From c965eafdb8c83453cc2a5f2b6c5a5acd7697d1b2 Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Fri, 28 Apr 2017 13:00:13 -0700 Subject: [PATCH 001/576] modify picklist to add additional select options --- modules/CmpdReg/src/client/src/PickList.js | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/modules/CmpdReg/src/client/src/PickList.js b/modules/CmpdReg/src/client/src/PickList.js index c18baa6c7..380e03297 100755 --- a/modules/CmpdReg/src/client/src/PickList.js +++ b/modules/CmpdReg/src/client/src/PickList.js @@ -64,6 +64,16 @@ $(function() { } else { this.insertFirstOption = null; } + if (this.options.insertSecondOption !=null) { + this.insertSecondOption = this.options.insertSecondOption; + } else { + this.insertSecondOption = null; + } + if (this.options.insertThirdOption !=null) { + this.insertThirdOption = this.options.insertThirdOption; + } else { + this.insertThirdOption = null; + } if (this.options.showIgnored !=null) { this.showIgnored = this.options.showIgnored; } else { @@ -72,10 +82,16 @@ $(function() { }, handleListReset: function() { + if (this.insertThirdOption) { + this.collection.add(this.insertThirdOption, {at: 0, silent: true}); + } + if (this.insertSecondOption) { + this.collection.add(this.insertSecondOption, {at: 0, silent: true}); + } if (this.insertFirstOption) { this.collection.add(this.insertFirstOption, {at: 0, silent: true}); } - this.render(); + this.render(); }, render: function() { From 0b3001cc24d0dc14900351be003e2d7b66603f1f Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Wed, 3 May 2017 22:08:17 -0700 Subject: [PATCH 002/576] add chem struct services --- .../server/routes/ChemStructureRoutes.coffee | 67 +++++++++++++++++-- 1 file changed, 62 insertions(+), 5 deletions(-) diff --git a/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee b/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee index ea1c56e61..b2a355a18 100644 --- a/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee +++ b/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee @@ -5,17 +5,19 @@ exports.setupAPIRoutes = (app) -> app.put '/api/chemStructure/:id', exports.putStructure app.post '/api/chemStructure/calculateMoleculeProperties', exports.calculateMoleculeProperties app.post '/api/chemStructure/renderMolStructure', exports.renderMolStructure - + app.post '/api/chemStructure/renderMolStructureBase64', exports.renderMolStructure exports.setupRoutes = (app, loginRoutes) -> app.get '/api/chemStructure/renderStructureByThingCode', loginRoutes.ensureAuthenticated, exports.renderStructureByThingCode + app.get '/api/chemStructure/renderStructureByCode', loginRoutes.ensureAuthenticated, exports.renderStructureByCode + app.get '/api/chemStructure/codename/:structureCode', loginRoutes.ensureAuthenticated, exports.getStructureByCode app.post '/api/chemStructure', loginRoutes.ensureAuthenticated, exports.postStructure app.put '/api/chemStructure/:id', loginRoutes.ensureAuthenticated, exports.putStructure app.post '/api/chemStructure/calculateMoleculeProperties', loginRoutes.ensureAuthenticated, exports.calculateMoleculeProperties app.post '/api/chemStructure/renderMolStructure', loginRoutes.ensureAuthenticated, exports.renderMolStructure - + app.post '/api/chemStructure/renderMolStructureBase64', loginRoutes.ensureAuthenticated, exports.renderMolStructureBase64 _ = require 'underscore' @@ -35,6 +37,19 @@ exports.renderStructureByThingCode = (req, resp) -> console.log rooUrl req.pipe(request(rooUrl)).pipe(resp) +exports.renderStructureByCode = (req, resp) -> + if global.specRunnerTestmode + console.debug process.cwd() + else + config = require '../conf/compiled/conf.js' + baseurl = "#{config.all.client.service.persistence.fullpath}structure/renderStructureByCodeName" + request = require 'request' + queryParams = req._parsedUrl.query + rooUrl = baseurl + '?' + queryParams + console.log '######## line 49 -- renderStructureByCode #########' + console.log rooUrl + req.pipe(request(rooUrl)).pipe(resp) + exports.getStructureByCode = (req, resp) -> if global.specRunnerTestmode console.debug process.cwd() @@ -42,6 +57,7 @@ exports.getStructureByCode = (req, resp) -> config = require '../conf/compiled/conf.js' baseurl = "#{config.all.client.service.persistence.fullpath}structure/getByCodeName/"+req.params.structureCode request = require 'request' +# req.pipe(request(baseurl)).pipe(resp) request( method: 'GET' url: baseurl @@ -132,22 +148,63 @@ exports.renderMolStructure = (req, resp) -> resp.json {molStructure: req.body[0].molStructure, height: req.body[0].height, width: req.body[0].width, format: req.body[0].format} else molecule = req.body + console.log 'incoming req.body' + console.log molecule config = require '../conf/compiled/conf.js' baseurl = config.all.client.service.persistence.fullpath+"structure/renderMolStructure" request = require 'request' + console.log 'line 136 ---- attempt to hit renderMolStructure -- how to handle reponse' request( method: 'POST' url: baseurl body: molecule +# encoding: null json: true - , (error, response, json) => + , (error, response, output) => if !error && response.statusCode == 200 - resp.json json + console.log '$$$$$$$$$$$$$$$$ READY TO RESPOND $$$$$$$$$$$$' +# console.log response + console.log output + resp.end output +# resp.writeHead 200, {'Content-Type': 'text/html'} +# resp.write '') +# resp.writeHead 200, 'Content-Type': 'image/png' +# resp.end buffer else - console.log 'got ajax error trying to render molStructure' + console.log '--- line 153: got ajax error trying to render molStructure' console.log error console.log json console.log response resp.statusCode = 500 resp.end JSON.stringify "render molStructure failed" ) + +exports.renderMolStructureBase64 = (req, resp) -> + if global.specRunnerTestmode + resp.json {molStructure: req.body[0].molStructure, height: req.body[0].height, width: req.body[0].width, format: req.body[0].format} + else + molecule = req.body + console.log 'incoming req.body' + console.log molecule + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"structure/renderMolStructureBase64" + request = require 'request' + console.log 'line 136 ---- attempt to hit renderMolStructure -- how to handle reponse' + request( + method: 'POST' + url: baseurl + body: molecule + json: true + , (error, response, output) => + if !error && response.statusCode == 200 + resp.end output + else + console.log '--- line 153: got ajax error trying to render molStructure' + console.log error + console.log json + console.log response + resp.statusCode = 500 + resp.end JSON.stringify "render molStructure failed" + ) \ No newline at end of file From 45ac9c43823041b62c77e5302a1e3208bea3237a Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Wed, 3 May 2017 22:14:05 -0700 Subject: [PATCH 003/576] add chem struct services --- .../server/routes/ChemStructureRoutes.coffee | 32 ++++++++++++++++--- 1 file changed, 27 insertions(+), 5 deletions(-) diff --git a/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee b/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee index b2a355a18..3c9b671fb 100644 --- a/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee +++ b/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee @@ -148,17 +148,13 @@ exports.renderMolStructure = (req, resp) -> resp.json {molStructure: req.body[0].molStructure, height: req.body[0].height, width: req.body[0].width, format: req.body[0].format} else molecule = req.body - console.log 'incoming req.body' - console.log molecule config = require '../conf/compiled/conf.js' baseurl = config.all.client.service.persistence.fullpath+"structure/renderMolStructure" request = require 'request' - console.log 'line 136 ---- attempt to hit renderMolStructure -- how to handle reponse' request( method: 'POST' url: baseurl body: molecule -# encoding: null json: true , (error, response, output) => if !error && response.statusCode == 200 @@ -181,6 +177,7 @@ exports.renderMolStructure = (req, resp) -> resp.end JSON.stringify "render molStructure failed" ) + exports.renderMolStructureBase64 = (req, resp) -> if global.specRunnerTestmode resp.json {molStructure: req.body[0].molStructure, height: req.body[0].height, width: req.body[0].width, format: req.body[0].format} @@ -207,4 +204,29 @@ exports.renderMolStructureBase64 = (req, resp) -> console.log response resp.statusCode = 500 resp.end JSON.stringify "render molStructure failed" - ) \ No newline at end of file + ) + +exports.acasStructureSearch = (req, resp) -> + if global.specRunnerTestmode + resp.json {queryMol: req.body[0].queryMol, searchType: req.body[0].searchType, maxResults: req.body[0].maxResults, similarity: req.body[0].similarity} + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"lsthings/structureSearch" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: req.body.reagentSearchParams + json: true + , (error, response, json) => + if !error && response.statusCode == 200 + resp.json json + else + console.log 'got ajax error trying to search for structures' + console.log error + console.log json + console.log response + resp.statusCode = 500 + resp.end JSON.stringify "ACAS structure search failed" + ) + From de46d29fc80fd71e47c783ed31c5e40a2f1216ee Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 5 May 2017 11:22:18 -0700 Subject: [PATCH 004/576] merging bitbucket compound-inventory, cmg-lims branches into oss feature/inventory --- .../BasicFileValidateReviewAndSave.coffee | 1 + modules/Components/src/client/PickList.coffee | 45 +- .../routes/InventoryServiceRoutes.coffee | 366 +++++++++-- .../routes/ServerUtilityFunctions.coffee | 21 + .../dist/select2-bootstrap.css | 610 ++++++++++++++++++ .../dist/select2-bootstrap.min.css | 1 + 6 files changed, 971 insertions(+), 73 deletions(-) create mode 100755 public/lib/select2-bootstrap-theme-0.1.0-beta.8/dist/select2-bootstrap.css create mode 100755 public/lib/select2-bootstrap-theme-0.1.0-beta.8/dist/select2-bootstrap.min.css diff --git a/modules/Components/src/client/BasicFileValidateReviewAndSave.coffee b/modules/Components/src/client/BasicFileValidateReviewAndSave.coffee index 0dbd9a1b5..d4a8f366b 100644 --- a/modules/Components/src/client/BasicFileValidateReviewAndSave.coffee +++ b/modules/Components/src/client/BasicFileValidateReviewAndSave.coffee @@ -1,6 +1,7 @@ class window.BasicFileValidateReviewAndSaveController extends BasicFileValidateAndSaveController template: _.template($("#BasicFileValidateReviewAndSaveView").html()) + initialize: -> console.log "BasicFileValidateReviewAndSaveController" super() diff --git a/modules/Components/src/client/PickList.coffee b/modules/Components/src/client/PickList.coffee index 470a84cad..c9fef94d3 100644 --- a/modules/Components/src/client/PickList.coffee +++ b/modules/Components/src/client/PickList.coffee @@ -90,10 +90,15 @@ class window.PickListOptionControllerForLsThing extends Backbone.View class window.PickListSelectController extends Backbone.View - initialize: -> + initialize: (options) -> @rendered = false @collection.bind "add", @addOne @collection.bind "reset", @handleListReset + # NOTE: Backbone 1.1.0 no longer automatically attaches options passed + # to View constructors as this.options. So, in order to be compatible + # with Backbone 1.0.0 and versions greater or equal to 1.1.0, we'll + # attach it ourselves here. + @options = options || {} unless @options.selectedCode is "" @selectedCode = @options.selectedCode @@ -228,17 +233,45 @@ class window.ComboBoxController extends PickListSelectController class window.PickListSelect2Controller extends PickListSelectController + # maps the 'code' property to the select2 required 'id' property and + # the 'name' property to the select2 required 'text' property + acasPropertyMap = + id: 'code' + text: 'name' + + # @param options.propertyMap String ('select2' or 'acas', where 'select2' + # does no mapping and 'acas' uses the 'acasPropertyMap' defined above) or + # an Object with 'id' and 'text' properties to use. If + # 'options.propertyMap' is not specified, it defaults to using the + # 'acasPropertyMap' + initialize: (options) -> + @propertyMap = acasPropertyMap + if options.propertyMap? + if _.isObject(options.propertyMap) and options.propertyMap.id? and options.propertyMap.text? + @propertyMap = options.propertyMap + else if options.propertyMap is 'select2' + @propertyMap = null + else if options.propertyMap isnt 'acas' + throw new Error ('PickListSelect2Controller.initialize(): Invalid propertyMap value encountered') + super(options) + render: => -# convert model objects to array of json objects which have 'id' and 'text' properties + # convert model objects to array of json objects which have 'id' and 'text' properties if propertyMap specified mappedData = [] for obj in @collection.toJSON() if (not obj.ignored? or (obj.ignored is false) or (@showIgnored? and @showIgnored is true)) - obj.id = obj.id || obj.code - obj.text = obj.text || obj.name + if @propertyMap? + obj.id = obj[@propertyMap.id] + obj.text = obj[@propertyMap.text] mappedData.push(obj) + # if a first option was inserted, use it for select's placeholder object + @placeholder = "" + if @insertFirstOption? + @placeholder = mappedData[0] + $(@el).select2 - placeholder: "" + placeholder: @placeholder data: mappedData openOnEnter: false allowClear: true @@ -256,7 +289,7 @@ class window.PickListSelect2Controller extends PickListSelectController result = $(@el).val() # if result is null then we'll return the "unassigned" instead if it # was inserted as the first option - if not result? and @insertFirstOption.get('code') is "unassigned" + if not result? and @insertFirstOption.get('code') is "unassigned" result = "unassigned" result diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index b94785c9a..67482e5b5 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -3,8 +3,11 @@ csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFuncti _ = require 'underscore' preferredEntityCodeService = require '../routes/PreferredEntityCodeService.js' config = require '../conf/compiled/conf.js' +RUN_CUSTOM_FLAG = "0" + exports.setupAPIRoutes = (app) -> + app.post '/api/getContainersInLocationWithTypeAndKind', exports.getContainersInLocationWithTypeAndKind app.post '/api/getContainersInLocation', exports.getContainersInLocation app.post '/api/getContainerCodesByLabels', exports.getContainerCodesByLabels app.post '/api/getContainersByLabels', exports.getContainersByLabels @@ -48,8 +51,10 @@ exports.setupAPIRoutes = (app) -> app.post '/api/createTube', exports.createTube app.post '/api/createTubes', exports.createTubes app.post '/api/throwInTrash', exports.throwInTrash + app.post '/api/updateContainerHistoryLogs', exports.updateContainerHistoryLogs exports.setupRoutes = (app, loginRoutes) -> + app.post '/api/getContainersInLocationWithTypeAndKind', loginRoutes.ensureAuthenticated, exports.getContainersInLocationWithTypeAndKind app.post '/api/getContainersInLocation', loginRoutes.ensureAuthenticated, exports.getContainersInLocation app.post '/api/getContainerCodesByLabels', loginRoutes.ensureAuthenticated, exports.getContainerCodesByLabels app.post '/api/getContainersByLabels', loginRoutes.ensureAuthenticated, exports.getContainersByLabels @@ -94,6 +99,8 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/createTube', loginRoutes.ensureAuthenticated, exports.createTube app.post '/api/createTubes', loginRoutes.ensureAuthenticated, exports.createTubes app.post '/api/throwInTrash', loginRoutes.ensureAuthenticated, exports.throwInTrash + app.post '/api/updateContainerHistoryLogs', loginRoutes.ensureAuthenticated, exports.updateContainerHistoryLogs + exports.getContainersInLocation = (req, resp) -> req.setTimeout 86400000 @@ -101,8 +108,14 @@ exports.getContainersInLocation = (req, resp) -> inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' resp.json inventoryServiceTestJSON.getContainersInLocationResponse else + queryParams = [] + if req.query.containerType? + queryParams.push "containerType="+req.query.containerType + if req.query.containerKind? + queryParams.push "containerKind="+req.query.containerKind + queryString = queryParams.join "&" config = require '../conf/compiled/conf.js' - baseurl = config.all.client.service.persistence.fullpath+"containers/getContainersInLocation" + baseurl = config.all.client.service.persistence.fullpath+"containers/getContainersInLocation?"+queryString request = require 'request' request( method: 'POST' @@ -121,6 +134,59 @@ exports.getContainersInLocation = (req, resp) -> resp.end JSON.stringify "getContainersInLocation failed" ) +exports.getContainersInLocationWithTypeAndKind = (req, resp) -> + req.setTimeout 86400000 + if global.specRunnerTestmode + inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' + resp.json inventoryServiceTestJSON.getContainersInLocationResponse + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containers/getContainersInLocation?containerType=location&containerKind=default" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: req.body.values + json: true + timeout: 86400000 + , (error, response, json) => + if !error && response.statusCode == 200 + resp.json json + else + console.error 'got ajax error trying to get getContainersInLocation' + console.error error + console.error json + console.error response + resp.end JSON.stringify "getContainersInLocation failed" + ) + +exports.getContainersInLocationWithTypeAndKindInternal = (values, callback) -> + #req.setTimeout 86400000 + if global.specRunnerTestmode + inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' + resp.json inventoryServiceTestJSON.getContainersInLocationResponse + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containers/getContainersInLocation?containerType=location&containerKind=default" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: values + json: true + timeout: 86400000 + , (error, response, json) => + if !error && response.statusCode == 200 + callback json, response.statusCode + else + console.error 'got ajax error trying to get getContainersInLocation' + console.error error + console.error json + console.error response + #resp.end JSON.stringify "getContainersInLocation failed" + callback response, response.statusCode + ) + exports.getContainersByLabels = (req, resp) -> req.setTimeout 86400000 exports.getContainersByLabelsInternal req.body, req.query.containerType, req.query.containerKind, req.query.labelType, req.query.labelKind, (json, statusCode) -> @@ -220,6 +286,32 @@ exports.getWellCodesByPlateBarcodes = (req, resp) -> else resp.json json +exports.getContainersInBoxPositionInternal = (values, callback) -> + if global.specRunnerTestmode + inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' + resp.json inventoryServiceTestJSON.getContainersInLocationResponse + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containers/getContainersInLocation?containerType=container&containerKind=tube" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: values + json: true + timeout: 86400000 + , (error, response, json) => + if !error && response.statusCode == 200 + callback json, response.statusCode + else + console.error 'got ajax error trying to get getContainersInLocation' + console.error error + console.error json + console.error response + #resp.end JSON.stringify "getContainersInLocation failed" + callback response, response.statusCode + ) + exports.getWellCodesByPlateBarcodes = (req, resp) -> req.setTimeout 86400000 if global.specRunnerTestmode @@ -426,7 +518,7 @@ exports.updateContainersByContainerCodesInternal = (updateInformation, callCusto else barcodes = _.pluck updateInformation, "barcode" console.debug "calling getContainerCodesByLabelsInternal" - exports.getContainerCodesByLabelsInternal barcodes, null, null, "barcode", "barcode", (containerCodes, statusCode) => + exports.getContainerCodesByLabelsInternal barcodes, "container", null, "barcode", "barcode", (containerCodes, statusCode) => if statusCode == 500 console.error "updateContainerMetadataByContainerCodeInternal failed: #{JSON.stringify containerCodes}" callback "updateContainersByContainerCodesInternal failed", 500 @@ -585,6 +677,8 @@ exports.getBreadCrumbByContainerCodeInternal = (codeNamesJSON, delimeter, callba headers: 'content-type': 'application/json' , (error, response, json) => if !error && response.statusCode == 200 + console.log 'json in getBreadCrumbByContainerCodeInternal' + console.log json callback json else console.error 'got ajax error trying to get getBreadCrumbByContainerCode' @@ -1161,41 +1255,52 @@ exports.moveToLocation = (req, resp) -> resp.json json exports.moveToLocationInternal = (input, callCustom, callback) -> - callCustom = callCustom != "0" - if global.specRunnerTestmode - inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' - resp.json inventoryServiceTestJSON.moveToLocationResponse - else - console.debug 'incoming moveToLocationJSON request: ', JSON.stringify(input) - config = require '../conf/compiled/conf.js' - baseurl = config.all.client.service.persistence.fullpath+"containers/moveToLocation" - console.debug 'base url: ', baseurl - request = require 'request' - request( - method: 'POST' - url: baseurl - body: input - json: true - timeout: 86400000 - headers: 'content-type': 'application/json' - , (error, response, json) => - console.debug "response statusCode: #{response.statusCode}" - if !error - if callCustom && csUtilities.moveToLocation? - console.log "running customer specific server function moveToLocation" - csUtilities.moveToLocation input, (customerResponse, statusCode) -> - json = _.extend json, customerResponse - callback json, statusCode + #exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> + # console.log 'updated history logs before moving to temp' + # ) + callCustom = callCustom != "0" + if global.specRunnerTestmode + inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' + resp.json inventoryServiceTestJSON.moveToLocationResponse + else + console.debug 'incoming moveToLocationJSON request: ', JSON.stringify(input) + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containers/moveToLocation" + console.debug 'base url: ', baseurl + request = require 'request' + console.log 'request into moveToLocation' + console.log input + request( + method: 'POST' + url: baseurl + body: input + json: true + timeout: 86400000 + headers: 'content-type': 'application/json' + , (error, response, json) => + #add the call to updateContainerHistoryLogs here... + console.debug "response statusCode: #{response.statusCode}" + if !error + console.log 'container down here...did it pull through??' + console.log input[0].containerCodeName + exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> + if callCustom && csUtilities.moveToLocation? + console.log "running customer specific server function moveToLocation" + csUtilities.moveToLocation input, (customerResponse, statusCode) -> + json = _.extend json, customerResponse + callback json, statusCode + else + console.warn "could not find customer specific server function moveToLocation so not running it" + callback json, response.statusCode + ) else - console.warn "could not find customer specific server function moveToLocation so not running it" - callback json, response.statusCode - else - console.error 'got ajax error trying to get moveToLocation' - console.error error - console.error json - console.error response - callback JSON.stringify("updateWellContent failed"), 500 - ) + console.error 'got ajax error trying to get moveToLocation' + console.error error + console.error json + console.error response + callback JSON.stringify("updateWellContent failed"), 500 + ) + #) exports.getWellContentByContainerLabel = (req, resp) -> req.setTimeout 86400000 @@ -1484,8 +1589,11 @@ exports.mergeContainersInternal = (input, callback) -> isOdd = (num) -> return (num % 2) == 1 alphabet = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' - _.map originWellContent, (originWells) -> - quadrant = _.findWhere input.quadrants, {"codeName": originWells.containerCodeName} + # for each quadrant + _.map input.quadrants, (quadrant) -> + # find plate whose name matches the quadrant name + originWells = _.findWhere originWellContent, {"containerCodeName": quadrant.codeName} + # map plate wells to merged plate wells _.map originWells.wellContent, (wellContent) -> wellContent = _.omit(wellContent, ['containerCodeName', 'wellName', 'recordedDate']) wellContent.recordedDate = 1455323242544 @@ -1623,6 +1731,7 @@ exports.containerLogsInternal = (inputs, callCustom, callback) -> callback json, statusCode exports.containerLocationHistory = (req, resp) -> + req.setTimeout 86400000 exports.containerLocationHistoryInternal req.body, req.query.callCustom, (json, statusCode) -> resp.statusCode = statusCode resp.json json @@ -1636,7 +1745,9 @@ exports.containerLocationHistoryInternal = (inputs, callCustom, callback) -> exports.addContainerLocationHistory inputs, callCustom, (json, statusCode) -> callback json, statusCode + exports.getContainerLogs = (req, resp) -> + req.setTimeout 86400000 exports.getContainerLogsInternal [req.params.label], req.query.containerType, req.query.containerKind, req.query.labelType, req.query.labelKind, (json, statusCode) -> resp.statusCode = statusCode resp.json json @@ -1754,7 +1865,6 @@ exports.addContainerLocationHistory = (inputs, callCustom, callback) -> if csUtilities.addContainerLocationHistory? console.log "running customer specific server function addContainerLocationHistory" csUtilities.addContainerLocationHistory inputs, (response) -> - console.log response else console.warn "could not find customer specific server function addContainerLocationHistory so not running it" callback json, statusCode @@ -1980,33 +2090,155 @@ exports.throwInTrash = (req, resp) -> resp.json json exports.throwInTrashInternal = (input, callCustom, callback) -> - config = require '../conf/compiled/conf.js' - baseurl = config.all.client.service.persistence.fullpath + "containers/throwInTrash" - console.log baseurl - request = require 'request' - request( - method: 'POST' - url: baseurl - body: JSON.stringify input - json: true - timeout: 6000000 - , (error, response, json) => - if !error && response.statusCode == 204 -# If call custom doesn't equal 0 then call custom - callCustom = callCustom != "0" - if callCustom && csUtilities.throwInTrash? - console.log "running customer specific server function throwInTrash" - csUtilities.throwInTrash input, (customerResponse, statusCode) -> -# json = _.extend json, customerResponse - callback json, response.statusCode + #exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath + "containers/throwInTrash" + console.log baseurl + request = require 'request' + request( + method: 'POST' + url: baseurl + body: JSON.stringify input + json: true + timeout: 6000000 + , (error, response, json) => + if !error && response.statusCode == 204 + exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> + # If call custom doesn't equal 0 then call custom + callCustom = callCustom != "0" + if callCustom && csUtilities.throwInTrash? + console.log "running customer specific server function throwInTrash" + csUtilities.throwInTrash input, (customerResponse, statusCode) -> + # json = _.extend json, customerResponse + callback json, response.statusCode + else + console.warn "could not find customer specific server function throwInTrash so not running it" + callback json, response.statusCode + ) + else if response.statusCode == 400 + callback response.body, response.statusCode else - console.warn "could not find customer specific server function throwInTrash so not running it" - callback json, response.statusCode - else if response.statusCode == 400 - callback response.body, response.statusCode - else - console.log 'got ajax error trying to create tube' - console.log error - console.log response - callback response.body, 500 + console.log 'got ajax error trying to create tube' + console.log error + console.log response + callback response.body, 500 + ) + #) + +exports.updateContainerHistoryLogsInternal = (containers, callback) -> + formattedContainers = [] + index = 0 + #_.each(containers, (container) -> + formatContainersForLocationHistoryUpdate(containers, (statusCode, formattedContainers) -> + exports.containerLocationHistoryInternal(formattedContainers, RUN_CUSTOM_FLAG, (json, statusCode) -> + return callback json,statusCode + ) + # else + # return callback null, 500 + ) + +formatContainersForLocationHistoryUpdate = (containers, callback) -> + createContainersWithBreadcrumb(containers, (containersWithBreadcrumb, modifiedBy, modifiedDate) -> + formatLocationStrings(containersWithBreadcrumb, (formattedContainersWithBreadcrumb) -> + formatContainers(formattedContainersWithBreadcrumb, modifiedBy, modifiedDate, (formattedContainers) -> + return callback 200, formattedContainers + ) + ) + ) + +createContainersWithBreadcrumb = (containers, callback) -> + containerCodeNames = [] + modifiedBy = containers[0].modifiedBy + modifiedDate = containers[0].modifiedDate + _.each(containers, (container) -> + containerCodeNames.push(container.containerCodeName) + ) + exports.getBreadCrumbByContainerCodeInternal(containerCodeNames, "<", (containersWithBreadcrumb) -> + return callback containersWithBreadcrumb, modifiedBy, modifiedDate + ) + +formatLocationStrings = (containersWithBreadcrumb, callback) -> + formattedContainersWithBreadcrumb = [] + _.each(containersWithBreadcrumb, (container) -> + locationArray = container.labelBreadCrumb.split("<") + locationArrayString = JSON.stringify(locationArray) + container.locationArrayString = locationArrayString + formattedContainersWithBreadcrumb.push(container) + ) + return callback formattedContainersWithBreadcrumb + +formatContainers = (containers, modifiedBy, modifiedDate, callback) -> + formattedContainers = [] + _.each(containers, (container) -> + formattedContainer = { + "codeName": container.containerCode + "recordedBy": modifiedBy + "recordedDate": modifiedDate + "location": container.locationArrayString + "movedBy": modifiedBy + "movedDate": modifiedDate + "additionalValues": [] + } + formattedContainers.push(formattedContainer) ) + statusCode = 200 + return callback formattedContainers + #callback(formattedContainers, statusCode) + + +# getLocationBreadcrumb = (container, callback) -> +# exports.getBreadCrumbByContainerCodeInternal([container.containerCodeName], "<", (breadcrumb) -> +# labelBreadCrumb = breadcrumb[0].labelBreadCrumb +# callback labelBreadCrumb +# # console.log 'breadcrumb for move to locations' +# # console.log breadcrumb[0].labelBreadCrumb +# # #test breadCrumb = 'CAGE00002 +# getLocationBreadcrumb(container, (labelBreadCrumb) -> +# createLocationArray(labelBreadCrumb, (locationArrayString) -> +# #buildLocationArrayString(locationArray, (locationArrayString) -> +# formatContainer(container, locationArrayString, (formattedContainer, statusCode) -> +# callback statusCode, formattedContainer +# ) +# ) +# ) +# +# createLocationArray = (labelBreadCrumb, callback) -> +# locationArray = labelBreadCrumb.split("<") +# locationArrayString = JSON.stringify(locationArray) +# callback locationArrayString.toUpperCase() +# +# formatContainer = (container, locationArrayString, callback) -> +# +# formattedContainer = { +# "codeName": container.containerCodeName +# "recordedBy": container.modifiedBy +# "recordedDate": container.modifiedDate +# "location": locationArrayString +# "movedBy": container.modifiedBy +# "movedDate": container.modifiedDate +# "additionalValues": [] +# } +# +# statusCode = 200 +# callback(formattedContainer, statusCode) + +# buildLocationArrayString = (locationArray, callback) -> +# locationSeparator = '\",\"' +# locationArrayString = '[\"' + +# locationArray[0] + +# locationSeparator + +# locationArray[1] + +# locationSeparator + +# locationArray[2] + +# locationSeparator + +# locationArray[3] + +# '\"]' +# +# console.log 'locationArrayString ' +# console.log locationArrayString +# callback locationArrayString diff --git a/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee b/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee index ae887c6fd..54766d26c 100644 --- a/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee +++ b/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee @@ -1429,6 +1429,27 @@ class Container extends Backbone.Model additionalValues: additionalValues response.push responseObject return response + + getLocationHistory: -> + lsStates = @get('lsStates').getStatesByTypeAndKind 'metadata', 'location history' + response = [] + if lsStates? + lsStates.forEach (lsState) => + additionalValues = lsState.get('lsValues').filter (value) -> + (!value.get('ignored')) and + !((value.get('lsType')=='stringValue') and (value.get('lsKind')=='location')) and + !((value.get('lsType')=='codeValue') and (value.get('lsKind')=='moved by')) and + !((value.get('lsType')=='dateValue') and (value.get('lsKind')=='moved date')) + responseObject = + codeName: @get('codeName') + recordedBy: lsState.get('recordedBy') + recordedDate: lsState.get('recordedDate') + location: lsState.getValuesByTypeAndKind('stringValue', 'location')[0].get('stringValue') + movedBy: lsState.getValuesByTypeAndKind('codeValue', 'moved by')[0]?.get('codeValue') + movedDate: lsState.getValuesByTypeAndKind('dateValue', 'moved date')[0]?.get('dateValue') + additionalValues: additionalValues + response.push responseObject + return response getLocationHistory: -> lsStates = @get('lsStates').getStatesByTypeAndKind 'metadata', 'location history' diff --git a/public/lib/select2-bootstrap-theme-0.1.0-beta.8/dist/select2-bootstrap.css b/public/lib/select2-bootstrap-theme-0.1.0-beta.8/dist/select2-bootstrap.css new file mode 100755 index 000000000..caf2b9abd --- /dev/null +++ b/public/lib/select2-bootstrap-theme-0.1.0-beta.8/dist/select2-bootstrap.css @@ -0,0 +1,610 @@ +/*! Select2 Bootstrap Theme v0.1.0-beta.8 | MIT License | github.com/select2/select2-bootstrap-theme */ +.select2-container--bootstrap { + display: block; + /*------------------------------------*\ + #COMMON STYLES + \*------------------------------------*/ + /** + * Search field in the Select2 dropdown. + */ + /** + * No outline for all search fields - in the dropdown + * and inline in multi Select2s. + */ + /** + * Adjust Select2's choices hover and selected styles to match + * Bootstrap 3's default dropdown styles. + * + * @see http://getbootstrap.com/components/#dropdowns + */ + /** + * Clear the selection. + */ + /** + * Address disabled Select2 styles. + * + * @see https://select2.github.io/examples.html#disabled + * @see http://getbootstrap.com/css/#forms-control-disabled + */ + /*------------------------------------*\ + #DROPDOWN + \*------------------------------------*/ + /** + * Dropdown border color and box-shadow. + */ + /** + * Limit the dropdown height. + */ + /*------------------------------------*\ + #SINGLE SELECT2 + \*------------------------------------*/ + /*------------------------------------*\ + #MULTIPLE SELECT2 + \*------------------------------------*/ + /** + * Address Bootstrap control sizing classes + * + * 1. Reset Bootstrap defaults. + * 2. Adjust the dropdown arrow button icon position. + * + * @see http://getbootstrap.com/css/#forms-control-sizes + */ + /* 1 */ + /*------------------------------------*\ + #RTL SUPPORT + \*------------------------------------*/ +} +.select2-container--bootstrap .select2-selection { + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + background-color: #fff; + border: 1px solid #ccc; + border-radius: 4px; + color: #555555; + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-size: 14px; + outline: 0; +} +.select2-container--bootstrap .select2-selection.form-control { + border-radius: 4px; +} +.select2-container--bootstrap .select2-search--dropdown .select2-search__field { + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + background-color: #fff; + border: 1px solid #ccc; + border-radius: 4px; + color: #555555; + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-size: 14px; +} +.select2-container--bootstrap .select2-search__field { + outline: 0; + /* Firefox 18- */ + /** + * Firefox 19+ + * + * @see http://stackoverflow.com/questions/24236240/color-for-styled-placeholder-text-is-muted-in-firefox + */ +} +.select2-container--bootstrap .select2-search__field::-webkit-input-placeholder { + color: #999; +} +.select2-container--bootstrap .select2-search__field:-moz-placeholder { + color: #999; +} +.select2-container--bootstrap .select2-search__field::-moz-placeholder { + color: #999; + opacity: 1; +} +.select2-container--bootstrap .select2-search__field:-ms-input-placeholder { + color: #999; +} +.select2-container--bootstrap .select2-results__option { + /** + * Disabled results. + * + * @see https://select2.github.io/examples.html#disabled-results + */ + /** + * Hover state. + */ + /** + * Selected state. + */ +} +.select2-container--bootstrap .select2-results__option[role=group] { + padding: 0; +} +.select2-container--bootstrap .select2-results__option[aria-disabled=true] { + color: #777777; + cursor: not-allowed; +} +.select2-container--bootstrap .select2-results__option[aria-selected=true] { + background-color: #f5f5f5; + color: #262626; +} +.select2-container--bootstrap .select2-results__option--highlighted[aria-selected] { + background-color: #337ab7; + color: #fff; +} +.select2-container--bootstrap .select2-results__option .select2-results__option { + padding: 6px 12px; +} +.select2-container--bootstrap .select2-results__option .select2-results__option .select2-results__group { + padding-left: 0; +} +.select2-container--bootstrap .select2-results__option .select2-results__option .select2-results__option { + margin-left: -12px; + padding-left: 24px; +} +.select2-container--bootstrap .select2-results__option .select2-results__option .select2-results__option .select2-results__option { + margin-left: -24px; + padding-left: 36px; +} +.select2-container--bootstrap .select2-results__option .select2-results__option .select2-results__option .select2-results__option .select2-results__option { + margin-left: -36px; + padding-left: 48px; +} +.select2-container--bootstrap .select2-results__option .select2-results__option .select2-results__option .select2-results__option .select2-results__option .select2-results__option { + margin-left: -48px; + padding-left: 60px; +} +.select2-container--bootstrap .select2-results__option .select2-results__option .select2-results__option .select2-results__option .select2-results__option .select2-results__option .select2-results__option { + margin-left: -60px; + padding-left: 72px; +} +.select2-container--bootstrap .select2-results__group { + color: #777777; + display: block; + padding: 6px 12px; + font-size: 12px; + line-height: 1.428571429; + white-space: nowrap; +} +.select2-container--bootstrap.select2-container--focus .select2-selection, .select2-container--bootstrap.select2-container--open .select2-selection { + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(102, 175, 233, 0.6); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(102, 175, 233, 0.6); + -webkit-transition: border-color ease-in-out 0.15s, box-shadow ease-in-out 0.15s; + -o-transition: border-color ease-in-out 0.15s, box-shadow ease-in-out 0.15s; + -webkit-transition: border-color ease-in-out 0.15s, -webkit-box-shadow ease-in-out 0.15s; + transition: border-color ease-in-out 0.15s, -webkit-box-shadow ease-in-out 0.15s; + transition: border-color ease-in-out 0.15s, box-shadow ease-in-out 0.15s; + transition: border-color ease-in-out 0.15s, box-shadow ease-in-out 0.15s, -webkit-box-shadow ease-in-out 0.15s; + border-color: #66afe9; +} +.select2-container--bootstrap.select2-container--open { + /** + * Make the dropdown arrow point up while the dropdown is visible. + */ + /** + * Handle border radii of the container when the dropdown is showing. + */ +} +.select2-container--bootstrap.select2-container--open .select2-selection .select2-selection__arrow b { + border-color: transparent transparent #999 transparent; + border-width: 0 4px 4px 4px; +} +.select2-container--bootstrap.select2-container--open.select2-container--below .select2-selection { + border-bottom-right-radius: 0; + border-bottom-left-radius: 0; + border-bottom-color: transparent; +} +.select2-container--bootstrap.select2-container--open.select2-container--above .select2-selection { + border-top-right-radius: 0; + border-top-left-radius: 0; + border-top-color: transparent; +} +.select2-container--bootstrap .select2-selection__clear { + color: #999; + cursor: pointer; + float: right; + font-weight: bold; + margin-right: 10px; +} +.select2-container--bootstrap .select2-selection__clear:hover { + color: #333; +} +.select2-container--bootstrap.select2-container--disabled .select2-selection { + border-color: #ccc; + -webkit-box-shadow: none; + box-shadow: none; +} +.select2-container--bootstrap.select2-container--disabled .select2-selection, +.select2-container--bootstrap.select2-container--disabled .select2-search__field { + cursor: not-allowed; +} +.select2-container--bootstrap.select2-container--disabled .select2-selection, +.select2-container--bootstrap.select2-container--disabled .select2-selection--multiple .select2-selection__choice { + background-color: #eeeeee; +} +.select2-container--bootstrap.select2-container--disabled .select2-selection__clear, +.select2-container--bootstrap.select2-container--disabled .select2-selection--multiple .select2-selection__choice__remove { + display: none; +} +.select2-container--bootstrap .select2-dropdown { + -webkit-box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175); + box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175); + border-color: #66afe9; + overflow-x: hidden; + margin-top: -1px; +} +.select2-container--bootstrap .select2-dropdown--above { + margin-top: 1px; +} +.select2-container--bootstrap .select2-results > .select2-results__options { + max-height: 200px; + overflow-y: auto; +} +.select2-container--bootstrap .select2-selection--single { + height: 34px; + line-height: 1.428571429; + padding: 6px 24px 6px 12px; + /** + * Adjust the single Select2's dropdown arrow button appearance. + */ +} +.select2-container--bootstrap .select2-selection--single .select2-selection__arrow { + position: absolute; + bottom: 0; + right: 12px; + top: 0; + width: 4px; +} +.select2-container--bootstrap .select2-selection--single .select2-selection__arrow b { + border-color: #999 transparent transparent transparent; + border-style: solid; + border-width: 4px 4px 0 4px; + height: 0; + left: 0; + margin-left: -4px; + margin-top: -2px; + position: absolute; + top: 50%; + width: 0; +} +.select2-container--bootstrap .select2-selection--single .select2-selection__rendered { + color: #555555; + padding: 0; +} +.select2-container--bootstrap .select2-selection--single .select2-selection__placeholder { + color: #999; +} +.select2-container--bootstrap .select2-selection--multiple { + min-height: 34px; + padding: 0; + height: auto; + /** + * Make Multi Select2's choices match Bootstrap 3's default button styles. + */ + /** + * Minus 2px borders. + */ + /** + * Clear the selection. + */ +} +.select2-container--bootstrap .select2-selection--multiple .select2-selection__rendered { + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + box-sizing: border-box; + display: block; + line-height: 1.428571429; + list-style: none; + margin: 0; + overflow: hidden; + padding: 0; + width: 100%; + text-overflow: ellipsis; + white-space: nowrap; +} +.select2-container--bootstrap .select2-selection--multiple .select2-selection__placeholder { + color: #999; + float: left; + margin-top: 5px; +} +.select2-container--bootstrap .select2-selection--multiple .select2-selection__choice { + color: #555555; + background: #fff; + border: 1px solid #ccc; + border-radius: 4px; + cursor: default; + float: left; + margin: 5px 0 0 6px; + padding: 0 6px; +} +.select2-container--bootstrap .select2-selection--multiple .select2-search--inline .select2-search__field { + background: transparent; + padding: 0 12px; + height: 32px; + line-height: 1.428571429; + margin-top: 0; + min-width: 5em; +} +.select2-container--bootstrap .select2-selection--multiple .select2-selection__choice__remove { + color: #999; + cursor: pointer; + display: inline-block; + font-weight: bold; + margin-right: 3px; +} +.select2-container--bootstrap .select2-selection--multiple .select2-selection__choice__remove:hover { + color: #333; +} +.select2-container--bootstrap .select2-selection--multiple .select2-selection__clear { + margin-top: 6px; +} +.select2-container--bootstrap .select2-selection--single.input-sm, .input-group-sm .select2-container--bootstrap .select2-selection--single, .form-group-sm .select2-container--bootstrap .select2-selection--single { + border-radius: 3px; + font-size: 12px; + height: 30px; + line-height: 1.5; + padding: 5px 22px 5px 10px; + /* 2 */ +} +.select2-container--bootstrap .select2-selection--single.input-sm .select2-selection__arrow b, .input-group-sm .select2-container--bootstrap .select2-selection--single .select2-selection__arrow b, .form-group-sm .select2-container--bootstrap .select2-selection--single .select2-selection__arrow b { + margin-left: -5px; +} +.select2-container--bootstrap .select2-selection--multiple.input-sm, .input-group-sm .select2-container--bootstrap .select2-selection--multiple, .form-group-sm .select2-container--bootstrap .select2-selection--multiple { + min-height: 30px; + border-radius: 3px; +} +.select2-container--bootstrap .select2-selection--multiple.input-sm .select2-selection__choice, .input-group-sm .select2-container--bootstrap .select2-selection--multiple .select2-selection__choice, .form-group-sm .select2-container--bootstrap .select2-selection--multiple .select2-selection__choice { + font-size: 12px; + line-height: 1.5; + margin: 4px 0 0 5px; + padding: 0 5px; +} +.select2-container--bootstrap .select2-selection--multiple.input-sm .select2-search--inline .select2-search__field, .input-group-sm .select2-container--bootstrap .select2-selection--multiple .select2-search--inline .select2-search__field, .form-group-sm .select2-container--bootstrap .select2-selection--multiple .select2-search--inline .select2-search__field { + padding: 0 10px; + font-size: 12px; + height: 28px; + line-height: 1.5; +} +.select2-container--bootstrap .select2-selection--multiple.input-sm .select2-selection__clear, .input-group-sm .select2-container--bootstrap .select2-selection--multiple .select2-selection__clear, .form-group-sm .select2-container--bootstrap .select2-selection--multiple .select2-selection__clear { + margin-top: 5px; +} +.select2-container--bootstrap .select2-selection--single.input-lg, .input-group-lg .select2-container--bootstrap .select2-selection--single, .form-group-lg .select2-container--bootstrap .select2-selection--single { + border-radius: 6px; + font-size: 18px; + height: 46px; + line-height: 1.3333333; + padding: 10px 31px 10px 16px; + /* 1 */ +} +.select2-container--bootstrap .select2-selection--single.input-lg .select2-selection__arrow, .input-group-lg .select2-container--bootstrap .select2-selection--single .select2-selection__arrow, .form-group-lg .select2-container--bootstrap .select2-selection--single .select2-selection__arrow { + width: 5px; +} +.select2-container--bootstrap .select2-selection--single.input-lg .select2-selection__arrow b, .input-group-lg .select2-container--bootstrap .select2-selection--single .select2-selection__arrow b, .form-group-lg .select2-container--bootstrap .select2-selection--single .select2-selection__arrow b { + border-width: 5px 5px 0 5px; + margin-left: -5px; + margin-left: -10px; + margin-top: -2.5px; +} +.select2-container--bootstrap .select2-selection--multiple.input-lg, .input-group-lg .select2-container--bootstrap .select2-selection--multiple, .form-group-lg .select2-container--bootstrap .select2-selection--multiple { + min-height: 46px; + border-radius: 6px; +} +.select2-container--bootstrap .select2-selection--multiple.input-lg .select2-selection__choice, .input-group-lg .select2-container--bootstrap .select2-selection--multiple .select2-selection__choice, .form-group-lg .select2-container--bootstrap .select2-selection--multiple .select2-selection__choice { + font-size: 18px; + line-height: 1.3333333; + border-radius: 4px; + margin: 9px 0 0 8px; + padding: 0 10px; +} +.select2-container--bootstrap .select2-selection--multiple.input-lg .select2-search--inline .select2-search__field, .input-group-lg .select2-container--bootstrap .select2-selection--multiple .select2-search--inline .select2-search__field, .form-group-lg .select2-container--bootstrap .select2-selection--multiple .select2-search--inline .select2-search__field { + padding: 0 16px; + font-size: 18px; + height: 44px; + line-height: 1.3333333; +} +.select2-container--bootstrap .select2-selection--multiple.input-lg .select2-selection__clear, .input-group-lg .select2-container--bootstrap .select2-selection--multiple .select2-selection__clear, .form-group-lg .select2-container--bootstrap .select2-selection--multiple .select2-selection__clear { + margin-top: 10px; +} +.select2-container--bootstrap .select2-selection.input-lg.select2-container--open .select2-selection--single { + /** + * Make the dropdown arrow point up while the dropdown is visible. + */ +} +.select2-container--bootstrap .select2-selection.input-lg.select2-container--open .select2-selection--single .select2-selection__arrow b { + border-color: transparent transparent #999 transparent; + border-width: 0 5px 5px 5px; +} +.input-group-lg .select2-container--bootstrap .select2-selection.select2-container--open .select2-selection--single { + /** + * Make the dropdown arrow point up while the dropdown is visible. + */ +} +.input-group-lg .select2-container--bootstrap .select2-selection.select2-container--open .select2-selection--single .select2-selection__arrow b { + border-color: transparent transparent #999 transparent; + border-width: 0 5px 5px 5px; +} +.select2-container--bootstrap[dir="rtl"] { + /** + * Single Select2 + * + * 1. Makes sure that .select2-selection__placeholder is positioned + * correctly. + */ + /** + * Multiple Select2 + */ +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--single { + padding-left: 24px; + padding-right: 12px; +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--single .select2-selection__rendered { + padding-right: 0; + padding-left: 0; + text-align: right; + /* 1 */ +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--single .select2-selection__clear { + float: left; +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--single .select2-selection__arrow { + left: 12px; + right: auto; +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--single .select2-selection__arrow b { + margin-left: 0; +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--multiple .select2-selection__choice, +.select2-container--bootstrap[dir="rtl"] .select2-selection--multiple .select2-selection__placeholder { + float: right; +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--multiple .select2-selection__choice { + margin-left: 0; + margin-right: 6px; +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--multiple .select2-selection__choice__remove { + margin-left: 2px; + margin-right: auto; +} + +/*------------------------------------*\ + #ADDITIONAL GOODIES +\*------------------------------------*/ +/** + * Address Bootstrap's validation states + * + * If a Select2 widget parent has one of Bootstrap's validation state modifier + * classes, adjust Select2's border colors and focus states accordingly. + * You may apply said classes to the Select2 dropdown (body > .select2-container) + * via JavaScript match Bootstraps' to make its styles match. + * + * @see http://getbootstrap.com/css/#forms-control-validation + */ +.has-warning .select2-dropdown, +.has-warning .select2-selection { + border-color: #8a6d3b; +} +.has-warning .select2-container--focus .select2-selection, +.has-warning .select2-container--open .select2-selection { + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #c0a16b; + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #c0a16b; + border-color: #66512c; +} +.has-warning.select2-drop-active { + border-color: #66512c; +} +.has-warning.select2-drop-active.select2-drop.select2-drop-above { + border-top-color: #66512c; +} + +.has-error .select2-dropdown, +.has-error .select2-selection { + border-color: #a94442; +} +.has-error .select2-container--focus .select2-selection, +.has-error .select2-container--open .select2-selection { + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #ce8483; + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #ce8483; + border-color: #843534; +} +.has-error.select2-drop-active { + border-color: #843534; +} +.has-error.select2-drop-active.select2-drop.select2-drop-above { + border-top-color: #843534; +} + +.has-success .select2-dropdown, +.has-success .select2-selection { + border-color: #3c763d; +} +.has-success .select2-container--focus .select2-selection, +.has-success .select2-container--open .select2-selection { + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #67b168; + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #67b168; + border-color: #2b542c; +} +.has-success.select2-drop-active { + border-color: #2b542c; +} +.has-success.select2-drop-active.select2-drop.select2-drop-above { + border-top-color: #2b542c; +} + +/** + * Select2 widgets in Bootstrap Input Groups + * + * When Select2 widgets are combined with other elements using Bootstraps + * "Input Group" component, we don't want specific edges of the Select2 + * container to have a border-radius. + * + * Use .select2-bootstrap-prepend and .select2-bootstrap-append on + * a Bootstrap 3 .input-group to let the contained Select2 widget know which + * edges should not be rounded as they are directly followed by another element. + * + * @see http://getbootstrap.com/components/#input-groups + */ +/** + * Mimick Bootstraps .input-group .form-control styles. + * + * @see https://github.com/twbs/bootstrap/blob/master/less/input-groups.less + */ +.input-group .select2-container--bootstrap { + display: table; + table-layout: fixed; + position: relative; + z-index: 2; + float: left; + width: 100%; + margin-bottom: 0; + /** + * Adjust z-index like Bootstrap does to show the focus-box-shadow + * above appended buttons in .input-group and .form-group. + */ +} +.input-group .select2-container--bootstrap.select2-container--open, .input-group .select2-container--bootstrap.select2-container--focus { + z-index: 3; +} + +.input-group.select2-bootstrap-prepend .select2-container--bootstrap .select2-selection { + border-bottom-left-radius: 0; + border-top-left-radius: 0; +} + +.input-group.select2-bootstrap-append .select2-container--bootstrap .select2-selection { + border-bottom-right-radius: 0; + border-top-right-radius: 0; +} + +/** + * Adjust alignment of Bootstrap buttons in Bootstrap Input Groups to address + * Multi Select2's height which - depending on how many elements have been selected - + * may grow taller than its initial size. + * + * @see http://getbootstrap.com/components/#input-groups + */ +.select2-bootstrap-append .select2-container--bootstrap, +.select2-bootstrap-append .input-group-btn, +.select2-bootstrap-append .input-group-btn .btn, +.select2-bootstrap-prepend .select2-container--bootstrap, +.select2-bootstrap-prepend .input-group-btn, +.select2-bootstrap-prepend .input-group-btn .btn { + vertical-align: top; +} + +/** + * Temporary fix for https://github.com/select2/select2-bootstrap-theme/issues/9 + * + * Provides `!important` for certain properties of the class applied to the + * original ` +
+ +
+ +
+
diff --git a/modules/ServerAPI/src/client/Experiment.coffee b/modules/ServerAPI/src/client/Experiment.coffee index d05c07530..322692c97 100644 --- a/modules/ServerAPI/src/client/Experiment.coffee +++ b/modules/ServerAPI/src/client/Experiment.coffee @@ -143,11 +143,31 @@ class window.Experiment extends BaseEntity attribute: 'recordedDate' message: attrs.subclass+" date must be set" if attrs.subclass? - notebook = @getNotebook().get('stringValue') - if notebook is "" or notebook is undefined or notebook is null - errors.push - attribute: 'notebook' - message: "Notebook must be set" + saveNotebook = true #default + if window.conf.entity?.notebook?.save? + saveNotebook= window.conf.entity.notebook.save + requireNotebook = true #default + if window.conf.entity?.notebook?.require? + requireNotebook= window.conf.entity.notebook.require + if saveNotebook and requireNotebook + notebook = @getNotebook().get('stringValue') + if notebook is "" or notebook is undefined or notebook is null + errors.push + attribute: 'notebook' + message: "Notebook must be set" + saveNotebookPage = true #default + if window.conf.entity?.notebookPage?.save? + saveNotebookPage = window.conf.entity.notebookPage.save + requireNotebookPage = false #default + if window.conf.entity?.notebookPage?.require? + requireNotebookPage= window.conf.entity.notebookPage.require + if saveNotebookPage and requireNotebookPage + notebookPage = @getNotebookPage().get('stringValue') + if notebookPage is "" or notebookPage is undefined or notebookPage is null + errors.push + attribute: 'notebookPage' + message: "Notebook Page must be set" + scientist = @getScientist().get('codeValue') if scientist is "unassigned" or scientist is undefined or scientist is "" or scientist is null errors.push diff --git a/modules/ServerAPI/src/client/Experiment.html b/modules/ServerAPI/src/client/Experiment.html index 2e8516ce5..7ff0eaebb 100644 --- a/modules/ServerAPI/src/client/Experiment.html +++ b/modules/ServerAPI/src/client/Experiment.html @@ -70,13 +70,13 @@
- +
- +
diff --git a/modules/ServerAPI/src/client/Protocol.html b/modules/ServerAPI/src/client/Protocol.html index c8811517a..ade4c32cc 100644 --- a/modules/ServerAPI/src/client/Protocol.html +++ b/modules/ServerAPI/src/client/Protocol.html @@ -59,13 +59,13 @@
- +
- +
diff --git a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee index 7b7b61fc5..377992073 100644 --- a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee @@ -172,7 +172,7 @@ updateExpt = (expt, testMode, callback) -> callback "saveFailed" ) -postExperiment = (exptToSave, testMode, callback) -> +exports.postExperimentInternal = (exptToSave, testMode, callback) -> console.log "posting experiment" serverUtilityFunctions = require './ServerUtilityFunctions.js' # exptToSave = req.body @@ -301,7 +301,7 @@ exports.postExperiment = (req, resp) -> newExptExptItxs = JSON.parse newExptExptItxs delete req.body.newExptExptItxs - postExperiment req.body, req.query.testMode, (response) => + exports.postExperimentInternal req.body, req.query.testMode, (response) => if response.codeName? and (newExptExptItxs.length > 0 or exptExptItxsToIgnore.length > 0) if response.lsKind is "study" _.each exptExptItxsToIgnore, (itx) => @@ -1022,7 +1022,7 @@ exports.postParentExperiment = (req, resp) -> #post parent experiment parentExperiment = JSON.parse req.body.parentExperiment - postExperiment parentExperiment, req.query.testMode, (saveParentExptResp) => + exports.postExperimentInternal parentExperiment, req.query.testMode, (saveParentExptResp) => console.log "post experiment response" console.log saveParentExptResp if typeof saveParentExptResp is "string" and saveParentExptResp.indexOf("saveFailed") > -1 From c294fb3252e0a11f5a61236e96d77d58ae6bd5f3 Mon Sep 17 00:00:00 2001 From: evagao Date: Wed, 10 May 2017 10:46:49 -0700 Subject: [PATCH 006/576] Added configs for showing/requiring notebook and notebook page attributes --- conf/config.properties.example | 7 ++ .../ServerAPI/src/client/BaseEntity.coffee | 65 +++++++++++++++++-- modules/ServerAPI/src/client/BaseEntity.html | 8 ++- .../ServerAPI/src/client/Experiment.coffee | 30 +++++++-- modules/ServerAPI/src/client/Experiment.html | 4 +- modules/ServerAPI/src/client/Protocol.html | 4 +- .../routes/ExperimentServiceRoutes.coffee | 6 +- 7 files changed, 104 insertions(+), 20 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index bc0752ea4..5fee97466 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -389,6 +389,13 @@ client.curvefit.modelfitparameter.classes=[{"code":"4 parameter D-R", "parameter # client.experiment.lockwhenapproved.filter=[{"lsType": "Bio Activity"}] +#Configs for whether notebook attributes for protocols and experiments should be visible and/or required +#Note that notebook page can't be visible if notebook is not visible and page can't be required if notebook is not required +client.entity.notebook.save=true +client.entity.notebook.require=true +client.entity.notebookPage.save=true +client.entity.notebookPage.require=false + # Protocols and experiments which should be hidden (to non-admin users) in the protocol/expt browser when the status is in the config below client.entity.hideStatuses=["deleted"] diff --git a/modules/ServerAPI/src/client/BaseEntity.coffee b/modules/ServerAPI/src/client/BaseEntity.coffee index 2ebdc270b..8b842b735 100644 --- a/modules/ServerAPI/src/client/BaseEntity.coffee +++ b/modules/ServerAPI/src/client/BaseEntity.coffee @@ -144,11 +144,32 @@ class window.BaseEntity extends Backbone.Model attribute: 'recordedDate' message: attrs.subclass+" date must be set" if attrs.subclass? - notebook = @getNotebook().get('stringValue') - if notebook is "" or notebook is undefined or notebook is null - errors.push - attribute: 'notebook' - message: "Notebook must be set" + saveNotebook = true #default + if window.conf.entity?.notebook?.save? + saveNotebook= window.conf.entity.notebook.save + requireNotebook = true #default + if window.conf.entity?.notebook?.require? + requireNotebook= window.conf.entity.notebook.require + if saveNotebook and requireNotebook + notebook = @getNotebook().get('stringValue') + if notebook is "" or notebook is undefined or notebook is null + errors.push + attribute: 'notebook' + message: "Notebook must be set" + + saveNotebookPage = true #default + if window.conf.entity?.notebookPage?.save? + saveNotebookPage = window.conf.entity.notebookPage.save + requireNotebookPage = false #default + if window.conf.entity?.notebookPage?.require? + requireNotebookPage= window.conf.entity.notebookPage.require + if saveNotebookPage and requireNotebookPage + notebookPage = @getNotebookPage().get('stringValue') + if notebookPage is "" or notebookPage is undefined or notebookPage is null + errors.push + attribute: 'notebookPage' + message: "Notebook Page must be set" + scientist = @getScientist().get('codeValue') if scientist is "unassigned" or scientist is undefined or scientist is "" or scientist is null errors.push @@ -278,8 +299,38 @@ class window.BaseEntityController extends AbstractThingFormController #TODO: che @$('.bv_'+subclass+'Kind').html(@model.get('lsKind')) #should get value from protocol create form @$('.bv_details').val(@model.getDetails().get('clobValue')) @$('.bv_comments').val(@model.getComments().get('clobValue')) - @$('.bv_notebook').val @model.getNotebook().get('stringValue') - @$('.bv_notebookPage').val @model.getNotebookPage().get('stringValue') + saveNotebook = true #default + if window.conf.entity?.notebook?.save? + saveNotebook= window.conf.entity.notebook.save + requireNotebook = true #default + if window.conf.entity?.notebook?.require? + requireNotebook= window.conf.entity.notebook.require + if saveNotebook + @$('.bv_notebook').val @model.getNotebook().get('stringValue') + if requireNotebook + console.log "require notebook" + @$('.bv_notebookLabel').html "*Notebook" + saveNotebookPage = true #default + if window.conf.entity?.notebookPage?.save? + saveNotebookPage = window.conf.entity.notebookPage.save + requireNotebookPage = false #default + if window.conf.entity?.notebookPage?.require? + requireNotebookPage= window.conf.entity.notebookPage.require + if saveNotebookPage + @$('.bv_notebookPage').val @model.getNotebookPage().get('stringValue') + if requireNotebookPage + @$('.bv_notebookPageLabel').html "*Notebook Page" + else + @$('.bv_notebookPageLabel').html "Notebook Page" + else + @$('.bv_group_notebookPage').hide() + else + @$('.bv_notebookLabel').html "Notebook" + + else + @$('.bv_group_notebook').hide() + @$('.bv_group_notebookPage').hide() + @$('.bv_status').val(@model.getStatus().get('codeValue')) if @model.isNew() @$('.bv_save').html("Save") diff --git a/modules/ServerAPI/src/client/BaseEntity.html b/modules/ServerAPI/src/client/BaseEntity.html index 646d2cd2c..446c5c110 100644 --- a/modules/ServerAPI/src/client/BaseEntity.html +++ b/modules/ServerAPI/src/client/BaseEntity.html @@ -51,11 +51,17 @@
- +
+
+ +
+ +
+
diff --git a/modules/ServerAPI/src/client/Experiment.coffee b/modules/ServerAPI/src/client/Experiment.coffee index d05c07530..322692c97 100644 --- a/modules/ServerAPI/src/client/Experiment.coffee +++ b/modules/ServerAPI/src/client/Experiment.coffee @@ -143,11 +143,31 @@ class window.Experiment extends BaseEntity attribute: 'recordedDate' message: attrs.subclass+" date must be set" if attrs.subclass? - notebook = @getNotebook().get('stringValue') - if notebook is "" or notebook is undefined or notebook is null - errors.push - attribute: 'notebook' - message: "Notebook must be set" + saveNotebook = true #default + if window.conf.entity?.notebook?.save? + saveNotebook= window.conf.entity.notebook.save + requireNotebook = true #default + if window.conf.entity?.notebook?.require? + requireNotebook= window.conf.entity.notebook.require + if saveNotebook and requireNotebook + notebook = @getNotebook().get('stringValue') + if notebook is "" or notebook is undefined or notebook is null + errors.push + attribute: 'notebook' + message: "Notebook must be set" + saveNotebookPage = true #default + if window.conf.entity?.notebookPage?.save? + saveNotebookPage = window.conf.entity.notebookPage.save + requireNotebookPage = false #default + if window.conf.entity?.notebookPage?.require? + requireNotebookPage= window.conf.entity.notebookPage.require + if saveNotebookPage and requireNotebookPage + notebookPage = @getNotebookPage().get('stringValue') + if notebookPage is "" or notebookPage is undefined or notebookPage is null + errors.push + attribute: 'notebookPage' + message: "Notebook Page must be set" + scientist = @getScientist().get('codeValue') if scientist is "unassigned" or scientist is undefined or scientist is "" or scientist is null errors.push diff --git a/modules/ServerAPI/src/client/Experiment.html b/modules/ServerAPI/src/client/Experiment.html index 2e8516ce5..7ff0eaebb 100644 --- a/modules/ServerAPI/src/client/Experiment.html +++ b/modules/ServerAPI/src/client/Experiment.html @@ -70,13 +70,13 @@
- +
- +
diff --git a/modules/ServerAPI/src/client/Protocol.html b/modules/ServerAPI/src/client/Protocol.html index c8811517a..ade4c32cc 100644 --- a/modules/ServerAPI/src/client/Protocol.html +++ b/modules/ServerAPI/src/client/Protocol.html @@ -59,13 +59,13 @@
- +
- +
diff --git a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee index 7b7b61fc5..377992073 100644 --- a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee @@ -172,7 +172,7 @@ updateExpt = (expt, testMode, callback) -> callback "saveFailed" ) -postExperiment = (exptToSave, testMode, callback) -> +exports.postExperimentInternal = (exptToSave, testMode, callback) -> console.log "posting experiment" serverUtilityFunctions = require './ServerUtilityFunctions.js' # exptToSave = req.body @@ -301,7 +301,7 @@ exports.postExperiment = (req, resp) -> newExptExptItxs = JSON.parse newExptExptItxs delete req.body.newExptExptItxs - postExperiment req.body, req.query.testMode, (response) => + exports.postExperimentInternal req.body, req.query.testMode, (response) => if response.codeName? and (newExptExptItxs.length > 0 or exptExptItxsToIgnore.length > 0) if response.lsKind is "study" _.each exptExptItxsToIgnore, (itx) => @@ -1022,7 +1022,7 @@ exports.postParentExperiment = (req, resp) -> #post parent experiment parentExperiment = JSON.parse req.body.parentExperiment - postExperiment parentExperiment, req.query.testMode, (saveParentExptResp) => + exports.postExperimentInternal parentExperiment, req.query.testMode, (saveParentExptResp) => console.log "post experiment response" console.log saveParentExptResp if typeof saveParentExptResp is "string" and saveParentExptResp.indexOf("saveFailed") > -1 From fde9338c31ef2e2896596c6b606ffe54b1f4b25b Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Fri, 19 May 2017 12:23:59 -0700 Subject: [PATCH 007/576] add chemDoodle json call --- .../src/client/ACASFormChemicalStructure.coffee | 7 +++++++ modules/Components/src/client/ACASFormFields.coffee | 10 +++++++++- 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormChemicalStructure.coffee b/modules/Components/src/client/ACASFormChemicalStructure.coffee index ba9333fb0..b523b3667 100644 --- a/modules/Components/src/client/ACASFormChemicalStructure.coffee +++ b/modules/Components/src/client/ACASFormChemicalStructure.coffee @@ -21,6 +21,10 @@ class window.ACASFormChemicalStructureExampleController extends Backbone.View setMol: (molStr) => @sketcher.setMol molStr + getChemDoodleJSON: => + mol = @sketcher.getChemDoodleJSON() + alert mol + class window.ACASFormChemicalStructureController extends Backbone.View tagName: "DIV" template: _.template($("#ACASFormChemicalStructureControllerView").html()) @@ -52,6 +56,9 @@ class window.ACASFormChemicalStructureController extends Backbone.View molStruct = @windowObj.ChemDoodle.readMOL molStr @windowObj.sketcher.loadMolecule(molStruct); + getChemDoodleJSON: -> + mol = @windowObj.sketcher.getMolecule(); + @windowObj.ChemDoodle.writeJSON([mol],[]) #TODO Why is it making a call to WebHQ outside our server, and make it stop diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 78042ffb0..58728900c 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -201,6 +201,10 @@ class window.ACASFormLSNumericValueFieldController extends ACASFormAbstractField value: null ignored: true + setInputValue: (inputValue) -> + @$('input').val inputValue + + renderModelContent: => @$('input').val @getModel().get('value') if @getModel().has 'unitKind' @@ -345,7 +349,7 @@ class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractF else opts.thingType = @thingType opts.thingKind = @thingKind - @thingSelectController = new ThingLabelComboBoxController opts + @thingSelectController = new ThingLabelComboBoxController opt @thingSelectController.render() render: => @@ -444,6 +448,10 @@ class window.ACASFormLSStringValueFieldController extends ACASFormAbstractFieldC value: null ignored: true + setInputValue: (inputValue) -> + @$('input').val inputValue + + renderModelContent: => @$('input').val @getModel().get('value') super() From 0493d732479270becacff59a9f4943017ee00fd9 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Mon, 22 May 2017 11:53:43 -0700 Subject: [PATCH 008/576] Added routes to bulk post/put experiments, refactored post/put experiment routes to only be for base experiments, changed picklistselect2controller to allow user to define width of picklist and to not have an automatic first option --- modules/Components/src/client/PickList.coffee | 12 +- .../routes/ExperimentServiceRoutes.coffee | 328 ++++-------------- 2 files changed, 69 insertions(+), 271 deletions(-) diff --git a/modules/Components/src/client/PickList.coffee b/modules/Components/src/client/PickList.coffee index 76bfa8c79..37cd72780 100644 --- a/modules/Components/src/client/PickList.coffee +++ b/modules/Components/src/client/PickList.coffee @@ -228,6 +228,14 @@ class window.ComboBoxController extends PickListSelectController class window.PickListSelect2Controller extends PickListSelectController + initialize: => + if @options.width? + @width = @options.width + else + @width = "100%" + + super() + render: => # convert model objects to array of json objects which have 'id' and 'text' properties mappedData = [] @@ -242,7 +250,7 @@ class window.PickListSelect2Controller extends PickListSelectController data: mappedData openOnEnter: false allowClear: true - width: "100%" + width: @width @setSelectedCode @selectedCode @rendered = true @@ -256,7 +264,7 @@ class window.PickListSelect2Controller extends PickListSelectController result = $(@el).val() # if result is null then we'll return the "unassigned" instead if it # was inserted as the first option - if not result? and @insertFirstOption.get('code') is "unassigned" + if not result? and @insertFirstOption != false and @insertFirstOption.get('code') is "unassigned" result = "unassigned" result diff --git a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee index 377992073..2b5f4e290 100644 --- a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee @@ -21,6 +21,8 @@ exports.setupAPIRoutes = (app) -> app.get '/api/experiments/genericSearch/:searchTerm', exports.genericExperimentSearch app.get '/api/experiments/:lsType/:lsKind', exports.experimentsByTypeKind app.post '/api/experiments/getExperimentCodeByLabel/:exptType/:exptKind', exports.getExperimentCodeByLabel + app.post '/api/bulkPostExperiments', exports.bulkPostExperiments + app.put '/api/bulkPostExperiments', exports.bulkPutExperiments exports.setupRoutes = (app, loginRoutes) -> app.get '/api/experiments/codename/:code', loginRoutes.ensureAuthenticated, exports.experimentByCodename @@ -46,6 +48,8 @@ exports.setupRoutes = (app, loginRoutes) -> app.put '/api/experiments/parentExperiment/:id', loginRoutes.ensureAuthenticated, exports.putParentExperiment app.get '/api/experiments/:lsType/:lsKind', loginRoutes.ensureAuthenticated, exports.experimentsByTypeKind app.post '/api/experiments/getExperimentCodeByLabel/:exptType/:exptKind', loginRoutes.ensureAuthenticated, exports.getExperimentCodeByLabel + app.post '/api/bulkPostExperiments', loginRoutes.ensureAuthenticated, exports.bulkPostExperiments + app.put '/api/bulkPostExperiments', loginRoutes.ensureAuthenticated, exports.bulkPutExperiments serverUtilityFunctions = require './ServerUtilityFunctions.js' csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFunctions.js' @@ -303,21 +307,15 @@ exports.postExperiment = (req, resp) -> exports.postExperimentInternal req.body, req.query.testMode, (response) => if response.codeName? and (newExptExptItxs.length > 0 or exptExptItxsToIgnore.length > 0) - if response.lsKind is "study" - _.each exptExptItxsToIgnore, (itx) => - itx.firstExperiment = {id: response.id} - _.each newExptExptItxs, (itx) => - itx.firstExperiment = {id: response.id} - else #is default/expt base - _.each exptExptItxsToIgnore, (itx) => - itx.secondExperiment = {id: response.id} - _.each newExptExptItxs, (itx) => - itx.secondExperiment = {id: response.id} + _.each exptExptItxsToIgnore, (itx) => + itx.secondExperiment = {id: response.id} + _.each newExptExptItxs, (itx) => + itx.secondExperiment = {id: response.id} console.log "exptExptItxsToIgnore" console.log exptExptItxsToIgnore console.log "newExptExptItxs" console.log JSON.stringify newExptExptItxs - createAndUpdateExptExptItxs JSON.stringify(exptExptItxsToIgnore), JSON.stringify(newExptExptItxs), req.query.testMode, (json) => + exports.createAndUpdateExptExptItxsInternal JSON.stringify(exptExptItxsToIgnore), JSON.stringify(newExptExptItxs), req.query.testMode, (json) => console.log "finished createAndUpdateExptExptItxs" console.log exptExptItxsToIgnore console.log newExptExptItxs @@ -326,46 +324,6 @@ exports.postExperiment = (req, resp) -> console.log "error creating and updating expt expt itxs" resp.statusCode = 500 resp.json "error creating and updating expt expt itxs" - else if response.lsKind is "default" - #if study step itx(s) was ignored/created, remove/add the study step(s) - #remove study step for ignored itx - studyStepItxToIgnore = _.filter exptExptItxsToIgnore, (itx) => - itx.lsType is "has member" and itx.lsKind is "parent_study child" - studyStepItxToCreate = _.filter newExptExptItxs, (itx) => - itx.lsType is "has member" and itx.lsKind is "parent_study child" - user = response.recordedBy - if studyStepItxToIgnore.length is 1 #only expect max of 1 study step itx to be affected - studyExptCodeNameToIgnoreStep = _.pluck(studyStepItxToIgnore, 'firstExperiment')[0].codeName - studyExptCodeNameToCreateStep = _.pluck(newExptExptItxs, 'firstExperiment')[0].codeName - secondExptCodeName = response.codeName - ignoreStudyStepInStudyExpt studyExptCodeNameToIgnoreStep, secondExptCodeName, (message1) => - if message1.indexOf 'Failed' > -1 - resp.statusCode = 500 - resp.json message1 - else if newExptExptItxs.length is 1 - createStudyStepInStudyExpt studyExptCodeNameToCreateStep, secondExptCodeName, user, (message2) => - if message2.indexOf 'Failed' > -1 - resp.statusCode = 500 - resp.json message2 - else - resp.json response - else - resp.json response - else if studyStepItxToCreate.length is 1 - studyExptCodeNameToCreateStep = _.pluck(newExptExptItxs, 'firstExperiment')[0].codeName - secondExptCodeName = response.codeName - console.log "first expt to create study step" - console.log _.pluck(studyStepItxToCreate,'firstExperiment')[0] - createStudyStepInStudyExpt studyExptCodeNameToCreateStep, secondExptCodeName, user, (message2) => - console.log "createStudyStepInStudyExpt - done" - console.log message2 - if message2.indexOf('Failed')> -1 - resp.statusCode = 500 - resp.json message2 - else - resp.json response - else - resp.json response else resp.json response else @@ -399,13 +357,15 @@ exports.putExperiment = (req, resp) -> console.log "put experiment" #remove the itxs attributes if needed - newExptExptItxs = "[]" - exptExptItxsToIgnore = "[]" + newExptExptItxs = [] + exptExptItxsToIgnore = [] if req.body.exptExptItxsToIgnore? exptExptItxsToIgnore = req.body.exptExptItxsToIgnore + exptExptItxsToIgnore = JSON.parse exptExptItxsToIgnore delete req.body.exptExptItxsToIgnore if req.body.newExptExptItxs? newExptExptItxs = req.body.newExptExptItxs + newExptExptItxs = JSON.parse newExptExptItxs delete req.body.newExptExptItxs exptToSave = req.body @@ -414,25 +374,13 @@ exports.putExperiment = (req, resp) -> completeExptUpdate = -> updateExpt exptToSave, req.query.testMode, (updatedExpt) -> - if updatedExpt.codeName? and (JSON.parse(newExptExptItxs).length > 0 or JSON.parse(exptExptItxsToIgnore).length > 0) - exptExptItxsToIgnore = JSON.parse exptExptItxsToIgnore - if updatedExpt.lsKind is "study" - _.each exptExptItxsToIgnore, (itx) => - itx.firstExperiment = {id: updatedExpt.id} - newExptExptItxs = JSON.parse newExptExptItxs - _.each newExptExptItxs, (itx) => - itx.firstExperiment = {id: updatedExpt.id} - else #is default/expt base - _.each exptExptItxsToIgnore, (itx) => - itx.secondExperiment = {id: updatedExpt.id} - newExptExptItxs = JSON.parse newExptExptItxs - _.each newExptExptItxs, (itx) => - itx.secondExperiment = {id: updatedExpt.id} - console.log "exptExptItxsToIgnore" - console.log JSON.stringify exptExptItxsToIgnore - console.log "newExptExptItxs" - console.log JSON.stringify newExptExptItxs - createAndUpdateExptExptItxs JSON.stringify(exptExptItxsToIgnore), JSON.stringify(newExptExptItxs), req.query.testMode, (json) => + if updatedExpt.codeName? and (newExptExptItxs.length > 0 or exptExptItxsToIgnore.length > 0) + #is default/expt base + _.each exptExptItxsToIgnore, (itx) => + itx.secondExperiment = {id: updatedExpt.id} + _.each newExptExptItxs, (itx) => + itx.secondExperiment = {id: updatedExpt.id} + exports.createAndUpdateExptExptItxsInternal JSON.stringify(exptExptItxsToIgnore), JSON.stringify(newExptExptItxs), req.query.testMode, (json) => console.log "finished createAndUpdateExptExptItxs" console.log exptExptItxsToIgnore console.log newExptExptItxs @@ -441,42 +389,6 @@ exports.putExperiment = (req, resp) -> console.log "error creating and updating expt expt itxs" resp.statusCode = 500 resp.json "error creating and updating expt expt itxs" - else if updatedExpt.lsKind is "default" - #if study step itx(s) was ignored/created, remove/add the study step(s) - #remove study step for ignored itx - studyStepItxToIgnore = _.filter exptExptItxsToIgnore, (itx) => - itx.lsType is "has member" and itx.lsKind is "parent_study child" - studyStepItxToCreate = _.filter newExptExptItxs, (itx) => - itx.lsType is "has member" and itx.lsKind is "parent_study child" - if studyStepItxToIgnore.length is 1 #only expect max of 1 study step itx to be affected - studyExptCodeNameToIgnoreStep = _.pluck(studyStepItxToIgnore, 'firstExperiment')[0].codeName - studyExptCodeNameToCreateStep = _.pluck(newExptExptItxs, 'firstExperiment')[0].codeName - secondExptCodeName = updatedExpt.codeName - user = updatedExpt.recordedBy - ignoreStudyStepInStudyExpt studyExptCodeNameToIgnoreStep, secondExptCodeName, (message1) => - if message1.indexOf('Failed') > -1 - resp.statusCode = 500 - resp.json message1 - else if newExptExptItxs.length is 1 - createStudyStepInStudyExpt studyExptCodeNameToCreateStep, secondExptCodeName, user, (message2) => - if message2.indexOf('Failed') > -1 - resp.statusCode = 500 - resp.json message2 - else - resp.json updatedExpt - else - resp.json updatedExpt - else if studyStepItxToCreate.length is 1 - studyExptCodeNameToCreateStep = _.pluck(newExptExptItxs, 'firstExperiment')[0].codeName - secondExptCodeName = updatedExpt.codeName - createStudyStepInStudyExpt studyExptCodeNameToCreateStep, secondExptCodeName, user, (message2) => - if message2.indexOf('Failed') > -1 - resp.statusCode = 500 - resp.json message2 - else - resp.json updatedExpt - else - resp.json updatedExpt else resp.json updatedExpt else @@ -783,7 +695,7 @@ exports.putExptExptItxs = (req, resp) -> resp.statusCode = 500 resp.json updatedExptExptItxs -createAndUpdateExptExptItxs = (exptExptItxsToIgnore, newExptExptItxs, testMode, callback) -> +exports.createAndUpdateExptExptItxsInternal = (exptExptItxsToIgnore, newExptExptItxs, testMode, callback) -> putExptExptItxs exptExptItxsToIgnore, testMode, (updatedExptExptItxs) -> if updatedExptExptItxs.indexOf("saveFailed") > -1 callback updatedExptExptItxs @@ -795,167 +707,19 @@ createAndUpdateExptExptItxs = (exptExptItxsToIgnore, newExptExptItxs, testMode, callback updatedExptExptItxs.concat newExptExptItxs exports.createAndUpdateExptExptItxs = (req, resp) -> - createAndUpdateExptExptItxs req.body.exptExptItxsToIgnore, req.body.newExptExptItxs, req.query.testMode, (json) => + exports.createAndUpdateExptExptItxsInternal req.body.exptExptItxsToIgnore, req.body.newExptExptItxs, req.query.testMode, (json) => if json.indexOf("saveFailed") > -1 resp.statusCode = 500 resp.json json -ignoreStudyStepInStudyExpt = (firstExptCodeName, secondExptCodeName, callback) -> - console.log "ignoreStudyStepInStudyExpt" - console.log "firstExptCodeName: " + firstExptCodeName - console.log "secondExptCodeName: " + secondExptCodeName - config = require '../conf/compiled/conf.js' - baseurl = config.all.client.service.persistence.fullpath+"experiments/codename/"+firstExptCodeName - request = require 'request' - request( - method: 'GET' - url: baseurl - json: true - , (error, response, firstExptJson) => - if !error && response.statusCode == 200 - #find state to ignore - lsStates = _.filter firstExptJson.lsStates, (state) => - !state.ignored and state.lsType is "study tracking" and state.lsKind is "study steps" - stepToIgnore = _.filter lsStates, (state) => - filteredVals = _.filter state.lsValues, (val) => - val.lsType is 'codeValue' and val.lsKind is "step experiment" and val.codeValue is secondExptCodeName and !(val.ignored) - filteredVals.length > 0 - if stepToIgnore.length > 0 - stepToIgnore = stepToIgnore[0] - stepToIgnore.ignored = true - firstExptJson.lsStates = [stepToIgnore] - console.log "ignoreStudyStepInStudyExpt: step to ignore" - #put study expt - updateExpt firstExptJson, false, (updatedFirstExpt) => - if updatedFirstExpt.codeName? - #success, create new step for newly added step expt - #get study expt to add the study step - callback "success: ignored study step for old expt" - else - callback "Failed: error ignoring study step for study experiment" - else - callback "Failed: could not get study experiment to update" - ) - -createStudyStepInStudyExpt = (firstExptCodeName, secondExptCodeName, user, callback) -> - console.log "createStudyStepInStudyExpt" - console.log "firstExptCodeName: " + firstExptCodeName - console.log "secondExptCodeName: " + secondExptCodeName - config = require '../conf/compiled/conf.js' - baseurl = config.all.client.service.persistence.fullpath+"experiments/codename/"+firstExptCodeName - request = require 'request' - request( - method: 'GET' - url: baseurl - json: true - , (error, response, firstExptJson) => - if !error && response.statusCode == 200 - lsStates = _.filter firstExptJson.lsStates, (state) => - !state.ignored and state.lsType is "study tracking" and state.lsKind is "study steps" - #find step order, filter for steps with uncategorized as step order - uncategorizedStates = _.filter lsStates, (state) => - filteredVals = _.filter state.lsValues, (val) => - val.lsType is 'stringValue' and val.lsKind is "step category" and val.stringValue is "Uncategorized" and !(val.ignored) - filteredVals.length > 0 - console.log "uncategorized states" - console.log JSON.stringify uncategorizedStates - stepOrder = uncategorizedStates.length - if uncategorizedStates.length > 0 - stepCategoryOrderVal = _.filter uncategorizedStates[0].lsValues, (val) => - val.lsType is 'numericValue' and val.lsKind is 'step category order' and !val.ignored - stepCategoryOrder = stepCategoryOrderVal[0].numericValue - else - #stepCategoryOrder = number of stepCategories - #group by stepCategory - groupedStepCategory = _.groupBy lsStates, (state) => - stepCategoryOrder = _.filter state.lsValues, (val) => - console.log "val - here" - console.log val - val.lsKind is 'step category order' and !val.ignored - stepCategoryOrder[0].numericValue - #find max key of returned object - console.log "groupedStepCategory" - console.log groupedStepCategory - stepCategoryOrder = Number(_.max Object.keys(groupedStepCategory))+1 - console.log "stepCategory Order: " - console.log stepCategoryOrder - firstExptJson.lsStates = [ - "ignored": false, - "lsKind": "study steps", - "lsType": "study tracking", - "lsValues": [ - { - "ignored": false, - "lsKind": "step order", - "lsType": "numericValue", - "numericValue": stepOrder, - "recordedBy": user, - "recordedDate": new Date().getTime(), - }, - { - "ignored": false, - "lsKind": "step category order", - "lsType": "numericValue", - "numericValue": stepCategoryOrder, - "recordedBy": user, - "recordedDate": new Date().getTime(), - }, - { - "ignored": false, - "lsKind": "step category", - "lsType": "stringValue", - "recordedBy": user, - "recordedDate": new Date().getTime(), - "stringValue": "Uncategorized", - }, - { - "ignored": false, - "lsKind": "step name", - "lsType": "stringValue", - "stringValue": secondExptCodeName - "recordedBy": user, - "recordedDate": new Date().getTime(), - }, - { - "ignored": false, - "lsKind": "step experiment", - "lsType": "codeValue", - "codeValue": secondExptCodeName - "recordedBy": user, - "recordedDate": new Date().getTime(), - } - ] - "recordedBy": user, - "recordedDate": new Date().getTime() - ] - - #put study expt - console.log "updatedFirstExpt - request" - console.log JSON.stringify firstExptJson -# console.log JSON.stringify firstExptJson2 - updateExpt firstExptJson, false, (updatedFirstExpt) => - console.log "updatedFirstExpt - response" - console.log JSON.stringify updatedFirstExpt - if updatedFirstExpt.codeName? - #success, create new step for newly added step expt - #get study expt to add the study step - callback "success: created new study step for study expt" - else - callback "Failed: error ignoring study step for study experiment" - else - callback "Failed: could not get study experiment to update" - ) - - - exports.experimentsByCodeNamesArray = (req, resp) -> - experimentsByCodeNamesArray req.body.data, req.query.option, req.query.testMode, (returnedExpts) -> + exports.experimentsByCodeNamesArrayInternal req.body.data, req.query.option, req.query.testMode, (returnedExpts) -> if returnedExpts.indexOf("Failed") > -1 resp.statusCode = 500 resp.json returnedExpts -experimentsByCodeNamesArray = (codeNamesArray, returnOption, testMode, callback) -> +exports.experimentsByCodeNamesArrayInternal = (codeNamesArray, returnOption, testMode, callback) -> if testMode or global.specRunnerTestmode callback JSON.stringify "stubsMode not implemented" else @@ -996,7 +760,7 @@ exports.getExptExptItxsToDisplay = (req, resp) -> exptExptItxs = _.filter JSON.parse(exptExptItxs), (itx) -> !itx.ignored secondExpts = _.pluck (_.pluck exptExptItxs, 'secondExperiment'), 'codeName' - experimentsByCodeNamesArray secondExpts, "stubwithprot", req.query.testMode, (returnedExpts) -> + exports.experimentsByCodeNamesArrayInternal secondExpts, "stubwithprot", req.query.testMode, (returnedExpts) -> #add returnedExpts information into the secondExperiment attribute _.each exptExptItxs, (itx) -> secondExptInfo = _.where(returnedExpts, experimentCodeName: itx.secondExperiment.codeName)[0] @@ -1045,7 +809,7 @@ exports.postParentExperiment = (req, resp) -> console.log childExperiments #bulk post of all the experiments - bulkPostExperiments childExperiments, (saveChildExptsResp) => + exports.bulkPostExperimentsInternal childExperiments, (saveChildExptsResp) => if typeof saveChildExptsResp is "string" and saveChildExptsResp.indexOf("saveFailed") > -1 resp.statusCode = 500 resp.json saveChildExptsResp @@ -1071,8 +835,11 @@ exports.postParentExperiment = (req, resp) -> #return resp.json saveParentExptResp +exports.bulkPostExperiments = (req, resp) -> + exports.bulkPostExperimentsInternal req.body, (response) => + resp.json response -bulkPostExperiments = (exptsArray, callback) -> +exports.bulkPostExperimentsInternal = (exptsArray, callback) -> console.log "bulkPostExperiments" console.log JSON.stringify exptsArray config = require '../conf/compiled/conf.js' @@ -1084,14 +851,37 @@ bulkPostExperiments = (exptsArray, callback) -> json: true , (error, response, json) => if !error && response.statusCode == 201 -#respond with the saved parent response - savedChildExperiments = json - console.log "savedChildExperiments" - console.log savedChildExperiments - callback savedChildExperiments + callback json else console.log "got error posting child experiments" - callback JSON.stringify "post child experiments saveFailed: " + JSON.stringify error + callback JSON.stringify "bulk post experiments saveFailed: " + JSON.stringify error + ) + +exports.bulkPutExperiments = (req, resp) -> + exports.bulkPutExperimentsInternal req.body, (response) => + resp.json response + +exports.bulkPutExperimentsInternal = (exptsArray, callback) -> + console.log "bulkPutExperiments" + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"/experiments/jsonArray" + console.log "bulkPutExperimentsInternal" + console.log baseurl + console.log exptsArray + request( + method: 'PUT' + url: baseurl + body: exptsArray + json: true + , (error, response, json) => + console.log "bulkPutExperimentsInternal" + console.log response.statusCode + if !error && response.statusCode == 200 + callback json + else + console.log "got error bulk updating experiments" + console.log error + callback JSON.stringify "bulk update experiments saveFailed: " + JSON.stringify error ) exports.putParentExperiment = (req, resp) -> From 6dccf7b27f94dd9d6fa2f7e126270fc27a7c6f3b Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Wed, 24 May 2017 14:54:38 -0600 Subject: [PATCH 009/576] Updating how ACAS starts up so websockets can be used. Configured websockets to have access to the passport / connect session. --- app_api_template.coffee | 6 ++--- app_template.coffee | 25 +++++++++++++++---- .../src/server/PrepareModuleIncludes.coffee | 7 +++++- .../routes/RequiredClientScripts_template.js | 3 ++- package.json | 4 +++ 5 files changed, 35 insertions(+), 10 deletions(-) diff --git a/app_api_template.coffee b/app_api_template.coffee index c6eae3270..48643f964 100644 --- a/app_api_template.coffee +++ b/app_api_template.coffee @@ -45,12 +45,12 @@ startApp = -> console.error 'Caught api exception: ' + err.stack return - ###TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES### - - http.createServer(app).listen(app.get('port'), -> + httpServer = http.createServer(app).listen(app.get('port'), -> console.log("ACAS API server listening on port " + app.get('port')) ) + io = require('socket.io')(httpServer) + ###TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES### csUtilities.logUsage("ACAS API server started", "started", "") diff --git a/app_template.coffee b/app_template.coffee index 555355120..5f1942e5f 100644 --- a/app_template.coffee +++ b/app_template.coffee @@ -57,7 +57,8 @@ startApp = -> # next() loginRoutes = require './routes/loginRoutes' - + MemoryStore = express.session.MemoryStore; + sessionStore = new MemoryStore(); global.app = express() app.configure -> app.set 'port', config.all.client.port @@ -70,6 +71,7 @@ startApp = -> app.use express.session secret: 'acas needs login' cookie: maxAge: 365 * 24 * 60 * 60 * 1000 + store: sessionStore # MemoryStore is used automatically if no "store" field is set, but we need a handle on the sessionStore object for Socket.IO, so we'll manually create the store so we have a handle on the object app.use flash() app.use passport.initialize() app.use passport.session pauseStream: true @@ -86,11 +88,11 @@ startApp = -> # index routes indexRoutes = require './routes/index.js' indexRoutes.setupRoutes(app, loginRoutes) - ###TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES### + if not config.all.client.use.ssl - http.createServer(app).listen(app.get('port'), -> - console.log("Express server listening on port " + app.get('port')) + httpServer = http.createServer(app).listen(app.get('port'), -> + console.log("ACAS API server listening on port " + app.get('port')) ) else console.log "------ Starting in SSL Mode" @@ -101,11 +103,24 @@ startApp = -> cert: fs.readFileSync config.all.server.ssl.cert.file.path ca: fs.readFileSync config.all.server.ssl.cert.authority.file.path passphrase: config.all.server.ssl.cert.passphrase - https.createServer(sslOptions, app).listen(app.get('port'), -> + httpServer = https.createServer(sslOptions, app).listen(app.get('port'), -> console.log("Express server listening on port " + app.get('port')) ) #TODO hack to prevent bug: https://github.com/mikeal/request/issues/418 process.env.NODE_TLS_REJECT_UNAUTHORIZED = "0" + io = require('socket.io')(httpServer) + bundle = require('socket.io-bundle') + passportSocketIo = require('passport.socketio') + cookieParser = require('cookie-parser') + + io.use(passportSocketIo.authorize({ + key: 'connect.sid', + secret: 'acas needs login', + store: sessionStore, + passport: passport, + cookieParser: cookieParser + })) + ###TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES### options = if stubsMode then ["stubsMode"] else [] options.push ['--color'] diff --git a/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee b/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee index dc69d0562..d81ca69f1 100644 --- a/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee +++ b/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee @@ -110,8 +110,13 @@ prepRouteIncludes = (apiMode) -> if apiMode includeStr += '\tif (routeSet_'+routeNum+'.setupAPIRoutes) {\n' includeStr += '\t\trouteSet_'+routeNum+'.setupAPIRoutes(app); }\n' + includeStr += '\tif (routeSet_'+routeNum+'.setupChannels) {\n' + includeStr += '\trouteSet_'+routeNum+'.setupChannels(io, loginRoutes); }\n' else - includeStr += '\trouteSet_'+routeNum+'.setupRoutes(app, loginRoutes);\n' + includeStr += '\tif (routeSet_'+routeNum+'.setupRoutes) {\n' + includeStr += '\trouteSet_'+routeNum+'.setupRoutes(app, loginRoutes);\n }' + includeStr += '\tif (routeSet_'+routeNum+'.setupChannels) {\n' + includeStr += '\trouteSet_'+routeNum+'.setupChannels(io, loginRoutes);\n }' routeLines += includeStr routeNum++ diff --git a/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js b/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js index e19e354ee..bbee713e2 100644 --- a/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js +++ b/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js @@ -25,7 +25,8 @@ exports.requiredScripts = [ '/lib/spin/js/spin.js', '/lib/spin/js/jquery-spin.js', '/lib/handsontable/dist/handsontable.full.js', - '/lib/select2-4.0.3/dist/js/select2.full.js' + '/lib/select2-4.0.3/dist/js/select2.full.js', + '/socket.io/socket.io.js' ]; exports.applicationScripts = [ diff --git a/package.json b/package.json index ac9580f0f..858a8ee2e 100644 --- a/package.json +++ b/package.json @@ -21,6 +21,7 @@ "backbone": "^1.2.3", "backbone-validation": "^0.11.5", "chai": "^3.5.0", + "cookie-parser": "^1.4.3", "connect-flash": "~0.1.0", "cron": "*", "csv-parse": "^1.1.1", @@ -51,6 +52,9 @@ "properties-parser": "*", "request": "2.34.0", "shelljs": "0.6.0", + "socket.io": "^1.7.3", + "passport.socketio": "^3.7.0", + "socket.io-bundle": "^0.1.2 ", "style-loader": "*", "temporary": ">= 0.0.0", "underscore": ">= 0.0.0", From 2ebf553af2bebf0d8e86df23c4f9fc5d89f7f8e5 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Wed, 24 May 2017 16:48:15 -0600 Subject: [PATCH 010/576] Adding feature to allow user to change their user name. --- app_template.coffee | 2 + .../ModuleMenus/src/client/ModuleMenus.coffee | 34 ++++++++++++++++ .../src/client/ModuleMenusView.html | 25 ++++++++++++ .../server/routes/ModuleMenusRoutes.coffee | 40 +++++++++++++++++++ package.json | 1 + 5 files changed, 102 insertions(+) create mode 100644 modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee diff --git a/app_template.coffee b/app_template.coffee index 5f1942e5f..2e42ff394 100644 --- a/app_template.coffee +++ b/app_template.coffee @@ -112,6 +112,8 @@ startApp = -> bundle = require('socket.io-bundle') passportSocketIo = require('passport.socketio') cookieParser = require('cookie-parser') +# sharedsession = require("express-socket.io-session") +# io.use(sharedsession(express.session)) io.use(passportSocketIo.authorize({ key: 'connect.sid', diff --git a/modules/ModuleMenus/src/client/ModuleMenus.coffee b/modules/ModuleMenus/src/client/ModuleMenus.coffee index 292709773..9d89ff327 100644 --- a/modules/ModuleMenus/src/client/ModuleMenus.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenus.coffee @@ -5,6 +5,8 @@ class window.ModuleMenusController extends Backbone.View events: -> 'click .bv_headerName': "handleHome" 'click .bv_toggleModuleMenuControl': "handleToggleMenus" + 'click .bv_loginUserFirstName': 'handleLoginUserFirstNameClick' + 'click .bv_changeNameBtn': 'handleChangeNameBtnClick' # 'click .bv_showModuleMenuControl': "handleShowMenus" window.onbeforeunload = () -> @@ -58,6 +60,15 @@ class window.ModuleMenusController extends Backbone.View modLink = '
  • '+module.displayName+'
    • ' @$('.bv_externalACASModules').append modLink + @socket = io('/user:loggedin') + @socket.on('connect', @handleConnected) + @socket.on('connect_error', @handleConnectError) + @socket.on('loggedOn', @handleLoggedOn) + @socket.on('loggedOff', @handleLoggedOn) + @socket.on('usernameUpdated', @handleNameChanged) + + @disconnectedAfterLogin = false + render: => if window.AppLaunchParams.deployMode? unless window.AppLaunchParams.deployMode.toUpperCase() =="PROD" @@ -88,5 +99,28 @@ class window.ModuleMenusController extends Backbone.View @$('.bv_mainModuleWellWrapper').removeClass 'span9' @$('.bv_mainModuleWellWrapper').addClass 'span11' + handleConnected: => + console.log "handleConnected" + + handleConnectError: => + @disconnectedAfterLogin = true + console.log "handleConnectError" + + handleLoggedOn: (numberOfLogins) -> + console.log "you're loggedin in this many places: ", numberOfLogins + + handleLoggedOff: (numberOfLogins) -> + console.log "you're loggedin in this many places: ", numberOfLogins + + handleLoginUserFirstNameClick: => + @$(".bv_changeUserName").modal "show" + handleChangeNameBtnClick: (e) => + e.preventDefault() + firstName = @$(".bv_firstName").val() + @socket.emit('changeUserName', firstName) + @$(".bv_firstName").val('') + @$(".bv_changeUserName").modal "hide" + handleNameChanged: (updatedFirstName) => + @$(".bv_loginUserFirstName").html updatedFirstName diff --git a/modules/ModuleMenus/src/client/ModuleMenusView.html b/modules/ModuleMenus/src/client/ModuleMenusView.html index 5bbe8c10e..38dcc798b 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusView.html +++ b/modules/ModuleMenus/src/client/ModuleMenusView.html @@ -5,6 +5,7 @@

    + Logged in as First Name Last Name @@ -58,4 +59,28 @@

    Welc

    © John McNeil & Company 2012-2015

    + +
    +
    +

    Error

    +
    +
    + ACAS is currently unavailable. +
    +
    + Login +
    +
    + +
    +
    +

    Change User Name

    +
    +
    + +
    +
    + Change My Name +
    +
    diff --git a/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee b/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee new file mode 100644 index 000000000..8a2a5a724 --- /dev/null +++ b/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee @@ -0,0 +1,40 @@ +_ = require 'underscore' + +exports.setupChannels = (io, loginRoutes) -> + nsp = io.of('/user:loggedin') + connectedUsers = {} + nsp.on('connection', (socket) => + userName = getUserNameFromSession(socket) + unless connectedUsers[userName]? + connectedUsers[userName] = [] + connectedUsers[userName].push socket.id + totalNumberOfConnectionsForUser = _.size(connectedUsers[userName]) + broadcastMessageToSpecificClients(connectedUsers[userName], 'loggedOn', totalNumberOfConnectionsForUser, socket) + socket.emit('loggedOn', totalNumberOfConnectionsForUser) + socket.on('disconnect', => + userName = getUserNameFromSession(socket) + clientConnections = connectedUsers[userName] + connectedUsers[userName] = _.without(clientConnections, socket.id) + totalNumberOfConnectionsForUser = _.size(connectedUsers[userName]) + broadcastMessageToSpecificClients(connectedUsers[userName], 'loggedOff', totalNumberOfConnectionsForUser, socket) + ) + + socket.on('changeUserName', (updatedUsername) => + userName = getUserNameFromSession(socket) + updateUserFirstNameInSession(updatedUsername, socket) + broadcastMessageToSpecificClients(connectedUsers[userName], 'usernameUpdated', updatedUsername, socket) + socket.emit('usernameUpdated', updatedUsername) + ) + ) + +getUserNameFromSession = (socket) -> + return socket.request.user.username + +updateUserFirstNameInSession = (updatedFirstName, socket) -> + socket.request.user.firstName = updatedFirstName + +broadcastMessageToSpecificClients = (socketIds, messageName, payload, socket) -> + console.log "broadcastMessageToSpecificClients" + _.each(socketIds, (socketId) -> + socket.broadcast.to(socketId).emit(messageName, payload) + ) \ No newline at end of file diff --git a/package.json b/package.json index 858a8ee2e..217fd329a 100644 --- a/package.json +++ b/package.json @@ -28,6 +28,7 @@ "each": ">= 0.0.0", "express": "3.0.2", "extract-text-webpack-plugin": "*", + "express-socket.io-session": "^1.3.2", "file-loader": "*", "flat": "*", "forever-monitor": "*", From e2c6db0b7e111a9572fa5fd6d856d63693dd745d Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Thu, 25 May 2017 09:40:25 -0600 Subject: [PATCH 011/576] Updated how the session store is accessed from socket.io Changes made to the session from within socket are now persisted to the session. --- app_template.coffee | 3 -- .../src/server/PrepareModuleIncludes.coffee | 4 +-- .../ModuleMenus/src/client/ModuleMenus.coffee | 1 + .../server/routes/ModuleMenusRoutes.coffee | 29 +++++++++++++------ package.json | 2 -- 5 files changed, 23 insertions(+), 16 deletions(-) diff --git a/app_template.coffee b/app_template.coffee index 2e42ff394..2594450bc 100644 --- a/app_template.coffee +++ b/app_template.coffee @@ -109,11 +109,8 @@ startApp = -> #TODO hack to prevent bug: https://github.com/mikeal/request/issues/418 process.env.NODE_TLS_REJECT_UNAUTHORIZED = "0" io = require('socket.io')(httpServer) - bundle = require('socket.io-bundle') passportSocketIo = require('passport.socketio') cookieParser = require('cookie-parser') -# sharedsession = require("express-socket.io-session") -# io.use(sharedsession(express.session)) io.use(passportSocketIo.authorize({ key: 'connect.sid', diff --git a/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee b/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee index d81ca69f1..b7ccfca4c 100644 --- a/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee +++ b/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee @@ -111,12 +111,12 @@ prepRouteIncludes = (apiMode) -> includeStr += '\tif (routeSet_'+routeNum+'.setupAPIRoutes) {\n' includeStr += '\t\trouteSet_'+routeNum+'.setupAPIRoutes(app); }\n' includeStr += '\tif (routeSet_'+routeNum+'.setupChannels) {\n' - includeStr += '\trouteSet_'+routeNum+'.setupChannels(io, loginRoutes); }\n' + includeStr += '\trouteSet_'+routeNum+'.setupChannels(io, {}, loginRoutes); }\n' else includeStr += '\tif (routeSet_'+routeNum+'.setupRoutes) {\n' includeStr += '\trouteSet_'+routeNum+'.setupRoutes(app, loginRoutes);\n }' includeStr += '\tif (routeSet_'+routeNum+'.setupChannels) {\n' - includeStr += '\trouteSet_'+routeNum+'.setupChannels(io, loginRoutes);\n }' + includeStr += '\trouteSet_'+routeNum+'.setupChannels(io, sessionStore, loginRoutes);\n }' routeLines += includeStr routeNum++ diff --git a/modules/ModuleMenus/src/client/ModuleMenus.coffee b/modules/ModuleMenus/src/client/ModuleMenus.coffee index 9d89ff327..1c9b9d8f8 100644 --- a/modules/ModuleMenus/src/client/ModuleMenus.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenus.coffee @@ -124,3 +124,4 @@ class window.ModuleMenusController extends Backbone.View handleNameChanged: (updatedFirstName) => @$(".bv_loginUserFirstName").html updatedFirstName + AppLaunchParams.loginUserName = updatedFirstName diff --git a/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee b/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee index 8a2a5a724..14545e71f 100644 --- a/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee +++ b/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee @@ -1,6 +1,6 @@ _ = require 'underscore' -exports.setupChannels = (io, loginRoutes) -> +exports.setupChannels = (io, sessionStore, loginRoutes) -> nsp = io.of('/user:loggedin') connectedUsers = {} nsp.on('connection', (socket) => @@ -11,8 +11,8 @@ exports.setupChannels = (io, loginRoutes) -> totalNumberOfConnectionsForUser = _.size(connectedUsers[userName]) broadcastMessageToSpecificClients(connectedUsers[userName], 'loggedOn', totalNumberOfConnectionsForUser, socket) socket.emit('loggedOn', totalNumberOfConnectionsForUser) + socket.on('disconnect', => - userName = getUserNameFromSession(socket) clientConnections = connectedUsers[userName] connectedUsers[userName] = _.without(clientConnections, socket.id) totalNumberOfConnectionsForUser = _.size(connectedUsers[userName]) @@ -20,21 +20,32 @@ exports.setupChannels = (io, loginRoutes) -> ) socket.on('changeUserName', (updatedUsername) => - userName = getUserNameFromSession(socket) - updateUserFirstNameInSession(updatedUsername, socket) + sessionID = getSessionID(socket) + updateUserNameInSession(updatedUsername, sessionStore, sessionID) broadcastMessageToSpecificClients(connectedUsers[userName], 'usernameUpdated', updatedUsername, socket) socket.emit('usernameUpdated', updatedUsername) ) ) getUserNameFromSession = (socket) -> - return socket.request.user.username + unless socket.request.user.originalLoginUserName? + console.log "using original login name" + return socket.request.user.originalLoginUserName + else + return socket.request.user.username -updateUserFirstNameInSession = (updatedFirstName, socket) -> - socket.request.user.firstName = updatedFirstName +updateUserNameInSession = (updatedUserName, sessionStore, sessionId) -> + parsedCookie = JSON.parse(sessionStore.sessions[sessionId]) + unless parsedCookie.passport.user.originalLoginUserName? + parsedCookie.passport.user.originalLoginUserName = parsedCookie.passport.user.username + parsedCookie.passport.user.username = updatedUserName + parsedCookie.passport.user.firstName = updatedUserName + sessionStore.sessions[sessionId] = JSON.stringify(parsedCookie) broadcastMessageToSpecificClients = (socketIds, messageName, payload, socket) -> - console.log "broadcastMessageToSpecificClients" _.each(socketIds, (socketId) -> socket.broadcast.to(socketId).emit(messageName, payload) - ) \ No newline at end of file + ) + +getSessionID = (socket) -> + socket.request.sessionID \ No newline at end of file diff --git a/package.json b/package.json index 217fd329a..d946dcfb0 100644 --- a/package.json +++ b/package.json @@ -28,7 +28,6 @@ "each": ">= 0.0.0", "express": "3.0.2", "extract-text-webpack-plugin": "*", - "express-socket.io-session": "^1.3.2", "file-loader": "*", "flat": "*", "forever-monitor": "*", @@ -55,7 +54,6 @@ "shelljs": "0.6.0", "socket.io": "^1.7.3", "passport.socketio": "^3.7.0", - "socket.io-bundle": "^0.1.2 ", "style-loader": "*", "temporary": ">= 0.0.0", "underscore": ">= 0.0.0", From cff54f42e6dcdf4d568b172415369fbf1cfea692 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Thu, 25 May 2017 10:06:50 -0600 Subject: [PATCH 012/576] Updated how user client ids are stored. --- .../RealtimeDeviceConnectionSockets.coffee | 205 ++++++++++++++++++ .../server/routes/ModuleMenusRoutes.coffee | 15 +- 2 files changed, 213 insertions(+), 7 deletions(-) create mode 100644 modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee diff --git a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee new file mode 100644 index 000000000..aaa96587e --- /dev/null +++ b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee @@ -0,0 +1,205 @@ + +request = require 'request' +_ = require 'underscore' + +promise = require 'promise' + + +class BalanceAccess + constructor: (balanceName, balanceUrl) -> + @balanceName = balanceName + @balanceUrl = balanceUrl + @isAvailable = true + @currentConnectedUser = null + @status = "idle" + @balanceConnectQueue = [] + + ### + get the current status of the balance from the node server connected to the balance + ### + getBalanceStatus: => + balanceStatusURL = @balanceUrl + "api/getBalanceStatus/#{@balanceName}" + return new Promise((resolve, reject) => + request( + method: 'GET' + url: balanceStatusURL + json: true + , (error, response, json) => + if error? + reject error + else + resolve json.message + ) + ) + + + removeUserFromQueue: (clientId) => + if @currentConnectedUser.clientId is clientId + @disconnectCurrentUser() + else + @balanceConnectQueue = _.filter(@balanceConnectQueue, (qu) -> + qu.clientId isnt clientId + ) + + disconnectCurrentUser: => + @balanceConnectQueue.shift() + @isAvailable = true + @currentConnectedUser = null + + getNextUser: => + return _.first(@balanceConnectQueue) + + ### + Attempt to connect the supplied client. + If client can connect, return null. + If client can't connect, return the ID of the currently connected user + ### + connectClient: (clientId, userName, socket) => + clientInQueue = _.findWhere(@balanceConnectQueue, {clientId: clientId}) + unless clientInQueue + @balanceConnectQueue.push {clientId: clientId, userName: userName, socket: socket} + return new Promise((resolve, reject) => + @getBalanceStatus().then((balanceStatus) => + @status = balanceStatus + switch @status + when "idle" + if @isAvailable + @currentConnectedUser = {clientId: clientId, userName: userName, socket: socket} + @isAvailable = false + resolve null + else + if _.first(@balanceConnectQueue).clientId is clientId + @currentConnectedUser = {clientId: clientId, userName: userName, socket: socket} + @isAvailable = false + resolve null + else + reject {status: 'not_available', connectedUser: @currentConnectedUser} + when "device_not_connected" + reject {status: "device_not_connected"} + when "in_use" + reject {status: "in_use"} + ).catch((err) => + reject {status: "device_server_offline"} + ) + ) + + swapCurrentUser: (userToAdd, socket) => + clientInQueue = _.findWhere(@balanceConnectQueue, {clientId: userToAdd.clientId}) + if clientInQueue + @removeUserToAddFromQueue(userToAdd.clientId) + + @removeCurrentUser() + @balanceConnectQueue.push {clientId: userToAdd.clientId, userName: userToAdd.userName, socket: socket} + @currentConnectedUser = {clientId: userToAdd.clientId, userName: userToAdd.userName, socket: socket} + @isAvailable = false + + + removeUserToAddFromQueue: (clientId) => + @balanceConnectQueue = _.reject(@balanceConnectQueue, (user) -> + return user.clientId is clientId + ) + + clearAllUsers: => + @balanceConnectQueue = [] + @isAvailable = true + @currentConnectedUser = null + + removeCurrentUser: => + @balanceConnectQueue.shift() + @currentConnectedUser = null + + +class DeviceSocketController + constructor: (io, nameSpace) -> + @io = io + @nameSpace = nameSpace + @nameSpacedRoom = @io.of(@nameSpace) + @balances = {} + @usersInRoom = {} + @currentlyConnectedSocket = null + + setupEventListeners: => + @nameSpacedRoom.on('connection', (socket) => + console.log "socket.request.username" + console.log socket.request.user + console.log socket.request.session + #console.log socket.request.session.passport.user + socket.on('connectToDevice', (payload, callback) => + @handleConnectToDevice(socket, payload, callback) + ) + socket.on('disconnected', => + @handleDisconnected(socket) + ) + socket.on('disconnect', => + @handleDisconnect(socket) + ) + socket.on('bootUser', (payload, callback) => + @handleBootUser(socket, payload, callback) + ) + socket.on('disconnectAllUsers', (callback) => + @handleDisconnectAllUsers(socket, callback) + ) + ) + + handleConnectToDevice: (socket, payload, callback) -> + unless @balances[payload.deviceName] + @balances[payload.deviceName] = new BalanceAccess(payload.deviceName, payload.deviceUrl) + socket.join(payload.deviceName) + @usersInRoom[socket.id] = payload.deviceName + balanceAccess = @balances[payload.deviceName] + balanceAccessPromise = balanceAccess.connectClient(socket.id, payload.userName, socket) + balanceAccessPromise.then(() => + @currentlyConnectedSocket = socket + return callback(null, 'Connected to device') + ) + balanceAccessPromise.catch((err) => + if err.status is "not_available" + return callback({status: "not_available", userName: err.connectedUser.userName, clientId: err.connectedUser.clientId}, null) + else + return callback({status: err.status}, null) + ) + + emitEventToCurrentlyConnectedClient: (eventName, payload) => + if payload? + @currentlyConnectedSocket.emit(eventName, payload) + else + @currentlyConnectedSocket.emit(eventName) + + handleDisconnected: (socket) -> + balanceAccess = @balances[@usersInRoom[socket.id]] + balanceAccess.disconnectCurrentUser() + nextUserInQueue = balanceAccess.getNextUser() + if nextUserInQueue? + socket.broadcast.to(nextUserInQueue.clientId).emit('youShouldTryConnecting') + else + socket.broadcast.emit('alertAllDisconnectedFromDevice') + socket.leave(@usersInRoom[socket.id]) + socket.emit('disconnectedFromDevice') + + handleDisconnect: (socket) -> + balanceAccess = @balances[@usersInRoom[socket.id]] + balanceAccess.removeUserFromQueue(socket.id) + + nextUserInQueue = balanceAccess.getNextUser() + if nextUserInQueue? + socket.broadcast.to(nextUserInQueue.clientId).emit('youShouldTryConnecting') + else + socket.broadcast.emit('alertAllDisconnectedFromDevice') + + handleBootUser: (socket, payload, callback) -> + balanceAccess = @balances[@usersInRoom[socket.id]] + balanceAccess.disconnectCurrentUser() + balanceAccess.swapCurrentUser({userName: payload.userNameToAdd, clientId: socket.id}) + @currentlyConnectedSocket = socket + socket.broadcast.to(payload.userToBootClientId).emit('disconnectedByAnotherUser', payload.userNameToAdd) + callback(null, 'did this connect? ') + + handleDisconnectAllUsers: (socket, callback) -> + balanceAccess = @balances[@usersInRoom[socket.id]] + balanceAccess.disconnectCurrentUser() + balanceAccess.clearAllUsers() + socket.broadcast.emit('alertAllDisconnectedFromDevice') + callback() + + +exports.DeviceSocketController = DeviceSocketController diff --git a/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee b/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee index 14545e71f..6aef3b89f 100644 --- a/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee +++ b/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee @@ -5,24 +5,25 @@ exports.setupChannels = (io, sessionStore, loginRoutes) -> connectedUsers = {} nsp.on('connection', (socket) => userName = getUserNameFromSession(socket) - unless connectedUsers[userName]? - connectedUsers[userName] = [] - connectedUsers[userName].push socket.id + sessionID = getSessionID(socket) + unless connectedUsers[sessionID]? + connectedUsers[sessionID] = [] + connectedUsers[sessionID].push socket.id totalNumberOfConnectionsForUser = _.size(connectedUsers[userName]) broadcastMessageToSpecificClients(connectedUsers[userName], 'loggedOn', totalNumberOfConnectionsForUser, socket) socket.emit('loggedOn', totalNumberOfConnectionsForUser) socket.on('disconnect', => clientConnections = connectedUsers[userName] - connectedUsers[userName] = _.without(clientConnections, socket.id) - totalNumberOfConnectionsForUser = _.size(connectedUsers[userName]) - broadcastMessageToSpecificClients(connectedUsers[userName], 'loggedOff', totalNumberOfConnectionsForUser, socket) + connectedUsers[sessionID] = _.without(clientConnections, socket.id) + totalNumberOfConnectionsForUser = _.size(connectedUsers[sessionID]) + broadcastMessageToSpecificClients(connectedUsers[sessionID], 'loggedOff', totalNumberOfConnectionsForUser, socket) ) socket.on('changeUserName', (updatedUsername) => sessionID = getSessionID(socket) updateUserNameInSession(updatedUsername, sessionStore, sessionID) - broadcastMessageToSpecificClients(connectedUsers[userName], 'usernameUpdated', updatedUsername, socket) + broadcastMessageToSpecificClients(connectedUsers[sessionID], 'usernameUpdated', updatedUsername, socket) socket.emit('usernameUpdated', updatedUsername) ) ) From e2dfac2887bc9b0ed1c060de5eebbf2af58daadc Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Thu, 25 May 2017 10:30:25 -0700 Subject: [PATCH 013/576] Implemented getContainerCodesByLbelsLikeMaxResults which has same function as getContainerCodesByLabels but with 2 additional parameters. --- .../routes/InventoryServiceRoutes.coffee | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 67482e5b5..8a25e42aa 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -6,10 +6,12 @@ config = require '../conf/compiled/conf.js' RUN_CUSTOM_FLAG = "0" + exports.setupAPIRoutes = (app) -> app.post '/api/getContainersInLocationWithTypeAndKind', exports.getContainersInLocationWithTypeAndKind app.post '/api/getContainersInLocation', exports.getContainersInLocation app.post '/api/getContainerCodesByLabels', exports.getContainerCodesByLabels + app.post '/api/getContainerCodesByLabelsLikeMaxResults', exports.getContainerCodesByLabelsLikeMaxResults app.post '/api/getContainersByLabels', exports.getContainersByLabels app.post '/api/getContainersByCodeNames', exports.getContainersByCodeNames app.post '/api/getWellCodesByPlateBarcodes', exports.getWellCodesByPlateBarcodes @@ -57,6 +59,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/getContainersInLocationWithTypeAndKind', loginRoutes.ensureAuthenticated, exports.getContainersInLocationWithTypeAndKind app.post '/api/getContainersInLocation', loginRoutes.ensureAuthenticated, exports.getContainersInLocation app.post '/api/getContainerCodesByLabels', loginRoutes.ensureAuthenticated, exports.getContainerCodesByLabels + app.post '/api/getContainerCodesByLabelsLikeMaxResults', loginRoutes.ensureAuthenticated, exports.getContainerCodesByLabelsLikeMaxResults app.post '/api/getContainersByLabels', loginRoutes.ensureAuthenticated, exports.getContainersByLabels app.post '/api/getContainersByCodeNames', loginRoutes.ensureAuthenticated, exports.getContainersByCodeNames app.post '/api/getWellCodesByPlateBarcodes', loginRoutes.ensureAuthenticated, exports.getWellCodesByPlateBarcodes @@ -198,6 +201,7 @@ exports.getContainersByLabelsInternal = (containerLabels, containerType, contain inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' resp.json inventoryServiceTestJSON.getContainersByLabelsInternalResponse else + console.warn "getContainerCodesByLabelsInternal is deprecated please use getContainerCodesByLabelsLikeMaxResultsInternal" console.debug 'incoming getContainersByLabelsInternal request: ', JSON.stringify(containerLabels), containerType, containerKind, labelType, labelKind exports.getContainerCodesByLabelsInternal containerLabels, containerType, containerKind, labelType, labelKind, (containerCodes, statusCode) => if statusCode == 500 @@ -234,6 +238,54 @@ exports.getContainersByLabelsInternal = (containerLabels, containerType, contain response.push resp callback response, statusCode +exports.getContainerCodesByLabelsLikeMaxResults = (req, resp) -> + #req.setTimeout 86400000 + exports.getContainerCodesByLabelsLikeMaxResultsInternal req.body, req.query.containerType, req.query.containerKind, req.query.labelType, req.query.labelKind, req.query.likeParameter, req.query.maxResults, (json, statusCode) -> + resp.statusCode = statusCode + resp.json json + +exports.getContainerCodesByLabelsLikeMaxResultsInternal = (containerCodesJSON, containerType, containerKind, labelType, labelKind, likeParameter, maxResults, callback) -> + if global.specRunnerTestmode + inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' + resp.json inventoryServiceTestJSON.getContainerCodesByLabelsResponse + else + console.debug 'incoming getContainerCodesByLabelsInternal request: ', JSON.stringify(containerCodesJSON), containerType, containerKind, labelType, labelKind, likeParameter, maxResults + config = require '../conf/compiled/conf.js' + queryParams = [] + if containerType? + queryParams.push "containerType="+containerType + if containerKind? + queryParams.push "containerKind="+containerKind + if labelType? + queryParams.push "labelType="+labelType + if labelKind? + queryParams.push "labelKind="+labelKind + if likeParameter? + queryParams.push "like="+likeParameter + if maxResults? + queryParams.push "maxResults="+maxResults + queryString = queryParams.join "&" + baseurl = config.all.client.service.persistence.fullpath+"containers/getContainerCodesByLabels?"+queryString + console.debug 'base url: ', baseurl + request = require 'request' + request( + method: 'POST' + url: baseurl + body: JSON.stringify containerCodesJSON + json: true + timeout: 86400000 + headers: 'content-type': 'application/json' + , (error, response, json) => + if !error && json[0] != "<" + callback json, response.statusCode + else + console.error 'got ajax error trying to get getContainerCodesByLabels' + console.error error + console.error json + console.error response + callback JSON.stringify("getContainerCodesByLabels failed"), 500 + ) + exports.getContainerCodesByLabels = (req, resp) -> req.setTimeout 86400000 exports.getContainerCodesByLabelsInternal req.body, req.query.containerType, req.query.containerKind, req.query.labelType, req.query.labelKind, (json, statusCode) -> From 2815900bafbf4077ebb2d4b3d3324c7857df7cd9 Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Thu, 25 May 2017 10:53:24 -0700 Subject: [PATCH 014/576] Fixed the debug message to indicate the new function name. --- .../ServerAPI/src/server/routes/InventoryServiceRoutes.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 8a25e42aa..05520c8ad 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -249,7 +249,7 @@ exports.getContainerCodesByLabelsLikeMaxResultsInternal = (containerCodesJSON, c inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' resp.json inventoryServiceTestJSON.getContainerCodesByLabelsResponse else - console.debug 'incoming getContainerCodesByLabelsInternal request: ', JSON.stringify(containerCodesJSON), containerType, containerKind, labelType, labelKind, likeParameter, maxResults + console.debug 'incoming getContainerCodesByLabelsLikeMaxResultsInternal request: ', JSON.stringify(containerCodesJSON), containerType, containerKind, labelType, labelKind, likeParameter, maxResults config = require '../conf/compiled/conf.js' queryParams = [] if containerType? From a4a07ec9debedaf58389dbf573dfbba337df334e Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Fri, 26 May 2017 09:18:04 -0700 Subject: [PATCH 015/576] Changed getContainerCodesByLabels to send to the new Internal function and send as an object. --- .../routes/InventoryServiceRoutes.coffee | 163 +++++++++++++----- 1 file changed, 119 insertions(+), 44 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 05520c8ad..21f431ac9 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -11,7 +11,6 @@ exports.setupAPIRoutes = (app) -> app.post '/api/getContainersInLocationWithTypeAndKind', exports.getContainersInLocationWithTypeAndKind app.post '/api/getContainersInLocation', exports.getContainersInLocation app.post '/api/getContainerCodesByLabels', exports.getContainerCodesByLabels - app.post '/api/getContainerCodesByLabelsLikeMaxResults', exports.getContainerCodesByLabelsLikeMaxResults app.post '/api/getContainersByLabels', exports.getContainersByLabels app.post '/api/getContainersByCodeNames', exports.getContainersByCodeNames app.post '/api/getWellCodesByPlateBarcodes', exports.getWellCodesByPlateBarcodes @@ -59,7 +58,6 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/getContainersInLocationWithTypeAndKind', loginRoutes.ensureAuthenticated, exports.getContainersInLocationWithTypeAndKind app.post '/api/getContainersInLocation', loginRoutes.ensureAuthenticated, exports.getContainersInLocation app.post '/api/getContainerCodesByLabels', loginRoutes.ensureAuthenticated, exports.getContainerCodesByLabels - app.post '/api/getContainerCodesByLabelsLikeMaxResults', loginRoutes.ensureAuthenticated, exports.getContainerCodesByLabelsLikeMaxResults app.post '/api/getContainersByLabels', loginRoutes.ensureAuthenticated, exports.getContainersByLabels app.post '/api/getContainersByCodeNames', loginRoutes.ensureAuthenticated, exports.getContainersByCodeNames app.post '/api/getWellCodesByPlateBarcodes', loginRoutes.ensureAuthenticated, exports.getWellCodesByPlateBarcodes @@ -192,6 +190,7 @@ exports.getContainersInLocationWithTypeAndKindInternal = (values, callback) -> exports.getContainersByLabels = (req, resp) -> req.setTimeout 86400000 + exports.getContainersByLabelsInternal req.body, req.query.containerType, req.query.containerKind, req.query.labelType, req.query.labelKind, (json, statusCode) -> resp.statusCode = statusCode resp.json json @@ -201,7 +200,6 @@ exports.getContainersByLabelsInternal = (containerLabels, containerType, contain inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' resp.json inventoryServiceTestJSON.getContainersByLabelsInternalResponse else - console.warn "getContainerCodesByLabelsInternal is deprecated please use getContainerCodesByLabelsLikeMaxResultsInternal" console.debug 'incoming getContainersByLabelsInternal request: ', JSON.stringify(containerLabels), containerType, containerKind, labelType, labelKind exports.getContainerCodesByLabelsInternal containerLabels, containerType, containerKind, labelType, labelKind, (containerCodes, statusCode) => if statusCode == 500 @@ -238,20 +236,73 @@ exports.getContainersByLabelsInternal = (containerLabels, containerType, contain response.push resp callback response, statusCode -exports.getContainerCodesByLabelsLikeMaxResults = (req, resp) -> - #req.setTimeout 86400000 - exports.getContainerCodesByLabelsLikeMaxResultsInternal req.body, req.query.containerType, req.query.containerKind, req.query.labelType, req.query.labelKind, req.query.likeParameter, req.query.maxResults, (json, statusCode) -> +exports.getContainerCodesByLabels = (req, resp) -> + req.setTimeout 86400000 + + containerLabels = req.body + containerType = req.query.containerType + containerKind = req.query.containerKind + labelType = req.query.labelType + labelKind = req.query.labelKind + likeParameter = req.query.like + maxResults = req.query.maxResults + + if !(containerLabels)? + containerLabels = null + if !(containerType)? + containerType = null + if !(containerKind)? + containerKind = null + if !(labelType)? + labelType = null + if !(labelKind)? + labelKind = null + if !(likeParameter)? + likeParameter = null + if !(maxResults)? + maxResults = null + + queryPayload = + containerLabels: req.body + containerType: containerType + containerKind: containerKind + labelType: labelType + labelKind: labelKind + likeParameter: likeParameter + maxResults: maxResults + + console.log 'queryPayload', queryPayload + + exports.getContainerCodesByLabelsLikeMaxResultsInternal(queryPayload, (json, statusCode) -> resp.statusCode = statusCode resp.json json + ) + #console.log 'queryPayload in getContainersByLabels', queryPayload -exports.getContainerCodesByLabelsLikeMaxResultsInternal = (containerCodesJSON, containerType, containerKind, labelType, labelKind, likeParameter, maxResults, callback) -> + + # exports.getContainerCodesByLabelsInternal req.body, req.query.containerType, req.query.containerKind, req.query.labelType, req.query.labelKind, (json, statusCode) -> + # resp.statusCode = statusCode + # resp.json json + +exports.getContainerCodesByLabelsLikeMaxResultsInternal = (requestObject, callback) -> if global.specRunnerTestmode inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' resp.json inventoryServiceTestJSON.getContainerCodesByLabelsResponse else - console.debug 'incoming getContainerCodesByLabelsLikeMaxResultsInternal request: ', JSON.stringify(containerCodesJSON), containerType, containerKind, labelType, labelKind, likeParameter, maxResults config = require '../conf/compiled/conf.js' + + containerLabels = requestObject.containerLabels + containerType = requestObject.containerType + containerKind = requestObject.containerKind + labelType = requestObject.labelType + labelKind = requestObject.labelKind + likeParameter = requestObject.likeParameter + maxResults = requestObject.maxResults + + console.debug 'incoming getContainerCodesByLabelsLikeMaxResultsInternal: ', JSON.stringify(containerLabels), containerType, containerKind, labelType, labelKind, likeParameter, maxResults + queryParams = [] + if containerType? queryParams.push "containerType="+containerType if containerKind? @@ -271,7 +322,7 @@ exports.getContainerCodesByLabelsLikeMaxResultsInternal = (containerCodesJSON, c request( method: 'POST' url: baseurl - body: JSON.stringify containerCodesJSON + body: JSON.stringify containerLabels json: true timeout: 86400000 headers: 'content-type': 'application/json' @@ -286,50 +337,74 @@ exports.getContainerCodesByLabelsLikeMaxResultsInternal = (containerCodesJSON, c callback JSON.stringify("getContainerCodesByLabels failed"), 500 ) -exports.getContainerCodesByLabels = (req, resp) -> - req.setTimeout 86400000 - exports.getContainerCodesByLabelsInternal req.body, req.query.containerType, req.query.containerKind, req.query.labelType, req.query.labelKind, (json, statusCode) -> - resp.statusCode = statusCode - resp.json json - exports.getContainerCodesByLabelsInternal = (containerCodesJSON, containerType, containerKind, labelType, labelKind, callback) -> if global.specRunnerTestmode inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' resp.json inventoryServiceTestJSON.getContainerCodesByLabelsResponse else + console.warn "getContainerCodesByLabelsInternal is deprecated please use getContainerCodesByLabelsLikeMaxResultsInternal" console.debug 'incoming getContainerCodesByLabelsInternal request: ', JSON.stringify(containerCodesJSON), containerType, containerKind, labelType, labelKind config = require '../conf/compiled/conf.js' - queryParams = [] - if containerType? - queryParams.push "containerType="+containerType - if containerKind? - queryParams.push "containerKind="+containerKind - if labelType? - queryParams.push "labelType="+labelType - if labelKind? - queryParams.push "labelKind="+labelKind - queryString = queryParams.join "&" - baseurl = config.all.client.service.persistence.fullpath+"containers/getContainerCodesByLabels?"+queryString - console.debug 'base url: ', baseurl - request = require 'request' - request( - method: 'POST' - url: baseurl - body: JSON.stringify containerCodesJSON - json: true - timeout: 86400000 - headers: 'content-type': 'application/json' - , (error, response, json) => - if !error && json[0] != "<" - callback json, response.statusCode - else - console.error 'got ajax error trying to get getContainerCodesByLabels' - console.error error - console.error json - console.error response - callback JSON.stringify("getContainerCodesByLabels failed"), 500 + + if !(containerCodesJSON)? + containerLabels = null + if !(containerType)? + containerType = null + if !(containerKind)? + containerKind = null + if !(labelType)? + labelType = null + if !(labelKind)? + labelKind = null + + likeParameter = null + maxResults = null + + queryPayload = + containerLabels: containerCodesJSON + containerType: containerType + containerKind: containerKind + labelType: labelType + labelKind: labelKind + likeParameter: likeParameter + maxResults: maxResults + + exports.getContainerCodesByLabelsLikeMaxResultsInternal(queryPayload, (json, statusCode) -> + callback json, statusCode ) + # + # queryParams = [] + # if containerType? + # queryParams.push "containerType="+containerType + # if containerKind? + # queryParams.push "containerKind="+containerKind + # if labelType? + # queryParams.push "labelType="+labelType + # if labelKind? + # queryParams.push "labelKind="+labelKind + # queryString = queryParams.join "&" + # baseurl = config.all.client.service.persistence.fullpath+"containers/getContainerCodesByLabels?"+queryString + # console.debug 'base url: ', baseurl + # request = require 'request' + # request( + # method: 'POST' + # url: baseurl + # body: JSON.stringify containerCodesJSON + # json: true + # timeout: 86400000 + # headers: 'content-type': 'application/json' + # , (error, response, json) => + # if !error && json[0] != "<" + # callback json, response.statusCode + # else + # console.error 'got ajax error trying to get getContainerCodesByLabels' + # console.error error + # console.error json + # console.error response + # callback JSON.stringify("getContainerCodesByLabels failed"), 500 + # ) + exports.getWellCodesByPlateBarcodes = (req, resp) -> req.setTimeout 86400000 exports.getWellCodesByPlateBarcodesInternal req.body, (json) -> From deacfebbbc0535909361dc5ae265edb35e4b00bf Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Fri, 26 May 2017 13:32:16 -0700 Subject: [PATCH 016/576] Removing extraneous comments. --- .../routes/InventoryServiceRoutes.coffee | 38 ------------------- 1 file changed, 38 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 21f431ac9..c01e4a9e5 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -277,12 +277,6 @@ exports.getContainerCodesByLabels = (req, resp) -> resp.statusCode = statusCode resp.json json ) - #console.log 'queryPayload in getContainersByLabels', queryPayload - - - # exports.getContainerCodesByLabelsInternal req.body, req.query.containerType, req.query.containerKind, req.query.labelType, req.query.labelKind, (json, statusCode) -> - # resp.statusCode = statusCode - # resp.json json exports.getContainerCodesByLabelsLikeMaxResultsInternal = (requestObject, callback) -> if global.specRunnerTestmode @@ -373,38 +367,6 @@ exports.getContainerCodesByLabelsInternal = (containerCodesJSON, containerType, callback json, statusCode ) - # - # queryParams = [] - # if containerType? - # queryParams.push "containerType="+containerType - # if containerKind? - # queryParams.push "containerKind="+containerKind - # if labelType? - # queryParams.push "labelType="+labelType - # if labelKind? - # queryParams.push "labelKind="+labelKind - # queryString = queryParams.join "&" - # baseurl = config.all.client.service.persistence.fullpath+"containers/getContainerCodesByLabels?"+queryString - # console.debug 'base url: ', baseurl - # request = require 'request' - # request( - # method: 'POST' - # url: baseurl - # body: JSON.stringify containerCodesJSON - # json: true - # timeout: 86400000 - # headers: 'content-type': 'application/json' - # , (error, response, json) => - # if !error && json[0] != "<" - # callback json, response.statusCode - # else - # console.error 'got ajax error trying to get getContainerCodesByLabels' - # console.error error - # console.error json - # console.error response - # callback JSON.stringify("getContainerCodesByLabels failed"), 500 - # ) - exports.getWellCodesByPlateBarcodes = (req, resp) -> req.setTimeout 86400000 exports.getWellCodesByPlateBarcodesInternal req.body, (json) -> From d1c909c178a2994cb91d638fc4e4c1c116aec02f Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Sat, 27 May 2017 23:48:42 -0500 Subject: [PATCH 017/576] new cmpdReg vendor routes --- .../src/client/CmpdRegVendor.coffee | 286 ++++++++++++++++++ .../src/client/CmpdRegVendor.html | 121 ++++++++ .../src/client/CmpdRegVendorBrowser.coffee | 233 ++++++++++++++ .../src/client/CmpdRegVendorBrowserView.html | 143 +++++++++ .../server/routes/CmpdRegAdminRoutes.coffee | 139 +++++++++ 5 files changed, 922 insertions(+) create mode 100644 modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee create mode 100644 modules/CmpdRegAdmin/src/client/CmpdRegVendor.html create mode 100644 modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowser.coffee create mode 100644 modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowserView.html create mode 100644 modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee new file mode 100644 index 000000000..362f24720 --- /dev/null +++ b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee @@ -0,0 +1,286 @@ +class window.Vendor extends Backbone.Model + urlRoot: "/api/cmpdRegAdmin/vendors" + defaults: + name: null + code: null + id: null + + isEditable: -> + return true + +class window.Vendors extends Backbone.Collection + model: Vendor + +class window.VendorController extends AbstractFormController + template: _.template($("#VendorView").html()) + moduleLaunchName: "vendor" + + events: -> + "change .bv_vendorCode": "handleVendorCodeNameChanged" + "keyup .bv_vendorName": "attributeChanged" + "keyup .bv_vendorDetails": "attributeChanged" + "click .bv_save": "handleSaveClicked" + "click .bv_newEntity": "handleNewEntityClicked" + "click .bv_cancel": "handleCancelClicked" + "click .bv_cancelClear": "handleCancelClearClicked" + "click .bv_confirmClear": "handleConfirmClearClicked" + + initialize: -> + console.log 'initialize vendorController -- line 30' + template = _.template( $("#VendorView").html()); + $(@el).empty() + $(@el).html template + if @model? + @completeInitialization() + + completeInitialization: => + unless @model? + @model=new Vendor() + @errorOwnerName = 'VendorController' + @setBindings() + if @options.readOnly? + @readOnly = @options.readOnly + else + @readOnly = false + @listenTo @model, 'saveFailed', @handleSaveFailed + @listenTo @model, 'change', @modelChangeCallback + $(@el).empty() + $(@el).html @template(@model.attributes) + @render() + + render: => + unless @model? + @model = new Vendor() + codeName = @model.get('code') + @$('.bv_vendorCode').val(codeName) + @$('.bv_vendorCode').html(codeName) + if @model.isNew() + console.log 'new vendor model -- line 56' + @$('.bv_vendorCode').removeAttr 'disabled' + @$('.bv_save').removeAttr('disabled') + @$('.bv_cancel').removeAttr('disabled') + @$('.VendorView').show() + @$('.bv_vendorCode').show() + @$('.bv_vendorName').show() + else + console.log 'old vendor model -- line 59' + @$('.bv_vendorCode').attr 'disabled', 'disabled' + bestName = @model.get('name') + if bestName? + @$('.bv_vendorName').val bestName + if @model.isNew() + @$('.bv_saveBeforeManagingPermissions').show() + if UtilityFunctions::testUserHasRole window.AppLaunchParams.loginUser, [window.conf.roles.cmpdreg.adminRole] + @$('.bv_saveBeforeManagingPermissions').show() + else + @updateEditable() + if @readOnly is true + @displayInReadOnlyMode() +# @$('.bv_save').attr('disabled','disabled') +# @$('.bv_cancel').attr('disabled','disabled') + @$('.VendorView').show() + @$('.bv_vendorCode').show() + + if @model.isNew() + @$('.bv_save').html("Save") + @$('.bv_newEntity').hide() + else + @$('.bv_save').html("Update") + @$('.bv_newEntity').show() + @ + + handleSaveFailed: => + @$('.bv_saveFailed').show() + @$('.bv_saveComplete').hide() + @$('.bv_saving').hide() + + modelSaveCallback: (method, model) => + @$('.bv_save').show() +# @$('.bv_save').attr('disabled', 'disabled') + unless @$('.bv_saveFailed').is(":visible") + @$('.bv_saveComplete').show() + @$('.bv_saving').hide() + @render() + @trigger 'amClean' + + modelChangeCallback: (method, model) => + @trigger 'amDirty' + @checkFormValid() + @$('.bv_saveComplete').hide() + @$('.bv_saveFailed').hide() + @$('.bv_cancel').removeAttr('disabled') + @$('.bv_cancelComplete').hide() + + updateEditable: => + if @model.isEditable() + if UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, [window.conf.roles.acas.adminRole]) + @enableAllInputs() + @$('.bv_vendorCode').attr 'disabled', 'disabled' + @$('.bv_saveBeforeManagingPermissions').hide() + else + @enableLimitedEditing() + @$('.bv_manageUserPermissions').hide() + else + @disableAllInputs() + @$('.bv_newEntity').removeAttr('disabled') + @$('.bv_status').attr 'disabled', 'disabled' #for now, don't allow status editing + + enableLimitedEditing: -> + @disableAllInputs() + + handleVendorCodeNameChanged: => + codeName = UtilityFunctions::getTrimmedInput @$('.bv_vendorCode') + if codeName is "" + delete @model.attributes.codeName + @model.trigger 'change' + else + #validate codeName + $.ajax + type: 'GET' + url: "/api/cmpdRegAdmin/vendors/findByCode/"+codeName + dataType: 'json' + error: (err) => + #codename is new + @model.set codeName: codeName + @clearValidationErrorStyles + success: (json) => + #codeName is not unique + @$('.bv_notUniqueModalTitle').html "Error: Vendor code is not unique" + @$('.bv_notUniqueModalBody').html "The entered vendor code is already used by another vendor. Please enter in a new code." + @$('.bv_notUniqueModal').modal('show') + @$('.bv_vendorCode').val @model.get 'codeName' + + handleNewEntityClicked: => + @$('.bv_confirmClearEntity').modal('show') + @$('.bv_confirmClear').removeAttr('disabled') + @$('.bv_cancelClear').removeAttr('disabled') + @$('.bv_closeModalButton').removeAttr('disabled') + @$('.bv_save').removeAttr('disabled') + + handleCancelClearClicked: => + @$('.bv_confirmClearEntity').modal('hide') + + handleConfirmClearClicked: => + @$('.bv_confirmClearEntity').modal('hide') + @model = null + @completeInitialization() + @trigger 'amClean' + + handleCancelClicked: => + if @model.isNew() + @model = null + @completeInitialization() + else + @$('.bv_canceling').show() + @model.fetch + success: @handleCancelComplete + @trigger 'amClean' + + handleCancelComplete: => + @$('.bv_canceling').hide() + @$('.bv_cancelComplete').show() + + updateModel: => + @model.set("name", UtilityFunctions::getTrimmedInput @$('.bv_vendorName')) + @model.set("code", UtilityFunctions::getTrimmedInput @$('.bv_vendorCode')) + + handleSaveClicked: => + @callNameValidationService() + + @$('.bv_saving').show() + @$('.bv_saveFailed').hide() + @$('.bv_saveComplete').hide() + + callNameValidationService: -> + @$('.bv_saving').show() + @$('.bv_save').attr('disabled', 'disabled') + reformattedModel = @model.clone() + reformattedModel.reformatBeforeSaving() + validateURL = "/api/cmpdRegAdmin/vendors/validate" + dataToPost = + data: #dataToPost needs wrapping key, not sure why + JSON.stringify( + lsThing: reformattedModel + uniqueName: true + ) + + $.ajax + type: 'POST' + url: validateURL + data: dataToPost + success: (response) => + @handleValidateReturn(response) + error: (err) => + @serviceReturn = null + dataType: 'json' + + handleValidateReturn: (validateResp) => + if validateResp?[0]?.errorLevel? + alert 'The requested vendor name has already been registered. Please choose a new vendor name.' + @$('.bv_saving').hide() + @$('.bv_saveFailed').show() + else if validateResp is "validate name failed" + alert 'There was an error validating the vendor name. Please try again and/or enter a different name.' + @$('.bv_saving').hide() + @$('.bv_saveFailed').show() + else + @saveVendorAndRoles() + + saveVendorAndRoles: => + console.log "saveVendorAndRoles - handle tags changed" + @model.prepareToSave() + @model.reformatBeforeSaving() + if @model.isNew() + @$('.bv_saveComplete').html('Save Complete') + newVendor = true + else + @$('.bv_saveComplete').html('Update Complete') + newVendor = false + @$('.bv_save').attr('disabled', 'disabled') + if @model.isNew() #if vendor was new, trigger roleKind and user/admin lsRole creation + @model.save null, + success: (model, response) => + if response is "update lsThing failed" + @model.trigger 'saveFailed' + else + if UtilityFunctions::testUserHasRoleTypeKindName(window.AppLaunchParams.loginUser, [@adminRole]) or UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, [window.conf.roles.acas.adminRole]) + @updateVendorRoles() + else + @model.save null, + success: (model, response) => + if response is "update lsThing failed" + @model.trigger 'saveFailed' + error: (err) => + @model.trigger 'saveFailed' + + validationError: => + super() + @$('.bv_save').attr('disabled', 'disabled') + + clearValidationErrorStyles: => + super() + @$('.bv_save').removeAttr('disabled') + + checkDisplayMode: => + if @readOnly is true + @displayInReadOnlyMode() + + displayInReadOnlyMode: => + @$(".bv_save").hide() + @$(".bv_cancel").hide() + @$(".bv_newEntity").hide() + @$('button').attr 'disabled', 'disabled' + @disableAllInputs() + + checkFormValid: => + if @isValid() + @$('.bv_save').removeAttr('disabled') + else + @$('.bv_save').attr('disabled', 'disabled') + + isValid: => + validCheck = super() + validCheck + + + diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html new file mode 100644 index 000000000..929b45c46 --- /dev/null +++ b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html @@ -0,0 +1,121 @@ + + diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowser.coffee b/modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowser.coffee new file mode 100644 index 000000000..744a8da16 --- /dev/null +++ b/modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowser.coffee @@ -0,0 +1,233 @@ +class window.VendorSearch extends Backbone.Model + defaults: + name: null + code: null + id: null + +class window.VendorList extends Backbone.Collection + model: VendorSearch + +class window.VendorSimpleSearchController extends AbstractFormController + template: _.template($("#VendorSimpleSearchView").html()) + genericSearchUrl: "/api/CmpdRegAdmin/vendors/" + + initialize: -> + @searchUrl = "" + @searchUrl = @genericSearchUrl + + events: + 'keyup .bv_vendorSearchTerm': 'updateVendorSearchTerm' + 'click .bv_doSearch': 'handleDoSearchClicked' + + render: => + $(@el).empty() + $(@el).html @template() + + updateVendorSearchTerm: (e) => + ENTER_KEY = 13 + vendorSearchTerm = $.trim(@$(".bv_vendorSearchTerm").val()) + if vendorSearchTerm isnt "" + @$(".bv_doSearch").attr("disabled", false) + if e.keyCode is ENTER_KEY + $(':focus').blur() + @handleDoSearchClicked() + else + @$(".bv_doSearch").attr("disabled", true) + + handleDoSearchClicked: => + $(".bv_vendorTableController").addClass "hide" + $(".bv_errorOccurredPerformingSearch").addClass "hide" + vendorSearchTerm = $.trim(@$(".bv_vendorSearchTerm").val()) + $(".bv_vendorSearchTerm").val "" + if vendorSearchTerm isnt "" + $(".bv_noMatchingVendorsFoundMessage").addClass "hide" + $(".bv_vendorBrowserSearchInstructions").addClass "hide" + $(".bv_searchVendorsStatusIndicator").removeClass "hide" + if !window.conf.browser.enableSearchAll and vendorSearchTerm is "*" + $(".bv_moreSpecificVendorSearchNeeded").removeClass "hide" + else + $(".bv_searchingVendorsMessage").removeClass "hide" + $(".bv_vendorSearchTerm").html vendorSearchTerm + $(".bv_moreSpecificVendorSearchNeeded").addClass "hide" + @doSearch vendorSearchTerm + + doSearch: (vendorSearchTerm) => +# disable the search text field while performing a search + @$(".bv_vendorSearchTerm").attr "disabled", true + @$(".bv_doSearch").attr "disabled", true + @trigger 'find' + unless vendorSearchTerm is "" + $.ajax + type: 'GET' + url: @searchUrl +# + vendorSearchTerm + dataType: "json" + data: + testMode: false +# lsType: "vendor" +# lsKind: "vendor" + +#fullObject: true + success: (vendor) => + @trigger "searchReturned", vendor + error: (result) => + @trigger "searchReturned", null + complete: => +# re-enable the search text field regardless of if any results found + @$(".bv_vendorSearchTerm").attr "disabled", false + @$(".bv_doSearch").attr "disabled", false + + + +class window.VendorRowSummaryController extends Backbone.View + tagName: 'tr' + className: 'dataTableRow' + events: + "click": "handleClick" + + handleClick: => + @trigger "gotClick", @model + $(@el).closest("table").find("tr").removeClass "info" + $(@el).addClass "info" + + initialize: -> + @template = _.template($('#VendorRowSummaryView').html()) + + render: => + toDisplay = + code: @model.get('code') + name: @model.get('name') + $(@el).html(@template(toDisplay)) + + @ + +class window.VendorSummaryTableController extends Backbone.View + initialize: -> + + selectedRowChanged: (row) => + @trigger "selectedRowUpdated", row + + render: => + @template = _.template($('#VendorSummaryTableView').html()) + $(@el).html @template + if @collection.models.length is 0 + $(".bv_noMatchingVendorsFoundMessage").removeClass "hide" + # display message indicating no results were found + else + $(".bv_noMatchingVendorsFoundMessage").addClass "hide" + @collection.each (vend) => + console.log vend + prsc = new VendorRowSummaryController + model: vend + prsc.on "gotClick", @selectedRowChanged + @$("tbody").append prsc.render().el + + @$("table").dataTable oLanguage: + sSearch: "Filter results: " #rename summary table's search bar + + @ + + +class window.VendorBrowserController extends Backbone.View + #template: _.template($("#VendorBrowserView").html()) + includeDuplicateAndEdit: false + events: + "click .bv_deleteVendor": "handleDeleteVendorClicked" + "click .bv_editVendor": "handleEditVendorClicked" + "click .bv_confirmDeleteVendorButton": "handleConfirmDeleteVendorClicked" + "click .bv_cancelDelete": "handleCancelDeleteClicked" + + moduleLaunchName: "vendor_browser" + + initialize: -> + template = _.template( $("#VendorBrowserView").html()); + $(@el).empty() + $(@el).html template + @searchController = new VendorSimpleSearchController + model: new VendorSearch() + el: @$('.bv_vendorSearchController') + @searchController.render() + @searchController.on "searchReturned", @setupVendorSummaryTable + #@searchController.on "resetSearch", @destroyVendorSummaryTable + + setupVendorSummaryTable: (vendors) => + @destroyVendorSummaryTable() + + $(".bv_searchingVendorsMessage").addClass "hide" + if vendors is null + @$(".bv_errorOccurredPerformingSearch").removeClass "hide" + + else if vendors.length is 0 + @$(".bv_noMatchingVendorsFoundMessage").removeClass "hide" + @$(".bv_vendorTableController").html "" + else + $(".bv_searchVendorsStatusIndicator").addClass "hide" + @$(".bv_vendorTableController").removeClass "hide" + @vendorSummaryTable = new VendorSummaryTableController + collection: new VendorList vendors + + @vendorSummaryTable.on "selectedRowUpdated", @selectedVendorUpdated + $(".bv_vendorTableController").html @vendorSummaryTable.render().el + + selectedVendorUpdated: (vendor) => + @trigger "selectedVendorUpdated" + @vendorController = new VendorController + model: new Vendor vendor.attributes + readOnly: true + + $('.bv_vendorController').html @vendorController.render().el + $(".bv_vendorController").removeClass("hide") + $(".bv_vendorControllerContainer").removeClass("hide") + @$('.bv_editVendor').show() + @$('.bv_deleteVendor').show() + + handleDeleteVendorClicked: => + @$(".bv_vendorCodeName").html @vendorController.model.get("code") + @$(".bv_deleteButtons").removeClass "hide" + @$(".bv_okayButton").addClass "hide" + @$(".bv_errorDeletingVendorMessage").addClass "hide" + @$(".bv_deleteWarningMessage").removeClass "hide" + @$(".bv_deletingStatusIndicator").addClass "hide" + @$(".bv_vendorDeletedSuccessfullyMessage").addClass "hide" + $(".bv_confirmDeleteVendor").removeClass "hide" + $('.bv_confirmDeleteVendor').modal({ + keyboard: false, + backdrop: true + }) + + handleConfirmDeleteVendorClicked: => + @$(".bv_deleteWarningMessage").addClass "hide" + @$(".bv_deletingStatusIndicator").removeClass "hide" + @$(".bv_deleteButtons").addClass "hide" + $.ajax( + url: "/api/vendors/#{@vendorController.model.get("id")}", + type: 'DELETE', + success: (result) => + @$(".bv_okayButton").removeClass "hide" + @$(".bv_deletingStatusIndicator").addClass "hide" + @$(".bv_vendorDeletedSuccessfullyMessage").removeClass "hide" + @searchController.handleDoSearchClicked() + error: (result) => + @$(".bv_okayButton").removeClass "hide" + @$(".bv_deletingStatusIndicator").addClass "hide" + @$(".bv_errorDeletingVendorMessage").removeClass "hide" + ) + + handleCancelDeleteClicked: => + @$(".bv_confirmDeleteVendor").modal('hide') + + handleEditVendorClicked: => + window.open("/vendor/codeName/#{@vendorController.model.get("code")}",'_blank'); + + destroyVendorSummaryTable: => + if @vendorSummaryTable? + @vendorSummaryTable.remove() + if @vendorController? + @vendorController.remove() + $(".bv_vendorController").addClass("hide") + $(".bv_vendorControllerContainer").addClass("hide") + $(".bv_noMatchingVendorsFoundMessage").addClass("hide") + + render: => + + @ diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowserView.html b/modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowserView.html new file mode 100644 index 000000000..d3e26cf9b --- /dev/null +++ b/modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowserView.html @@ -0,0 +1,143 @@ + + + + + + + diff --git a/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee b/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee new file mode 100644 index 000000000..ca6ae0375 --- /dev/null +++ b/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee @@ -0,0 +1,139 @@ +exports.setupAPIRoutes = (app, loginRoutes) -> + app.get '/api/cmpdRegAdmin/vendors', exports.getCmpdRegVendors + app.get '/api/cmpdRegAdmin/vendors/validate/:code', exports.validateCmpdRegVendor + app.get '/api/cmpdRegAdmin/vendors/findByCode/:code', exports.getCmpdRegVendorByCode + +exports.setupRoutes = (app, loginRoutes) -> + app.get '/api/cmpdRegAdmin/vendors/validate/:code', loginRoutes.ensureAuthenticated, exports.validateCmpdRegVendor + app.get '/api/cmpdRegAdmin/vendors/findByCode/:code', loginRoutes.ensureAuthenticated, exports.getCmpdRegVendorByCode + app.get '/api/cmpdRegAdmin/vendors', loginRoutes.ensureAuthenticated, exports.getCmpdRegVendors + app.get '/api/cmpdRegAdmin/vendors/:searchTerm', loginRoutes.ensureAuthenticated, exports.searchCmpdRegVendors + app.post '/api/cmpdRegAdmin/vendors', loginRoutes.ensureAuthenticated, exports.saveCmpdRegVendors + app.put '/api/cmpdRegAdmin/vendors', loginRoutes.ensureAuthenticated, exports.updateCmpdRegVendors + app.delete '/api/cmpdRegAdmin/vendors', loginRoutes.ensureAuthenticated, exports.deleteCmpdRegVendors + +exports.validateCmpdRegVendor = (req, resp) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors/validate?code=' + req.params.code + console.log 'attempting vendor call to the following route' + console.log cmpdRegCall + request( + method: 'GET' + url: cmpdRegCall + json: false + timeout: 6000000 + , (error, response, validVendor) => + if !error + console.log validVendor + resp.statusCode = response.statusCode + resp.setHeader('Content-Type', 'application/json') + resp.end validVendor + else + console.log 'got ajax error trying to do validate vendor' + console.log error + console.log validVendor + console.log response + resp.end JSON.stringify {error: "something went wrong :("} + ) + +exports.getCmpdRegVendorByCode = (req, resp) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors/findByCodeEquals?code=' + req.params.code + console.log 'attempting vendor call to the following route' + console.log cmpdRegCall + request( + method: 'GET' + url: cmpdRegCall + json: true + timeout: 6000000 + , (error, response, json) => + if !error + console.log JSON.stringify json + resp.statusCode = response.statusCode + resp.setHeader('Content-Type', 'application/json') + resp.json json + else + console.log 'got ajax error trying to do get vendor' + console.log error + console.log json + console.log response + resp.end JSON.stringify {error: "something went wrong :("} + ) + + +exports.getCmpdRegVendors = (req, resp) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors' + console.log 'attempting vendor call to the following route' + console.log cmpdRegCall + request( + method: 'GET' + url: cmpdRegCall + json: true + timeout: 6000000 + , (error, response, json) => + if !error + console.log JSON.stringify json + resp.statusCode = response.statusCode + resp.setHeader('Content-Type', 'application/json') + resp.json json + else + console.log 'got ajax error trying to do get vendors' + console.log error + console.log json + console.log response + resp.end JSON.stringify {error: "something went wrong :("} + ) + +exports.saveParent = (req, resp) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + console.log "exports.updateParent" + + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors' + request( + method: 'POST' + url: cmpdRegCall + body: req.body + json: true + timeout: 6000000 + , (error, response, json) => + if !error + resp.setHeader('Content-Type', 'plain/text') + resp.json json + else + console.log 'got ajax error trying to save the vendor' + console.log error + console.log json + console.log response + resp.statusCode = 500 + resp.end "Error trying to save vendor: " + error; + ) + +exports.updateParent = (req, resp) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + console.log "exports.updateParent" + + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/parents/updateParent' + request( + method: 'POST' + url: cmpdRegCall + body: req.body + json: true + timeout: 6000000 + , (error, response, json) => + if !error + resp.setHeader('Content-Type', 'plain/text') + resp.json json + else + console.log 'got ajax error trying to update vendor' + console.log error + console.log json + console.log response + resp.statusCode = 500 + resp.end "Error trying to update vendor: " + error; + ) \ No newline at end of file From adbd4c25848c39addef9d55ec13671b1d5b56d93 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Tue, 30 May 2017 10:37:33 -0600 Subject: [PATCH 018/576] #101 Added base "device connection" controller and html template content. --- .../RealtimeDeviceConnectionController.coffee | 195 ++++++++++++++++++ .../client/RealtimeDeviceConnectionView.html | 123 +++++++++++ 2 files changed, 318 insertions(+) create mode 100644 modules/Components/src/client/RealtimeDeviceConnectionController.coffee create mode 100644 modules/Components/src/client/RealtimeDeviceConnectionView.html diff --git a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee new file mode 100644 index 000000000..79f4d293b --- /dev/null +++ b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee @@ -0,0 +1,195 @@ +class window.DeviceCollection extends PickListList + +deviceStubs = [ + { + code: 'balanceIsIdle', + name: 'Balance Is Idle' + url: 'http://192.168.0.193:1337/' + }, { + code: 'balanceNotConnected', + name: 'Balance Not Connected' + url: 'http://192.168.0.193:1337/' + }, { + code: 'balanceNotAvailable', + name: 'Balance Not Available' + url: 'http://192.168.0.193:1337/' + } + +] + + +class window.RealtimeDeviceConnectionController extends Backbone.View + template: _.template($("#RealtimeDeviceConnectionView").html()) + + events: + "click .bv_disconnect": "handleDisconnectClicked" + "click .bv_bootCurrentUserOffDevice": "handleBootCurrentUserOffDevice" + "click .bv_disconnectedByAnotherUserDismiss": "hideDisconnectedModal" + "click .bv_kickUserOff": "displayInUseModal" + "click .bv_deviceInUseDismiss": "dismissDeviceInUse" + "change .bv_deviceSelectContainer": "handleDeviceSelectChange" + "click .bv_dismissDisconnectMessage": "handleDismissDisconnectMessage" + + initialize: -> + @isConnectedToDevice = false + @testMode = @options.testMode + @deviceCollection = new DeviceCollection(deviceStubs) + unless @testMode + @setupSocketEventHandlers() + + + setupSocketEventHandlers: => + @socket = io('/deviceChannel') + @socket.on('connect', @handleDeviceSelectChange) + @socket.on('connect_error', @handleConnectError) + @socket.on('youShouldTryConnecting', @connectToDevice) + @socket.on('disconnectedFromDevice', @disconnectedFromDevice) + @socket.on('alertAllDisconnectedFromDevice', @alertAllDisconnectedFromDevice) + @socket.on('disconnectedByAnotherUser', @disconnectedByAnotherUser) + + connectToDevice: => + selectedDevice = @devicePickList.getSelectedModel() + @$(".bv_connecting").removeClass "hide" + @socket.emit('connectToDevice', {deviceName: selectedDevice.get('code'), deviceUrl: selectedDevice.get('url'), userName: AppLaunchParams.loginUserName}, @connectToDeviceCallback) + + connectToDeviceCallback: (err, data) => + console.log "err", err + console.log "data", data + if err + @setStateToDisconnected() + console.log "err.status", err.status + switch err.status + when "not_available" + @clientIdOfConnectedUser = err.clientId + @userNameOfConnectedUser = err.userName + @displayInUseMessage() + when "device_not_connected" + @displayStatusMessage(".bv_deviceNotConnected") + when "device_server_offline" + @displayStatusMessage(".bv_deviceServerOffline") + when "in_use" + @displayStatusMessage(".bv_deviceServerInUse") + + else + @setStateToConnected() + + @$(".bv_connectionStatusAlert").addClass "hide" + + displayStatusMessage: (messageSelector) => + @resetStatusMessages() + + @$(messageSelector).removeClass "hide" + + resetStatusMessages: => + @$(".bv_connecting").addClass "hide" + @$(".bv_connected").addClass "hide" + @$(".bv_disconnected").addClass "hide" + @$(".bv_deviceNotConnected").addClass "hide" + @$(".bv_deviceServerInUse").addClass "hide" + @$(".bv_deviceServerOffline").addClass "hide" + @$(".bv_deviceServerInUseButIdle").addClass "hide" + @handleDismissDisconnectMessage() + + displayInUseMessage: => + @resetStatusMessages() + @displayStatusMessage(".bv_deviceServerInUseButIdle") + @$(".bv_deviceUsedBy").html @userNameOfConnectedUser + + + handleDeviceSelectChange: => + deviceName = @devicePickList.getSelectedCode() + unless deviceName is "" + @connectToDevice() + + handleBootCurrentUserOffDevice: => + @socket.emit('bootUser', {userToBootClientId: @clientIdOfConnectedUser, userNameToAdd: AppLaunchParams.loginUserName}, (err, data) => + @setStateToConnected() + @$(".bv_deviceInUse").modal "hide" + ) + + handleDismissDisconnectMessage: => + @$(".bv_disconnectedByAUserMessage").hide() + + displayInUseModal: => + @$(".bv_alreadyConnectedUserName").html @userNameOfConnectedUser + @$(".bv_deviceInUse").modal "show" + + handleConnectError: => + @$(".bv_connectionStatusAlert").removeClass "hide" + + getDeviceName: => + return @$(".bv_deviceSelect").val() + + disableDisconnectButton: => + @$(".bv_disconnect").addClass "hide" +#@disableButton(".bv_disconnect") + + enableDisconnectButton: => +#@enableButton(".bv_disconnect") + @$(".bv_disconnect").removeClass "hide" + + disableButton: (cssSelector) => + @$(cssSelector).prop "disabled", true + @$(cssSelector).addClass "disabled" + + enableButton: (cssSelector) => + @$(cssSelector).prop "disabled", false + @$(cssSelector).removeClass "disabled" + + handleDisconnectClicked: (e) => + e.preventDefault() + console.log "handleDisconnectClicked" + @socket.emit('disconnected') + + setStateToDisconnected: => + @disableDisconnectButton() + @isConnectedToDevice = false + @$(".bv_connecting").addClass "hide" + @$(".bv_connected").addClass "hide" + @$(".bv_disconnected").removeClass "hide" + + setStateToConnected: => + @enableDisconnectButton() + @isConnectedToDevice = true + @displayStatusMessage ".bv_connected" + + disconnectedFromDevice: => + console.log "you've been successfully disconnected" + @setStateToDisconnected() + + alertAllDisconnectedFromDevice: => + console.log "alertAllDisconnectedFromDevice" + console.log "@isConnectedToDevice", @isConnectedToDevice + unless @isConnectedToDevice + @connectToDevice() + + disconnectedByAnotherUser: (disconnectingUserName) => + @displayDisconnectedModal(disconnectingUserName) + @setStateToDisconnected() + + displayDisconnectedModal: (disconnectingUserName) => + @$(".bv_disconnectingUserName").html disconnectingUserName + @$(".bv_disconnectedByAUserMessage").show "slide", {direction: "right"} +#@$(".bv_disconnectedByAnotherUser").modal "show" + + dismissDeviceInUse: => + @$(".bv_deviceInUse").modal "hide" + + hideDisconnectedModal: => + @$(".bv_disconnectedByAnotherUser").modal "hide" + + render: => + $(@el).empty() + $(@el).html @template() + + @devicePickList = new PickListSelectController({collection: @deviceCollection, autoFetch: false, el: @$(".bv_deviceSelectContainer")}) + @renderSubform() + + @ + + renderSubform: => + + @$(".bv_subformContainer").html @subFormTemplate() + @completeInitialization() + + @ \ No newline at end of file diff --git a/modules/Components/src/client/RealtimeDeviceConnectionView.html b/modules/Components/src/client/RealtimeDeviceConnectionView.html new file mode 100644 index 000000000..1cb34f85d --- /dev/null +++ b/modules/Components/src/client/RealtimeDeviceConnectionView.html @@ -0,0 +1,123 @@ + \ No newline at end of file From 5502837025a1e3ccbdfca2b22f3b5071aff05d6b Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Tue, 30 May 2017 15:59:51 -0600 Subject: [PATCH 019/576] #101 Code cleanup, adding tests. --- ...ltimeDeviceConnectionControllerSpec.coffee | 96 +++++++++++++++++++ .../RealtimeDeviceConnectionController.coffee | 18 ++-- 2 files changed, 105 insertions(+), 9 deletions(-) create mode 100644 modules/Components/spec/RealtimeDeviceConnectionControllerSpec.coffee diff --git a/modules/Components/spec/RealtimeDeviceConnectionControllerSpec.coffee b/modules/Components/spec/RealtimeDeviceConnectionControllerSpec.coffee new file mode 100644 index 000000000..6c9de298b --- /dev/null +++ b/modules/Components/spec/RealtimeDeviceConnectionControllerSpec.coffee @@ -0,0 +1,96 @@ +describe 'Realtime Device Connection Controller testing', -> + beforeEach -> + @fixture = $.clone($("#fixture").get(0)) + @waitForServiceReturn = -> + typeof @serviceReturn != 'undefined' + + afterEach -> + $("#fixture").remove() + $(".modal-backdrop").remove() + $("body").append $(@fixture) + + describe 'when instantiated', -> + beforeEach -> + @rtdc = new RealtimeDeviceConnectionController() + @rtdc.subFormTemplate = _.template("

    Subform...

    ") + $("#fixture").html @rtdc.render().el + + it 'should exist', -> + expect(@rtdc).toBeTruthy() + + it 'should have template content', -> + expect($("#fixture").find('.bv_deviceSelectContainer').length).toEqual(1) + + describe 'connecting to a device server', -> + beforeEach -> + @rtdc = new RealtimeDeviceConnectionController() + @rtdc.subFormTemplate = _.template("

    Subform...

    ") + $("#fixture").html @rtdc.render().el + + describe 'and device status is "not_available"', -> + beforeEach -> + @rtdc.connectToDeviceCallback({status: "not_available", userName: 'bob'}, null) + + it 'should display a message indicating the device is in use', -> + expect($('.bv_deviceServerInUseButIdle').hasClass('hide')).toBeFalsy() + + it 'should display the username of the user currently using the device', -> + expect($('.bv_deviceUsedBy').html()).toContain('bob') + + describe 'disconnect other user and reserve balance workflow', -> + describe 'clicking the "Kick off user" button', -> + it 'should prompt the user to verify that they want to kick the current user off', -> + expect($('.bv_deviceInUse').css('display') is 'none').toBeTruthy() + $('.bv_kickUserOff').click() + expect($('.bv_deviceInUse').css('display') is 'none').toBeFalsy() + + describe 'clicking the "no" button', -> + beforeEach -> + $('.bv_deviceInUseDismiss').click() + it 'should close the modal', -> + expect($('.bv_deviceInUse').css('display') is 'none').toBeTruthy() + + it 'should continue displaying a message indicating the device is in use', -> + expect($('.bv_deviceServerInUseButIdle').hasClass('hide')).toBeFalsy() + + it 'should continue displaying a message indicating the user currently using the device', -> + expect($('.bv_deviceUsedBy').html()).toContain('bob') + + describe 'clicking the "yes" button', -> + beforeEach -> + $('.bv_bootCurrentUserOffDevice').click() + @rtdc.handleBootCurrentUserOffDeviceCallback() + it 'should close the modal', -> + expect($('.bv_deviceInUse').css('display') is 'none').toBeTruthy() + + it 'should displaying a message indicating the user is currently connected to the selected device', -> + expect($('.bv_deviceServerInUseButIdle').hasClass('hide')).toBeTruthy() + expect($('.bv_connected').hasClass('hide')).toBeFalsy() + + describe 'and device status is "device_not_connected"', -> + beforeEach -> + @rtdc.connectToDeviceCallback({status: "device_not_connected"}, null) + + it 'should display a message indicating the device is not connected', -> + expect($('.bv_deviceNotConnected').hasClass('hide')).toBeFalsy() + + describe 'and device status is "device_server_offline"', -> + beforeEach -> + @rtdc.connectToDeviceCallback({status: "device_server_offline"}, null) + + it 'should display a message indicating the device is not connected', -> + expect($('.bv_deviceServerOffline').hasClass('hide')).toBeFalsy() + + describe 'and device status is "in_use"', -> + beforeEach -> + @rtdc.connectToDeviceCallback({status: "in_use"}, null) + + it 'should display a message indicating the device is not connected', -> + expect($('.bv_deviceServerInUse').hasClass('hide')).toBeFalsy() + + describe 'and device is available and not in use', -> + beforeEach -> + @rtdc.connectToDeviceCallback(null, null) + + it 'should display a message indicating the user is connected to the device', -> + expect($('.bv_connected').hasClass('hide')).toBeFalsy() \ No newline at end of file diff --git a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee index 79f4d293b..ab649455d 100644 --- a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee +++ b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee @@ -14,7 +14,6 @@ deviceStubs = [ name: 'Balance Not Available' url: 'http://192.168.0.193:1337/' } - ] @@ -53,11 +52,8 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @socket.emit('connectToDevice', {deviceName: selectedDevice.get('code'), deviceUrl: selectedDevice.get('url'), userName: AppLaunchParams.loginUserName}, @connectToDeviceCallback) connectToDeviceCallback: (err, data) => - console.log "err", err - console.log "data", data if err @setStateToDisconnected() - console.log "err.status", err.status switch err.status when "not_available" @clientIdOfConnectedUser = err.clientId @@ -102,10 +98,11 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @connectToDevice() handleBootCurrentUserOffDevice: => - @socket.emit('bootUser', {userToBootClientId: @clientIdOfConnectedUser, userNameToAdd: AppLaunchParams.loginUserName}, (err, data) => - @setStateToConnected() - @$(".bv_deviceInUse").modal "hide" - ) + @socket.emit('bootUser', {userToBootClientId: @clientIdOfConnectedUser, userNameToAdd: AppLaunchParams.loginUserName}, @handleBootCurrentUserOffDeviceCallback) + + handleBootCurrentUserOffDeviceCallback: (err, data) => + @setStateToConnected() + @$(".bv_deviceInUse").modal "hide" handleDismissDisconnectMessage: => @$(".bv_disconnectedByAUserMessage").hide() @@ -192,4 +189,7 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @$(".bv_subformContainer").html @subFormTemplate() @completeInitialization() - @ \ No newline at end of file + @ + + completeInitialization: => + console.info "override in concrete instance of controller" \ No newline at end of file From 25acc7a62ad324703e3905194f44bc738c2beab6 Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Tue, 30 May 2017 22:00:32 -0700 Subject: [PATCH 020/576] Removed the unnecessary changes to null. --- .../routes/InventoryServiceRoutes.coffee | 27 ------------------- 1 file changed, 27 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index c01e4a9e5..c344b237a 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -247,21 +247,6 @@ exports.getContainerCodesByLabels = (req, resp) -> likeParameter = req.query.like maxResults = req.query.maxResults - if !(containerLabels)? - containerLabels = null - if !(containerType)? - containerType = null - if !(containerKind)? - containerKind = null - if !(labelType)? - labelType = null - if !(labelKind)? - labelKind = null - if !(likeParameter)? - likeParameter = null - if !(maxResults)? - maxResults = null - queryPayload = containerLabels: req.body containerType: containerType @@ -340,17 +325,6 @@ exports.getContainerCodesByLabelsInternal = (containerCodesJSON, containerType, console.debug 'incoming getContainerCodesByLabelsInternal request: ', JSON.stringify(containerCodesJSON), containerType, containerKind, labelType, labelKind config = require '../conf/compiled/conf.js' - if !(containerCodesJSON)? - containerLabels = null - if !(containerType)? - containerType = null - if !(containerKind)? - containerKind = null - if !(labelType)? - labelType = null - if !(labelKind)? - labelKind = null - likeParameter = null maxResults = null @@ -596,7 +570,6 @@ exports.updateContainersByContainerCodesInternal = (updateInformation, callCusto codeNames = _.pluck updateInformation, "codeName" console.debug "calling getContainersByCodeNamesInternal" exports.getContainersByCodeNamesInternal codeNames, (containers, statusCode) => - console.debug "containers from service" if statusCode == 400 console.error "got errors requesting code names: #{JSON.stringify containers}" callback "error when requesting code names", 400 From 418bce8b9145b92f03f861cb816adf76f9f11107 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 31 May 2017 14:40:21 -0700 Subject: [PATCH 021/576] notify user of error by making noise and printing error in color --- docker-compose.yml | 16 ++++++++-------- gulpfile.coffee | 24 ++++++++++++++++++++---- package.json | 16 ++++------------ 3 files changed, 32 insertions(+), 24 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 541cecf51..e6f83506d 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -2,7 +2,7 @@ version: '2' services: acas: # build: . - image: mcneilco/acas-oss:1.10.0 + image: mcneilco/acas-oss:develop restart: always ports: - "3000:3000" @@ -12,7 +12,7 @@ services: - APP_NAME=ACAS-OPEN - PREPARE_MODULE_CONF_JSON=true - PREPARE_CONFIG_FILES=true - - RUN_SYSTEM_TEST=true + - RUN_SYSTEM_TEST=false - DOCKER_HOST_IP=localhost - NODE_ENV=integration volumes: @@ -24,16 +24,16 @@ services: # Add chemaxon marvinjs here - ./chemaxon/marvinjs:/home/runner/build/public/CmpdReg/marvinjs # Please add any dev volumes below this line - # - ./:/home/runner/acas + - ./:/home/runner/acas # - ./modules/BuildUtilities/:/home/runner/acas/modules/BuildUtilities env_file: - ./conf/docker/acas/environment/acas.env # Dev Command # command: ["bin/acas.sh", "run", "acas", "dev"] # Start command - command: ["bin/acas.sh", "run", "acas", "start"] + command: ["bin/acas.sh", "run", "acas", "dev"] rservices: - image: mcneilco/racas-oss:1.10.0 + image: mcneilco/racas-oss:develop restart: always ports: - "1080:1080" @@ -60,7 +60,7 @@ services: ports: - "5432:5432" tomcat: - image: mcneilco/tomcat-maven + image: mcneilco/tomcat-maven:develop restart: always depends_on: - db @@ -81,12 +81,12 @@ services: - ./conf/docker/cmpdreg/environment/cmpdreg.env command: catalina.sh run roo: - image: mcneilco/acas-roo-server-oss:1.10.0 + image: mcneilco/acas-roo-server-oss:develop volumes: - /usr/local/tomcat/webapps/acas command: /bin/true cmpdreg: - image: mcneilco/cmpdreg-oss:1.10.0 + image: mcneilco/acas-cmpdreg-roo-server-oss:1.10.0 volumes: - /usr/local/tomcat/webapps/cmpdreg # Add chemaxon license files here diff --git a/gulpfile.coffee b/gulpfile.coffee index 2ac0e85eb..c41e00360 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -1,19 +1,18 @@ # ---------------------------------------------- Requires gulp = require('gulp') -gutil = require('gutil') coffee = require('gulp-coffee') -del = require('del') flatten = require('gulp-flatten') rename = require('gulp-rename') plumber = require('gulp-plumber') jeditor = require('gulp-json-editor') argv = require('yargs').argv path = require('path') -run = require('gulp-run') gulpif = require('gulp-if') _ = require('underscore') +notify = require("gulp-notify") node = undefined +os = require('os'); # ---------------------------------------------- Functions getGlob = (paths) -> @@ -352,6 +351,23 @@ createExecuteTask = (options) => watchTasks.push watchTaskName return taskName + +onError = (err) -> + process.stdout.write '\x07' + if os.platform() == 'darwins' + return notify.onError( + title: '<%= error.message %>' + # subtitle: 'Failure!' + message: 'Error: <%= error.stack %>' + sound: false) err + else + return notify.onError((options, callback) -> + console.log "\x1b[34m[#{options.message}]\x1b[0m \x1b[31mError: #{options.stack}\x1b[0m" + return + ) err + @emit 'end' + + createTask = (options, type) -> taskName = "#{type}:#{options.taskName}" taskOptions = options.options @@ -362,7 +378,7 @@ createTask = (options, type) -> renameFunction = options.renameFunction gulp.task taskName, -> gulp.src(src, _.extend(taskOptions, {since: gulp.lastRun(taskName)})) - .pipe(plumber()) + .pipe(plumber({errorHandler: onError})) .pipe(gulpif(shouldFlatten,flatten())) .pipe(gulpif(renameFunction?,rename(renameFunction))) .pipe(gulpif(type=="coffee",coffee(bare: true))) diff --git a/package.json b/package.json index ac9580f0f..9b173f29e 100644 --- a/package.json +++ b/package.json @@ -26,7 +26,6 @@ "csv-parse": "^1.1.1", "each": ">= 0.0.0", "express": "3.0.2", - "extract-text-webpack-plugin": "*", "file-loader": "*", "flat": "*", "forever-monitor": "*", @@ -35,7 +34,7 @@ "jasmine-core": "^2.4.1", "jasmine-jquery": "^2.1.1", "jquery": "^2.2.0", - "jquery-file-upload-middleware": ">=0.1.7", + "jquery-file-upload-middleware": "https://github.com/mcneilco/jquery-file-upload-middleware.git", "jszip": "*", "less": "^2.6.0", "lodash": "^4.0.0", @@ -57,34 +56,27 @@ "underscore-deep-extend": ">= 0.0.0", "winston": "*", "winston-mongodb": "*", - "style-loader": "*", "bootstrap": "*", "exports-loader": "*", - "extract-text-webpack-plugin": "*", "url-loader": "*", - "file-loader": "*", - "jquery-file-upload-middleware": "https://github.com/mcneilco/jquery-file-upload-middleware.git", "yamljs": "*", "request-promise": "*", - "bluebird": "*" + "bluebird": "*" }, "devDependencies": { - "del": "^2.2.2", + "coffee-script": "^1.12.4", "gulp": "github:gulpjs/gulp#4.0", - "gulp-browserify": "^0.5.1", "gulp-coffee": "^2.3.3", "gulp-copy": "^1.0.0", "gulp-exec": "^2.1.3", "gulp-flatten": "^0.3.1", "gulp-if": "^2.0.2", "gulp-json-editor": "^2.2.1", + "gulp-notify": "^3.0.0", "gulp-plumber": "^1.1.0", "gulp-rename": "^1.2.2", "gulp-replace": "^0.5.4", - "gulp-run": "^1.7.1", "gulp-watch": "^4.3.11", - "gutil": "^1.6.4", - "coffee-script": "^1.12.4", "yargs": "^7.0.2" } } From 66baf53659f413fef43d115865c9e7b4b5e7d921 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 31 May 2017 14:47:33 -0700 Subject: [PATCH 022/576] fixing os version #108 --- gulpfile.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gulpfile.coffee b/gulpfile.coffee index c41e00360..9ee420283 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -354,7 +354,7 @@ createExecuteTask = (options) => onError = (err) -> process.stdout.write '\x07' - if os.platform() == 'darwins' + if os.platform() == 'darwin' return notify.onError( title: '<%= error.message %>' # subtitle: 'Failure!' From 69d57881b7b38695a5ddd20f77e99cbefa9398cd Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 31 May 2017 14:47:33 -0700 Subject: [PATCH 023/576] fixing os version #108 --- gulpfile.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gulpfile.coffee b/gulpfile.coffee index c41e00360..9ee420283 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -354,7 +354,7 @@ createExecuteTask = (options) => onError = (err) -> process.stdout.write '\x07' - if os.platform() == 'darwins' + if os.platform() == 'darwin' return notify.onError( title: '<%= error.message %>' # subtitle: 'Failure!' From bbf8e54b3a0b0d410b4196e5a91921753652fc76 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Wed, 31 May 2017 16:36:55 -0600 Subject: [PATCH 024/576] #101 Added missing promise npm module to package.json Updated behavior of selecting a balance. --- .../client/RealtimeDeviceConnectionController.coffee | 11 ++++++----- package.json | 1 + 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee index ab649455d..7345c100c 100644 --- a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee +++ b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee @@ -4,15 +4,15 @@ deviceStubs = [ { code: 'balanceIsIdle', name: 'Balance Is Idle' - url: 'http://192.168.0.193:1337/' + url: 'http://192.168.0.193:1337/api/weigh/balanceIsIdle' }, { code: 'balanceNotConnected', name: 'Balance Not Connected' - url: 'http://192.168.0.193:1337/' + url: 'http://192.168.0.193:1337/api/weigh/balanceNotConnected' }, { code: 'balanceNotAvailable', name: 'Balance Not Available' - url: 'http://192.168.0.193:1337/' + url: 'http://192.168.0.193:1337/api/weigh/balanceNotAvailable' } ] @@ -47,9 +47,9 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @socket.on('disconnectedByAnotherUser', @disconnectedByAnotherUser) connectToDevice: => - selectedDevice = @devicePickList.getSelectedModel() + @selectedDevice = @devicePickList.getSelectedModel() @$(".bv_connecting").removeClass "hide" - @socket.emit('connectToDevice', {deviceName: selectedDevice.get('code'), deviceUrl: selectedDevice.get('url'), userName: AppLaunchParams.loginUserName}, @connectToDeviceCallback) + @socket.emit('connectToDevice', {deviceName: @selectedDevice.get('code'), deviceUrl: @selectedDevice.get('url'), userName: AppLaunchParams.loginUserName}, @connectToDeviceCallback) connectToDeviceCallback: (err, data) => if err @@ -67,6 +67,7 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @displayStatusMessage(".bv_deviceServerInUse") else + @setStateToConnected() @$(".bv_connectionStatusAlert").addClass "hide" diff --git a/package.json b/package.json index d946dcfb0..c182081b5 100644 --- a/package.json +++ b/package.json @@ -54,6 +54,7 @@ "shelljs": "0.6.0", "socket.io": "^1.7.3", "passport.socketio": "^3.7.0", + "promise": "7.1.1", "style-loader": "*", "temporary": ">= 0.0.0", "underscore": ">= 0.0.0", From 2d26552c96e230e754553963cb53d9b0fdf48253 Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Fri, 2 Jun 2017 11:12:35 -0700 Subject: [PATCH 025/576] Updating getContainerCodeNamesByContainerValue to handle new query parameters (like, rightLike and maxResults) --- .../src/server/routes/InventoryServiceRoutes.coffee | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index c344b237a..6250524cc 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -2013,8 +2013,17 @@ exports.getContainerCodeNamesByContainerValueInternal = (requestObject, callback inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' callback inventoryServiceTestJSON.getContainerCodeNamesByContainerValueResponse else + queryParams = [] + if requestObject.like? + queryParams.push "like="+requestObject.like + if requestObject.rightLike? + queryParams.push "rightLike="+requestObject.rightLike + if requestObject.maxResults? + queryParams.push "maxResults="+requestObject.maxResults + queryString = queryParams.join "&" + console.log 'request object in getContainerCodeNamesByContainerValue', requestObject config = require '../conf/compiled/conf.js' - baseurl = config.all.client.service.persistence.fullpath+"containers/getContainerCodeNamesByContainerValue" + baseurl = config.all.client.service.persistence.fullpath+"containers/getContainerCodeNamesByContainerValue?"+queryString request = require 'request' console.debug 'calling service', baseurl request( From 8875377e3514f210e87475dd3fb7d764a5eece73 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 2 Jun 2017 14:30:30 -0700 Subject: [PATCH 026/576] adding excel app --- modules/ExcelApp/conf/main.md | 8 ++ modules/ExcelApp/spec/ExcelApp.coffee | 135 ++++++++++++++++++ modules/ExcelApp/src/client/ExcelApp.coffee | 21 +++ modules/ExcelApp/src/client/ExcelApp.html | 5 + modules/ExcelApp/src/client/ExcelApp.jade | 20 +++ .../server/MSOfficeManifests/ExcelApps.xml | 23 +++ .../src/server/routes/ExcelApp.coffee | 28 ++++ 7 files changed, 240 insertions(+) create mode 100644 modules/ExcelApp/conf/main.md create mode 100644 modules/ExcelApp/spec/ExcelApp.coffee create mode 100644 modules/ExcelApp/src/client/ExcelApp.coffee create mode 100644 modules/ExcelApp/src/client/ExcelApp.html create mode 100644 modules/ExcelApp/src/client/ExcelApp.jade create mode 100644 modules/ExcelApp/src/server/MSOfficeManifests/ExcelApps.xml create mode 100644 modules/ExcelApp/src/server/routes/ExcelApp.coffee diff --git a/modules/ExcelApp/conf/main.md b/modules/ExcelApp/conf/main.md new file mode 100644 index 000000000..a1d342098 --- /dev/null +++ b/modules/ExcelApp/conf/main.md @@ -0,0 +1,8 @@ +Logout + + +Compound Properties Apps +* [Parent/Batch/Alias Properties][CIExcelCompoundPropertiesApp] - Get properties by providing batch, parent and alias ids + + +[CIExcelCompoundPropertiesApp]: diff --git a/modules/ExcelApp/spec/ExcelApp.coffee b/modules/ExcelApp/spec/ExcelApp.coffee new file mode 100644 index 000000000..ca6061c53 --- /dev/null +++ b/modules/ExcelApp/spec/ExcelApp.coffee @@ -0,0 +1,135 @@ +beforeEach -> + @fixture = $.clone($("#fixture").get(0)) + window.logger = + log: (message) -> + window.Office = + context: + document: + getSelectedDataAsync: (type, callback) -> + callback(window.resultMockObject) + + window.successfulResultMockObject = + status: 'succeeded' + value: 'mockResultValue' + + window.unsuccessfulResultMockObject = + status: 'failed' + value: null + error: + name: "error message name" + value: "mock error message" + +afterEach -> + $("#fixture").remove() + $("body").append $(@fixture) + +describe "Excel Compound Info App module testing", -> + describe "Attributes Controller", -> + beforeEach -> + @attributesController = new AttributesController + el: $("#fixture") + @attributesController.render() + + describe "Basic existence tests and defaults", -> + it "should be defined", -> + expect(@attributesController).toBeDefined() + it "insert column headers and include requested ids should be checked by default", -> + expect(@attributesController.$('.bv_insertColumnHeaders').attr("checked")).toEqual "checked" + expect(@attributesController.$('.bv_includeRequestedID').attr("checked")).toBeUndefined() + describe "Property Descriptor Controller", -> + beforeEach -> + @pdc = new PropertyDescriptorController + el: $("#fixture") + model: new PropertyDescriptor window.parentPropertyDescriptorsTestJSON.parentPropertyDescriptors[0] + @pdc.render() + describe 'basic existence testing', (done) -> + it "should have a Property Descriptor as a model", -> + expect(@pdc.model instanceof PropertyDescriptor).toBeTruthy() + describe 'rendering testing', () -> + it "should set the description label to the models pretty name", -> + modelPrettyName = @pdc.model.get('valueDescriptor').prettyName + descriptorLabel = @pdc.$('.bv_descriptorLabel').html() + expect(descriptorLabel).toEqual(modelPrettyName) + it "should set the description label title attribute to the models description", -> + modelDescription = @pdc.model.get('valueDescriptor').description + descriptorTitle = @pdc.$('.bv_descriptorLabel').attr 'title' + expect(descriptorTitle).toEqual(modelDescription) + describe 'clicking on the property descriptor checkbox', () -> + it "should trigger handleDescriptorCheckboxChanged", -> + spyOn @pdc, "handleDescriptorCheckboxChanged" + @pdc.delegateEvents() + @pdc.$('.bv_propertyDescriptorCheckbox').click() + expect(@pdc.handleDescriptorCheckboxChanged).toHaveBeenCalled() + describe "Property Descriptor List Controller", -> + beforeEach (done) -> + setTimeout (-> + window.propertyDescriptorListController = new PropertyDescriptorListController + el: $("#fixture") + title: 'Parent Properties' + url: '/api/compound/parent/property/descriptors' + window.propertyDescriptorListController.on 'ready', -> + window.propertyDescriptorListController.render() + done() + return + ), 100 + return + describe 'basic existence testing', (done) -> + it "should populate a collection", -> + expect(window.propertyDescriptorListController.collection.length).toBeGreaterThan(0) + describe 'basic rendering', (done) -> + it "should have a title", -> + expect(window.propertyDescriptorListController.$('.propertyDescriptorListControllerTitle').html()).toEqual 'Parent Properties' + it "should render the property descriptor list", -> + expect(window.propertyDescriptorListController.$('.bv_propertyDescriptorList .bv_descriptorLabel').length).toBeGreaterThan(0) + + describe "Excel Compound Info App controller", -> + beforeEach (done) -> + setTimeout (-> + window.insertCompoundPropertiesController = new ExcelInsertCompoundPropertiesController + el: $("#fixture") + window.insertCompoundPropertiesController.render() + numberReady = 0 + window.insertCompoundPropertiesController.batchPropertyDescriptorListController.on 'ready', -> + if numberReady == 1 + done() + else + numberReady = 1 + window.insertCompoundPropertiesController.parentPropertyDescriptorListController.on 'ready', -> + if numberReady == 1 + done() + else + numberReady = 1 + return + ), 100 + return +# beforeEach (done)-> +# window.insertCompoundPropertiesController = new ExcelInsertCompoundPropertiesController +# el: $("#fixture") +# +# insertCompoundPropertiesController.render() + describe "Basic existence tests", -> + it "should be defined", -> + expect(insertCompoundPropertiesController).toBeDefined() + expect(insertCompoundPropertiesController.attributesController).toBeDefined() + expect(insertCompoundPropertiesController.parentPropertyDescriptorListController).toBeDefined() + expect(insertCompoundPropertiesController.batchPropertyDescriptorListController).toBeDefined() + describe "getSelectedProperties", -> + it "should return an array of properties with a batch and parent key", -> + console.log window.insertCompoundPropertiesController.$('.bv_parentProperties') + window.insertCompoundPropertiesController.$('.bv_batchProperties .bv_propertyDescriptorList .bv_propertyDescriptorCheckbox')[0].click() + window.insertCompoundPropertiesController.$('.bv_batchProperties .bv_propertyDescriptorList .bv_propertyDescriptorCheckbox')[1].click() + window.insertCompoundPropertiesController.$('.bv_parentProperties .bv_propertyDescriptorList .bv_propertyDescriptorCheckbox')[0].click() + window.insertCompoundPropertiesController.getSelectedProperties (selectedProperties) -> + expect(selectedProperties.parentNames.length).toEqual(1) + expect(selectedProperties.batchNames.length).toEqual(2) + describe "handleGetPropertiesClicked", -> + it "should call fetchPrepared if result.status is 'succeeded'", -> + window.resultMockObject = window.successfulResultMockObject + spyOn insertCompoundPropertiesController, "getPropertiesAndRequestData" + insertCompoundPropertiesController.handleGetPropertiesClicked() + expect(insertCompoundPropertiesController.getPropertiesAndRequestData).toHaveBeenCalled() + it "should not call fetchPrepared if result.status is not 'succeeded'", -> + window.resultMockObject = window.unsuccessfulResultMockObject + spyOn insertCompoundPropertiesController, "getPropertiesAndRequestData" + insertCompoundPropertiesController.handleGetPropertiesClicked() + expect(insertCompoundPropertiesController.getPropertiesAndRequestData).not.toHaveBeenCalled() diff --git a/modules/ExcelApp/src/client/ExcelApp.coffee b/modules/ExcelApp/src/client/ExcelApp.coffee new file mode 100644 index 000000000..158ccab58 --- /dev/null +++ b/modules/ExcelApp/src/client/ExcelApp.coffee @@ -0,0 +1,21 @@ +marked = require 'marked' + +window.onload = -> + window.excelAppController = new ExcelAppController + el: $('.bv_excelAppView') + excelAppController.render() + +class window.ExcelAppController extends Backbone.View + initialize: -> + @template = _.template($("#ExcelAppView").html()) + + render: => + @$el.empty() + @$el.html @template() + $.ajax + type: 'GET' + url: "/conf/ExcelApp/main.md" + success: (markdown) => + console.log markdown + appHTML = marked(markdown) + @$('.bv_excelApp').html appHTML diff --git a/modules/ExcelApp/src/client/ExcelApp.html b/modules/ExcelApp/src/client/ExcelApp.html new file mode 100644 index 000000000..96ab63b6c --- /dev/null +++ b/modules/ExcelApp/src/client/ExcelApp.html @@ -0,0 +1,5 @@ + + diff --git a/modules/ExcelApp/src/client/ExcelApp.jade b/modules/ExcelApp/src/client/ExcelApp.jade new file mode 100644 index 000000000..a9281b646 --- /dev/null +++ b/modules/ExcelApp/src/client/ExcelApp.jade @@ -0,0 +1,20 @@ +doctype html +html + head + meta(charset="UTF-8") + meta(http-equiv="X-UA-Compatible", content="IE=Edge") + link(rel='stylesheet', href='/lib/jquery-ui-1.10.2.custom/css/smoothness/jquery-ui-1.10.2.custom.css') + link(rel='stylesheet', href='/lib/bootstrap-3.3.5-dist/css/bootstrap.css') + script(type='text/javascript', src="https://appsforoffice.microsoft.com/lib/1.0/hosted/office.js") + script(type='text/javascript', src="/lib/json2.js") + script(type='text/javascript', src="/lib/jquery-ui-1.10.2.custom/js/jquery-1.9.1.js") + script(type='text/javascript', src="/lib/underscore.js") + script(type='text/javascript', src="/lib/bootstrap-3.3.5-dist/js/bootstrap.min.js") + script(type='text/javascript', src="/lib/backbone-min.js") + include ../public/html/ExcelApp/ExcelApp.html + script(type='text/javascript', src="/javascripts/src/ExcelApp/ExcelApp.js") + + body + script + window.AppLaunchParams = !{JSON.stringify(AppLaunchParams)}; + div( class="bv_excelAppView" ) diff --git a/modules/ExcelApp/src/server/MSOfficeManifests/ExcelApps.xml b/modules/ExcelApp/src/server/MSOfficeManifests/ExcelApps.xml new file mode 100644 index 000000000..4d9246fe5 --- /dev/null +++ b/modules/ExcelApp/src/server/MSOfficeManifests/ExcelApps.xml @@ -0,0 +1,23 @@ + + + aaaaaaaa-1111-bbbb-2222-cccccccccccd + 1.0 + John McNeil and Co + EN-US + + + + + + + + + + + + + ReadWriteDocument + \ No newline at end of file diff --git a/modules/ExcelApp/src/server/routes/ExcelApp.coffee b/modules/ExcelApp/src/server/routes/ExcelApp.coffee new file mode 100644 index 000000000..bb0b08e94 --- /dev/null +++ b/modules/ExcelApp/src/server/routes/ExcelApp.coffee @@ -0,0 +1,28 @@ +exports.setupRoutes = (app, loginRoutes) -> + app.get '/excelApps', loginRoutes.ensureAuthenticated, exports.excelAppIndex + +exports.excelAppIndex = (req, resp) -> + csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFunctions.js' + csUtilities.logUsage "Index requested", "#{req.url}", req.body.user + + global.specRunnerTestmode = if global.stubsMode then true else false + config = require '../conf/compiled/conf.js' + if config.all.client.require.login + loginUserName = req.user.username + loginUser = req.user + else + loginUserName = "nouser" + loginUser = + id: 0, + username: "nouser", + email: "nouser@nowhere.com", + firstName: "no", + lastName: "user" + + return resp.render 'ExcelApp', + title: 'ExcelApps' + AppLaunchParams: + loginUserName: loginUserName + loginUser: loginUser + testMode: global.specRunnerTestmode + deployMode: global.deployMode From 5727f239252b80af8739e61722bf966ed9596b97 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 5 Jun 2017 09:39:19 -0700 Subject: [PATCH 027/576] fixing browserify --- gulpfile.coffee | 21 ++++++++++++++++++++- package.json | 13 +++++++------ 2 files changed, 27 insertions(+), 7 deletions(-) diff --git a/gulpfile.coffee b/gulpfile.coffee index 9ee420283..b6b4b9eee 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -11,6 +11,8 @@ path = require('path') gulpif = require('gulp-if') _ = require('underscore') notify = require("gulp-notify") +coffeeify = require('gulp-coffeeify') + node = undefined os = require('os'); @@ -239,6 +241,12 @@ taskConfigs = src: getGlob('conf/**', '!conf/*.coffee') dest: build + '/conf' options: _.extend _.clone(globalCopyOptions), {} + , + taskName: "moduleConf" + src: getGlob('modules/**/conf/**', '!modules/**/conf/*.coffee') + dest: build + '/public/conf' + options: _.extend _.clone(globalCopyOptions), {} + renameFunction: getFirstFolderName , taskName: "nodeModulesCustomized" src: getGlob('node_modules_customized/**') @@ -376,12 +384,23 @@ createTask = (options, type) -> watch = options.watch shouldFlatten = options.flatten ? false renameFunction = options.renameFunction + shouldCoffeify = (file) -> + if type=="coffee" && (file.path.indexOf("client/ExcelApp") > -1) + return true + else + return false + shouldCoffee = (file) -> + if type=="coffee" && !(file.path.indexOf("client/ExcelApp") > -1) + return true + else + return false gulp.task taskName, -> gulp.src(src, _.extend(taskOptions, {since: gulp.lastRun(taskName)})) .pipe(plumber({errorHandler: onError})) .pipe(gulpif(shouldFlatten,flatten())) + .pipe(gulpif(shouldCoffeify, coffeeify({options:{paths:[build]}}))) + .pipe(gulpif(shouldCoffee,coffee(bare: true))) .pipe(gulpif(renameFunction?,rename(renameFunction))) - .pipe(gulpif(type=="coffee",coffee(bare: true))) .pipe gulp.dest(dest) unless watch == false watchTaskName = "watch:#{taskName}" diff --git a/package.json b/package.json index 9b173f29e..eb82dcb6d 100644 --- a/package.json +++ b/package.json @@ -20,11 +20,14 @@ "asyncblock": "*", "backbone": "^1.2.3", "backbone-validation": "^0.11.5", + "bluebird": "*", + "bootstrap": "*", "chai": "^3.5.0", "connect-flash": "~0.1.0", "cron": "*", "csv-parse": "^1.1.1", "each": ">= 0.0.0", + "exports-loader": "*", "express": "3.0.2", "file-loader": "*", "flat": "*", @@ -49,24 +52,22 @@ "properties": "*", "properties-parser": "*", "request": "2.34.0", + "request-promise": "*", "shelljs": "0.6.0", "style-loader": "*", "temporary": ">= 0.0.0", "underscore": ">= 0.0.0", "underscore-deep-extend": ">= 0.0.0", + "url-loader": "*", "winston": "*", "winston-mongodb": "*", - "bootstrap": "*", - "exports-loader": "*", - "url-loader": "*", - "yamljs": "*", - "request-promise": "*", - "bluebird": "*" + "yamljs": "*" }, "devDependencies": { "coffee-script": "^1.12.4", "gulp": "github:gulpjs/gulp#4.0", "gulp-coffee": "^2.3.3", + "gulp-coffeeify": "^0.1.8", "gulp-copy": "^1.0.0", "gulp-exec": "^2.1.3", "gulp-flatten": "^0.3.1", From 19bd9e75e4a899a25e876ca4112dff294a7b00d6 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Wed, 7 Jun 2017 13:46:38 -0600 Subject: [PATCH 028/576] #101 Added heartbeat / watchdog feature that periodically checks the status of the balance server and updates the client with the current state. --- .../RealtimeDeviceConnectionController.coffee | 40 ++++++++++--------- .../RealtimeDeviceConnectionSockets.coffee | 36 +++++++++++++---- 2 files changed, 49 insertions(+), 27 deletions(-) diff --git a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee index 7345c100c..a73280b46 100644 --- a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee +++ b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee @@ -4,15 +4,15 @@ deviceStubs = [ { code: 'balanceIsIdle', name: 'Balance Is Idle' - url: 'http://192.168.0.193:1337/api/weigh/balanceIsIdle' + url: 'http://192.168.0.193:1337/' }, { code: 'balanceNotConnected', name: 'Balance Not Connected' - url: 'http://192.168.0.193:1337/api/weigh/balanceNotConnected' + url: 'http://192.168.0.193:1337/' }, { code: 'balanceNotAvailable', name: 'Balance Not Available' - url: 'http://192.168.0.193:1337/api/weigh/balanceNotAvailable' + url: 'http://192.168.0.193:1337/' } ] @@ -32,7 +32,10 @@ class window.RealtimeDeviceConnectionController extends Backbone.View initialize: -> @isConnectedToDevice = false @testMode = @options.testMode + if @options.socket? + @socket = @options.socket @deviceCollection = new DeviceCollection(deviceStubs) + @connected = false unless @testMode @setupSocketEventHandlers() @@ -45,14 +48,19 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @socket.on('disconnectedFromDevice', @disconnectedFromDevice) @socket.on('alertAllDisconnectedFromDevice', @alertAllDisconnectedFromDevice) @socket.on('disconnectedByAnotherUser', @disconnectedByAnotherUser) + @socket.on('in_use', @displayUnavailableMessage) + + connectToDevice: => - @selectedDevice = @devicePickList.getSelectedModel() - @$(".bv_connecting").removeClass "hide" - @socket.emit('connectToDevice', {deviceName: @selectedDevice.get('code'), deviceUrl: @selectedDevice.get('url'), userName: AppLaunchParams.loginUserName}, @connectToDeviceCallback) + unless @connected + @selectedDevice = @devicePickList.getSelectedModel() + @$(".bv_connecting").removeClass "hide" + @socket.emit('connectToDevice', {deviceName: @selectedDevice.get('code'), deviceUrl: @selectedDevice.get('url'), userName: AppLaunchParams.loginUserName}, @connectToDeviceCallback) connectToDeviceCallback: (err, data) => if err + @connected = false @setStateToDisconnected() switch err.status when "not_available" @@ -67,14 +75,17 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @displayStatusMessage(".bv_deviceServerInUse") else - + @connected = true @setStateToConnected() @$(".bv_connectionStatusAlert").addClass "hide" + displayUnavailableMessage: => + unless @connected + @displayStatusMessage(".bv_deviceServerInUse") + displayStatusMessage: (messageSelector) => @resetStatusMessages() - @$(messageSelector).removeClass "hide" resetStatusMessages: => @@ -92,7 +103,6 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @displayStatusMessage(".bv_deviceServerInUseButIdle") @$(".bv_deviceUsedBy").html @userNameOfConnectedUser - handleDeviceSelectChange: => deviceName = @devicePickList.getSelectedCode() unless deviceName is "" @@ -120,23 +130,20 @@ class window.RealtimeDeviceConnectionController extends Backbone.View disableDisconnectButton: => @$(".bv_disconnect").addClass "hide" -#@disableButton(".bv_disconnect") enableDisconnectButton: => -#@enableButton(".bv_disconnect") @$(".bv_disconnect").removeClass "hide" - disableButton: (cssSelector) => + disableElement: (cssSelector) => @$(cssSelector).prop "disabled", true @$(cssSelector).addClass "disabled" - enableButton: (cssSelector) => + enableElement: (cssSelector) => @$(cssSelector).prop "disabled", false @$(cssSelector).removeClass "disabled" handleDisconnectClicked: (e) => e.preventDefault() - console.log "handleDisconnectClicked" @socket.emit('disconnected') setStateToDisconnected: => @@ -152,12 +159,9 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @displayStatusMessage ".bv_connected" disconnectedFromDevice: => - console.log "you've been successfully disconnected" @setStateToDisconnected() alertAllDisconnectedFromDevice: => - console.log "alertAllDisconnectedFromDevice" - console.log "@isConnectedToDevice", @isConnectedToDevice unless @isConnectedToDevice @connectToDevice() @@ -168,7 +172,6 @@ class window.RealtimeDeviceConnectionController extends Backbone.View displayDisconnectedModal: (disconnectingUserName) => @$(".bv_disconnectingUserName").html disconnectingUserName @$(".bv_disconnectedByAUserMessage").show "slide", {direction: "right"} -#@$(".bv_disconnectedByAnotherUser").modal "show" dismissDeviceInUse: => @$(".bv_deviceInUse").modal "hide" @@ -186,7 +189,6 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @ renderSubform: => - @$(".bv_subformContainer").html @subFormTemplate() @completeInitialization() diff --git a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee index aaa96587e..c18e0efb7 100644 --- a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee +++ b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee @@ -2,23 +2,25 @@ request = require 'request' _ = require 'underscore' -promise = require 'promise' +Promise = require 'promise' class BalanceAccess - constructor: (balanceName, balanceUrl) -> + constructor: (balanceName, balanceUrl, room) -> @balanceName = balanceName @balanceUrl = balanceUrl @isAvailable = true @currentConnectedUser = null @status = "idle" @balanceConnectQueue = [] + @room = room + @heartBeat = null ### get the current status of the balance from the node server connected to the balance ### getBalanceStatus: => - balanceStatusURL = @balanceUrl + "api/getBalanceStatus/#{@balanceName}" + balanceStatusURL = @balanceUrl + "api/getBalanceStatus?balanceId=#{@balanceName}" return new Promise((resolve, reject) => request( method: 'GET' @@ -32,6 +34,25 @@ class BalanceAccess ) ) + startHeartBeat: => + unless @heartBeat? + @heartBeat = setInterval( => + @getBalanceStatus().then((balanceStatus) => + unless balanceStatus is @status + @status = balanceStatus + switch @status + when "idle" + @room.emit('youShouldTryConnecting') + when "in_use" + @room.emit('in_use') + ).catch((err) => + @room.emit("device_server_offline") + ) + , 1000) + + clearHeartBeat: => + clearInterval(@heartBeat) + @heartBeat = null removeUserFromQueue: (clientId) => if @currentConnectedUser.clientId is clientId @@ -61,6 +82,7 @@ class BalanceAccess return new Promise((resolve, reject) => @getBalanceStatus().then((balanceStatus) => @status = balanceStatus + @startHeartBeat() switch @status when "idle" if @isAvailable @@ -120,10 +142,6 @@ class DeviceSocketController setupEventListeners: => @nameSpacedRoom.on('connection', (socket) => - console.log "socket.request.username" - console.log socket.request.user - console.log socket.request.session - #console.log socket.request.session.passport.user socket.on('connectToDevice', (payload, callback) => @handleConnectToDevice(socket, payload, callback) ) @@ -143,7 +161,7 @@ class DeviceSocketController handleConnectToDevice: (socket, payload, callback) -> unless @balances[payload.deviceName] - @balances[payload.deviceName] = new BalanceAccess(payload.deviceName, payload.deviceUrl) + @balances[payload.deviceName] = new BalanceAccess(payload.deviceName, payload.deviceUrl, @nameSpacedRoom) socket.join(payload.deviceName) @usersInRoom[socket.id] = payload.deviceName balanceAccess = @balances[payload.deviceName] @@ -173,6 +191,7 @@ class DeviceSocketController socket.broadcast.to(nextUserInQueue.clientId).emit('youShouldTryConnecting') else socket.broadcast.emit('alertAllDisconnectedFromDevice') + balanceAccess.clearHeartBeat() socket.leave(@usersInRoom[socket.id]) socket.emit('disconnectedFromDevice') @@ -185,6 +204,7 @@ class DeviceSocketController socket.broadcast.to(nextUserInQueue.clientId).emit('youShouldTryConnecting') else socket.broadcast.emit('alertAllDisconnectedFromDevice') + balanceAccess.clearHeartBeat() handleBootUser: (socket, payload, callback) -> balanceAccess = @balances[@usersInRoom[socket.id]] From c0ebc28588bb0d5c74966d402da85e99660d8374 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Wed, 7 Jun 2017 13:21:07 -0700 Subject: [PATCH 029/576] Fast User Switching Feature Complete --- conf/config.properties.example | 5 + .../src/server/routes/loginRoutes.coffee | 1 - .../ModuleMenus/src/client/ModuleMenus.coffee | 123 +++++++++++++----- .../src/client/ModuleMenusView.html | 7 +- modules/ModuleMenus/src/client/style.css | 11 +- .../server/routes/ModuleMenusRoutes.coffee | 47 +++++-- .../CustomerSpecificServerFunctions.coffee | 6 +- 7 files changed, 151 insertions(+), 49 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 431a6ad42..504307d19 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -511,3 +511,8 @@ client.projectEditor.restrictedCheckbox.show=true client.projectEditor.isRestricted.default=false client.roles.crossProjectLoaderRole=ROLE_ACAS-CROSS-PROJECT-LOADER + +#Add user roles that represent groups allowed to fast user switch +#client.moduleMenus.fastUserSwitchingRoles=[] +client.moduleMenus.fastUserSwitchingRoles=[{"lsKind":"PROJ-00000001","lsType":"Project","roleName":"User"},{"lsKind":"PROJ-00000002","lsType":"Project","roleName":"User"}] +client.moduleMenus.fastUserSwitchingChangeUserRoles=true \ No newline at end of file diff --git a/modules/Login/src/server/routes/loginRoutes.coffee b/modules/Login/src/server/routes/loginRoutes.coffee index ed8970603..300317cfb 100644 --- a/modules/Login/src/server/routes/loginRoutes.coffee +++ b/modules/Login/src/server/routes/loginRoutes.coffee @@ -62,7 +62,6 @@ exports.loginPost = (req, res) -> else res.redirect '/' - exports.changePost = (req, res) -> console.log req.session # res.redirect '/' diff --git a/modules/ModuleMenus/src/client/ModuleMenus.coffee b/modules/ModuleMenus/src/client/ModuleMenus.coffee index 1c9b9d8f8..0a1885692 100644 --- a/modules/ModuleMenus/src/client/ModuleMenus.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenus.coffee @@ -5,8 +5,7 @@ class window.ModuleMenusController extends Backbone.View events: -> 'click .bv_headerName': "handleHome" 'click .bv_toggleModuleMenuControl': "handleToggleMenus" - 'click .bv_loginUserFirstName': 'handleLoginUserFirstNameClick' - 'click .bv_changeNameBtn': 'handleChangeNameBtnClick' + 'change .bv_fastUserSelect': 'handleLoginUserChange' # 'click .bv_showModuleMenuControl': "handleShowMenus" window.onbeforeunload = () -> @@ -16,7 +15,6 @@ class window.ModuleMenusController extends Backbone.View return initialize: -> - $(@el).html @template() @moduleLauncherList = new ModuleLauncherList(@options.menuListJSON) @@ -27,12 +25,6 @@ class window.ModuleMenusController extends Backbone.View el: @$('.bv_mainModuleWrapper') collection: @moduleLauncherList - if window.conf.require.login - @$('.bv_loginUserFirstName').html window.AppLaunchParams.loginUser.firstName - @$('.bv_loginUserLastName').html window.AppLaunchParams.loginUser.lastName - else - @$('.bv_userInfo').hide() - unless window.conf.roologin.showpasswordchange @$('.bv_changePassword').hide() @@ -60,14 +52,17 @@ class window.ModuleMenusController extends Backbone.View modLink = '
  • '+module.displayName+'
    • ' @$('.bv_externalACASModules').append modLink - @socket = io('/user:loggedin') - @socket.on('connect', @handleConnected) - @socket.on('connect_error', @handleConnectError) - @socket.on('loggedOn', @handleLoggedOn) - @socket.on('loggedOff', @handleLoggedOn) - @socket.on('usernameUpdated', @handleNameChanged) - - @disconnectedAfterLogin = false + if window.conf.require.login + if @fastUserSwitchingAllowed() + @$('.bv_loginUserFirstName').hide() + @$('.bv_loginUserLastName').hide() + @setupFastUserSwitching() + else + @$('.bv_fastUserSelect').hide() + @$('.bv_loginUserFirstName').html window.AppLaunchParams.loginUser.firstName + @$('.bv_loginUserLastName').html window.AppLaunchParams.loginUser.lastName + else + @$('.bv_userInfo').hide() render: => if window.AppLaunchParams.deployMode? @@ -81,7 +76,6 @@ class window.ModuleMenusController extends Backbone.View $('.bv_homePageWrapper').show() handleHideMenus: => - console.log "got handleHideMenus" @$('.bv_moduleMenuWellWrapper').hide() @$('.bv_showModuleMenuControl').show() @@ -99,6 +93,43 @@ class window.ModuleMenusController extends Backbone.View @$('.bv_mainModuleWellWrapper').removeClass 'span9' @$('.bv_mainModuleWellWrapper').addClass 'span11' +# Fast User Switching Methods + + setupFastUserSwitching: -> + @socket = io('/user:loggedin') + @socket.on('connect', @handleConnected) + @socket.on('connect_error', @handleConnectError) + @socket.on('loggedOn', @handleLoggedOn) + @socket.on('tabClosed', @handleOtherTabClosed) + @socket.on('loggedOff', @handleLoggedOff) + @socket.on('usernameUpdated', @handleUserChanged) + @disconnectedAfterLogin = false + @setupUserSwitchingSelect() + + setupUserSwitchingSelect: -> + @altUserList = new PickListList() + @getAllAvailableUsers @altUserList, => + @altUserListController = new PickListSelectController + el: @$('.bv_fastUserSelect') + collection: @altUserList + autoFetch: false + selectedCode: window.AppLaunchParams.loginUserName + + getAllAvailableUsers: (userList, callback) -> + roles = @getMatchingFastUserSwitchingRoles() + @getNextGroup roles, 0, userList, callback + + getNextGroup: (roles, index, userList, finalCallback) -> + if index >= roles.length + finalCallback() + else + role = roles[index++] + tList = new PickListList() + tList.url = "/api/authors?roleType=#{role.lsType}&roleKind=#{role.lsKind}&roleName=#{role.roleName}" + tList.fetch success: => + userList.add tList.models + @getNextGroup roles, index, userList, finalCallback + handleConnected: => console.log "handleConnected" @@ -107,21 +138,47 @@ class window.ModuleMenusController extends Backbone.View console.log "handleConnectError" handleLoggedOn: (numberOfLogins) -> - console.log "you're loggedin in this many places: ", numberOfLogins + console.log "you're logged in this many places: ", numberOfLogins - handleLoggedOff: (numberOfLogins) -> - console.log "you're loggedin in this many places: ", numberOfLogins - - handleLoginUserFirstNameClick: => - @$(".bv_changeUserName").modal "show" + handleOtherTabClosed: (numberOfLogins) -> + console.log "Tab closed elsewhere, you're logged in this many places: ", numberOfLogins - handleChangeNameBtnClick: (e) => - e.preventDefault() - firstName = @$(".bv_firstName").val() - @socket.emit('changeUserName', firstName) - @$(".bv_firstName").val('') - @$(".bv_changeUserName").modal "hide" + handleLoggedOff: (numberOfLogins) -> + console.log "you're logged in this many places: ", numberOfLogins + window.location = "/login"; + + handleLoginUserChange: => + newUserName = @$('.bv_fastUserSelect').val() + console.log "user change requested to: "+newUserName + unless newUserName == window.AppLaunchParams.loginUserName + @socket.emit('changeUserName', newUserName) + + handleUserChanged: (updatedUser) => + console.log "handleUserChanged" + console.dir updatedUser +# updatedUser = JSON.parse updatedUserStr + console.log "got user change to: "+updatedUser.username + AppLaunchParams.loginUserName = updatedUser.username + AppLaunchParams.loginUser = updatedUser + @setupUserSwitchingSelect() + + fastUserSwitchingAllowed: -> + switchingRoles = JSON.parse(window.conf.moduleMenus.fastUserSwitchingRoles) + allowed = false + if switchingRoles.length > 0 && window.AppLaunchParams.loginUser.roles? + allowed = UtilityFunctions::testUserHasRoleTypeKindName window.AppLaunchParams.loginUser, switchingRoles + return allowed + + getMatchingFastUserSwitchingRoles: -> + matches = [] + for role in JSON.parse(window.conf.moduleMenus.fastUserSwitchingRoles) + for userRole in window.AppLaunchParams.loginUser.roles + if userRole.roleEntry.lsType == role.lsType and userRole.roleEntry.lsKind == role.lsKind and userRole.roleEntry.roleName == role.roleName + matches.push role + matches + + + +#TODO config docs in readme.md file +#TODO should some code in mmroutes be rafactored to a general socket utility? - handleNameChanged: (updatedFirstName) => - @$(".bv_loginUserFirstName").html updatedFirstName - AppLaunchParams.loginUserName = updatedFirstName diff --git a/modules/ModuleMenus/src/client/ModuleMenusView.html b/modules/ModuleMenus/src/client/ModuleMenusView.html index 38dcc798b..177003207 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusView.html +++ b/modules/ModuleMenus/src/client/ModuleMenusView.html @@ -7,8 +7,11 @@

    Logged in as - First Name - Last Name + + First Name + Last Name + + Logout

      diff --git a/modules/ModuleMenus/src/client/style.css b/modules/ModuleMenus/src/client/style.css index 0ace50164..00a8a137c 100644 --- a/modules/ModuleMenus/src/client/style.css +++ b/modules/ModuleMenus/src/client/style.css @@ -63,4 +63,13 @@ body { .bv_BulkLoadSampleTransfersController { background-color: green; -}*/ \ No newline at end of file +}*/ + +.bv_fastUserSelect { + background-color: transparent; + color: #999999; + margin-top: 0px; + margin-bottom: 6px; + height: 0px; + border: none; +} \ No newline at end of file diff --git a/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee b/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee index 6aef3b89f..f10c498f4 100644 --- a/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee +++ b/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee @@ -9,22 +9,29 @@ exports.setupChannels = (io, sessionStore, loginRoutes) -> unless connectedUsers[sessionID]? connectedUsers[sessionID] = [] connectedUsers[sessionID].push socket.id - totalNumberOfConnectionsForUser = _.size(connectedUsers[userName]) - broadcastMessageToSpecificClients(connectedUsers[userName], 'loggedOn', totalNumberOfConnectionsForUser, socket) + totalNumberOfConnectionsForUser = _.size(connectedUsers[sessionID]) + broadcastMessageToSpecificClients(connectedUsers[sessionID], 'loggedOn', totalNumberOfConnectionsForUser, socket) socket.emit('loggedOn', totalNumberOfConnectionsForUser) socket.on('disconnect', => - clientConnections = connectedUsers[userName] + parsedCookie = JSON.parse(sessionStore.sessions[sessionID]) + + clientConnections = connectedUsers[sessionID] connectedUsers[sessionID] = _.without(clientConnections, socket.id) totalNumberOfConnectionsForUser = _.size(connectedUsers[sessionID]) - broadcastMessageToSpecificClients(connectedUsers[sessionID], 'loggedOff', totalNumberOfConnectionsForUser, socket) + if parsedCookie.passport.user? + console.log "got disconnect" + broadcastMessageToSpecificClients(connectedUsers[sessionID], 'tabClosed', totalNumberOfConnectionsForUser, socket) + else + console.log "got logoff" + broadcastMessageToSpecificClients(connectedUsers[sessionID], 'loggedOff', totalNumberOfConnectionsForUser, socket) ) socket.on('changeUserName', (updatedUsername) => sessionID = getSessionID(socket) - updateUserNameInSession(updatedUsername, sessionStore, sessionID) - broadcastMessageToSpecificClients(connectedUsers[sessionID], 'usernameUpdated', updatedUsername, socket) - socket.emit('usernameUpdated', updatedUsername) + updateUserNameInSession updatedUsername, sessionStore, sessionID, (newUser) -> + broadcastMessageToSpecificClients(connectedUsers[sessionID], 'usernameUpdated', newUser, socket) + socket.emit('usernameUpdated', newUser) ) ) @@ -35,13 +42,31 @@ getUserNameFromSession = (socket) -> else return socket.request.user.username -updateUserNameInSession = (updatedUserName, sessionStore, sessionId) -> +updateUserNameInSession = (updatedUserName, sessionStore, sessionId, callback) -> parsedCookie = JSON.parse(sessionStore.sessions[sessionId]) + if updatedUserName == parsedCookie.passport.user.username + return #nothing to change + unless parsedCookie.passport.user.originalLoginUserName? parsedCookie.passport.user.originalLoginUserName = parsedCookie.passport.user.username - parsedCookie.passport.user.username = updatedUserName - parsedCookie.passport.user.firstName = updatedUserName - sessionStore.sessions[sessionId] = JSON.stringify(parsedCookie) + + config = require '../conf/compiled/conf.js' + csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFunctions.js' + csUtilities.getUser updatedUserName, (messgage, user) -> + newUser = + id: user.id + username: user.username + email: user.email + firstName: user.firstName + lastName: user.lastName + if config.all.client.moduleMenus.fastUserSwitchingChangeUserRoles + newUser.roles = user.roles + else + newUser.roles = parsedCookie.passport.user.roles + + parsedCookie.passport.user = newUser + sessionStore.sessions[sessionId] = JSON.stringify(parsedCookie) + callback newUser broadcastMessageToSpecificClients = (socketIds, messageName, payload, socket) -> _.each(socketIds, (socketId) -> diff --git a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee index ac81dcba2..e612fe222 100644 --- a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee +++ b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee @@ -227,7 +227,11 @@ exports.getAuthors = (req, resp) -> #req passed in as input to be able to filter config = require "#{ACAS_HOME}/conf/compiled/conf.js" serverUtilityFunctions = require "#{ACAS_HOME}/routes/ServerUtilityFunctions.js" baseurl = config.all.client.service.persistence.fullpath+"authors/codeTable" - #TODO: need to change if want to filter users by roles + + if req.query.roleType? and req.query.roleKind? and req.query.roleName? + baseurl = config.all.client.service.persistence.fullpath+"authors/findByRoleTypeKindAndName" + baseurl += "?roleType=#{req.query.roleType}&roleKind=#{req.query.roleKind}&roleName=#{req.query.roleName}&format=codeTable" + serverUtilityFunctions.getFromACASServer(baseurl, resp) exports.relocateEntityFile = (fileValue, entityCodePrefix, entityCode, callback) -> From 21b80c8130c961574381d7280428004e5688969e Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 8 Jun 2017 10:20:16 -0700 Subject: [PATCH 030/576] moving cron script runner to open source --- .../conf/StartupCronJobsConfJSON.coffee | 34 ++ .../CronScriptRunnerServicesSpec.coffee | 459 ++++++++++++++++++ .../CronScriptRunnerTestJSON.coffee | 45 ++ .../routes/CronScriptRunnerRoutes.coffee | 246 ++++++++++ 4 files changed, 784 insertions(+) create mode 100644 modules/CronScriptRunner/conf/StartupCronJobsConfJSON.coffee create mode 100644 modules/CronScriptRunner/spec/serviceTests/CronScriptRunnerServicesSpec.coffee create mode 100644 modules/CronScriptRunner/spec/testFixtures/CronScriptRunnerTestJSON.coffee create mode 100644 modules/CronScriptRunner/src/server/routes/CronScriptRunnerRoutes.coffee diff --git a/modules/CronScriptRunner/conf/StartupCronJobsConfJSON.coffee b/modules/CronScriptRunner/conf/StartupCronJobsConfJSON.coffee new file mode 100644 index 000000000..36b1d739a --- /dev/null +++ b/modules/CronScriptRunner/conf/StartupCronJobsConfJSON.coffee @@ -0,0 +1,34 @@ +exports.jobsToStart = [ +# schedule: "0-59/2 * * * * *" +# scriptType: "R" +# scriptFile: "public/src/modules/ServerAPI/src/server/RunRFunctionTestStub.R" +# functionName: "runRFunctionTest" +# scriptJSONData: '{"fileToParse": "public/src/modules/BulkLoadSampleTransfers/spec/specFiles/shortTransfer.csv", "dryRun": "true", "user": "jmcneil" }' +# active: true +# , +# schedule: "0-59/2 * * * * *" +# scriptType: "R" +# scriptFile: "public/src/modules/ServerAPI/src/server/RunRFunctionTestStub.R" +# functionName: "runRFunctionTest" +# scriptJSONData: '{"fileToParse": "public/src/modules/BulkLoadSampleTransfers/spec/specFiles/SampleTransfers_good.csv", "dryRun": "true", "user": "jmcneil" }' +# active: false +# , +# schedule: "0-59/3 * * * * *" +# scriptType: "R" +# scriptFile: "public/src/modules/ServerAPI/src/server/RunRFunctionTestStub.R" +# functionName: "runRFunctionTest" +# scriptJSONData: '{"fileToParse": "public/src/modules/BulkLoadSampleTransfers/spec/specFiles/KilroyTransfers_good.csv", "dryRun": "true", "user": "kilroy" }' +# active: true +] +exports.typeKindList = + labelsequences: + [ + "digits":8 + "groupDigits":false + "labelPrefix":"CRON" + "labelSeparator":"-" + "labelTypeAndKind":"id_codeName" + "latestNumber":1 + "thingTypeAndKind":"document_cronJob" + ] + diff --git a/modules/CronScriptRunner/spec/serviceTests/CronScriptRunnerServicesSpec.coffee b/modules/CronScriptRunner/spec/serviceTests/CronScriptRunnerServicesSpec.coffee new file mode 100644 index 000000000..794560589 --- /dev/null +++ b/modules/CronScriptRunner/spec/serviceTests/CronScriptRunnerServicesSpec.coffee @@ -0,0 +1,459 @@ +### + This subsystem runs scripts on a periodic basis. Examples of uses: +- Check the status of external data analysis jobs running on a grid system +- Check for files added to a directory that need to be processed +- Check to see if ACAS should send a user a reminder to do something +- Kick off the ping-pong table generator + +Basic requirements: +- Programmatically add and remove periodic jobs +- Call R script (other languages in the future) +- Queue has to survive system ACAS and server reboots, so should be stored permanently in the database or a file +- API should be usable from within node or from outside processes like R scripts, so need REST API +- Must call through services. Direct function calls won't work because we have to keep global cron hash +- When called, there will be no context, so function names and arguments need to be strings or numbers, not live functions. +- R script call should be formatted like every other wrapped R script in ACAS, + the caller supplies the script, the function name, and the arguments as a JSON formatted string +### + +assert = require 'assert' +request = require 'request' + +config = require '../../../../conf/compiled/conf.js' +cronScriptRunnerTestJSON = require '../testFixtures/CronScriptRunnerTestJSON.js' +cronFunctions = require '../../../../routes/CronScriptRunnerRoutes.js' + +baseURL = "http://"+config.all.client.host+":"+config.all.server.nodeapi.port + +parseResponse = (jsonStr) -> + try + return JSON.parse jsonStr + catch error + console.log "response unparsable: " + error + return null + +copyJSON = (json) -> + JSON.parse(JSON.stringify(json)) + +describe "Cron Script Runner Services Spec", -> + describe "Create new cron script runner, saves to databases and schedules the job, unless active = false", -> + unsavedReq = copyJSON cronScriptRunnerTestJSON.savedCronEntry + delete unsavedReq.codeName + before (done) -> + request.post + url: baseURL+"/api/cronScriptRunner" + json: true + body: unsavedReq + , (error, response, body) => + @serverError = error + @responseJSON = body + @serverResponse = response + request + url: baseURL+"/api/cronScriptRunner" + json: true + , (error, response, body) => + @allJSON = body + #cleanup + request.put + url: baseURL+"/api/cronScriptRunner/"+@responseJSON.codeName + json: true + body: + active: false + ignored: true + , (error, response, body) => + done() + it "should return a success status code of 200", -> + assert.equal @serverResponse.statusCode, 200 + it "should supply a new code", -> + assert.equal @responseJSON.codeName?, true + it "should list the cron in the list of all", -> + allCodes = (spec.code for spec in @allJSON) + assert allCodes.indexOf @responseJSON.codeName > 0 + + describe "updating jobs", -> + describe "disable current cron and delete", -> + #save a job to stop + unsavedReq = copyJSON cronScriptRunnerTestJSON.savedCronEntry + delete unsavedReq.codeName + before (done) -> + request.post + url: baseURL+"/api/cronScriptRunner" + json: true + body: unsavedReq + , (error, response, body) => + request.put + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + body: + active: false + ignored: true # if you just want to disable, then leave this false + , (error, response, body) => + @responseJSON = body + @serverResponse = response + done() + it "should return a success status code of 200", -> + assert.equal @serverResponse.statusCode, 200 + it "should return the updated active value", -> + assert.equal @responseJSON.active, false + it "should return the updated ignored value", -> + assert.equal @responseJSON.ignored, true + + describe "try to update non-existant job", -> + before (done) -> + request.put + url: baseURL+"/api/cronScriptRunner/"+"errorNonExistant" + json: true + body: + active: false + ignored: true # if you just want to disable, then leave this false + , (error, response, body) => + @responseJSON = body + @serverResponse = response + done() + it "should return a success error code of 404", -> + assert.equal @serverResponse.statusCode, 404 + + + describe "create and run cron and get run status", -> + #save a job to run + unsavedReq = copyJSON cronScriptRunnerTestJSON.savedCronEntry + delete unsavedReq.codeName + before (done) -> + @.timeout(25000) + request.post + url: baseURL+"/api/cronScriptRunner" + json: true + body: unsavedReq + , (error, response, body) => + setTimeout => + request.get + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + , (error, response, body) => + @responseJSON = body + @serverResponse = response + #cleanup + request.put + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + body: + active: false + ignored: true + , (error, response, body) => + done() + , 3000 + it "should return the cron object with the last start time", -> + assert.equal @responseJSON.lastStartTime>0, true + it "should return the cron object with the last duration", -> + assert.equal @responseJSON.lastDuration>0, true + it "should return the cron object result JSON", -> + assert.equal @responseJSON.lastResultJSON.indexOf('}')>0, true + it "should return success of the R script run", -> + assert.equal parseResponse(@responseJSON.lastResultJSON).hasError, false + it "should increment the run count", -> + assert.equal @responseJSON.numberOfExecutions > 0 , true + + describe "create and run cron then stop", -> + #save a job to run + unsavedReq = copyJSON cronScriptRunnerTestJSON.savedCronEntry + delete unsavedReq.codeName + before (done) -> + @.timeout(25000) + request.post + url: baseURL+"/api/cronScriptRunner" + json: true + body: unsavedReq + , (error, response, body) => + setTimeout => + request.get + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + , (error, response, body1) => + @numRuns1 = body1.numberOfExecutions + #cleanup + request.put + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + body: + active: false + ignored: false + , (error, response, body) => + setTimeout => + request.get + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + , (error, response, body2) => + @numRuns2 = body2.numberOfExecutions + done() + , 2500 + , 2500 + it "should run once", -> + assert.equal @numRuns1, @numRuns2 + + + describe "create active job then change it", -> + #save a job to run + unsavedReq = copyJSON cronScriptRunnerTestJSON.savedCronEntry + delete unsavedReq.codeName + before (done) -> + @.timeout(25000) + request.post + url: baseURL+"/api/cronScriptRunner" + json: true + body: unsavedReq + , (error, response, body) => + setTimeout => + request.get + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + , (error, response, body1) => + @numRuns1 = body1.numberOfExecutions + request.put + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + body: + active: true + ignored: false + scriptJSONData: '{"fileToParse": "public/src/modules/BulkLoadSampleTransfers/spec/specFiles/KilroyWasHere_good.csv", "dryRun": "true", "user": "jmcneil" }' + , (error, response, body) => + setTimeout => + request.get + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + , (error, response, body2) => + @numRuns2 = body2.numberOfExecutions + @lastResultJSON = body2.lastResultJSON + #cleanup + request.put + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + body: + active: false + ignored: false + , (error, response, body) => + done() + , 4500 + , 2500 + it "should run at first", -> + assert.equal @numRuns1>0, true + it "should run later", -> + assert.equal @numRuns2>@numRuns1, true + it "should return an error the second run", -> + assert.equal @lastResultJSON.indexOf("KilroyWasHere")>-1, true + + + + describe "create inactive job then set active", -> + #save a job to run + unsavedReq = copyJSON cronScriptRunnerTestJSON.savedCronEntry + delete unsavedReq.codeName + unsavedReq.active = false + before (done) -> + @.timeout(25000) + request.post + url: baseURL+"/api/cronScriptRunner" + json: true + body: unsavedReq + , (error, response, body) => + setTimeout => + request.get + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + , (error, response, body1) => + @numRuns1 = body1.numberOfExecutions + request.put + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + body: + active: true + ignored: false + , (error, response, body) => + setTimeout => + request.get + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + , (error, response, body2) => + @numRuns2 = body2.numberOfExecutions + #cleanup + request.put + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + body: + active: false + ignored: false + , (error, response, body) => + done() + , 2500 + , 2500 + it "should not run at first", -> + assert.equal @numRuns1, 0 + it "should run later", -> + assert.equal @numRuns2>0, true + + + describe "create active job then set inactive, then active", -> + #save a job to run + unsavedReq = copyJSON cronScriptRunnerTestJSON.savedCronEntry + delete unsavedReq.codeName + before (done) -> + @.timeout(25000) + request.post + url: baseURL+"/api/cronScriptRunner" + json: true + body: unsavedReq + , (error, response, body) => + setTimeout => + request.get + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + , (error, response, body1) => + @numRuns1 = body1.numberOfExecutions + request.put + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + body: + active: false + ignored: false + , (error, response, body) => + setTimeout => + request.get + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + , (error, response, body2) => + @numRuns2 = body2.numberOfExecutions + request.put + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + body: + active: true + ignored: false + , (error, response, body3) => + setTimeout => + request.get + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + , (error, response, body3) => + @numRuns3 = body3.numberOfExecutions + #cleanup + request.put + url: baseURL+"/api/cronScriptRunner/"+body.codeName + json: true + body: + active: false + ignored: false + , (error, response, body) => + done() + , 2500 + , 2500 + , 2500 + it "should run at first", -> + assert.equal @numRuns1> 0, true + it "should stop later", -> + assert.equal @numRuns1, @numRuns2 + it "should start after that", -> + assert.equal @numRuns3>@numRuns2, true + + + + describe "Post bogus or missing cron spec", -> + describe "missing schedule", -> + unsavedReq = copyJSON cronScriptRunnerTestJSON.savedCronEntry + delete unsavedReq.codeName + delete unsavedReq.schedule + before (done) -> + request.post + url: baseURL+"/api/cronScriptRunner" + json: true + body: unsavedReq + , (error, response, body) => + @serverError = error + @responseJSON = body + @serverResponse = response + done() + it "should return a success status code of 500", -> + assert.equal @serverResponse.statusCode, 500 + describe "missing scriptType", -> + unsavedReq = copyJSON cronScriptRunnerTestJSON.savedCronEntry + delete unsavedReq.codeName + delete unsavedReq.scriptType + before (done) -> + request.post + url: baseURL+"/api/cronScriptRunner" + json: true + body: unsavedReq + , (error, response, body) => + @serverError = error + @responseJSON = body + @serverResponse = response + done() + it "should return a success status code of 500", -> + assert.equal @serverResponse.statusCode, 500 + describe "missing scriptFile", -> + unsavedReq = copyJSON cronScriptRunnerTestJSON.savedCronEntry + delete unsavedReq.codeName + delete unsavedReq.scriptFile + before (done) -> + request.post + url: baseURL+"/api/cronScriptRunner" + json: true + body: unsavedReq + , (error, response, body) => + @serverError = error + @responseJSON = body + @serverResponse = response + done() + it "should return a success status code of 500", -> + assert.equal @serverResponse.statusCode, 500 + describe "missing functionName", -> + unsavedReq = copyJSON cronScriptRunnerTestJSON.savedCronEntry + delete unsavedReq.codeName + delete unsavedReq.functionName + before (done) -> + request.post + url: baseURL+"/api/cronScriptRunner" + json: true + body: unsavedReq + , (error, response, body) => + @serverError = error + @responseJSON = body + @serverResponse = response + done() + it "should return a success status code of 500", -> + assert.equal @serverResponse.statusCode, 500 + describe "missing scriptJSONData", -> + unsavedReq = copyJSON cronScriptRunnerTestJSON.savedCronEntry + delete unsavedReq.codeName + delete unsavedReq.scriptJSONData + before (done) -> + request.post + url: baseURL+"/api/cronScriptRunner" + json: true + body: unsavedReq + , (error, response, body) => + @serverError = error + @responseJSON = body + @serverResponse = response + done() + it "should return a success status code of 500", -> + assert.equal @serverResponse.statusCode, 500 + describe "missing active", -> + unsavedReq = copyJSON cronScriptRunnerTestJSON.savedCronEntry + delete unsavedReq.codeName + delete unsavedReq.active + before (done) -> + request.post + url: baseURL+"/api/cronScriptRunner" + json: true + body: unsavedReq + , (error, response, body) => + @serverError = error + @responseJSON = body + @serverResponse = response + done() + it "should return a success status code of 500", -> + assert.equal @serverResponse.statusCode, 500 + + + + + diff --git a/modules/CronScriptRunner/spec/testFixtures/CronScriptRunnerTestJSON.coffee b/modules/CronScriptRunner/spec/testFixtures/CronScriptRunnerTestJSON.coffee new file mode 100644 index 000000000..5b641b450 --- /dev/null +++ b/modules/CronScriptRunner/spec/testFixtures/CronScriptRunnerTestJSON.coffee @@ -0,0 +1,45 @@ +((exports) -> + #This is an example of a saved cron job spec that has not executed yet + exports.savedCronEntry = +#The requestor must provide these attributes + schedule: "0-59/2 * * * * *" + #cron format string + #This example runs every 2 seconds + #mocha tests depend on this timing example + scriptType: "R" + #only choice for now, later python, knime, etc + scriptFile: "public/src/modules/ServerAPI/src/server/RunRFunctionTestStub.R" + #the acas_home relative path and filename to the script file to be run + functionName: "runRFunctionTest" + #function name to call within the script file + #Required for R scripts + scriptJSONData: '{"fileToParse": "public/src/modules/BulkLoadSampleTransfers/spec/specFiles/SampleTransfers_good.csv", "dryRun": "true", "user": "jmcneil" }' + #JSON string passed to the script as arguments. + #This will be converted to language-native data structure when script is run. + # e.g. R runner will convert this to nested list objects + active: true + #true if should run, false otherwise, essentially pause + ignored: false + #true is logical delete state. Job will be dequeued + runUser: 'jmcneil' + #required login user of person whose actions caused this cron to be created +#Attributes below this are filled in by the service and not required from the requestor + codeName: "CRON123456789" + #identifier we will also use as a key to lookup the handle to the cron job in memory + #generated sequentially by the persistence + lastStartTime: null + #last time script was started in ms of the unix epoch in the local time zone + #null if not run + lastDuration: null + #execution time in ms otherwise + #null if not run + lastResultJSON: null + #JSON format string of last run results + #null if not run + numberOfExecutions: null + #number of times script has been executed for this job + #null if not run + +) (if (typeof process is "undefined" or not process.versions) then window.cronScriptRunnerTestJSON = window.cronScriptRunnerTestJSON or {} else exports) + + diff --git a/modules/CronScriptRunner/src/server/routes/CronScriptRunnerRoutes.coffee b/modules/CronScriptRunner/src/server/routes/CronScriptRunnerRoutes.coffee new file mode 100644 index 000000000..fb5426249 --- /dev/null +++ b/modules/CronScriptRunner/src/server/routes/CronScriptRunnerRoutes.coffee @@ -0,0 +1,246 @@ +exports.setupAPIRoutes = (app) -> + app.get '/api/cronScriptRunner', exports.getAllCronScriptRunner + app.post '/api/cronScriptRunner', exports.postCronScriptRunner + app.get '/api/cronScriptRunner/:code', exports.getCronScriptRunner + app.put '/api/cronScriptRunner/:code', exports.putCronScriptRunner + global.cronJobs = {} + console.log "just declared global cronJobs in setup" + if config.all.server.service?.cron?.enable + addJobsOnStartup() + +exports.setupRoutes = (app, loginRoutes) -> + #no public routes, and none can be added, they won't work since global is in context of api server + +# Must call through services. Direct function calls won't work because we have to keep global cron hash + +config = require '../conf/compiled/conf.js' +request = require 'request' +CRON_CONFIG_PREFIX = "CONF_CRON" + +addJobsOnStartup = -> + cronConfig = require '../public/javascripts/conf/CronScriptRunner/StartupCronJobsConfJSON.js' + persistenceURL = config.all.client.service.persistence.fullpath + "cronjobs" + + #We don't want to save these to the database, so make our own special cronCodes and launch + codeInt = 1 + if cronConfig.jobsToStart? + for spec in cronConfig.jobsToStart + newCode = CRON_CONFIG_PREFIX + codeInt++ + + newCron = + spec: spec + newCron.spec.codeName = newCode + newCron.spec.numberOfExcutions = 0 + newCron.spec.ignored = false + + global.cronJobs[newCode] = newCron + + if newCron.spec.active + setupNewCron newCron + + # Get existing jobs + if not global.specRunnerTestmode + request.get + url: persistenceURL + json: true + , (error, response, body) => + if not error and response.statusCode < 400 + for spec in body + newCron = spec: spec + global.cronJobs[newCron.spec.codeName] = newCron + # Default startOnRestart to true + startOnRestart = config.all.server.service?.cron?.startOnRestart + if not startOnRestart? + startOnRestart = true + if not newCron.spec.ignored and newCron.spec.active and startOnRestart + setupNewCron newCron + else + console.log 'Failed to get list of existing cronjobs, error:' + error + '\n body: ' + body + + +exports.getAllCronScriptRunner = (req, resp) -> + allSavedSpecs = (job.spec for code, job of global.cronJobs) + resp.json allSavedSpecs + +exports.postCronScriptRunner = (req, resp) -> + console.log "global.specRunnerTestmode: " + global.specRunnerTestmode + validation = validateSpec(JSON.parse(JSON.stringify(req.body))) + if !validation.valid + console.log validation + resp.send JSON.stringify(validation.messages), 500 + return + + if (req.query.testMode is true) or (global.specRunnerTestmode is true) + cronScriptRunnerTestJSON = require '../public/javascripts/spec/testFixtures/CronScriptRunnerTestJSON.js' + resp.json cronScriptRunnerTestJSON.savedCronEntry + else + unsavedReq = req.body + persistenceURL = config.all.client.service.persistence.fullpath + "cronjobs" + if not unsavedReq.numberOfExecutions + unsavedReq.numberOfExecutions = 0 + request.post + url: persistenceURL + json: true + body: unsavedReq + , (error, response, body) => + @serverError = error + @responseJSON = body + @serverResponse = response + if not error and response.statusCode < 400 and body.codeName? + newCron = spec: body + newCode = body.codeName + + global.cronJobs[newCode] = newCron + + if newCron.spec.active + setupNewCron newCron + + resp.json newCron.spec + else + resp.statusCode = 500 + resp.end response.body + +exports.putCronScriptRunner = (req, resp) -> + if (req.query.testMode is true) or (global.specRunnerTestmode is true) + cronScriptRunnerTestJSON = require '../public/javascripts/spec/testFixtures/CronScriptRunnerTestJSON.js' + if req.params.code.indexOf('error') > -1 + resp.send "codeName #{code} not found", 404 + return + respCron = JSON.parse(JSON.stringify(cronScriptRunnerTestJSON.savedCronEntry)) + respCron.codeName = req.params.code + if req.body.active? then respCron.active = req.body.active + if req.body.ignored? then respCron.ignored = req.body.ignored + resp.json respCron + return + else + code = req.params.code + cronJob = global.cronJobs[code] + unless cronJob? + resp.send "codeName #{code} not found", 404 + return + + updateCronScriptRunner code, req.body, (err, response) -> + if err + resp.send 500, err + else + resp.json response + + + +exports.getCronScriptRunner = (req, resp) -> + if (req.query.testMode is true) or (global.specRunnerTestmode is true) + cronScriptRunnerTestJSON = require '../public/javascripts/spec/testFixtures/CronScriptRunnerTestJSON.js' + respCron = JSON.parse(JSON.stringify(cronScriptRunnerTestJSON.savedCronEntry)) + respCron.lastStartTime = 1234 + respCron.lastDuration = 42 + respCron.lastResultJSON = '{"someKey": "someValue", "hasError": false}' + respCron.numberOfExcutions = 1 + resp.json respCron + return + else + code = req.params.code + cronJob = global.cronJobs[code] + if cronJob? + resp.json cronJob.spec + else + resp.status(400).send "Cron Job not found" + +updateCronScriptRunner = (code, newSpec, callback) -> + cronJob = global.cronJobs[code] + unless cronJob? + callback "codeName #{code} not found" + return + + #Update supplied attributes + for key, value of newSpec +# console.log key + ": "+value + cronJob.spec[key] = value + #no matter what, stop job. Who knows what changes we got? + if cronJob.job? + cronJob.job.stop() + delete cronJob.job + persistenceURL = config.all.client.service.persistence.fullpath + "cronjobs/" + #Skip if cron defined in config + delete cronJob.spec.running + if code.indexOf CRON_CONFIG_PREFIX < 0 + request.put + url: persistenceURL + code + json: true + body: cronJob.spec + , (error, response, body) => + if not error and response.statusCode < 400 and body.codeName? + cronJob.spec = body + if not cronJob.spec.ignored and cronJob.spec.active? and cronJob.spec.active + setupNewCron cronJob + callback null, cronJob.spec + else + callback "Failed put request to server: " + body + else + if not cronJob.spec.ignored and cronJob.spec.active? and cronJob.spec.active + setupNewCron cronJob + callback null, cronJob.spec + +setupNewCron = (cron) -> + CronJob = require('cron').CronJob + cron.job = new CronJob + cronTime: cron.spec.schedule + start: true + onTick: -> + launchRScript cron.spec + +launchRScript = (spec) -> + serverUtilityFunctions = require './ServerUtilityFunctions.js' + jobStart = new Date() + if spec.running? && spec.running + console.log "#{spec.codeName} already running, skipping this run" + else + spec.running = true + console.log 'started cron r script ' + spec.codeName + serverUtilityFunctions.runRFunctionOutsideRequest spec.user, JSON.parse(spec.scriptJSONData), spec.scriptFile, spec.functionName, (rReturn) -> + console.log 'finished cron r script ' + spec.codeName + duration = new Date() - jobStart + scriptComplete spec.codeName, jobStart.getTime(), duration, rReturn + +scriptComplete = (codeName, startTime, duration, resultJSON) -> + cronJob = global.cronJobs[codeName] + if cronJob? and cronJob.spec? + cronJob.spec.lastStartTime = startTime + cronJob.spec.lastDuration = duration + cronJob.spec.lastResultJSON = resultJSON + if cronJob.spec.numberOfExecutions? + cronJob.spec.numberOfExecutions++ + else + cronJob.spec.numberOfExecutions = 1 + updateCronScriptRunner codeName, cronJob.spec, (err, res) -> + if err + console.log 'unable to update job in database in scriptComplete: ' + err + + +validateSpec = (spec) -> + valid = true + messages = [] + + if !spec.schedule? + valid = false + messages.push {attribute: "schedule", level: "error", message: "schedule must be supplied"} + if !spec.scriptType? + valid = false + messages.push {attribute: "scriptType", level: "error", message: "scriptType must be supplied"} + if spec.scriptType? + if spec.scriptType != "R" + valid = false + messages.push {attribute: "scriptType", level: "error", message: "Only scriptType supported is R"} + if !spec.scriptFile? + valid = false + messages.push {attribute: "scriptFile", level: "error", message: "scriptFile must be supplied"} + if !spec.functionName? + valid = false + messages.push {attribute: "functionName", level: "error", message: "functionName must be supplied"} + if !spec.scriptJSONData? + valid = false + messages.push {attribute: "scriptJSONData", level: "error", message: "scriptJSONData must be supplied"} + if !spec.active? + valid = false + messages.push {attribute: "active", level: "error", message: "active must be supplied"} + + return {valid: valid, messages: messages} \ No newline at end of file From 67a23bcf447732a54e1ac0cfcf995e7f270e2de5 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Mon, 12 Jun 2017 09:59:30 -0700 Subject: [PATCH 031/576] removed review request notification route, added getAllAuthorObjectsRoute --- .../CustomerSpecificServerFunctions.coffee | 6 ++++ .../routes/BaseEntityServiceRoutes.coffee | 36 ------------------- 2 files changed, 6 insertions(+), 36 deletions(-) diff --git a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee index ac81dcba2..1ef19e639 100644 --- a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee +++ b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee @@ -230,6 +230,12 @@ exports.getAuthors = (req, resp) -> #req passed in as input to be able to filter #TODO: need to change if want to filter users by roles serverUtilityFunctions.getFromACASServer(baseurl, resp) +exports.getAllAuthorObjects = (req, resp) -> + config = require "#{ACAS_HOME}/conf/compiled/conf.js" + serverUtilityFunctions = require "#{ACAS_HOME}/routes/ServerUtilityFunctions.js" + baseurl = config.all.client.service.persistence.fullpath+"authors" + serverUtilityFunctions.getFromACASServer(baseurl, resp) + exports.relocateEntityFile = (fileValue, entityCodePrefix, entityCode, callback) -> config = require "#{ACAS_HOME}/conf/compiled/conf.js" uploadsPath = serverUtilityFunctions.makeAbsolutePath config.all.server.datafiles.relative_path diff --git a/modules/ServerAPI/src/server/routes/BaseEntityServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/BaseEntityServiceRoutes.coffee index 527f47206..776d75cbe 100644 --- a/modules/ServerAPI/src/server/routes/BaseEntityServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/BaseEntityServiceRoutes.coffee @@ -1,9 +1,5 @@ -exports.setupAPIRoutes = (app) -> - app.post '/api/entityReviewRequestNotification', exports.exptReadyForReviewNotification - exports.setupRoutes = (app, loginRoutes) -> app.get '/api/authors', loginRoutes.ensureAuthenticated, exports.getAuthors - app.post '/api/entityReviewRequestNotification', loginRoutes.ensureAuthenticated, exports.exptReadyForReviewNotification exports.getAuthors = (req, resp) -> console.log "getting authors" @@ -13,35 +9,3 @@ exports.getAuthors = (req, resp) -> else csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFunctions.js' csUtilities.getAuthors req, resp - -exports.exptReadyForReviewNotification = (request, response) -> - request.connection.setTimeout 600000 - serverUtilityFunctions = require './ServerUtilityFunctions.js' - - response.writeHead(200, {'Content-Type': 'application/json'}); - if global.specRunnerTestmode - console.log "test mode: "+global.specRunnerTestmode - serverUtilityFunctions.runRFunction( - request, - "src/r/ELN/ExptReadyForReviewNotification.R", - "deleteComponentRequestNotification", - (rReturn) -> - response.end rReturn - ) - else - authorRoutes = require './AuthorRoutes.js' - console.log "getting username in exptReadyForReviewNotification" - console.log request.body.userName - authorRoutes.getAuthorByUsernameInternal request.body.reviewer, (json, statusCode) => - console.log "author" - console.log json - console.log request.body - request.body.reviewerEmail = json.emailAddress - console.log request.body - serverUtilityFunctions.runRFunction( - request, - "src/r/ELN/ExptReadyForReviewNotification.R", - "exptReadyForReviewNotification", - (rReturn) -> - response.end rReturn - ) From df7e522ec475a7a8d2ee5de02824e893ffba3146 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Tue, 13 Jun 2017 21:13:38 -0700 Subject: [PATCH 032/576] added config for autolaunching module --- conf/config.properties.example | 2 ++ modules/ModuleMenus/src/client/ModuleMenus.coffee | 3 +++ 2 files changed, 5 insertions(+) diff --git a/conf/config.properties.example b/conf/config.properties.example index 5fee97466..9154921e3 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -329,6 +329,8 @@ client.moduleMenus.summaryStats=false # For navigation to external ACAS modules from ACAS homepage client.moduleMenus.modules.external=[{"displayName": "Compound Registration", "href": "/cmpdreg/"},\ {"displayName": "Compound Registration Bulk Loader", "href":"/CmpdRegBulkLoader"}] +# For auto-starting a module when opening up ACAS +client.moduleMenus.moduleAutoLaunchName= client.leaveACASMessage=There are no unsaved changes. client.scientistCodeOrigin=ACAS authors diff --git a/modules/ModuleMenus/src/client/ModuleMenus.coffee b/modules/ModuleMenus/src/client/ModuleMenus.coffee index 292709773..777c657f4 100644 --- a/modules/ModuleMenus/src/client/ModuleMenus.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenus.coffee @@ -58,6 +58,9 @@ class window.ModuleMenusController extends Backbone.View modLink = '
    • '+module.displayName+'
      • ' @$('.bv_externalACASModules').append modLink + if window.conf.moduleMenus?.moduleAutoLaunchName? + @$(".bv_launch_#{window.conf.moduleMenus.moduleAutoLaunchName}").click() + render: => if window.AppLaunchParams.deployMode? unless window.AppLaunchParams.deployMode.toUpperCase() =="PROD" From a611475ad058fe6904c9a0f429358dd8ece41162 Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Wed, 14 Jun 2017 10:51:51 -0700 Subject: [PATCH 033/576] add acas meta structure search routes --- .../server/routes/ChemStructureRoutes.coffee | 41 +++++++++++++++---- 1 file changed, 32 insertions(+), 9 deletions(-) diff --git a/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee b/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee index 3c9b671fb..2361bc1e4 100644 --- a/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee +++ b/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee @@ -1,28 +1,30 @@ exports.setupAPIRoutes = (app) -> app.get '/api/chemStructure/renderStructureByThingCode', exports.renderStructureByThingCode + app.get '/api/chemStructure/renderStructureByCode', exports.renderStructureByCode app.get '/api/chemStructure/codename/:structureCode', exports.getStructureByCode app.post '/api/chemStructure', exports.postStructure app.put '/api/chemStructure/:id', exports.putStructure app.post '/api/chemStructure/calculateMoleculeProperties', exports.calculateMoleculeProperties app.post '/api/chemStructure/renderMolStructure', exports.renderMolStructure - app.post '/api/chemStructure/renderMolStructureBase64', exports.renderMolStructure - + app.post '/api/chemStructure/renderMolStructureBase64', exports.renderMolStructureBase64 + app.post '/api/chemStructure/acasStructureMetaSearch', loginRoutes.ensureAuthenticated, exports.acasStructureMetaSearch + app.post '/api/chemStructure/acasStructureSearch', loginRoutes.ensureAuthenticated, exports.acasStructureSearch exports.setupRoutes = (app, loginRoutes) -> app.get '/api/chemStructure/renderStructureByThingCode', loginRoutes.ensureAuthenticated, exports.renderStructureByThingCode app.get '/api/chemStructure/renderStructureByCode', loginRoutes.ensureAuthenticated, exports.renderStructureByCode - app.get '/api/chemStructure/codename/:structureCode', loginRoutes.ensureAuthenticated, exports.getStructureByCode app.post '/api/chemStructure', loginRoutes.ensureAuthenticated, exports.postStructure app.put '/api/chemStructure/:id', loginRoutes.ensureAuthenticated, exports.putStructure app.post '/api/chemStructure/calculateMoleculeProperties', loginRoutes.ensureAuthenticated, exports.calculateMoleculeProperties app.post '/api/chemStructure/renderMolStructure', loginRoutes.ensureAuthenticated, exports.renderMolStructure app.post '/api/chemStructure/renderMolStructureBase64', loginRoutes.ensureAuthenticated, exports.renderMolStructureBase64 + app.post '/api/chemStructure/acasStructureMetaSearch', loginRoutes.ensureAuthenticated, exports.acasStructureMetaSearch + app.post '/api/chemStructure/acasStructureSearch', loginRoutes.ensureAuthenticated, exports.acasStructureSearch _ = require 'underscore' acasHome = '../../../..' -#reagentData = require "/home/runner/build/public/javascripts/spec/ReagentRegistration/testFixtures/ReagentRegistrationServiceTestJSON.js" exports.renderStructureByThingCode = (req, resp) -> @@ -34,7 +36,6 @@ exports.renderStructureByThingCode = (req, resp) -> request = require 'request' queryParams = req._parsedUrl.query rooUrl = baseurl + '?' + queryParams - console.log rooUrl req.pipe(request(rooUrl)).pipe(resp) exports.renderStructureByCode = (req, resp) -> @@ -46,8 +47,6 @@ exports.renderStructureByCode = (req, resp) -> request = require 'request' queryParams = req._parsedUrl.query rooUrl = baseurl + '?' + queryParams - console.log '######## line 49 -- renderStructureByCode #########' - console.log rooUrl req.pipe(request(rooUrl)).pipe(resp) exports.getStructureByCode = (req, resp) -> @@ -143,6 +142,7 @@ exports.calculateMoleculeProperties = (req, resp) -> resp.end JSON.stringify "calculate molecule properties failed" ) +#TODO FIX this route exports.renderMolStructure = (req, resp) -> if global.specRunnerTestmode resp.json {molStructure: req.body[0].molStructure, height: req.body[0].height, width: req.body[0].width, format: req.body[0].format} @@ -169,7 +169,7 @@ exports.renderMolStructure = (req, resp) -> # resp.writeHead 200, 'Content-Type': 'image/png' # resp.end buffer else - console.log '--- line 153: got ajax error trying to render molStructure' + console.log '--- line 176: got ajax error trying to render molStructure' console.log error console.log json console.log response @@ -216,7 +216,7 @@ exports.acasStructureSearch = (req, resp) -> request( method: 'POST' url: baseurl - body: req.body.reagentSearchParams + body: req.body.structureSearchParams json: true , (error, response, json) => if !error && response.statusCode == 200 @@ -230,3 +230,26 @@ exports.acasStructureSearch = (req, resp) -> resp.end JSON.stringify "ACAS structure search failed" ) +exports.acasStructureMetaSearch = (req, resp) -> + if global.specRunnerTestmode + resp.json {queryMol: req.body[0].queryMol, searchType: req.body[0].searchType, maxResults: req.body[0].maxResults, similarity: req.body[0].similarity} + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"lsthings/structureAndMetaSearch" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: req.body.structureSearchParams + json: true + , (error, response, json) => + if !error && response.statusCode == 200 + resp.json json + else + console.log 'got ajax error trying to search for structures' + console.log error + console.log json + console.log response + resp.statusCode = 500 + resp.end JSON.stringify "ACAS structure search failed" + ) From 2c490aa961c8eeb7b34a031ff05b52dd413c064c Mon Sep 17 00:00:00 2001 From: Fiona McNeil Date: Wed, 14 Jun 2017 12:11:15 -0700 Subject: [PATCH 034/576] Made it prettier. --- .../ModuleMenus/src/client/ModuleMenus.coffee | 3 +- .../src/client/ModuleMenusView.html | 11 +++-- modules/ModuleMenus/src/client/style.css | 45 ++++++++++++++++--- 3 files changed, 46 insertions(+), 13 deletions(-) diff --git a/modules/ModuleMenus/src/client/ModuleMenus.coffee b/modules/ModuleMenus/src/client/ModuleMenus.coffee index 0a1885692..1d9b0212e 100644 --- a/modules/ModuleMenus/src/client/ModuleMenus.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenus.coffee @@ -109,7 +109,7 @@ class window.ModuleMenusController extends Backbone.View setupUserSwitchingSelect: -> @altUserList = new PickListList() @getAllAvailableUsers @altUserList, => - @altUserListController = new PickListSelectController + @altUserListController = new PickListSelect2Controller el: @$('.bv_fastUserSelect') collection: @altUserList autoFetch: false @@ -181,4 +181,3 @@ class window.ModuleMenusController extends Backbone.View #TODO config docs in readme.md file #TODO should some code in mmroutes be rafactored to a general socket utility? - diff --git a/modules/ModuleMenus/src/client/ModuleMenusView.html b/modules/ModuleMenus/src/client/ModuleMenusView.html index 177003207..b1ea5193d 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusView.html +++ b/modules/ModuleMenus/src/client/ModuleMenusView.html @@ -4,16 +4,19 @@
      -

      - Logged in as +

      + + Logged in as First Name Last Name - Logout -

      + Logout +
      + +
      • diff --git a/modules/ModuleMenus/src/client/style.css b/modules/ModuleMenus/src/client/style.css index 00a8a137c..fcc00748a 100644 --- a/modules/ModuleMenus/src/client/style.css +++ b/modules/ModuleMenus/src/client/style.css @@ -66,10 +66,41 @@ body { }*/ .bv_fastUserSelect { - background-color: transparent; - color: #999999; - margin-top: 0px; - margin-bottom: 6px; - height: 0px; - border: none; -} \ No newline at end of file + width: 150px; + height: 30px; + border-color: #999999; + background-color: transparent; + margin-bottom: 2px; +} + +.bv_userInfo select2-hidden-accessible { + display: none; +} + +.bv_userInfo .select2-container { + width: 175px !important; +} + +.bv_userInfo .select2-container .select2-selection--single { + width: 175px; + height: 30px; + border-color: #999999; + background-color: transparent; +} + +.bv_userInfo .select2-container--default .select2-selection--single .select2-selection__rendered { + color: #999999; +} + +.bv_userInfo .select2-container--default .select2-selection--single .select2-selection__clear { + display: none; +} + +.bv_userInfo .select2-container { + margin-bottom: 2px; +} + +.bv_userInfo .bv_logout { + margin-top:0px; + margin-bottom: 2px; +} From 0f8c24dc3d0787de9460467fc0fce78fecbda55d Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Wed, 14 Jun 2017 15:03:51 -0700 Subject: [PATCH 035/576] create new corpName with user initials for Protocol and Experiment leans on config: client.entity.saveInitialsCorpName --- .../src/server/generic_data_parser.R | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index b4a60ac55..edba5ab7a 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -1753,6 +1753,22 @@ createNewProtocol <- function(metaData, lsTransaction, recordedBy) { lsKind="protocol name", labelText=metaData$'Protocol Name'[1], preferred=TRUE) + + if (toupper(configList$client.entity.saveInitialsCorpName) == "TRUE"){ + protocolCorpNameList <- unlist(getAutoLabels(thingTypeAndKind="document_protocol", + labelTypeAndKind=paste0("corpName initials_", recordedBy), + numberOfLabels=1), + use.names=FALSE) + + protocolLabels[[length(protocolLabels)+1]] <- createProtocolLabel(lsTransaction = lsTransaction, + recordedBy=recordedBy, + lsType="corpName", + lsKind="protocol corpName", + labelText=protocolCorpNameList[1], + preferred=FALSE) + } + + # Create the protocol protocol <- createProtocol(lsTransaction = lsTransaction, @@ -1881,6 +1897,22 @@ createNewExperiment <- function(metaData, protocol, lsTransaction, pathToGeneric labelText=experimentName, preferred=TRUE) + if (toupper(configList$client.entity.saveInitialsCorpName) == "TRUE"){ + experimentCorpNameList <- unlist(getAutoLabels(thingTypeAndKind="document_experiment", + labelTypeAndKind=paste0("corpName initials_", recordedBy), + numberOfLabels=1), + use.names=FALSE) + + experimentLabels[[length(experimentLabels)+1]] <- createExperimentLabel(lsTransaction = lsTransaction, + recordedBy=recordedBy, + lsType="corpName", + lsKind="experiment corpName", + labelText=experimentCorpNameList[1], + preferred=FALSE) + + } + + # Create LS Tags if("Experiment Keywords" %in% names(metaData)) { tagList <- splitOnSemicolon(metaData$"Experiment Keywords"[[1]]) From 48c88afd2a6acb4f025642aef186fb3e3fe559fc Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Thu, 15 Jun 2017 13:57:07 -0700 Subject: [PATCH 036/576] fixed bugs for feature to autolaunch module --- .../ModuleMenus/src/client/ModuleMenus.coffee | 5 ++--- .../CustomerSpecificServerFunctions.coffee | 5 +++-- .../routes/ControllerRedirectRoutes.coffee | 6 ++++++ .../routes/ExperimentServiceRoutes.coffee | 21 +++++++++++++++++++ .../routes/ProtocolServiceRoutes.coffee | 21 +++++++++++++++++++ 5 files changed, 53 insertions(+), 5 deletions(-) diff --git a/modules/ModuleMenus/src/client/ModuleMenus.coffee b/modules/ModuleMenus/src/client/ModuleMenus.coffee index 777c657f4..35c805dbe 100644 --- a/modules/ModuleMenus/src/client/ModuleMenus.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenus.coffee @@ -44,6 +44,8 @@ class window.ModuleMenusController extends Backbone.View if window.AppLaunchParams.moduleLaunchParams? @moduleLauncherMenuListController.launchModule window.AppLaunchParams.moduleLaunchParams.moduleName + else if window.conf.moduleMenus?.moduleAutoLaunchName? + @$(".bv_launch_#{window.conf.moduleMenus.moduleAutoLaunchName}").click() else @$('.bv_homePageWrapper').show() @@ -58,9 +60,6 @@ class window.ModuleMenusController extends Backbone.View modLink = '
      • '+module.displayName+'
        • ' @$('.bv_externalACASModules').append modLink - if window.conf.moduleMenus?.moduleAutoLaunchName? - @$(".bv_launch_#{window.conf.moduleMenus.moduleAutoLaunchName}").click() - render: => if window.AppLaunchParams.deployMode? unless window.AppLaunchParams.deployMode.toUpperCase() =="PROD" diff --git a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee index 1ef19e639..21c3d8a8b 100644 --- a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee +++ b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee @@ -230,11 +230,12 @@ exports.getAuthors = (req, resp) -> #req passed in as input to be able to filter #TODO: need to change if want to filter users by roles serverUtilityFunctions.getFromACASServer(baseurl, resp) -exports.getAllAuthorObjects = (req, resp) -> +exports.getAllAuthorObjectsInternal = (callback) -> config = require "#{ACAS_HOME}/conf/compiled/conf.js" serverUtilityFunctions = require "#{ACAS_HOME}/routes/ServerUtilityFunctions.js" baseurl = config.all.client.service.persistence.fullpath+"authors" - serverUtilityFunctions.getFromACASServer(baseurl, resp) + serverUtilityFunctions.getFromACASServerInternal baseurl, (statusCode, json) -> + callback statusCode, json exports.relocateEntityFile = (fileValue, entityCodePrefix, entityCode, callback) -> config = require "#{ACAS_HOME}/conf/compiled/conf.js" diff --git a/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee b/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee index 6c0275873..31ca85c4b 100644 --- a/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee @@ -25,8 +25,14 @@ exports.redirectToEditor = (req, resp) -> else prefixKeyIndex +=1 + console.log "in redirectToEditor" if req.params.code.substring(0,5) is "STUDY" resp.redirect "/study_tracker_experiment/codeName/#{req.params.code}" + else if req.params.code.substring(0,3) is "EXP" #TODO: refactor to get expt and then figure out kind and deeplink appropriately + resp.redirect "/experiment_base/codeName/#{req.params.code}" + else if req.params.code.substring(0,3) is "PRT" #TODO: refactor to get prot and then figure out kind and deeplink appropriately + resp.redirect "/protocol_base/codeName/#{req.params.code}" + else if queryPrefix != null request json: true diff --git a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee index 2b5f4e290..e5b2b195c 100644 --- a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee @@ -20,6 +20,7 @@ exports.setupAPIRoutes = (app) -> app.put '/api/experiments/parentExperiment/:id', exports.putParentExperiment app.get '/api/experiments/genericSearch/:searchTerm', exports.genericExperimentSearch app.get '/api/experiments/:lsType/:lsKind', exports.experimentsByTypeKind + app.get '/api/getExperimentByLabel/:exptLabel', exports.getExperimentByLabel app.post '/api/experiments/getExperimentCodeByLabel/:exptType/:exptKind', exports.getExperimentCodeByLabel app.post '/api/bulkPostExperiments', exports.bulkPostExperiments app.put '/api/bulkPostExperiments', exports.bulkPutExperiments @@ -47,6 +48,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/experiments/parentExperiment', loginRoutes.ensureAuthenticated, exports.postParentExperiment app.put '/api/experiments/parentExperiment/:id', loginRoutes.ensureAuthenticated, exports.putParentExperiment app.get '/api/experiments/:lsType/:lsKind', loginRoutes.ensureAuthenticated, exports.experimentsByTypeKind + app.get '/api/getExperimentByLabel/:exptLabel', loginRoutes.ensureAuthenticated, exports.getExperimentByLabel app.post '/api/experiments/getExperimentCodeByLabel/:exptType/:exptKind', loginRoutes.ensureAuthenticated, exports.getExperimentCodeByLabel app.post '/api/bulkPostExperiments', loginRoutes.ensureAuthenticated, exports.bulkPostExperiments app.put '/api/bulkPostExperiments', loginRoutes.ensureAuthenticated, exports.bulkPutExperiments @@ -900,6 +902,25 @@ exports.experimentsByTypeKind = (req, resp) -> console.log baseurl serverUtilityFunctions.getFromACASServer(baseurl, resp) +exports.getExperimentByLabel = (req, resp) -> + config = require '../conf/compiled/conf.js' + url = config.all.client.service.persistence.fullpath+"experiments?FindByExperimentName&experimentName=#{req.params.exptLabel}" + request = require 'request' + request( + method: 'GET' + url: url + json: true + , (error, response, json) => + console.log response.statusCode + console.log json + if !error and !json.error + resp.json json + else + console.log 'got ajax error trying to get experiment by label' + resp.statusCode = 500 + resp.json json.errorMessages + ) + exports.getExperimentCodeByLabel = (req, resp) -> if global.specRunnerTestmode results = [] diff --git a/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee index 076867da9..fb2057a73 100644 --- a/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee @@ -8,6 +8,7 @@ exports.setupAPIRoutes = (app) -> app.get '/api/protocolKindCodes', exports.protocolKindCodeList app.get '/api/protocols/genericSearch/:searchTerm', exports.genericProtocolSearch app.delete '/api/protocols/browser/:id', exports.deleteProtocol + app.get '/api/getProtocolByLabel/:protLabel', exports.getProtocolByLabel exports.setupRoutes = (app, loginRoutes) -> @@ -20,6 +21,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.get '/api/protocolKindCodes', loginRoutes.ensureAuthenticated, exports.protocolKindCodeList app.get '/api/protocols/genericSearch/:searchTerm', loginRoutes.ensureAuthenticated, exports.genericProtocolSearch app.delete '/api/protocols/browser/:id', loginRoutes.ensureAuthenticated, exports.deleteProtocol + app.get '/api/getProtocolByLabel/:protLabel', loginRoutes.ensureAuthenticated, exports.getProtocolByLabel serverUtilityFunctions = require './ServerUtilityFunctions.js' csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFunctions.js' @@ -467,3 +469,22 @@ exports.deleteProtocol = (req, res) -> console.log error console.log response ) + +exports.getProtocolByLabel = (req, resp) -> + config = require '../conf/compiled/conf.js' + url = config.all.client.service.persistence.fullpath+"protocols?FindByProtocolName&protocolName=#{req.params.protLabel}" + request = require 'request' + request( + method: 'GET' + url: url + json: true + , (error, response, json) => + console.log response.statusCode + console.log json + if !error and !json.error + resp.json json + else + console.log 'got ajax error trying to get protocol by label' + resp.statusCode = 500 + resp.json json.errorMessages + ) \ No newline at end of file From 04dbd5bf3fb602c4685ae4156b7763de28214763 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Fri, 16 Jun 2017 13:08:42 -0700 Subject: [PATCH 037/576] updating ControllerRedirectRoutes for when config.all.client.entity.saveInitialsCorpName is true, added getExperimentByLabelInternal and getProtocolByLabelInternal routes --- .../routes/ControllerRedirectRoutes.coffee | 57 +++++++++++++++---- .../routes/ExperimentServiceRoutes.coffee | 14 +++-- .../routes/ProtocolServiceRoutes.coffee | 12 ++-- 3 files changed, 64 insertions(+), 19 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee b/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee index 31ca85c4b..efa7f2f1f 100644 --- a/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee @@ -14,36 +14,71 @@ config = require '../conf/compiled/conf.js' exports.redirectToEditor = (req, resp) -> + code = req.params.code controllerRedirectConfFile = require '../src/javascripts/ServerAPI/ControllerRedirectConf.js' controllerRedirectConf = controllerRedirectConfFile.controllerRedirectConf queryPrefix = null prefixKeyIndex = 0 while queryPrefix is null and prefixKeyIndex < (Object.keys(controllerRedirectConf)).length prefix = Object.keys(controllerRedirectConf)[prefixKeyIndex] #prefix = possible entity prefix - if req.params.code.indexOf(prefix) > -1 #the requested route has a known entity prefix + if code.indexOf(prefix) > -1 #the requested route has a known entity prefix queryPrefix = prefix else prefixKeyIndex +=1 console.log "in redirectToEditor" - if req.params.code.substring(0,5) is "STUDY" - resp.redirect "/study_tracker_experiment/codeName/#{req.params.code}" - else if req.params.code.substring(0,3) is "EXP" #TODO: refactor to get expt and then figure out kind and deeplink appropriately - resp.redirect "/experiment_base/codeName/#{req.params.code}" - else if req.params.code.substring(0,3) is "PRT" #TODO: refactor to get prot and then figure out kind and deeplink appropriately - resp.redirect "/protocol_base/codeName/#{req.params.code}" - - else if queryPrefix != null + console.log config.all.client.entity.saveInitialsCorpName + + getEntityByName = (protOrExpt, resp) => + console.log "getEntityByName" + protocolServiceRoutes = require './ProtocolServiceRoutes.js' + experimentServiceRoutes = require './ExperimentServiceRoutes.js' + if protOrExpt is 'protocols' + protocolServiceRoutes.getProtocolByLabelInternal code, (statusCode, json) -> + console.log "getEntityByName - getProtocolByLabelInternal " + if statusCode is 500 + resp.redirect "/" + else + kind = json[0].lsKind + deepLink = controllerRedirectConf[queryPrefix][kind]["deepLink"] + console.log "/"+deepLink+"/codeName/"+code + resp.redirect "/"+deepLink+"/codeName/"+code + + else if protOrExpt is 'experiments' + experimentServiceRoutes.getExperimentByLabelInternal code, (statusCode, json) -> + console.log "getEntityByName - getExperimentByLabelInternal" + if statusCode is 500 + resp.redirect "/" + else + kind = json[0].lsKind + deepLink = controllerRedirectConf[queryPrefix][kind]["deepLink"] + console.log controllerRedirectConf[queryPrefix][kind]["deepLink"] + resp.redirect "/"+deepLink+"/codeName/"+code + + getEntityByCodeName = (resp) => request json: true - url: config.all.server.nodeapi.path+"/api/"+controllerRedirectConf[queryPrefix]["entityName"]+"/codename/"+req.params.code #get protocol + url: config.all.server.nodeapi.path+"/api/"+controllerRedirectConf[queryPrefix]["entityName"]+"/codename/"+code , (error, response, body) => console.log error console.log response console.log body kind = response.body.lsKind deepLink = controllerRedirectConf[queryPrefix][kind]["deepLink"] - resp.redirect "/"+deepLink+"/codeName/"+req.params.code + resp.redirect "/"+deepLink+"/codeName/"+code + + if queryPrefix != null + console.log "url to get entity - in redirectToEditor" + + if config.all.client.entity.saveInitialsCorpName + entityName = controllerRedirectConf[queryPrefix]["entityName"] + if entityName is "protocols" or entityName is "experiments" + #get entity by name + getEntityByName entityName, resp + else + getEntityByCodeName resp + else + getEntityByCodeName resp else resp.redirect "/#" diff --git a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee index e5b2b195c..7cb4a9bb3 100644 --- a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee @@ -903,8 +903,15 @@ exports.experimentsByTypeKind = (req, resp) -> serverUtilityFunctions.getFromACASServer(baseurl, resp) exports.getExperimentByLabel = (req, resp) -> + exports.getExperimentByLabelInternal req.params.exptLabel, (statusCode, json) -> + resp.statusCode = statusCode + resp.json json + +exports.getExperimentByLabelInternal = (label, callback) -> config = require '../conf/compiled/conf.js' - url = config.all.client.service.persistence.fullpath+"experiments?FindByExperimentName&experimentName=#{req.params.exptLabel}" + url = config.all.client.service.persistence.fullpath+"experiments?FindByExperimentName&experimentName=#{label}" + console.log "getExperimentByLabelInternal url" + console.log url request = require 'request' request( method: 'GET' @@ -914,11 +921,10 @@ exports.getExperimentByLabel = (req, resp) -> console.log response.statusCode console.log json if !error and !json.error - resp.json json + callback response.statusCode, json else console.log 'got ajax error trying to get experiment by label' - resp.statusCode = 500 - resp.json json.errorMessages + callback 500, json.errorMessages ) exports.getExperimentCodeByLabel = (req, resp) -> diff --git a/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee index fb2057a73..311842146 100644 --- a/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee @@ -471,8 +471,13 @@ exports.deleteProtocol = (req, res) -> ) exports.getProtocolByLabel = (req, resp) -> + exports.getProtocolByLabelInternal req.params.protLabel, (statusCode, json) -> + resp.statusCode = statusCode + resp.json json + +exports.getProtocolByLabelInternal = (label, callback) -> config = require '../conf/compiled/conf.js' - url = config.all.client.service.persistence.fullpath+"protocols?FindByProtocolName&protocolName=#{req.params.protLabel}" + url = config.all.client.service.persistence.fullpath+"protocols?FindByProtocolName&protocolName=#{label}" request = require 'request' request( method: 'GET' @@ -482,9 +487,8 @@ exports.getProtocolByLabel = (req, resp) -> console.log response.statusCode console.log json if !error and !json.error - resp.json json + callback response.statusCode, json else console.log 'got ajax error trying to get protocol by label' - resp.statusCode = 500 - resp.json json.errorMessages + callback 500, json.errorMessages ) \ No newline at end of file From d2fa51618f97e478c38801931929b3ea0337958e Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Fri, 16 Jun 2017 15:28:21 -0700 Subject: [PATCH 038/576] get client config to generate experiment/protocol corpName --- modules/GenericDataParser/src/server/generic_data_parser.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index edba5ab7a..064f0c5c7 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -1754,7 +1754,7 @@ createNewProtocol <- function(metaData, lsTransaction, recordedBy) { labelText=metaData$'Protocol Name'[1], preferred=TRUE) - if (toupper(configList$client.entity.saveInitialsCorpName) == "TRUE"){ + if (toupper(racas::applicationSettings$client.entity.saveInitialsCorpName) == "TRUE"){ protocolCorpNameList <- unlist(getAutoLabels(thingTypeAndKind="document_protocol", labelTypeAndKind=paste0("corpName initials_", recordedBy), numberOfLabels=1), @@ -1897,7 +1897,7 @@ createNewExperiment <- function(metaData, protocol, lsTransaction, pathToGeneric labelText=experimentName, preferred=TRUE) - if (toupper(configList$client.entity.saveInitialsCorpName) == "TRUE"){ + if (toupper(racas::applicationSettings$client.entity.saveInitialsCorpName) == "TRUE"){ experimentCorpNameList <- unlist(getAutoLabels(thingTypeAndKind="document_experiment", labelTypeAndKind=paste0("corpName initials_", recordedBy), numberOfLabels=1), From bfb0bc5435ace31c410ee288de5245f88c636f3c Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Fri, 16 Jun 2017 15:37:04 -0700 Subject: [PATCH 039/576] fixed bugs in ChemStructureRoutes, Thing.coffee (deleting empty labels should be determined by instance variable), and ProtocolServiceRoutes --- .../server/routes/ChemStructureRoutes.coffee | 4 +-- modules/ServerAPI/src/client/Thing.coffee | 11 ++++--- .../routes/ProtocolServiceRoutes.coffee | 32 +++++++++---------- 3 files changed, 24 insertions(+), 23 deletions(-) diff --git a/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee b/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee index 2361bc1e4..57aa53247 100644 --- a/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee +++ b/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee @@ -7,8 +7,8 @@ exports.setupAPIRoutes = (app) -> app.post '/api/chemStructure/calculateMoleculeProperties', exports.calculateMoleculeProperties app.post '/api/chemStructure/renderMolStructure', exports.renderMolStructure app.post '/api/chemStructure/renderMolStructureBase64', exports.renderMolStructureBase64 - app.post '/api/chemStructure/acasStructureMetaSearch', loginRoutes.ensureAuthenticated, exports.acasStructureMetaSearch - app.post '/api/chemStructure/acasStructureSearch', loginRoutes.ensureAuthenticated, exports.acasStructureSearch + app.post '/api/chemStructure/acasStructureMetaSearch', exports.acasStructureMetaSearch + app.post '/api/chemStructure/acasStructureSearch', exports.acasStructureSearch exports.setupRoutes = (app, loginRoutes) -> app.get '/api/chemStructure/renderStructureByThingCode', loginRoutes.ensureAuthenticated, exports.renderStructureByThingCode diff --git a/modules/ServerAPI/src/client/Thing.coffee b/modules/ServerAPI/src/client/Thing.coffee index e0a638da2..2d65192eb 100644 --- a/modules/ServerAPI/src/client/Thing.coffee +++ b/modules/ServerAPI/src/client/Thing.coffee @@ -1,6 +1,7 @@ class window.Thing extends Backbone.Model lsProperties: {} className: "Thing" + deleteEmptyLabelsBeforeSave: true # urlRoot: "/api/things" defaults: () -> @@ -68,11 +69,11 @@ class window.Thing extends Backbone.Model toJSON: (options) -> attsToSave = super(options) - - toDel = attsToSave.lsLabels.filter (lab) -> - (lab.get('ignored') || lab.get('labelText')=="") && lab.isNew() - for lab in toDel - attsToSave.lsLabels.remove lab + if @deleteEmptyLabelsBeforeSave + toDel = attsToSave.lsLabels.filter (lab) -> + (lab.get('ignored') || lab.get('labelText')=="") && lab.isNew() + for lab in toDel + attsToSave.lsLabels.remove lab if attsToSave.firstLsThings? toDel = attsToSave.firstLsThings.filter (itx) -> diff --git a/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee index e133dc46d..9f446fd07 100644 --- a/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee @@ -11,6 +11,7 @@ exports.setupAPIRoutes = (app) -> app.get '/api/getProtocolByLabel/:protLabel', exports.getProtocolByLabel + exports.setupRoutes = (app, loginRoutes) -> app.get '/api/protocols/codename/:code', loginRoutes.ensureAuthenticated, exports.protocolByCodename app.get '/api/protocols/:id', loginRoutes.ensureAuthenticated, exports.protocolById @@ -62,25 +63,24 @@ exports.protocolByCodename = (req, resp) -> if req.user? && config.all.server.project.roles.enable serverUtilityFunctions.getRestrictedEntityFromACASServerInternal baseurl, req.user.username, "metadata", "protocol metadata", (statusCode, json) => #if prot is deleted, need to check if user has privs to view deleted protocols - if json.codeName? and json.ignored and !json.deleted - if config.all.client.entity?.viewDeletedRoles? - viewDeletedRoles = config.all.client.entity.viewDeletedRoles.split(",") - else - viewDeletedRoles = [] - grantedRoles = _.map req.user.roles, (role) -> - role.roleEntry.roleName - canViewDeleted = (config.all.client.entity?.viewDeletedRoles? && config.all.client.entity.viewDeletedRoles in grantedRoles) - if canViewDeleted - resp.statusCode = statusCode - resp.end JSON.stringify json - else - resp.statusCode = 500 - resp.end JSON.stringify "Protocol does not exist" + if json.codeName? and json.ignored and !json.deleted + if config.all.client.entity?.viewDeletedRoles? + viewDeletedRoles = config.all.client.entity.viewDeletedRoles.split(",") else + viewDeletedRoles = [] + grantedRoles = _.map req.user.roles, (role) -> + role.roleEntry.roleName + canViewDeleted = (config.all.client.entity?.viewDeletedRoles? && config.all.client.entity.viewDeletedRoles in grantedRoles) + if canViewDeleted resp.statusCode = statusCode resp.end JSON.stringify json - - else + else + resp.statusCode = 500 + resp.end JSON.stringify "Protocol does not exist" + else + resp.statusCode = statusCode + resp.end JSON.stringify json + else serverUtilityFunctions.getFromACASServer baseurl, resp exports.protocolById = (req, resp) -> From 732241816040bb78a836cd6d6ba593426c3f0f68 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 16 Jun 2017 16:10:28 -0700 Subject: [PATCH 040/576] Allowed PickListSelect2Controller to have a placeholder mapped in. Added method to specifically get "code" in case model has different id and code, since "getSelectedCode" actually gets the id attribute for select2. Added alphabetical sorting to ThingLabelComboBoxController. Appended empty option to all ThingLabelComboBoxController html elements, which fixes #82 --- modules/Components/src/client/PickList.coffee | 27 ++++++++++++++++--- 1 file changed, 24 insertions(+), 3 deletions(-) diff --git a/modules/Components/src/client/PickList.coffee b/modules/Components/src/client/PickList.coffee index 151e58753..abe46ee0d 100644 --- a/modules/Components/src/client/PickList.coffee +++ b/modules/Components/src/client/PickList.coffee @@ -252,9 +252,11 @@ class window.PickListSelect2Controller extends PickListSelectController obj.id = obj.id || obj.code obj.text = obj.text || obj.name mappedData.push(obj) - + @placeholder = "" + if @options.placeholder? + @placeholder = @options.placeholder $(@el).select2 - placeholder: "" + placeholder: @placeholder data: mappedData openOnEnter: false allowClear: true @@ -276,6 +278,16 @@ class window.PickListSelect2Controller extends PickListSelectController result = "unassigned" result + getSelectedCodeNotId: -> + results = $(@el).select2('data') + if results.length > 0 + results[0].code + else + if @insertFirstOption.get('code') is "unassigned" + "unassigned" + else + null + setSelectedCode: (code) -> if code? @selectedCode = code @@ -557,7 +569,7 @@ class window.EditablePickListSelect2Controller extends EditablePickListSelectCon name: "Select "+pascalCaseParameterName selectedCode: @options.selectedCode -class window.ThingLabelComboBoxController extends Backbone.View +class window.ThingLabelComboBoxController extends PickListSelect2Controller initialize: -> @thingType = @options.thingType @@ -567,6 +579,7 @@ class window.ThingLabelComboBoxController extends Backbone.View @queryUrl = if @options.queryUrl? then @options.queryUrl else null unless @queryUrl? or (@thingType? and @thingKind?) alert("ThingLabelComboBoxController URL misconfigured - crash to follow") + @$el.append('') render: => @selectController = @$el.select2 @@ -593,6 +606,14 @@ class window.ThingLabelComboBoxController extends Backbone.View results = for option in data {id: option.code, text: option.name} return {results: results} + sorter: (data) -> + data.sort( (a, b) -> + if a.text.toUpperCase() > b.text.toUpperCase() + return 1 + if a.text.toUpperCase() < b.text.toUpperCase() + return -1 + return 0 + ) @ getSelectedCode: -> From 3b93f96e2641cb5813f57aaade4248654f3fde67 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 16 Jun 2017 17:07:22 -0700 Subject: [PATCH 041/576] add call to racas function to clean environment before call to R functions --- gulpfile.coffee | 25 +++++++++++++++++++++++++ package.json | 11 ++++------- 2 files changed, 29 insertions(+), 7 deletions(-) diff --git a/gulpfile.coffee b/gulpfile.coffee index 73d491e09..42c0340f4 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -13,6 +13,8 @@ path = require('path') run = require('gulp-run') gulpif = require('gulp-if') _ = require('underscore') +through = require('through2') + node = undefined # ---------------------------------------------- Functions @@ -66,6 +68,26 @@ getPythonPath = (path) -> path.dirname = outputDirname return +addREnvironmentCleanUp = (file,contents) -> + # file contents are handed + # over as buffers + if path.extname(file.path) in [".R",".r"] && contents.match('# ROUTE:.*') + cleanFunction = "racas::cleanEnvironment()" + contents = "#{cleanFunction}\n\r#{contents}\r\n#{cleanFunction}" + return contents + +modify = (options = {}) -> + through.obj (file, enc, next) -> + error = null + if file.isBuffer() + if fileModifier = options.fileModifier + try + content = fileModifier file, file.contents.toString 'utf8' + file.contents = new Buffer content + catch _error + console.log _error + next error, file + # ------------------------------------------------- Read Inputs build = argv.buildPath or process.env.BUILD_PATH or '' @@ -257,6 +279,7 @@ taskConfigs = dest: build + '/src/r' options: _.extend _.clone(globalCopyOptions), {} renameFunction: getFirstFolderName + modifyFunction: addREnvironmentCleanUp , taskName: "html" src: getGlob('modules/**/src/client/*.html') @@ -340,10 +363,12 @@ createTask = (options, type) -> watch = options.watch shouldFlatten = options.flatten ? false renameFunction = options.renameFunction + modifyFunction = options.modifyFunction gulp.task taskName, -> gulp.src(src, _.extend(taskOptions, {since: gulp.lastRun(taskName)})) .pipe(plumber()) .pipe(gulpif(shouldFlatten,flatten())) + .pipe(gulpif(modifyFunction?, modify(fileModifier: modifyFunction))) .pipe(gulpif(renameFunction?,rename(renameFunction))) .pipe(gulpif(type=="coffee",coffee(bare: true))) .pipe gulp.dest(dest) diff --git a/package.json b/package.json index ac9580f0f..31ae5baa9 100644 --- a/package.json +++ b/package.json @@ -35,7 +35,7 @@ "jasmine-core": "^2.4.1", "jasmine-jquery": "^2.1.1", "jquery": "^2.2.0", - "jquery-file-upload-middleware": ">=0.1.7", + "jquery-file-upload-middleware": "https://github.com/mcneilco/jquery-file-upload-middleware.git", "jszip": "*", "less": "^2.6.0", "lodash": "^4.0.0", @@ -57,18 +57,15 @@ "underscore-deep-extend": ">= 0.0.0", "winston": "*", "winston-mongodb": "*", - "style-loader": "*", "bootstrap": "*", "exports-loader": "*", - "extract-text-webpack-plugin": "*", "url-loader": "*", - "file-loader": "*", - "jquery-file-upload-middleware": "https://github.com/mcneilco/jquery-file-upload-middleware.git", "yamljs": "*", "request-promise": "*", - "bluebird": "*" + "bluebird": "*" }, "devDependencies": { + "coffee-script": "^1.12.4", "del": "^2.2.2", "gulp": "github:gulpjs/gulp#4.0", "gulp-browserify": "^0.5.1", @@ -84,7 +81,7 @@ "gulp-run": "^1.7.1", "gulp-watch": "^4.3.11", "gutil": "^1.6.4", - "coffee-script": "^1.12.4", + "through2": "^2.0.3", "yargs": "^7.0.2" } } From 6b9bf2e00e8d0f60bf7ed23a8b998f5344603d0c Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 16 Jun 2017 17:33:22 -0700 Subject: [PATCH 042/576] add an extra line at the endof file --- gulpfile.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gulpfile.coffee b/gulpfile.coffee index 42c0340f4..c4c318524 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -73,7 +73,7 @@ addREnvironmentCleanUp = (file,contents) -> # over as buffers if path.extname(file.path) in [".R",".r"] && contents.match('# ROUTE:.*') cleanFunction = "racas::cleanEnvironment()" - contents = "#{cleanFunction}\n\r#{contents}\r\n#{cleanFunction}" + contents = "#{cleanFunction}\n\r#{contents}\r\n#{cleanFunction}\r\n" return contents modify = (options = {}) -> From 68588f894484914907d41d62925130075bd1a0b9 Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Sat, 17 Jun 2017 00:21:05 -0700 Subject: [PATCH 043/576] Service to get container information from batch code. --- .../routes/InventoryServiceRoutes.coffee | 43 ++++++++++++++++++- 1 file changed, 42 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index c344b237a..a3d1b89ad 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -53,6 +53,7 @@ exports.setupAPIRoutes = (app) -> app.post '/api/createTubes', exports.createTubes app.post '/api/throwInTrash', exports.throwInTrash app.post '/api/updateContainerHistoryLogs', exports.updateContainerHistoryLogs + app.post '/api/getContainerInfoFromBatchCode', exports.getContainerInfoFromBatchCode exports.setupRoutes = (app, loginRoutes) -> app.post '/api/getContainersInLocationWithTypeAndKind', loginRoutes.ensureAuthenticated, exports.getContainersInLocationWithTypeAndKind @@ -101,7 +102,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/createTubes', loginRoutes.ensureAuthenticated, exports.createTubes app.post '/api/throwInTrash', loginRoutes.ensureAuthenticated, exports.throwInTrash app.post '/api/updateContainerHistoryLogs', loginRoutes.ensureAuthenticated, exports.updateContainerHistoryLogs - + app.post '/api/getContainerInfoFromBatchCode', loginRoutes.ensureAuthenticated, exports.getContainerInfoFromBatchCode exports.getContainersInLocation = (req, resp) -> req.setTimeout 86400000 @@ -2304,3 +2305,43 @@ formatContainers = (containers, modifiedBy, modifiedDate, callback) -> # console.log 'locationArrayString ' # console.log locationArrayString # callback locationArrayString + +exports.getContainerInfoFromBatchCode = (req, resp) => + + requestObject = + batchCode: req.body.batchCode + + exports.getContainerInfoFromBatchCodeInternal(requestObject, (json, statusCode) => + resp.statusCode = statusCode + resp.json json + ) + +exports.getContainerInfoFromBatchCodeInternal = (requestObject, callback) => + + queryPayload = + { + "containerType": "well", + "containerKind": "default", + "stateType": "status", + "stateKind": "content", + "valueType": "codeValue", + "valueKind": "batch code", + "value": requestObject.batchCode, + "maxResults": 600, + "like": true, + "rightLike": true + } + + exports.getContainerCodeNamesByContainerValueInternal(queryPayload, (json) => + statusCode = 200 + if json.maxResults? + warningMessage = "Max results of #{maxResults} reached." + return callback {warningMessage: warningMessage, statusMessage: ""},statusCode + else + if json.length > 0 + exports.getWellContentInternal(json, (response) => + return callback response, statusCode + ) + else + return callback {warningMessage: "No results found for #{queryPayload.value}", statusMessage: ""}, statusCode + ) From 95d5ef79be93fe64f8ed247c5bd5eb045989dbfb Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Mon, 19 Jun 2017 13:13:41 -0700 Subject: [PATCH 044/576] add expt corpName to results HTML --- .../GenericDataParser/src/server/generic_data_parser.R | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 064f0c5c7..12a2b2df5 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -2911,7 +2911,15 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, summaryInfo$info$"Flagged Data Points" <- sum(subjectData$valueKind == "flag") } if(!dryRun) { - summaryInfo$info$"Experiment Code Name" <- experiment$codeName + if (toupper(racas::applicationSettings$client.entity.saveInitialsCorpName) == "TRUE"){ + exptLabels <- flattenLabels(experiment$lsLabels) + exptCorpName <- exptLabels$labelText[exptLabels$lsType=='corpName' && exptLabels$lsKind=='experiment corpName' && exptLabels$ignored==FALSE] + summaryInfo$info$"Experiment Corp Name" <- exptCorpName + viewerLink <- paste0("/openExptInQueryTool?experiment=", URLencode(exptCorpName, reserved = TRUE)) + } else { + summaryInfo$info$"Experiment Code Name" <- experiment$codeName + } + if (!is.null(viewerLink)) { summaryInfo$viewerLink <- viewerLink } From f42267b71cdfd74373e93e2d0c0e37427764c15d Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Mon, 19 Jun 2017 14:37:38 -0700 Subject: [PATCH 045/576] Fixed protocol and expt browsers to deep link and display properly when expts/prots have corpNames, fixed bugs with using @deleteEmptyLabelsAndValsBeforeSave --- .../src/client/ExperimentBrowser.coffee | 124 ++++++++++++++---- .../src/client/ProtocolBrowser.coffee | 73 +++++++++-- modules/ServerAPI/src/client/Thing.coffee | 27 ++-- 3 files changed, 174 insertions(+), 50 deletions(-) diff --git a/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee b/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee index 1b5b1fdd2..3d33bc7c8 100644 --- a/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee +++ b/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee @@ -240,15 +240,19 @@ class window.ExperimentRowSummaryController extends Backbone.View protocolBestName = @model.get('protocol').get('lsLabels').pickBestName() if protocolBestName protocolBestName = @model.get('protocol').get('lsLabels').pickBestName().get('labelText') - if @model.get('lsKind') is "study" - if @model.get('lsLabels') not instanceof LabelList - @model.set 'lsLabels', new LabelList @model.get('lsLabels') - if @model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 - code = @model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') + if @model.get('lsLabels') not instanceof LabelList + @model.set 'lsLabels', new LabelList @model.get('lsLabels') + subclass = @model.get('subclass') + if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true + if @model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 + code = @model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') else code = @model.get("codeName") + else if @model.get('lsKind') is "study" and @model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 + code = @model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') else - code = @model.get("codeName") + code = @model.get('codeName') + toDisplay = experimentName: experimentBestName experimentCode: code @@ -484,15 +488,28 @@ class window.ExperimentBrowserController extends Backbone.View return true handleDeleteExperimentClicked: => - if @experimentController.model.get('lsKind') is "study" - if @experimentController.model.get('lsLabels') not instanceof LabelList - @experimentController.model.set 'lsLabels', new LabelList @model.get('lsLabels') - if @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 - code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') + if @experimentController.model.get('lsLabels') not instanceof LabelList + @experimentController.model.set 'lsLabels', new LabelList @experimentController.model.get('lsLabels') + subclass = @experimentController.model.get('subclass') + if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true + if @experimentController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') else code = @experimentController.model.get("codeName") + else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') else - code = @experimentController.model.get("codeName") + code = @experimentController.model.get('codeName') + +# if @experimentController.model.get('lsKind') is "study" +# if @experimentController.model.get('lsLabels') not instanceof LabelList +# @experimentController.model.set 'lsLabels', new LabelList @model.get('lsLabels') +# if @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 +# code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') +# else +# code = @experimentController.model.get("codeName") +# else +# code = @experimentController.model.get("codeName") @$(".bv_experimentCodeName").html code @$(".bv_deleteButtons").removeClass "hide" @$(".bv_okayButton").addClass "hide" @@ -529,19 +546,45 @@ class window.ExperimentBrowserController extends Backbone.View @$(".bv_confirmDeleteExperiment").modal('hide') handleEditExperimentClicked: => - if @experimentController.model.get('lsKind') is 'study' - if @experimentController.model.get('lsLabels') not instanceof LabelList - @experimentController.model.set 'lsLabels', new LabelList @experimentController.model.get('lsLabels') - if @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 - code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') + if @experimentController.model.get('lsLabels') not instanceof LabelList + @experimentController.model.set 'lsLabels', new LabelList @experimentController.model.get('lsLabels') + subclass = @experimentController.model.get('subclass') + if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true + if @experimentController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') else code = @experimentController.model.get("codeName") + else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') else - code = @experimentController.model.get("codeName") + code = @experimentController.model.get('codeName') +# +# if @experimentController.model.get('lsKind') is 'study' +# if @experimentController.model.get('lsLabels') not instanceof LabelList +# @experimentController.model.set 'lsLabels', new LabelList @experimentController.model.get('lsLabels') +# if @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 +# code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') +# else +# code = @experimentController.model.get("codeName") +# else +# code = @experimentController.model.get("codeName") window.open("/entity/edit/codeName/#{code}",'_blank'); - handleDuplicateExperimentClicked: => + handleDuplicateExperimentClicked: => #TODO: refactor experimentKind = @experimentController.model.get('lsKind') + if @experimentController.model.get('lsLabels') not instanceof LabelList + @experimentController.model.set 'lsLabels', new LabelList @experimentController.model.get('lsLabels') + subclass = @experimentController.model.get('subclass') + if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true + if @experimentController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') + else + code = @experimentController.model.get("codeName") + else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') + else + code = @experimentController.model.get('codeName') + if experimentKind is "Bio Activity" window.open("/entity/copy/primary_screen_experiment/#{@experimentController.model.get("codeName")}",'_blank'); else if experimentKind is "study" @@ -557,16 +600,30 @@ class window.ExperimentBrowserController extends Backbone.View handleOpenInQueryToolClicked: => unless @$('.bv_openInQueryToolButton').hasClass 'dropdown-toggle' - experimentKind = @experimentController.model.get('lsKind') - if experimentKind is "study" - if @experimentController.model.get('lsLabels') not instanceof LabelList - @experimentController.model.set 'lsLabels', new LabelList @experimentController.model.get('lsLabels') - if @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 - code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') + if @experimentController.model.get('lsLabels') not instanceof LabelList + @experimentController.model.set 'lsLabels', new LabelList @experimentController.model.get('lsLabels') + subclass = @experimentController.model.get('subclass') + if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true + if @experimentController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') else code = @experimentController.model.get("codeName") + else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') else - code = @experimentController.model.get("codeName") + code = @experimentController.model.get('codeName') + + + # experimentKind = @experimentController.model.get('lsKind') +# if experimentKind is "study" +# if @experimentController.model.get('lsLabels') not instanceof LabelList +# @experimentController.model.set 'lsLabels', new LabelList @experimentController.model.get('lsLabels') +# if @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 +# code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') +# else +# code = @experimentController.model.get("codeName") +# else +# code = @experimentController.model.get("codeName") window.open("/openExptInQueryTool?experiment=#{code}",'_blank') formatOpenInQueryToolButton: => @@ -577,7 +634,20 @@ class window.ExperimentBrowserController extends Backbone.View if configuredViewers? and configuredViewers.length>1 for viewer in configuredViewers viewerName = $.trim viewer - href = "'/openExptInQueryTool?tool=#{viewerName}&experiment=#{@experimentController.model.get("codeName")}','_blank'" + if @experimentController.model.get('lsLabels') not instanceof LabelList + @experimentController.model.set 'lsLabels', new LabelList @experimentController.model.get('lsLabels') + subclass = @experimentController.model.get('subclass') + if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true + if @experimentController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') + else + code = @experimentController.model.get("codeName") + else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') + else + code = @experimentController.model.get('codeName') + + href = "'/openExptInQueryTool?tool=#{viewerName}&experiment=#{code}','_blank'" if @experimentController.model.getStatus().get('codeValue') != "approved" and viewerName is "LiveDesign" @$('.bv_viewerOptions').append '
      • '+viewerName+'
        • ' else diff --git a/modules/ProtocolBrowser/src/client/ProtocolBrowser.coffee b/modules/ProtocolBrowser/src/client/ProtocolBrowser.coffee index da2c4cf69..e658ff348 100644 --- a/modules/ProtocolBrowser/src/client/ProtocolBrowser.coffee +++ b/modules/ProtocolBrowser/src/client/ProtocolBrowser.coffee @@ -90,6 +90,16 @@ class window.ProtocolRowSummaryController extends Backbone.View date = "not recorded" else date = UtilityFunctions::convertMSToYMDDate(date.get('dateValue')) + if @model.get('lsLabels') not instanceof LabelList + @model.set 'lsLabels', new LabelList @model.get('lsLabels') + subclass = @model.get('subclass') + if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true + if @model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 + code = @model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') + else + code = @model.get("codeName") + else + code = @model.get('codeName') toDisplay = protocolName: @model.get('lsLabels').pickBestName().get('labelText') @@ -320,7 +330,17 @@ class window.ProtocolBrowserController extends Backbone.View return true handleDeleteProtocolClicked: => - @$(".bv_protocolCodeName").html @protocolController.model.get("codeName") + if @protocolController.model.get('lsLabels') not instanceof LabelList + @protocolController.model.set 'lsLabels', new LabelList @protocolController.model.get('lsLabels') + subclass = @protocolController.model.get('subclass') + if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true + if @protocolController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 + code = @protocolController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') + else + code = @protocolController.model.get("codeName") + else + code = @protocolController.model.get('codeName') + @$(".bv_protocolCodeName").html code @$(".bv_deleteButtons").removeClass "hide" @$(".bv_okayButton").addClass "hide" @$(".bv_errorDeletingProtocolMessage").addClass "hide" @@ -356,29 +376,62 @@ class window.ProtocolBrowserController extends Backbone.View @$(".bv_confirmDeleteProtocol").modal('hide') handleEditProtocolClicked: => - window.open("/entity/edit/codeName/#{@protocolController.model.get("codeName")}",'_blank'); + if @protocolController.model.get('lsLabels') not instanceof LabelList + @protocolController.model.set 'lsLabels', new LabelList @protocolController.model.get('lsLabels') + subclass = @protocolController.model.get('subclass') + if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true + if @protocolController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 + code = @protocolController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') + else + code = @protocolController.model.get("codeName") + else + code = @protocolController.model.get('codeName') + + window.open("/entity/edit/codeName/#{code}",'_blank'); handleDuplicateProtocolClicked: => protocolKind = @protocolController.model.get('lsKind') + if @protocolController.model.get('lsLabels') not instanceof LabelList + @protocolController.model.set 'lsLabels', new LabelList @protocolController.model.get('lsLabels') + subclass = @protocolController.model.get('subclass') + if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true + if @protocolController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 + code = @protocolController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') + else + code = @protocolController.model.get("codeName") + else + code = @protocolController.model.get('codeName') + if protocolKind is "Bio Activity" - window.open("/entity/copy/primary_screen_protocol/#{@protocolController.model.get("codeName")}",'_blank'); + window.open("/entity/copy/primary_screen_protocol/#{code}",'_blank'); else if protocolKind is "Parent Bio Activity" - window.open("/entity/copy/parent_protocol/#{@protocolController.model.get("codeName")}",'_blank'); + window.open("/entity/copy/parent_protocol/#{code}",'_blank'); else if protocolKind is "study" - window.open("/entity/copy/study_tracker_protocol/#{@protocolController.model.get("codeName")}",'_blank'); + window.open("/entity/copy/study_tracker_protocol/#{code}",'_blank'); else - window.open("/entity/copy/protocol_base/#{@protocolController.model.get("codeName")}",'_blank'); + window.open("/entity/copy/protocol_base/#{code}",'_blank'); handleCreateExperimentClicked: => protocolKind = @protocolController.model.get('lsKind') + if @protocolController.model.get('lsLabels') not instanceof LabelList + @protocolController.model.set 'lsLabels', new LabelList @protocolController.model.get('lsLabels') + subclass = @protocolController.model.get('subclass') + if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true + if @protocolController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 + code = @protocolController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') + else + code = @protocolController.model.get("codeName") + else + code = @protocolController.model.get('codeName') + if protocolKind is "Bio Activity" - window.open("/primary_screen_experiment/createFrom/#{@protocolController.model.get("codeName")}",'_blank') + window.open("/primary_screen_experiment/createFrom/#{code}",'_blank') else if protocolKind is "Parent Bio Activity" - window.open("/parent_experiment/createFrom/#{@protocolController.model.get("codeName")}",'_blank') + window.open("/parent_experiment/createFrom/#{code}",'_blank') else if protocolKind is "study" - window.open("/study_tracker_experiment/createFrom/#{@protocolController.model.get("codeName")}",'_blank') + window.open("/study_tracker_experiment/createFrom/#{code}",'_blank') else - window.open("/experiment_base/createFrom/#{@protocolController.model.get("codeName")}",'_blank') + window.open("/experiment_base/createFrom/#{code}",'_blank') destroyProtocolSummaryTable: => if @protocolSummaryTable? diff --git a/modules/ServerAPI/src/client/Thing.coffee b/modules/ServerAPI/src/client/Thing.coffee index 2d65192eb..f39bcf3bc 100644 --- a/modules/ServerAPI/src/client/Thing.coffee +++ b/modules/ServerAPI/src/client/Thing.coffee @@ -1,7 +1,7 @@ class window.Thing extends Backbone.Model lsProperties: {} className: "Thing" - deleteEmptyLabelsBeforeSave: true + deleteEmptyLabelsAndValsBeforeSave: true # urlRoot: "/api/things" defaults: () -> @@ -69,7 +69,7 @@ class window.Thing extends Backbone.Model toJSON: (options) -> attsToSave = super(options) - if @deleteEmptyLabelsBeforeSave + if @deleteEmptyLabelsAndValsBeforeSave toDel = attsToSave.lsLabels.filter (lab) -> (lab.get('ignored') || lab.get('labelText')=="") && lab.isNew() for lab in toDel @@ -103,17 +103,18 @@ class window.Thing extends Backbone.Model for itx in @lsProperties.defaultSecondLsThingItx delete attsToSave[itx.key] - if @lsProperties.defaultValues? - for dValue in @lsProperties.defaultValues - if attsToSave[dValue.key]? - val = attsToSave[dValue.key].get('value') - if val is undefined or val is "" or val is null - lsStates = attsToSave.lsStates.getStatesByTypeAndKind dValue.stateType, dValue.stateKind - values = lsStates[0].getValuesByTypeAndKind dValue.type, dValue.kind - if values[0]? - if values[0].isNew() - lsStates[0].get('lsValues').remove values[0] - delete attsToSave[dValue.key] + if @deleteEmptyLabelsAndValsBeforeSave + if @lsProperties.defaultValues? + for dValue in @lsProperties.defaultValues + if attsToSave[dValue.key]? + val = attsToSave[dValue.key].get('value') + if val is undefined or val is "" or val is null + lsStates = attsToSave.lsStates.getStatesByTypeAndKind dValue.stateType, dValue.stateKind + values = lsStates[0].getValuesByTypeAndKind dValue.type, dValue.kind + if values[0]? + if values[0].isNew() + lsStates[0].get('lsValues').remove values[0] + delete attsToSave[dValue.key] if attsToSave.attributes? delete attsToSave.attributes From bdb5152de959936940b7ea4cfd955f97441fd0c4 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 19 Jun 2017 14:39:41 -0700 Subject: [PATCH 046/576] fixing broken system tests --- Dockerfile-rservices | 2 +- docker-compose.yml | 6 ++--- gulpfile.coffee | 22 +++++++++++++++++++ .../RunRFunctionServiceTestJSON.coffee | 2 +- .../server/routes/ThingServiceRoutes.coffee | 2 +- .../spec/serviceTests/SystemTest.coffee | 2 +- .../src/server/routes/SystemTestRoutes.coffee | 8 +++---- 7 files changed, 33 insertions(+), 11 deletions(-) diff --git a/Dockerfile-rservices b/Dockerfile-rservices index fd2aa8e3f..5ca7c84f5 100644 --- a/Dockerfile-rservices +++ b/Dockerfile-rservices @@ -1,4 +1,4 @@ -FROM mcneilco/racas-oss:${ACAS_TAG} +FROM mcneilco/racas-oss:develop # RSTUDIO INSTALL USER root diff --git a/docker-compose.yml b/docker-compose.yml index 4bc3b9fd9..89c6d032e 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -24,14 +24,14 @@ services: # Add chemaxon marvinjs here - ./chemaxon/marvinjs:/home/runner/build/public/CmpdReg/marvinjs # Please add any dev volumes below this line - # - ./:/home/runner/acas + - ./:/home/runner/acas # - ./modules/BuildUtilities/:/home/runner/acas/modules/BuildUtilities env_file: - ./conf/docker/acas/environment/acas.env # Dev Command -# command: ["bin/acas.sh", "run", "acas", "dev"] + command: ["bin/acas.sh", "run", "acas", "dev"] # Start command - command: ["bin/acas.sh", "run", "acas", "start"] +# command: ["bin/acas.sh", "run", "acas", "start"] rservices: image: mcneilco/racas-oss:${ACAS_TAG} restart: always diff --git a/gulpfile.coffee b/gulpfile.coffee index 73d491e09..d07e85eb5 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -66,6 +66,16 @@ getPythonPath = (path) -> path.dirname = outputDirname return +getAssetsPath = (path) -> + module = path.dirname.split('/')[0] + if path.basename == 'assets' and path.extname == '' + path.basename = '' + path.dirname = '' + outputDirname = module + '/' + path.dirname.replace(module + '/src/server/assets', '') + path.dirname = outputDirname + return + + # ------------------------------------------------- Read Inputs build = argv.buildPath or process.env.BUILD_PATH or '' @@ -286,6 +296,18 @@ taskConfigs = src: getGlob('modules/CmpdReg/src/**') dest: build + '/public/CmpdReg' options: _.extend _.clone(globalCopyOptions), {} + , + taskName: "serverAssets" + src: getGlob('modules/**/src/server/assets/**') + dest: build + '/src/assets' + options: _.extend _.clone(globalCopyOptions), {} + renameFunction: getAssetsPath + , + taskName: "clientAssets" + src: getGlob('modules/**/src/client/assets/**') + dest: build + '/public/assets' + options: _.extend _.clone(globalCopyOptions), {} + renameFunction: getFirstFolderName ], others: packageJSON: diff --git a/modules/ServerAPI/spec/testFixtures/RunRFunctionServiceTestJSON.coffee b/modules/ServerAPI/spec/testFixtures/RunRFunctionServiceTestJSON.coffee index abca877c3..35c419362 100644 --- a/modules/ServerAPI/spec/testFixtures/RunRFunctionServiceTestJSON.coffee +++ b/modules/ServerAPI/spec/testFixtures/RunRFunctionServiceTestJSON.coffee @@ -1,7 +1,7 @@ ((exports) -> exports.runRFunctionRequest = - rScript:"src/r/spec/ServerAPI/serviceTests/runRApacheFunction.R" + rScript:"src/r/spec/ServerAPI/runRApacheFunction.R" rFunction:"testFunction" request: "{\"smartMode\":true,\"inactiveThresholdMode\":true,\"inactiveThreshold\":20,\"inverseAgonistMode\":false,\"max\":{\"limitType\":\"none\"},\"min\":{\"limitType\":\"none\"},\"slope\":{\"limitType\":\"none\"}}" diff --git a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee index 6bbf9c812..edc35fa64 100644 --- a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee @@ -259,7 +259,7 @@ postThing = (isBatch, req, resp) -> transactionOptions = { comments: "new experiment" } - transactionOptions.recordedBy = req.session.passport.user.username + transactionOptions.recordedBy = if req.session?.passport?.user?.username? then req.session.passport.user.username else "acas" transactionOptions.status = "PENDING" transactionOptions.type = "NEW" serverUtilityFunctions.createLSTransaction2 thingToSave.recordedDate, transactionOptions, (transaction) -> diff --git a/modules/SystemTest/spec/serviceTests/SystemTest.coffee b/modules/SystemTest/spec/serviceTests/SystemTest.coffee index 39995642e..b3d9c6cea 100644 --- a/modules/SystemTest/spec/serviceTests/SystemTest.coffee +++ b/modules/SystemTest/spec/serviceTests/SystemTest.coffee @@ -251,7 +251,7 @@ describe "D. Access to rApache", -> @responseJSON = body done() it "should not return an error", -> - assert.equal(@responseJSON,undefined,@responseJSON) + assert.equal(@responseJSON,"",@responseJSON) ############################# # E. System Tests # diff --git a/modules/SystemTest/src/server/routes/SystemTestRoutes.coffee b/modules/SystemTest/src/server/routes/SystemTestRoutes.coffee index 8e8a8c962..12324f665 100644 --- a/modules/SystemTest/src/server/routes/SystemTestRoutes.coffee +++ b/modules/SystemTest/src/server/routes/SystemTestRoutes.coffee @@ -440,7 +440,7 @@ exports.getOrCreateCmpdRegBobInternal = (callback)-> code: bob.username name: bob.firstName + " " + bob.lastName isChemist: !config.all.client.roles.cmpdreg?.chemistRole? || (config.all.client.roles.cmpdreg?.chemistRole? && config.all.client.roles.cmpdreg.chemistRole in grantedRoles) - isAdmin = !config.all.client.roles.cmpdreg?.adminRole? || (config.all.client.roles.cmpdreg?.adminRole? && config.all.client.roles.cmpdreg.adminRole in grantedRoles) + isAdmin: !config.all.client.roles.cmpdreg?.adminRole? || (config.all.client.roles.cmpdreg?.adminRole? && config.all.client.roles.cmpdreg.adminRole in grantedRoles) ] json: true request options, (error, response, body) -> @@ -575,7 +575,7 @@ exports.getOrCreateCmpdsInternal = (callback) -> headers: accept: 'application/json, text/javascript, */*; q=0.01' 'content-type': 'application/x-www-form-urlencoded; charset=UTF-8' - body: "fileName=#{encodeURIComponent(body[0].name)}&mappings%5B0%5D%5BdbProperty%5D=Parent+Corp+Name&mappings%5B0%5D%5Brequired%5D=false&mappings%5B0%5D%5BsdfProperty%5D=Parent+Corp+Name&mappings%5B0%5D%5BdefaultVal%5D=&mappings%5B1%5D%5BdbProperty%5D=Lot+Corp+Name&mappings%5B1%5D%5Brequired%5D=false&mappings%5B1%5D%5BsdfProperty%5D=Lot+Corp+Name&mappings%5B1%5D%5BdefaultVal%5D=&mappings%5B2%5D%5BsdfProperty%5D=&mappings%5B2%5D%5BdbProperty%5D=Lot+Chemist&mappings%5B2%5D%5BdefaultVal%5D=bob&mappings%5B2%5D%5Brequired%5D=true&mappings%5B3%5D%5BsdfProperty%5D=&mappings%5B3%5D%5BdbProperty%5D=Parent+Stereo+Category&mappings%5B3%5D%5BdefaultVal%5D=racemic&mappings%5B3%5D%5Brequired%5D=true&mappings%5B4%5D%5BdbProperty%5D=Project&mappings%5B4%5D%5Brequired%5D=true&mappings%5B4%5D%5BsdfProperty%5D=&mappings%5B4%5D%5BdefaultVal%5D=#{globalProjectCode}&userName=bob&fileDate=1472799600000" + body: "fileName=#{encodeURIComponent(body.files[0].name)}&mappings%5B0%5D%5BdbProperty%5D=Parent+Corp+Name&mappings%5B0%5D%5Brequired%5D=false&mappings%5B0%5D%5BsdfProperty%5D=Parent+Corp+Name&mappings%5B0%5D%5BdefaultVal%5D=&mappings%5B1%5D%5BdbProperty%5D=Lot+Corp+Name&mappings%5B1%5D%5Brequired%5D=false&mappings%5B1%5D%5BsdfProperty%5D=Lot+Corp+Name&mappings%5B1%5D%5BdefaultVal%5D=&mappings%5B2%5D%5BsdfProperty%5D=&mappings%5B2%5D%5BdbProperty%5D=Lot+Chemist&mappings%5B2%5D%5BdefaultVal%5D=bob&mappings%5B2%5D%5Brequired%5D=true&mappings%5B3%5D%5BsdfProperty%5D=&mappings%5B3%5D%5BdbProperty%5D=Parent+Stereo+Category&mappings%5B3%5D%5BdefaultVal%5D=racemic&mappings%5B3%5D%5Brequired%5D=true&mappings%5B4%5D%5BdbProperty%5D=Project&mappings%5B4%5D%5Brequired%5D=true&mappings%5B4%5D%5BsdfProperty%5D=&mappings%5B4%5D%5BdefaultVal%5D=#{globalProjectCode}&userName=bob&fileDate=1472799600000" request options, (error, response, body) -> if error throw new Error(error) @@ -672,7 +672,7 @@ exports.loadSELFileInternal = (username, callback)-> headers: accept: 'application/json, text/javascript, */*; q=0.01' 'content-type': 'application/x-www-form-urlencoded; charset=UTF-8' - body: "fileToParse=#{encodeURIComponent(body[0].name)}&reportFile=&imagesFile=&dryRunMode=false&user=#{username}&requireDoseResponse=true" + body: "fileToParse=#{encodeURIComponent(body.files[0].name)}&reportFile=&imagesFile=&dryRunMode=false&user=#{username}&requireDoseResponse=true" request options, (error, response, body) => if error throw new Error(error) @@ -881,7 +881,7 @@ exports.runSystemTestInternal = (force, callback) -> exports.systemReport = (req, resp) -> - fs.readFile path.resolve(path.join(config.all.server.datafiles.relative_path, "systemReport/systemReport.html")), (err, data) => + fs.readFile path.resolve(path.join(config.all.server.datafiles.relative_path, "systemReport/mochawesome.html")), (err, data) => if err? resp.send 400, "no system report found" else From a0831f03e8cc03ef81026935cb8fce826b39249d Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Mon, 19 Jun 2017 16:41:28 -0700 Subject: [PATCH 047/576] Fixed bug in protocol browser to display corpName labels if config set --- modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee | 2 +- modules/ProtocolBrowser/src/client/ProtocolBrowser.coffee | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee b/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee index 3d33bc7c8..3e1f397da 100644 --- a/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee +++ b/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee @@ -570,7 +570,7 @@ class window.ExperimentBrowserController extends Backbone.View # code = @experimentController.model.get("codeName") window.open("/entity/edit/codeName/#{code}",'_blank'); - handleDuplicateExperimentClicked: => #TODO: refactor + handleDuplicateExperimentClicked: => experimentKind = @experimentController.model.get('lsKind') if @experimentController.model.get('lsLabels') not instanceof LabelList @experimentController.model.set 'lsLabels', new LabelList @experimentController.model.get('lsLabels') diff --git a/modules/ProtocolBrowser/src/client/ProtocolBrowser.coffee b/modules/ProtocolBrowser/src/client/ProtocolBrowser.coffee index e658ff348..89bddcb17 100644 --- a/modules/ProtocolBrowser/src/client/ProtocolBrowser.coffee +++ b/modules/ProtocolBrowser/src/client/ProtocolBrowser.coffee @@ -103,7 +103,7 @@ class window.ProtocolRowSummaryController extends Backbone.View toDisplay = protocolName: @model.get('lsLabels').pickBestName().get('labelText') - protocolCode: @model.get('codeName') + protocolCode: code protocolKind: @model.get('lsKind') scientist: @model.getScientist().get('codeValue') assayStage: @model.getAssayStage().get("codeValue") From 35f1a5d2412b9a76d9463d91d76d1f4205a648c6 Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Mon, 19 Jun 2017 18:15:25 -0700 Subject: [PATCH 048/576] correct naming of exp corpName --- modules/GenericDataParser/src/server/generic_data_parser.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 12a2b2df5..94f449701 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -2913,7 +2913,7 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, if(!dryRun) { if (toupper(racas::applicationSettings$client.entity.saveInitialsCorpName) == "TRUE"){ exptLabels <- flattenLabels(experiment$lsLabels) - exptCorpName <- exptLabels$labelText[exptLabels$lsType=='corpName' && exptLabels$lsKind=='experiment corpName' && exptLabels$ignored==FALSE] + exptCorpName <- exptLabels$labelText[exptLabels$lsType=='corpName' & exptLabels$lsKind=='experiment corpName' & exptLabels$ignored==FALSE] summaryInfo$info$"Experiment Corp Name" <- exptCorpName viewerLink <- paste0("/openExptInQueryTool?experiment=", URLencode(exptCorpName, reserved = TRUE)) } else { From d1458c493b5d3c1fef9d76f7ecdb74b742f64e75 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Tue, 20 Jun 2017 18:18:30 -0700 Subject: [PATCH 049/576] cleaned up and simplified example thing --- .../client/ModuleMenusConfiguration.coffee | 2 +- .../conf/ExampleThingConfJSON.coffee | 94 ++++++++ .../ServerAPI/src/client/ExampleThing.coffee | 215 ++++++++---------- 3 files changed, 196 insertions(+), 115 deletions(-) create mode 100644 modules/ServerAPI/conf/ExampleThingConfJSON.coffee diff --git a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee index 6efb6c6f7..fb75e6b4b 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee @@ -31,7 +31,7 @@ window.ModuleMenusConfiguration = , isHeader: false, menuName: "Example Thing" mainControllerClassName: "ExampleThingController" - autoLaunchName:"cationic_block" + autoLaunchName:"example_thing" , isHeader: true menuName: "Search and Edit" diff --git a/modules/ServerAPI/conf/ExampleThingConfJSON.coffee b/modules/ServerAPI/conf/ExampleThingConfJSON.coffee new file mode 100644 index 000000000..acbea5e5b --- /dev/null +++ b/modules/ServerAPI/conf/ExampleThingConfJSON.coffee @@ -0,0 +1,94 @@ +((exports) -> + exports.typeKindList = + thingkinds: + [ + typeName: "parent" + kindName: "example thing" + ] + + statetypes: + [ + typeName: "metadata" + ] + + statekinds: + [ + typeName: "metadata" + kindName: "example thing parent" + ] + + valuetypes: + [ + typeName: "dateValue" + , + typeName: "codeValue" + , + typeName: "stringValue" + , + typeName: "clobValue" + , + typeName: "fileValue" + ] + + valuekinds: + [ + typeName: "codeValue" + kindName: "scientist" + , + typeName: "dateValue" + kindName: "completion date" + , + typeName: "stringValue" + kindName: "notebook" + , + typeName: "stringValue" + kindName: "notebook page" + , + typeName: "fileValue" + kindName: "structural file" + ] + + labeltypes: + [ + typeName: "name" + ] + + labelkinds: + [ + typeName: "name" + kindName: "experiment thing" + ] + + ddicttypes: + [ + ] + + ddictkinds: + [ + ] + + codetables: + [ + ] + + labelsequences: + [ + digits: 6 + groupDigits: false + labelPrefix: "ET" + labelSeparator: "-" + labelTypeAndKind: "corpName_Example Thing" + thingTypeAndKind: "parent_Example Thing" + latestNumber:1 + , + digits: 8 + groupDigits: false + labelPrefix: "THING" + labelSeparator: "" + labelTypeAndKind: "id_codeName" + thingTypeAndKind: "parent_Example Thing" + latestNumber:1 + ] + +) (if (typeof process is "undefined" or not process.versions) then window.exampleThingConfJSON = window.exampleThingConfJSON or {} else exports) + diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index 20d66d980..06411746e 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -1,25 +1,30 @@ -class window.ExampleThing extends Thing - urlRoot: "/api/things/parent/cationic block" - className: "CationicBlockParent" +class window.ExampleThingParent extends Thing + urlRoot: "/api/things/parent/example thing" + url: -> + if @isNew() and !@has('codeName') + return "/api/things/Material/example thing?nestedstub=true" + else + return "/api/things/parent/thing/#{@get 'codeName'}?nestedstub=true" + className: "ExampleThingParent" initialize: -> @.set lsType: "parent" - lsKind: "cationic block" + lsKind: "Example Thing" super() lsProperties: defaultLabels: [ - key: 'cationic block name' + key: 'example thing name' type: 'name' - kind: 'cationic block' + kind: 'example thing' preferred: true # labelText: "" #gets created when createDefaultLabels is called ] defaultValues: [ key: 'scientist' stateType: 'metadata' - stateKind: 'cationic block parent' + stateKind: 'example thing parent' type: 'codeValue' kind: 'scientist' codeOrigin: window.conf.scientistCodeOrigin @@ -27,31 +32,24 @@ class window.ExampleThing extends Thing , key: 'completion date' stateType: 'metadata' - stateKind: 'cationic block parent' + stateKind: 'example thing parent' type: 'dateValue' kind: 'completion date' value: NaN , key: 'notebook' stateType: 'metadata' - stateKind: 'cationic block parent' + stateKind: 'example thing parent' type: 'stringValue' kind: 'notebook' value: "" , key: 'structural file' stateType: 'metadata' - stateKind: 'cationic block parent' + stateKind: 'example thing parent' type: 'fileValue' kind: 'structural file' value: "" - , - key: 'batch number' - stateType: 'metadata' - stateKind: 'cationic block parent' - type: 'numericValue' - kind: 'batch number' - value: 0 ] defaultFirstLsThingItx: [ @@ -62,8 +60,6 @@ class window.ExampleThing extends Thing ] - - validate: (attrs) -> errors = [] bestName = attrs.lsLabels.pickBestName() @@ -100,34 +96,14 @@ class window.ExampleThing extends Thing else return null - prepareToSave: -> - rBy = @get('recordedBy') - rDate = new Date().getTime() - @set recordedDate: rDate - @get('lsLabels').each (lab) -> - unless lab.get('recordedBy') != "" - lab.set recordedBy: rBy - unless lab.get('recordedDate') != null - lab.set recordedDate: rDate - @get('lsStates').each (state) -> - unless state.get('recordedBy') != "" - state.set recordedBy: rBy - unless state.get('recordedDate') != null - state.set recordedDate: rDate - state.get('lsValues').each (val) -> - unless val.get('recordedBy') != "" - val.set recordedBy: rBy - unless val.get('recordedDate') != null - val.set recordedDate: rDate - duplicate: => copiedThing = super() - copiedThing.get("batch number").set value: 0 +# copiedThing.get("batch number").set value: 0 copiedThing class window.ExampleThingController extends AbstractFormController template: _.template($("#ExampleThingView").html()) - moduleLaunchName: "cationic_block" + moduleLaunchName: "example_thing" events: -> "keyup .bv_thingName": "attributeChanged" @@ -139,42 +115,17 @@ class window.ExampleThingController extends AbstractFormController "click .bv_deleteSavedFile": "handleDeleteSavedStructuralFile" initialize: => - if @model? - @completeInitialization() - else - if window.AppLaunchParams.moduleLaunchParams? - if window.AppLaunchParams.moduleLaunchParams.moduleName == @moduleLaunchName - launchCode = window.AppLaunchParams.moduleLaunchParams.code - if launchCode.indexOf("-") == -1 - @batchCodeName = "new batch" - else - @batchCodeName = launchCode - launchCode =launchCode.split("-")[0] - $.ajax - type: 'GET' - url: "/api/things/parent/cationic block/codename/"+launchCode - dataType: 'json' - error: (err) -> - alert 'Could not get parent for code in this URL, creating new one' - @completeInitialization() - success: (json) => - if json.length == 0 - alert 'Could not get parent for code in this URL, creating new one' - else - #TODO Once server is upgraded to not wrap in an array, use the commented out line. It is consistent with specs and tests -# cbp = new CationicBlockParent json - cbp = new ExampleThing json - cbp.set cbp.parse(cbp.attributes) - @model = cbp - @completeInitialization() - else - @completeInitialization() - else - @completeInitialization() - - completeInitialization: => + @hasRendered = false + if window.AppLaunchParams.moduleLaunchParams? + if window.AppLaunchParams.moduleLaunchParams.moduleName == @moduleLaunchName + launchCode = window.AppLaunchParams.moduleLaunchParams.code + @model = new ExampleThingParent {codeName: launchCode} + @model.fetch() + unless @model? - @model=new ExampleThing() + @model = new ExampleThingParent() + @modelSaveCallback() + @errorOwnerName = 'ExampleThingController' @setBindings() if @options.readOnly? @@ -182,17 +133,68 @@ class window.ExampleThingController extends AbstractFormController else @readOnly = false @listenTo @model, 'sync', @modelSaveCallback - @listenTo @model, 'change', @modelChangeCallback - $(@el).empty() - $(@el).html @template(@model.attributes) - @setupScientistSelect() - @render() - +# @listenTo @model, 'change', @modelChangeCallback + + +# if @model? +# @completeInitialization() +# else +# if window.AppLaunchParams.moduleLaunchParams? +# if window.AppLaunchParams.moduleLaunchParams.moduleName == @moduleLaunchName +# launchCode = window.AppLaunchParams.moduleLaunchParams.code +# if launchCode.indexOf("-") == -1 +# @batchCodeName = "new batch" +# else +# @batchCodeName = launchCode +# launchCode =launchCode.split("-")[0] +# $.ajax +# type: 'GET' +# url: "/api/things/parent/Example Thing/codename/"+launchCode +# dataType: 'json' +# error: (err) => +# alert 'Could not get parent for code in this URL, creating new one' +# @completeInitialization() +# success: (json) => +# if json.length == 0 +# alert 'Could not get parent for code in this URL, creating new one' +# else +# #TODO Once server is upgraded to not wrap in an array, use the commented out line. It is consistent with specs and tests +## cbp = new CationicBlockParent json +# cbp = new ExampleThing json +# cbp.set cbp.parse(cbp.attributes) +# @model = cbp +# @completeInitialization() +# else +# @completeInitialization() +# else +# @completeInitialization() + +# completeInitialization: => +# unless @model? +# @model=new ExampleThing() +# @errorOwnerName = 'ExampleThingController' +# @setBindings() +# if @options.readOnly? +# @readOnly = @options.readOnly +# else +# @readOnly = false +# @listenTo @model, 'sync', @modelSaveCallback +# @listenTo @model, 'change', @modelChangeCallback +# @render() render: => - unless @model? - @model = new ExampleThing() - @setupStructuralFileController() + unless @hasRendered + $(@el).empty() + $(@el).html @template(@model.attributes) + @setupScientistSelect() + @setupStructuralFileController() + @$('.bv_completionDate').datepicker(); + @$('.bv_completionDate').datepicker( "option", "dateFormat", "yy-mm-dd" ); + @hasRendered = true + + @ + + renderModelContent: -> codeName = @model.get('codeName') @$('.bv_thingCode').val(codeName) @$('.bv_thingCode').html(codeName) @@ -200,8 +202,6 @@ class window.ExampleThingController extends AbstractFormController if bestName? @$('.bv_thingName').val bestName.get('labelText') @$('.bv_scientist').val @model.get('scientist').get('value') - @$('.bv_completionDate').datepicker(); - @$('.bv_completionDate').datepicker( "option", "dateFormat", "yy-mm-dd" ); compDate = @model.get('completion date').get('value') if compDate? unless isNaN(compDate) @@ -214,16 +214,20 @@ class window.ExampleThingController extends AbstractFormController @$('.bv_saveThing').html("Save") else @$('.bv_saveThing').html("Update") - @ modelSaveCallback: (method, model) => + console.log "got model save callback" + if @model.isNew() # model not found + @model.set codeName: null + return + @$('.bv_saveThing').show() @$('.bv_saveThing').attr('disabled', 'disabled') @$('.bv_saveThingComplete').show() @$('.bv_updatingThing').hide() @trigger 'amClean' @trigger 'thingSaved' - @render() + @renderModelContent() modelChangeCallback: (method, model) => @trigger 'amDirty' @@ -271,7 +275,7 @@ class window.ExampleThingController extends AbstractFormController @structuralFileController.on('fileDeleted', @handleFileRemoved) #update model with filename handleFileUpload: (nameOnServer) => - newFileValue = @model.get('lsStates').getOrCreateValueByTypeAndKind "metadata", "cationic block parent", "fileValue", "structural file" + newFileValue = @model.get('lsStates').getOrCreateValueByTypeAndKind "metadata", "example thing parent", "fileValue", "structural file" @model.set "structural file", newFileValue @model.get("structural file").set("value", nameOnServer) @@ -285,7 +289,7 @@ class window.ExampleThingController extends AbstractFormController @createNewFileChooser() updateModel: => - @model.get("cationic block name").set("labelText", UtilityFunctions::getTrimmedInput @$('.bv_thingName')) + @model.get("example thing name").set("labelText", UtilityFunctions::getTrimmedInput @$('.bv_thingName')) @model.get("scientist").set("value", @scientistListController.getSelectedCode()) @model.get("notebook").set("value", UtilityFunctions::getTrimmedInput @$('.bv_notebook')) @model.get("completion date").set("value", UtilityFunctions::convertYMDDateToMs(UtilityFunctions::getTrimmedInput @$('.bv_completionDate'))) @@ -298,27 +302,6 @@ class window.ExampleThingController extends AbstractFormController super() @$('.bv_saveThing').removeAttr('disabled') - validateThingName: -> - @$('.bv_saveThing').attr('disabled', 'disabled') - lsKind = @model.get('lsKind') - name= [@model.get(lsKind+' name').get('labelText')] - $.ajax - type: 'POST' - url: "/api/validateName/"+lsKind - data: - requestName: name - success: (response) => - @handleValidateReturn(response) - error: (err) => - @serviceReturn = null - dataType: 'json' - - handleValidateReturn: (validNewLabel) => - if validNewLabel is true - @handleUpdateThing() - else - alert 'The requested thing name has already been registered. Please choose a new thing name.' - handleUpdateThing: => @model.prepareToSave() @model.reformatBeforeSaving() @@ -335,5 +318,9 @@ class window.ExampleThingController extends AbstractFormController return false @disableAllInputs() - updateBatchNumber: => - @model.fetch() + +#TODO switch to form fields +#TODO add state table example +#TODO add pick list/ddict example +#TODO add thing interaction to project with field +#TODO file upload is broken \ No newline at end of file From 8ff32a3d78f0cf1f8e6f35a80593ab51a525452d Mon Sep 17 00:00:00 2001 From: John McNeil Date: Tue, 20 Jun 2017 20:57:22 -0700 Subject: [PATCH 050/576] changed example thing to use form fields. Added dataValue form field. Added URL override for picklist form field --- .../src/client/ACASFormFields.coffee | 57 ++++- .../src/client/ACASFormFieldsView.html | 10 + .../src/client/AbstractFormController.coffee | 2 + .../ServerAPI/src/client/ExampleThing.coffee | 230 +++++++----------- .../ServerAPI/src/client/ExampleThing.html | 32 +-- 5 files changed, 157 insertions(+), 174 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 58728900c..bb0a0e0ec 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -222,6 +222,11 @@ class window.ACASFormLSCodeValueFieldController extends ACASFormAbstractFieldCon template: _.template($("#ACASFormLSCodeValueFieldView").html()) + applyOptions: -> + super() + if @options.url? + @url = @options.url + handleInputChanged: => @clearError() value = @pickListController.getSelectedCode() @@ -245,7 +250,10 @@ class window.ACASFormLSCodeValueFieldController extends ACASFormAbstractFieldCon setupSelect: -> @pickList = new PickListList() mdl = @getModel() - @pickList.url = "/api/codetables/#{mdl.get 'codeType'}/#{mdl.get 'codeKind'}" + if @url? + @pickList.url = @url + else + @pickList.url = "/api/codetables/#{mdl.get 'codeType'}/#{mdl.get 'codeKind'}" plOptions = el: @$('select') collection: @pickList @@ -455,3 +463,50 @@ class window.ACASFormLSStringValueFieldController extends ACASFormAbstractFieldC renderModelContent: => @$('input').val @getModel().get('value') super() + + +class window.ACASFormLSDateValueFieldController extends ACASFormAbstractFieldController + ### + Launching controller must: + - Initialize the model with an LSValue + Do whatever else is required or optional in ACASFormAbstractFieldController + ### + + template: _.template($("#ACASFormLSDateValueFieldView").html()) + events: -> + "change input": "handleInputChanged" + "click .bv_dateIcon": "handleDateIconClicked" + + render: -> + super() + @$('input').datepicker(); + @$('input').datepicker( "option", "dateFormat", "yy-mm-dd" ); + + @ + + handleInputChanged: => + @clearError() + @userInputEvent = true + value = UtilityFunctions::convertYMDDateToMs(UtilityFunctions::getTrimmedInput(@$('input'))) + if value == "" || isNaN(value) + @setEmptyValue() + else + @getModel().set + value: value + ignored: false + super() + + setEmptyValue: -> + @getModel().set + value: null + ignored: true + + renderModelContent: => + compDate = @getModel().get('value') + if compDate? + unless isNaN(compDate) + @$('input').val UtilityFunctions::convertMSToYMDDate(compDate) + super() + + handleDateIconClicked: => + @$('input').datepicker( "show" ) diff --git a/modules/Components/src/client/ACASFormFieldsView.html b/modules/Components/src/client/ACASFormFieldsView.html index 668282a20..86a50c112 100644 --- a/modules/Components/src/client/ACASFormFieldsView.html +++ b/modules/Components/src/client/ACASFormFieldsView.html @@ -31,6 +31,15 @@
      + + + diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index f21aebf49..9ac9eaa70 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -100,6 +100,7 @@ class window.AbstractThingFormController extends AbstractFormController formLabel: field.fieldSettings.formLabel placeholder: field.fieldSettings.placeholder required: field.fieldSettings.required + url: field.fieldSettings.url thingRef: @model insertUnassigned: field.fieldSettings.insertUnassigned @@ -117,6 +118,7 @@ class window.AbstractThingFormController extends AbstractFormController opts.labelType = field.fieldSettings.labelType newField = new ACASFormLSThingInteractionFieldController opts when 'stringValue' then newField = new ACASFormLSStringValueFieldController opts + when 'dateValue' then newField = new ACASFormLSDateValueFieldController opts @$("."+field.fieldSettings.fieldWrapper).append newField.render().el newField.afterRender() diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index 06411746e..cb470c25c 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -1,3 +1,71 @@ +ExampleThingConf = + formFieldDefinitions: + labels: [ + key: 'example thing name' + modelDefaults: + type: 'name' + kind: 'example thing' + preferred: true + fieldSettings: + fieldType: 'label' + required: true + inputClass: "" + formLabel: "*Name" + placeholder: "name" + fieldWrapper: "bv_thingName" + ] + values: [ + key: 'scientist' + modelDefaults: + stateType: 'metadata' + stateKind: 'example thing parent' + type: 'codeValue' + kind: 'scientist' + codeOrigin: window.conf.scientistCodeOrigin + value: "unassigned" + fieldSettings: + fieldType: 'codeValue' + required: true + formLabel: "*Scientist" + fieldWrapper: "bv_scientist_date" + url: "/api/authors" + , + key: 'completion date' + modelDefaults: + stateType: 'metadata' + stateKind: 'example thing parent' + type: 'dateValue' + kind: 'completion date' + value: null + fieldSettings: + fieldType: 'dateValue' + formLabel: "*Date" + fieldWrapper: "bv_scientist_date" + placeholder: "yyyy-mm-dd" + required: true + , + key: 'notebook' + modelDefaults: + stateType: 'metadata' + stateKind: 'example thing parent' + type: 'stringValue' + kind: 'notebook' + value: "" + fieldSettings: + fieldType: 'stringValue' + formLabel: "Notebook" + fieldWrapper: "bv_notebook" + placeholder: "notebook and page" + required: false + ] + + + stateTables: [] + firstLsThingItxs: [] + secondLsThingItxs: [] + + + class window.ExampleThingParent extends Thing urlRoot: "/api/things/parent/example thing" url: -> @@ -11,39 +79,24 @@ class window.ExampleThingParent extends Thing @.set lsType: "parent" lsKind: "Example Thing" + for label in ExampleThingConf.formFieldDefinitions.labels + label.modelDefaults.key = label.key + @lsProperties.defaultLabels.push label.modelDefaults + for value in ExampleThingConf.formFieldDefinitions.values + value.modelDefaults.key = value.key + @lsProperties.defaultValues.push value.modelDefaults + for itx in ExampleThingConf.formFieldDefinitions.firstLsThingItxs + itx.modelDefaults.key = itx.key + @lsProperties.defaultFirstLsThingItx.push itx.modelDefaults + for itx in ExampleThingConf.formFieldDefinitions.secondLsThingItxs + itx.modelDefaults.key = itx.key + @lsProperties.defaultSecondLsThingItx.push itx.modelDefaults super() lsProperties: defaultLabels: [ - key: 'example thing name' - type: 'name' - kind: 'example thing' - preferred: true -# labelText: "" #gets created when createDefaultLabels is called ] defaultValues: [ - key: 'scientist' - stateType: 'metadata' - stateKind: 'example thing parent' - type: 'codeValue' - kind: 'scientist' - codeOrigin: window.conf.scientistCodeOrigin - value: "unassigned" - , - key: 'completion date' - stateType: 'metadata' - stateKind: 'example thing parent' - type: 'dateValue' - kind: 'completion date' - value: NaN - , - key: 'notebook' - stateType: 'metadata' - stateKind: 'example thing parent' - type: 'stringValue' - kind: 'notebook' - value: "" - , key: 'structural file' stateType: 'metadata' stateKind: 'example thing parent' @@ -62,35 +115,7 @@ class window.ExampleThingParent extends Thing validate: (attrs) -> errors = [] - bestName = attrs.lsLabels.pickBestName() - nameError = true - if bestName? - nameError = true - if bestName.get('labelText') != "" - nameError = false - if nameError - errors.push - attribute: 'thingName' - message: "Name must be set" - if attrs.scientist? - scientist = attrs.scientist.get('value') - if scientist is "" or scientist is "unassigned" or scientist is undefined or scientist is null - errors.push - attribute: 'scientist' - message: "Scientist must be set" - if attrs["completion date"]? - cDate = attrs["completion date"].get('value') - if cDate is undefined or cDate is "" or cDate is null then cDate = "fred" - if isNaN(cDate) - errors.push - attribute: 'completionDate' - message: "Date must be set" - if attrs.notebook? - notebook = attrs.notebook.get('value') - if notebook is "" or notebook is undefined or notebook is null - errors.push - attribute: 'notebook' - message: "Notebook must be set" + if errors.length > 0 return errors else @@ -98,19 +123,13 @@ class window.ExampleThingParent extends Thing duplicate: => copiedThing = super() -# copiedThing.get("batch number").set value: 0 copiedThing -class window.ExampleThingController extends AbstractFormController +class window.ExampleThingController extends AbstractThingFormController template: _.template($("#ExampleThingView").html()) moduleLaunchName: "example_thing" events: -> - "keyup .bv_thingName": "attributeChanged" - "change .bv_scientist": "attributeChanged" - "keyup .bv_completionDate": "attributeChanged" - "click .bv_completionDateIcon": "handleCompletionDateIconClicked" - "keyup .bv_notebook": "attributeChanged" "click .bv_saveThing": "handleUpdateThing" "click .bv_deleteSavedFile": "handleDeleteSavedStructuralFile" @@ -133,63 +152,13 @@ class window.ExampleThingController extends AbstractFormController else @readOnly = false @listenTo @model, 'sync', @modelSaveCallback -# @listenTo @model, 'change', @modelChangeCallback - - -# if @model? -# @completeInitialization() -# else -# if window.AppLaunchParams.moduleLaunchParams? -# if window.AppLaunchParams.moduleLaunchParams.moduleName == @moduleLaunchName -# launchCode = window.AppLaunchParams.moduleLaunchParams.code -# if launchCode.indexOf("-") == -1 -# @batchCodeName = "new batch" -# else -# @batchCodeName = launchCode -# launchCode =launchCode.split("-")[0] -# $.ajax -# type: 'GET' -# url: "/api/things/parent/Example Thing/codename/"+launchCode -# dataType: 'json' -# error: (err) => -# alert 'Could not get parent for code in this URL, creating new one' -# @completeInitialization() -# success: (json) => -# if json.length == 0 -# alert 'Could not get parent for code in this URL, creating new one' -# else -# #TODO Once server is upgraded to not wrap in an array, use the commented out line. It is consistent with specs and tests -## cbp = new CationicBlockParent json -# cbp = new ExampleThing json -# cbp.set cbp.parse(cbp.attributes) -# @model = cbp -# @completeInitialization() -# else -# @completeInitialization() -# else -# @completeInitialization() - -# completeInitialization: => -# unless @model? -# @model=new ExampleThing() -# @errorOwnerName = 'ExampleThingController' -# @setBindings() -# if @options.readOnly? -# @readOnly = @options.readOnly -# else -# @readOnly = false -# @listenTo @model, 'sync', @modelSaveCallback -# @listenTo @model, 'change', @modelChangeCallback -# @render() render: => unless @hasRendered $(@el).empty() $(@el).html @template(@model.attributes) - @setupScientistSelect() + @setupFormFields(ExampleThingConf.formFieldDefinitions) @setupStructuralFileController() - @$('.bv_completionDate').datepicker(); - @$('.bv_completionDate').datepicker( "option", "dateFormat", "yy-mm-dd" ); @hasRendered = true @ @@ -198,15 +167,6 @@ class window.ExampleThingController extends AbstractFormController codeName = @model.get('codeName') @$('.bv_thingCode').val(codeName) @$('.bv_thingCode').html(codeName) - bestName = @model.get('lsLabels').pickBestName() - if bestName? - @$('.bv_thingName').val bestName.get('labelText') - @$('.bv_scientist').val @model.get('scientist').get('value') - compDate = @model.get('completion date').get('value') - if compDate? - unless isNaN(compDate) - @$('.bv_completionDate').val UtilityFunctions::convertMSToYMDDate(@model.get('completion date').get('value')) - @$('.bv_notebook').val @model.get('notebook').get('value') if @readOnly is true @displayInReadOnlyMode() @$('.bv_saveThing').attr('disabled','disabled') @@ -221,6 +181,7 @@ class window.ExampleThingController extends AbstractFormController @model.set codeName: null return + @fillFieldsFromModels() @$('.bv_saveThing').show() @$('.bv_saveThing').attr('disabled', 'disabled') @$('.bv_saveThingComplete').show() @@ -242,21 +203,6 @@ class window.ExampleThingController extends AbstractFormController @$('.bv_structuralFile').html ''+@model.get('structural file').get('comments')+'' @$('.bv_deleteSavedFile').show() - setupScientistSelect: -> - defaultOption = "Select Scientist" - @scientistList = new PickListList() - @scientistList.url = "/api/authors" - @scientistListController = new PickListSelectController - el: @$('.bv_scientist') - collection: @scientistList - insertFirstOption: new PickList - code: "unassigned" - name: defaultOption - selectedCode: @model.get('scientist').get('value') - - handleCompletionDateIconClicked: => - @$( ".bv_completionDate" ).datepicker( "show" ) - createNewFileChooser: => @structuralFileController = new LSFileChooserController el: @$('.bv_structuralFile') @@ -289,10 +235,7 @@ class window.ExampleThingController extends AbstractFormController @createNewFileChooser() updateModel: => - @model.get("example thing name").set("labelText", UtilityFunctions::getTrimmedInput @$('.bv_thingName')) - @model.get("scientist").set("value", @scientistListController.getSelectedCode()) - @model.get("notebook").set("value", UtilityFunctions::getTrimmedInput @$('.bv_notebook')) - @model.get("completion date").set("value", UtilityFunctions::convertYMDDateToMs(UtilityFunctions::getTrimmedInput @$('.bv_completionDate'))) + validationError: => super() @@ -319,8 +262,7 @@ class window.ExampleThingController extends AbstractFormController @disableAllInputs() -#TODO switch to form fields #TODO add state table example #TODO add pick list/ddict example #TODO add thing interaction to project with field -#TODO file upload is broken \ No newline at end of file +#TODO file upload is broken diff --git a/modules/ServerAPI/src/client/ExampleThing.html b/modules/ServerAPI/src/client/ExampleThing.html index d52225a7c..d7583a4f4 100644 --- a/modules/ServerAPI/src/client/ExampleThing.html +++ b/modules/ServerAPI/src/client/ExampleThing.html @@ -8,36 +8,10 @@
      Thing RegistrationAutofilled when saved
      -
      - -
      - -
      -
      +
      -
      - -
      - -
      -
      -
      - -
      -
      - - -
      -
      -
      -
      - -
      - -
      -
      +
      +
      From d7726dad4ba98f76c6b1a0ede8cb3acfd26db1f7 Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Wed, 21 Jun 2017 11:32:21 -0700 Subject: [PATCH 051/576] Corrected the queryPayload for getContainerInfoFromBatchCode (3 parameters were not required or necessary for this purpose). --- .../routes/InventoryServiceRoutes.coffee | 29 +++++++++---------- 1 file changed, 13 insertions(+), 16 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 435c791c6..f75a807a2 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -2257,6 +2257,16 @@ formatContainers = (containers, modifiedBy, modifiedDate, callback) -> return callback formattedContainers #callback(formattedContainers, statusCode) +exports.getContainerInfoFromBatchCode = (req, resp) => + + requestObject = + batchCode: req.body.batchCode + + exports.getContainerInfoFromBatchCodeInternal(requestObject, (json, statusCode) => + resp.statusCode = statusCode + resp.json json + ) + # getLocationBreadcrumb = (container, callback) -> # exports.getBreadCrumbByContainerCodeInternal([container.containerCodeName], "<", (breadcrumb) -> @@ -2315,16 +2325,6 @@ formatContainers = (containers, modifiedBy, modifiedDate, callback) -> # console.log locationArrayString # callback locationArrayString -exports.getContainerInfoFromBatchCode = (req, resp) => - - requestObject = - batchCode: req.body.batchCode - - exports.getContainerInfoFromBatchCodeInternal(requestObject, (json, statusCode) => - resp.statusCode = statusCode - resp.json json - ) - exports.getContainerInfoFromBatchCodeInternal = (requestObject, callback) => queryPayload = @@ -2335,22 +2335,19 @@ exports.getContainerInfoFromBatchCodeInternal = (requestObject, callback) => "stateKind": "content", "valueType": "codeValue", "valueKind": "batch code", - "value": requestObject.batchCode, - "maxResults": 600, - "like": true, - "rightLike": true + "value": requestObject.batchCode } exports.getContainerCodeNamesByContainerValueInternal(queryPayload, (json) => statusCode = 200 if json.maxResults? warningMessage = "Max results of #{maxResults} reached." - return callback {warningMessage: warningMessage, statusMessage: ""},statusCode + return callback {warningMessage: warningMessage}, statusCode else if json.length > 0 exports.getWellContentInternal(json, (response) => return callback response, statusCode ) else - return callback {warningMessage: "No results found for #{queryPayload.value}", statusMessage: ""}, statusCode + return callback {warningMessage: "No results found for #{queryPayload.value}"}, statusCode ) From 3e680ed555d0a8441ffafde0b00939882b9a731a Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 22 Jun 2017 07:50:03 -0700 Subject: [PATCH 052/576] adding copy test fixtures to src/spec folder --- gulpfile.coffee | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gulpfile.coffee b/gulpfile.coffee index 73d491e09..3d0a52048 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -286,6 +286,12 @@ taskConfigs = src: getGlob('modules/CmpdReg/src/**') dest: build + '/public/CmpdReg' options: _.extend _.clone(globalCopyOptions), {} + , + taskName: "spec" + src: getGlob("modules/**/spec/**", "!modules/**/spec/**/*.coffee", "!modules/**/spec/testFixtures/*.coffee") + dest: build + '/src/spec' + options: _.extend _.clone(globalCopyOptions), {} + renameFunction: getTestFixuresPath ], others: packageJSON: From 29508f0274c8e41e0902f5aa725993ae2348a9b6 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Thu, 22 Jun 2017 13:17:29 -0700 Subject: [PATCH 053/576] added state table and picklist form field examples to Example Thing --- .../src/client/ACASFormStateTable.coffee | 15 +++- .../conf/ExampleThingConfJSON.coffee | 62 +++++++++++++- .../ServerAPI/src/client/ExampleThing.coffee | 83 ++++++++++++++++++- .../ServerAPI/src/client/ExampleThing.html | 1 + 4 files changed, 154 insertions(+), 7 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index bf231a634..61e413f02 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -19,6 +19,8 @@ class window.ACASFormStateTableController extends Backbone.View initialize: -> @thingRef = @options.thingRef @tableDef = @options.tableDef + @tableSetupComplete = false + @callWhenSetupComplete = null getCollection: -> #TODO get states by type and kind @@ -33,6 +35,12 @@ class window.ACASFormStateTableController extends Backbone.View #Subclass to extend renderModelContent: => + if @tableSetupComplete + @completeRenderModelContent() + else + @callWhenSetupComplete = @completeRenderModelContent + + completeRenderModelContent: -> for state in @getCurrentStates() @renderState state @@ -59,6 +67,10 @@ class window.ACASFormStateTableController extends Backbone.View @fetchPickLists => @defineColumns() @setupHot() + @tableSetupComplete = true + if @callWhenSetupComplete? + @callWhenSetupComplete.call @ + @callWhenSetupComplete = null fetchPickLists: (callback) => @pickLists = {} @@ -90,12 +102,10 @@ class window.ACASFormStateTableController extends Backbone.View json: true self: @ kind: kind -# success: makeRetFunct() success: (response) -> this.self.pickLists[this.kind] = new PickListList response doneYet() - defineColumns: -> unless @colHeaders? @colHeaders = [] @@ -301,7 +311,6 @@ class window.ACASFormStateTableController extends Backbone.View if rowValues.length == 1 rowValues[0].set numericValue: rowNum + amount - handleRowRemoved: (index, amount) => for rowNum in [index..(index+amount-1)] state = @getStateForRow rowNum, false diff --git a/modules/ServerAPI/conf/ExampleThingConfJSON.coffee b/modules/ServerAPI/conf/ExampleThingConfJSON.coffee index acbea5e5b..ba62d9484 100644 --- a/modules/ServerAPI/conf/ExampleThingConfJSON.coffee +++ b/modules/ServerAPI/conf/ExampleThingConfJSON.coffee @@ -15,6 +15,9 @@ [ typeName: "metadata" kindName: "example thing parent" + , + typeName: "metadata" + kindName: "example thing data" ] valuetypes: @@ -28,6 +31,8 @@ typeName: "clobValue" , typeName: "fileValue" + , + typeName: "numericValue" ] valuekinds: @@ -46,6 +51,28 @@ , typeName: "fileValue" kindName: "structural file" + , + typeName: "stringValue" + kindName: "media component" + , + typeName: "numericValue" + kindName: "Volume" + , + typeName: "codeValue" + kindName: "performed by" + , + typeName: "dateValue" + kindName: "performed date" + ] + unittypes: + [ + typeName: "volume" + ] + + unitkinds: + [ + typeName: "volume" + kindName: "mL" ] labeltypes: @@ -61,14 +88,47 @@ ddicttypes: [ + typeName: "metadata" ] ddictkinds: [ + typeName: "metadata" + kindName: "category" + , + typeName: "metadata" + kindName: "color" ] codetables: [ + codeType: "metadata" + codeKind: "category" + codeOrigin: "ACAS DDICT" + code: "alpha" + name: "Alpha" + ignored: false + , + codeType: "metadata" + codeKind: "category" + codeOrigin: "ACAS DDICT" + code: "beta" + name: "Beta" + ignored: false + , + codeType: "metadata" + codeKind: "color" + codeOrigin: "ACAS DDICT" + code: "blue" + name: "Blue" + ignored: false + , + codeType: "metadata" + codeKind: "color" + codeOrigin: "ACAS DDICT" + code: "purple" + name: "Purple" + ignored: false ] labelsequences: @@ -80,7 +140,7 @@ labelTypeAndKind: "corpName_Example Thing" thingTypeAndKind: "parent_Example Thing" latestNumber:1 - , + , digits: 8 groupDigits: false labelPrefix: "THING" diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index cb470c25c..a71e17eb0 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -43,6 +43,22 @@ ExampleThingConf = fieldWrapper: "bv_scientist_date" placeholder: "yyyy-mm-dd" required: true + , + key: 'color' + modelDefaults: + stateType: 'metadata' + stateKind: 'example thing parent' + type: 'codeValue' + kind: 'color' + codeType: 'metadata' + codeKind: "color" + codeOrigin: 'ACAS DDict' + value: null + fieldSettings: + fieldType: 'codeValue' + required: false + formLabel: "Color" + fieldWrapper: "bv_scientist_date" , key: 'notebook' modelDefaults: @@ -60,7 +76,70 @@ ExampleThingConf = ] - stateTables: [] + stateTables: [ + key: 'exampleThingTable' + stateType: 'metadata' + stateKind: 'example thing data' + tableWrapper: "bv_dataTable" + tableLabel: "Example Thing Data Table" + values: [ + modelDefaults: + type: 'stringValue' + kind: 'media component' + value: "" + fieldSettings: + fieldType: 'stringValue' + formLabel: "Media Component" + required: true + width: 215 + , + modelDefaults: + type: 'numericValue' + kind: 'volume' + value: null + unitType: 'volume' + unitKind: 'mL' + fieldSettings: + fieldType: 'numericValue' + formLabel: "Volume" + required: false + , + modelDefaults: + type: 'codeValue' + kind: 'category' + codeType: 'metadata' + codeKind: "category" + codeOrigin: 'ACAS DDict' + value: null + fieldSettings: + fieldType: 'codeValue' + required: false + formLabel: "Category" + required: true + width:150 + , + modelDefaults: + type: 'codeValue' + kind: 'performed by' + value: "" + fieldSettings: + fieldType: 'stringValue' + formLabel: "Performed By" + required: true + width: 150 + , + modelDefaults: + type: 'dateValue' + kind: 'performed time' + value: null + codeOrigin: window.conf.scientistCodeOrigin + fieldSettings: + fieldType: 'dateValue' + formLabel: "Added date" + required: true + width: 150 + ] + ] firstLsThingItxs: [] secondLsThingItxs: [] @@ -262,7 +341,5 @@ class window.ExampleThingController extends AbstractThingFormController @disableAllInputs() -#TODO add state table example -#TODO add pick list/ddict example #TODO add thing interaction to project with field #TODO file upload is broken diff --git a/modules/ServerAPI/src/client/ExampleThing.html b/modules/ServerAPI/src/client/ExampleThing.html index d7583a4f4..90ebebdb0 100644 --- a/modules/ServerAPI/src/client/ExampleThing.html +++ b/modules/ServerAPI/src/client/ExampleThing.html @@ -12,6 +12,7 @@
      Thing Registration
      +
      From 950ec83d4bc79708cbaf3bb650f9f3916f8e3f98 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Thu, 22 Jun 2017 16:39:18 -0700 Subject: [PATCH 054/576] Added feature to disconnect from balance. Added feature to zero balance out. --- .../RealtimeDeviceConnectionController.coffee | 141 ++++++++++++++---- .../client/RealtimeDeviceConnectionView.html | 57 ++----- .../RealtimeDeviceConnectionSockets.coffee | 68 ++++++++- .../src/server/routes/loginRoutes.coffee | 21 +++ .../routes/InventoryServiceRoutes.coffee | 17 +++ 5 files changed, 226 insertions(+), 78 deletions(-) diff --git a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee index a73280b46..9d9261f02 100644 --- a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee +++ b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee @@ -1,21 +1,55 @@ class window.DeviceCollection extends PickListList -deviceStubs = [ - { - code: 'balanceIsIdle', - name: 'Balance Is Idle' - url: 'http://192.168.0.193:1337/' - }, { - code: 'balanceNotConnected', - name: 'Balance Not Connected' - url: 'http://192.168.0.193:1337/' - }, { - code: 'balanceNotAvailable', - name: 'Balance Not Available' - url: 'http://192.168.0.193:1337/' - } -] +class window.DeviceModel extends Container + urlRoot: "/api/containers" + initialize: -> + @.set + lsType: "instrument" + lsKind: "balance" + super() + + lsProperties: + defaultLabels: [ + key: 'common' + type: 'name' + kind: 'common' + preferred: true + , + key: 'corpName' + type: 'corpName' + kind: 'ACAS LsContainer' + preferred: false + ] + defaultValues: [ + key: 'description' + stateType: 'metadata' + stateKind: 'information' + type: 'stringValue' + kind: 'description' + , + key: 'url' + stateType: 'metadata' + stateKind: 'information' + type: 'stringValue' + kind: 'url' + , + key: 'createdUser' + stateType: 'metadata' + stateKind: 'information' + type: 'codeValue' + kind: 'created user' + , + key: 'person responsible' + stateType: 'metadata' + stateKind: 'information' + type: 'codeValue' + kind: 'person responsible' + ] + +class window.DeviceCollection extends Backbone.Collection + url: 'api/containers/instrument/balance' + model: DeviceModel class window.RealtimeDeviceConnectionController extends Backbone.View template: _.template($("#RealtimeDeviceConnectionView").html()) @@ -28,37 +62,85 @@ class window.RealtimeDeviceConnectionController extends Backbone.View "click .bv_deviceInUseDismiss": "dismissDeviceInUse" "change .bv_deviceSelectContainer": "handleDeviceSelectChange" "click .bv_dismissDisconnectMessage": "handleDismissDisconnectMessage" + "click .bv_zeroBalance": "handleZeroBalanceClick" initialize: -> @isConnectedToDevice = false @testMode = @options.testMode if @options.socket? @socket = @options.socket - @deviceCollection = new DeviceCollection(deviceStubs) + + @deviceCollection = new DeviceCollection() + @deviceCollection.comparator = (instrument) => + return instrument.get("lsLabels").pickBestName().get("labelText").toLowerCase() + + @listenTo @deviceCollection, "sync", @renderSelectListOfExistingInstruments @connected = false unless @testMode @setupSocketEventHandlers() + renderSelectListOfExistingInstruments: => + @$(".bv_loadingMessage").addClass "hide" + @$(".bv_formContainer").removeClass "hide" + deviceSelectList = '' + @$(".bv_deviceSelectContainer").empty() + @deviceCollection.sort() + _.each(@deviceCollection.models, (instrument) => + deviceSelectList += "" + ) + @$(".bv_deviceSelectContainer").append deviceSelectList + @$(".bv_loadingMessage").addClass "hide" + @$(".bv_formContainer").removeClass "hide" + + @handleDeviceSelectChange() setupSocketEventHandlers: => @socket = io('/deviceChannel') - @socket.on('connect', @handleDeviceSelectChange) + #@socket.on('connect', @handleDeviceSelectChange) @socket.on('connect_error', @handleConnectError) @socket.on('youShouldTryConnecting', @connectToDevice) @socket.on('disconnectedFromDevice', @disconnectedFromDevice) @socket.on('alertAllDisconnectedFromDevice', @alertAllDisconnectedFromDevice) @socket.on('disconnectedByAnotherUser', @disconnectedByAnotherUser) @socket.on('in_use', @displayUnavailableMessage) - + @socket.on('zeroingComplete', => + console.log "zeroingComplete" + if @connected + console.log "zeroingComplete" + @resetForm() + @enableElement(".bv_disconnect") + @enableElement(".bv_zeroBalance") + @$(".bv_zeroBalance").html "Zero Balance" + else + @displayInUseMessage() + ) + + + handleZeroBalanceClick: => + if @connected + @disableAllFields() + @disableElement(".bv_disconnect") + @disableElement(".bv_zeroBalance") + @$(".bv_zeroBalance").html "Zeroing..." + @socket.emit('zeroBalance', {deviceName: @selectedDevice.get('description').get('value'), deviceUrl: @selectedDevice.get('url').get('value'), userName: AppLaunchParams.loginUserName}, @zeroBalanceCallback) + + zeroBalanceCallback: (err, data) => connectToDevice: => unless @connected - @selectedDevice = @devicePickList.getSelectedModel() + #@selectedDevice = @devicePickList.getSelectedModel() + @selectedInstrumentCode = @$('.bv_deviceSelectContainer').val() + @selectedDevice = @deviceCollection.findWhere({"codeName": @selectedInstrumentCode}) + console.log "@selectedDevice.get('url').get('value')" + console.log @selectedDevice.get('url').get('value') @$(".bv_connecting").removeClass "hide" - @socket.emit('connectToDevice', {deviceName: @selectedDevice.get('code'), deviceUrl: @selectedDevice.get('url'), userName: AppLaunchParams.loginUserName}, @connectToDeviceCallback) + @$(".bv_deviceServerOffline").addClass "hide" + @socket.emit('connectToDevice', {deviceName: @selectedDevice.get('description').get('value'), deviceUrl: @selectedDevice.get('url').get('value'), userName: AppLaunchParams.loginUserName}, @connectToDeviceCallback) connectToDeviceCallback: (err, data) => + console.log "err", err + console.log "data", data if err @connected = false @setStateToDisconnected() @@ -77,7 +159,7 @@ class window.RealtimeDeviceConnectionController extends Backbone.View else @connected = true @setStateToConnected() - + @enableElement(".bv_deviceSelectContainer") @$(".bv_connectionStatusAlert").addClass "hide" displayUnavailableMessage: => @@ -96,6 +178,8 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @$(".bv_deviceServerInUse").addClass "hide" @$(".bv_deviceServerOffline").addClass "hide" @$(".bv_deviceServerInUseButIdle").addClass "hide" + @$(".bv_disconnect").addClass "hide" + @$(".bv_zeroBalance").addClass "hide" @handleDismissDisconnectMessage() displayInUseMessage: => @@ -104,8 +188,13 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @$(".bv_deviceUsedBy").html @userNameOfConnectedUser handleDeviceSelectChange: => - deviceName = @devicePickList.getSelectedCode() - unless deviceName is "" + @disableElement(".bv_deviceSelectContainer") + @selectedInstrumentCode = @$('.bv_deviceSelectContainer').val() + selectedInstrument = @deviceCollection.findWhere({"codeName": @selectedInstrumentCode}) + @connected = false + @resetStatusMessages() + @socket.emit('disconnected') + unless selectedInstrument is "" @connectToDevice() handleBootCurrentUserOffDevice: => @@ -151,12 +240,15 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @isConnectedToDevice = false @$(".bv_connecting").addClass "hide" @$(".bv_connected").addClass "hide" + @$(".bv_zeroBalance").addClass "hide" @$(".bv_disconnected").removeClass "hide" setStateToConnected: => @enableDisconnectButton() @isConnectedToDevice = true @displayStatusMessage ".bv_connected" + @$(".bv_zeroBalance").removeClass "hide" + @$(".bv_disconnect").removeClass "hide" disconnectedFromDevice: => @setStateToDisconnected() @@ -182,8 +274,7 @@ class window.RealtimeDeviceConnectionController extends Backbone.View render: => $(@el).empty() $(@el).html @template() - - @devicePickList = new PickListSelectController({collection: @deviceCollection, autoFetch: false, el: @$(".bv_deviceSelectContainer")}) + @deviceCollection.fetch() @renderSubform() @ diff --git a/modules/Components/src/client/RealtimeDeviceConnectionView.html b/modules/Components/src/client/RealtimeDeviceConnectionView.html index 1cb34f85d..6977f5908 100644 --- a/modules/Components/src/client/RealtimeDeviceConnectionView.html +++ b/modules/Components/src/client/RealtimeDeviceConnectionView.html @@ -5,7 +5,7 @@

      Tare Single Vial

      -
      +
    @@ -41,56 +42,16 @@

    Tare Single Vial

    -
    -
    -

    Error

    -
    -
    - Vial is already expired: -
    -
    - OK +
    +
    + Loading .... +
    +
    +
    -
    -
    -

    Error

    -
    -
    - Vial is already registered with contents: -
    -
    - OK -
    -
    -
    -
    -

    Warning

    -
    -
    - Vial has already been tared: -
    - Retare? -
    -
    - OK - Cancel -
    -
    - -
    -
    -

    Error

    -
    -
    - Vial does not have numeric weight value: -
    -
    - OK -
    -
    diff --git a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee index c18e0efb7..fbf89d675 100644 --- a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee +++ b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee @@ -26,7 +26,10 @@ class BalanceAccess method: 'GET' url: balanceStatusURL json: true + timeout: 2000 , (error, response, json) => +# console.log "error", error +# console.log "json", json if error? reject error else @@ -54,6 +57,22 @@ class BalanceAccess clearInterval(@heartBeat) @heartBeat = null + disconnectFromBalance: => + disconnectFromBalanceURL = @balanceUrl + "api/disconnectFromBalance" + return new Promise((resolve, reject) => + request( + method: 'POST' + url: disconnectFromBalanceURL + json: true + body: {'callbackURL': global.app.get('port') + '/api/tareSingleVia/disconnectFromBalanceComplete'} + , (error, response, json) -> + if error? + reject error + else + resolve json.message + ) + ) + removeUserFromQueue: (clientId) => if @currentConnectedUser.clientId is clientId @disconnectCurrentUser() @@ -81,6 +100,8 @@ class BalanceAccess @balanceConnectQueue.push {clientId: clientId, userName: userName, socket: socket} return new Promise((resolve, reject) => @getBalanceStatus().then((balanceStatus) => + console.log "balanceStatus" + console.log balanceStatus @status = balanceStatus @startHeartBeat() switch @status @@ -101,6 +122,8 @@ class BalanceAccess when "in_use" reject {status: "in_use"} ).catch((err) => + console.log "err" + console.log err reject {status: "device_server_offline"} ) ) @@ -130,6 +153,20 @@ class BalanceAccess @balanceConnectQueue.shift() @currentConnectedUser = null + zeroBalance: => + zeroBalanceURL = @balanceUrl + "api/zeroBalance" + console.log "zeroBalanceURL", zeroBalanceURL + return new Promise((resolve, reject) => + request( + method: 'POST' + url: zeroBalanceURL + json: true + body: {'callbackURL': global.app.get('port') + '/api/tareSingleVial/zeroBalanceComplete'} + , (error, response, json) -> + resolve json + ) + ) + class DeviceSocketController constructor: (io, nameSpace) -> @@ -157,20 +194,25 @@ class DeviceSocketController socket.on('disconnectAllUsers', (callback) => @handleDisconnectAllUsers(socket, callback) ) + socket.on('zeroBalance', (payload) => + @handleZeroBalance(socket, payload) + ) ) handleConnectToDevice: (socket, payload, callback) -> - unless @balances[payload.deviceName] - @balances[payload.deviceName] = new BalanceAccess(payload.deviceName, payload.deviceUrl, @nameSpacedRoom) - socket.join(payload.deviceName) - @usersInRoom[socket.id] = payload.deviceName - balanceAccess = @balances[payload.deviceName] + unless @balances[payload.deviceUrl] + @balances[payload.deviceUrl] = new BalanceAccess(payload.deviceName, payload.deviceUrl, @nameSpacedRoom) + socket.join(payload.deviceUrl) + @usersInRoom[socket.id] = payload.deviceUrl + balanceAccess = @balances[payload.deviceUrl] balanceAccessPromise = balanceAccess.connectClient(socket.id, payload.userName, socket) balanceAccessPromise.then(() => + console.log "balanceAccessPromise.then" @currentlyConnectedSocket = socket return callback(null, 'Connected to device') ) balanceAccessPromise.catch((err) => + console.log "balanceAccessPromise.catch err" if err.status is "not_available" return callback({status: "not_available", userName: err.connectedUser.userName, clientId: err.connectedUser.clientId}, null) else @@ -192,6 +234,7 @@ class DeviceSocketController else socket.broadcast.emit('alertAllDisconnectedFromDevice') balanceAccess.clearHeartBeat() + balanceAccess.disconnectFromBalance() socket.leave(@usersInRoom[socket.id]) socket.emit('disconnectedFromDevice') @@ -221,5 +264,20 @@ class DeviceSocketController socket.broadcast.emit('alertAllDisconnectedFromDevice') callback() + broadCastToAllUsers: (eventName) -> + @nameSpacedRoom.emit(eventName) + + handleZeroBalance: (socket) -> + console.log "handleZeroBalance" + balanceAccess = @balances[@usersInRoom[socket.id]] + balanceAccessPromise = balanceAccess.zeroBalance() + balanceAccessPromise.then(() => + console.log "balanceAccessPromise.then" + ) + balanceAccessPromise.catch((err) => + console.log "balanceAccessPromise.catch err" + ) + socket.broadcast.emit('in_use') + exports.DeviceSocketController = DeviceSocketController diff --git a/modules/Login/src/server/routes/loginRoutes.coffee b/modules/Login/src/server/routes/loginRoutes.coffee index ed8970603..c43f6b97c 100644 --- a/modules/Login/src/server/routes/loginRoutes.coffee +++ b/modules/Login/src/server/routes/loginRoutes.coffee @@ -79,6 +79,8 @@ exports.logout = (req, res) -> exports.ensureAuthenticated = (req, res, next) -> console.log "checking for login for path: "+req.url + console.log "req" + console.log req if req.isAuthenticated() return next() if req.session? @@ -120,6 +122,25 @@ exports.authenticationService = (req, resp) -> else csUtilities.authCheck req.body.user, req.body.password, callback +exports.ensureAuthenticatedService = (req, resp, next) -> + callback = (results) -> + console.log results + if results.indexOf("Success")>=0 + console.log "in authentication service success" + next() + else + console.log "in authentication service fail" + resp.json + status: "Fail" + + console.log "ensureAuthenticatedService -- req.body" + console.log req.body + + if global.specRunnerTestmode + callback("Success") + else + csUtilities.authCheck req.body.user, req.body.password, callback + exports.resetAuthenticationService = (req, resp) -> callback = (results) -> console.log results diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 67482e5b5..167e394e1 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -849,6 +849,23 @@ exports.containerByCodeName = (req, resp) -> baseurl = config.all.client.service.persistence.fullpath+"containers/"+req.params.code serverUtilityFunctions.getFromACASServer(baseurl, resp) +exports.containerByCodeNameInteral = (containerCodeName, callback) -> + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containers/" + containerCodeName + request = require 'request' + request( + method: 'GET' + url: baseurl + json: true + , (error, response, json) => + if !error && response.statusCode == 200 + callback response.statusCode, json + else + console.log 'got ajax error' + console.log error + console.log json + callback 500, {error: true, message:error} + ) updateContainer = (container, testMode, callback) -> if testMode or global.specRunnerTestmode From fa86a11ef4d3aa166e9537e722fd148fe6c39aa8 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Fri, 23 Jun 2017 11:40:14 -0700 Subject: [PATCH 055/576] Fixed bugs in Zero Balance and Disconnect Balance features --- .../server/routes/RealtimeDeviceConnectionSockets.coffee | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee index fbf89d675..5a33a90a9 100644 --- a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee +++ b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee @@ -61,10 +61,8 @@ class BalanceAccess disconnectFromBalanceURL = @balanceUrl + "api/disconnectFromBalance" return new Promise((resolve, reject) => request( - method: 'POST' + method: 'GET' url: disconnectFromBalanceURL - json: true - body: {'callbackURL': global.app.get('port') + '/api/tareSingleVia/disconnectFromBalanceComplete'} , (error, response, json) -> if error? reject error @@ -100,8 +98,6 @@ class BalanceAccess @balanceConnectQueue.push {clientId: clientId, userName: userName, socket: socket} return new Promise((resolve, reject) => @getBalanceStatus().then((balanceStatus) => - console.log "balanceStatus" - console.log balanceStatus @status = balanceStatus @startHeartBeat() switch @status @@ -248,6 +244,7 @@ class DeviceSocketController else socket.broadcast.emit('alertAllDisconnectedFromDevice') balanceAccess.clearHeartBeat() + balanceAccess.disconnectFromBalance() handleBootUser: (socket, payload, callback) -> balanceAccess = @balances[@usersInRoom[socket.id]] @@ -268,7 +265,6 @@ class DeviceSocketController @nameSpacedRoom.emit(eventName) handleZeroBalance: (socket) -> - console.log "handleZeroBalance" balanceAccess = @balances[@usersInRoom[socket.id]] balanceAccessPromise = balanceAccess.zeroBalance() balanceAccessPromise.then(() => From 2cd2c723b9763180f9024fbff296c31312e7d506 Mon Sep 17 00:00:00 2001 From: jmcneil86043 Date: Fri, 23 Jun 2017 16:53:12 -0700 Subject: [PATCH 056/576] Update ACASFormFields.coffee --- modules/Components/src/client/ACASFormFields.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index bb0a0e0ec..de724b2a4 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -357,7 +357,7 @@ class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractF else opts.thingType = @thingType opts.thingKind = @thingKind - @thingSelectController = new ThingLabelComboBoxController opt + @thingSelectController = new ThingLabelComboBoxController opts @thingSelectController.render() render: => From 25228403607b7940d30ab802995361a621703f73 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Sat, 24 Jun 2017 17:13:55 -0700 Subject: [PATCH 057/576] stateDisplayTable in progress, probably to be abandoned --- .../client/ACASFormStateDisplayUpdate.coffee | 67 +++++++++++++++++++ .../src/client/ACASFormStateDisplayView.html | 28 ++++++++ .../src/client/ACASFormStateTable.coffee | 5 ++ .../src/client/AbstractFormController.coffee | 16 +++++ .../ServerAPI/src/client/ExampleThing.coffee | 64 ++++++++++++++++++ .../ServerAPI/src/client/ExampleThing.html | 1 + 6 files changed, 181 insertions(+) create mode 100644 modules/Components/src/client/ACASFormStateDisplayUpdate.coffee create mode 100644 modules/Components/src/client/ACASFormStateDisplayView.html diff --git a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee new file mode 100644 index 000000000..dcc3b245a --- /dev/null +++ b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee @@ -0,0 +1,67 @@ +class window.ACASFormStateDisplayUpdateRowController extends Backbone.View + tagName: 'tr' + + render: => + @collection.each (val) => + value = val.get(val.get('lsType')) + $(@el).append "#{value}" + console.log @el + + @ + + + +class window.ACASFormStateDisplayUpdateController extends Backbone.View + + template: _.template($("#ACASFormStateDisplayUpdateView").html()) + + initialize: -> + @thingRef = @options.thingRef + @tableDef = @options.tableDef + @tableSetupComplete = false + @callWhenSetupComplete = null + + render: => + $(@el).empty() + $(@el).html @template() + @applyOptions() + @tableSetupComplete = true + + @ + + renderModelContent: => + if @tableSetupComplete + @completeRenderModelContent() + else + @callWhenSetupComplete = @completeRenderModelContent + + completeRenderModelContent: -> + for state in @getCurrentStates() + rowController = new ACASFormStateDisplayUpdateRowController + collection: state.get 'lsValues' + @$("tbody").append rowController.render().el + console.log @$("tbody") + + applyOptions: -> + if @tableDef?.tableLabel? + @setTableLabel @tableDef.tableLabel + if @tableDef?.tableLabelClass? + @addFormLabelClass @options.tableDef.tableLabelClass + + setTableLabel: (value) -> + @$('.bv_tableLabel').html value + + addTableLabelClass: (value) -> + @$('.bv_tableLabel').addClass value + + removeTableLabelClass: (value) -> + @$('.bv_tableLabel').removeClass value + + getCurrentStates: -> + @thingRef.get('lsStates').getStatesByTypeAndKind @tableDef.stateType, @tableDef.stateKind + +#TODO Build header row +#TODO value editor +#TODO show/hide edited states +#TODO option to set order of values +#TODO implement enable/disable editing \ No newline at end of file diff --git a/modules/Components/src/client/ACASFormStateDisplayView.html b/modules/Components/src/client/ACASFormStateDisplayView.html new file mode 100644 index 000000000..3bc766125 --- /dev/null +++ b/modules/Components/src/client/ACASFormStateDisplayView.html @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 61e413f02..42d51b0f2 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -213,6 +213,7 @@ class window.ACASFormStateTableController extends Backbone.View for valDef in @tableDef.values cellInfo = [] value = state.getOrCreateValueByTypeAndKind valDef.modelDefaults.type, valDef.modelDefaults.kind + #TODO look for ignored values of the same type and kind. Add styling if this was edited if valDef.modelDefaults.type == 'codeValue' if valDef.fieldSettings.fieldType == 'stringValue' displayVal = value.get 'codeValue' @@ -247,6 +248,10 @@ class window.ACASFormStateTableController extends Backbone.View return null handleCellChanged: (changes, source) => + #TODO if audit mode call configured function after change +# that function shoiuld popup a panel to capture a reason, then update the thing +# there should be a cancel option, and this function will have to have undo if cancel pushed +# so I'll have to save the old value ( I have oldValue in a vairable) if changes? for change in changes unless change[2] == change[3] or source == "autofill" diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 9ac9eaa70..dc12665eb 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -124,12 +124,15 @@ class window.AbstractThingFormController extends AbstractFormController newField.afterRender() @formFields[field.key] = newField @setupFormTables fieldDefs.stateTables + @setupFormStateDisplayTables fieldDefs.stateDisplayTables fillFieldsFromModels: => for modelKey, formField of @formFields formField.renderModelContent() for stateKey, formTable of @formTables formTable.renderModelContent() + for stateKey, formDisplayTable of @formDisplayTables + formDisplayTable.renderModelContent() setupFormTables: (tableDefs) -> unless @formTables? @@ -144,6 +147,19 @@ class window.AbstractThingFormController extends AbstractFormController fTable.render() @formTables[tDef.key] = fTable + setupFormStateDisplayTables: (tableDefs) -> + unless @formDisplayTables? + @formDisplayTables = {} + for tDef in tableDefs + tdiv = $("
    ") + @$("."+tDef.tableWrapper).append tdiv + fTable = new ACASFormStateDisplayUpdateController + el: tdiv + tableDef: tDef + thingRef: @model + fTable.render() + @formDisplayTables[tDef.key] = fTable + disableAllInputs: -> super() for key, tbl of @formTables diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index a71e17eb0..c35120fd1 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -140,6 +140,70 @@ ExampleThingConf = width: 150 ] ] + stateDisplayTables: [ + key: 'exampleStateDisplay' + stateType: 'metadata' + stateKind: 'example thing data' + tableWrapper: "bv_stateDisplayTable" + tableLabel: "Example Thing State Display Table" + values: [ + modelDefaults: + type: 'stringValue' + kind: 'media component' + value: "" + fieldSettings: + fieldType: 'stringValue' + formLabel: "Media Component" + required: true + width: 215 + , + modelDefaults: + type: 'numericValue' + kind: 'volume' + value: null + unitType: 'volume' + unitKind: 'mL' + fieldSettings: + fieldType: 'numericValue' + formLabel: "Volume" + required: false + , + modelDefaults: + type: 'codeValue' + kind: 'category' + codeType: 'metadata' + codeKind: "category" + codeOrigin: 'ACAS DDict' + value: null + fieldSettings: + fieldType: 'codeValue' + required: false + formLabel: "Category" + required: true + width:150 + , + modelDefaults: + type: 'codeValue' + kind: 'performed by' + value: "" + fieldSettings: + fieldType: 'stringValue' + formLabel: "Performed By" + required: true + width: 150 + , + modelDefaults: + type: 'dateValue' + kind: 'performed time' + value: null + codeOrigin: window.conf.scientistCodeOrigin + fieldSettings: + fieldType: 'dateValue' + formLabel: "Added date" + required: true + width: 150 + ] + ] firstLsThingItxs: [] secondLsThingItxs: [] diff --git a/modules/ServerAPI/src/client/ExampleThing.html b/modules/ServerAPI/src/client/ExampleThing.html index 90ebebdb0..8ab808588 100644 --- a/modules/ServerAPI/src/client/ExampleThing.html +++ b/modules/ServerAPI/src/client/ExampleThing.html @@ -13,6 +13,7 @@
    Thing Registration
    +
    From dbea50e613a9da9ba6b8277b988406adbd98e9c3 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Sun, 25 Jun 2017 14:42:52 -0700 Subject: [PATCH 058/576] back to state display/audit table idea - starting to work --- .../client/ACASFormStateDisplayUpdate.coffee | 156 ++++++++++++-- .../src/client/ACASFormStateDisplayView.html | 45 ++-- .../src/client/AbstractFormController.coffee | 6 +- modules/Components/src/client/style.css | 4 + .../ServerAPI/src/client/ExampleThing.coffee | 193 ++++++++++++------ .../ServerAPI/src/client/ExampleThing.html | 20 +- modules/ServerAPI/src/client/Label.coffee | 3 + 7 files changed, 327 insertions(+), 100 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee index dcc3b245a..7cba51ea6 100644 --- a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee +++ b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee @@ -1,18 +1,61 @@ -class window.ACASFormStateDisplayUpdateRowController extends Backbone.View +# This component displays states with the same value kinds in a table based on the supplied configuration +# Clickin a cell shows the value (editing) history of that cell +# This can be configured to allow editing of individual values +# This ignores ignored states, and neither shows them, nor allows them to be edited + + +class window.ACASFormStateDisplayUpdateHeaderRowController extends Backbone.View tagName: 'tr' render: => - @collection.each (val) => - value = val.get(val.get('lsType')) - $(@el).append "#{value}" - console.log @el + for val in @options.tableDef.values + displayName = val.fieldSettings.formLabel + if @options.showUnits + if val.modelDefaults.unitKind? + displayName += "
    (#{val.modelDefaults.unitKind})" + $(@el).append "#{displayName}" @ +class window.ACASFormStateDisplayUpdateCellController extends Backbone.View + tagName: 'td' + events: -> + "click": "handleCellClicked" -class window.ACASFormStateDisplayUpdateController extends Backbone.View + render: => + $(@el).empty() + if @collection.length == 0 + content = "NA" + else + val = @collection.findWhere ignored: false + content = val.get(val.get('lsType')) + $(@el).html content + $(@el).addClass if @collection.length > 1 then "valueWasEdited" else "" + + + @ + + handleCellClicked: => + @trigger 'cellClicked', @collection +class window.ACASFormStateDisplayUpdateRowController extends Backbone.View + tagName: 'tr' + + render: => + for valDef in @options.tableDef.values + vals = @collection.where lsKind: valDef.modelDefaults.kind + cellController = new ACASFormStateDisplayUpdateCellController + collection: new ValueList vals + cellDef: valDef + $(@el).append cellController.render().el + cellController.on 'cellClicked', (values) => + @trigger 'cellClicked', values + + @ + +class window.ACASFormStateDisplayUpdateController extends Backbone.View + rowNumberKind: 'row number' template: _.template($("#ACASFormStateDisplayUpdateView").html()) initialize: -> @@ -36,17 +79,30 @@ class window.ACASFormStateDisplayUpdateController extends Backbone.View @callWhenSetupComplete = @completeRenderModelContent completeRenderModelContent: -> - for state in @getCurrentStates() + @headerController = new ACASFormStateDisplayUpdateHeaderRowController + tableDef: @options.tableDef + showUnits: @options.showUnits + @$("thead").append @headerController.render().el + + @getCurrentStates().each (state) => rowController = new ACASFormStateDisplayUpdateRowController collection: state.get 'lsValues' + tableDef: @options.tableDef @$("tbody").append rowController.render().el - console.log @$("tbody") + + rowController.on 'cellClicked', (values) => + @currentCellEditor = new ACASFormStateDisplayValueEditController + collection: values + el: @$('.bv_valueEditor') + @currentCellEditor.render() applyOptions: -> if @tableDef?.tableLabel? @setTableLabel @tableDef.tableLabel if @tableDef?.tableLabelClass? @addFormLabelClass @options.tableDef.tableLabelClass + if @tableDef?.sortKind? + @sortKind = @tableDef?.sortKind setTableLabel: (value) -> @$('.bv_tableLabel').html value @@ -58,10 +114,82 @@ class window.ACASFormStateDisplayUpdateController extends Backbone.View @$('.bv_tableLabel').removeClass value getCurrentStates: -> - @thingRef.get('lsStates').getStatesByTypeAndKind @tableDef.stateType, @tableDef.stateKind + states = new StateList(@thingRef.get('lsStates').getStatesByTypeAndKind(@tableDef.stateType, @tableDef.stateKind)) + + sortKindCount = 0 + rowKindCount = 0 + states.each (state) => + if @sortKind? + if state.getFirstValueOfKind(@sortKind)? then sortKindCount++ + if state.getFirstValueOfKind(@rowNumberKind)? then rowKindCount++ + + if sortKindCount == states.length then kindToSort = @sortKind + else if rowKindCount == states.length then kindToSort = @rowNumberKind + else kindToSort = 'id' + + states.comparator = (state) => + if kindToSort == 'id' + return state.id + else + val = state.getFirstValueOfKind(kindToSort) + return val.get (val.get('lsType')) + states.sort() + return states + +class window.ACASFormStateDisplayOldValueController extends Backbone.View + tagName: 'tr' + template: _.template($("#ACASFormStateDisplayOldValueView").html()) + + render: => + attrs = + value: @model.get(@model.get('lsType')) + attrs.valueClass = if @model.get 'ignored' then "valueWasEdited" else "" + + if @model.has('modifiedBy') && @model.get('modifiedBy')!="" + attrs.changedBy = @model.get('modifiedBy') + else + attrs.changedBy = @model.get('recordedBy') + + if @model.has('modifiedDate') && !isNaN(@model.get('modifiedBy')) + attrs.changedDate = UtilityFunctions::convertMSToYMDDate @model.get('modifiedDate') + else + attrs.changedDate = UtilityFunctions::convertMSToYMDDate @model.get('recordedDate') + + if @model.get 'ignored' + attrs.reason = "not implemented" + else + attrs.reason = "current value" + + $(@el).empty() + $(@el).html @template(attrs) + + @ + +class window.ACASFormStateDisplayValueEditController extends Backbone.View + + template: _.template($("#ACASFormStateDisplayValueEditView").html()) + + initialize: -> + + render: => + $(@el).empty() + $(@el).html @template() + + @collection.comparator = 'id' + @collection.sort() + @collection.each (val) => + oldRow = new ACASFormStateDisplayOldValueController + model: val + @$("tbody").append oldRow.render().el + + @ + +#TODO value editor: +# - new node service to fetch transaction to display change reason +# http://localhost:8080/acas/lstransactions/42 +# - maybe show transaction creator as modified by and date? +# - style value editor so it floats or slides down from top of table or something. It should be modal +# - trigger save at thing level, wait for success to close +# - pass reason to thing to add to transaction +# - add new value where none existed? -#TODO Build header row -#TODO value editor -#TODO show/hide edited states -#TODO option to set order of values -#TODO implement enable/disable editing \ No newline at end of file diff --git a/modules/Components/src/client/ACASFormStateDisplayView.html b/modules/Components/src/client/ACASFormStateDisplayView.html index 3bc766125..bb5358c44 100644 --- a/modules/Components/src/client/ACASFormStateDisplayView.html +++ b/modules/Components/src/client/ACASFormStateDisplayView.html @@ -1,28 +1,39 @@ - - - - - - - - - - - - - - + + + + diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index dc12665eb..66eb51180 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -123,8 +123,10 @@ class window.AbstractThingFormController extends AbstractFormController @$("."+field.fieldSettings.fieldWrapper).append newField.render().el newField.afterRender() @formFields[field.key] = newField - @setupFormTables fieldDefs.stateTables - @setupFormStateDisplayTables fieldDefs.stateDisplayTables + if fieldDefs.stateTables? + @setupFormTables fieldDefs.stateTables + if fieldDefs.stateDisplayTables? + @setupFormStateDisplayTables fieldDefs.stateDisplayTables fillFieldsFromModels: => for modelKey, formField of @formFields diff --git a/modules/Components/src/client/style.css b/modules/Components/src/client/style.css index 0ed2905fa..3429cf280 100644 --- a/modules/Components/src/client/style.css +++ b/modules/Components/src/client/style.css @@ -41,3 +41,7 @@ border-color: #bbbbbb; /* base width matches edit prot and expt */ } + +.bv_stateDisplayUpdateTable .valueWasEdited { + color: red; +} \ No newline at end of file diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index c35120fd1..ac2df8f44 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -140,70 +140,6 @@ ExampleThingConf = width: 150 ] ] - stateDisplayTables: [ - key: 'exampleStateDisplay' - stateType: 'metadata' - stateKind: 'example thing data' - tableWrapper: "bv_stateDisplayTable" - tableLabel: "Example Thing State Display Table" - values: [ - modelDefaults: - type: 'stringValue' - kind: 'media component' - value: "" - fieldSettings: - fieldType: 'stringValue' - formLabel: "Media Component" - required: true - width: 215 - , - modelDefaults: - type: 'numericValue' - kind: 'volume' - value: null - unitType: 'volume' - unitKind: 'mL' - fieldSettings: - fieldType: 'numericValue' - formLabel: "Volume" - required: false - , - modelDefaults: - type: 'codeValue' - kind: 'category' - codeType: 'metadata' - codeKind: "category" - codeOrigin: 'ACAS DDict' - value: null - fieldSettings: - fieldType: 'codeValue' - required: false - formLabel: "Category" - required: true - width:150 - , - modelDefaults: - type: 'codeValue' - kind: 'performed by' - value: "" - fieldSettings: - fieldType: 'stringValue' - formLabel: "Performed By" - required: true - width: 150 - , - modelDefaults: - type: 'dateValue' - kind: 'performed time' - value: null - codeOrigin: window.conf.scientistCodeOrigin - fieldSettings: - fieldType: 'dateValue' - formLabel: "Added date" - required: true - width: 150 - ] - ] firstLsThingItxs: [] secondLsThingItxs: [] @@ -333,6 +269,11 @@ class window.ExampleThingController extends AbstractThingFormController @trigger 'thingSaved' @renderModelContent() + @auditTableController = new ExampleTableAuditController + el: @$('.bv_exampleTableAudit') + thingCode: @model.get 'codeName' + @auditTableController.render() + modelChangeCallback: (method, model) => @trigger 'amDirty' @$('.bv_saveThingComplete').hide() @@ -379,7 +320,6 @@ class window.ExampleThingController extends AbstractThingFormController updateModel: => - validationError: => super() @$('.bv_saveThing').attr('disabled', 'disabled') @@ -407,3 +347,126 @@ class window.ExampleThingController extends AbstractThingFormController #TODO add thing interaction to project with field #TODO file upload is broken + + +ExampleTableAuditConf = + formFieldDefinitions: + stateTables: [] + stateDisplayTables: [ + key: 'exampleThingTable' + stateType: 'metadata' + stateKind: 'example thing data' + tableWrapper: "bv_dataTable" + tableLabel: "Example Thing Data Table - Audit Mode" + auditMode: true +# sortKind: 'media component' + values: [ + modelDefaults: + type: 'stringValue' + kind: 'media component' + value: "" + fieldSettings: + fieldType: 'stringValue' + formLabel: "Media Component" + required: true + width: 215 + , + modelDefaults: + type: 'numericValue' + kind: 'volume' + value: null + unitType: 'volume' + unitKind: 'mL' + fieldSettings: + fieldType: 'numericValue' + formLabel: "Volume" + required: false + , + modelDefaults: + type: 'codeValue' + kind: 'category' + codeType: 'metadata' + codeKind: "category" + codeOrigin: 'ACAS DDict' + value: null + fieldSettings: + fieldType: 'codeValue' + required: false + formLabel: "Category" + required: true + width:150 + , + modelDefaults: + type: 'codeValue' + kind: 'performed by' + value: "" + fieldSettings: + fieldType: 'stringValue' + formLabel: "Performed By" + required: true + width: 150 + , + modelDefaults: + type: 'dateValue' + kind: 'performed time' + value: null + codeOrigin: window.conf.scientistCodeOrigin + fieldSettings: + fieldType: 'dateValue' + formLabel: "Added date" + required: true + width: 150 + ] + ] + firstLsThingItxs: [] + secondLsThingItxs: [] + + +class window.ExampleTableAuditController extends AbstractThingFormController + template: _.template($("#ExampleTableAuditView").html()) + + events: -> + + initialize: => + @hasRendered = false + @model = new ExampleThingParent codeName: @options.thingCode + @model.fetch() + + @errorOwnerName = 'ExampleTableAuditController' + @setBindings() + @listenTo @model, 'sync', @modelSaveCallback + + render: => + unless @hasRendered + $(@el).empty() + $(@el).html @template() + @setupFormFields(ExampleTableAuditConf.formFieldDefinitions) + @hasRendered = true + + @ + + renderModelContent: -> + codeName = @model.get('codeName') + @$('.bv_thingCode').html(codeName) + + modelSaveCallback: (method, model) => + console.log "got model save callback" + if @model.isNew() # model not found + @model.set codeName: null + return + + @fillFieldsFromModels() + @trigger 'amClean' + @trigger 'thingSaved' + @renderModelContent() + + modelChangeCallback: (method, model) => + @trigger 'amDirty' + + + updateModel: => + + handleUpdateThing: => + @model.prepareToSave() + @model.reformatBeforeSaving() + @model.save() diff --git a/modules/ServerAPI/src/client/ExampleThing.html b/modules/ServerAPI/src/client/ExampleThing.html index 8ab808588..08662d0bd 100644 --- a/modules/ServerAPI/src/client/ExampleThing.html +++ b/modules/ServerAPI/src/client/ExampleThing.html @@ -1,6 +1,5 @@ + + diff --git a/modules/ServerAPI/src/client/Label.coffee b/modules/ServerAPI/src/client/Label.coffee index 3be20c1e0..81890ed63 100644 --- a/modules/ServerAPI/src/client/Label.coffee +++ b/modules/ServerAPI/src/client/Label.coffee @@ -227,6 +227,9 @@ class window.State extends Backbone.Model @get('lsValues').filter (value) -> (value.get('lsType')==type) and (value.get('lsKind')==kind) + getFirstValueOfKind: (kind) -> + @get('lsValues').findWhere lsKind: kind + getOrCreateValueByTypeAndKind: (vType, vKind) -> descVals = @getValuesByTypeAndKind vType, vKind descVal = descVals[0] #TODO should do something smart if there are more than one From b2ed71b604f396e901286478b93ada7c3262a85c Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Mon, 26 Jun 2017 11:12:57 -0700 Subject: [PATCH 059/576] Merged 1.10-release-oss into RC/1.12.0. Changes include: adding config for dataViewerDeepLink, picklist select and select2 changes, new inventory service routes, inventory service route to get location history, and select2 css files --- conf/config.properties.example | 1 + .../BasicFileValidateReviewAndSave.coffee | 1 + modules/Components/src/client/PickList.coffee | 45 +- .../src/client/ModuleLauncher.coffee | 6 +- .../routes/InventoryServiceRoutes.coffee | 366 +++++++++-- .../routes/ServerUtilityFunctions.coffee | 21 + .../dist/select2-bootstrap.css | 610 ++++++++++++++++++ .../dist/select2-bootstrap.min.css | 1 + 8 files changed, 975 insertions(+), 76 deletions(-) create mode 100755 public/lib/select2-bootstrap-theme-0.1.0-beta.8/dist/select2-bootstrap.css create mode 100755 public/lib/select2-bootstrap-theme-0.1.0-beta.8/dist/select2-bootstrap.min.css diff --git a/conf/config.properties.example b/conf/config.properties.example index ab39e2f19..95851ae25 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -331,6 +331,7 @@ client.moduleMenus.summaryStats=false # For navigation to external ACAS modules from ACAS homepage client.moduleMenus.modules.external=[{"displayName": "Compound Registration", "href": "/cmpdreg/"},\ {"displayName": "Compound Registration Bulk Loader", "href":"/CmpdRegBulkLoader"}] +client.moduleMenus.dataViewerDeepLink=/dataViewer # For auto-starting a module when opening up ACAS client.moduleMenus.moduleAutoLaunchName= diff --git a/modules/Components/src/client/BasicFileValidateReviewAndSave.coffee b/modules/Components/src/client/BasicFileValidateReviewAndSave.coffee index 0dbd9a1b5..d4a8f366b 100644 --- a/modules/Components/src/client/BasicFileValidateReviewAndSave.coffee +++ b/modules/Components/src/client/BasicFileValidateReviewAndSave.coffee @@ -1,6 +1,7 @@ class window.BasicFileValidateReviewAndSaveController extends BasicFileValidateAndSaveController template: _.template($("#BasicFileValidateReviewAndSaveView").html()) + initialize: -> console.log "BasicFileValidateReviewAndSaveController" super() diff --git a/modules/Components/src/client/PickList.coffee b/modules/Components/src/client/PickList.coffee index 2375dd806..7f703497b 100644 --- a/modules/Components/src/client/PickList.coffee +++ b/modules/Components/src/client/PickList.coffee @@ -90,10 +90,15 @@ class window.PickListOptionControllerForLsThing extends Backbone.View class window.PickListSelectController extends Backbone.View - initialize: -> + initialize: (options) -> @rendered = false @collection.bind "add", @addOne @collection.bind "reset", @handleListReset + # NOTE: Backbone 1.1.0 no longer automatically attaches options passed + # to View constructors as this.options. So, in order to be compatible + # with Backbone 1.0.0 and versions greater or equal to 1.1.0, we'll + # attach it ourselves here. + @options = options || {} unless @options.selectedCode is "" @selectedCode = @options.selectedCode @@ -244,25 +249,49 @@ class window.ComboBoxController extends PickListSelectController class window.PickListSelect2Controller extends PickListSelectController - initialize: => + # maps the 'code' property to the select2 required 'id' property and + # the 'name' property to the select2 required 'text' property + acasPropertyMap = + id: 'code' + text: 'name' + + # @param options.propertyMap String ('select2' or 'acas', where 'select2' + # does no mapping and 'acas' uses the 'acasPropertyMap' defined above) or + # an Object with 'id' and 'text' properties to use. If + # 'options.propertyMap' is not specified, it defaults to using the + # 'acasPropertyMap' + initialize: (options) -> if @options.width? @width = @options.width else @width = "100%" - - super() + @propertyMap = acasPropertyMap + if options.propertyMap? + if _.isObject(options.propertyMap) and options.propertyMap.id? and options.propertyMap.text? + @propertyMap = options.propertyMap + else if options.propertyMap is 'select2' + @propertyMap = null + else if options.propertyMap isnt 'acas' + throw new Error ('PickListSelect2Controller.initialize(): Invalid propertyMap value encountered') + super(options) render: => -# convert model objects to array of json objects which have 'id' and 'text' properties + # convert model objects to array of json objects which have 'id' and 'text' properties if propertyMap specified mappedData = [] for obj in @collection.toJSON() if (not obj.ignored? or (obj.ignored is false) or (@showIgnored? and @showIgnored is true)) - obj.id = obj.id || obj.code - obj.text = obj.text || obj.name + if @propertyMap? + obj.id = obj[@propertyMap.id] + obj.text = obj[@propertyMap.text] mappedData.push(obj) + # if a first option was inserted, use it for select's placeholder object + @placeholder = "" + if @insertFirstOption? + @placeholder = mappedData[0] + $(@el).select2 - placeholder: "" + placeholder: @placeholder data: mappedData openOnEnter: false allowClear: true diff --git a/modules/ModuleMenus/src/client/ModuleLauncher.coffee b/modules/ModuleMenus/src/client/ModuleLauncher.coffee index 563322f99..1afc0c3d6 100644 --- a/modules/ModuleMenus/src/client/ModuleLauncher.coffee +++ b/modules/ModuleMenus/src/client/ModuleLauncher.coffee @@ -13,7 +13,11 @@ class window.ModuleLauncher extends Backbone.Model if @get('externalLink')? window.open(@get('externalLink'),'_blank'); else if @get('autoLaunchName') is "dataViewer" - window.open("/dataViewer",'_blank'); + if window.conf.moduleMenus?.dataViewerDeepLink? + dataViewerDeepLink = window.conf.moduleMenus.dataViewerDeepLink + else + dataViewerDeepLink = '/dataViewer' + window.open(dataViewerDeepLink,'_blank'); else @trigger 'activationRequested', @ @set isActive: true diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index b94785c9a..67482e5b5 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -3,8 +3,11 @@ csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFuncti _ = require 'underscore' preferredEntityCodeService = require '../routes/PreferredEntityCodeService.js' config = require '../conf/compiled/conf.js' +RUN_CUSTOM_FLAG = "0" + exports.setupAPIRoutes = (app) -> + app.post '/api/getContainersInLocationWithTypeAndKind', exports.getContainersInLocationWithTypeAndKind app.post '/api/getContainersInLocation', exports.getContainersInLocation app.post '/api/getContainerCodesByLabels', exports.getContainerCodesByLabels app.post '/api/getContainersByLabels', exports.getContainersByLabels @@ -48,8 +51,10 @@ exports.setupAPIRoutes = (app) -> app.post '/api/createTube', exports.createTube app.post '/api/createTubes', exports.createTubes app.post '/api/throwInTrash', exports.throwInTrash + app.post '/api/updateContainerHistoryLogs', exports.updateContainerHistoryLogs exports.setupRoutes = (app, loginRoutes) -> + app.post '/api/getContainersInLocationWithTypeAndKind', loginRoutes.ensureAuthenticated, exports.getContainersInLocationWithTypeAndKind app.post '/api/getContainersInLocation', loginRoutes.ensureAuthenticated, exports.getContainersInLocation app.post '/api/getContainerCodesByLabels', loginRoutes.ensureAuthenticated, exports.getContainerCodesByLabels app.post '/api/getContainersByLabels', loginRoutes.ensureAuthenticated, exports.getContainersByLabels @@ -94,6 +99,8 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/createTube', loginRoutes.ensureAuthenticated, exports.createTube app.post '/api/createTubes', loginRoutes.ensureAuthenticated, exports.createTubes app.post '/api/throwInTrash', loginRoutes.ensureAuthenticated, exports.throwInTrash + app.post '/api/updateContainerHistoryLogs', loginRoutes.ensureAuthenticated, exports.updateContainerHistoryLogs + exports.getContainersInLocation = (req, resp) -> req.setTimeout 86400000 @@ -101,8 +108,14 @@ exports.getContainersInLocation = (req, resp) -> inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' resp.json inventoryServiceTestJSON.getContainersInLocationResponse else + queryParams = [] + if req.query.containerType? + queryParams.push "containerType="+req.query.containerType + if req.query.containerKind? + queryParams.push "containerKind="+req.query.containerKind + queryString = queryParams.join "&" config = require '../conf/compiled/conf.js' - baseurl = config.all.client.service.persistence.fullpath+"containers/getContainersInLocation" + baseurl = config.all.client.service.persistence.fullpath+"containers/getContainersInLocation?"+queryString request = require 'request' request( method: 'POST' @@ -121,6 +134,59 @@ exports.getContainersInLocation = (req, resp) -> resp.end JSON.stringify "getContainersInLocation failed" ) +exports.getContainersInLocationWithTypeAndKind = (req, resp) -> + req.setTimeout 86400000 + if global.specRunnerTestmode + inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' + resp.json inventoryServiceTestJSON.getContainersInLocationResponse + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containers/getContainersInLocation?containerType=location&containerKind=default" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: req.body.values + json: true + timeout: 86400000 + , (error, response, json) => + if !error && response.statusCode == 200 + resp.json json + else + console.error 'got ajax error trying to get getContainersInLocation' + console.error error + console.error json + console.error response + resp.end JSON.stringify "getContainersInLocation failed" + ) + +exports.getContainersInLocationWithTypeAndKindInternal = (values, callback) -> + #req.setTimeout 86400000 + if global.specRunnerTestmode + inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' + resp.json inventoryServiceTestJSON.getContainersInLocationResponse + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containers/getContainersInLocation?containerType=location&containerKind=default" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: values + json: true + timeout: 86400000 + , (error, response, json) => + if !error && response.statusCode == 200 + callback json, response.statusCode + else + console.error 'got ajax error trying to get getContainersInLocation' + console.error error + console.error json + console.error response + #resp.end JSON.stringify "getContainersInLocation failed" + callback response, response.statusCode + ) + exports.getContainersByLabels = (req, resp) -> req.setTimeout 86400000 exports.getContainersByLabelsInternal req.body, req.query.containerType, req.query.containerKind, req.query.labelType, req.query.labelKind, (json, statusCode) -> @@ -220,6 +286,32 @@ exports.getWellCodesByPlateBarcodes = (req, resp) -> else resp.json json +exports.getContainersInBoxPositionInternal = (values, callback) -> + if global.specRunnerTestmode + inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' + resp.json inventoryServiceTestJSON.getContainersInLocationResponse + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containers/getContainersInLocation?containerType=container&containerKind=tube" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: values + json: true + timeout: 86400000 + , (error, response, json) => + if !error && response.statusCode == 200 + callback json, response.statusCode + else + console.error 'got ajax error trying to get getContainersInLocation' + console.error error + console.error json + console.error response + #resp.end JSON.stringify "getContainersInLocation failed" + callback response, response.statusCode + ) + exports.getWellCodesByPlateBarcodes = (req, resp) -> req.setTimeout 86400000 if global.specRunnerTestmode @@ -426,7 +518,7 @@ exports.updateContainersByContainerCodesInternal = (updateInformation, callCusto else barcodes = _.pluck updateInformation, "barcode" console.debug "calling getContainerCodesByLabelsInternal" - exports.getContainerCodesByLabelsInternal barcodes, null, null, "barcode", "barcode", (containerCodes, statusCode) => + exports.getContainerCodesByLabelsInternal barcodes, "container", null, "barcode", "barcode", (containerCodes, statusCode) => if statusCode == 500 console.error "updateContainerMetadataByContainerCodeInternal failed: #{JSON.stringify containerCodes}" callback "updateContainersByContainerCodesInternal failed", 500 @@ -585,6 +677,8 @@ exports.getBreadCrumbByContainerCodeInternal = (codeNamesJSON, delimeter, callba headers: 'content-type': 'application/json' , (error, response, json) => if !error && response.statusCode == 200 + console.log 'json in getBreadCrumbByContainerCodeInternal' + console.log json callback json else console.error 'got ajax error trying to get getBreadCrumbByContainerCode' @@ -1161,41 +1255,52 @@ exports.moveToLocation = (req, resp) -> resp.json json exports.moveToLocationInternal = (input, callCustom, callback) -> - callCustom = callCustom != "0" - if global.specRunnerTestmode - inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' - resp.json inventoryServiceTestJSON.moveToLocationResponse - else - console.debug 'incoming moveToLocationJSON request: ', JSON.stringify(input) - config = require '../conf/compiled/conf.js' - baseurl = config.all.client.service.persistence.fullpath+"containers/moveToLocation" - console.debug 'base url: ', baseurl - request = require 'request' - request( - method: 'POST' - url: baseurl - body: input - json: true - timeout: 86400000 - headers: 'content-type': 'application/json' - , (error, response, json) => - console.debug "response statusCode: #{response.statusCode}" - if !error - if callCustom && csUtilities.moveToLocation? - console.log "running customer specific server function moveToLocation" - csUtilities.moveToLocation input, (customerResponse, statusCode) -> - json = _.extend json, customerResponse - callback json, statusCode + #exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> + # console.log 'updated history logs before moving to temp' + # ) + callCustom = callCustom != "0" + if global.specRunnerTestmode + inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' + resp.json inventoryServiceTestJSON.moveToLocationResponse + else + console.debug 'incoming moveToLocationJSON request: ', JSON.stringify(input) + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containers/moveToLocation" + console.debug 'base url: ', baseurl + request = require 'request' + console.log 'request into moveToLocation' + console.log input + request( + method: 'POST' + url: baseurl + body: input + json: true + timeout: 86400000 + headers: 'content-type': 'application/json' + , (error, response, json) => + #add the call to updateContainerHistoryLogs here... + console.debug "response statusCode: #{response.statusCode}" + if !error + console.log 'container down here...did it pull through??' + console.log input[0].containerCodeName + exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> + if callCustom && csUtilities.moveToLocation? + console.log "running customer specific server function moveToLocation" + csUtilities.moveToLocation input, (customerResponse, statusCode) -> + json = _.extend json, customerResponse + callback json, statusCode + else + console.warn "could not find customer specific server function moveToLocation so not running it" + callback json, response.statusCode + ) else - console.warn "could not find customer specific server function moveToLocation so not running it" - callback json, response.statusCode - else - console.error 'got ajax error trying to get moveToLocation' - console.error error - console.error json - console.error response - callback JSON.stringify("updateWellContent failed"), 500 - ) + console.error 'got ajax error trying to get moveToLocation' + console.error error + console.error json + console.error response + callback JSON.stringify("updateWellContent failed"), 500 + ) + #) exports.getWellContentByContainerLabel = (req, resp) -> req.setTimeout 86400000 @@ -1484,8 +1589,11 @@ exports.mergeContainersInternal = (input, callback) -> isOdd = (num) -> return (num % 2) == 1 alphabet = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' - _.map originWellContent, (originWells) -> - quadrant = _.findWhere input.quadrants, {"codeName": originWells.containerCodeName} + # for each quadrant + _.map input.quadrants, (quadrant) -> + # find plate whose name matches the quadrant name + originWells = _.findWhere originWellContent, {"containerCodeName": quadrant.codeName} + # map plate wells to merged plate wells _.map originWells.wellContent, (wellContent) -> wellContent = _.omit(wellContent, ['containerCodeName', 'wellName', 'recordedDate']) wellContent.recordedDate = 1455323242544 @@ -1623,6 +1731,7 @@ exports.containerLogsInternal = (inputs, callCustom, callback) -> callback json, statusCode exports.containerLocationHistory = (req, resp) -> + req.setTimeout 86400000 exports.containerLocationHistoryInternal req.body, req.query.callCustom, (json, statusCode) -> resp.statusCode = statusCode resp.json json @@ -1636,7 +1745,9 @@ exports.containerLocationHistoryInternal = (inputs, callCustom, callback) -> exports.addContainerLocationHistory inputs, callCustom, (json, statusCode) -> callback json, statusCode + exports.getContainerLogs = (req, resp) -> + req.setTimeout 86400000 exports.getContainerLogsInternal [req.params.label], req.query.containerType, req.query.containerKind, req.query.labelType, req.query.labelKind, (json, statusCode) -> resp.statusCode = statusCode resp.json json @@ -1754,7 +1865,6 @@ exports.addContainerLocationHistory = (inputs, callCustom, callback) -> if csUtilities.addContainerLocationHistory? console.log "running customer specific server function addContainerLocationHistory" csUtilities.addContainerLocationHistory inputs, (response) -> - console.log response else console.warn "could not find customer specific server function addContainerLocationHistory so not running it" callback json, statusCode @@ -1980,33 +2090,155 @@ exports.throwInTrash = (req, resp) -> resp.json json exports.throwInTrashInternal = (input, callCustom, callback) -> - config = require '../conf/compiled/conf.js' - baseurl = config.all.client.service.persistence.fullpath + "containers/throwInTrash" - console.log baseurl - request = require 'request' - request( - method: 'POST' - url: baseurl - body: JSON.stringify input - json: true - timeout: 6000000 - , (error, response, json) => - if !error && response.statusCode == 204 -# If call custom doesn't equal 0 then call custom - callCustom = callCustom != "0" - if callCustom && csUtilities.throwInTrash? - console.log "running customer specific server function throwInTrash" - csUtilities.throwInTrash input, (customerResponse, statusCode) -> -# json = _.extend json, customerResponse - callback json, response.statusCode + #exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath + "containers/throwInTrash" + console.log baseurl + request = require 'request' + request( + method: 'POST' + url: baseurl + body: JSON.stringify input + json: true + timeout: 6000000 + , (error, response, json) => + if !error && response.statusCode == 204 + exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> + # If call custom doesn't equal 0 then call custom + callCustom = callCustom != "0" + if callCustom && csUtilities.throwInTrash? + console.log "running customer specific server function throwInTrash" + csUtilities.throwInTrash input, (customerResponse, statusCode) -> + # json = _.extend json, customerResponse + callback json, response.statusCode + else + console.warn "could not find customer specific server function throwInTrash so not running it" + callback json, response.statusCode + ) + else if response.statusCode == 400 + callback response.body, response.statusCode else - console.warn "could not find customer specific server function throwInTrash so not running it" - callback json, response.statusCode - else if response.statusCode == 400 - callback response.body, response.statusCode - else - console.log 'got ajax error trying to create tube' - console.log error - console.log response - callback response.body, 500 + console.log 'got ajax error trying to create tube' + console.log error + console.log response + callback response.body, 500 + ) + #) + +exports.updateContainerHistoryLogsInternal = (containers, callback) -> + formattedContainers = [] + index = 0 + #_.each(containers, (container) -> + formatContainersForLocationHistoryUpdate(containers, (statusCode, formattedContainers) -> + exports.containerLocationHistoryInternal(formattedContainers, RUN_CUSTOM_FLAG, (json, statusCode) -> + return callback json,statusCode + ) + # else + # return callback null, 500 + ) + +formatContainersForLocationHistoryUpdate = (containers, callback) -> + createContainersWithBreadcrumb(containers, (containersWithBreadcrumb, modifiedBy, modifiedDate) -> + formatLocationStrings(containersWithBreadcrumb, (formattedContainersWithBreadcrumb) -> + formatContainers(formattedContainersWithBreadcrumb, modifiedBy, modifiedDate, (formattedContainers) -> + return callback 200, formattedContainers + ) + ) + ) + +createContainersWithBreadcrumb = (containers, callback) -> + containerCodeNames = [] + modifiedBy = containers[0].modifiedBy + modifiedDate = containers[0].modifiedDate + _.each(containers, (container) -> + containerCodeNames.push(container.containerCodeName) + ) + exports.getBreadCrumbByContainerCodeInternal(containerCodeNames, "<", (containersWithBreadcrumb) -> + return callback containersWithBreadcrumb, modifiedBy, modifiedDate + ) + +formatLocationStrings = (containersWithBreadcrumb, callback) -> + formattedContainersWithBreadcrumb = [] + _.each(containersWithBreadcrumb, (container) -> + locationArray = container.labelBreadCrumb.split("<") + locationArrayString = JSON.stringify(locationArray) + container.locationArrayString = locationArrayString + formattedContainersWithBreadcrumb.push(container) + ) + return callback formattedContainersWithBreadcrumb + +formatContainers = (containers, modifiedBy, modifiedDate, callback) -> + formattedContainers = [] + _.each(containers, (container) -> + formattedContainer = { + "codeName": container.containerCode + "recordedBy": modifiedBy + "recordedDate": modifiedDate + "location": container.locationArrayString + "movedBy": modifiedBy + "movedDate": modifiedDate + "additionalValues": [] + } + formattedContainers.push(formattedContainer) ) + statusCode = 200 + return callback formattedContainers + #callback(formattedContainers, statusCode) + + +# getLocationBreadcrumb = (container, callback) -> +# exports.getBreadCrumbByContainerCodeInternal([container.containerCodeName], "<", (breadcrumb) -> +# labelBreadCrumb = breadcrumb[0].labelBreadCrumb +# callback labelBreadCrumb +# # console.log 'breadcrumb for move to locations' +# # console.log breadcrumb[0].labelBreadCrumb +# # #test breadCrumb = 'CAGE00002 +# getLocationBreadcrumb(container, (labelBreadCrumb) -> +# createLocationArray(labelBreadCrumb, (locationArrayString) -> +# #buildLocationArrayString(locationArray, (locationArrayString) -> +# formatContainer(container, locationArrayString, (formattedContainer, statusCode) -> +# callback statusCode, formattedContainer +# ) +# ) +# ) +# +# createLocationArray = (labelBreadCrumb, callback) -> +# locationArray = labelBreadCrumb.split("<") +# locationArrayString = JSON.stringify(locationArray) +# callback locationArrayString.toUpperCase() +# +# formatContainer = (container, locationArrayString, callback) -> +# +# formattedContainer = { +# "codeName": container.containerCodeName +# "recordedBy": container.modifiedBy +# "recordedDate": container.modifiedDate +# "location": locationArrayString +# "movedBy": container.modifiedBy +# "movedDate": container.modifiedDate +# "additionalValues": [] +# } +# +# statusCode = 200 +# callback(formattedContainer, statusCode) + +# buildLocationArrayString = (locationArray, callback) -> +# locationSeparator = '\",\"' +# locationArrayString = '[\"' + +# locationArray[0] + +# locationSeparator + +# locationArray[1] + +# locationSeparator + +# locationArray[2] + +# locationSeparator + +# locationArray[3] + +# '\"]' +# +# console.log 'locationArrayString ' +# console.log locationArrayString +# callback locationArrayString diff --git a/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee b/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee index ae887c6fd..54766d26c 100644 --- a/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee +++ b/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee @@ -1429,6 +1429,27 @@ class Container extends Backbone.Model additionalValues: additionalValues response.push responseObject return response + + getLocationHistory: -> + lsStates = @get('lsStates').getStatesByTypeAndKind 'metadata', 'location history' + response = [] + if lsStates? + lsStates.forEach (lsState) => + additionalValues = lsState.get('lsValues').filter (value) -> + (!value.get('ignored')) and + !((value.get('lsType')=='stringValue') and (value.get('lsKind')=='location')) and + !((value.get('lsType')=='codeValue') and (value.get('lsKind')=='moved by')) and + !((value.get('lsType')=='dateValue') and (value.get('lsKind')=='moved date')) + responseObject = + codeName: @get('codeName') + recordedBy: lsState.get('recordedBy') + recordedDate: lsState.get('recordedDate') + location: lsState.getValuesByTypeAndKind('stringValue', 'location')[0].get('stringValue') + movedBy: lsState.getValuesByTypeAndKind('codeValue', 'moved by')[0]?.get('codeValue') + movedDate: lsState.getValuesByTypeAndKind('dateValue', 'moved date')[0]?.get('dateValue') + additionalValues: additionalValues + response.push responseObject + return response getLocationHistory: -> lsStates = @get('lsStates').getStatesByTypeAndKind 'metadata', 'location history' diff --git a/public/lib/select2-bootstrap-theme-0.1.0-beta.8/dist/select2-bootstrap.css b/public/lib/select2-bootstrap-theme-0.1.0-beta.8/dist/select2-bootstrap.css new file mode 100755 index 000000000..caf2b9abd --- /dev/null +++ b/public/lib/select2-bootstrap-theme-0.1.0-beta.8/dist/select2-bootstrap.css @@ -0,0 +1,610 @@ +/*! Select2 Bootstrap Theme v0.1.0-beta.8 | MIT License | github.com/select2/select2-bootstrap-theme */ +.select2-container--bootstrap { + display: block; + /*------------------------------------*\ + #COMMON STYLES + \*------------------------------------*/ + /** + * Search field in the Select2 dropdown. + */ + /** + * No outline for all search fields - in the dropdown + * and inline in multi Select2s. + */ + /** + * Adjust Select2's choices hover and selected styles to match + * Bootstrap 3's default dropdown styles. + * + * @see http://getbootstrap.com/components/#dropdowns + */ + /** + * Clear the selection. + */ + /** + * Address disabled Select2 styles. + * + * @see https://select2.github.io/examples.html#disabled + * @see http://getbootstrap.com/css/#forms-control-disabled + */ + /*------------------------------------*\ + #DROPDOWN + \*------------------------------------*/ + /** + * Dropdown border color and box-shadow. + */ + /** + * Limit the dropdown height. + */ + /*------------------------------------*\ + #SINGLE SELECT2 + \*------------------------------------*/ + /*------------------------------------*\ + #MULTIPLE SELECT2 + \*------------------------------------*/ + /** + * Address Bootstrap control sizing classes + * + * 1. Reset Bootstrap defaults. + * 2. Adjust the dropdown arrow button icon position. + * + * @see http://getbootstrap.com/css/#forms-control-sizes + */ + /* 1 */ + /*------------------------------------*\ + #RTL SUPPORT + \*------------------------------------*/ +} +.select2-container--bootstrap .select2-selection { + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + background-color: #fff; + border: 1px solid #ccc; + border-radius: 4px; + color: #555555; + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-size: 14px; + outline: 0; +} +.select2-container--bootstrap .select2-selection.form-control { + border-radius: 4px; +} +.select2-container--bootstrap .select2-search--dropdown .select2-search__field { + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075); + background-color: #fff; + border: 1px solid #ccc; + border-radius: 4px; + color: #555555; + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + font-size: 14px; +} +.select2-container--bootstrap .select2-search__field { + outline: 0; + /* Firefox 18- */ + /** + * Firefox 19+ + * + * @see http://stackoverflow.com/questions/24236240/color-for-styled-placeholder-text-is-muted-in-firefox + */ +} +.select2-container--bootstrap .select2-search__field::-webkit-input-placeholder { + color: #999; +} +.select2-container--bootstrap .select2-search__field:-moz-placeholder { + color: #999; +} +.select2-container--bootstrap .select2-search__field::-moz-placeholder { + color: #999; + opacity: 1; +} +.select2-container--bootstrap .select2-search__field:-ms-input-placeholder { + color: #999; +} +.select2-container--bootstrap .select2-results__option { + /** + * Disabled results. + * + * @see https://select2.github.io/examples.html#disabled-results + */ + /** + * Hover state. + */ + /** + * Selected state. + */ +} +.select2-container--bootstrap .select2-results__option[role=group] { + padding: 0; +} +.select2-container--bootstrap .select2-results__option[aria-disabled=true] { + color: #777777; + cursor: not-allowed; +} +.select2-container--bootstrap .select2-results__option[aria-selected=true] { + background-color: #f5f5f5; + color: #262626; +} +.select2-container--bootstrap .select2-results__option--highlighted[aria-selected] { + background-color: #337ab7; + color: #fff; +} +.select2-container--bootstrap .select2-results__option .select2-results__option { + padding: 6px 12px; +} +.select2-container--bootstrap .select2-results__option .select2-results__option .select2-results__group { + padding-left: 0; +} +.select2-container--bootstrap .select2-results__option .select2-results__option .select2-results__option { + margin-left: -12px; + padding-left: 24px; +} +.select2-container--bootstrap .select2-results__option .select2-results__option .select2-results__option .select2-results__option { + margin-left: -24px; + padding-left: 36px; +} +.select2-container--bootstrap .select2-results__option .select2-results__option .select2-results__option .select2-results__option .select2-results__option { + margin-left: -36px; + padding-left: 48px; +} +.select2-container--bootstrap .select2-results__option .select2-results__option .select2-results__option .select2-results__option .select2-results__option .select2-results__option { + margin-left: -48px; + padding-left: 60px; +} +.select2-container--bootstrap .select2-results__option .select2-results__option .select2-results__option .select2-results__option .select2-results__option .select2-results__option .select2-results__option { + margin-left: -60px; + padding-left: 72px; +} +.select2-container--bootstrap .select2-results__group { + color: #777777; + display: block; + padding: 6px 12px; + font-size: 12px; + line-height: 1.428571429; + white-space: nowrap; +} +.select2-container--bootstrap.select2-container--focus .select2-selection, .select2-container--bootstrap.select2-container--open .select2-selection { + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(102, 175, 233, 0.6); + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(102, 175, 233, 0.6); + -webkit-transition: border-color ease-in-out 0.15s, box-shadow ease-in-out 0.15s; + -o-transition: border-color ease-in-out 0.15s, box-shadow ease-in-out 0.15s; + -webkit-transition: border-color ease-in-out 0.15s, -webkit-box-shadow ease-in-out 0.15s; + transition: border-color ease-in-out 0.15s, -webkit-box-shadow ease-in-out 0.15s; + transition: border-color ease-in-out 0.15s, box-shadow ease-in-out 0.15s; + transition: border-color ease-in-out 0.15s, box-shadow ease-in-out 0.15s, -webkit-box-shadow ease-in-out 0.15s; + border-color: #66afe9; +} +.select2-container--bootstrap.select2-container--open { + /** + * Make the dropdown arrow point up while the dropdown is visible. + */ + /** + * Handle border radii of the container when the dropdown is showing. + */ +} +.select2-container--bootstrap.select2-container--open .select2-selection .select2-selection__arrow b { + border-color: transparent transparent #999 transparent; + border-width: 0 4px 4px 4px; +} +.select2-container--bootstrap.select2-container--open.select2-container--below .select2-selection { + border-bottom-right-radius: 0; + border-bottom-left-radius: 0; + border-bottom-color: transparent; +} +.select2-container--bootstrap.select2-container--open.select2-container--above .select2-selection { + border-top-right-radius: 0; + border-top-left-radius: 0; + border-top-color: transparent; +} +.select2-container--bootstrap .select2-selection__clear { + color: #999; + cursor: pointer; + float: right; + font-weight: bold; + margin-right: 10px; +} +.select2-container--bootstrap .select2-selection__clear:hover { + color: #333; +} +.select2-container--bootstrap.select2-container--disabled .select2-selection { + border-color: #ccc; + -webkit-box-shadow: none; + box-shadow: none; +} +.select2-container--bootstrap.select2-container--disabled .select2-selection, +.select2-container--bootstrap.select2-container--disabled .select2-search__field { + cursor: not-allowed; +} +.select2-container--bootstrap.select2-container--disabled .select2-selection, +.select2-container--bootstrap.select2-container--disabled .select2-selection--multiple .select2-selection__choice { + background-color: #eeeeee; +} +.select2-container--bootstrap.select2-container--disabled .select2-selection__clear, +.select2-container--bootstrap.select2-container--disabled .select2-selection--multiple .select2-selection__choice__remove { + display: none; +} +.select2-container--bootstrap .select2-dropdown { + -webkit-box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175); + box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175); + border-color: #66afe9; + overflow-x: hidden; + margin-top: -1px; +} +.select2-container--bootstrap .select2-dropdown--above { + margin-top: 1px; +} +.select2-container--bootstrap .select2-results > .select2-results__options { + max-height: 200px; + overflow-y: auto; +} +.select2-container--bootstrap .select2-selection--single { + height: 34px; + line-height: 1.428571429; + padding: 6px 24px 6px 12px; + /** + * Adjust the single Select2's dropdown arrow button appearance. + */ +} +.select2-container--bootstrap .select2-selection--single .select2-selection__arrow { + position: absolute; + bottom: 0; + right: 12px; + top: 0; + width: 4px; +} +.select2-container--bootstrap .select2-selection--single .select2-selection__arrow b { + border-color: #999 transparent transparent transparent; + border-style: solid; + border-width: 4px 4px 0 4px; + height: 0; + left: 0; + margin-left: -4px; + margin-top: -2px; + position: absolute; + top: 50%; + width: 0; +} +.select2-container--bootstrap .select2-selection--single .select2-selection__rendered { + color: #555555; + padding: 0; +} +.select2-container--bootstrap .select2-selection--single .select2-selection__placeholder { + color: #999; +} +.select2-container--bootstrap .select2-selection--multiple { + min-height: 34px; + padding: 0; + height: auto; + /** + * Make Multi Select2's choices match Bootstrap 3's default button styles. + */ + /** + * Minus 2px borders. + */ + /** + * Clear the selection. + */ +} +.select2-container--bootstrap .select2-selection--multiple .select2-selection__rendered { + -webkit-box-sizing: border-box; + -moz-box-sizing: border-box; + box-sizing: border-box; + display: block; + line-height: 1.428571429; + list-style: none; + margin: 0; + overflow: hidden; + padding: 0; + width: 100%; + text-overflow: ellipsis; + white-space: nowrap; +} +.select2-container--bootstrap .select2-selection--multiple .select2-selection__placeholder { + color: #999; + float: left; + margin-top: 5px; +} +.select2-container--bootstrap .select2-selection--multiple .select2-selection__choice { + color: #555555; + background: #fff; + border: 1px solid #ccc; + border-radius: 4px; + cursor: default; + float: left; + margin: 5px 0 0 6px; + padding: 0 6px; +} +.select2-container--bootstrap .select2-selection--multiple .select2-search--inline .select2-search__field { + background: transparent; + padding: 0 12px; + height: 32px; + line-height: 1.428571429; + margin-top: 0; + min-width: 5em; +} +.select2-container--bootstrap .select2-selection--multiple .select2-selection__choice__remove { + color: #999; + cursor: pointer; + display: inline-block; + font-weight: bold; + margin-right: 3px; +} +.select2-container--bootstrap .select2-selection--multiple .select2-selection__choice__remove:hover { + color: #333; +} +.select2-container--bootstrap .select2-selection--multiple .select2-selection__clear { + margin-top: 6px; +} +.select2-container--bootstrap .select2-selection--single.input-sm, .input-group-sm .select2-container--bootstrap .select2-selection--single, .form-group-sm .select2-container--bootstrap .select2-selection--single { + border-radius: 3px; + font-size: 12px; + height: 30px; + line-height: 1.5; + padding: 5px 22px 5px 10px; + /* 2 */ +} +.select2-container--bootstrap .select2-selection--single.input-sm .select2-selection__arrow b, .input-group-sm .select2-container--bootstrap .select2-selection--single .select2-selection__arrow b, .form-group-sm .select2-container--bootstrap .select2-selection--single .select2-selection__arrow b { + margin-left: -5px; +} +.select2-container--bootstrap .select2-selection--multiple.input-sm, .input-group-sm .select2-container--bootstrap .select2-selection--multiple, .form-group-sm .select2-container--bootstrap .select2-selection--multiple { + min-height: 30px; + border-radius: 3px; +} +.select2-container--bootstrap .select2-selection--multiple.input-sm .select2-selection__choice, .input-group-sm .select2-container--bootstrap .select2-selection--multiple .select2-selection__choice, .form-group-sm .select2-container--bootstrap .select2-selection--multiple .select2-selection__choice { + font-size: 12px; + line-height: 1.5; + margin: 4px 0 0 5px; + padding: 0 5px; +} +.select2-container--bootstrap .select2-selection--multiple.input-sm .select2-search--inline .select2-search__field, .input-group-sm .select2-container--bootstrap .select2-selection--multiple .select2-search--inline .select2-search__field, .form-group-sm .select2-container--bootstrap .select2-selection--multiple .select2-search--inline .select2-search__field { + padding: 0 10px; + font-size: 12px; + height: 28px; + line-height: 1.5; +} +.select2-container--bootstrap .select2-selection--multiple.input-sm .select2-selection__clear, .input-group-sm .select2-container--bootstrap .select2-selection--multiple .select2-selection__clear, .form-group-sm .select2-container--bootstrap .select2-selection--multiple .select2-selection__clear { + margin-top: 5px; +} +.select2-container--bootstrap .select2-selection--single.input-lg, .input-group-lg .select2-container--bootstrap .select2-selection--single, .form-group-lg .select2-container--bootstrap .select2-selection--single { + border-radius: 6px; + font-size: 18px; + height: 46px; + line-height: 1.3333333; + padding: 10px 31px 10px 16px; + /* 1 */ +} +.select2-container--bootstrap .select2-selection--single.input-lg .select2-selection__arrow, .input-group-lg .select2-container--bootstrap .select2-selection--single .select2-selection__arrow, .form-group-lg .select2-container--bootstrap .select2-selection--single .select2-selection__arrow { + width: 5px; +} +.select2-container--bootstrap .select2-selection--single.input-lg .select2-selection__arrow b, .input-group-lg .select2-container--bootstrap .select2-selection--single .select2-selection__arrow b, .form-group-lg .select2-container--bootstrap .select2-selection--single .select2-selection__arrow b { + border-width: 5px 5px 0 5px; + margin-left: -5px; + margin-left: -10px; + margin-top: -2.5px; +} +.select2-container--bootstrap .select2-selection--multiple.input-lg, .input-group-lg .select2-container--bootstrap .select2-selection--multiple, .form-group-lg .select2-container--bootstrap .select2-selection--multiple { + min-height: 46px; + border-radius: 6px; +} +.select2-container--bootstrap .select2-selection--multiple.input-lg .select2-selection__choice, .input-group-lg .select2-container--bootstrap .select2-selection--multiple .select2-selection__choice, .form-group-lg .select2-container--bootstrap .select2-selection--multiple .select2-selection__choice { + font-size: 18px; + line-height: 1.3333333; + border-radius: 4px; + margin: 9px 0 0 8px; + padding: 0 10px; +} +.select2-container--bootstrap .select2-selection--multiple.input-lg .select2-search--inline .select2-search__field, .input-group-lg .select2-container--bootstrap .select2-selection--multiple .select2-search--inline .select2-search__field, .form-group-lg .select2-container--bootstrap .select2-selection--multiple .select2-search--inline .select2-search__field { + padding: 0 16px; + font-size: 18px; + height: 44px; + line-height: 1.3333333; +} +.select2-container--bootstrap .select2-selection--multiple.input-lg .select2-selection__clear, .input-group-lg .select2-container--bootstrap .select2-selection--multiple .select2-selection__clear, .form-group-lg .select2-container--bootstrap .select2-selection--multiple .select2-selection__clear { + margin-top: 10px; +} +.select2-container--bootstrap .select2-selection.input-lg.select2-container--open .select2-selection--single { + /** + * Make the dropdown arrow point up while the dropdown is visible. + */ +} +.select2-container--bootstrap .select2-selection.input-lg.select2-container--open .select2-selection--single .select2-selection__arrow b { + border-color: transparent transparent #999 transparent; + border-width: 0 5px 5px 5px; +} +.input-group-lg .select2-container--bootstrap .select2-selection.select2-container--open .select2-selection--single { + /** + * Make the dropdown arrow point up while the dropdown is visible. + */ +} +.input-group-lg .select2-container--bootstrap .select2-selection.select2-container--open .select2-selection--single .select2-selection__arrow b { + border-color: transparent transparent #999 transparent; + border-width: 0 5px 5px 5px; +} +.select2-container--bootstrap[dir="rtl"] { + /** + * Single Select2 + * + * 1. Makes sure that .select2-selection__placeholder is positioned + * correctly. + */ + /** + * Multiple Select2 + */ +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--single { + padding-left: 24px; + padding-right: 12px; +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--single .select2-selection__rendered { + padding-right: 0; + padding-left: 0; + text-align: right; + /* 1 */ +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--single .select2-selection__clear { + float: left; +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--single .select2-selection__arrow { + left: 12px; + right: auto; +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--single .select2-selection__arrow b { + margin-left: 0; +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--multiple .select2-selection__choice, +.select2-container--bootstrap[dir="rtl"] .select2-selection--multiple .select2-selection__placeholder { + float: right; +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--multiple .select2-selection__choice { + margin-left: 0; + margin-right: 6px; +} +.select2-container--bootstrap[dir="rtl"] .select2-selection--multiple .select2-selection__choice__remove { + margin-left: 2px; + margin-right: auto; +} + +/*------------------------------------*\ + #ADDITIONAL GOODIES +\*------------------------------------*/ +/** + * Address Bootstrap's validation states + * + * If a Select2 widget parent has one of Bootstrap's validation state modifier + * classes, adjust Select2's border colors and focus states accordingly. + * You may apply said classes to the Select2 dropdown (body > .select2-container) + * via JavaScript match Bootstraps' to make its styles match. + * + * @see http://getbootstrap.com/css/#forms-control-validation + */ +.has-warning .select2-dropdown, +.has-warning .select2-selection { + border-color: #8a6d3b; +} +.has-warning .select2-container--focus .select2-selection, +.has-warning .select2-container--open .select2-selection { + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #c0a16b; + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #c0a16b; + border-color: #66512c; +} +.has-warning.select2-drop-active { + border-color: #66512c; +} +.has-warning.select2-drop-active.select2-drop.select2-drop-above { + border-top-color: #66512c; +} + +.has-error .select2-dropdown, +.has-error .select2-selection { + border-color: #a94442; +} +.has-error .select2-container--focus .select2-selection, +.has-error .select2-container--open .select2-selection { + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #ce8483; + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #ce8483; + border-color: #843534; +} +.has-error.select2-drop-active { + border-color: #843534; +} +.has-error.select2-drop-active.select2-drop.select2-drop-above { + border-top-color: #843534; +} + +.has-success .select2-dropdown, +.has-success .select2-selection { + border-color: #3c763d; +} +.has-success .select2-container--focus .select2-selection, +.has-success .select2-container--open .select2-selection { + -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #67b168; + box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #67b168; + border-color: #2b542c; +} +.has-success.select2-drop-active { + border-color: #2b542c; +} +.has-success.select2-drop-active.select2-drop.select2-drop-above { + border-top-color: #2b542c; +} + +/** + * Select2 widgets in Bootstrap Input Groups + * + * When Select2 widgets are combined with other elements using Bootstraps + * "Input Group" component, we don't want specific edges of the Select2 + * container to have a border-radius. + * + * Use .select2-bootstrap-prepend and .select2-bootstrap-append on + * a Bootstrap 3 .input-group to let the contained Select2 widget know which + * edges should not be rounded as they are directly followed by another element. + * + * @see http://getbootstrap.com/components/#input-groups + */ +/** + * Mimick Bootstraps .input-group .form-control styles. + * + * @see https://github.com/twbs/bootstrap/blob/master/less/input-groups.less + */ +.input-group .select2-container--bootstrap { + display: table; + table-layout: fixed; + position: relative; + z-index: 2; + float: left; + width: 100%; + margin-bottom: 0; + /** + * Adjust z-index like Bootstrap does to show the focus-box-shadow + * above appended buttons in .input-group and .form-group. + */ +} +.input-group .select2-container--bootstrap.select2-container--open, .input-group .select2-container--bootstrap.select2-container--focus { + z-index: 3; +} + +.input-group.select2-bootstrap-prepend .select2-container--bootstrap .select2-selection { + border-bottom-left-radius: 0; + border-top-left-radius: 0; +} + +.input-group.select2-bootstrap-append .select2-container--bootstrap .select2-selection { + border-bottom-right-radius: 0; + border-top-right-radius: 0; +} + +/** + * Adjust alignment of Bootstrap buttons in Bootstrap Input Groups to address + * Multi Select2's height which - depending on how many elements have been selected - + * may grow taller than its initial size. + * + * @see http://getbootstrap.com/components/#input-groups + */ +.select2-bootstrap-append .select2-container--bootstrap, +.select2-bootstrap-append .input-group-btn, +.select2-bootstrap-append .input-group-btn .btn, +.select2-bootstrap-prepend .select2-container--bootstrap, +.select2-bootstrap-prepend .input-group-btn, +.select2-bootstrap-prepend .input-group-btn .btn { + vertical-align: top; +} + +/** + * Temporary fix for https://github.com/select2/select2-bootstrap-theme/issues/9 + * + * Provides `!important` for certain properties of the class applied to the + * original ` -
    -
    - Change My Name -
    -
    diff --git a/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee b/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee deleted file mode 100644 index 6aef3b89f..000000000 --- a/modules/ModuleMenus/src/server/routes/ModuleMenusRoutes.coffee +++ /dev/null @@ -1,52 +0,0 @@ -_ = require 'underscore' - -exports.setupChannels = (io, sessionStore, loginRoutes) -> - nsp = io.of('/user:loggedin') - connectedUsers = {} - nsp.on('connection', (socket) => - userName = getUserNameFromSession(socket) - sessionID = getSessionID(socket) - unless connectedUsers[sessionID]? - connectedUsers[sessionID] = [] - connectedUsers[sessionID].push socket.id - totalNumberOfConnectionsForUser = _.size(connectedUsers[userName]) - broadcastMessageToSpecificClients(connectedUsers[userName], 'loggedOn', totalNumberOfConnectionsForUser, socket) - socket.emit('loggedOn', totalNumberOfConnectionsForUser) - - socket.on('disconnect', => - clientConnections = connectedUsers[userName] - connectedUsers[sessionID] = _.without(clientConnections, socket.id) - totalNumberOfConnectionsForUser = _.size(connectedUsers[sessionID]) - broadcastMessageToSpecificClients(connectedUsers[sessionID], 'loggedOff', totalNumberOfConnectionsForUser, socket) - ) - - socket.on('changeUserName', (updatedUsername) => - sessionID = getSessionID(socket) - updateUserNameInSession(updatedUsername, sessionStore, sessionID) - broadcastMessageToSpecificClients(connectedUsers[sessionID], 'usernameUpdated', updatedUsername, socket) - socket.emit('usernameUpdated', updatedUsername) - ) - ) - -getUserNameFromSession = (socket) -> - unless socket.request.user.originalLoginUserName? - console.log "using original login name" - return socket.request.user.originalLoginUserName - else - return socket.request.user.username - -updateUserNameInSession = (updatedUserName, sessionStore, sessionId) -> - parsedCookie = JSON.parse(sessionStore.sessions[sessionId]) - unless parsedCookie.passport.user.originalLoginUserName? - parsedCookie.passport.user.originalLoginUserName = parsedCookie.passport.user.username - parsedCookie.passport.user.username = updatedUserName - parsedCookie.passport.user.firstName = updatedUserName - sessionStore.sessions[sessionId] = JSON.stringify(parsedCookie) - -broadcastMessageToSpecificClients = (socketIds, messageName, payload, socket) -> - _.each(socketIds, (socketId) -> - socket.broadcast.to(socketId).emit(messageName, payload) - ) - -getSessionID = (socket) -> - socket.request.sessionID \ No newline at end of file From 7b2a92693b0c15b7cd54a15d625970efe73c654d Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Mon, 26 Jun 2017 15:56:54 -0700 Subject: [PATCH 062/576] develop: adding optional config client.moduleMenus.dataViewerDeepLink --- conf/config.properties.example | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/config.properties.example b/conf/config.properties.example index 6cf0491d3..0e20e2f7d 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -331,6 +331,7 @@ client.moduleMenus.summaryStats=false # For navigation to external ACAS modules from ACAS homepage client.moduleMenus.modules.external=[{"displayName": "Compound Registration", "href": "/cmpdreg/"},\ {"displayName": "Compound Registration Bulk Loader", "href":"/CmpdRegBulkLoader"}] +client.moduleMenus.dataViewerDeepLink=/dataViewer client.leaveACASMessage=There are no unsaved changes. client.scientistCodeOrigin=ACAS authors From 2b065c34741f2ba1b143fb8a4f891cd4e2bf6dd3 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Tue, 27 Jun 2017 08:51:45 -0600 Subject: [PATCH 063/576] Removed extra indent in socket.io/socket.io.js include line. --- .../src/server/routes/RequiredClientScripts_template.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js b/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js index bbee713e2..593d77a5d 100644 --- a/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js +++ b/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js @@ -26,7 +26,7 @@ exports.requiredScripts = [ '/lib/spin/js/jquery-spin.js', '/lib/handsontable/dist/handsontable.full.js', '/lib/select2-4.0.3/dist/js/select2.full.js', - '/socket.io/socket.io.js' + '/socket.io/socket.io.js' ]; exports.applicationScripts = [ From dbb8d2ee1b6a238a60ee31ff301f5563dde8d32a Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Tue, 27 Jun 2017 08:53:04 -0600 Subject: [PATCH 064/576] Removed extra indent in socket.io/socket.io.js include line. --- .../src/server/routes/RequiredClientScripts_template.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js b/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js index bbee713e2..593d77a5d 100644 --- a/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js +++ b/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js @@ -26,7 +26,7 @@ exports.requiredScripts = [ '/lib/spin/js/jquery-spin.js', '/lib/handsontable/dist/handsontable.full.js', '/lib/select2-4.0.3/dist/js/select2.full.js', - '/socket.io/socket.io.js' + '/socket.io/socket.io.js' ]; exports.applicationScripts = [ From be564fd7622f56df2d553661e46471b44e8f26cd Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Tue, 27 Jun 2017 11:19:36 -0600 Subject: [PATCH 065/576] Set fastUserSwitchingRoles to empty array by default in the example conf --- conf/config.properties.example | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 24a0e2113..56c8d66f8 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -515,6 +515,6 @@ client.projectEditor.isRestricted.default=false client.roles.crossProjectLoaderRole=ROLE_ACAS-CROSS-PROJECT-LOADER #Add user roles that represent groups allowed to fast user switch -#client.moduleMenus.fastUserSwitchingRoles=[] -client.moduleMenus.fastUserSwitchingRoles=[{"lsKind":"PROJ-00000001","lsType":"Project","roleName":"User"},{"lsKind":"PROJ-00000002","lsType":"Project","roleName":"User"}] +client.moduleMenus.fastUserSwitchingRoles=[] +#client.moduleMenus.fastUserSwitchingRoles=[{"lsKind":"PROJ-00000001","lsType":"Project","roleName":"User"},{"lsKind":"PROJ-00000002","lsType":"Project","roleName":"User"}] client.moduleMenus.fastUserSwitchingChangeUserRoles=true \ No newline at end of file From ff235e5f89a297b7a07a5926742ba075f7393825 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Tue, 27 Jun 2017 12:57:47 -0600 Subject: [PATCH 066/576] Set fastUserSwitchingRoles to empty array by default in the example conf --- conf/config.properties.example | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 56c8d66f8..adb5768ae 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -517,4 +517,4 @@ client.roles.crossProjectLoaderRole=ROLE_ACAS-CROSS-PROJECT-LOADER #Add user roles that represent groups allowed to fast user switch client.moduleMenus.fastUserSwitchingRoles=[] #client.moduleMenus.fastUserSwitchingRoles=[{"lsKind":"PROJ-00000001","lsType":"Project","roleName":"User"},{"lsKind":"PROJ-00000002","lsType":"Project","roleName":"User"}] -client.moduleMenus.fastUserSwitchingChangeUserRoles=true \ No newline at end of file +client.moduleMenus.fastUserSwitchingChangeUserRoles=false \ No newline at end of file From 228de84840b9fb5523995f15dc4ab1b455df7225 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Tue, 27 Jun 2017 13:02:07 -0600 Subject: [PATCH 067/576] Fixed select2 reference to point to the correct version (4.0.2 instead of 4.0.3) --- .../src/server/routes/RequiredClientScripts_template.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js b/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js index 593d77a5d..58da06749 100644 --- a/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js +++ b/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js @@ -25,7 +25,7 @@ exports.requiredScripts = [ '/lib/spin/js/spin.js', '/lib/spin/js/jquery-spin.js', '/lib/handsontable/dist/handsontable.full.js', - '/lib/select2-4.0.3/dist/js/select2.full.js', + '/lib/select2-4.0.2/dist/js/select2.full.js', '/socket.io/socket.io.js' ]; From 41a238a2ec06b3317bfecb7aa8d72be6904dd90a Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Tue, 27 Jun 2017 13:42:00 -0600 Subject: [PATCH 068/576] Removed configuration that added socket io routes to api routes. --- app_api_template.coffee | 3 --- 1 file changed, 3 deletions(-) diff --git a/app_api_template.coffee b/app_api_template.coffee index 48643f964..66c3a66a5 100644 --- a/app_api_template.coffee +++ b/app_api_template.coffee @@ -49,9 +49,6 @@ startApp = -> httpServer = http.createServer(app).listen(app.get('port'), -> console.log("ACAS API server listening on port " + app.get('port')) ) - io = require('socket.io')(httpServer) - ###TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES### - csUtilities.logUsage("ACAS API server started", "started", "") startApp() From bfbf4c830c7dbc063599c2243fe04f03e6ce6e32 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Tue, 27 Jun 2017 13:45:04 -0600 Subject: [PATCH 069/576] Removed configuration that added socket io routes to api routes. --- app_api_template.coffee | 3 +++ modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee | 2 -- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/app_api_template.coffee b/app_api_template.coffee index 66c3a66a5..a13b2277a 100644 --- a/app_api_template.coffee +++ b/app_api_template.coffee @@ -49,6 +49,9 @@ startApp = -> httpServer = http.createServer(app).listen(app.get('port'), -> console.log("ACAS API server listening on port " + app.get('port')) ) + + ###TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES### + csUtilities.logUsage("ACAS API server started", "started", "") startApp() diff --git a/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee b/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee index b7ccfca4c..64c3c8af7 100644 --- a/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee +++ b/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee @@ -110,8 +110,6 @@ prepRouteIncludes = (apiMode) -> if apiMode includeStr += '\tif (routeSet_'+routeNum+'.setupAPIRoutes) {\n' includeStr += '\t\trouteSet_'+routeNum+'.setupAPIRoutes(app); }\n' - includeStr += '\tif (routeSet_'+routeNum+'.setupChannels) {\n' - includeStr += '\trouteSet_'+routeNum+'.setupChannels(io, {}, loginRoutes); }\n' else includeStr += '\tif (routeSet_'+routeNum+'.setupRoutes) {\n' includeStr += '\trouteSet_'+routeNum+'.setupRoutes(app, loginRoutes);\n }' From d4a91074d30fc1768ca16412b90b540ca58b4bce Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Tue, 27 Jun 2017 16:57:54 -0700 Subject: [PATCH 070/576] RC/1.12.0: fixing bug in initializing options for PickListForLsThingsSelectController, renamed deleteEmptyLabelsAndValsBeforeSave to deleteEmptyLabelsValsItxsBeforeSave in order to control when empty labels/values/itxs are removed, fixed bug in ThingInteraction to inherit defaults --- modules/Components/src/client/PickList.coffee | 4 +- modules/ServerAPI/src/client/Thing.coffee | 55 ++++++++++--------- .../src/client/ThingInteraction.coffee | 11 ++-- 3 files changed, 36 insertions(+), 34 deletions(-) diff --git a/modules/Components/src/client/PickList.coffee b/modules/Components/src/client/PickList.coffee index 7f703497b..eec78277b 100644 --- a/modules/Components/src/client/PickList.coffee +++ b/modules/Components/src/client/PickList.coffee @@ -204,8 +204,8 @@ class window.PickListSelectController extends Backbone.View class window.PickListForLsThingsSelectController extends PickListSelectController - initialize: -> - super() + initialize: (options) -> + super(options) if @options.displayName? #examples are codeName, corpName @displayName = @options.displayName else diff --git a/modules/ServerAPI/src/client/Thing.coffee b/modules/ServerAPI/src/client/Thing.coffee index f39bcf3bc..5db59aa21 100644 --- a/modules/ServerAPI/src/client/Thing.coffee +++ b/modules/ServerAPI/src/client/Thing.coffee @@ -1,7 +1,7 @@ class window.Thing extends Backbone.Model lsProperties: {} className: "Thing" - deleteEmptyLabelsAndValsBeforeSave: true + deleteEmptyLabelsValsItxsBeforeSave: true # urlRoot: "/api/things" defaults: () -> @@ -69,41 +69,42 @@ class window.Thing extends Backbone.Model toJSON: (options) -> attsToSave = super(options) - if @deleteEmptyLabelsAndValsBeforeSave + if @deleteEmptyLabelsValsItxsBeforeSave toDel = attsToSave.lsLabels.filter (lab) -> (lab.get('ignored') || lab.get('labelText')=="") && lab.isNew() for lab in toDel attsToSave.lsLabels.remove lab - if attsToSave.firstLsThings? - toDel = attsToSave.firstLsThings.filter (itx) -> - !itx.getItxThing().id? - for itx in toDel - attsToSave.firstLsThings.remove itx - if attsToSave.firstLsThings.length == 0 - delete attsToSave.firstLsThings - - if attsToSave.secondLsThings? - toDel = attsToSave.secondLsThings.filter (itx) -> - !itx.getItxThing().id? - for itx in toDel - attsToSave.secondLsThings.remove itx - if attsToSave.secondLsThings.length == 0 - delete attsToSave.secondLsThings + if attsToSave.firstLsThings? + toDel = attsToSave.firstLsThings.filter (itx) -> + !itx.getItxThing().id? + for itx in toDel + attsToSave.firstLsThings.remove itx + if attsToSave.firstLsThings.length == 0 + delete attsToSave.firstLsThings - if @lsProperties.defaultLabels? - for dLabel in @lsProperties.defaultLabels - delete attsToSave[dLabel.key] + if attsToSave.secondLsThings? + toDel = attsToSave.secondLsThings.filter (itx) -> + !itx.getItxThing().id? + for itx in toDel + attsToSave.secondLsThings.remove itx + if attsToSave.secondLsThings.length == 0 + delete attsToSave.secondLsThings - if @lsProperties.defaultFirstLsThingItx? - for itx in @lsProperties.defaultFirstLsThingItx - delete attsToSave[itx.key] + if @lsProperties.defaultLabels? + for dLabel in @lsProperties.defaultLabels + delete attsToSave[dLabel.key] - if @lsProperties.defaultSecondLsThingItx? - for itx in @lsProperties.defaultSecondLsThingItx - delete attsToSave[itx.key] + if @lsProperties.defaultFirstLsThingItx? + for itx in @lsProperties.defaultFirstLsThingItx + delete attsToSave[itx.key] + + if @lsProperties.defaultSecondLsThingItx? + console.log "deleting empty 2nd ls thing itxs" + + for itx in @lsProperties.defaultSecondLsThingItx + delete attsToSave[itx.key] - if @deleteEmptyLabelsAndValsBeforeSave if @lsProperties.defaultValues? for dValue in @lsProperties.defaultValues if attsToSave[dValue.key]? diff --git a/modules/ServerAPI/src/client/ThingInteraction.coffee b/modules/ServerAPI/src/client/ThingInteraction.coffee index a29b6e7e6..b85aad45f 100644 --- a/modules/ServerAPI/src/client/ThingInteraction.coffee +++ b/modules/ServerAPI/src/client/ThingInteraction.coffee @@ -30,9 +30,9 @@ class window.FirstThingItx extends ThingItx className: "FirstThingItx" defaults: -> - super() - firstLsThing: {} - + _(super()).extend( + firstLsThing: {} + ) getItxThing: -> @get 'firstLsThing' @@ -43,8 +43,9 @@ class window.SecondThingItx extends ThingItx className: "SecondThingItx" defaults: -> - super() - secondLsThing: {} + _(super()).extend( + secondLsThing: {} + ) getItxThing: -> @get 'secondLsThing' From 5b28999fc3c5c2001c05fdd5c34fe46ffd368b82 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Thu, 29 Jun 2017 10:55:02 -0700 Subject: [PATCH 071/576] continued development of state edit table --- .../client/ACASFormStateDisplayUpdate.coffee | 23 ++++++++++------ .../src/client/ACASFormStateDisplayView.html | 27 +++++++++++++++---- .../ServerAPI/src/client/ExampleThing.coffee | 5 ++-- .../server/routes/ThingServiceRoutes.coffee | 10 ++++++- 4 files changed, 48 insertions(+), 17 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee index 7cba51ea6..d574bd8e0 100644 --- a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee +++ b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee @@ -154,21 +154,27 @@ class window.ACASFormStateDisplayOldValueController extends Backbone.View attrs.changedDate = UtilityFunctions::convertMSToYMDDate @model.get('modifiedDate') else attrs.changedDate = UtilityFunctions::convertMSToYMDDate @model.get('recordedDate') - - if @model.get 'ignored' - attrs.reason = "not implemented" - else - attrs.reason = "current value" + attrs.reason = "current value" $(@el).empty() $(@el).html @template(attrs) + if @model.get 'ignored' + $.ajax + type: 'GET' + url: "/api/transaction/"+@model.get 'lsTransaction' + json: true + success: (response) => + @$('.bv_reason').html response.comments + @ class window.ACASFormStateDisplayValueEditController extends Backbone.View - template: _.template($("#ACASFormStateDisplayValueEditView").html()) + events: -> + "keyup .bv_reasonForUpdate": "reasonForUpdateChanged" + initialize: -> render: => @@ -184,9 +190,10 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View @ + setupEditor: -> + + #TODO value editor: -# - new node service to fetch transaction to display change reason -# http://localhost:8080/acas/lstransactions/42 # - maybe show transaction creator as modified by and date? # - style value editor so it floats or slides down from top of table or something. It should be modal # - trigger save at thing level, wait for success to close diff --git a/modules/Components/src/client/ACASFormStateDisplayView.html b/modules/Components/src/client/ACASFormStateDisplayView.html index bb5358c44..88998b28e 100644 --- a/modules/Components/src/client/ACASFormStateDisplayView.html +++ b/modules/Components/src/client/ACASFormStateDisplayView.html @@ -16,14 +16,14 @@
    launching controller must provide or set table label"><%=value%> <%=changedBy%> <%=changedDate%> - <%=reason%> + <%=reason%> diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index ac2df8f44..bdfcdb34d 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -357,8 +357,8 @@ ExampleTableAuditConf = stateType: 'metadata' stateKind: 'example thing data' tableWrapper: "bv_dataTable" - tableLabel: "Example Thing Data Table - Audit Mode" - auditMode: true + tableLabel: "Example Thing Data Table - Edit Mode" + allowEdit: true # sortKind: 'media component' values: [ modelDefaults: @@ -463,7 +463,6 @@ class window.ExampleTableAuditController extends AbstractThingFormController modelChangeCallback: (method, model) => @trigger 'amDirty' - updateModel: => handleUpdateThing: => diff --git a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee index 6bbf9c812..77bd0f5bd 100644 --- a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee @@ -43,6 +43,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.get '/api/getThingCodeTablesByLabelText/:lsType/:lsKind/:labelText', loginRoutes.ensureAuthenticated, exports.getThingsByTypeAndKindAndLabelTypeAndLabelText app.post '/api/things/:lsType/:lsKind/codeNames/jsonArray', loginRoutes.ensureAuthenticated, exports.getThingsByCodeNames app.get '/api/thingKinds', loginRoutes.ensureAuthenticated, exports.getThingKinds + app.get '/api/transaction/:id', loginRoutes.ensureAuthenticated, exports.getTransaction exports.thingsByTypeKind = (req, resp) -> @@ -636,4 +637,11 @@ exports.getThingKinds = (req, resp) -> code: kind.kindName name: kind.kindName codeTables.push codeTable - resp.json codeTables \ No newline at end of file + resp.json codeTables + +exports.getTransaction = (req, resp) -> + config = require '../conf/compiled/conf.js' + serverUtilityFunctions = require './ServerUtilityFunctions.js' + baseurl = config.all.client.service.persistence.fullpath+"lstransactions/"+req.params.id + serverUtilityFunctions.getFromACASServer baseurl, resp + From 55f4f135a9721bddee812966ea365f55cc2fcb3e Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 29 Jun 2017 12:01:42 -0700 Subject: [PATCH 072/576] fixing bad merge with developement for bugfix/fix-system-tests --- gulpfile.coffee | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gulpfile.coffee b/gulpfile.coffee index ec0a3edf7..47b9dc8ad 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -89,6 +89,25 @@ getAssetsPath = (path) -> path.dirname = outputDirname return +addREnvironmentCleanUp = (file,contents) -> + # file contents are handed + # over as buffers + if path.extname(file.path) in [".R",".r"] && contents.match('# ROUTE:.*') + cleanFunction = "racas::cleanEnvironment()" + contents = "#{cleanFunction}\n\r#{contents}\r\n#{cleanFunction}\r\n" + return contents + +modify = (options = {}) -> + through.obj (file, enc, next) -> + error = null + if file.isBuffer() + if fileModifier = options.fileModifier + try + content = fileModifier file, file.contents.toString 'utf8' + file.contents = new Buffer content + catch _error + console.log _error + next error, file # ------------------------------------------------- Read Inputs From c1ff95e1a17f939621cbf2627edd27211b52fbba Mon Sep 17 00:00:00 2001 From: jmcneil86043 Date: Thu, 29 Jun 2017 13:27:14 -0700 Subject: [PATCH 073/576] Fixes #137 (#138) * Fixes #137 * removed extraneous console.logs --- conf/config.properties.example | 1 + .../SystemTest/spec/serviceTests/SystemTest.coffee | 12 ++++++------ .../src/server/routes/SystemTestRoutes.coffee | 11 +++++++---- 3 files changed, 14 insertions(+), 10 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 95851ae25..efb25e100 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -509,6 +509,7 @@ flyway.database.password=${server.database.password} server.acas.license=/home/runner/build/conf/acas.lic server.systemTest.runOnStart=${env.RUN_SYSTEM_TEST} +server.systemTest.runDestructive=false # Required configs for which base entity to use diff --git a/modules/SystemTest/spec/serviceTests/SystemTest.coffee b/modules/SystemTest/spec/serviceTests/SystemTest.coffee index b3d9c6cea..8f11e7455 100644 --- a/modules/SystemTest/spec/serviceTests/SystemTest.coffee +++ b/modules/SystemTest/spec/serviceTests/SystemTest.coffee @@ -25,7 +25,7 @@ prefix = "http" if config.all.client.use.ssl? && config.all.client.use.ssl prefix = "https" -describe "A. Connecting to ACAS", -> +describe "A. Connecting to ACAS -nondestructive", -> describe "by requesting #{prefix}://client.host:client.port", -> before (done) -> request "#{prefix}://"+config.all.client.host+":"+config.all.client.port, (error, response, body) => @@ -43,7 +43,7 @@ describe "A. Connecting to ACAS", -> # B. Database Communication # ############################# -describe "B. Connecting to the database", -> +describe "B. Connecting to the database -nondestructive", -> describe "through tomcat", -> before (done) -> @timeout 600000 @@ -195,7 +195,7 @@ describe "C. Writing a file to", -> # D. Communication with rApache # ################################# -describe "D. Access to rApache", -> +describe "D. Access to rApache -nondestructive", -> @timeout 10000 before (done) -> request config.all.client.service.rapache.fullpath + "hello", (error, response, body) => @@ -366,8 +366,8 @@ describe "E. System Tests", => if @output.results.htmlSummary.indexOf("Upload completed.") != -1 global.cleanup.sel = true - describe "check result viewers", -> - describe "check live design", -> + describe "check result viewers", => + describe "check live design", => if "LiveDesign" not in config.all.client.service.result.viewer.configuredViewers.split(',') @.pending = true describe "install live design python client", -> @@ -381,7 +381,7 @@ describe "E. System Tests", => assert(!@output.hasError) it "Successfully installed ldclient", -> assert(@output.messages.indexOf("Successfully installed") != -1) - describe "check live design sel report", -> + describe "check live design sel report", => before (done) -> waitToStart = 60000 repeat = 10 diff --git a/modules/SystemTest/src/server/routes/SystemTestRoutes.coffee b/modules/SystemTest/src/server/routes/SystemTestRoutes.coffee index 12324f665..b6d5dde41 100644 --- a/modules/SystemTest/src/server/routes/SystemTestRoutes.coffee +++ b/modules/SystemTest/src/server/routes/SystemTestRoutes.coffee @@ -826,15 +826,18 @@ exports.runSystemTestInternal = (force, callback) -> else if force || err.code == 'ENOENT' Mocha = require('mocha') # Instantiate a Mocha instance. - mocha = new Mocha { + mochaOpts = reporter: 'mochawesome' - reporterOptions: { + reporterOptions: reportDir: path.resolve(path.join(config.all.server.datafiles.relative_path, "systemReport/")), reportName: 'systemReport', reportTitle: 'ACAS System Report', inlineAssets: true - } - } + + unless config.all.server.systemTest.runDestructive + mochaOpts.grep = "-nondestructive" + + mocha = new Mocha mochaOpts testDir = "src/spec/SystemTest/serviceTests" # Add each .js file to the mocha instance From 6539e2995490d48e7baa75a987ce6391dc698cfc Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 29 Jun 2017 15:16:10 -0700 Subject: [PATCH 074/576] Imported Ketcher from EPAM (GNU Affero GPL) and created new basic controller and view for it. --- .../client/ACASFormChemicalStructure.coffee | 25 + .../client/ACASFormChemicalStructureView.html | 4 + public/lib/ketcher-2.0.0-alpha.3/LICENSE | 632 ++++++++ public/lib/ketcher-2.0.0-alpha.3/demo.html | 126 ++ public/lib/ketcher-2.0.0-alpha.3/favicon.ico | Bin 0 -> 1078 bytes public/lib/ketcher-2.0.0-alpha.3/ketcher.css | 1 + public/lib/ketcher-2.0.0-alpha.3/ketcher.eot | Bin 0 -> 26576 bytes public/lib/ketcher-2.0.0-alpha.3/ketcher.html | 1322 +++++++++++++++++ public/lib/ketcher-2.0.0-alpha.3/ketcher.js | 1068 +++++++++++++ public/lib/ketcher-2.0.0-alpha.3/ketcher.py | 330 ++++ public/lib/ketcher-2.0.0-alpha.3/ketcher.svg | 138 ++ public/lib/ketcher-2.0.0-alpha.3/ketcher.ttf | Bin 0 -> 17072 bytes public/lib/ketcher-2.0.0-alpha.3/ketcher.woff | Bin 0 -> 16164 bytes public/lib/ketcher-2.0.0-alpha.3/logo.jpg | Bin 0 -> 5816 bytes .../ketcher-2.0.0-alpha.3/prototype-min.js | 8 + .../lib/ketcher-2.0.0-alpha.3/raphael.min.js | 3 + .../lib/ketcher-2.0.0-alpha.3/templates.sdf | 368 +++++ 17 files changed, 4025 insertions(+) create mode 100644 public/lib/ketcher-2.0.0-alpha.3/LICENSE create mode 100644 public/lib/ketcher-2.0.0-alpha.3/demo.html create mode 100644 public/lib/ketcher-2.0.0-alpha.3/favicon.ico create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.css create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.eot create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.html create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.js create mode 100755 public/lib/ketcher-2.0.0-alpha.3/ketcher.py create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.svg create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.ttf create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.woff create mode 100644 public/lib/ketcher-2.0.0-alpha.3/logo.jpg create mode 100644 public/lib/ketcher-2.0.0-alpha.3/prototype-min.js create mode 100644 public/lib/ketcher-2.0.0-alpha.3/raphael.min.js create mode 100644 public/lib/ketcher-2.0.0-alpha.3/templates.sdf diff --git a/modules/Components/src/client/ACASFormChemicalStructure.coffee b/modules/Components/src/client/ACASFormChemicalStructure.coffee index b523b3667..54ca2da13 100644 --- a/modules/Components/src/client/ACASFormChemicalStructure.coffee +++ b/modules/Components/src/client/ACASFormChemicalStructure.coffee @@ -63,3 +63,28 @@ class window.ACASFormChemicalStructureController extends Backbone.View #TODO Why is it making a call to WebHQ outside our server, and make it stop +class window.KetcherChemicalStructureController extends Backbone.View + tagName: "DIV" + template: _.template($("#KetcherChemicalStructureControllerView").html()) + + render: => + $(@el).empty() + $(@el).html @template() + + searchFrameURL = "/lib/ketcher-2.0.0-alpha.3/ketcher.html" + + @$('.bv_sketcherIFrame').attr 'src', searchFrameURL + + @$('.bv_sketcherIFrame').on 'load', @startSketcher + + @ + + startSketcher: => + @windowObj = @$('.bv_sketcherIFrame')[0].contentWindow + @trigger 'sketcherLoaded' + + getMol: -> + @windowObj.ketcher.getMolfile(); + + setMol: (molStr) -> + molStruct = @windowObj.ketcher.setMolecule molStr diff --git a/modules/Components/src/client/ACASFormChemicalStructureView.html b/modules/Components/src/client/ACASFormChemicalStructureView.html index 94e7147f1..269c44ff3 100644 --- a/modules/Components/src/client/ACASFormChemicalStructureView.html +++ b/modules/Components/src/client/ACASFormChemicalStructureView.html @@ -9,3 +9,7 @@

    Test sketcher thingy

    + + diff --git a/public/lib/ketcher-2.0.0-alpha.3/LICENSE b/public/lib/ketcher-2.0.0-alpha.3/LICENSE new file mode 100644 index 000000000..677c7cd75 --- /dev/null +++ b/public/lib/ketcher-2.0.0-alpha.3/LICENSE @@ -0,0 +1,632 @@ + Ketcher is Copyright (C) of EPAM Systems 2009-2015. + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published + by the Free Software Foundation, version 3 of the License. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS diff --git a/public/lib/ketcher-2.0.0-alpha.3/demo.html b/public/lib/ketcher-2.0.0-alpha.3/demo.html new file mode 100644 index 000000000..b72332b6a --- /dev/null +++ b/public/lib/ketcher-2.0.0-alpha.3/demo.html @@ -0,0 +1,126 @@ + + + + + + Ketcher demo + + + + + + + +

    Ketcher example

    + + +

    Ketcher interaction example

    +
    + +
      + + + + + + + +
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kbd{display:inline-block;position:absolute;right:.5em}#bond-common,#bond-stereo,#bond-query{position:static;overflow:visible;height:auto;width:auto}#bond-common:after,#bond-stereo:after,#bond-query:after{content:none}#bond{position:relative;overflow:hidden;height:40px;width:100%}#bond:after{font-size:7px;width:7px;height:7px;display:block;font-family:ketcher;content:'\e818';position:absolute;z-index:10;right:0;bottom:0}#bond:hover:after{color:#1a7090}#bond.opened{overflow:visible}}@media (max-height:700px) and (max-width:850px){li.opened button,li.opened #open-file .open,li.opened #save-file .save{font-size:12px}li.opened button:before,li.opened button:after,li.opened #open-file .open:before,li.opened #open-file .open:after,li.opened #save-file .save:before,li.opened #save-file .save:after{font-size:16px}#bond{height:32px;width:100%}}@media (max-height:600px){#rgroup,#transform,#bond{height:32px;width:100%}}@media 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.save:before{content:'\e826'}#rgroup-attpoints button:before,#rgroup-attpoints #open-file .open:before,#rgroup-attpoints #save-file .save:before{content:'\e827'}#rgroup-fragment button:before,#rgroup-fragment #open-file .open:before,#rgroup-fragment #save-file .save:before{content:'\e828'}#save button:before,#save #open-file .open:before,#save #save-file .save:before{content:'\e82b'}#select-fragment button:before,#select-fragment #open-file .open:before,#select-fragment #save-file .save:before{content:'\e82c'}#select-lasso button:before,#select-lasso #open-file .open:before,#select-lasso #save-file .save:before{content:'\e82d'}#select-rectangle button:before,#select-rectangle #open-file .open:before,#select-rectangle #save-file .save:before{content:'\e82e'}#settings button:before,#settings #open-file .open:before,#settings #save-file .save:before{content:'\e82f'}#sgroup button:before,#sgroup #open-file .open:before,#sgroup #save-file .save:before{content:'\e830'}#template-0 button:before,#template-0 #open-file .open:before,#template-0 #save-file .save:before{content:'\e831'}#template-1 button:before,#template-1 #open-file .open:before,#template-1 #save-file .save:before{content:'\e832'}#template-2 button:before,#template-2 #open-file .open:before,#template-2 #save-file .save:before{content:'\e833'}#template-3 button:before,#template-3 #open-file .open:before,#template-3 #save-file .save:before{content:'\e834'}#template-4 button:before,#template-4 #open-file .open:before,#template-4 #save-file .save:before{content:'\e835'}#template-5 button:before,#template-5 #open-file .open:before,#template-5 #save-file .save:before{content:'\e836'}#template-6 button:before,#template-6 #open-file .open:before,#template-6 #save-file .save:before{content:'\e837'}#template-7 button:before,#template-7 #open-file .open:before,#template-7 #save-file .save:before{content:'\e838'}#template-custom button:before,#template-custom #open-file .open:before,#template-custom #save-file .save:before{content:'\e839'}#transform-flip-h button:before,#transform-flip-h #open-file .open:before,#transform-flip-h #save-file .save:before{content:'\e83a'}#transform-flip-v button:before,#transform-flip-v #open-file .open:before,#transform-flip-v #save-file .save:before{content:'\e83b'}#transform-rotate button:before,#transform-rotate #open-file .open:before,#transform-rotate #save-file .save:before{content:'\e83c'}#undo button:before,#undo #open-file .open:before,#undo #save-file .save:before{content:'\e83d'}#zoom-in button:before,#zoom-in #open-file .open:before,#zoom-in #save-file .save:before{content:'\e83e'}#zoom-out button:before,#zoom-out #open-file .open:before,#zoom-out #save-file .save:before{content:'\e83f'}#rgroup-label button:before,#rgroup-label #open-file .open:before,#rgroup-label #save-file .save:before{content:'\e829';color:#739fc6}#rgroup-label button:after,#rgroup-label #open-file .open:after,#rgroup-label #save-file 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      • +       +
      • +       + + + + + diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.js b/public/lib/ketcher-2.0.0-alpha.3/ketcher.js new file mode 100644 index 000000000..2c9589f28 --- /dev/null +++ b/public/lib/ketcher-2.0.0-alpha.3/ketcher.js @@ -0,0 +1,1068 @@ +/**************************************************************************** + * Copyright (C) 2009-2017. EPAM Systems. + * + * This file may be distributed and/or modified under the terms of the + * GNU Affero General Public License version 3 as published by the Free + * Software Foundation and appearing in the file LICENSE included in + * the packaging of this file. + * + * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE + * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. + ***************************************************************************/ + +(function(f){if(typeof exports==="object"&&typeof module!=="undefined"){module.exports=f()}else if(typeof define==="function"&&define.amd){define([],f)}else{var g;if(typeof window!=="undefined"){g=window}else if(typeof global!=="undefined"){g=global}else if(typeof self!=="undefined"){g=self}else{g=this}g.ketcher = f()}})(function(){var define,module,exports;return (function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o= 0; i--) { + chains = getNestedChains(allChains, scope.slice(0, i)); + if (!chains) { + continue; + } + matched = true; + for (var j = 0; j < seq.length; j++) { + key = seq[j]; + if (!chains[key]) { + matched = false; + break; + } + chains = chains[key]; + } + + if (matched) { + break; + } + } + + var definitionScope = scope.slice(0, i).join('.'); + var preventDefault = chains.preventDefault; + + // partial match, save the sequence + if (matched && !chains.handlers) { + sequence = seq; + if (preventDefault) { + e.preventDefault(); + } + return; + } + + if (matched) { + for (i = 0; i < chains.handlers.length; i++) { + var handler = chains.handlers[i]; + var options = handler._keymage; + + var res = handler.call(options.context, e, { + shortcut: options.original, + scope: currentScope, + definitionScope: definitionScope + }); + + if (res === false || preventDefault) { + e.preventDefault(); + } + } + } + + // either matched or not, drop the sequence + sequence = []; + } + + function getHandlers(scope, keychain, fn) { + var bits = scope.split('.'); + var chains = allChains; + bits = bits.concat(keychain); + + for (var i = 0, l = bits.length; i < l; i++) { + var bit = bits[i]; + if (!bit) continue; + + chains = chains[bit] || (chains[bit] = {}); + if (fn && fn._keymage.preventDefault) { + chains.preventDefault = true; + } + + if (i === l - 1) { + var handlers = chains.handlers || (chains.handlers = []); + return handlers; + } + } + } + + function assignKey(scope, keychain, fn) { + var handlers = getHandlers(scope, keychain, fn); + handlers.push(fn); + } + + function unassignKey(scope, keychain, fn) { + var handlers = getHandlers(scope, keychain); + var idx = handlers.indexOf(fn); + if (~idx) { + handlers.splice(idx, 1); + } + } + + function parsed(scope, keychain, fn, options) { + if (keychain === undefined && fn === undefined) { + return function(keychain, fn) { + return keymage(scope, keychain, fn); + }; + } + + if (typeof keychain === 'function') { + options = fn; + fn = keychain; + keychain = scope; + scope = ''; + } + + var normalized = normalizeKeyChain(keychain); + + return [scope, normalized, fn, options]; + } + + // optional arguments: scope, options. + function keymage(scope, keychain, fn, options) { + var args = parsed(scope, keychain, fn, options); + fn = args[2]; + options = args[3]; + fn._keymage = options || {}; + fn._keymage.original = keychain; + assignKey.apply(null, args); + + return function () { + unassignKey.apply(null, args); + }; + } + + keymage.unbind = function(scope, keychain, fn) { + var args = parsed(scope, keychain, fn); + unassignKey.apply(null, args); + }; + + keymage.parse = parseKeyString; + keymage.stringify = stringifyKey; + + keymage.bindings = allChains; + + keymage.setScope = function(scope) { + currentScope = scope ? scope : ''; + }; + + keymage.getScope = function() { return currentScope; }; + + keymage.pushScope = function(scope) { + currentScope = (currentScope ? currentScope + '.' : '') + scope; + return currentScope; + }; + + keymage.popScope = function(scope) { + var i; + + if (!scope) { + i = currentScope.lastIndexOf('.'); + scope = currentScope.slice(i + 1); + currentScope = i == -1 ? '' : currentScope.slice(0, i); + return scope; + } + + currentScope = currentScope.replace( + new RegExp('(^|\\.)' + scope + '(\\.|$).*'), ''); + return scope; + }; + + keymage.version = VERSION; + + window.addEventListener('keydown', dispatch, false); + + return keymage; +}); +})(typeof define !== 'undefined' ? define : function(factory) { + if (typeof module !== 'undefined') { + module.exports = factory(); + } else { + window.keymage = factory(); + } +}); + +},{}],3:[function(require,module,exports){ +(function(root) { + + // Use polyfill for setImmediate for performance gains + var asap = (typeof setImmediate === 'function' && setImmediate) || + function(fn) { setTimeout(fn, 1); }; + + // Polyfill for Function.prototype.bind + function bind(fn, thisArg) { + return function() { + fn.apply(thisArg, arguments); + } + } + + var isArray = Array.isArray || function(value) { return Object.prototype.toString.call(value) === "[object Array]" }; + + function Promise(fn) { + if (typeof this !== 'object') throw new TypeError('Promises must be constructed via new'); + if (typeof fn !== 'function') throw new TypeError('not a function'); + this._state = null; + this._value = null; + this._deferreds = [] + + doResolve(fn, bind(resolve, this), bind(reject, this)) + } + + function handle(deferred) { + var me = this; + if (this._state === null) { + this._deferreds.push(deferred); + return + } + asap(function() { + var cb = me._state ? deferred.onFulfilled : deferred.onRejected + if (cb === null) { + (me._state ? deferred.resolve : deferred.reject)(me._value); + return; + } + var ret; + try { + ret = cb(me._value); + } + catch (e) { + deferred.reject(e); + return; + } + deferred.resolve(ret); + }) + } + + function resolve(newValue) { + try { //Promise Resolution Procedure: https://github.com/promises-aplus/promises-spec#the-promise-resolution-procedure + if (newValue === this) throw new TypeError('A promise cannot be resolved with itself.'); + if (newValue && (typeof newValue === 'object' || typeof newValue === 'function')) { + var then = newValue.then; + if (typeof then === 'function') { + doResolve(bind(then, newValue), bind(resolve, this), bind(reject, this)); + return; + } + } + this._state = true; + this._value = newValue; + finale.call(this); + } catch (e) { reject.call(this, e); } + } + + function reject(newValue) { + this._state = false; + this._value = newValue; + finale.call(this); + } + + function finale() { + for (var i = 0, len = this._deferreds.length; i < len; i++) { + handle.call(this, this._deferreds[i]); + } + this._deferreds = null; + } + + function Handler(onFulfilled, onRejected, resolve, reject){ + this.onFulfilled = typeof onFulfilled === 'function' ? onFulfilled : null; + this.onRejected = typeof onRejected === 'function' ? onRejected : null; + this.resolve = resolve; + this.reject = reject; + } + + /** + * Take a potentially misbehaving resolver function and make sure + * onFulfilled and onRejected are only called once. + * + * Makes no guarantees about asynchrony. + */ + function doResolve(fn, onFulfilled, onRejected) { + var done = false; + try { + fn(function (value) { + if (done) return; + done = true; + onFulfilled(value); + }, function (reason) { + if (done) return; + done = true; + onRejected(reason); + }) + } catch (ex) { + if (done) return; + done = true; + onRejected(ex); + } + } + + Promise.prototype['catch'] = function (onRejected) { + return this.then(null, onRejected); + }; + + Promise.prototype.then = function(onFulfilled, onRejected) { + var me = this; + return new Promise(function(resolve, reject) { + handle.call(me, new Handler(onFulfilled, onRejected, resolve, reject)); + }) + }; + + Promise.all = function () { + var args = Array.prototype.slice.call(arguments.length === 1 && isArray(arguments[0]) ? arguments[0] : arguments); + + return new Promise(function (resolve, reject) { + if (args.length === 0) return resolve([]); + var remaining = args.length; + function res(i, val) { + try { + if (val && (typeof val === 'object' || typeof val === 'function')) { + var then = val.then; + if (typeof then === 'function') { + then.call(val, function (val) { res(i, val) }, reject); + return; + } + } + args[i] = val; + if (--remaining === 0) { + resolve(args); + } + } catch (ex) { + reject(ex); + } + } + for (var i = 0; i < args.length; i++) { + res(i, args[i]); + } + }); + }; + + Promise.resolve = function (value) { + if (value && typeof value === 'object' && value.constructor === Promise) { + return value; + } + + return new Promise(function (resolve) { + resolve(value); + }); + }; + + Promise.reject = function (value) { + return new Promise(function (resolve, reject) { + reject(value); + }); + }; + + Promise.race = function (values) { + return new Promise(function (resolve, reject) { + for(var i = 0, len = values.length; i < len; i++) { + values[i].then(resolve, reject); + } + }); + }; + + /** + * Set the immediate function to execute callbacks + * @param fn {function} Function to execute + * @private + */ + Promise._setImmediateFn = function _setImmediateFn(fn) { + asap = fn; + }; + + if (typeof module !== 'undefined' && module.exports) { + module.exports = Promise; + } else if (!root.Promise) { + root.Promise = Promise; + } + +})(this); +},{}],4:[function(require,module,exports){ +'use strict'; +var strictUriEncode = require('strict-uri-encode'); + +exports.extract = function (str) { + return str.split('?')[1] || ''; +}; + +exports.parse = function (str) { + if (typeof str !== 'string') { + return {}; + } + + str = str.trim().replace(/^(\?|#|&)/, ''); + + if (!str) { + return {}; + } + + return str.split('&').reduce(function (ret, param) { + var parts = param.replace(/\+/g, ' ').split('='); + // Firefox (pre 40) decodes `%3D` to `=` + // https://github.com/sindresorhus/query-string/pull/37 + var key = parts.shift(); + var val = parts.length > 0 ? parts.join('=') : undefined; + + key = decodeURIComponent(key); + + // missing `=` should be `null`: + // http://w3.org/TR/2012/WD-url-20120524/#collect-url-parameters + val = val === undefined ? null : decodeURIComponent(val); + + if (!ret.hasOwnProperty(key)) { + ret[key] = val; + } else if (Array.isArray(ret[key])) { + ret[key].push(val); + } else { + ret[key] = [ret[key], val]; + } + + return ret; + }, {}); +}; + +exports.stringify = function (obj) { + return obj ? Object.keys(obj).sort().map(function (key) { + var val = obj[key]; + + if (Array.isArray(val)) { + return val.sort().map(function (val2) { + return strictUriEncode(key) + '=' + strictUriEncode(val2); + }).join('&'); + } + + return strictUriEncode(key) + '=' + strictUriEncode(val); + }).filter(function (x) { + return x.length > 0; + }).join('&') : ''; +}; + +},{"strict-uri-encode":5}],5:[function(require,module,exports){ +'use strict'; +module.exports = function (str) { + return encodeURIComponent(str).replace(/[!'()*]/g, function (c) { + return '%' + c.charCodeAt(0).toString(16).toUpperCase(); + }); +}; + +},{}],6:[function(require,module,exports){ +var xhrFactory = (function getXHRfactory (factories) { + for (var i=0, xhr, X, len=factories.length; i0?1:-1},chem.CisTrans.prototype._sameside=function(e,t,s,i){return this.sameside(this.molecule.atoms.get(e).pp,this.molecule.atoms.get(t).pp,this.molecule.atoms.get(s).pp,this.molecule.atoms.get(i).pp)},chem.CisTrans.prototype._sortSubstituents=function(e){var t=this.molecule.atoms.get(e[0]).pureHydrogen(),s=e[1]<0||this.molecule.atoms.get(e[1]).pureHydrogen(),i=this.molecule.atoms.get(e[2]).pureHydrogen(),r=e[3]<0||this.molecule.atoms.get(e[3]).pureHydrogen();return(!t||!s)&&((!i||!r)&&(s?e[1]=-1:t?(e[0]=e[1],e[1]=-1):e[0]>e[1]&&e.swap(0,1),r?e[3]=-1:i?(e[2]=e[3],e[3]=-1):e[2]>e[3]&&e.swap(2,3),!0))},chem.CisTrans.prototype.isGeomStereoBond=function(e,t){var s=this.molecule.bonds.get(e);if(s.type!=chem.Struct.BOND.TYPE.DOUBLE)return!1;var i=this.molecule.atoms.get(s.begin).label,r=this.molecule.atoms.get(s.end).label;if("C"!=i&&"N"!=i&&"Si"!=i&&"Ge"!=i)return!1;if("C"!=r&&"N"!=r&&"Si"!=r&&"Ge"!=r)return!1;var n=this.getNeighbors.call(this.context,s.begin),o=this.getNeighbors.call(this.context,s.end);if(n.length<2||n.length>3||o.length<2||o.length>3)return!1;t[0]=-1,t[1]=-1,t[2]=-1,t[3]=-1;var u,a;for(u=0;u=0&&this.vertices[v].branches--}this.vertices[h].branches++,this.vertices[f].parent_vertex=h,this.vertices[f].parent_edge=u,this.vertices[f].dfs_state=1,s.push(f)}}}},chem.Dfs.prototype.edgeClosingCycle=function(e){return 0!=this.edges[e].closing_cycle},chem.Dfs.prototype.numBranches=function(e){return this.vertices[e].branches},chem.Dfs.prototype.numOpeningCycles=function(e){return this.edges[e].opening_cycles},chem.Dfs.prototype.toString=function(){var e="";return this.v_seq.each(function(t){e+=t.idx+" -> "}),e+="*"}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../util/":39,"../util/set":42,"./element":10}],10:[function(require,module,exports){ +function el(e,l,f,a,b){return{label:e,period:l,group:f,putHydrogenOnTheLeft:a,color:b||"#000000"}}var Map=require("../util/map"),element=new Map({1:el("H",1,1,!1,"#000000"),2:el("He",1,8,!1,"#d9ffff"),3:el("Li",2,1,!1,"#cc80ff"),4:el("Be",2,2,!1,"#c2ff00"),5:el("B",2,3,!1,"#ffb5b5"),6:el("C",2,4,!1,"#000000"),7:el("N",2,5,!1,"#304ff7"),8:el("O",2,6,!0,"#ff0d0d"),9:el("F",2,7,!0,"#8fe04f"),10:el("Ne",2,8,!1,"#b3e3f5"),11:el("Na",3,1,!1,"#ab5cf2"),12:el("Mg",3,2,!1,"#8aff00"),13:el("Al",3,3,!1,"#bfa6a6"),14:el("Si",3,4,!1,"#f0c7a1"),15:el("P",3,5,!1,"#ff8000"),16:el("S",3,6,!0,"#d9a61a"),17:el("Cl",3,7,!0,"#1fd01f"),18:el("Ar",3,8,!1,"#80d1e3"),19:el("K",4,1,!1,"#8f40d4"),20:el("Ca",4,2,!1,"#3dff00"),21:el("Sc",4,3,!1,"#e6e6e6"),22:el("Ti",4,4,!1,"#bfc2c7"),23:el("V",4,5,!1,"#a6a6ab"),24:el("Cr",4,6,!1,"#8a99c7"),25:el("Mn",4,7,!1,"#9c7ac7"),26:el("Fe",4,8,!1,"#e06633"),27:el("Co",4,8,!1,"#f08fa1"),28:el("Ni",4,8,!1,"#4fd14f"),29:el("Cu",4,1,!1,"#c78033"),30:el("Zn",4,2,!1,"#7d80b0"),31:el("Ga",4,3,!1,"#c28f8f"),32:el("Ge",4,4,!1,"#668f8f"),33:el("As",4,5,!1,"#bd80e3"),34:el("Se",4,6,!0,"#ffa100"),35:el("Br",4,7,!0,"#a62929"),36:el("Kr",4,8,!1,"#5cb8d1"),37:el("Rb",5,1,!1,"#702eb0"),38:el("Sr",5,2,!1,"#00ff00"),39:el("Y",5,3,!1,"#94ffff"),40:el("Zr",5,4,!1,"#94e0e0"),41:el("Nb",5,5,!1,"#73c2c9"),42:el("Mo",5,6,!1,"#54b5b5"),43:el("Tc",5,7,!1,"#3b9e9e"),44:el("Ru",5,8,!1,"#248f8f"),45:el("Rh",5,8,!1,"#0a7d8c"),46:el("Pd",5,8,!1,"#006985"),47:el("Ag",5,1,!1,"#bfbfbf"),48:el("Cd",5,2,!1,"#ffd98f"),49:el("In",5,3,!1,"#a67573"),50:el("Sn",5,4,!1,"#668080"),51:el("Sb",5,5,!1,"#9e63b5"),52:el("Te",5,6,!1,"#d47a00"),53:el("I",5,7,!0,"#940094"),54:el("Xe",5,8,!1,"#429eb0"),55:el("Cs",6,1,!1,"#57178f"),56:el("Ba",6,2,!1,"#00c900"),57:el("La",6,3,!1,"#70d4ff"),58:el("Ce",6,3,!1,"#ffffc7"),59:el("Pr",6,3,!1,"#d9ffc7"),60:el("Nd",6,3,!1,"#c7ffc7"),61:el("Pm",6,3,!1,"#a3ffc7"),62:el("Sm",6,3,!1,"#8fffc7"),63:el("Eu",6,3,!1,"#61ffc7"),64:el("Gd",6,3,!1,"#45ffc7"),65:el("Tb",6,3,!1,"#30ffc7"),66:el("Dy",6,3,!1,"#1fffc7"),67:el("Ho",6,3,!1,"#00ff9c"),68:el("Er",6,3,!1,"#00e675"),69:el("Tm",6,3,!1,"#00d452"),70:el("Yb",6,3,!1,"#00bf38"),71:el("Lu",6,3,!1,"#00ab24"),72:el("Hf",6,4,!1,"#4dc2ff"),73:el("Ta",6,5,!1,"#4da6ff"),74:el("W",6,6,!1,"#2194d6"),75:el("Re",6,7,!1,"#267dab"),76:el("Os",6,8,!1,"#266696"),77:el("Ir",6,8,!1,"#175487"),78:el("Pt",6,8,!1,"#d1d1e0"),79:el("Au",6,1,!1,"#ffd124"),80:el("Hg",6,2,!1,"#b8b8d1"),81:el("Tl",6,3,!1,"#a6544d"),82:el("Pb",6,4,!1,"#575961"),83:el("Bi",6,5,!1,"#9e4fb5"),84:el("Po",6,6,!1,"#ab5c00"),85:el("At",6,7,!1,"#754f45"),86:el("Rn",6,8,!1,"#428296"),87:el("Fr",7,1,!1,"#420066"),88:el("Ra",7,2,!1,"#007d00"),89:el("Ac",7,3,!1,"#70abfa"),90:el("Th",7,3,!1,"#00baff"),91:el("Pa",7,3,!1,"#00a1ff"),92:el("U",7,3,!1,"#008fff"),93:el("Np",7,3,!1,"#0080ff"),94:el("Pu",7,3,!1,"#006bff"),95:el("Am",7,3,!1,"#545cf2"),96:el("Cm",7,3,!1,"#785ce3"),97:el("Bk",7,3,!1,"#8a4fe3"),98:el("Cf",7,3,!1,"#a136d4"),99:el("Es",7,3,!1,"#b31fd4"),100:el("Fm",7,3,!1,"#000000"),101:el("Md",7,3,!1,"#000000"),102:el("No",7,3,!1,"#000000"),103:el("Lr",7,3,!1,"#000000"),104:el("Rf",7,4,!1,"#4dc2ff"),105:el("Db",7,5,!1,"#4da6ff"),106:el("Sg",7,6,!1,"#2194d6"),107:el("Bh",7,7,!1,"#267dab"),108:el("Hs",7,8,!1,"#266696"),109:el("Mt",7,8,!1,"#175487"),110:el("Ds",7,8,!1,"#d1d1e0"),111:el("Rg",7,1,!1,"#ffd124"),112:el("Cn",7,2,!1,"#b8b8d1"),113:el("Uut",7,3,!1),114:el("Fl",7,4,!1),115:el("Uup",7,5,!1),116:el("Lv",7,6,!1),117:el("Uus",7,7,!1),118:el("Uuo",7,8,!1)}),labelMap=null;element.getElementByLabel=function(e){return labelMap||(labelMap={},element.each(function(e,l){labelMap[l.label]=e-0})),labelMap[e]||null},module.exports=element; + +},{"../util/map":40}],11:[function(require,module,exports){ +(function (global){ +require("./struct"),require("./cis_trans"),require("./dfs"),require("./molfile"),require("./sgroup"),require("./smiles"),require("./stereocenters"),require("./struct_valence"),global.chem=global.chem||{}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"./cis_trans":8,"./dfs":9,"./molfile":12,"./sgroup":13,"./smiles":14,"./stereocenters":15,"./struct":16,"./struct_valence":17}],12:[function(require,module,exports){ +(function (global){ +var Map=require("../util/map"),Set=require("../util/set"),Vec2=require("../util/vec2"),element=require("./element"),util=require("../util"),chem=global.chem=global.chem||{};chem.Molfile=function(){},chem.Molfile.loadRGroupFragments=!0,chem.Molfile.parseDecimalInt=function(e){var t=parseInt(e,10);return isNaN(t)?0:t},chem.Molfile.partitionLine=function(e,t,r){for(var i=[],a=0,n=0;a0&&(M.ifthen=g),M.resth=1==w,M.range=S,n[d]=M}else if("APO"==c)o.get("attpnt")||o.set("attpnt",new Map),o.get("attpnt").update(l.readKeyValuePairs(p));else if("ALS"==c){o.get("atomList")||o.set("atomList",new Map);var v=l.parsePropertyLineAtomList(l.partitionLine(p,[1,3,3,1,1,1]),l.partitionLineFixed(p.slice(10),4,!1));o.get("atomList").update(v),o.get("label")||o.set("label",new Map);for(var D in v)o.get("label").set(D,"L#")}else if("STY"==c)l.initSGroup(a,p);else if("SST"==c)l.applySGroupProp(a,"subtype",p);else if("SLB"==c)l.applySGroupProp(a,"label",p,!0);else if("SPL"==c)l.applySGroupProp(a,"parent",p,!0,!0);else if("SCN"==c)l.applySGroupProp(a,"connectivity",p);else if("SAL"==c)l.applySGroupArrayProp(a,"atoms",p,-1);else if("SBL"==c)l.applySGroupArrayProp(a,"bonds",p,-1);else if("SPA"==c)l.applySGroupArrayProp(a,"patoms",p,-1);else if("SMT"==c){var b=l.parseDecimalInt(p.slice(0,4))-1;a[b].data.subscript=p.slice(4).strip()}else"SDT"==c?l.applyDataSGroupDesc(a,p):"SDD"==c?l.applyDataSGroupInfoLine(a,p):"SCD"==c?l.applyDataSGroupDataLine(a,p,!1):"SED"==c&&l.applyDataSGroupDataLine(a,p,!0)}++r}return o},chem.Molfile.applyAtomProp=function(e,t,r,i){t.each(function(t,i){e.get(t)[r]=i})},chem.Molfile.parseCTabV2000=function(e,t){var r,i=new chem.Struct,a=chem.Molfile,n=a.parseDecimalInt(t[0]),l=a.parseDecimalInt(t[1]),o=a.parseDecimalInt(t[2]);i.isChiral=0!=a.parseDecimalInt(t[4]);var s=a.parseDecimalInt(t[5]),c=a.parseDecimalInt(t[10]),p=0,h=e.slice(p,p+n);p+=n;var u=e.slice(p,p+l);p+=l;var m=e.slice(p,p+o);p+=o+s;var f=h.map(a.parseAtomLine);for(r=0;r=0){var b=g[D-1];"GEN"===b.type&&(v.atoms=util.array(b.atoms))}}}for(S in g)chem.SGroup.addGroup(i,g[S],M);var N=[];for(S in g)chem.SGroup.filter(i,g[S],M),0!=g[S].atoms.length||g[S].allAtoms||N.push(S);for(r=0;rn+1&&i.push(e.slice(n+1,r)),n=r);return r>n+1&&i.push(e.slice(n+1,r)),n=r,i},chem.Molfile.splitonce=function(e,t){var r=e.indexOf(t);return[e.slice(0,r),e.slice(r+1)]},chem.Molfile.splitSGroupDef=function(e){for(var t=[],r=0,i=!1,a=0;a0&&t.push(e.strip()),t},chem.Molfile.parseBracedNumberList=function(e,t){if(!e)return null;var r=[];e=e.strip(),e=e.substr(1,e.length-2);var i=e.split(" ");t=t||0;for(var a=1;a0&&(d.ifthen=u),d.resth=1==m,d.range=f,i[l]=d,a++}}}for(var g in r)for(var w=0;wr[s];)++s;n[s]=n[s]||{},Set.mergeIn(n[s],t[a])}var c=[],p=[],h=[];for(a=0;a0,e.rxnArrows.count()>1)throw new Error("Reaction may not contain more than one arrow");if(this.molfile="",this.reaction){if(e.rgroups.count()>0)throw new Error("Unable to save the structure - reactions with r-groups are not supported at the moment");var a=chem.MolfileSaver.getComponents(e),n=a.reactants,l=a.products,o=n.concat(l);this.molfile="$RXN\n\n\n\n"+util.paddedInt(n.length,3)+util.paddedInt(l.length,3)+util.paddedInt(0,3)+"\n";for(var s=0;s0){if(!r){var u=new chem.MolfileSaver(!1).getCTab(e.getScaffold(),e.rgroups);return this.molfile="$MDL REV 1\n$MOL\n$HDR\n\n\n\n$END HDR\n",this.molfile+="$CTAB\n"+u+"$END CTAB\n",e.rgroups.each(function(t,r){this.molfile+="$RGP\n",this.writePaddedNumber(t,3),this.molfile+="\n",r.frags.each(function(t,r){var i=new chem.MolfileSaver(!1).getCTab(e.getFragment(r));this.molfile+="$CTAB\n"+i+"$END CTAB\n"},this),this.molfile+="$END RGP\n"},this),this.molfile+="$END MOL\n",this.molfile}e=e.getScaffold()}return this.molecule=e.clone(),this.prepareSGroups(t,i),this.writeHeader(),this.writeCTab2000(),this.molfile},chem.MolfileSaver.prototype.writeHeader=function(){var e=new Date;this.writeCR(),this.writeWhiteSpace(2),this.write("Ketcher"),this.writeWhiteSpace(),this.writeCR((e.getMonth()+1).toPaddedString(2)+e.getDate().toPaddedString(2)+(e.getFullYear()%100).toPaddedString(2)+e.getHours().toPaddedString(2)+e.getMinutes().toPaddedString(2)+"2D 1 1.00000 0.00000 0"),this.writeCR()},chem.MolfileSaver.prototype.write=function(e){this.molfile+=e},chem.MolfileSaver.prototype.writeCR=function(e){0==arguments.length&&(e=""),this.molfile+=e+"\n"},chem.MolfileSaver.prototype.writeWhiteSpace=function(e){0==arguments.length&&(e=1),e.times(function(){this.write(" ")},this)},chem.MolfileSaver.prototype.writePadded=function(e,t){this.write(e),this.writeWhiteSpace(t-e.length)},chem.MolfileSaver.prototype.writePaddedNumber=function(e,t){var r=(e-0).toString();this.writeWhiteSpace(t-r.length),this.write(r)},chem.MolfileSaver.prototype.writePaddedFloat=function(e,t,r){this.write(util.paddedFloat(e,t,r))},chem.MolfileSaver.prototype.writeCTab2000Header=function(){this.writePaddedNumber(this.molecule.atoms.count(),3),this.writePaddedNumber(this.molecule.bonds.count(),3),this.writePaddedNumber(0,3),this.writeWhiteSpace(3),this.writePaddedNumber(this.molecule.isChiral?1:0,3),this.writePaddedNumber(0,3),this.writeWhiteSpace(12),this.writePaddedNumber(999,3),this.writeCR(" V2000")},chem.MolfileSaver.prototype.writeCTab2000=function(e){this.writeCTab2000Header(),this.mapping={};var t=1,r=[],i=[];for(this.molecule.atoms.each(function(e,a){this.writePaddedFloat(a.pp.x,10,4),this.writePaddedFloat(-a.pp.y,10,4),this.writePaddedFloat(0,10,4),this.writeWhiteSpace();var n=a.label;null!=a.atomList?(n="L",r.push(e)):null==element.getElementByLabel(n)&&-1==["A","Q","X","*","R#"].indexOf(n)&&(n="C",i.push(e)),this.writePadded(n,3),this.writePaddedNumber(0,2),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),Object.isUndefined(a.hCount)&&(a.hCount=0),this.writePaddedNumber(a.hCount,3),Object.isUndefined(a.stereoCare)&&(a.stereoCare=0),this.writePaddedNumber(a.stereoCare,3),this.writePaddedNumber(a.explicitValence<0?0:0==a.explicitValence?15:a.explicitValence,3),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),Object.isUndefined(a.aam)&&(a.aam=0),this.writePaddedNumber(a.aam,3),Object.isUndefined(a.invRet)&&(a.invRet=0),this.writePaddedNumber(a.invRet,3),Object.isUndefined(a.exactChangeFlag)&&(a.exactChangeFlag=0),this.writePaddedNumber(a.exactChangeFlag,3),this.writeCR(),this.mapping[e]=t,t++},this),this.bondMapping={},t=1,this.molecule.bonds.each(function(e,r){this.bondMapping[e]=t++,this.writePaddedNumber(this.mapping[r.begin],3),this.writePaddedNumber(this.mapping[r.end],3),this.writePaddedNumber(r.type,3),Object.isUndefined(r.stereo)&&(r.stereo=0),this.writePaddedNumber(r.stereo,3),this.writeWhiteSpace(3),Object.isUndefined(r.topology)&&(r.topology=0),this.writePaddedNumber(r.topology,3),Object.isUndefined(r.reactingCenterStatus)&&(r.reactingCenterStatus=0),this.writePaddedNumber(r.reactingCenterStatus,3),this.writeCR()},this);i.length>0;)this.write("A "),this.writePaddedNumber(i[0]+1,3),this.writeCR(),this.writeCR(this.molecule.atoms.get(i[0]).label),i.splice(0,1);var a=new Array,n=new Array,l=new Array,o=new Array,s=new Array,c=new Array,p=new Array,h=new Array,u=new Array;this.molecule.atoms.each(function(e,t){if(0!=t.charge&&a.push([e,t.charge]),0!=t.isotope&&n.push([e,t.isotope]),0!=t.radical&&l.push([e,t.radical]),null!=t.rglabel&&"R#"==t.label)for(var r=0;r<32;r++)t.rglabel&1<0||t.range.length>0){var r=" 1 "+util.paddedInt(e,3)+" "+util.paddedInt(t.ifthen,3)+" "+util.paddedInt(t.resth?1:0,3)+" "+t.range;s.push(r)}});var m=function(e,t){for(;t.length>0;){for(var r=new Array;t.length>0&&r.length<8;)r.push(t[0]),t.splice(0,1);this.write(e),this.writePaddedNumber(r.length,3),r.each(function(e){this.writeWhiteSpace(),this.writePaddedNumber(this.mapping[e[0]],3),this.writeWhiteSpace(),this.writePaddedNumber(e[1],3)},this),this.writeCR()}};m.call(this,"M CHG",a),m.call(this,"M ISO",n),m.call(this,"M RAD",l),m.call(this,"M RGP",o);for(var f=0;f0)for(f=0;f=0&&(this.write("M SPL"),this.writePaddedNumber(1,3),this.writeWhiteSpace(1),this.writePaddedNumber(N,3),this.writeWhiteSpace(1),this.writePaddedNumber(M[T],3),this.writeCR()),"SRU"==A.type&&A.data.connectivity){var C="";C+=" ",C+=util.stringPadded(N.toString(),3),C+=" ",C+=util.stringPadded(A.data.connectivity,3,!0),this.write("M SCN"),this.writePaddedNumber(1,3),this.write(C.toUpperCase()),this.writeCR()}"SRU"==A.type&&(this.write("M SMT "),this.writePaddedNumber(N,3),this.writeWhiteSpace(),this.write(A.data.subscript||"n"),this.writeCR()),this.writeCR(A.saveToMolfile(this.molecule,M,this.mapping,this.bondMapping))}this.writeCR("M END")},chem.Molfile.parseRxn=function(e){var t=chem.Molfile,r=e[0].strip().split(" ");return r.length>1&&"V3000"==r[1]?t.parseRxn3000(e):t.parseRxn2000(e)},chem.Molfile.parseRxn2000=function(e){var t=chem.Molfile;e=e.slice(4);var r=t.partitionLine(e[0],t.fmtInfo.rxnItemsPartition),i=r[0]-0,a=r[1]-0,n=r[2]-0;e=e.slice(1);for(var l=[];e.length>0&&"$MOL"==e[0].substr(0,4);){e=e.slice(1);for(var o=0;o2?r[2]-0:0,l=function(e){util.assert(e,"CTab format invalid")},o=[],s=[],c=null,p=[],h=0;h=0?s.push(e[o]):s.push(-1)}return s},chem.SGroup.removeNegative=function(t){for(var e=[],s=0;s=0&&e.push(t[s]);return e},chem.SGroup.filter=function(t,e,s){e.atoms=chem.SGroup.removeNegative(chem.SGroup.filterAtoms(e.atoms,s))},chem.SGroup.clone=function(t,e,s){var r=new chem.SGroup(t.type);for(var o in t.data)r.data[o]=t.data[o];return r.atoms=util.mapArray(t.atoms,e),r.pp=t.pp,r.bracketBox=t.bracketBox,r.patoms=null,r.bonds=null,r.allAtoms=t.allAtoms,r},chem.SGroup.addAtom=function(t,e){t.atoms.push(e)},chem.SGroup.removeAtom=function(t,e){for(var s=0;sm.d.y)&&(l=p)}var f=d[l],S=function(s,r){var o=e.ps(f.c.addScaled(f.n,r*f.h)),i=e.paper.text(o.x,o.y,s).attr({font:e.settings.font,"font-size":e.settings.fontszsub});c&&i.attr(c);var n=Box2Abs.fromRelBox(rnd.relBox(i.getBBox())),a=Math.max(Vec2.shiftRayBox(o,f.d.negated(),n),3)+2;i.translateAbs(a*f.d.x,a*f.d.y),t.push(i)};h&&S(h,.5),u&&S(u,-.5)},chem.SGroup.drawBracket=function(t,e,s,r,o,i,n,a){n=n||.25,a=a||1;var h=i.addScaled(o,-.5*a),u=i.addScaled(o,.5*a),c=h.addScaled(r,-n),d=u.addScaled(r,-n);return h=t.obj2scaled(h),u=t.obj2scaled(u),c=t.obj2scaled(c),d=t.obj2scaled(d),e.path("M {0}, {1} L {2} , {3} L {4} , {5} L {6} , {7}",c.x,c.y,h.x,h.y,u.x,u.y,d.x,d.y).attr(s.sgroupBracketStyle)},chem.SGroup.getBracketParameters=function(t,e,s,r,o,i,n,a){var h=function(t,e,s,r){this.c=t,this.d=e,this.n=e.rotateSC(1,0),this.w=s,this.h=r},u=[];return e.length<2?function(){o=o||new Vec2(1,0),i=i||o.rotateSC(1,0);var t=Math.min(.25,.3*r.sz().x),e=Vec2.lc2(o,r.p0.x,i,.5*(r.p0.y+r.p1.y)),s=Vec2.lc2(o,r.p1.x,i,.5*(r.p0.y+r.p1.y)),n=r.sz().y;u.push(new h(e,o.negated(),t,n),new h(s,o,t,n))}():2===e.length?function(){var s=t.bonds.get(e[0]),r=t.bonds.get(e[1]),o=s.getCenter(t),i=r.getCenter(t),c=-1,d=-1,l=-1,p=-1,m=Vec2.centre(o,i),g=Vec2.diff(i,o).normalized(),f=g.negated(),S=g.rotateSC(1,0),v=S.negated();util.each(t.sGroupForest.children.get(a),function(t){var e=n?n.ctab.sgroups.get(t).visel.boundingBox:null;util.isNull(e)||(e=e.translate((n.offset||new Vec2).negated()).transform(n.scaled2obj,n),c=Math.max(c,Vec2.shiftRayBox(o,f,e)),d=Math.max(d,Vec2.shiftRayBox(i,g,e)),l=Math.max(l,Vec2.shiftRayBox(m,S,e)),p=Math.max(p,Vec2.shiftRayBox(m,v,e)))},this),c=Math.max(c+.2,0),d=Math.max(d+.2,0),l=Math.max(Math.max(l,p)+.1,0);var b=1.5+l;u.push(new h(o.addScaled(f,c),f,.25,b),new h(i.addScaled(g,d),g,.25,b))}():function(){for(var r=0;r=0&&s.indexOf(e.end)>=0&&r.push(t)}),r},chem.SGroup.GroupMul={draw:function(t){var e=t.render,s=e.paper.set(),r=[],o=[],i=Set.fromList(this.atoms);chem.SGroup.getCrossBonds(r,o,t.molecule,i),chem.SGroup.bracketPos(this,e,t.molecule,o);var n=this.bracketBox,a=this.bracketDir,h=a.rotateSC(1,0);return this.areas=[n],chem.SGroup.drawBrackets(s,e,this,o,i,n,a,h,this.data.mul),s},saveToMolfile:function(t,e,s,r){var o=util.stringPadded(e[this.id],3),i=[];i=i.concat(chem.SGroup.makeAtomBondLines("SAL",o,util.idList(this.atomSet),s)),i=i.concat(chem.SGroup.makeAtomBondLines("SPA",o,util.idList(this.parentAtomSet),s)),i=i.concat(chem.SGroup.makeAtomBondLines("SBL",o,this.bonds,r));var n="M SMT "+o+" "+this.data.mul;return i.push(n),i=i.concat(chem.SGroup.bracketsToMolfile(t,this,o)),i.join("\n")},prepareForSaving:function(t){var e;this.atoms.sort(),this.atomSet=Set.fromList(this.atoms),this.parentAtomSet=Set.clone(this.atomSet);var s=[],r=[];if(t.bonds.each(function(t,e){Set.contains(this.parentAtomSet,e.begin)&&Set.contains(this.parentAtomSet,e.end)?s.push(t):(Set.contains(this.parentAtomSet,e.begin)||Set.contains(this.parentAtomSet,e.end))&&r.push(t)},this),0!=r.length&&2!=r.length)throw{id:this.id,"error-type":"cross-bond-number",message:"Unsupported cross-bonds number"};var o=-1,i=-1,n=null;if(2==r.length){var a=t.bonds.get(r[0]);o=Set.contains(this.parentAtomSet,a.begin)?a.begin:a.end;var h=t.bonds.get(r[1]);i=Set.contains(this.parentAtomSet,h.begin)?h.begin:h.end,n=h}var u=null,c=o,d=[];for(e=0;e=0){var p=t.bonds.get(r[0]);p.begin==o?p.begin=c:p.end=c}this.bonds=r},postLoad:function(t,e){this.data.mul=this.data.subscript-0;var s={};this.atoms=chem.SGroup.filterAtoms(this.atoms,e),this.patoms=chem.SGroup.filterAtoms(this.patoms,e);for(var r=1;r=0?util.paddedInt(i.nCharnCharsToDisplay,3):"ALL")+" 1 "+util.stringPadded(i.tagChar,1)+" "+util.paddedInt(i.daspPos,1)+" ";a.push(u);var c=util.normalizeNewlines(i.fieldValue).replace(/\n*$/,"");return c.split("\n").each(function(t){for(;t.length>69;)a.push("M SCD "+o+" "+t.slice(0,69)),t=t.slice(69);a.push("M SED "+o+" "+t)}),a.join("\n")},prepareForSaving:function(t){this.atoms=chem.SGroup.getAtoms(t,this)},postLoad:function(t,e){this.data.absolute||(this.pp=this.pp.add(chem.SGroup.getMassCentre(t,this.atoms)))}},chem.SGroup.TYPES={MUL:chem.SGroup.GroupMul,SRU:chem.SGroup.GroupSru,SUP:chem.SGroup.GroupSup,DAT:chem.SGroup.GroupDat,GEN:chem.SGroup.GroupGen},chem.SGroupForest=function(t){this.parent=new Map,this.children=new Map,this.children.set(-1,[]),this.molecule=t},chem.SGroupForest.prototype.getSGroupsBFS=function(){var t=[],e=[],s=-1;for(e=util.array(this.children.get(-1));e.length>0;){var s=e.shift();e=e.concat(this.children.get(s)),t.push(s)}return t},chem.SGroupForest.prototype.getAtomSets=function(){return this.molecule.sgroups.map(function(t,e){return Set.fromList(e.atoms)})},chem.SGroupForest.prototype.getAtomSetRelations=function(t,e,s){var r=new Map,o=new Map,s=this.getAtomSets();s.unset(t),s.each(function(t,s){o.set(t,Set.subset(e,s)),r.set(t,Set.subset(s,e)&&!Set.eq(s,e))},this);var i=s.findAll(function(t){return!!o.get(t)&&!(util.findIndex(this.children.get(t),function(t){return o.get(t)},this)>=0)},this);return util.assert(i.length<=1),{children:s.findAll(function(t,e){return r.get(t)&&!r.get(this.parent.get(t))},this),parent:0===i.length?-1:i[0]}},chem.SGroupForest.prototype.getPathToRoot=function(t){for(var e=[],s=t;s>=0;s=this.parent.get(s))util.assert(e.indexOf(s)<0,"SGroupForest: loop detected"),e.push(s);return e},chem.SGroupForest.prototype.validate=function(){var t=this.getAtomSets();this.molecule.sgroups.each(function(t){this.getPathToRoot(t)},this);var e=!0;return this.parent.each(function(s,r){r>=0&&!Set.subset(t.get(s),t.get(r))&&(e=!1)},this),this.children.each(function(s){for(var r=this.children.get(s),o=0;o=0){var l=this.atoms[c],g=h.numOpeningCycles(b);for(i=0;i=4)throw new Error("internal: pyramid overflow");o[r++]=n;break}if(4==r)r=o[0],o[0]=o[1],o[1]=o[2],o[2]=o[3],o[3]=r;else if(3!=r)throw new Error("cannot calculate chirality");chem.Stereocenters.isPyramidMappingRigid(o)?this.atoms[t].chirality=1:this.atoms[t].chirality=2},this)}catch(t){alert("Warning: "+t.message)}var _=[];_.push(0);var p=!0;for(s=0;s=0){for(h.numBranches(m)>1&&this.atoms[m].branch_cnt>0&&this.atoms[m].paren_written&&(this.smiles+=")"),g=h.numOpeningCycles(b),i=0;i=0){var v=h.numBranches(m);if(v>1&&this.atoms[m].branch_cntv)throw new Error("unexpected branch")}var S=t.bonds.get(b),w=0;if(S.type==chem.Struct.BOND.TYPE.SINGLE&&(w=this._calcBondDirection(t,b,m)),1==w&&c==S.end||2==w&&c==S.begin?this.smiles+="/":2==w&&c==S.end||1==w&&c==S.begin?this.smiles+="\\":S.type==chem.Struct.BOND.TYPE.ANY?this.smiles+="~":S.type==chem.Struct.BOND.TYPE.DOUBLE?this.smiles+="=":S.type==chem.Struct.BOND.TYPE.TRIPLE?this.smiles+="#":S.type!=chem.Struct.BOND.TYPE.AROMATIC||this.atoms[S.begin].lowercase&&this.atoms[S.end].lowercase&&this.isBondInRing(b)?S.type==chem.Struct.BOND.TYPE.SINGLE&&this.atoms[S.begin].aromatic&&this.atoms[S.end].aromatic?this.smiles+="-":!1:this.smiles+=":",h.edgeClosingCycle(b)){for(i=1;i<_.length&&_[i]!=c;i++);if(i==_.length)throw new Error("cycle number not found");this._writeCycleNumber(i),_[i]=-1,f=!1}}else p||(this.smiles+=this._written_components==h.nComponentsInReactants?">>":"."),p=!1,this._written_components++;f&&(this._writeAtom(t,c,this.atoms[c].aromatic,this.atoms[c].lowercase,this.atoms[c].chirality),this._written_atoms.push(d.idx))}return this.comma=!1,this._writeRadicals(t),this.comma&&(this.smiles+="|"),this.smiles},chem.SmilesSaver.prototype._writeCycleNumber=function(t){if(t>0&&t<10)this.smiles+=t;else if(t>=10&&t<100)this.smiles+="%"+t;else{if(!(t>=100&&t<1e3))throw new Error("bad cycle number: "+t);this.smiles+="%%"+t}},chem.SmilesSaver.prototype._writeAtom=function(t,e,s,i,n){var o=t.atoms.get(e),r=!1,a=-1,h=0;if("A"==o.label)return void(this.smiles+="*");if("R"==o.label||"R#"==o.label)return void(this.smiles+="[*]");h=o.aam,"C"!=o.label&&"P"!=o.label&&"N"!=o.label&&"S"!=o.label&&"O"!=o.label&&"Cl"!=o.label&&"F"!=o.label&&"Br"!=o.label&&"B"!=o.label&&"I"!=o.label&&(r=!0),(o.explicitValence>=0||0!=o.radical||n>0||s&&"C"!=o.label&&"O"!=o.label||s&&"C"==o.label&&this.atoms[e].neighbours.length<3&&0==this.atoms[e].h_count)&&(a=this.atoms[e].h_count);var d=o.label;if(o.atomList&&!o.atomList.notList?(d=o.atomList.label(),r=!1):o.isPseudo()||o.atomList&&o.atomList.notList?(d="*",r=!0):(n||0!=o.charge||o.isotope>0||a>=0||h>0)&&(r=!0),r&&(-1==a&&(a=this.atoms[e].h_count),this.smiles+="["),o.isotope>0&&(this.smiles+=o.isotope),this.smiles+=i?d.toLowerCase():d,n>0&&(this.smiles+=1==n?"@":"@@",o.implicitH>1))throw new Error(o.implicitH+" implicit H near stereocenter");"H"!=o.label&&(a>1||0==a&&!r?this.smiles+="H"+a:1==a&&(this.smiles+="H")),o.charge>1?this.smiles+="+"+o.charge:o.charge<-1?this.smiles+=o.charge:1==o.charge?this.smiles+="+":-1==o.charge&&(this.smiles+="-"),h>0&&(this.smiles+=":"+h),r&&(this.smiles+="]")},chem.SmilesSaver.prototype._markCisTrans=function(t){this.cis_trans=new chem.CisTrans(t,function(t){return this.atoms[t].neighbours},this),this.cis_trans.build(),this._dbonds=new Array(t.bonds.count()),t.bonds.each(function(t){this._dbonds[t]={ctbond_beg:-1,ctbond_end:-1,saved:0}},this),this.cis_trans.each(function(e,s){var i=t.bonds.get(e);if(0!=s.parity&&!this.isBondInRing(e)){var n=this.atoms[i.begin].neighbours,o=this.atoms[i.end].neighbours,r=!0,a=!0;if(n.each(function(s){s.bid!=e&&t.bonds.get(s.bid).type==chem.Struct.BOND.TYPE.SINGLE&&(r=!1)},this),o.each(function(s){s.bid!=e&&t.bonds.get(s.bid).type==chem.Struct.BOND.TYPE.SINGLE&&(a=!1)},this),r||a)return;n.each(function(s){s.bid!=e&&(t.bonds.get(s.bid).begin==i.begin?this._dbonds[s.bid].ctbond_beg=e:this._dbonds[s.bid].ctbond_end=e)},this),o.each(function(s){s.bid!=e&&(t.bonds.get(s.bid).begin==i.end?this._dbonds[s.bid].ctbond_beg=e:this._dbonds[s.bid].ctbond_end=e)},this)}},this)},chem.SmilesSaver.prototype._updateSideBonds=function(t,e){var s=t.bonds.get(e),i=this.cis_trans.getSubstituents(e),n=this.cis_trans.getParity(e),o=[-1,-1,-1,-1];o[0]=t.findBondId(i[0],s.begin),-1!=i[1]&&(o[1]=t.findBondId(i[1],s.begin)),o[2]=t.findBondId(i[2],s.end),-1!=i[3]&&(o[3]=t.findBondId(i[3],s.end));var r=0,a=0,h=0,d=0;if(0!=this._dbonds[o[0]].saved&&(1==this._dbonds[o[0]].saved&&t.bonds.get(o[0]).begin==s.begin||2==this._dbonds[o[0]].saved&&t.bonds.get(o[0]).end==s.begin?r++:a++),-1!=o[1]&&0!=this._dbonds[o[1]].saved&&(2==this._dbonds[o[1]].saved&&t.bonds.get(o[1]).begin==s.begin||1==this._dbonds[o[1]].saved&&t.bonds.get(o[1]).end==s.begin?r++:a++),0!=this._dbonds[o[2]].saved&&(1==this._dbonds[o[2]].saved&&t.bonds.get(o[2]).begin==s.end||2==this._dbonds[o[2]].saved&&t.bonds.get(o[2]).end==s.end?h++:d++),-1!=o[3]&&0!=this._dbonds[o[3]].saved&&(2==this._dbonds[o[3]].saved&&t.bonds.get(o[3]).begin==s.end||1==this._dbonds[o[3]].saved&&t.bonds.get(o[3]).end==s.end?h++:d++),n==chem.CisTrans.PARITY.CIS?(r+=h,a+=d):(r+=d,a+=h),r>0&&a>0)throw new Error("incompatible cis-trans configuration");return(0!=r||0!=a)&&(r>0&&(this._dbonds[o[0]].saved=t.bonds.get(o[0]).begin==s.begin?1:2,-1!=o[1]&&(this._dbonds[o[1]].saved=t.bonds.get(o[1]).begin==s.begin?2:1),this._dbonds[o[2]].saved=t.bonds.get(o[2]).begin==s.end==(n==chem.CisTrans.PARITY.CIS)?1:2,-1!=o[3]&&(this._dbonds[o[3]].saved=t.bonds.get(o[3]).begin==s.end==(n==chem.CisTrans.PARITY.CIS)?2:1)),a>0&&(this._dbonds[o[0]].saved=t.bonds.get(o[0]).begin==s.begin?2:1,-1!=o[1]&&(this._dbonds[o[1]].saved=t.bonds.get(o[1]).begin==s.begin?1:2),this._dbonds[o[2]].saved=t.bonds.get(o[2]).begin==s.end==(n==chem.CisTrans.PARITY.CIS)?2:1,-1!=o[3]&&(this._dbonds[o[3]].saved=t.bonds.get(o[3]).begin==s.end==(n==chem.CisTrans.PARITY.CIS)?1:2)),!0)},chem.SmilesSaver.prototype._calcBondDirection=function(t,e,s){var i;if(-1==this._dbonds[e].ctbond_beg&&-1==this._dbonds[e].ctbond_end)return 0;if(t.bonds.get(e).type!=chem.Struct.BOND.TYPE.SINGLE)throw new Error("internal: directed bond type "+t.bonds.get(e).type);for(;;){if(i=0,this.cis_trans.each(function(e,s){0==s.parity||this.isBondInRing(e)||this._updateSideBonds(t,e)&&i++},this),i==this._touched_cistransbonds)break;this._touched_cistransbonds=i}return 0==this._dbonds[e].saved&&(s==t.bonds.get(e).begin?this._dbonds[e].saved=1:this._dbonds[e].saved=2),this._dbonds[e].saved},chem.SmilesSaver.prototype._writeRadicals=function(t){var e,s,i=new Array(this._written_atoms.length);for(e=0;e=0)return!1;if(util.findIndex([c.bid,d.bid],function(e){return t.get(e).type!=chem.Struct.BOND.TYPE.DOUBLE},this)>=0)return!1;var a=util.findAll(this.getNeighbors.call(this.context,c.aid),function(r){return r.aid!=e},this),s=util.findAll(this.getNeighbors.call(this.context,d.aid),function(r){return r.aid!=e},this);return!(a.length<1||a.length>2||s.length<1||s.length>2)&&(!(util.findIndex(a.concat(s),function(e){return t.get(e.bid).type!=chem.Struct.BOND.TYPE.SINGLE},this)>=0)&&(!(util.findIndex(a.concat(s),function(e){return t.get(e.bid).stereo==chem.Struct.BOND.STEREO.EITHER},this)>=0)&&(Set.add(n,c.aid),void Set.add(n,d.aid))))},this),Set.size(n)>0&&alert("This structure may contain allenes, which cannot be represented in the SMILES notation. Relevant stereo-information will be discarded."),r.each(function(e){if(!Set.contains(n,e)){var r=this.getNeighbors.call(this.context,e),t=!1;r.find(function(r){var n=this.molecule.bonds.get(r.bid);return n.type==chem.Struct.BOND.TYPE.SINGLE&&n.begin==e&&(n.stereo==chem.Struct.BOND.STEREO.UP||n.stereo==chem.Struct.BOND.STEREO.DOWN)&&(t=!0,!0)},this),t&&this._buildOneCenter(e)}},this)},chem.Stereocenters.allowed_stereocenters=[{elem:"C",charge:0,degree:3,n_double_bonds:0,implicit_degree:4},{elem:"C",charge:0,degree:4,n_double_bonds:0,implicit_degree:4},{elem:"Si",charge:0,degree:3,n_double_bonds:0,implicit_degree:4},{elem:"Si",charge:0,degree:4,n_double_bonds:0,implicit_degree:4},{elem:"N",charge:1,degree:3,n_double_bonds:0,implicit_degree:4},{elem:"N",charge:1,degree:4,n_double_bonds:0,implicit_degree:4},{elem:"N",charge:0,degree:3,n_double_bonds:0,implicit_degree:3},{elem:"S",charge:0,degree:4,n_double_bonds:2,implicit_degree:4},{elem:"S",charge:1,degree:3,n_double_bonds:0,implicit_degree:3},{elem:"S",charge:0,degree:3,n_double_bonds:1,implicit_degree:3},{elem:"P",charge:0,degree:3,n_double_bonds:0,implicit_degree:3},{elem:"P",charge:1,degree:4,n_double_bonds:0,implicit_degree:4},{elem:"P",charge:0,degree:4,n_double_bonds:1,implicit_degree:4}],chem.Stereocenters.prototype._buildOneCenter=function(e){var r=this.molecule.atoms.get(e),t=this.getNeighbors.call(this.context,e),n=t.length,i=-1,o={group:0,type:0,pyramid:new Array(4)},c=0,d=new Array(4),a=0,s=0;o.pyramid[0]=-1,o.pyramid[1]=-1,o.pyramid[2]=-1,o.pyramid[3]=-1;var h=0;if(n>4)throw new Error("stereocenter with %d bonds are not supported"+n);if(t.each(function(e){var t=this.molecule.atoms.get(e.aid),n=this.molecule.bonds.get(e.bid);if(d[c]={edge_idx:e.bid,nei_idx:e.aid,rank:e.aid,vec:Vec2.diff(t.pp,r.pp).yComplement()},t.pureHydrogen()?(h++,d[c].rank=1e4):"H"==t.label&&(d[c].rank=5e3),!d[c].vec.normalize())throw new Error("zero bond length");if(n.type==chem.Struct.BOND.TYPE.TRIPLE)throw new Error("non-single bonds not allowed near stereocenter");if(n.type==chem.Struct.BOND.TYPE.AROMATIC)throw new Error("aromatic bonds not allowed near stereocenter");n.type==chem.Struct.BOND.TYPE.DOUBLE&&s++,c++},this),chem.Stereocenters.allowed_stereocenters.find(function(e){return e.elem==r.label&&e.charge==r.charge&&e.degree==n&&e.n_double_bonds==s&&(i=e.implicit_degree,!0)},this),-1==i)throw new Error("unknown stereocenter configuration: "+r.label+", charge "+r.charge+", "+n+" bonds ("+s+" double)");if(4==n&&h>1)throw new Error(h+" hydrogens near stereocenter");if(3==n&&4==i&&h>0)throw new Error("have hydrogen(s) besides implicit hydrogen near stereocenter");if(4==n){d[0].rank>d[1].rank&&d.swap(0,1),d[1].rank>d[2].rank&&d.swap(1,2),d[2].rank>d[3].rank&&d.swap(2,3),d[1].rank>d[2].rank&&d.swap(1,2),d[0].rank>d[1].rank&&d.swap(0,1),d[1].rank>d[2].rank&&d.swap(1,2);var m=-1,l=-1,u=-1,g=-1,S=0;for(c=0;c<4;c++){var p=this._getBondStereo(e,d[c].edge_idx);if(p==chem.Struct.BOND.STEREO.UP||p==chem.Struct.BOND.STEREO.DOWN){m=c,S=p;break}}if(-1==m)throw new Error("none of 4 bonds going from stereocenter is stereobond");var _,E;if(-1==l&&(_=chem.Stereocenters._xyzzy(d[m].vec,d[(m+1)%4].vec,d[(m+2)%4].vec),E=chem.Stereocenters._xyzzy(d[m].vec,d[(m+1)%4].vec,d[(m+3)%4].vec),_+E!=3&&_+E!=12||(l=(m+1)%4,u=(m+2)%4,g=(m+3)%4)),-1==l&&(_=chem.Stereocenters._xyzzy(d[m].vec,d[(m+2)%4].vec,d[(m+1)%4].vec),E=chem.Stereocenters._xyzzy(d[m].vec,d[(m+2)%4].vec,d[(m+3)%4].vec),_+E!=3&&_+E!=12||(l=(m+2)%4,u=(m+1)%4,g=(m+3)%4)),-1==l&&(_=chem.Stereocenters._xyzzy(d[m].vec,d[(m+3)%4].vec,d[(m+1)%4].vec),E=chem.Stereocenters._xyzzy(d[m].vec,d[(m+3)%4].vec,d[(m+2)%4].vec),_+E!=3&&_+E!=12||(l=(m+3)%4,u=(m+2)%4,g=(m+1)%4)),-1==l)throw new Error("internal error: can not find opposite bond");if(S==chem.Struct.BOND.STEREO.UP&&this._getBondStereo(e,d[l].edge_idx)==chem.Struct.BOND.STEREO.DOWN)throw new Error("stereo types of the opposite bonds mismatch");if(S==chem.Struct.BOND.STEREO.DOWN&&this._getBondStereo(e,d[l].edge_idx)==chem.Struct.BOND.STEREO.UP)throw new Error("stereo types of the opposite bonds mismatch");if(S==this._getBondStereo(e,d[u].edge_idx))throw new Error("stereo types of non-opposite bonds match");if(S==this._getBondStereo(e,d[g].edge_idx))throw new Error("stereo types of non-opposite bonds match");a=3==m||3==l?S:S==chem.Struct.BOND.STEREO.UP?chem.Struct.BOND.STEREO.DOWN:chem.Struct.BOND.STEREO.UP,N=chem.Stereocenters._sign(d[0].vec,d[1].vec,d[2].vec),a==chem.Struct.BOND.STEREO.UP&&N>0||a==chem.Struct.BOND.STEREO.DOWN&&N<0?(o.pyramid[0]=d[0].nei_idx,o.pyramid[1]=d[1].nei_idx,o.pyramid[2]=d[2].nei_idx):(o.pyramid[0]=d[0].nei_idx,o.pyramid[1]=d[2].nei_idx,o.pyramid[2]=d[1].nei_idx),o.pyramid[3]=d[3].nei_idx}else if(3==n){d[0].rank>d[1].rank&&d.swap(0,1),d[1].rank>d[2].rank&&d.swap(1,2),d[0].rank>d[1].rank&&d.swap(0,1);var b=this._getBondStereo(e,d[0].edge_idx),O=this._getBondStereo(e,d[1].edge_idx),f=this._getBondStereo(e,d[2].edge_idx),w=0,y=0;if(w+=b==chem.Struct.BOND.STEREO.UP?1:0,w+=O==chem.Struct.BOND.STEREO.UP?1:0,w+=f==chem.Struct.BOND.STEREO.UP?1:0,y+=b==chem.Struct.BOND.STEREO.DOWN?1:0,y+=O==chem.Struct.BOND.STEREO.DOWN?1:0,y+=f==chem.Struct.BOND.STEREO.DOWN?1:0,4==i){if(3==w)throw new Error("all 3 bonds up near stereoatom");if(3==y)throw new Error("all 3 bonds down near stereoatom");if(0==w&&0==y)throw new Error("no up/down bonds near stereoatom -- indefinite case");if(1==w&&1==y)throw new Error("one bond up, one bond down -- indefinite case");if(S=0,2==w)a=chem.Struct.BOND.STEREO.DOWN;else if(2==y)a=chem.Struct.BOND.STEREO.UP;else{for(m=-1,u=-1,g=-1,c=0;c<3;c++)if((x=this._getBondStereo(e,d[c].edge_idx))==chem.Struct.BOND.STEREO.UP||x==chem.Struct.BOND.STEREO.DOWN){m=c,S=x,u=(c+1)%3,g=(c+2)%3;break}if(-1==m)throw new Error("internal error: can not find up or down bond");var v=chem.Stereocenters._xyzzy(d[u].vec,d[g].vec,d[m].vec);if(3==v||4==v)throw new Error("degenerate case for 3 bonds near stereoatom");a=1==v?S:S==chem.Struct.BOND.STEREO.UP?chem.Struct.BOND.STEREO.DOWN:chem.Struct.BOND.STEREO.UP}var N=chem.Stereocenters._sign(d[0].vec,d[1].vec,d[2].vec);a==chem.Struct.BOND.STEREO.UP&&N>0||a==chem.Struct.BOND.STEREO.DOWN&&N<0?(o.pyramid[0]=d[0].nei_idx,o.pyramid[1]=d[1].nei_idx,o.pyramid[2]=d[2].nei_idx):(o.pyramid[0]=d[0].nei_idx,o.pyramid[1]=d[2].nei_idx,o.pyramid[2]=d[1].nei_idx),o.pyramid[3]=-1}else{var x;if(y>0&&w>0)throw new Error("one bond up, one bond down -- indefinite case");if(0==y&&0==w)throw new Error("no up-down bonds attached to stereocenter");x=w>0?1:-1,1!=chem.Stereocenters._xyzzy(d[0].vec,d[1].vec,d[2].vec)&&1!=chem.Stereocenters._xyzzy(d[0].vec,d[2].vec,d[1].vec)&&1!=chem.Stereocenters._xyzzy(d[2].vec,d[1].vec,d[0].vec)||(x=-x),N=chem.Stereocenters._sign(d[0].vec,d[1].vec,d[2].vec),N==x?(o.pyramid[0]=d[0].nei_idx,o.pyramid[1]=d[2].nei_idx,o.pyramid[2]=d[1].nei_idx):(o.pyramid[0]=d[0].nei_idx,o.pyramid[1]=d[1].nei_idx,o.pyramid[2]=d[2].nei_idx),o.pyramid[3]=-1}}this.atoms.set(e,o)},chem.Stereocenters.prototype._getBondStereo=function(e,r){var t=this.molecule.bonds.get(r);return e!=t.begin?0:t.stereo},chem.Stereocenters._xyzzy=function(e,r,t){var n=Vec2.cross(e,r),i=Vec2.dot(e,r),o=Vec2.cross(e,t),c=Vec2.dot(e,t);if(Math.abs(n)<.001){if(Math.abs(o)<.001)throw new Error("degenerate case -- bonds overlap");return o>0?4:8}return n*o<-1e-6?2:c.001)return 1;if(n<-.001)return-1;throw new Error("degenerate triangle")},chem.Stereocenters.isPyramidMappingRigid=function(e){var r=e.clone(),t=!0;return r[0]>r[1]&&(r.swap(0,1),t=!t),r[1]>r[2]&&(r.swap(1,2),t=!t),r[2]>r[3]&&(r.swap(2,3),t=!t),r[1]>r[2]&&(r.swap(1,2),t=!t),r[0]>r[1]&&(r.swap(0,1),t=!t),r[1]>r[2]&&(r.swap(1,2),t=!t),t}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../util":39,"../util/map":40,"../util/set":42,"../util/vec2":43,"./struct":16}],16:[function(require,module,exports){ +(function (global){ +var Map=require("../util/map"),Pool=require("../util/pool"),Set=require("../util/set"),Vec2=require("../util/vec2"),util=require("../util"),element=require("./element"),chem=global.chem=global.chem||{};chem.Struct=function(){this.atoms=new Pool,this.bonds=new Pool,this.sgroups=new Pool,this.halfBonds=new Map,this.loops=new Pool,this.isChiral=!1,this.isReaction=!1,this.rxnArrows=new Pool,this.rxnPluses=new Pool,this.frags=new Pool,this.rgroups=new Map,this.name="",this.sGroupForest=new chem.SGroupForest(this)},chem.Struct.prototype.hasRxnProps=function(){return this.atoms.find(function(t,e){return e.hasRxnProps()},this)>=0||this.bonds.find(function(t,e){return e.hasRxnProps()},this)>=0},chem.Struct.prototype.hasRxnArrow=function(){return this.rxnArrows.count()>0},chem.Struct.prototype.addRxnArrowIfNecessary=function(){var t=!this.hasRxnArrow()&&this.hasRxnProps();return t&&this.rxnArrows.add(new chem.Struct.RxnArrow),t},chem.Struct.prototype.getSGroupsInAtomSet=function(t){var e=new Hash;util.each(t,function(t){Set.list(this.atoms.get(t).sgs).each(function(t){var n=e.get(t);Object.isUndefined(n)?n=1:n++,e.set(t,n)},this)},this);var n=[];return e.each(function(t){var e=parseInt(t.key,10),i=this.sgroups.get(e),o=chem.SGroup.getAtoms(this,i);t.value==o.length&&n.push(e)},this),n},chem.Struct.prototype.isBlank=function(){return 0===this.atoms.count()&&0===this.rxnArrows.count()&&0===this.rxnPluses.count()&&!this.isChiral},chem.Struct.prototype.toLists=function(){var t={},e=[];this.atoms.each(function(n,i){t[n]=e.length,e.push(i)});var n=[];return this.bonds.each(function(e,i){var o=new chem.Struct.Bond(i);o.begin=t[i.begin],o.end=t[i.end],n.push(o)}),{atoms:e,bonds:n}},chem.Struct.prototype.clone=function(t,e,n,i){var o=new chem.Struct;return this.mergeInto(o,t,e,n,!1,i)},chem.Struct.prototype.getScaffold=function(){var t=Set.empty();return this.atoms.each(function(e){Set.add(t,e)},this),this.rgroups.each(function(e,n){n.frags.each(function(e,n){this.atoms.each(function(e,i){i.fragment==n&&Set.remove(t,e)},this)},this)},this),this.clone(t)},chem.Struct.prototype.getFragmentIds=function(t){var e=Set.empty();return this.atoms.each(function(n,i){i.fragment==t&&Set.add(e,n)},this),e},chem.Struct.prototype.getFragment=function(t){return this.clone(this.getFragmentIds(t))},chem.Struct.prototype.mergeInto=function(t,e,n,i,o,s){e=e||Set.keySetInt(this.atoms),n=n||Set.keySetInt(this.bonds),n=Set.filter(n,function(t){var n=this.bonds.get(t);return Set.contains(e,n.begin)&&Set.contains(e,n.end)},this);var r={};this.atoms.each(function(t,n){Set.contains(e,t)&&(r[n.fragment]=1)});var h={};this.frags.each(function(e,n){r[e]&&(h[e]=t.frags.add(n.clone()))}),this.rgroups.each(function(e,n){var i=o;if(i||(n.frags.each(function(t,e){r[e]&&(i=!0)}),i)){var s=t.rgroups.get(e);s?n.frags.each(function(t,e){r[e]&&s.frags.add(h[e])}):t.rgroups.set(e,n.clone(h))}}),void 0!==s&&null!==s||(s={}),this.atoms.each(function(n,i){Set.contains(e,n)&&(s[n]=t.atoms.add(i.clone(h)))});var c={};return this.bonds.each(function(e,i){Set.contains(n,e)&&(c[e]=t.bonds.add(i.clone(s)))}),this.sgroups.each(function(n,i){var o;for(o=0;o1e-4?o:new Vec2(1,0),e.norm=e.dir.turnLeft(),e.ang=e.dir.oxAngle(),e.loop<0&&(e.loop=-1)},chem.Struct.prototype.initHalfBonds=function(){this.halfBonds.clear(),this.bonds.each(this.bondInitHalfBonds,this)},chem.Struct.prototype.setHbNext=function(t,e){this.halfBonds.get(this.halfBonds.get(t).contra).next=e},chem.Struct.prototype.halfBondSetAngle=function(t,e){var n=this.halfBonds.get(t),i=this.halfBonds.get(e);i.rightCos=n.leftCos=Vec2.dot(i.dir,n.dir),i.rightSin=n.leftSin=Vec2.cross(i.dir,n.dir),n.leftNeighbor=e,i.rightNeighbor=t},chem.Struct.prototype.atomAddNeighbor=function(t){var e=this.halfBonds.get(t),n=this.atoms.get(e.begin),i=0;for(i=0;ie.ang);++i);n.neighbors.splice(i,0,t);var o=n.neighbors[(i+1)%n.neighbors.length],s=n.neighbors[(i+n.neighbors.length-1)%n.neighbors.length];this.setHbNext(s,t),this.setHbNext(t,o),this.halfBondSetAngle(t,s),this.halfBondSetAngle(o,t)},chem.Struct.prototype.atomSortNeighbors=function(t){var e=this.atoms.get(t);e.neighbors=e.neighbors.sortBy(function(t){return this.halfBonds.get(t).ang},this);var n;for(n=0;n0?t.totalLength/t.cnt:-1},chem.Struct.prototype.getAvgClosestAtomDistance=function(){var t,e,n,i=0,o=0,s=this.atoms.keys();for(e=0;eo)&&(t=o));i+=t}return s.length>0?i/s.length:-1},chem.Struct.prototype.checkBondExists=function(t,e){var n=!1;return this.bonds.each(function(i,o){(o.begin==t&&o.end==e||o.end==t&&o.begin==e)&&(n=!0)},this),n},chem.Loop=function(t,e,n){this.hbs=t,this.dblBonds=0,this.aromatic=!0,this.convex=n||!1,t.each(function(t){var n=e.bonds.get(e.halfBonds.get(t).bid);n.type!=chem.Struct.BOND.TYPE.AROMATIC&&(this.aromatic=!1),n.type==chem.Struct.BOND.TYPE.DOUBLE&&this.dblBonds++},this)},chem.Struct.RxnPlus=function(t){t=t||{},this.pp=t.pp?new Vec2(t.pp):new Vec2},chem.Struct.RxnPlus.prototype.clone=function(){return new chem.Struct.RxnPlus(this)},chem.Struct.RxnArrow=function(t){t=t||{},this.pp=t.pp?new Vec2(t.pp):new Vec2},chem.Struct.RxnArrow.prototype.clone=function(){return new chem.Struct.RxnArrow(this)},chem.Struct.prototype.findConnectedComponent=function(t){for(var e={},n=[t],i=Set.empty();n.length>0;)(function(){var t=n.pop();e[t]=1,Set.add(i,t);for(var o=this.atoms.get(t),s=0;s0)return!1}return!0},chem.Struct.prototype.loopIsInner=function(t){for(var e=2*Math.PI,n=0;n0&&t==r){var c=this.partitionLoop(n);util.each(c,function(t){this.loopIsInner(t)&&!this.loopHasSelfIntersections(t)?(i=util.arrayMin(t),this.loops.set(i,new chem.Loop(t,this,this.loopIsConvex(t)))):i=-2,t.each(function(t){this.halfBonds.get(t).loop=i,Set.add(s,this.halfBonds.get(t).bid)},this),i>=0&&o.push(i)},this);break}n.push(t)}},this),{newLoops:o,bondsToMark:Set.list(s)}},chem.Struct.prototype.prepareLoopStructure=function(){this.initHalfBonds(),this.initNeighbors(),this.updateHalfBonds(this.atoms.keys()),this.sortNeighbors(this.atoms.keys()),this.findLoops()},chem.Struct.prototype.atomAddToSGroup=function(t,e){chem.SGroup.addAtom(this.sgroups.get(t),e),Set.add(this.atoms.get(e).sgs,t)}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../util":39,"../util/map":40,"../util/pool":41,"../util/set":42,"../util/vec2":43,"./element":10}],17:[function(require,module,exports){ +(function (global){ +var util=require("../util"),element=require("./element");require("./struct");var chem=global.chem=global.chem||{};chem.Struct.prototype.calcConn=function(e){for(var t=0,i=this.atoms.get(e),r=!1,l=0;l=1?(a=3,u=3-n-e):(a=2,u=2-n-e-s):"S"==r||"Se"==r||"Po"==r?1==i?e<=3?(a=3,u=3-n-e):(a=5,u=5-n-e):e+n+s<=2?(a=2,u=2-n-e-s):e+n+s<=4?(a=4,u=4-n-e-s):(a=6,u=6-n-e-s):"Te"==r&&(-1==i?e<=2&&(a=2,u=2-n-e-s):0!=i&&2!=i||(e<=2?(a=2,u=2-n-e-s):e<=4?(a=4,u=4-n-e-s):0==i&&e<=6?(a=6,u=6-n-e-s):u=-1)):7==c&&("F"==r?(a=1,u=1-n-e-s):"Cl"!=r&&"Br"!=r&&"I"!=r&&"At"!=r||(1==i?e<=2?(a=2,u=2-n-e):(3==e||5==e||e>=7)&&(u=-1):0==i&&(e<=1?(a=1,u=1-n-e):2==e||4==e||6==e?1==n?(a=e,u=0):u=-1:e>7&&(u=-1)))),this.valence=a,this.implicitH=u,!(this.implicitH<0)||(this.valence=e,this.implicitH=0,this.badConn=!0,!1)},chem.Struct.Atom.prototype.calcValenceMinusHyd=function(e){var t=this,i=t.charge,r=t.label,l=element.getElementByLabel(r);if(null==l)throw new Error("Element "+r+" unknown");if(l<0)return this.implicitH=0,null;var c=element.get(l).group,n=chem.Struct.radicalElectrons(t.radical);if(3==c){if(("B"==r||"Al"==r||"Ga"==r||"In"==r)&&-1==i&&n+e<=4)return n+e}else if(5==c){if("N"==r||"P"==r){if(1==i)return n+e;if(2==i)return n+e}else if("Sb"==r||"Bi"==r||"As"==r){if(1==i)return n+e;if(2==i)return n+e}}else if(6==c){if("O"==r){if(i>=1)return n+e}else if(("S"==r||"Se"==r||"Po"==r)&&1==i)return n+e}else if(7==c&&("Cl"==r||"Br"==r||"I"==r||"At"==r)&&1==i)return n+e;return n+e+Math.abs(i)},chem.Struct.prototype.calcImplicitHydrogen=function(e){var t=this.calcConn(e),i=this.atoms.get(e);if(i.badConn=!1,t<0||i.isQuery())return void(i.implicitH=0);if(i.explicitValence>=0){var r=element.getElementByLabel(i.label);i.implicitH=0,null!=r&&(i.implicitH=i.explicitValence-i.calcValenceMinusHyd(t),i.implicitH<0&&(i.implicitH=0,i.badConn=!0))}else i.calcValence(t)},chem.Struct.prototype.setImplicitHydrogen=function(e){var t=function(e){this.calcImplicitHydrogen(e)};util.isNullOrUndefined(e)?this.atoms.each(t,this):util.each(e,t,this)}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../util":39,"./element":10,"./struct":16}],18:[function(require,module,exports){ +(function (global){ +function getSmiles(e){var t=ui.standalone||e,i=t?new chem.SmilesSaver:new chem.MolfileSaver,r=i.saveMolecule(ui.ctab,!0);return t?r:ketcher.server.smiles.sync({moldata:r})}function getMolfile(){return(new chem.MolfileSaver).saveMolecule(ui.ctab,!0)}function setMolecule(e){Object.isString(e)&&ui.loadMolecule(e)}function addFragment(e){Object.isString(e)&&ui.loadFragment(e)}function showMolfile(e,t,i){var r=util.extend({bondLength:75,showSelectionRegions:!1,showBondIds:!1,showHalfBondIds:!1,showLoopIds:!1,showAtomIds:!1,autoScale:!1,autoScaleMargin:4,hideImplicitHydrogen:!1},i),l=new rnd.Render(e,r.bondLength,r);if(t){var n=chem.Molfile.parseCTFile(t);l.setMolecule(n)}return l.update(),l}function onStructChange(e){util.assert(e),ui.render.addStructChangeHandler(e)}var queryString=require("query-string"),util=require("./util"),api=require("./api.js");require("./ui"),require("./chem"),require("./rnd");var ui=global.ui,chem=global.chem,rnd=global.rnd;window.onload=function(){var e=queryString.parse(document.location.search);e.api_path&&(ketcher.api_path=e.api_path),ketcher.server=api(ketcher.api_path),ui.init(util.extend({},e),ketcher.server)};var ketcher=module.exports={version:"2.0.0-alpha.3",api_path:"",build_date:"2017-06-28 16-34-14",build_number:null,build_options:"__BUILD_NUMBER__",getSmiles:getSmiles,getMolfile:getMolfile,setMolecule:setMolecule,addFragment:addFragment,showMolfile:showMolfile,onStructChange:onStructChange}; +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"./api.js":7,"./chem":11,"./rnd":21,"./ui":34,"./util":39,"query-string":4}],19:[function(require,module,exports){ +(function (global){ +var Raphael=(typeof window !== "undefined" ? window['Raphael'] : typeof global !== "undefined" ? global['Raphael'] : null),Vec2=require("./util/vec2");Raphael.el.translateAbs=function(t,a){this.delta=this.delta||new Vec2,this.delta.x+=t-0,this.delta.y+=a-0,this.transform("t"+this.delta.x.toString()+","+this.delta.y.toString())},Raphael.st.translateAbs=function(t,a){this.forEach(function(e){e.translateAbs(t,a)})},module.exports=Raphael; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"./util/vec2":43}],20:[function(require,module,exports){ +(function (global){ +function bondFlipRequired(t,e){return e.type==chem.Struct.BOND.TYPE.SINGLE&&t.stereo==chem.Struct.BOND.STEREO.NONE&&e.stereo!=chem.Struct.BOND.STEREO.NONE&&ui.ctab.atoms.get(t.begin).neighbors.length0&&(!t||"sgroupData"!==e))return!0;return!1},rnd.Editor.prototype.getSelection=function(t){var e={};if("selection"in this._selectionHelper)for(var o in this._selectionHelper.selection)e[o]=this._selectionHelper.selection[o].slice(0);if(t){var i=this.render.ctab.molecule;"bonds"in e&&e.bonds.each(function(t){var o=i.bonds.get(t);e.atoms=e.atoms||[],e.atoms.indexOf(o.begin)<0&&e.atoms.push(o.begin),e.atoms.indexOf(o.end)<0&&e.atoms.push(o.end)},this),"atoms"in e&&"bonds"in e&&i.bonds.each(function(t){if(!("bonds"in e)||e.bonds.indexOf(t)<0){var o=i.bonds.get(t);e.atoms.indexOf(o.begin)>=0&&e.atoms.indexOf(o.end)>=0&&(e.bonds=e.bonds||[],e.bonds.push(t))}},this)}return e},rnd.Editor.prototype.getSelectionStruct=function(){console.assert(ui.ctab==this.render.ctab.molecule,"Another ctab");var t=ui.ctab,e=this.getSelection(!0),o=t.clone(Set.fromList(e.atoms),Set.fromList(e.bonds),!0);return t.rxnArrows.each(function(t,i){-1!=e.rxnArrows.indexOf(t)&&o.rxnArrows.add(i.clone())}),t.rxnPluses.each(function(t,i){-1!=e.rxnPluses.indexOf(t)&&o.rxnPluses.add(i.clone())}),o.isReaction=t.isReaction&&(o.rxnArrows.count()||o.rxnPluses.count()),o},rnd.Editor.SelectionHelper=function(t){this.editor=t},rnd.Editor.SelectionHelper.prototype.setSelection=function(t,e){if(!("selection"in this&&e)){this.selection={};for(var o in rnd.ReStruct.maps)this.selection[o]=[]}if(t&&"id"in t&&"map"in t&&(t[t.map]=t[t.map]||[]).push(t.id),t)for(var i in this.selection)if(i in t)for(var r=0;r-1},rnd.Editor.EditorTool=function(t){this.editor=t},rnd.Editor.EditorTool.prototype.processEvent=function(t,e,o){if("touches"in e&&1!=e.touches.length){if("lastEvent"in this.OnMouseDown0)return this.OnMouseUp0(e,o)}else{if(t+"0"in this)return this[t+"0"](e,o);if(t in this)return this[t](e,o);console.log("EditorTool.dispatchEvent: event '"+t+"' is not handled.")}},rnd.Editor.EditorTool.prototype.OnMouseDown=function(){},rnd.Editor.EditorTool.prototype.OnMouseMove=function(){},rnd.Editor.EditorTool.prototype.OnMouseUp=function(){},rnd.Editor.EditorTool.prototype.OnClick=function(){},rnd.Editor.EditorTool.prototype.OnDblClick=function(){},rnd.Editor.EditorTool.prototype.OnMouseLeave=function(){this.OnCancel()},rnd.Editor.EditorTool.prototype.OnKeyPress=function(){},rnd.Editor.EditorTool.prototype.OnCancel=function(){},rnd.Editor.EditorTool.prototype.OnMouseDown0=function(t){return!!ui.hideBlurredControls()||(this.OnMouseDown0.lastEvent=t,this.OnMouseMove0.lastEvent=t,"OnMouseDown"in this?this.OnMouseDown(t):void 0)},rnd.Editor.EditorTool.prototype.OnMouseMove0=function(t){if(this.OnMouseMove0.lastEvent=t,"OnMouseMove"in this)return this.OnMouseMove(t)},rnd.Editor.EditorTool.prototype.OnMouseUp0=function(t){if(!("lastEvent"in this.OnMouseDown0))return!0;"lastEvent"in this.OnMouseMove0&&(t=Object.clone(t),t.pageX=this.OnMouseMove0.lastEvent.pageX,t.pageY=this.OnMouseMove0.lastEvent.pageY);try{if("OnMouseUp"in this)return this.OnMouseUp(t)}finally{delete this.OnMouseDown0.lastEvent}},rnd.Editor.EditorTool.atom_label_map={atom_tool_any:"A",atom_tool_h:"H",atom_tool_c:"C",atom_tool_n:"N",atom_tool_o:"O",atom_tool_s:"S",atom_tool_p:"P",atom_tool_f:"F",atom_tool_br:"Br",atom_tool_cl:"Cl",atom_tool_i:"I"},rnd.Editor.EditorTool.prototype.OnKeyPress0=function(t,e){if("rgroup_tool_label"===e&&"lastEvent"in this.OnMouseMove0)return rnd.Editor.RGroupAtomTool.prototype.OnMouseUp.call(this,this.OnMouseMove0.lastEvent);if(e in rnd.Editor.EditorTool.atom_label_map){var o=rnd.Editor.EditorTool.atom_label_map[e],i=this.editor.getSelection();if(i&&"atoms"in i&&i.atoms.length>0)return ui.addUndoAction(Action.fromAtomsAttrs(i.atoms,{label:o},!0),!0),ui.render.update(),!0;var r=this.editor.render.findItem(this.OnMouseMove0.lastEvent);if(r)return r.label={label:o},"atoms"===r.map?ui.addUndoAction(Action.fromAtomsAttrs(r.id,r.label,!0),!0):-1==r.id&&ui.addUndoAction(Action.fromAtomAddition(ui.page2obj(this.OnMouseMove0.lastEvent),r.label),!0),ui.render.update(),!0}return"OnKeyPress"in this&&this.OnKeyPress(t)},rnd.Editor.EditorTool.prototype._calcAngle=function(t,e){var o=Vec2.diff(e,t),i=Math.atan2(o.y,o.x),r=i<0?-1:1,n=Math.floor(Math.abs(i)/(Math.PI/12))*(Math.PI/12);return i=r*(n+(Math.abs(i)-n=0){var e=this.editor.render.findItem(t,[this.dragCtx.item.map],this.dragCtx.item);this._hoverHelper.hover(e.map==this.dragCtx.item.map?e:null)}this.editor.render.update()}else this._lassoHelper.running()?this.editor._selectionHelper.setSelection(this._lassoHelper.addPoint(t),t.shiftKey):this._hoverHelper.hover(this.editor.render.findItem(t,this._lassoHelper.fragment||t.ctrlKey?["frags","sgroups","sgroupData","rgroups","rxnArrows","rxnPluses","chiralFlags"]:["atoms","bonds","sgroups","sgroupData","rgroups","rxnArrows","rxnPluses","chiralFlags"]));return!0},rnd.Editor.LassoTool.prototype.OnMouseUp=function(t){if("dragCtx"in this){if("stopTapping"in this.dragCtx&&this.dragCtx.stopTapping(),["atoms"].indexOf(this.dragCtx.item.map)>=0){var e=this.editor.render.findItem(t,[this.dragCtx.item.map],this.dragCtx.item);e.map==this.dragCtx.item.map&&(this._hoverHelper.hover(null),this.editor._selectionHelper.setSelection(),this.dragCtx.action=this.dragCtx.action?Action.fromAtomMerge(this.dragCtx.item.id,e.id).mergeWith(this.dragCtx.action):Action.fromAtomMerge(this.dragCtx.item.id,e.id))}ui.addUndoAction(this.dragCtx.action,!0),this.editor.render.update(),delete this.dragCtx}else this._lassoHelper.running()?this.editor._selectionHelper.setSelection(this._lassoHelper.end(),t.shiftKey):this._lassoHelper.fragment&&this.editor._selectionHelper.setSelection();return!0},rnd.Editor.LassoTool.prototype.OnDblClick=function(t){var e=this.editor.render.findItem(t);if("atoms"==e.map){this.editor._selectionHelper.setSelection(e);var o=ui.ctab.atoms.get(e.id);"R#"==o.label?rnd.Editor.RGroupAtomTool.prototype.OnMouseUp.call(this,t):"L#"==o.label?ui.showElemTable({selection:o,onOk:function(t){return o.label==t.label&&o.atomList.equals(t.atomList)||(ui.addUndoAction(Action.fromAtomsAttrs(e.id,t)),ui.render.update()),!0}.bind(this)}):(element.getElementByLabel(o.label)||121)<120?ui.showAtomProperties(e.id):ui.showReaGenericsTable({values:[o.label],onOk:function(t){var i=t.values[0];return o.label!=i&&(ui.addUndoAction(Action.fromAtomsAttrs(e.id,{label:i})),ui.render.update()),!0}.bind(this)})}else"bonds"==e.map?(this.editor._selectionHelper.setSelection(e),ui.showBondProperties(e.id)):"sgroups"==e.map&&(this.editor._selectionHelper.setSelection(e),this._sGroupHelper.showPropertiesDialog(e.id));return!0},rnd.Editor.LassoTool.prototype.OnCancel=function(){"dragCtx"in this?("stopTapping"in this.dragCtx&&this.dragCtx.stopTapping(),ui.addUndoAction(this.dragCtx.action,!0),this.editor.render.update(),delete this.dragCtx):this._lassoHelper.running()&&this.editor._selectionHelper.setSelection(this._lassoHelper.end()),this._hoverHelper.hover(null)},rnd.Editor.LassoTool.LassoHelper=function(t,e,o){this.mode=t,this.fragment=o,this.editor=e},rnd.Editor.LassoTool.LassoHelper.prototype.getSelection=function(){if(0==this.mode)return ui.render.getElementsInPolygon(this.points);if(1==this.mode)return ui.render.getElementsInRectangle(this.points[0],this.points[1]);throw new Error("Selector mode unknown")},rnd.Editor.LassoTool.LassoHelper.prototype.begin=function(t){this.points=[ui.page2obj(t)],1==this.mode&&this.points.push(this.points[0])},rnd.Editor.LassoTool.LassoHelper.prototype.running=function(){return"points"in this},rnd.Editor.LassoTool.LassoHelper.prototype.addPoint=function(t){return!!this.running()&&(0==this.mode?(this.points.push(ui.page2obj(t)),this.editor.render.drawSelectionPolygon(this.points)):1==this.mode&&(this.points=[this.points[0],ui.page2obj(t)],this.editor.render.drawSelectionRectangle(this.points[0],this.points[1])),this.getSelection())},rnd.Editor.LassoTool.LassoHelper.prototype.end=function(){var t=this.getSelection();return"points"in this&&(this.editor.render.drawSelectionPolygon(null),delete this.points),t},rnd.Editor.EraserTool=function(t,e){this.editor=t,this.maps=["atoms","bonds","rxnArrows","rxnPluses","sgroups","sgroupData","chiralFlags"],this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this),this._lassoHelper=new rnd.Editor.LassoTool.LassoHelper(e||0,t)},rnd.Editor.EraserTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.EraserTool.prototype.OnMouseDown=function(t){var e=this.editor.render.findItem(t,this.maps);e&&"Canvas"!=e.type||this._lassoHelper.begin(t)},rnd.Editor.EraserTool.prototype.OnMouseMove=function(t){this._lassoHelper.running()?this.editor._selectionHelper.setSelection(this._lassoHelper.addPoint(t)):this._hoverHelper.hover(this.editor.render.findItem(t,this.maps))},rnd.Editor.EraserTool.prototype.OnMouseUp=function(t){if(this._lassoHelper.running())ui.addUndoAction(Action.fromFragmentDeletion(this._lassoHelper.end(t))),this.editor.deselectAll(),ui.render.update();else{var e=this.editor.render.findItem(t,this.maps);if(e&&"Canvas"!=e.type){if(this._hoverHelper.hover(null),"atoms"==e.map)ui.addUndoAction(Action.fromAtomDeletion(e.id));else if("bonds"==e.map)ui.addUndoAction(Action.fromBondDeletion(e.id));else if("sgroups"==e.map||"sgroupData"==e.map)ui.addUndoAction(Action.fromSgroupDeletion(e.id));else if("rxnArrows"==e.map)ui.addUndoAction(Action.fromArrowDeletion(e.id));else if("rxnPluses"==e.map)ui.addUndoAction(Action.fromPlusDeletion(e.id));else{if("chiralFlags"!=e.map)return void console.log("EraserTool: unable to delete the object "+e.map+"["+e.id+"]");ui.addUndoAction(Action.fromChiralFlagDeletion())}this.editor.deselectAll(),ui.render.update()}}},rnd.Editor.AtomTool=function(t,e){this.editor=t,this.atomProps=e,this.bondProps={type:1,stereo:chem.Struct.BOND.STEREO.NONE},this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.AtomTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.AtomTool.prototype.OnMouseDown=function(t){this._hoverHelper.hover(null);var e=this.editor.render.findItem(t,["atoms"]);e&&"Canvas"!=e.type?"atoms"==e.map&&(this.dragCtx={item:e,xy0:ui.page2obj(t)}):this.dragCtx={xy0:ui.page2obj(t)}},rnd.Editor.AtomTool.prototype.OnMouseMove=function(t){var e=this.editor,o=e.render;if("dragCtx"in this&&"item"in this.dragCtx){var i=this.dragCtx,r=this._calcNewAtomPos(o.atomGetPos(i.item.id),ui.page2obj(t));"action"in i&&i.action.perform();var n=Action.fromBondAddition(this.bondProps,i.item.id,Object.clone(this.atomProps),r,r);i.action=n[0],i.aid2=n[2],o.update()}else this._hoverHelper.hover(o.findItem(t,["atoms"]))},rnd.Editor.AtomTool.prototype.OnMouseUp=function(t){if("dragCtx"in this){var e=this.dragCtx;ui.addUndoAction("action"in e?e.action:"item"in e?Action.fromAtomsAttrs(e.item.id,this.atomProps,!0):Action.fromAtomAddition(ui.page2obj(t),this.atomProps),!0),this.editor.render.update(),delete this.dragCtx}},rnd.Editor.BondTool=function(t,e){this.editor=t,this.atomProps={label:"C"},this.bondProps=e,this.plainBondTypes=[chem.Struct.BOND.TYPE.SINGLE,chem.Struct.BOND.TYPE.DOUBLE,chem.Struct.BOND.TYPE.TRIPLE],this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.BondTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.BondTool.prototype.OnMouseDown=function(t){return this._hoverHelper.hover(null),this.dragCtx={xy0:ui.page2obj(t),item:this.editor.render.findItem(t,["atoms","bonds"])},this.dragCtx.item&&"Canvas"!=this.dragCtx.item.type||delete this.dragCtx.item,!0},rnd.Editor.BondTool.prototype.OnMouseMove=function(t){var e=this.editor,o=e.render;if("dragCtx"in this){var i=this.dragCtx;if(!("item"in i)||"atoms"==i.item.map){"action"in i&&i.action.perform();var r,n,s,d;"item"in i&&"atoms"==i.item.map?(r=i.item.id,n=o.findItem(t,["atoms"],i.item)):(r=this.atomProps,s=i.xy0,n=o.findItem(t,["atoms"]));var a=Number.MAX_VALUE;if(n&&"atoms"==n.map)n=n.id;else{n=this.atomProps;var l=ui.page2obj(t);a=Vec2.dist(i.xy0,l),s?d=this._calcNewAtomPos(s,l):s=this._calcNewAtomPos(o.atomGetPos(r),l)}return a>.3?i.action=Action.fromBondAddition(this.bondProps,r,n,s,d)[0]:delete i.action,o.update(),!0}}return this._hoverHelper.hover(o.findItem(t,["atoms","bonds"])),!0},rnd.Editor.BondTool.prototype.OnMouseUp=function(t){if("dragCtx"in this){var e=this.dragCtx;if("action"in e)ui.addUndoAction(e.action);else if("item"in e){if("atoms"==e.item.map)ui.addUndoAction(Action.fromBondAddition(this.bondProps,e.item.id)[0]);else if("bonds"==e.item.map){var o=Object.clone(this.bondProps),i=ui.ctab.bonds.get(e.item.id);if(o.stereo!=chem.Struct.BOND.STEREO.NONE&&i.type==chem.Struct.BOND.TYPE.SINGLE&&o.type==chem.Struct.BOND.TYPE.SINGLE&&i.stereo==o.stereo)ui.addUndoAction(Action.fromBondFlipping(e.item.id));else{if(o.type===chem.Struct.BOND.TYPE.SINGLE&&i.stereo===chem.Struct.BOND.STEREO.NONE&&o.stereo===chem.Struct.BOND.STEREO.NONE){var r=this.plainBondTypes.indexOf(o.type)>=0?this.plainBondTypes:null;r&&(o.type=r[(r.indexOf(i.type)+1)%r.length])}ui.addUndoAction(Action.fromBondAttrs(e.item.id,o,bondFlipRequired(i,o)),!0)}}}else{var n=ui.page2obj(t),s=new Vec2(.5,0).rotate(this.bondProps.type==chem.Struct.BOND.TYPE.SINGLE?-Math.PI/6:0),d=Action.fromBondAddition(this.bondProps,{label:"C"},{label:"C"},{x:n.x-s.x,y:n.y-s.y},{x:n.x+s.x,y:n.y+s.y});ui.addUndoAction(d[0])}this.editor.render.update(),delete this.dragCtx}return!0},rnd.Editor.ChainTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.ChainTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.ChainTool.prototype.OnMouseDown=function(t){return this._hoverHelper.hover(null),this.dragCtx={xy0:ui.page2obj(t),item:this.editor.render.findItem(t,["atoms"])},this.dragCtx.item&&"Canvas"!=this.dragCtx.item.type||delete this.dragCtx.item,!0},rnd.Editor.ChainTool.prototype.OnMouseMove=function(t){var e=this.editor,o=e.render;if("dragCtx"in this){var i=this.dragCtx;"action"in i&&i.action.perform();var r="item"in i?o.atomGetPos(i.item.id):i.xy0,n=ui.page2obj(t);return i.action=Action.fromChain(r,this._calcAngle(r,n),Math.ceil(Vec2.diff(n,r).length()),"item"in i?i.item.id:null),o.update(),!0}return this._hoverHelper.hover(o.findItem(t,["atoms"])),!0},rnd.Editor.ChainTool.prototype.OnMouseUp=function(){return"dragCtx"in this&&("action"in this.dragCtx&&ui.addUndoAction(this.dragCtx.action),delete this.dragCtx),!0},rnd.Editor.ChainTool.prototype.OnCancel=function(){this.OnMouseUp()},rnd.Editor.TemplateTool=function(t,e){if(this.editor=t,this.template=e,!this.template.molecule){var o=chem.Molfile.parseCTFile(this.template.molfile);o.rescale();var i=new Vec2;o.atoms.each(function(t,e){i.add_(e.pp)}),this.template.molecule=o,this.template.xy0=i.scaled(1/o.atoms.count()),this.template.angle0=this._calcAngle(o.atoms.get(this.template.aid).pp,this.template.xy0);var r=o.bonds.get(this.template.bid);this.template.sign=this._getSign(o,r,this.template.xy0)}this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.TemplateTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.TemplateTool.prototype._getSign=function(t,e,o){var i=t.atoms.get(e.begin).pp,r=t.atoms.get(e.end).pp,n=Vec2.cross(Vec2.diff(i,r),Vec2.diff(o,r));return n>0?1:n<0?-1:0},rnd.Editor.TemplateTool.prototype.OnMouseDown=function(t){var e=this.editor,o=e.render;this._hoverHelper.hover(null),this.dragCtx={xy0:ui.page2obj(t),item:o.findItem(t,["atoms","bonds"])};var i=this.dragCtx,r=i.item;if(r&&"Canvas"!=r.type){if("bonds"==r.map){var n=o.ctab.molecule,s=new Vec2,d=n.bonds.get(r.id),a=o.atomGetAttr(d.begin,"fragment"),l=n.getFragmentIds(a),h=0,p=n.halfBonds.get(d.hb1).loop;if(p<0&&(p=n.halfBonds.get(d.hb2).loop),p>=0){var u=n.loops.get(p).hbs;u.each(function(t){s.add_(n.atoms.get(n.halfBonds.get(t).begin).pp),h++})}else Set.each(l,function(t){s.add_(n.atoms.get(t).pp),h++});i.v0=s.scaled(1/h);var c=this._getSign(n,d,i.v0);i.sign1=c||1,i.sign2=this.template.sign}}else delete i.item;return!0},rnd.Editor.TemplateTool.prototype.OnMouseMove=function(t){var e=this.editor,o=e.render;if("dragCtx"in this){var i,r,n,s=this.dragCtx,d=s.item,a=ui.page2obj(t);if(s.mouse_moved=!0,d&&"Canvas"!=d.type){if("atoms"==d.map)i=o.atomGetPos(d.id),n=Vec2.dist(i,a)>1;else if("bonds"==d.map){var l=o.ctab.molecule,h=l.bonds.get(d.id),p=this._getSign(l,h,a);return s.sign1*this.template.sign>0&&(p=-p),p==s.sign2&&s.action||("action"in s&&s.action.perform(),s.sign2=p,s.action=Action.fromTemplateOnBond(d.id,this.template,this._calcAngle,s.sign1*s.sign2>0),o.update()),!0}}else i=s.xy0;r=this._calcAngle(i,a);var u=Math.round(180/Math.PI*r);if("angle"in s&&s.angle==u){if(!("extra_bond"in s))return!0;if(s.extra_bond==n)return!0}return"action"in s&&s.action.perform(),s.angle=u,d&&"Canvas"!=d.type?"atoms"==d.map&&(s.action=Action.fromTemplateOnAtom(d.id,r,n,this.template,this._calcAngle),s.extra_bond=n):s.action=Action.fromTemplateOnCanvas(i,r,this.template),o.update(),!0}return this._hoverHelper.hover(o.findItem(t,["atoms","bonds"])),!0},rnd.Editor.TemplateTool.prototype.OnMouseUp=function(t){var e=this.editor,o=e.render;if("dragCtx"in this){var i=this.dragCtx,r=i.item;if(!i.action){if(r&&"Canvas"!=r.type)if("atoms"==r.map){var n=o.atomGetDegree(r.id);if(n>1)i.action=Action.fromTemplateOnAtom(r.id,null,!0,this.template,this._calcAngle);else if(1==n){var s=o.ctab.molecule,d=s.halfBonds.get(s.atoms.get(r.id).neighbors[0]).end,a=s.atoms.get(r.id),l=s.atoms.get(d);i.action=Action.fromTemplateOnAtom(r.id,this._calcAngle(l.pp,a.pp),!1,this.template,this._calcAngle)}else i.action=Action.fromTemplateOnAtom(r.id,0,!1,this.template,this._calcAngle)}else"bonds"==r.map&&(i.action=Action.fromTemplateOnBond(r.id,this.template,this._calcAngle,i.sign1*i.sign2>0));else i.action=Action.fromTemplateOnCanvas(i.xy0,0,this.template);o.update()}"action"in this.dragCtx&&(this.dragCtx.action.isDummy()||ui.addUndoAction(this.dragCtx.action)),delete this.dragCtx}},rnd.Editor.TemplateTool.prototype.OnCancel=function(){this.OnMouseUp()},rnd.Editor.ChargeTool=function(t,e){this.editor=t,this.charge=e,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.ChargeTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.ChargeTool.prototype.OnMouseMove=function(t){var e=this.editor.render.findItem(t,["atoms"]);return e&&"atoms"==e.map&&null!=element.getElementByLabel(ui.ctab.atoms.get(e.id).label)?this._hoverHelper.hover(e):this._hoverHelper.hover(null),!0},rnd.Editor.ChargeTool.prototype.OnMouseUp=function(t){var e=this.editor,o=e.render,i=o.findItem(t,["atoms"]);return i&&"atoms"==i.map&&null!=element.getElementByLabel(ui.ctab.atoms.get(i.id).label)&&(this._hoverHelper.hover(null),ui.addUndoAction(Action.fromAtomsAttrs(i.id,{charge:o.ctab.molecule.atoms.get(i.id).charge+this.charge})),o.update()),!0},rnd.Editor.RGroupAtomTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.RGroupAtomTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.RGroupAtomTool.prototype.OnMouseMove=function(t){this._hoverHelper.hover(this.editor.render.findItem(t,["atoms"]))},rnd.Editor.RGroupAtomTool.prototype.OnMouseUp=function(t){function e(t){var e=0;return t.values.forEach(function(t){var o=t.substr(1)-1;e|=1<,<,=]?[0-9]+$/g)||t.match(/^[0-9]+\-[0-9]+$/g)}))return alert("Bad occurrence value"),!1;o.range=t.occurrence}return n.resth!=t.resth&&(o.resth=t.resth),n.ifthen!=t.ifthen&&(o.ifthen=t.ifthen),("range"in o||"resth"in o||"ifthen"in o)&&(ui.addUndoAction(Action.fromRGroupAttrs(e.id,o)),this.editor.render.update()),!0}.bind(this)}),!0}},rnd.Editor.APointTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.APointTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.APointTool.prototype.OnMouseMove=function(t){this._hoverHelper.hover(this.editor.render.findItem(t,["atoms"]))},rnd.Editor.APointTool.prototype.OnMouseUp=function(t){var e=this.editor.render.findItem(t,["atoms"]);if(e&&"atoms"==e.map){this._hoverHelper.hover(null);var o=this.editor.render.ctab.molecule.atoms.get(e.id).attpnt;return ui.showAtomAttachmentPoints({selection:o,onOk:function(t){o!=t&&(ui.addUndoAction(Action.fromAtomsAttrs(e.id,{attpnt:t}),!0),ui.render.update())}.bind(this)}),!0}},rnd.Editor.ReactionArrowTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.ReactionArrowTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.ReactionArrowTool.prototype.OnMouseDown=function(t){var e=this.editor.render.findItem(t,["rxnArrows"]);e&&"rxnArrows"==e.map&&(this._hoverHelper.hover(null),this.editor._selectionHelper.setSelection(e),this.dragCtx={xy0:ui.page2obj(t)})},rnd.Editor.ReactionArrowTool.prototype.OnMouseMove=function(t){"dragCtx"in this?(this.dragCtx.action&&this.dragCtx.action.perform(),this.dragCtx.action=Action.fromMultipleMove(this.editor._selectionHelper.selection,ui.page2obj(t).sub(this.dragCtx.xy0)),ui.render.update()):this._hoverHelper.hover(this.editor.render.findItem(t,["rxnArrows"]))},rnd.Editor.ReactionArrowTool.prototype.OnMouseUp=function(t){"dragCtx"in this?(ui.addUndoAction(this.dragCtx.action,!1),this.editor.render.update(),delete this.dragCtx):this.editor.render.ctab.molecule.rxnArrows.count()<1&&(ui.addUndoAction(Action.fromArrowAddition(ui.page2obj(t))),this.editor.render.update())},rnd.Editor.ReactionPlusTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.ReactionPlusTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.ReactionPlusTool.prototype.OnMouseDown=function(t){var e=this.editor.render.findItem(t,["rxnPluses"]);e&&"rxnPluses"==e.map&&(this._hoverHelper.hover(null),this.editor._selectionHelper.setSelection(e),this.dragCtx={xy0:ui.page2obj(t)})},rnd.Editor.ReactionPlusTool.prototype.OnMouseMove=function(t){"dragCtx"in this?(this.dragCtx.action&&this.dragCtx.action.perform(),this.dragCtx.action=Action.fromMultipleMove(this.editor._selectionHelper.selection,ui.page2obj(t).sub(this.dragCtx.xy0)),ui.render.update()):this._hoverHelper.hover(this.editor.render.findItem(t,["rxnPluses"]))},rnd.Editor.ReactionPlusTool.prototype.OnMouseUp=function(t){"dragCtx"in this?(ui.addUndoAction(this.dragCtx.action,!1),this.editor.render.update(),delete this.dragCtx):(ui.addUndoAction(Action.fromPlusAddition(ui.page2obj(t))),this.editor.render.update())},rnd.Editor.ReactionMapTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this),this.editor._selectionHelper.setSelection(null),this.rcs=chem.MolfileSaver.getComponents(this.editor.render.ctab.molecule)},rnd.Editor.ReactionMapTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.ReactionMapTool.prototype.OnMouseDown=function(t){var e=this.editor.render.findItem(t,["atoms"]);e&&"atoms"==e.map&&(this._hoverHelper.hover(null),this.dragCtx={item:e,xy0:ui.page2obj(t)})},rnd.Editor.ReactionMapTool.prototype.OnMouseMove=function(t){var e=this.editor.render;if("dragCtx"in this){var o=e.findItem(t,["atoms"],this.dragCtx.item);o&&"atoms"==o.map&&this._isValidMap(this.dragCtx.item.id,o.id)?(this._hoverHelper.hover(o),e.drawSelectionLine(e.atomGetPos(this.dragCtx.item.id),e.atomGetPos(o.id))):(this._hoverHelper.hover(null),e.drawSelectionLine(e.atomGetPos(this.dragCtx.item.id),ui.page2obj(t)))}else this._hoverHelper.hover(e.findItem(t,["atoms"]))},rnd.Editor.ReactionMapTool.prototype.OnMouseUp=function(t){if("dragCtx"in this){var e=this.editor.render,o=e.findItem(t,["atoms"],this.dragCtx.item);if(o&&"atoms"==o.map&&this._isValidMap(this.dragCtx.item.id,o.id)){var i=new Action,r=e.ctab.molecule.atoms,n=r.get(this.dragCtx.item.id),s=r.get(o.id),d=n.aam,a=s.aam;if(!d||d!=a){if((d&&d!=a||!d&&a)&&r.each(function(t,e){t!=this.dragCtx.item.id&&(d&&e.aam==d||a&&e.aam==a)&&i.mergeWith(Action.fromAtomsAttrs(t,{aam:0}))},this),d)i.mergeWith(Action.fromAtomsAttrs(o.id,{aam:d}));else{var l=0;r.each(function(t,e){l=Math.max(l,e.aam||0)}),i.mergeWith(Action.fromAtomsAttrs(this.dragCtx.item.id,{aam:l+1})),i.mergeWith(Action.fromAtomsAttrs(o.id,{aam:l+1}))}ui.addUndoAction(i,!0),e.update()}}e.drawSelectionLine(null),delete this.dragCtx}this._hoverHelper.hover(null)},rnd.Editor.ReactionMapTool.prototype._isValidMap=function(t,e){for(var o,i,r=0;(!o||!i)&&r=0&&(o="r"),!i&&n.indexOf(e)>=0&&(i="r")}for(var s=0;(!o||!i)&&s=0&&(o="p"),!i&&d.indexOf(e)>=0&&(i="p")}return o&&i&&o!=i},rnd.Editor.ReactionUnmapTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this),this.editor._selectionHelper.setSelection(null)},rnd.Editor.ReactionUnmapTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.ReactionUnmapTool.prototype.OnMouseMove=function(t){var e=this.editor.render.findItem(t,["atoms"]);e&&"atoms"==e.map?this._hoverHelper.hover(this.editor.render.ctab.molecule.atoms.get(e.id).aam?e:null):this._hoverHelper.hover(null)},rnd.Editor.ReactionUnmapTool.prototype.OnMouseUp=function(t){var e=this.editor.render.findItem(t,["atoms"]),o=this.editor.render.ctab.molecule.atoms;if(e&&"atoms"==e.map&&o.get(e.id).aam){var i=new Action,r=o.get(e.id).aam;o.each(function(t,e){e.aam==r&&i.mergeWith(Action.fromAtomsAttrs(t,{aam:0}))},this),ui.addUndoAction(i,!0),this.editor.render.update()}this._hoverHelper.hover(null)},rnd.Editor.SGroupTool=function(t){this.editor=t,this.maps=["atoms","bonds","sgroups","sgroupData"],this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this),this._lassoHelper=new rnd.Editor.LassoTool.LassoHelper(1,t),this._sGroupHelper=new rnd.Editor.SGroupTool.SGroupHelper(t) +;var e=this.editor.getSelection();e.atoms&&e.atoms.length>0?this._sGroupHelper.showPropertiesDialog(null,e):this.editor.deselectAll()},rnd.Editor.SGroupTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.SGroupTool.prototype.OnMouseDown=function(t){var e=this.editor.render.findItem(t,this.maps);e&&"Canvas"!=e.type||this._lassoHelper.begin(t)},rnd.Editor.SGroupTool.prototype.OnMouseMove=function(t){this._lassoHelper.running()?this.editor._selectionHelper.setSelection(this._lassoHelper.addPoint(t)):this._hoverHelper.hover(this.editor.render.findItem(t,this.maps))},rnd.Editor.SGroupTool.SGroupHelper=function(t){this.editor=t,this.selection=null},rnd.Editor.SGroupTool.SGroupHelper.prototype.showPropertiesDialog=function(t,e){this.selection=e;var o=this.editor.render;if(null==t){var i={},r={};if(e.atoms.each(function(t){r[t]=!0},this),!Object.isUndefined(e.atoms.detect(function(t){var n=o.atomGetSGroups(t);return!Object.isUndefined(n.detect(function(t){if(t in i)return!1;var n=o.sGroupGetAtoms(t);if(n.length0)&&this._sGroupHelper.showPropertiesDialog(e,o)},rnd.Editor.PasteTool=function(t,e){this.editor=t,this.struct=e,this.action=Action.fromPaste(this.struct,"lastEvent"in this.OnMouseMove0?ui.page2obj(this.OnMouseMove0.lastEvent):void 0),this.editor.render.update()},rnd.Editor.PasteTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.PasteTool.prototype.OnMouseMove=function(t){"action"in this&&this.action.perform(this.editor),this.action=Action.fromPaste(this.struct,ui.page2obj(t)),this.editor.render.update()},rnd.Editor.PasteTool.prototype.OnMouseUp=function(){ui.addUndoAction(this.action),delete this.action,ui.selectAction(null)},rnd.Editor.PasteTool.prototype.OnCancel=function(){"action"in this&&(this.action.perform(this.editor),delete this.action)},rnd.Editor.RotateTool=function(t){this.editor=t,this._lassoHelper=new rnd.Editor.LassoTool.LassoHelper(1,t);var e=this.editor._selectionHelper.selection;e.atoms&&e.atoms.length||this.editor._selectionHelper.setSelection(null)},rnd.Editor.RotateTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.RotateTool.prototype.OnMouseDown=function(t){var e=this.editor._selectionHelper.selection;if(e.atoms&&e.atoms.length){var o=this.editor.render.ctab.molecule,i=new Vec2;if(!e.atoms||!e.atoms.length)return!0;var r=null,n=!1;e.atoms.each(function(t){var s=o.atoms.get(t);i.add_(s.pp),n||s.neighbors.find(function(i){var s=o.halfBonds.get(i);if(-1==e.atoms.indexOf(s.end)){if(s.loop>=0){var d=o.atoms.get(t);if(!Object.isUndefined(d.neighbors.find(function(t){var i=o.halfBonds.get(t);return i.loop>=0&&-1!=e.atoms.indexOf(i.end)})))return n=!0,!0}if(null==r)r=t;else if(r!=t)return n=!0,!0}return!1})}),i=n||null==r?i.scaled(1/e.atoms.length):o.atoms.get(r).pp,this.dragCtx={xy0:i,angle1:this._calcAngle(i,ui.page2obj(t)),all:n}}else this._lassoHelper.begin(t);return!0},rnd.Editor.RotateTool.prototype.OnMouseMove=function(t){if(this._lassoHelper.running())this.editor._selectionHelper.setSelection(this._lassoHelper.addPoint(t));else if("dragCtx"in this){var e=this.editor,o=e.render,i=this.dragCtx,r=ui.page2obj(t),n=this._calcAngle(i.xy0,r)-i.angle1,s=Math.round(n/Math.PI*180);if(s>180?s-=360:s<=-180&&(s+=360),"angle"in i&&i.angle==s)return!0;"action"in i&&i.action.perform(),i.angle=s,i.action=Action.fromRotate(i.all?o.ctab.molecule:this.editor.getSelection(),i.xy0,n),$("toolText").update(s+"º"),o.update()}return!0},rnd.Editor.RotateTool.prototype.OnMouseUp=function(t){return this._lassoHelper.running()?this._lassoHelper.end(t):"dragCtx"in this&&("action"in this.dragCtx?(ui.addUndoAction(this.dragCtx.action,!0),$("toolText").update("")):this.editor._selectionHelper.setSelection(),delete this.dragCtx),!0},rnd.Editor.RotateTool.prototype.OnCancel=function(){"dragCtx"in this&&("action"in this.dragCtx&&(ui.addUndoAction(this.dragCtx.action,!0),$("toolText").update("")),delete this.dragCtx)}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../chem":11,"../chem/element":10,"../ui":34,"../ui/action":26,"../util":39,"../util/set":42,"../util/vec2":43,"./restruct":23}],21:[function(require,module,exports){ +(function (global){ +require("./visel"),require("./restruct"),require("./editor"),require("./render"),require("./restruct_rendering"),global.rnd=global.rnd||{}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"./editor":20,"./render":22,"./restruct":23,"./restruct_rendering":24,"./visel":25}],22:[function(require,module,exports){ +(function (global){ +var Raphael=require("../raphael-ext.js"),Box2Abs=require("../util/box2abs"),Set=require("../util/set"),Vec2=require("../util/vec2"),util=require("../util");require("./restruct"),require("../ui"),require("../chem"),require("./restruct_rendering");var rnd=global.rnd=global.rnd||{},chem=global.chem=global.chem||{},ui=global.ui,tfx=util.tfx;rnd.DEBUG=!1,rnd.logcnt=0,rnd.logmouse=!1,rnd.hl=!1;var EventMap={mousemove:"mousemove",mousedown:"mousedown",mouseup:"mouseup"};rnd.logMethod=function(){},rnd.RenderDummy=function(t,e,o,s){this.clientArea=t=$(t),t.innerHTML="",this.paper=new Raphael(t),this.paper.rect(0,0,100,100).attr({fill:"#0F0",stroke:"none"}),this.setMolecule=function(){},this.update=function(){}},rnd.RenderOptions=function(t){t=t||{},this.showSelectionRegions=t.showSelectionRegions||!1,this.showAtomIds=t.showAtomIds||!1,this.showBondIds=t.showBondIds||!1,this.showHalfBondIds=t.showHalfBondIds||!1,this.showLoopIds=t.showLoopIds||!1,this.hideChiralFlag=t.hideChiralFlag||!1,this.showValenceWarnings=!!Object.isUndefined(t.showValenceWarnings)||t.showValenceWarnings,this.autoScale=t.autoScale||!1,this.autoScaleMargin=t.autoScaleMargin||0,this.maxBondLength=t.maxBondLength||0,this.atomColoring=t.atomColoring||0,this.hideImplicitHydrogen=t.hideImplicitHydrogen||!1,this.hideTerminalLabels=t.hideTerminalLabels||!1,this.ignoreMouseEvents=t.ignoreMouseEvents||!1,this.selectionDistanceCoefficient=(t.selectionDistanceCoefficient||.4)-0},rnd.Render=function(t,e,o,s){this.opt=new rnd.RenderOptions(o),this.useOldZoom=Prototype.Browser.IE,this.scale=e||100,this.baseScale=this.scale,this.offset=new Vec2,this.clientArea=t=$(t),t.innerHTML="",this.paper=new Raphael(t),this.size=new Vec2,this.viewSz=s||new Vec2(t.clientWidth||100,t.clientHeight||100),this.bb=new Box2Abs(new Vec2,this.viewSz),this.dirty=!0,this.selectionRect=null,this.rxnArrow=null,this.rxnMode=!1,this.zoom=1,this.structChangeHandlers=[];var n=this,i=0,r=0,a=t;do{i+=a.offsetTop||0,r+=a.offsetLeft||0,a=a.offsetParent}while(a);this.clientAreaPos=new Vec2(r,i);var h=this;h.longTapFlag=!1,h.longTapTimeout=null,h.longTapTouchstart=null,h.setLongTapTimeout=function(t){h.longTapFlag=!1,h.longTapTouchstart=t,h.longTapTimeout=setTimeout(function(){h.longTapFlag=!0,h.longTapTimeout=null},500)},h.resetLongTapTimeout=function(t){clearTimeout(h.longTapTimeout),h.longTapTimeout=null,t&&(h.longTapTouchstart=null,h.longTapFlag=!1)},"hiddenPaths"in rnd.ReStruct.prototype&&t.observe("touchend",function(t){if(0==t.touches.length)for(;rnd.ReStruct.prototype.hiddenPaths.length>0;)rnd.ReStruct.prototype.hiddenPaths.pop().remove()}),this.opt.ignoreMouseEvents||(t.observe("selectstart",function(t){return util.stopEventPropagation(t),util.preventDefault(t)}),t.observe("touchstart",function(t){h.resetLongTapTimeout(!0),2==t.touches.length?(this._tui=this._tui||{},this._tui.center={pageX:(t.touches[0].pageX+t.touches[1].pageX)/2,pageY:(t.touches[0].pageY+t.touches[1].pageY)/2},ui.setZoomStaticPointInit(ui.page2obj(this._tui.center))):1==t.touches.length&&h.setLongTapTimeout(t)}),t.observe("touchmove",function(t){h.resetLongTapTimeout(!0),"_tui"in this&&2==t.touches.length&&(this._tui.center={pageX:(t.touches[0].pageX+t.touches[1].pageX)/2,pageY:(t.touches[0].pageY+t.touches[1].pageY)/2})}),t.observe("gesturestart",function(t){this._tui=this._tui||{},this._tui.scale0=ui.render.zoom,t.preventDefault()}),t.observe("gesturechange",function(t){ui.setZoomStaticPoint(this._tui.scale0*t.scale,ui.page2canvas2(this._tui.center)),ui.render.update(),t.preventDefault()}),t.observe("gestureend",function(t){delete this._tui,t.preventDefault()}),t.observe("onresize",function(t){n.onResize()}),["Click","DblClick","MouseDown","MouseMove","MouseUp","MouseLeave"].each(function(e){var o=e.toLowerCase();o=EventMap[o]||o,t.observe(o,function(s){if(!("MouseLeave"==e||ui&&ui.is_touch)){var n=t.cumulativeOffset();n=new Vec2(n[0],n[1]);var i=new Vec2(s.clientX,s.clientY).sub(n),r=new Vec2(t.clientWidth,t.clientHeight);if(!(i.x>0&&i.y>0&&i.x=0&&this.ctab.loopRemove(o),s>=0&&this.ctab.loopRemove(s)},rnd.Render.prototype.invalidateBond=function(t){var e=this.ctab.bonds.get(t);this.invalidateLoop(t),this.invalidateAtom(e.b.begin,0),this.invalidateAtom(e.b.end,0)},rnd.Render.prototype.invalidateItem=function(t,e,o){"atoms"==t?this.invalidateAtom(e,o):"bonds"==t?(this.invalidateBond(e),o>0&&this.invalidateLoop(e)):this.ctab.markItem(t,e,o)},rnd.Render.prototype.atomGetDegree=function(t){return rnd.logMethod("atomGetDegree"),this.ctab.atoms.get(t).a.neighbors.length},rnd.Render.prototype.isBondInRing=function(t){var e=this.ctab.bonds.get(t);return this.ctab.molecule.halfBonds.get(e.b.hb1).loop>=0||this.ctab.molecule.halfBonds.get(e.b.hb2).loop>=0},rnd.Render.prototype.atomGetNeighbors=function(t){for(var e=this.ctab.atoms.get(t),o=[],s=0;s-1))return!1;var o=this.ctab[t.map].get(t.id);if(null==o)return!0;if("sgroups"==t.map&&"DAT"==o.item.type||"sgroupData"==t.map){var s=this.ctab.sgroups.get(t.id),n=this.ctab.sgroupData.get(t.id);null!=s&&s.setHighlight(e,this),null!=n&&n.setHighlight(e,this)}else o.setHighlight(e,this);return!0},rnd.Render.prototype.itemGetPos=function(t,e){return this.ctab.molecule[t].get(e).pp},rnd.Render.prototype.atomGetPos=function(t){return rnd.logMethod("atomGetPos"),this.itemGetPos("atoms",t)},rnd.Render.prototype.rxnArrowGetPos=function(t){return rnd.logMethod("rxnArrowGetPos"),this.itemGetPos("rxnArrows",t)},rnd.Render.prototype.rxnPlusGetPos=function(t){return rnd.logMethod("rxnPlusGetPos"),this.itemGetPos("rxnPluses",t)},rnd.Render.prototype.getAdjacentBonds=function(t){for(var e=Set.fromList(t),o=Set.empty(),s=Set.empty(),n=0;nn&&s.xr&&s.yn&&e.a.pp.xr&&e.a.pp.yn&&e.item.pp.xr&&e.item.pp.yn&&e.item.pp.xr&&e.item.pp.yn&&e.pp.xr&&e.pp.yn&&e.sgroup.pp.xr&&e.sgroup.pp.y1){for(var e=this.obj2scaled(t[t.length-1]).add(this.offset),o="M"+tfx(e.x)+","+tfx(e.y),s=0;s-1e-5?r>-1e-5&&(l=!0):(Math.abs(i)*Math.abs(f)-Math.abs(g)*Math.abs(r))*f>0&&(l=!0)),l&&d&&Vec2.dot(p,s)*Vec2(a,s)>=0&&(l=!1),l&&h++,n=u,i=g,r=f,a=p,d=l}return h%2!=0},rnd.Render.prototype.ps=function(t){return t.scaled(this.settings.scaleFactor)},rnd.Render.prototype.getElementsInPolygon=function(t){rnd.logMethod("getElementsInPolygon");for(var e=[],o=[],s=[],n=0;n0?.8*this.viewSz.y/(e.max.y-e.min.y):100,s=e.max.x-e.min.x>0?.8*this.viewSz.x/(e.max.x-e.min.x):100;this.scale=Math.min(o,s),this.opt.maxBondLength>0&&this.scale>this.opt.maxBondLength&&(this.scale=this.opt.maxBondLength)}this.initSettings(),this.initStyles(),this.dirty=!1,t=!0}var n=(new Date).getTime(),i=this.ctab.update(t);this.setSelection(null);var r=(new Date).getTime()-n;if(t&&$("log")&&($("log").innerHTML=r.toString()+"\n"),i){var a=this.settings.scaleFactor,h=this.ctab.getVBoxObj().transform(this.obj2scaled,this).translate(this.offset||new Vec2);if(this.opt.autoScale){var l=h.sz(),d=this.opt.autoScaleMargin,c=new Vec2(d,d),u=this.viewSz;if(u.x<2*d+1||u.y<2*d+1)throw new Error("View box too small for the given margin");var p=Math.max(l.x/(u.x-2*d),l.y/(u.y-2*d));this.opt.maxBondLength/p>1&&(p=1);var g=l.add(c.scaled(2*p));this.paper.setViewBox(h.pos().x-d*p-(u.x*p-g.x)/2,h.pos().y-d*p-(u.y*p-g.y)/2,u.x*p,u.y*p)}else{var f=Vec2.UNIT.scaled(a),m=h.sz().length()>0?h.extend(f,f):h;console.assert(ui.zoom==this.zoom);var b=new Box2Abs(ui.scrollPos(),this.viewSz.scaled(1/ui.zoom).sub(Vec2.UNIT.scaled(20))),y=Box2Abs.union(b,m);this.oldCb||(this.oldCb=new Box2Abs);var v=y.sz().floor(),x=this.oldCb.p0.sub(y.p0).ceil();this.oldBb=h,this.sz&&v.x==this.sz.x&&v.y==this.sz.y||this.setPaperSize(v),this.offset=this.offset||new Vec2,0==x.x&&0==x.y||(this.setOffset(this.offset.add(x)),this.ctab.translate(x))}}},rnd.Render.prototype.checkBondExists=function(t,e){return this.ctab.molecule.checkBondExists(t,e)},rnd.Render.prototype.findClosestAtom=function(t,e,o){var s=null,n=this.opt.selectionDistanceCoefficient;return e=e||n,e=Math.min(e,n),this.ctab.atoms.each(function(n,i){if(n!=o){var r=Vec2.dist(t,i.a.pp);re.dist||o)&&(s={type:t,id:e.id,dist:e.dist})};if(!e||e.indexOf("atoms")>=0){n("Atom",this.findClosestAtom(t,void 0,Object.isUndefined(o)||"atoms"!=o.map?void 0:o.id))}if(!e||e.indexOf("bonds")>=0){var i=this.findClosestBond(t);i&&(null!==i.cid&&n("Bond",{id:i.cid,dist:i.cdist}),(null==s||s.dist>.4*this.scale)&&n("Bond",i))}if(!e||e.indexOf("chiralFlags")>=0){n("ChiralFlag",rnd.ReChiralFlag.findClosest(this,t))}if(!e||e.indexOf("sgroupData")>=0){n("DataSGroupData",rnd.ReDataSGroupData.findClosest(this,t))}if(!e||e.indexOf("sgroups")>=0){n("SGroup",rnd.ReSGroup.findClosest(this,t))}if(!e||e.indexOf("rxnArrows")>=0){n("RxnArrow",rnd.ReRxnArrow.findClosest(this,t))}if(!e||e.indexOf("rxnPluses")>=0){n("RxnPlus",rnd.ReRxnPlus.findClosest(this,t))}if(!e||e.indexOf("frags")>=0){n("Fragment",rnd.ReFrag.findClosest(this,t,o&&"atoms"==o.map?o.id:void 0))}if(!e||e.indexOf("rgroups")>=0){n("RGroup",rnd.ReRGroup.findClosest(this,t))}return s=s||{type:"Canvas",id:-1}},rnd.Render.prototype.setZoom=function(t){this.zoom=t,this._setPaperSize(this.sz)},rnd.Render.prototype.extendCanvas=function(t,e,o,s){var n=0,i=0,r=0,a=0;t-=0,o-=0,e-=0,s-=0,t<0&&(n+=-t,r+=-t),e<0&&(i+=-e,a+=-e);var h=this.sz.x*this.zoom,l=this.sz.y*this.zoom;h0||n>0){var c=new Vec2(n,i).scaled(1/this.zoom),u=this.sz.add(c);this.setPaperSize(u),(d.x>0||d.y>0)&&(this.ctab.translate(d),this.setOffset(this.offset.add(d)))}return d},rnd.Render.prototype.setScale=function(t){this.offset&&(this.offset=this.offset.scaled(1/t).scaled(this.zoom)),this.scale=this.baseScale*this.zoom,this.settings=null,this.update(!0)},rnd.Render.prototype.setViewBox=function(t){this.useOldZoom?this.setScale(t):this.paper.canvas.setAttribute("viewBox","0 0 "+this.sz.x+" "+this.sz.y)}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../chem":11,"../raphael-ext.js":19,"../ui":34,"../util":39,"../util/box2abs":38,"../util/set":42,"../util/vec2":43,"./restruct":23,"./restruct_rendering":24}],23:[function(require,module,exports){ +(function (global){ +var Box2Abs=require("../util/box2abs"),Map=require("../util/map"),Pool=require("../util/pool"),Set=require("../util/set"),Vec2=require("../util/vec2"),util=require("../util"),element=require("../chem/element");require("../chem");var rnd=global.rnd=global.rnd||{},chem=global.chem,tfx=util.tfx;rnd.ReObject=function(){this.__ext=new Vec2(.05*3,.05*3)},rnd.ReObject.prototype.init=function(t){this.visel=new rnd.Visel(t),this.highlight=!1,this.highlighting=null,this.selected=!1,this.selectionPlate=null},rnd.ReObject.prototype.getVBoxObj=function(t){var e=this.visel.boundingBox;return util.isNull(e)?null:(t.offset&&(e=e.translate(t.offset.negated())),e.transform(t.scaled2obj,t))},rnd.ReObject.prototype.drawHighlight=function(t){console.log("ReObject.drawHighlight is not overridden")},rnd.ReObject.prototype.setHighlight=function(t,e){if(t){var n="highlighting"in this&&null!=this.highlighting;n&&(n="set"==this.highlighting.type?!this.highlighting[0].removed:!this.highlighting.removed),n=n&&(!("hiddenPaths"in rnd.ReStruct.prototype)||rnd.ReStruct.prototype.hiddenPaths.indexOf(this.highlighting)<0),n?this.highlighting.show():(e.paper.setStart(),this.drawHighlight(e),this.highlighting=e.paper.setFinish())}else this.highlighting&&this.highlighting.hide();this.highlight=t},rnd.ReObject.prototype.makeSelectionPlate=function(t){console.log("ReObject.makeSelectionPlate is not overridden")},rnd.ReAtom=function(t){this.init(rnd.Visel.TYPE.ATOM),this.a=t,this.showLabel=!1,this.hydrogenOnTheLeft=!1,this.component=-1},rnd.ReAtom.prototype=new rnd.ReObject,rnd.ReAtom.isSelectable=function(){return!0},rnd.ReAtom.prototype.getVBoxObj=function(t){return this.visel.boundingBox?rnd.ReObject.prototype.getVBoxObj.call(this,t):new Box2Abs(this.a.pp,this.a.pp)},rnd.ReAtom.prototype.drawHighlight=function(t){var e=this.makeHighlightPlate(t);return t.ctab.addReObjectPath("highlighting",this.visel,e),e},rnd.ReAtom.prototype.makeHighlightPlate=function(t){var e=t.paper,n=t.styles,r=t.ps(this.a.pp);return e.circle(r.x,r.y,n.atomSelectionPlateRadius).attr(n.highlightStyle)},rnd.ReAtom.prototype.makeSelectionPlate=function(t,e,n){var r=t.render.ps(this.a.pp);return e.circle(r.x,r.y,n.atomSelectionPlateRadius).attr(n.selectionStyle)},rnd.ReBond=function(t){this.init(rnd.Visel.TYPE.BOND),this.b=t,this.doubleBondShift=0},rnd.ReBond.prototype=new rnd.ReObject,rnd.ReBond.isSelectable=function(){return!0},rnd.ReBond.prototype.drawHighlight=function(t){var e=this.makeHighlightPlate(t);return t.ctab.addReObjectPath("highlighting",this.visel,e),e},rnd.ReBond.prototype.makeHighlightPlate=function(t){t.ctab.bondRecalc(t.settings,this);var e=t.ps(this.b.center);return t.paper.circle(e.x,e.y,.8*t.styles.atomSelectionPlateRadius).attr(t.styles.highlightStyle)},rnd.ReBond.prototype.makeSelectionPlate=function(t,e,n){t.bondRecalc(t.render.settings,this);var r=t.render.ps(this.b.center);return e.circle(r.x,r.y,.8*n.atomSelectionPlateRadius).attr(n.selectionStyle)},rnd.ReStruct=function(t,e,n){this.render=e,this.atoms=new Map,this.bonds=new Map,this.reloops=new Map,this.rxnPluses=new Map,this.rxnArrows=new Map,this.frags=new Map,this.rgroups=new Map,this.sgroups=new Map,this.sgroupData=new Map,this.chiralFlags=new Map,this.molecule=t||new chem.Struct,this.initialized=!1,this.layers=[],this.initLayers(),this.connectedComponents=new Pool,this.ccFragmentType=new Map;for(var r in rnd.ReStruct.maps)this[r+"Changed"]={};if(this.structChanged=!1,t.atoms.each(function(t,e){this.atoms.set(t,new rnd.ReAtom(e))},this),t.bonds.each(function(t,e){this.bonds.set(t,new rnd.ReBond(e))},this),t.loops.each(function(t,e){this.reloops.set(t,new rnd.ReLoop(e))},this),t.rxnPluses.each(function(t,e){this.rxnPluses.set(t,new rnd.ReRxnPlus(e))},this),t.rxnArrows.each(function(t,e){this.rxnArrows.set(t,new rnd.ReRxnArrow(e))},this),t.frags.each(function(t,e){this.frags.set(t,new rnd.ReFrag(e))},this),t.rgroups.each(function(t,e){this.rgroups.set(t,new rnd.ReRGroup(e))},this),t.sgroups.each(function(t,e){this.sgroups.set(t,new rnd.ReSGroup(e)),"DAT"!=e.type||e.data.attached||this.sgroupData.set(t,new rnd.ReDataSGroupData(e))},this),t.isChiral&&!this.render.opt.hideChiralFlag){var i=t.getCoordBoundingBox();this.chiralFlags.set(0,new rnd.ReChiralFlag(new Vec2(i.max.x,i.min.y-1)))}this.coordProcess(n)},rnd.ReStruct.prototype.connectedComponentRemoveAtom=function(t,e){if(e=e||this.atoms.get(t),!(e.component<0)){var n=this.connectedComponents.get(e.component);Set.remove(n,t),Set.size(n)<1&&this.connectedComponents.remove(e.component),e.component=-1}},rnd.ReStruct.prototype.printConnectedComponents=function(){var t=[];this.connectedComponents.each(function(e,n){t.push(" "+e+":["+Set.list(n).toString()+"]."+Set.size(n).toString())},this),console.log(t.toString())},rnd.ReStruct.prototype.clearConnectedComponents=function(){this.connectedComponents.clear(),this.atoms.each(function(t,e){e.component=-1})},rnd.ReStruct.prototype.getConnectedComponent=function(t,e){for(var n="number"==typeof t.length?util.array(t):[t],r=Set.empty();n.length>0;)(function(){var t=n.pop();Set.add(r,t);var i=this.atoms.get(t);i.component>=0&&Set.add(e,i.component);for(var o=0;o=0)){var n=Set.empty(),r=this.getConnectedComponent(t,n);Set.each(n,function(t){this.removeConnectedComponent(t)},this),this.addConnectedComponent(r)}},this)},rnd.ReStruct.prototype.connectedComponentGetBoundingBox=function(t,e,n){return e=e||this.connectedComponents.get(t),n=n||{min:null,max:null},Set.each(e,function(t){var e=this.render.ps(this.atoms.get(t).a.pp);null==n.min?n.min=n.max=e:(n.min=n.min.min(e),n.max=n.max.max(e))},this),n},rnd.ReStruct.prototype.initLayers=function(){for(var t in rnd.ReStruct.layerMap)this.layers[rnd.ReStruct.layerMap[t]]=this.render.paper.rect(0,0,10,10).attr({fill:"#000",opacity:"0.0"}).toFront()},rnd.ReStruct.prototype.insertInLayer=function(t,e){e.insertBefore(this.layers[t])},rnd.ReStruct.prototype.clearMarks=function(){for(var t in rnd.ReStruct.maps)this[t+"Changed"]={};this.structChanged=!1},rnd.ReStruct.prototype.markItemRemoved=function(){this.structChanged=!0},rnd.ReStruct.prototype.markBond=function(t,e){this.markItem("bonds",t,e)},rnd.ReStruct.prototype.markAtom=function(t,e){this.markItem("atoms",t,e)},rnd.ReStruct.prototype.markItem=function(t,e,n){var r=this[t+"Changed"];r[e]=void 0!==r[e]?Math.max(n,r[e]):n,this[t].has(e)&&this.clearVisel(this[t].get(e).visel)},rnd.ReStruct.prototype.eachVisel=function(t,e){for(var n in rnd.ReStruct.maps)this[n].each(function(n,r){t.call(e,r.visel)},this)},rnd.ReStruct.prototype.getVBoxObj=function(t){if(t=t||{},this.selectionIsEmpty(t))for(var e in rnd.ReStruct.maps)t[e]=this[e].keys();var n=null;for(var e in rnd.ReStruct.maps)t[e]&&util.each(t[e],function(t){var r=this[e].get(t).getVBoxObj(this.render);r&&(n=n?Box2Abs.union(n,r):r.clone())},this);return n=n||new Box2Abs(0,0,0,0)},rnd.ReStruct.prototype.selectionIsEmpty=function(t){if(util.assert(!util.isUndefined(t),"'selection' is not defined"),util.isNull(t))return!0;for(var e in rnd.ReStruct.maps)if(t[e]&&t[e].length>0)return!1;return!0},rnd.ReStruct.prototype.translate=function(t){this.eachVisel(function(e){e.translate(t)},this)},rnd.ReStruct.prototype.scale=function(t){this.eachVisel(function(e){this.scaleVisel(e,t)},this)},rnd.ReStruct.prototype.scaleRPath=function(t,e){if("set"==t.type)for(var n=0;n=0&&n[1]>=0},rnd.ReStruct.prototype.findIncomingUpBonds=function(t,e){var n=util.map([e.b.begin,e.b.end],function(e){var n=this.molecule.atoms.get(e),r=this.findIncomingStereoUpBond(n,t,!0);return r<0?-1:n.neighbors[r]},this);util.assert(2===n.length),e.neihbid1=this.atoms.get(e.b.begin).showLabel?-1:n[0],e.neihbid2=this.atoms.get(e.b.end).showLabel?-1:n[1]},rnd.ReStruct.prototype.checkStereoBoldBonds=function(){this.bonds.each(this.checkStereoBold,this)},rnd.ReStruct.prototype.update=function(t){t=t||!this.initialized;var e;t?function(){for(var t in rnd.ReStruct.maps){var e=this[t+"Changed"];this[t].each(function(t){e[t]=1},this)}}.call(this):function(){for(var t in rnd.ReStruct.maps){var n=this[t+"Changed"];for(e in n)this[t].has(e)||delete n[e]}}.call(this);for(e in this.atomsChanged)this.connectedComponentRemoveAtom(e);for(var n=this.frags.findAll(function(t,e){return!e.calcBBox(this.render,t)},this),r=0;r0}}).call(this),this.structChanged&&util.each(this.render.structChangeHandlers,function(t){t.call()}),this.sgroups.each(function(t,e){this.clearVisel(e.visel),e.highlighting=null,e.selectionPlate=null},this),this.frags.each(function(t,e){this.clearVisel(e.visel)},this),this.rgroups.each(function(t,e){this.clearVisel(e.visel)},this),t&&(this.clearConnectedComponents(),this.molecule.initHalfBonds(),this.molecule.initNeighbors()),this.molecule.updateHalfBonds(new Map(this.atomsChanged).findAll(function(t,e){return e>=0},this)),this.molecule.sortNeighbors(new Map(this.atomsChanged).findAll(function(t,e){return e>=1},this)),this.assignConnectedComponents(),this.setImplicitHydrogen(),this.setHydrogenPos(),this.initialized=!0,this.verifyLoops();var o=t||this.structChanged;return o&&this.updateLoops(),this.setDoubleBondShift(),this.checkLabelsToShow(),this.checkStereoBoldBonds(),this.showLabels(),this.showBonds(),o&&this.renderLoops(),this.drawReactionSymbols(),this.drawSGroups(),this.drawFragments(),this.drawRGroups(),this.chiralFlags.each(function(t,e){this.chiralFlagsChanged[t]>0&&e.draw(this.render)},this),this.clearMarks(),!0},rnd.ReStruct.prototype.drawReactionSymbols=function(){var t,e;for(e in this.rxnArrowsChanged)t=this.rxnArrows.get(e),this.drawReactionArrow(e,t);for(e in this.rxnPlusesChanged)t=this.rxnPluses.get(e),this.drawReactionPlus(e,t)},rnd.ReStruct.prototype.drawReactionArrow=function(t,e){var n=this.render.ps(e.item.pp),r=this.drawArrow(new Vec2(n.x-this.render.scale,n.y),new Vec2(n.x+this.render.scale,n.y));e.visel.add(r,Box2Abs.fromRelBox(rnd.relBox(r.getBBox())));var i=this.render.offset;null!=i&&r.translateAbs(i.x,i.y)},rnd.ReStruct.prototype.drawReactionPlus=function(t,e){var n=this.render.ps(e.item.pp),r=this.drawPlus(n);e.visel.add(r,Box2Abs.fromRelBox(rnd.relBox(r.getBBox())));var i=this.render.offset;null!=i&&r.translateAbs(i.x,i.y)},rnd.ReStruct.prototype.drawSGroups=function(){util.each(this.molecule.sGroupForest.getSGroupsBFS().reverse(),function(t){var e=this.sgroups.get(t),n=e.draw(this.render);this.addReObjectPath("data",e.visel,n,null,!0),e.setHighlight(e.highlight,this.render)},this)},rnd.ReStruct.prototype.drawFragments=function(){this.frags.each(function(t,e){var n=e.draw(this.render,t);n&&this.addReObjectPath("data",e.visel,n,null,!0)},this)},rnd.ReStruct.prototype.drawRGroups=function(){this.rgroups.each(function(t,e){var n=e.draw(this.render);for(var r in n)for(;n[r].length>0;)this.addReObjectPath(r,e.visel,n[r].shift(),null,!0)},this)},rnd.ReStruct.prototype.eachCC=function(t,e,n){this.connectedComponents.each(function(r,i){e&&this.ccFragmentType.get(r)!=e||t.call(n||this,r,i)},this)},rnd.ReStruct.prototype.getGroupBB=function(t){var e={min:null,max:null};return this.eachCC(function(t,n){e=this.connectedComponentGetBoundingBox(t,n,e)},t,this),e},rnd.ReStruct.prototype.setHydrogenPos=function(){for(var t in this.atomsChanged){var e=this.atoms.get(t);if(0!=e.a.neighbors.length){for(var n=1,r=1,i=0,o=0,s=0;si}else{var h=element.getElementByLabel(e.a.label);null!=h&&(e.hydrogenOnTheLeft=element.get(h).putHydrogenOnTheLeft)}}},rnd.ReStruct.prototype.setImplicitHydrogen=function(){this.molecule.setImplicitHydrogen(util.idList(this.atomsChanged))},rnd.ReLoop=function(t){this.loop=t,this.visel=new rnd.Visel(rnd.Visel.TYPE.LOOP),this.centre=new Vec2,this.radius=new Vec2},rnd.ReLoop.prototype=new rnd.ReObject,rnd.ReLoop.isSelectable=function(){return!1},rnd.ReStruct.prototype.coordProcess=function(t){t||this.molecule.rescale()},rnd.ReStruct.prototype.notifyAtomAdded=function(t){var e=new rnd.ReAtom(this.molecule.atoms.get(t));e.component=this.connectedComponents.add(Set.single(t)),this.atoms.set(t,e),this.markAtom(t,1)},rnd.ReStruct.prototype.notifyRxnPlusAdded=function(t){this.rxnPluses.set(t,new rnd.ReRxnPlus(this.molecule.rxnPluses.get(t)))},rnd.ReStruct.prototype.notifyRxnArrowAdded=function(t){this.rxnArrows.set(t,new rnd.ReRxnArrow(this.molecule.rxnArrows.get(t)))},rnd.ReStruct.prototype.notifyRxnArrowRemoved=function(t){this.markItemRemoved(),this.clearVisel(this.rxnArrows.get(t).visel),this.rxnArrows.unset(t)},rnd.ReStruct.prototype.notifyRxnPlusRemoved=function(t){this.markItemRemoved(),this.clearVisel(this.rxnPluses.get(t).visel),this.rxnPluses.unset(t)},rnd.ReStruct.prototype.notifyBondAdded=function(t){this.bonds.set(t,new rnd.ReBond(this.molecule.bonds.get(t))),this.markBond(t,1)},rnd.ReStruct.prototype.notifyAtomRemoved=function(t){var e=this.atoms.get(t),n=this.connectedComponents.get(e.component);Set.remove(n,t),0==Set.size(n)&&this.connectedComponents.remove(e.component),this.clearVisel(e.visel),this.atoms.unset(t),this.markItemRemoved()},rnd.ReStruct.prototype.notifyBondRemoved=function(t){var e=this.bonds.get(t);[e.b.hb1,e.b.hb2].each(function(t){var e=this.molecule.halfBonds.get(t);e.loop>=0&&this.loopRemove(e.loop)},this),this.clearVisel(e.visel),this.bonds.unset(t),this.markItemRemoved()},rnd.ReStruct.prototype.loopRemove=function(t){if(this.reloops.has(t)){var e=this.reloops.get(t);this.clearVisel(e.visel);for(var n=[],r=0;r0;){var o=r.shift();t.call(n,o);for(var s=this.atoms.get(o),a=0;ae.y&&a.p0.xe.x){var h=Math.min(Math.abs(a.p0.x-e.x),Math.abs(a.p1.x-e.x));(!i||h0?"IF ":"")+"R"+a.toString()+(this.item.range.length>0?this.item.range.startsWith(">")||this.item.range.startsWith("<")||this.item.range.startsWith("=")?this.item.range:"="+this.item.range:">0")+(this.item.resth?" (RestH)":"")+(this.item.ifthen>0?"\nTHEN R"+this.item.ifthen.toString():""));for(var u=l.height/2+n.lineWidth/2,g=0;ga.y&&c.p0.xa.x,d=Math.min(Math.abs(c.p0.x-a.x),Math.abs(c.p1.x-a.x));l&&(null==n||de.y&&o.p0.xe.x,a=Math.min(Math.abs(o.p0.x-e.x),Math.abs(o.p1.x-e.x));s&&(null==r||a=0){var p=this.stereoUpBondGetCoordinates(e,r.neihbid2);l=p[0],c=p[1]}return o.path("M{0},{1}L{2},{3}L{4},{5}Z",tfx(a.x),tfx(a.y),tfx(l.x),tfx(l.y),tfx(c.x),tfx(c.y)).attr(s.lineattr).attr({fill:"#000"})},rnd.ReStruct.prototype.drawVec=function(t,e,r,a){var n=this.render.settings,d=this.render.paper,i=this.render.styles,o=n.bondSpace,s=t.addScaled(e,a||3*o);return d.path("M{0},{1}L{2},{3}",tfx(t.x),tfx(t.y),tfx(s.x),tfx(s.y)).attr(i.lineattr).attr({stroke:r||"#0F0"})},rnd.ReStruct.prototype.stereoUpBondGetCoordinates=function(t,e){var r=this.render.settings.bondSpace,a=this.molecule.halfBonds.get(e),n=Vec2.dot(t.dir,a.dir),d=Vec2.cross(t.dir,a.dir),i=Math.sqrt(.5*(1-n)),o=a.dir.rotateSC((d>=0?-1:1)*i,Math.sqrt(.5*(1+n))),s=t.p.addScaled(o,.7*r/(i+.3)),h=t.p.addScaled(o.negated(),.7*r/(i+.3));return d>0?[s,h]:[h,s]},rnd.ReStruct.prototype.drawBondSingleStereoBold=function(t,e,r,a){var n=this.render.paper,d=this.render.settings,i=this.render.styles,o=this.stereoUpBondGetCoordinates(t,r.neihbid1),s=this.stereoUpBondGetCoordinates(e,r.neihbid2),h=o[0],l=o[1],c=s[0],p=s[1],b=n.path("M{0},{1}L{2},{3}L{4},{5}L{6},{7}Z",tfx(h.x),tfx(h.y),tfx(l.x),tfx(l.y),tfx(c.x),tfx(c.y),tfx(p.x),tfx(p.y)).attr(i.lineattr).attr({stroke:"#000",fill:"#000"});if(a){var u=t.p,f=e.p,S=t.norm,x=r.doubleBondShift,g=1.5*d.bondSpace,B=u.addScaled(S,g*x),v=f.addScaled(S,g*x),R=!this.atoms.get(t.begin).showLabel,y=!this.atoms.get(e.begin).showLabel;return x>0?(R&&(B=B.addScaled(t.dir,g*this.getBondLineShift(t.rightCos,t.rightSin))),y&&(v=v.addScaled(t.dir,-g*this.getBondLineShift(e.leftCos,e.leftSin)))):x<0&&(R&&(B=B.addScaled(t.dir,g*this.getBondLineShift(t.leftCos,t.leftSin))),y&&(v=v.addScaled(t.dir,-g*this.getBondLineShift(e.rightCos,e.rightSin)))),n.set([b,n.path("M{0},{1}L{2},{3}",tfx(B.x),tfx(B.y),tfx(v.x),tfx(v.y)).attr(i.lineattr)])}return b},rnd.ReStruct.prototype.drawBondSingleDown=function(t,e){var r=t.p,a=e.p,n=t.norm,d=this.render.settings,i=this.render.paper,o=this.render.styles,s=.7*d.bondSpace,h=a.sub(r),l=h.length()+.2;h=h.normalized();for(var c,p,b=1.2*d.lineWidth,u=Math.max(Math.floor((l-d.lineWidth)/(d.lineWidth+b)),0)+2,f=l/(u-1),S="",x=r,g=0;g.9?0:e/(1-t)},rnd.ReStruct.prototype.drawBondDouble=function(t,e,r,a){var n=t.p,d=e.p,i=t.norm,o=a?0:r.doubleBondShift,s=this.render.settings,h=this.render.paper,l=this.render.styles,c=s.bondSpace/2,p=c,b=-c;p+=o*c,b+=o*c;var u=n.addScaled(i,p),f=d.addScaled(i,p),S=n.addScaled(i,b),x=d.addScaled(i,b),g=!this.atoms.get(t.begin).showLabel,B=!this.atoms.get(e.begin).showLabel;return o>0?(g&&(u=u.addScaled(t.dir,s.bondSpace*this.getBondLineShift(t.rightCos,t.rightSin))),B&&(f=f.addScaled(t.dir,-s.bondSpace*this.getBondLineShift(e.leftCos,e.leftSin)))):o<0&&(g&&(S=S.addScaled(t.dir,s.bondSpace*this.getBondLineShift(t.leftCos,t.leftSin))),B&&(x=x.addScaled(t.dir,-s.bondSpace*this.getBondLineShift(e.rightCos,e.rightSin)))),h.path(a?"M{0},{1}L{6},{7}M{4},{5}L{2},{3}":"M{0},{1}L{2},{3}M{4},{5}L{6},{7}",tfx(u.x),tfx(u.y),tfx(f.x),tfx(f.y),tfx(S.x),tfx(S.y),tfx(x.x),tfx(x.y)).attr(l.lineattr)},rnd.ReStruct.makeStroke=function(t,e){return"M"+tfx(t.x)+","+tfx(t.y)+"L"+tfx(e.x)+","+tfx(e.y)+"\t"},rnd.ReStruct.prototype.drawBondSingleOrDouble=function(t,e){var r=t.p,a=e.p,n=t.norm,d=this.render,i=d.settings,o=d.paper,s=d.styles,h=i.bondSpace/2,l=(Vec2.dist(r,a)/(i.bondSpace+i.lineWidth)).toFixed()-0;1&l||(l+=1);for(var c="",p=r,b=1;b<=l;++b){var u=Vec2.lc2(r,(l-b)/l,a,b/l);1&b?c+=rnd.ReStruct.makeStroke(p,u):(c+=rnd.ReStruct.makeStroke(p.addScaled(n,h),u.addScaled(n,h)),c+=rnd.ReStruct.makeStroke(p.addScaled(n,-h),u.addScaled(n,-h))),p=u}return o.path(c).attr(s.lineattr)},rnd.ReStruct.prototype.drawBondTriple=function(t,e){var r=t.p,a=e.p,n=t.norm,d=this.render,i=d.settings,o=d.paper,s=d.styles,h=r.addScaled(n,i.bondSpace),l=a.addScaled(n,i.bondSpace),c=r.addScaled(n,-i.bondSpace),p=a.addScaled(n,-i.bondSpace);return o.path(rnd.ReStruct.makeStroke(r,a)+rnd.ReStruct.makeStroke(h,l)+rnd.ReStruct.makeStroke(c,p)).attr(s.lineattr)},rnd.dashedPath=function(t,e,r){for(var a=0,n=Vec2.dist(t,e),d=Vec2.diff(e,t).normalized(),i=!0,o="",s=0;a0?o:s).attr({"stroke-dasharray":"- "}),d.set([o,s])},rnd.dashdotPattern=[.125,.125,.005,.125],rnd.ReStruct.prototype.drawBondSingleOrAromatic=function(t,e,r){var a=r.doubleBondShift,n=this.render.paper,d=this.render.settings.scaleFactor,i=util.map(rnd.dashdotPattern,function(t){return t*d}),o=this.preparePathsForAromaticBond(t,e,a,a>0?1:2,i),s=o[0],h=o[1];return n.set([s,h])},rnd.ReStruct.prototype.preparePathsForAromaticBond=function(t,e,r,a,n){var d=this.render.settings,i=this.render.paper,o=this.render.styles,s=t.p,h=e.p,l=t.norm,c=d.bondSpace/2,p=c,b=-c;p+=r*c,b+=r*c;var u=s.addScaled(l,p),f=h.addScaled(l,p),S=s.addScaled(l,b),x=h.addScaled(l,b),g=!this.atoms.get(t.begin).showLabel,B=!this.atoms.get(e.begin).showLabel;return r>0?(g&&(u=u.addScaled(t.dir,d.bondSpace*this.getBondLineShift(t.rightCos,t.rightSin))),B&&(f=f.addScaled(t.dir,-d.bondSpace*this.getBondLineShift(e.leftCos,e.leftSin)))):r<0&&(g&&(S=S.addScaled(t.dir,d.bondSpace*this.getBondLineShift(t.leftCos,t.leftSin))),B&&(x=x.addScaled(t.dir,-d.bondSpace*this.getBondLineShift(e.rightCos,e.rightSin)))),[i.path(n&&1&a?rnd.dashedPath(u,f,n):rnd.ReStruct.makeStroke(u,f)).attr(o.lineattr),i.path(n&&2&a?rnd.dashedPath(S,x,n):rnd.ReStruct.makeStroke(S,x)).attr(o.lineattr)]},rnd.ReStruct.prototype.drawBondDoubleOrAromatic=function(t,e,r){var a=r.doubleBondShift,n=this.render.paper,d=this.render.settings.scaleFactor,i=util.map(rnd.dashdotPattern,function(t){return t*d}),o=this.preparePathsForAromaticBond(t,e,a,3,i),s=o[0],h=o[1];return n.set([s,h])},rnd.ReStruct.prototype.drawBondAny=function(t,e){var r=t.p,a=e.p,n=this.render.paper,d=this.render.styles;return n.path(rnd.ReStruct.makeStroke(r,a)).attr(d.lineattr).attr({"stroke-dasharray":"- "})},rnd.ReStruct.prototype.drawReactingCenter=function(t,e,r){var a=e.p,n=r.p,d=n.add(a).scaled(.5),i=n.sub(a).normalized(),o=i.rotateSC(1,0),s=this.render.paper,h=this.render.styles,l=this.render.settings,c=[],p=l.lineWidth,b=l.bondSpace/2,u=p,f=2*p,S=1.5*b,x=1.5*b,g=3*b;switch(t.b.reactingCenterStatus){case chem.Struct.BOND.REACTING_CENTER.NOT_CENTER:c.push(d.addScaled(o,g).addScaled(i,.2*g)),c.push(d.addScaled(o,-g).addScaled(i,-.2*g)),c.push(d.addScaled(o,g).addScaled(i,-.2*g)),c.push(d.addScaled(o,-g).addScaled(i,.2*g));break;case chem.Struct.BOND.REACTING_CENTER.CENTER:c.push(d.addScaled(o,g).addScaled(i,.2*g).addScaled(i,u)),c.push(d.addScaled(o,-g).addScaled(i,-.2*g).addScaled(i,u)),c.push(d.addScaled(o,g).addScaled(i,.2*g).addScaled(i,-u)),c.push(d.addScaled(o,-g).addScaled(i,-.2*g).addScaled(i,-u)),c.push(d.addScaled(i,S).addScaled(o,x)),c.push(d.addScaled(i,-S).addScaled(o,x)),c.push(d.addScaled(i,S).addScaled(o,-x)),c.push(d.addScaled(i,-S).addScaled(o,-x));break;case chem.Struct.BOND.REACTING_CENTER.MADE_OR_BROKEN:c.push(d.addScaled(o,g).addScaled(i,f)),c.push(d.addScaled(o,-g).addScaled(i,f)),c.push(d.addScaled(o,g).addScaled(i,-f)),c.push(d.addScaled(o,-g).addScaled(i,-f));break;case chem.Struct.BOND.REACTING_CENTER.ORDER_CHANGED:c.push(d.addScaled(o,g)),c.push(d.addScaled(o,-g));break;case chem.Struct.BOND.REACTING_CENTER.MADE_OR_BROKEN_AND_CHANGED:c.push(d.addScaled(o,g).addScaled(i,f)),c.push(d.addScaled(o,-g).addScaled(i,f)),c.push(d.addScaled(o,g).addScaled(i,-f)),c.push(d.addScaled(o,-g).addScaled(i,-f)),c.push(d.addScaled(o,g)),c.push(d.addScaled(o,-g));break;default:return null}for(var B="",v=0;v0?l=l.scaled(-t.doubleBondShift):0==t.doubleBondShift&&(c+=d.bondSpace/2);var p=new Vec2(2,1).scaled(d.bondSpace);t.b.type==chem.Struct.BOND.TYPE.TRIPLE&&(c+=d.bondSpace);var b=s.add(new Vec2(l.x*(p.x+c),l.y*(p.y+c))),u=n.text(b.x,b.y,a).attr({font:d.font,"font-size":d.fontszsub,fill:"#000"}),f=rnd.relBox(u.getBBox());return this.centerText(u,f),u},rnd.ReStruct.prototype.drawBond=function(t,e,r){var a=null,n=this.molecule;switch(t.b.type){case chem.Struct.BOND.TYPE.SINGLE:switch(t.b.stereo){case chem.Struct.BOND.STEREO.UP:this.findIncomingUpBonds(e.bid,t),a=t.boldStereo&&t.neihbid1>=0&&t.neihbid2>=0?this.drawBondSingleStereoBold(e,r,t):this.drawBondSingleUp(e,r,t);break;case chem.Struct.BOND.STEREO.DOWN:a=this.drawBondSingleDown(e,r,t);break;case chem.Struct.BOND.STEREO.EITHER:a=this.drawBondSingleEither(e,r,t);break;default:a=this.drawBondSingle(e,r)}break;case chem.Struct.BOND.TYPE.DOUBLE:this.findIncomingUpBonds(e.bid,t),a=t.b.stereo===chem.Struct.BOND.STEREO.NONE&&t.boldStereo&&t.neihbid1>=0&&t.neihbid2>=0?this.drawBondSingleStereoBold(e,r,t,!0):this.drawBondDouble(e,r,t,t.b.stereo===chem.Struct.BOND.STEREO.CIS_TRANS);break;case chem.Struct.BOND.TYPE.TRIPLE:a=this.drawBondTriple(e,r,t);break;case chem.Struct.BOND.TYPE.AROMATIC:var d=e.loop>=0&&n.loops.get(e.loop).aromatic||r.loop>=0&&n.loops.get(r.loop).aromatic;a=this.drawBondAromatic(e,r,t,!d);break;case chem.Struct.BOND.TYPE.SINGLE_OR_DOUBLE:a=this.drawBondSingleOrDouble(e,r,t);break;case chem.Struct.BOND.TYPE.SINGLE_OR_AROMATIC:a=this.drawBondSingleOrAromatic(e,r,t);break;case chem.Struct.BOND.TYPE.DOUBLE_OR_AROMATIC:a=this.drawBondDoubleOrAromatic(e,r,t);break;case chem.Struct.BOND.TYPE.ANY:a=this.drawBondAny(e,r,t);break;default:throw new Error("Bond type "+t.b.type+" not supported")}return a},rnd.ReStruct.prototype.radicalCap=function(t){var e=this.render.settings,r=this.render.paper,a=.9*e.lineWidth,n=a,d=2*a;return r.path("M{0},{1}L{2},{3}L{4},{5}",tfx(t.x-n),tfx(t.y+d),tfx(t.x),tfx(t.y),tfx(t.x+n),tfx(t.y+d)).attr({stroke:"#000","stroke-width":.7*e.lineWidth,"stroke-linecap":"square","stroke-linejoin":"miter"})},rnd.ReStruct.prototype.radicalBullet=function(t){var e=this.render.settings;return this.render.paper.circle(t.x,t.y,e.lineWidth).attr({stroke:null,fill:"#000"})},rnd.ReStruct.prototype.centerText=function(t,e){this.render.paper.raphael.vml&&this.pathAndRBoxTranslate(t,e,0,.16*e.height)},rnd.ReStruct.prototype.showItemSelection=function(t,e,r){var a=null!=e.selectionPlate&&!e.selectionPlate.removed;if(a=a&&(!("hiddenPaths"in rnd.ReStruct.prototype)||rnd.ReStruct.prototype.hiddenPaths.indexOf(e.selectionPlate)<0),r){if(!a){var n=this.render,d=n.styles,i=n.paper;e.selectionPlate=e.makeSelectionPlate(this,i,d),this.addReObjectPath("selection-plate",e.visel,e.selectionPlate)}e.selectionPlate&&e.selectionPlate.show()}else a&&e.selectionPlate&&e.selectionPlate.hide()},rnd.ReStruct.prototype.pathAndRBoxTranslate=function(t,e,r,a){t.translateAbs(r,a),e.x+=r,e.y+=a};var markerColors=["black","cyan","magenta","red","green","blue","green"];rnd.ReStruct.prototype.showLabels=function(){var t=this.render,e=t.settings,r=t.styles,a=t.opt,n=t.paper,d=.5*e.lineWidth;for(var i in this.atomsChanged){var o=this.atoms.get(i),s=t.ps(o.a.pp),h=null;a.showAtomIds&&(h={},h.text=i.toString(),h.path=n.text(s.x,s.y,h.text).attr({font:e.font,"font-size":e.fontszsub,fill:"#070"}),h.rbb=rnd.relBox(h.path.getBBox()),this.centerText(h.path,h.rbb),this.addReObjectPath("indices",o.visel,h.path,s)),o.setHighlight(o.highlight,t);var l="#000000";if(o.showLabel){var c=0,p=0,b={};if(null!=o.a.atomList)b.text=o.a.atomList.label();else if("R#"==o.a.label&&null!=o.a.rglabel){b.text="";for(var u=0;u<32;u++)o.a.rglabel&1<0&&(B={},B.text=(S+1).toString(),B.path=n.text(s.x,s.y,B.text).attr({font:e.font,"font-size":e.fontszsub,fill:l}),B.rbb=rnd.relBox(B.path.getBBox()),this.centerText(B.path,B.rbb),this.pathAndRBoxTranslate(B.path,B.rbb,c+.5*B.rbb.width+d,.2*b.rbb.height),c+=B.rbb.width+d,this.addReObjectPath("data",o.visel,B.path,s,!0));var R={};if(0!=o.a.radical){var y;switch(o.a.radical){case 1:R.path=n.set(),y=1.6*e.lineWidth,R.path.push(this.radicalBullet(s.add(new Vec2(-y,0))),this.radicalBullet(s.add(new Vec2(y,0)))),R.path.attr("fill",l);break;case 2:R.path=this.radicalBullet(s).attr("fill",l);break;case 3:R.path=n.set(),y=1.6*e.lineWidth,R.path.push(this.radicalCap(s.add(new Vec2(-y,0))),this.radicalCap(s.add(new Vec2(y,0)))),R.path.attr("stroke",l)}R.rbb=rnd.relBox(R.path.getBBox());var m=-.5*(b.rbb.height+R.rbb.height);3==o.a.radical&&(m-=e.lineWidth/2),this.pathAndRBoxTranslate(R.path,R.rbb,0,m),this.addReObjectPath("data",o.visel,R.path,s,!0)}var w={};0!=o.a.isotope&&(w.text=o.a.isotope.toString(),w.path=n.text(s.x,s.y,w.text).attr({font:e.font,"font-size":e.fontszsub,fill:l}),w.rbb=rnd.relBox(w.path.getBBox()),this.centerText(w.path,w.rbb),this.pathAndRBoxTranslate(w.path,w.rbb,p-.5*w.rbb.width-d,-.3*b.rbb.height),p-=w.rbb.width+d,this.addReObjectPath("data",o.visel,w.path,s,!0)),!x&&S>0&&!t.opt.hideImplicitHydrogen&&(g.text="H",g.path=n.text(s.x,s.y,g.text).attr({font:e.font,"font-size":e.fontsz,fill:l}),g.rbb=rnd.relBox(g.path.getBBox()),this.centerText(g.path,g.rbb),v||(this.pathAndRBoxTranslate(g.path,g.rbb,c+.5*g.rbb.width+d,0),c+=g.rbb.width+d),S>1&&(B={},B.text=S.toString(),B.path=n.text(s.x,s.y,B.text).attr({font:e.font,"font-size":e.fontszsub,fill:l}),B.rbb=rnd.relBox(B.path.getBBox()),this.centerText(B.path,B.rbb),v||(this.pathAndRBoxTranslate(B.path,B.rbb,c+.5*B.rbb.width+d,.2*b.rbb.height),c+=B.rbb.width+d)),v&&(null!=B&&(this.pathAndRBoxTranslate(B.path,B.rbb,p-.5*B.rbb.width-d,.2*b.rbb.height),p-=B.rbb.width+d),this.pathAndRBoxTranslate(g.path,g.rbb,p-.5*g.rbb.width-d,0),p-=g.rbb.width+d),this.addReObjectPath("data",o.visel,g.path,s,!0),null!=B&&this.addReObjectPath("data",o.visel,B.path,s,!0));var O={};if(0!=o.a.charge){O.text="";var T=Math.abs(o.a.charge);1!=T&&(O.text=T.toString()),o.a.charge<0?O.text+="–":O.text+="+",O.path=n.text(s.x,s.y,O.text).attr({font:e.font,"font-size":e.fontszsub,fill:l}),O.rbb=rnd.relBox(O.path.getBBox()),this.centerText(O.path,O.rbb),this.pathAndRBoxTranslate(O.path,O.rbb,c+.5*O.rbb.width+d,-.3*b.rbb.height),c+=O.rbb.width+d,this.addReObjectPath("data",o.visel,O.path,s,!0)}var E={},L={0:"0",1:"I",2:"II",3:"III",4:"IV",5:"V",6:"VI",7:"VII",8:"VIII",9:"IX",10:"X",11:"XI",12:"XII",13:"XIII",14:"XIV"};if(o.a.explicitValence>=0){if(E.text=L[o.a.explicitValence],!E.text)throw new Error("invalid valence "+o.a.explicitValence.toString());E.text="("+E.text+")",E.path=n.text(s.x,s.y,E.text).attr({font:e.font,"font-size":e.fontszsub,fill:l}),E.rbb=rnd.relBox(E.path.getBBox()),this.centerText(E.path,E.rbb),this.pathAndRBoxTranslate(E.path,E.rbb,c+.5*E.rbb.width+d,-.3*b.rbb.height),c+=E.rbb.width+d,this.addReObjectPath("data",o.visel,E.path,s,!0)}if(o.a.badConn&&a.showValenceWarnings){var C={},k=s.y+b.rbb.height/2+d;C.path=n.path("M{0},{1}L{2},{3}",tfx(s.x+p),tfx(k),tfx(s.x+c),tfx(k)).attr(this.render.styles.lineattr).attr({stroke:"#F00"}),C.rbb=rnd.relBox(C.path.getBBox()),this.addReObjectPath("warnings",o.visel,C.path,s,!0)}h&&this.pathAndRBoxTranslate(h.path,h.rbb,-.5*b.rbb.width-.5*h.rbb.width-d,.3*b.rbb.height)}var P=this.bisectLargestSector(o),I=Prototype.Browser.IE?"*":"∗";if(o.a.attpnt){var M,A;for(M=0,0;M<4;++M){var N="";if(o.a.attpnt&1<0&&(N+=" "),N+=I,A=0;A<(0==M?0:M+1);++A)N+="'";var V=new Vec2(s),D=s.addScaled(P,.7*e.scaleFactor),z=n.text(D.x,D.y,N).attr({font:e.font,"font-size":e.fontsz,fill:l}),W=rnd.relBox(z.getBBox());this.centerText(z,W);var j=P.negated();D=D.addScaled(j,Vec2.shiftRayBox(D,j,Box2Abs.fromRelBox(W))+e.lineWidth/2),V=this.shiftBondEnd(o,V,P,e.lineWidth);var _=P.rotateSC(1,0),F=D.addScaled(_,.05*e.scaleFactor).addScaled(j,.09*e.scaleFactor),G=D.addScaled(_,-.05*e.scaleFactor).addScaled(j,.09*e.scaleFactor),U=n.set();U.push(z,n.path("M{0},{1}L{2},{3}M{4},{5}L{2},{3}L{6},{7}",tfx(V.x),tfx(V.y),tfx(D.x),tfx(D.y),tfx(F.x),tfx(F.y),tfx(G.x),tfx(G.y)).attr(r.lineattr).attr({"stroke-width":e.lineWidth/2})),this.addReObjectPath("indices",o.visel,U,s),P=P.rotate(Math.PI/6)}}}var Y="";if(o.a.aam>0&&(Y+=o.a.aam),o.a.invRet>0)if(Y.length>0&&(Y+=","),1==o.a.invRet)Y+="Inv";else{if(2!=o.a.invRet)throw new Error("Invalid value for the invert/retain flag");Y+="Ret"}var H="";if(0!=o.a.ringBondCount)if(o.a.ringBondCount>0)H+="rb"+o.a.ringBondCount.toString();else if(-1==o.a.ringBondCount)H+="rb0";else{if(-2!=o.a.ringBondCount)throw new Error("Ring bond count invalid");H+="rb*"}if(0!=o.a.substitutionCount)if(H.length>0&&(H+=","),o.a.substitutionCount>0)H+="s"+o.a.substitutionCount.toString();else if(-1==o.a.substitutionCount)H+="s0";else{if(-2!=o.a.substitutionCount)throw new Error("Substitution count invalid");H+="s*"}if(o.a.unsaturatedAtom>0){if(H.length>0&&(H+=","),1!=o.a.unsaturatedAtom)throw new Error("Unsaturated atom invalid value");H+="u"}if(o.a.hCount>0&&(H.length>0&&(H+=","),H+="H"+(o.a.hCount-1).toString()),o.a.exactChangeFlag>0){if(Y.length>0&&(Y+=","),1!=o.a.exactChangeFlag)throw new Error("Invalid value for the exact change flag");Y+="ext"}if(Y=(H.length>0?H+"\n":"")+(Y.length>0?"."+Y+".":""),Y.length>0){var q=n.text(s.x,s.y,Y).attr({font:e.font,"font-size":e.fontszsub,fill:l}),X=rnd.relBox(q.getBBox());this.centerText(q,X);var Z=this.bisectLargestSector(o),K=o.visel,J=3;for(M=0;M0&&(e=e.addScaled(r,n+a)),e},rnd.ReStruct.prototype.bisectLargestSector=function(t){var e=[];t.a.neighbors.each(function(t){var r=this.molecule.halfBonds.get(t);e.push(r.ang)},this),e=e.sort(function(t,e){return t-e});for(var r=[],a=0;an&&(n=r[a],d=e[a]+r[a]/2);return new Vec2(Math.cos(d),Math.sin(d))},rnd.ReStruct.prototype.bondRecalc=function(t,e){var r=this.render,a=this.atoms.get(e.b.begin),n=this.atoms.get(e.b.end),d=r.ps(a.a.pp),i=r.ps(n.a.pp),o=this.molecule.halfBonds.get(e.b.hb1),s=this.molecule.halfBonds.get(e.b.hb2);o.p=this.shiftBondEnd(a,d,o.dir,2*t.lineWidth),s.p=this.shiftBondEnd(n,i,s.dir,2*t.lineWidth),e.b.center=Vec2.lc2(a.a.pp,.5,n.a.pp,.5),e.b.len=Vec2.dist(d,i),e.b.sb=5*t.lineWidth,e.b.sa=Math.max(e.b.sb,e.b.len/2-2*t.lineWidth),e.b.angle=180*Math.atan2(o.dir.y,o.dir.x)/Math.PI},rnd.ReStruct.prototype.showBonds=function(){var t=this.render,e=t.settings,r=t.paper,a=t.opt;for(var n in this.bondsChanged){var d=this.bonds.get(n),i=this.molecule.halfBonds.get(d.b.hb1),o=this.molecule.halfBonds.get(d.b.hb2);this.bondRecalc(e,d),d.path=this.drawBond(d,i,o),d.rbb=rnd.relBox(d.path.getBBox()),this.addReObjectPath("data",d.visel,d.path,null,!0);var s={};s.path=this.drawReactingCenter(d,i,o),s.path&&(s.rbb=rnd.relBox(s.path.getBBox()),this.addReObjectPath("data",d.visel,s.path,null,!0));var h={};h.path=this.drawTopologyMark(d,i,o),h.path&&(h.rbb=rnd.relBox(h.path.getBBox()),this.addReObjectPath("data",d.visel,h.path,null,!0)),d.setHighlight(d.highlight,t);var l=.6*e.subFontSize,c=null,p=null;if(a.showBondIds){var b=Vec2.lc(i.p,.5,o.p,.5,i.norm,l);c=r.text(b.x,b.y,n.toString()),p=rnd.relBox(c.getBBox()),this.centerText(c,p),this.addReObjectPath("indices",d.visel,c)}if(a.showHalfBondIds){var u=Vec2.lc(i.p,.8,o.p,.2,i.norm,l);c=r.text(u.x,u.y,d.b.hb1.toString()),p=rnd.relBox(c.getBBox()),this.centerText(c,p),this.addReObjectPath("indices",d.visel,c);var f=Vec2.lc(i.p,.2,o.p,.8,o.norm,l);c=r.text(f.x,f.y,d.b.hb2.toString()),p=rnd.relBox(c.getBBox()),this.centerText(c,p),this.addReObjectPath("indices",d.visel,c)}if(a.showLoopIds&&!a.showBondIds){var S=Vec2.lc(i.p,.5,o.p,.5,o.norm,l);c=r.text(S.x,S.y,i.loop.toString()),p=rnd.relBox(c.getBBox()),this.centerText(c,p),this.addReObjectPath("indices",d.visel,c);var x=Vec2.lc(i.p,.5,o.p,.5,i.norm,l);c=r.text(x.x,x.y,o.loop.toString()),p=rnd.relBox(c.getBBox()),this.centerText(c,p),this.addReObjectPath("indices",d.visel,c)}}},rnd.ReStruct.prototype.labelIsVisible=function(t,e){if(0==e.a.neighbors.length||e.a.neighbors.length<2&&!this.render.opt.hideTerminalLabels||"c"!=e.a.label.toLowerCase()||e.a.badConn&&this.render.opt.showValenceWarnings||0!=e.a.isotope||0!=e.a.radical||0!=e.a.charge||e.a.explicitValence>=0||null!=e.a.atomList||null!=e.a.rglabel)return!0;if(2==e.a.neighbors.length){var r=e.a.neighbors[0],a=e.a.neighbors[1],n=this.molecule.halfBonds.get(r),d=this.molecule.halfBonds.get(a),i=this.bonds.get(n.bid),o=this.bonds.get(d.bid);if(i.b.type==o.b.type&&i.b.stereo==chem.Struct.BOND.STEREO.NONE&&o.b.stereo==chem.Struct.BOND.STEREO.NONE&&Math.abs(Vec2.cross(n.dir,d.dir))<.2)return!0}return!1},rnd.ReStruct.prototype.checkLabelsToShow=function(){for(var t in this.atomsChanged){var e=this.atoms.get(t);e.showLabel=this.labelIsVisible(t,e)}},rnd.ReStruct.layerMap={background:0,"selection-plate":1,highlighting:2,warnings:3,data:4,indices:5},rnd.ReStruct.prototype.addReObjectPath=function(t,e,r,a,n){if(r){var d=this.render.offset,i=n?Box2Abs.fromRelBox(rnd.relBox(r.getBBox())):null,o=a&&i?i.translate(a.negated()):null;null!==d&&(r.translateAbs(d.x,d.y),i=i?i.translate(d):null),e.add(r,i,o),this.insertInLayer(rnd.ReStruct.layerMap[t],r)}},rnd.ReStruct.prototype.clearVisel=function(t){for(var e=0;e1||1==a)?-1:6==e&&6!=t&&(a>1||1==r)?1:e*r>t*a?-1:e*rt?-1:1},rnd.ReStruct.prototype.selectDoubleBondShift_Chain=function(t){var e=this.molecule,r=e.halfBonds.get(t.b.hb1),a=e.halfBonds.get(t.b.hb2),n=(r.leftSin>.3?1:0)+(a.rightSin>.3?1:0),d=(a.leftSin>.3?1:0)+(r.rightSin>.3?1:0);return n>d?-1:n.3?1:0)+(r.rightSin>.3?1:0)==1?1:0},rnd.ReStruct.prototype.setDoubleBondShift=function(){var t=this.molecule;for(var e in this.bondsChanged){var r,a,n=this.bonds.get(e);if(r=t.halfBonds.get(n.b.hb1).loop,a=t.halfBonds.get(n.b.hb2).loop,r>=0&&a>=0){var d=t.loops.get(r).dblBonds,i=t.loops.get(a).dblBonds,o=t.loops.get(r).hbs.length,s=t.loops.get(a).hbs.length;n.doubleBondShift=this.selectDoubleBondShift(o,s,d,i)}else n.doubleBondShift=r>=0?-1:a>=0?1:this.selectDoubleBondShift_Chain(n)}},rnd.ReStruct.prototype.updateLoops=function(){this.reloops.each(function(t,e){this.clearVisel(e.visel)},this);var t=this.molecule.findLoops();util.each(t.bondsToMark,function(t){this.markBond(t,1)},this),util.each(t.newLoops,function(t){this.reloops.set(t,new rnd.ReLoop(this.molecule.loops.get(t)))},this)},rnd.ReStruct.prototype.renderLoops=function(){var t=this.render,e=t.settings,r=t.paper,a=this.molecule;this.reloops.each(function(n,d){var i=d.loop;d.centre=new Vec2,i.hbs.each(function(e){var r=a.halfBonds.get(e),n=this.bonds.get(r.bid),o=t.ps(this.atoms.get(r.begin).a.pp);n.b.type!=chem.Struct.BOND.TYPE.AROMATIC&&(i.aromatic=!1),d.centre.add_(o)},this),i.convex=!0;for(var o=0;o0&&(i.convex=!1)}if(d.centre=d.centre.scaled(1/i.hbs.length),d.radius=-1,i.hbs.each(function(e){var r=a.halfBonds.get(e),n=t.ps(this.atoms.get(r.begin).a.pp),i=t.ps(this.atoms.get(r.end).a.pp),o=Vec2.diff(i,n).rotateSC(1,0).normalized(),s=Vec2.dot(Vec2.diff(n,d.centre),o);d.radius<0?d.radius=s:d.radius=Math.min(d.radius,s)},this),d.radius*=.7,i.aromatic){var c=null;if(i.convex)c=r.circle(d.centre.x,d.centre.y,d.radius).attr({stroke:"#000","stroke-width":e.lineWidth});else{var p="";for(o=0;o2)throw new Error("One vector or two scalar arguments expected");if(void 0===s)this.translate(t.x,t.y);else{for(var n=new Vec2(t,s),i=0;i=0&&Set.add(p,r)},this)):Set.contains(u,t.b.begin)?Set.add(m,t.b.begin):Set.contains(u,t.b.end)&&Set.add(m,t.b.end)},this),r=0;ri&&(a=o,i=n);var d=new Vec2(1,0);if(t.length>0){if(1==t.length){i=-4*Math.PI/3;var p=ui.render.atomGetNeighbors(e)[0];if(ui.render.atomGetDegree(p.aid)>1){var m=[],u=ui.render.atomGetPos(p.aid),s=Vec2.diff(r,u),f=Math.atan2(s.y,s.x);ui.render.atomGetNeighbors(p.aid).each(function(e){var t=ui.render.atomGetPos(e.aid);if(!(e.bid==p.bid||Vec2.dist(u,t)<.1)){var r=Vec2.diff(t,u),o=Math.atan2(r.y,r.x)-f;o<0&&(o+=2*Math.PI),m.push(o)}}),m.sort(function(e,t){return e-t}),m[0]<=1.01*Math.PI&&m[m.length-1]<=1.01*Math.PI&&(i*=-1)}}n=i/2+Math.atan2(t[a].v.y,t[a].v.x),d=d.rotate(n)}d.add_(r);var c=ui.render.findClosestAtom(d,.1);return c=null==c?{label:"C"}:c.id,{atom:c,pos:d}}function fromBondAddition(e,t,r,o,n){if(void 0===r){var a=atomForNewBond(t);r=a.atom,o=a.pos}var i=new Action,d=null;if(Object.isNumber(t)){if(d=ui.render.atomGetAttr(t,"fragment"),Object.isNumber(r)){var p=ui.render.atomGetAttr(r,"fragment");mergeFragments(i,d,p)}}else Object.isNumber(r)&&(d=ui.render.atomGetAttr(r,"fragment"));null==d&&(d=i.addOp((new op.FragmentAdd).perform(ui.editor)).frid),Object.isNumber(t)?"*"==ui.render.atomGetAttr(t,"label")&&i.addOp(new op.AtomAttr(t,"label","C").perform(ui.editor)):(t.fragment=d,t=i.addOp(new op.AtomAdd(t,o).perform(ui.editor)).data.aid,o=n),Object.isNumber(r)?"*"==ui.render.atomGetAttr(r,"label")&&i.addOp(new op.AtomAttr(r,"label","C").perform(ui.editor)):(r.fragment=d,r=i.addOp(new op.AtomAdd(r,o).perform(ui.editor)).data.aid,Object.isNumber(t)&&ui.render.atomGetSGroups(t).each(function(e){i.addOp(new op.SGroupAtomAdd(e,r).perform(ui.editor))},this));var m=i.addOp(new op.BondAdd(t,r,e).perform(ui.editor)).data.bid;return i.operations.reverse(),[i,t,r,m]}function fromArrowAddition(e){var t=new Action;return ui.ctab.rxnArrows.count()<1&&t.addOp(new op.RxnArrowAdd(e).perform(ui.editor)),t}function fromArrowDeletion(e){var t=new Action;return t.addOp(new op.RxnArrowDelete(e)),t.perform()}function fromChiralFlagAddition(e){var t=new Action;return ui.render.ctab.chiralFlags.count()<1&&t.addOp(new op.ChiralFlagAdd(e).perform(ui.editor)),t}function fromChiralFlagDeletion(){var e=new Action;return e.addOp(new op.ChiralFlagDelete),e.perform()}function fromPlusAddition(e){var t=new Action;return t.addOp(new op.RxnPlusAdd(e).perform(ui.editor)),t}function fromPlusDeletion(e){var t=new Action;return t.addOp(new op.RxnPlusDelete(e)),t.perform()}function fromAtomDeletion(e){var t=new Action,r=new Array,o=ui.ctab.atoms.get(e).fragment;return ui.render.atomGetNeighbors(e).each(function(e){t.addOp(new op.BondDelete(e.bid)),1==ui.render.atomGetDegree(e.aid)&&(t.removeAtomFromSgroupIfNeeded(e.aid)&&r.push(e.aid),t.addOp(new op.AtomDelete(e.aid)))},this),t.removeAtomFromSgroupIfNeeded(e)&&r.push(e),t.addOp(new op.AtomDelete(e)),t.removeSgroupIfNeeded(r),t=t.perform(),t.mergeWith(fromFragmentSplit(o)),t}function fromBondDeletion(e){var t=new Action,r=ui.ctab.bonds.get(e),o=ui.ctab.atoms.get(r.begin).fragment,n=new Array;return t.addOp(new op.BondDelete(e)),1==ui.render.atomGetDegree(r.begin)&&(t.removeAtomFromSgroupIfNeeded(r.begin)&&n.push(r.begin),t.addOp(new op.AtomDelete(r.begin))),1==ui.render.atomGetDegree(r.end)&&(t.removeAtomFromSgroupIfNeeded(r.end)&&n.push(r.end),t.addOp(new op.AtomDelete(r.end))),t.removeSgroupIfNeeded(n),t=t.perform(),t.mergeWith(fromFragmentSplit(o)),t}function fromFragmentSplit(e){var t=new Action,r=chem.Struct.RGroup.findRGroupByFragment(ui.ctab.rgroups,e);return ui.ctab.atoms.each(function(o,n){if(n.fragment==e){var a=t.addOp((new op.FragmentAdd).perform(ui.editor)).frid,i=function(r){t.addOp(new op.AtomAttr(r,"fragment",a).perform(ui.editor)),ui.render.atomGetNeighbors(r).each(function(t){ui.ctab.atoms.get(t.aid).fragment==e&&i(t.aid)})};i(o),r&&t.mergeWith(fromRGroupFragment(r,a))}}),-1!=e&&(t.mergeWith(fromRGroupFragment(0,e)),t.addOp(new op.FragmentDelete(e).perform(ui.editor))),t}function fromFragmentAddition(e,t,r,o,n){var a=new Action;return r.each(function(e){a.addOp(new op.SGroupRemoveFromHierarchy(e)),a.addOp(new op.SGroupDelete(e))},this),t.each(function(e){a.addOp(new op.BondDelete(e))},this),e.each(function(e){a.addOp(new op.AtomDelete(e))},this),o.each(function(e){a.addOp(new op.RxnArrowDelete(e))},this),n.each(function(e){a.addOp(new op.RxnPlusDelete(e))},this),a.mergeWith(new fromFragmentSplit(-1)),a}function fromFragmentDeletion(e){e=e||ui.editor.getSelection();var t=new Action,r=new Array,o=[],n=new Action;for(e.sgroupData&&e.sgroupData.each(function(e){n.mergeWith(fromSgroupDeletion(e))},this),e.atoms.each(function(t){ui.render.atomGetNeighbors(t).each(function(t){-1==e.bonds.indexOf(t.bid)&&(e.bonds=e.bonds.concat([t.bid]))},this)},this),e.bonds.each(function(n){t.addOp(new op.BondDelete(n));var a=ui.ctab.bonds.get(n);if(-1==e.atoms.indexOf(a.begin)&&1==ui.render.atomGetDegree(a.begin)){var i=ui.ctab.atoms.get(a.begin).fragment;o.indexOf(i)<0&&o.push(i),t.removeAtomFromSgroupIfNeeded(a.begin)&&r.push(a.begin),t.addOp(new op.AtomDelete(a.begin))}if(-1==e.atoms.indexOf(a.end)&&1==ui.render.atomGetDegree(a.end)){var d=ui.ctab.atoms.get(a.end).fragment;o.indexOf(d)<0&&o.push(d),t.removeAtomFromSgroupIfNeeded(a.end)&&r.push(a.end),t.addOp(new op.AtomDelete(a.end))}},this),e.atoms.each(function(e){var n=ui.ctab.atoms.get(e).fragment;o.indexOf(n)<0&&o.push(n),t.removeAtomFromSgroupIfNeeded(e)&&r.push(e),t.addOp(new op.AtomDelete(e))},this),t.removeSgroupIfNeeded(r),e.rxnArrows.each(function(e){t.addOp(new op.RxnArrowDelete(e))},this),e.rxnPluses.each(function(e){t.addOp(new op.RxnPlusDelete(e))},this),e.chiralFlags.each(function(e){t.addOp(new op.ChiralFlagDelete(e))},this),t=t.perform();o.length>0;)t.mergeWith(new fromFragmentSplit(o.pop()));return t.mergeWith(n),t}function fromAtomMerge(e,t){var r=new Action,o=ui.render.atomGetAttr(e,"fragment"),n=ui.render.atomGetAttr(t,"fragment");o!=n&&mergeFragments(r,o,n);var a=new Action;ui.render.atomGetNeighbors(e).each(function(e){var r,o,n=ui.ctab.bonds.get(e.bid);n.begin==e.aid?(r=e.aid,o=t):(r=t,o=e.aid),t!=n.begin&&t!=n.end&&-1==ui.ctab.findBondId(r,o)&&a.addOp(new op.BondAdd(r,o,n)),a.addOp(new op.BondDelete(e.bid))},this);var i=chem.Struct.Atom.getAttrHash(ui.ctab.atoms.get(e));1==ui.render.atomGetDegree(e)&&"*"==i.get("label")&&i.set("label","C"),i.each(function(e){a.addOp(new op.AtomAttr(t,e.key,e.value))},this);var d=a.removeAtomFromSgroupIfNeeded(e);return a.addOp(new op.AtomDelete(e)),d&&a.removeSgroupIfNeeded([e]),a.perform().mergeWith(r)}function toBondFlipping(e){var t=ui.ctab.bonds.get(e),r=new Action;return r.addOp(new op.BondDelete(e)),r.addOp(new op.BondAdd(t.end,t.begin,t)).data.bid=e,r}function fromBondFlipping(e){return toBondFlipping(e).perform()}function fromTemplateOnCanvas(e,t,r){var o=new Action,n=r.molecule,a=(new op.FragmentAdd).perform(ui.editor),i={};return n.atoms.each(function(n,d){var p,m=chem.Struct.Atom.getAttrHash(d).toObject();m.fragment=a.frid,o.addOp(p=new op.AtomAdd(m,Vec2.diff(d.pp,r.xy0).rotate(t).add(e)).perform(ui.editor)),i[n]=p.data.aid}),n.bonds.each(function(e,t){o.addOp(new op.BondAdd(i[t.begin],i[t.end],t).perform(ui.editor))}),o.operations.reverse(),o.addOp(a),o}function atomAddToSGroups(e,t){var r=new Action;return util.each(e,function(e){r.addOp(new op.SGroupAtomAdd(e,t).perform(ui.editor))},this),r}function fromTemplateOnAtom(e,t,r,o,n){var a=new Action,i=o.molecule,d=ui.render,p=d.ctab,m=p.molecule,u=m.atoms.get(e),s=e,f=null,c=ui.render.atomGetSGroups(e),g=d.atomGetAttr(e,"fragment"),l={},h=i.atoms.get(o.aid).pp;if(r){if(null==t){var A=atomForNewBond(e),w=fromBondAddition({type:1},e,A.atom,A.pos);a=w[0],a.operations.reverse(),f=e=w[2]}else{var v;a.addOp(v=new op.AtomAdd({label:"C",fragment:g},new Vec2(1,0).rotate(t).add(u.pp)).perform(ui.editor)),a.addOp(new op.BondAdd(e,v.data.aid,{type:1}).perform(ui.editor)),f=e=v.data.aid,a.mergeWith(atomAddToSGroups(c,e))}var b=u;u=m.atoms.get(e);var O=n(b.pp,u.pp)-o.angle0}else null==t&&(A=atomForNewBond(e),t=n(u.pp,A.pos)),O=t-o.angle0;return i.atoms.each(function(t,r){var n=chem.Struct.Atom.getAttrHash(r).toObject();if(n.fragment=g,t==o.aid)a.mergeWith(fromAtomsAttrs(e,n,!0)),l[t]=e;else{var i;i=Vec2.diff(r.pp,h).rotate(O).add(u.pp),a.addOp(v=new op.AtomAdd(n,i).perform(ui.editor)),l[t]=v.data.aid}l[t]-0!=s-0&&l[t]-0!=f-0&&a.mergeWith(atomAddToSGroups(c,l[t]))}),i.bonds.each(function(e,t){a.addOp(new op.BondAdd(l[t.begin],l[t.end],t).perform(ui.editor))}),a.operations.reverse(),a}function fromTemplateOnBond(e,t,r,o){var n,a,i=new Action,d=t.molecule,p=ui.render,m=p.ctab,u=m.molecule,s=u.bonds.get(e),f=u.atoms.get(s.begin),c=u.atoms.get(s.end),g=Set.list(Set.intersection(Set.fromList(ui.render.atomGetSGroups(s.begin)),Set.fromList(ui.render.atomGetSGroups(s.end)))),l=d.bonds.get(t.bid),h=p.atomGetAttr(s.begin,"fragment"),A={};o?(n=d.atoms.get(l.end),a=d.atoms.get(l.begin),A[l.end]=s.begin,A[l.begin]=s.end):(n=d.atoms.get(l.begin),a=d.atoms.get(l.end),A[l.begin]=s.begin,A[l.end]=s.end);var w=r(f.pp,c.pp)-r(n.pp,a.pp),v=Vec2.dist(f.pp,c.pp)/Vec2.dist(n.pp,a.pp);n.pp;return d.atoms.each(function(e,t){var r=chem.Struct.Atom.getAttrHash(t).toObject();if(r.fragment=h,e==l.begin||e==l.end)return void i.mergeWith(fromAtomsAttrs(A[e],r,!0));var o;o=Vec2.diff(t.pp,n.pp).rotate(w).scaled(v).add(f.pp);var a=p.findClosestAtom(o,.1);if(null==a){var d;i.addOp(d=new op.AtomAdd(r,o).perform(ui.editor)),A[e]=d.data.aid,i.mergeWith(atomAddToSGroups(g,A[e]))}else A[e]=a.id,i.mergeWith(fromAtomsAttrs(A[e],r,!0))}),d.bonds.each(function(e,t){var r=u.findBondId(A[t.begin],A[t.end]);-1==r?i.addOp(new op.BondAdd(A[t.begin],A[t.end],t).perform(ui.editor)):i.mergeWith(fromBondAttrs(r,l,!1,!0))}),i.operations.reverse(),i}function fromChain(e,t,r,o){var n,a=Math.PI/6,i=Math.cos(a),d=Math.sin(a),p=new Action;n=null!=o?ui.render.atomGetAttr(o,"fragment"):p.addOp((new op.FragmentAdd).perform(ui.editor)).frid;var m=-1;return m=null!=o?o:p.addOp(new op.AtomAdd({label:"C",fragment:n},e).perform(ui.editor)).data.aid,p.operations.reverse(),r.times(function(r){var o=new Vec2(i*(r+1),1&r?0:d).rotate(t).add(e),n=ui.render.findClosestAtom(o,.1),a=fromBondAddition({},m,n?n.id:{},o);p=a[0].mergeWith(p),m=a[2]},this),p}function fromNewCanvas(e){var t=new Action;return t.addOp(new op.CanvasLoad(e)),t.perform()}function fromSgroupType(e,t){var r=ui.render,o=r.sGroupGetType(e);if(t&&t!=o){var n=util.array(r.sGroupGetAtoms(e)),a=r.sGroupGetAttrs(e),i=fromSgroupDeletion(e);return fromSgroupAddition(t,n,a,e).mergeWith(i)}return new Action}function fromSgroupAttrs(e,t){var r=new Action,o=ui.render,n=o.ctab;n.sgroups.get(e).item;return new Hash(t).each(function(t){r.addOp(new op.SGroupAttr(e,t.key,t.value))},this),r.perform()}function sGroupAttributeAction(e,t){var r=new Action;return new Hash(t).each(function(t){r.addOp(new op.SGroupAttr(e,t.key,t.value))},this),r}function fromSgroupDeletion(e){var t=new Action,r=ui.render,o=r.ctab,n=o.molecule;if("SRU"==ui.render.sGroupGetType(e)){ui.render.sGroupsFindCrossBonds();ui.render.sGroupGetNeighborAtoms(e).each(function(e){"*"==ui.render.atomGetAttr(e,"label")&&t.addOp(new op.AtomAttr(e,"label","C"))},this)}var a=n.sgroups.get(e),i=chem.SGroup.getAtoms(n,a),d=a.getAttrs();t.addOp(new op.SGroupRemoveFromHierarchy(e));for(var p=0;p=0;S--)n.addOp(O.operations[S])}if(ui.editor.render.ctab.rxnArrows.count()<1)for(var G=0;G0&&(t.each(function(t){this.addOp(new op.SGroupAtomRemove(t,e))},this),!0)},Action.prototype.removeSgroupIfNeeded=function(e){var t=ui.render,r=t.ctab,o=r.molecule,n=new Hash;e.each(function(e){ui.render.atomGetSGroups(e).each(function(e){var t=n.get(e);Object.isUndefined(t)?t=1:t++,n.set(e,t)},this)},this),n.each(function(e){var t=parseInt(e.key);if(ui.render.sGroupGetAtoms(t).length==e.value){var r=o.sgroups.get(t);this.mergeWith(sGroupAttributeAction(t,r.getAttrs())),this.addOp(new op.SGroupRemoveFromHierarchy(t)),this.addOp(new op.SGroupDelete(t))}},this)},module.exports=util.extend(Action,{fromMultipleMove:fromMultipleMove,fromAtomAddition:fromAtomAddition,fromArrowAddition:fromArrowAddition,fromArrowDeletion:fromArrowDeletion,fromChiralFlagDeletion:fromChiralFlagDeletion,fromPlusAddition:fromPlusAddition,fromPlusDeletion:fromPlusDeletion,fromAtomDeletion:fromAtomDeletion,fromBondDeletion:fromBondDeletion,fromFragmentDeletion:fromFragmentDeletion,fromAtomMerge:fromAtomMerge,fromBondFlipping:fromBondFlipping,fromTemplateOnCanvas:fromTemplateOnCanvas,fromTemplateOnAtom:fromTemplateOnAtom,fromTemplateOnBond:fromTemplateOnBond,fromAtomsAttrs:fromAtomsAttrs,fromBondAttrs:fromBondAttrs,fromChain:fromChain,fromBondAddition:fromBondAddition,fromNewCanvas:fromNewCanvas,fromSgroupType:fromSgroupType,fromSgroupDeletion:fromSgroupDeletion,fromSgroupAttrs:fromSgroupAttrs,fromRGroupFragment:fromRGroupFragment,fromPaste:fromPaste,fromRGroupAttrs:fromRGroupAttrs,fromSgroupAddition:fromSgroupAddition,fromFlip:fromFlip,fromRotate:fromRotate}); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../chem":11,"../util":39,"../util/set":42,"../util/vec2":43,"./op":35}],27:[function(require,module,exports){ +(function (global){ +function initDialogs(){$("input_label").observe("blur",function(){keymage.setScope("editor"),this.hide()}),$("input_label").observe("keypress",onKeyPress_InputLabel),$("input_label").observe("keyup",onKeyUp_InputLabel),$("atom_label").observe("change",onChange_AtomLabel),$("atom_charge").observe("change",onChange_AtomCharge),$("atom_isotope").observe("change",onChange_AtomIsotope),$("atom_valence").observe("change",onChange_AtomValence),$("atom_prop_cancel").observe("click",function(){ui.hideDialog("atom_properties")}),$("atom_prop_ok").observe("click",function(){applyAtomProperties()}),$("bond_prop_cancel").observe("click",function(){ui.hideDialog("bond_properties")}),$("bond_prop_ok").observe("click",function(){applyBondProperties()})}function showAtomAttachmentPoints(e){$("atom_ap1").checked=(1&(e.selection||0))>0,$("atom_ap2").checked=(2&(e.selection||0))>0,ui.showDialog("atom_attpoints");var t=new Event.Handler("atom_attpoints_ok","click",void 0,function(){t.stop(),o.stop(),ui.hideDialog("atom_attpoints"),"onOk"in e&&e.onOk(($("atom_ap1").checked?1:0)+($("atom_ap2").checked?2:0))}).start(),o=new Event.Handler("atom_attpoints_cancel","click",void 0,function(){t.stop(),o.stop(),ui.hideDialog("atom_attpoints"),"onCancel"in e&&e.onCancel()}).start();$("atom_attpoints_ok").focus()}function showAtomProperties(e){$("atom_properties").atom_id=e,$("atom_label").value=ui.render.atomGetAttr(e,"label"),onChange_AtomLabel.call($("atom_label"));var t=ui.render.atomGetAttr(e,"charge")-0;$("atom_charge").value=0==t?"":t,t=ui.render.atomGetAttr(e,"isotope")-0,$("atom_isotope").value=0==t?"":t,t=ui.render.atomGetAttr(e,"explicitValence")-0,$("atom_valence").value=t<0?"":t,$("atom_radical").value=ui.render.atomGetAttr(e,"radical"),$("atom_inversion").value=ui.render.atomGetAttr(e,"invRet"),$("atom_exactchange").value=ui.render.atomGetAttr(e,"exactChangeFlag")?1:0,$("atom_ringcount").value=ui.render.atomGetAttr(e,"ringBondCount"),$("atom_substitution").value=ui.render.atomGetAttr(e,"substitutionCount"),$("atom_unsaturation").value=ui.render.atomGetAttr(e,"unsaturatedAtom"),$("atom_hcount").value=ui.render.atomGetAttr(e,"hCount"),ui.showDialog("atom_properties"),$("atom_label").activate()}function applyAtomProperties(){ui.hideDialog("atom_properties");var e=$("atom_properties").atom_id;ui.addUndoAction(Action.fromAtomsAttrs(e,{label:$("atom_label").value,charge:""==$("atom_charge").value?0:parseInt($("atom_charge").value,10),isotope:""==$("atom_isotope").value?0:parseInt($("atom_isotope").value,10),explicitValence:""==$("atom_valence").value?-1:parseInt($("atom_valence").value,10),radical:parseInt($("atom_radical").value,10),invRet:parseInt($("atom_inversion").value,10),exactChangeFlag:!!parseInt($("atom_exactchange").value,10),ringBondCount:parseInt($("atom_ringcount").value,10),substitutionCount:parseInt($("atom_substitution").value,10),unsaturatedAtom:parseInt($("atom_unsaturation").value,10),hCount:parseInt($("atom_hcount").value,10)}),!0),ui.render.update()}function onChange_AtomLabel(){this.value=this.value.strip().capitalize();var e=element.getElementByLabel(this.value);null==e&&"A"!==this.value&&"*"!==this.value&&"Q"!==this.value&&"X"!==this.value&&"R"!==this.value&&(this.value=ui.render.atomGetAttr($("atom_properties").atom_id,"label"),"A"!==this.value&&"*"!==this.value&&(e=element.getElementByLabel(this.value))),"A"==this.value||"*"==this.value?$("atom_number").value="any":$("atom_number").value=e?e.toString():""}function onChange_AtomCharge(){""===this.value.strip()||"0"==this.value?this.value="":this.value.match(/^[1-9][0-9]{0,1}[-+]$/)?this.value=(this.value.endsWith("-")?"-":"")+this.value.substr(0,this.value.length-1):this.value.match(/^[+-]?[1-9][0-9]{0,1}$/)||(this.value=ui.render.atomGetAttr($("atom_properties").atom_id,"charge"))}function onChange_AtomIsotope(){this.value==util.getElementTextContent($("atom_number"))||""==this.value.strip()||"0"==this.value?this.value="":this.value.match(/^[1-9][0-9]{0,2}$/)||(this.value=ui.render.atomGetAttr($("atom_properties").atom_id,"isotope"))}function onChange_AtomValence(){}function showBondProperties(e){var t;$("bond_properties").bond_id=e;var o=ui.render.bondGetAttr(e,"type"),a=ui.render.bondGetAttr(e,"stereo");for(t in ui.bondTypeMap)if(ui.bondTypeMap[t].type==o&&ui.bondTypeMap[t].stereo==a)break;$("bond_type").value=t,$("bond_topology").value=ui.render.bondGetAttr(e,"topology")||0,$("bond_center").value=ui.render.bondGetAttr(e,"reactingCenterStatus")||0,ui.showDialog("bond_properties"),$("bond_type").activate()}function applyBondProperties(){ui.hideDialog("bond_properties");var e=$("bond_properties").bond_id,t=Object.clone(ui.bondTypeMap[$("bond_type").value]);t.topology=parseInt($("bond_topology").value,10),t.reactingCenterStatus=parseInt($("bond_center").value,10),ui.addUndoAction(Action.fromBondAttrs(e,t),!0),ui.render.update()}function showAutomapProperties(e){ui.showDialog("automap_properties");var t,o;t=new Event.Handler("automap_ok","click",void 0,function(){t.stop(),o.stop(),e&&"onOk"in e&&e.onOk($("automap_mode").value),ui.hideDialog("automap_properties")}).start(),o=new Event.Handler("automap_cancel","click",void 0,function(){t.stop(),o.stop(),ui.hideDialog("automap_properties"),e&&"onCancel"in e&&e.onCancel()}).start(),$("automap_mode").activate()}function showRLogicTable(e){var t=e||{};t.rlogic=t.rlogic||{},$("rlogic_occurrence").value=t.rlogic.occurrence||">0",$("rlogic_resth").value=t.rlogic.resth?"1":"0";for(var o='',a=1;a<=32;a++)a!=t.rgid&&0!=(t.rgmask&1<IF R'+t.rgid+" THEN R"+a+"");$("rlogic_if").outerHTML='",$("rlogic_if").value=t.rlogic.ifthen,ui.showDialog("rlogic_table");var i=new Event.Handler("rlogic_ok","click",void 0,function(){var e={occurrence:$("rlogic_occurrence").value.replace(/\s*/g,"").replace(/,+/g,",").replace(/^,/,"").replace(/,$/,""),resth:"1"==$("rlogic_resth").value,ifthen:parseInt($("rlogic_if").value,10)};t&&"onOk"in t&&!t.onOk(e)||(i.stop(),n.stop(),ui.hideDialog("rlogic_table"))}).start(),n=new Event.Handler("rlogic_cancel","click",void 0,function(){i.stop(),n.stop(),ui.hideDialog("rlogic_table"),t&&"onCancel"in t&&t.onCancel()}).start();$("rlogic_occurrence").activate()}function onKeyPress_Dialog(e){if(util.stopEventPropagation(e),27===e.keyCode)return ui.hideDialog(this.id),util.preventDefault(e)}function onKeyPress_InputLabel(e){if(util.stopEventPropagation(e),13==e.keyCode){keymage.setScope("editor"),this.hide();var t="",o=0,a=this.value.toArray();if("*"==this.value)t="A";else if(this.value.match(/^[*][1-9]?[+-]$/i))t="A",o=2==this.value.length?1:parseInt(a[1]),"-"==a[2]&&(o*=-1);else if(this.value.match(/^[A-Z]{1,2}$/i))t=this.value.capitalize();else if(this.value.match(/^[A-Z]{1,2}[0][+-]?$/i))t=this.value.match(/^[A-Z]{2}/i)?this.value.substr(0,2).capitalize():a[0].capitalize();else if(this.value.match(/^[A-Z]{1,2}[1-9]?[+-]$/i)){t=this.value.match(/^[A-Z]{2}/i)?this.value.substr(0,2).capitalize():a[0].capitalize();var i=this.value.match(/[0-9]/i);o=null!=i?parseInt(i[0]):1,"-"==a[this.value.length-1]&&(o*=-1)}return"A"!=t&&"Q"!=t&&"X"!=t&&"R"!=t&&null==element.getElementByLabel(t)||(ui.addUndoAction(Action.fromAtomsAttrs(this.atom_id,{label:t,charge:o}),!0),ui.render.update()),util.preventDefault(e)}if(27==e.keyCode)return this.hide(),keymage.setScope("editor"),util.preventDefault(e)}function onKeyUp_InputLabel(e){if(util.stopEventPropagation(e),27==e.keyCode)return this.hide(),keymage.setScope("editor"),util.preventDefault(e)}function showLabelEditor(e){var t=$("input_label");keymage.setScope("label");var o=Math.min(7*ui.render.zoom,16);t.atom_id=e,t.value=ui.render.atomGetAttr(e,"label"),t.style.fontSize=2*o+"px",t.show();var a=ui.render.obj2view(ui.render.atomGetPos(e)),i={left:0,top:0},n=Element.cumulativeOffset(t.offsetParent);t.style.left=a.x+i.left-n.left-o-0+"px",t.style.top=a.y+i.top-n.top-o-0+"px",t.activate()}var keymage=require("keymage"),element=require("../../chem/element"),util=require("../../util"),Action=require("../action"),ui=global.ui;module.exports={initDialogs:initDialogs,showAtomAttachmentPoints:showAtomAttachmentPoints,showAtomProperties:showAtomProperties,showBondProperties:showBondProperties,showAutomapProperties:showAutomapProperties,showRLogicTable:showRLogicTable,showLabelEditor:showLabelEditor}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../../chem/element":10,"../../util":39,"../action":26,"keymage":2}],28:[function(require,module,exports){ +(function (global){ +function dialog(e){var n,i=ui.showDialog("open-file"),t=i.select("input[value=OK]")[0],o=i.select("textarea")[0],l=i.select("input[type=file]")[0],a=i.select("input[name=fragment]")[0],r=[];r[0]=i.on("click","input[type=button]",function(n,i){r.forEach(function(e){e.stop()}),ui.hideDialog("open-file");var t="on"+i.value.capitalize();e&&t in e&&e[t]({fragment:a.checked,value:o.value})}),r[1]=l.on("change",function(e,t){console.assert(n,"No valid file opener"),t.files.length&&(i.select("input").each(function(e){e.disabled=!0}),n(t.files[0]).then(function(e){o.value=e,i.select("input").each(function(e){e.disabled=!1})},ui.echo))}),r[2]=o.on("input",function(e,n){var i=o.value.trim();t.disabled=!i}),o.value="",a.checked=!1,t.disabled=!0,l.disabled=!0,l.parentNode.addClassName("disabled"),fileOpener().then(function(e){n=e,l.disabled=!1,l.parentNode.removeClassName("disabled")})}function fileOpener(){function e(e){return new Promise(function(n,i){var t=new FileReader;t.onload=function(e){n(e.target.result)},t.onerror=function(e){i(e)},t.readAsText(e,"UTF-8")})}function n(e,n){var i=e.OpenTextFile(n.name,1),t=i.ReadAll();return i.Close(),t}function i(e){}return new Promise(function(t,o){if(global.FileReader)return t(e);if(global.ActiveXObject)try{var l=new global.ActiveXObject("Scripting.FileSystemObject");return t(function(e){return Promise.resolve(n(l,e))})}catch(e){}return ui.standalone?o("Standalone mode!"):t(i)})}function loadHook(){}var Promise=require("promise-polyfill"),ui=global.ui;dialog.loadHook=loadHook,module.exports=dialog; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"promise-polyfill":3}],29:[function(require,module,exports){ +(function (global){ +function saveDialog(e,l){function i(e,l){l=l||"mol",n.value=e,n.className=l,n.activate()}var a,o=ui.showDialog("save-file"),n=o.select("textarea")[0],t=o.select("select")[0],c=o.select(".save")[0],s=[];s[0]=o.on("click","input[type=button]",function(l,i){s.forEach(function(e){e.stop()}),ui.hideDialog("save-file");var a="on"+i.value.capitalize();e&&a in e&&e[a]({})}),s[1]=t.on("change",function(a,o){var n=t.value;convertMolecule(l,e.molecule,n).then(function(e){i(e,n)},ui.echo)}),s[2]=c.on("click",function(e){a&&(a(n.value,t.value),o.select("input[type=button]")[0].click()),e.preventDefault()}),i((new chem.MolfileSaver).saveMolecule(e.molecule)),c.addClassName("disabled"),fileSaver(l).then(function(e){a=e,c.removeClassName("disabled")}),t.select("[value=inchi]")[0].disabled=ui.standalone}function fileSaver(e){var l={smi:"chemical/x-daylight-smiles",mol:"chemical/x-mdl-molfile",rxn:"chemical/x-mdl-rxnfile",inchi:"chemical/x-inchi"};return new Promise(function(i,a){global.Blob&&fs.saveAs?i(function(e,i){"mol"==i&&0==e.indexOf("$RXN")&&(i="rxn"),console.assert(l[i],"Unknown chemical file type");var a=new Blob([e],{type:l[i]});fs.saveAs(a,"ketcher."+i)}):ui.standalone?a("Standalone mode!"):i(function(l,i){e.save({filedata:[i,l].join("\n")})})})}function convertMolecule(e,l,i){return new Promise(function(a,o){var n=(new chem.MolfileSaver).saveMolecule(l);if("mol"==i)a(n);else if("smi"==i)a(ui.standalone?(new chem.SmilesSaver).saveMolecule(l):e.smiles({moldata:n}));else if("inchi"==i){if(ui.standalone)throw Error("InChI is not supported in the standalone mode");0!==l.rgroups.count()&&ui.echo("R-group fragments are not supported and will be discarded"),l=l.getScaffold(),0===l.atoms.count()?a(""):(l=l.clone(),l.sgroups.each(function(e,l){if("MUL"!=l.type&&!/^INDIGO_.+_DESC$/i.test(l.data.fieldName))throw Error("InChi data format doesn't support s-groups")}),a(e.inchi({moldata:n})))}})}var Promise=require("promise-polyfill"),fs=require("filesaver.js");require("../../chem");var chem=global.chem,ui=global.ui;module.exports=saveDialog; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../../chem":11,"filesaver.js":1,"promise-polyfill":3}],30:[function(require,module,exports){ +(function (global){ +function dialog(e,n){function t(e){a.select(".selected").each(function(e){e.removeClassName("selected")}),e?a.select("button").each(function(n){var t=n.value||n.textContent||n.innerText;e.indexOf(t)>=0&&n.addClassName("selected")}):n.required&&(i.disabled=!0)}function l(){var e=[];return a.select(".selected").each(function(n){var t=n.value||n.textContent||n.innerText;e.push(t)}),e}var a=ui.showDialog(e),i=a.select("input[value=OK]")[0],c=n.mode||"single",o=[];o[0]=a.on("click","input[type=button]",function(t,a){o.forEach(function(e){e.stop()}),ui.hideDialog(e);var i="on"+a.value.capitalize();console.assert("onOk"!=i||!n.required||0!=l().length,"No elements selected"),n&&i in n&&n[i]({mode:c,values:l()})}),o[1]=a.on("click","button",function(e,l){"single"===c&&(l.hasClassName("selected")?n.required&&i.click():t(null)),l.toggleClassName("selected"),n.required&&(i.disabled=0===a.select(".selected").length),e.stop()}),o[2]=a.on("click","input[name=mode]",function(e,n){n.value!=c&&("single"==n.value&&t(null),c=n.value)}),t(n.values),a.select("input[name=mode]").each(function(e){e.value==c&&(e.checked=!0)})}var ui=global.ui;module.exports=dialog; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{}],31:[function(require,module,exports){ +(function (global){ +function dialog(e){var t=ui.showDialog("sgroup_special"),a={},l=[];console.assert(!e.type||"DAT"==e.type),console.assert(!e.type||e.attrs.fieldName),setContext(e.type&&matchContext(e.attrs.fieldName,e.attrs.fieldValue)||e.context||"Fragment",a,!0),e.attrs.fieldName&&setField(e.attrs.fieldName,a,!0),$("sgroup_special_value").value=e.attrs.fieldValue,e.attrs.attached?$("sgroup_special_attached").checked=!0:e.attrs.absolute?$("sgroup_special_absolute").checked=!0:$("sgroup_special_relative").checked=!0,l[0]=t.on("click","input[type=button]",function(t,a){var n="on"+a.value.capitalize(),i="onOk"!=n||getValidateAttrs();i&&(l.forEach(function(e){e.stop()}),ui.hideDialog("sgroup_special"),n in e&&i&&e[n](i))}),l[1]=t.on("change","select",function(e,t){"sgroup_context"==t.id&&setContext($("sgroup_context").value,a),"sgroup_special_name"==t.id&&setField($("sgroup_special_name").value,a)})}function getValidateAttrs(){var e={mul:null,connectivity:"",name:"",subscript:""};return e.fieldName=$("sgroup_special_name").value.strip(),e.fieldValue=$("sgroup_special_value").value.strip(),e.absolute=$("sgroup_special_absolute").checked,e.attached=$("sgroup_special_attached").checked,""==e.fieldValue?(alert("Please, specify data field value."),null):{type:"DAT",attrs:e}}function setContext(e,t,a){if(console.info("set context:",e,t),console.assert(t.context||a,"Field setup should be forced"),a||e!=t.context.name){t.context=util.find(special_choices,function(t){return t.name==e}),console.assert(t.context,"Can't find such context");var l=t.context.value.reduce(function(e,t){return e+'"},"");$("sgroup_special_name").update(l),setField(t.context.value[0].name,t,!0),a&&($("sgroup_context").value=e)}}function setField(e,t,a){if(console.info("set field:",e,t),console.assert(t.field||a,"Field setup should be forced"),e||e!=t.field.name){if(t.field=util.find(t.context.value,function(t){return t.name==e}),console.assert(t.field,"Can't find such field"),t.field.value){var l=t.field.value.reduce(function(e,t){return e+'"},"");$("sgroup_special_value").outerHTML='"}else $("sgroup_special_value").outerHTML='';$("sgroup_special_name").value=e}}function matchContext(e,t){console.info("search:",util.unicodeLiteral(e),util.unicodeLiteral(t));var a=util.find(special_choices,function(a){var l=util.find(a.value,function(t){return t.name==e});return!!l&&(!t||!l.value||!!util.find(l.value,function(e){return e==t}))});return a&&a.name}var util=require("../../util"),ui=global.ui,special_choices=[{name:"Fragment",value:[{name:"MDLBG_FRAGMENT_STEREO",value:["abs","(+)-enantiomer","(-)-enantiomer","steric","rel","R(a)","S(a)","R(p)","S(p)"]},{name:"MDLBG_FRAGMENT_COEFFICIENT",value:null},{name:"MDLBG_FRAGMENT_CHARGE",value:null},{name:"MDLBG_FRAGMENT_RADICALS",value:null}]},{name:"Single Bond",value:[{name:"MDLBG_STEREO_KEY",value:["erythro","threo","alpha","beta","endo","exo","anti","syn","ECL","STG"]},{name:"MDLBG_BOND_KEY",value:["Value=4"]}]},{name:"Atom",value:[{name:"MDLBG_STEREO_KEY",value:["RS","SR","P-3","P-3-PI","SP-4","SP-4-PI","T-4","T-4-PI","SP-5","SP-5-PI","TB-5","TB-5-PI","OC-6","TB-5-PI","TP-6","PB-7","CU-8","SA-8","DD-8","HB-9","TPS-9","HB-9"]}]},{name:"Group",value:[{name:"MDLBG_STEREO_KEY",value:["cis","trans"]}]}];dialog.match=function(e){return!e.type||"DAT"==e.type&&!!matchContext(e.attrs.fieldName,e.attrs.fieldValue)},module.exports=dialog; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../../util":39}],32:[function(require,module,exports){ +(function (global){ +function dialog(e){var a=ui.showDialog("sgroup_properties"),t=e.type||"GEN";switch($("sgroup_type").value=t,$("sgroup_type").activate(),onChange_SGroupType.call($("sgroup_type")),t){case"SRU":$("sgroup_connection").value=e.attrs.connectivity,$("sgroup_label").value=e.attrs.subscript;break;case"MUL":$("sgroup_label").value=e.attrs.mul;break;case"SUP":$("sgroup_label").value=e.attrs.name;break;case"DAT":$("sgroup_field_name").value=e.attrs.fieldName,$("sgroup_field_value").value=e.attrs.fieldValue,e.attrs.attached?$("sgroup_pos_attached").checked=!0:e.attrs.absolute?$("sgroup_pos_absolute").checked=!0:$("sgroup_pos_relative").checked=!0}"DAT"!=t&&($("sgroup_field_name").value="",$("sgroup_field_value").value="");var s=[];s[0]=a.on("click","input[type=button]",function(a,t){var l="on"+t.value.capitalize(),u="onOk"!=l||getValidateAttrs();u&&(s.forEach(function(e){e.stop()}),ui.hideDialog("sgroup_properties"),l in e&&u&&e[l](u))}),s[1]=$("sgroup_type").on("change",onChange_SGroupType),s[2]=$("sgroup_label").on("change",onChange_SGroupLabel)}function getValidateAttrs(){var e=$("sgroup_type").value,a={mul:null,connectivity:"",name:"",subscript:"",fieldName:"",fieldValue:"",attached:!1,absolute:!1};switch(e){case"SRU":if(a.connectivity=$("sgroup_connection").value.strip(),a.subscript=$("sgroup_label").value.strip(),1!=a.subscript.length||!a.subscript.match(/^[a-zA-Z]$/))return alert(a.subscript.length?"SRU subscript should consist of a single letter.":"Please provide an SRU subscript."),null;break;case"MUL":a.mul=parseInt($("sgroup_label").value);break;case"SUP":if(a.name=$("sgroup_label").value.strip(),!a.name)return alert("Please provide a name for the superatom."),null;break;case"DAT":if(a.fieldName=$("sgroup_field_name").value.strip(),a.fieldValue=$("sgroup_field_value").value.strip(),a.absolute=$("sgroup_pos_absolute").checked,a.attached=$("sgroup_pos_attached").checked,""==a.fieldName||""==a.fieldValue)return alert("Please, specify data field name and value."),null}return{type:e,attrs:a}}function onChange_SGroupLabel(){"MUL"!=$("sgroup_type").value||this.value.match(/^[1-9][0-9]{0,2}$/)||(this.value="1")}function onChange_SGroupType(){var e=$("sgroup_type").value;if("DAT"==e)return $$("#sgroup_properties .base")[0].hide(),void $$("#sgroup_properties .data")[0].show();$$("#sgroup_properties .base")[0].show(),$$("#sgroup_properties .data")[0].hide(),$("sgroup_label").disabled="SRU"!=e&&"MUL"!=e&&"SUP"!=e,$("sgroup_connection").disabled="SRU"!=e,"MUL"!=e||$("sgroup_label").value.match(/^[1-9][0-9]{0,2}$/)?"SRU"==e?$("sgroup_label").value="n":"GEN"!=e&&"SUP"!=e||($("sgroup_label").value=""):$("sgroup_label").value="1"}var ui=global.ui;module.exports=dialog; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{}],33:[function(require,module,exports){ +(function (global){ +function parseSdf(e){var t=e.split(/^[$][$][$][$]$/m),i=[];return t.each(function(e){e=e.replace(/\r/g,""),e=e.strip();var t=e.indexOf("M END");if(-1!=t){var n={};n.molfile=e.substring(0,t+6),n.name=e.substring(0,e.indexOf("\n")).strip(),e=e.substr(t+7).strip();e.split(/^$/m).each(function(e){if(e=e.strip(),e.startsWith("> <")){var t=e.split("\n"),i=t[0].strip().substring(3,t[0].lastIndexOf(">")).strip();n[i]=parseInt(t[1].strip())||t[1].strip()}}),i.push(n)}}),i}function fetchTemplateCustom(e){return ajax(e+"templates.sdf").then(function(e){var t=parseSdf(e.responseText),i=[],n=0;return t.each(function(e){i.push({name:(e.name||"customtemplate "+ ++n).capitalize(),molfile:e.molfile,aid:(e.atomid||1)-1,bid:(e.bondid||1)-1})}),i})}function initTemplateCustom(e,t){return fetchTemplateCustom(t).then(function(t){return custom_templates=t,eachAsync(t,function(t,i){var n=new Element("li");n.title=t.name,e.insert({bottom:n});var a=chem.Molfile.parseCTFile(t.molfile),l=new rnd.Render(n,0,{autoScale:!0,autoScaleMargin:0,ignoreMouseEvents:!0,hideChiralFlag:!0,maxBondLength:30});l.setMolecule(a),l.update()},50)})}function eachAsync(e,t,i,n){return new Promise(function(a){function l(){s",r.forEach(function(e){var t=e.toLowerCase();Array.isArray(o[t])?o[t].push(l):o[t]=[l]})}else e.title=e.title||t}),o=util.extend(o,{a:["atom-any"],"defmod-a":["select-all"],"defmod-shift-a":["deselect-all"],"ctrl-alt-r":["force-update"]}),Object.keys(o).forEach(function(e){keymage("editor",e,1==o[e].length?function(t){var n=o[e][0];-1==clipActions.indexOf(n)&&(selectAction(o[e][0]),t.preventDefault())}:function(){console.info("actions",o[e])})}),keymage.setScope("editor"),toolbar.select("li").each(function(e){e.on("click",function(e){"BUTTON"==e.target.tagName&&e.target.parentNode==this&&(this.hasClassName("selected")||e.stop(),selectAction(this.id)),hideBlurredControls()?e.stop():"hidden"==this.getStyle("overflow")&&(this.addClassName("opened"),dropdownOpened=this,e.stop())})}),initCliparea(ketcherWindow),initZoom(),updateHistoryButtons(),clientArea.on("scroll",onScroll_ClientArea),clientArea.on("mousedown",function(){keymage.setScope("editor")});var n=new rnd.RenderOptions(e);n.atomColoring=!0,ui.render=new rnd.Render(clientArea,SCALE,n),ui.editor=new rnd.Editor(ui.render),ui.render.onCanvasOffsetChanged=onOffsetChanged,selectAction("select-lasso"),setScrollOffset(0,0),ui.render.setMolecule(ui.ctab),ui.render.update()}function shortcutStr(e){var t=navigator.platform.toUpperCase().indexOf("MAC")>=0;return e.replace(/Defmod/g,t?"⌘":"Ctrl").replace(/-(?!$)/g,"+")}function subEl(e){return $(e).children[0]}function hideBlurredControls(){if(!dropdownOpened)return!1;dropdownOpened.removeClassName("opened");var e=dropdownOpened.select(".selected");if(1==e.length){var t=subEl(dropdownOpened);t.style.marginTop=-e[0].offsetTop+t.offsetTop+"px"}return clientArea.style.visibility="hidden",setTimeout(function(){clientArea.style.visibility="visible"},0),dropdownOpened=null,!0}function selectAction(e){e=e||lastSelected;var t=$(e),o=[].slice.call(arguments,1);if(console.assert(e.startsWith,"id is not a string",e),-1!=clipActions.indexOf(e)&&0==o.length)return delegateCliparea(e);if(!t||!subEl(t).disabled){o.unshift(e);var n=mapTool.apply(null,o);if(n instanceof rnd.Editor.EditorTool){var r=toolbar.select(".selected")[0];t==r&&t||(ui.render.current_tool&&ui.render.current_tool.OnCancel(),ui.render.current_tool=n,e.startsWith("select-")&&(lastSelected=e),t&&t.addClassName("selected"),r&&r.removeClassName("selected"))}return n}return null}function delegateCliparea(e){var t=document.queryCommandSupported(e);if(t)try{document.execCommand(e)}catch(e){t=!1}if(!t){var o=subEl(e);echo("These action is unavailble via menu.\nInstead, use "+shortcutStr(o.dataset?o.dataset.keys:o.getAttribute("data-keys"))+" to "+e+".")}return null}function initCliparea(e){var t=new Element("input",{type:"text",class:"cliparea",autofocus:!0}),o=window.clipboardData,n=["chemical/x-mdl-molfile","chemical/x-mdl-rxnfile","chemical/x-cml","text/plain","chemical/x-daylight-smiles","chemical/x-inchi"],r=function(){return"editor"==keymage.getScope()&&(t.value=" ",t.focus(),t.select(),!0)},i=function(e,t){var n=(new chem.MolfileSaver).saveMolecule(e);if(!t&&o)o.setData("text",n);else{t.setData("text/plain",n);try{t.setData(e.isReaction?"chemical/x-mdl-rxnfile":"chemical/x-mdl-molfile",n),t.setData("chemical/x-daylight-smiles",(new chem.SmilesSaver).saveMolecule(e))}catch(e){console.info("Could not write exact type",e)}}},l=function(e){var t="";if(!e&&o)t=o.getData("text");else for(var r=0;r=0&&n[r],t.slice(0,50),".."),t};e.insert(t),e.on("mouseup",r),["copy","cut"].forEach(function(t){e.on(t,function(e){if(r()){var o=selectAction(t,!0);o&&i(o,e.clipboardData),e.preventDefault()}})}),e.on("paste",function(e){if(r()){var t=l(e.clipboardData);t&&loadFragment(t),e.preventDefault()}})}function updateClipboardButtons(){subEl("copy").disabled=subEl("cut").disabled=!ui.editor.hasSelection(!0)}function updateHistoryButtons(){subEl("undo").disabled=0==undoStack.length,subEl("redo").disabled=0==redoStack.length}function updateServerButtons(){serverActions.forEach(function(e){subEl(e).disabled=ui.standalone})}function transitionEndEvent(){var e,t=document.createElement("transitionTest"),o={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"};for(e in o)if(void 0!==t.style[e])return o[e];return!1}function animateToggle(e,t){ketcherWindow.addClassName("animate");var o=transitionEndEvent(),n=function(e){setTimeout(function(){e&&e(),ketcherWindow.removeClassName("animate")},0)};if(t&&o){var r=function(){n(t),e.removeEventListener(o,r,!1)};e.addEventListener(o,r,!1)}else n(t),t||e()}function showDialog(e){var t=$(e);return keymage.setScope("dialog"),animateToggle(function(){$$(".overlay")[0].show(),t.style.display=""}),t}function hideDialog(e){var t=$$(".overlay")[0];animateToggle(t,function(){$(e).style.display="none",t.hide(),keymage.setScope("editor")})}function showElemTable(e){e.required=!0,selectDialog("elem-table",e)}function showRGroupTable(e){selectDialog("rgroup-table",e)}function showReaGenericsTable(e){e.required=!0,selectDialog("generics-table",e)}function echo(e){alert(e)}function updateMolecule(e){if(void 0!==e&&null!=e){ui.editor.deselectAll(),addUndoAction(Action.fromNewCanvas(e)),showDialog("loading");try{ui.render.onResize(),ui.render.update(),setZoomCentered(null,ui.render.getStructCenter())}catch(e){alert(e.message)}finally{hideDialog("loading")}}}function addUndoAction(e,t){null!=e&&(1==t&&e.isDummy()||(undoStack.push(e),redoStack.clear(),undoStack.length>HISTORY_LENGTH&&undoStack.splice(0,1),updateHistoryButtons()))}function onClick_NewFile(){selectAction(null),ui.ctab.isBlank()||(addUndoAction(Action.fromNewCanvas(new chem.Struct)),ui.render.update())}function onClick_OpenFile(){openDialog({onOk:function(e){e.fragment?loadFragment(e.value,!0):loadMolecule(e.value,!0)}})}function onClick_SaveFile(){saveDialog({molecule:ui.ctab},server)}function aromatize(e,t){e=e.clone();var o=e.addRxnArrowIfNecessary(),n=(new chem.MolfileSaver).saveMolecule(e);if(ui.standalone)throw new Error("Aromatization and dearomatization are not supported in the standalone mode.");server[t?"aromatize":"dearomatize"]({moldata:n}).then(function(e){var t=parseMayBeCorruptedCTFile(e);o&&t.rxnArrows.clear(),updateMolecule(t)},echo)}function calculateCip(){util.assert(!ui.standalone,"Can't calculate in standalone mode!");var e=ui.ctab.clone(),t=e.addRxnArrowIfNecessary(),o=(new chem.MolfileSaver).saveMolecule(e);server.calculateCip({moldata:o}).then(function(e){var o=parseMayBeCorruptedCTFile(e);t&&o.rxnArrows.clear(),updateMolecule(o)},echo)}function initZoom(){var e=subEl("zoom-list");e.on("focus",function(){keymage.pushScope("zoom")}),e.on("blur",function(){keymage.popScope("zoom")}),e.on("change",updateZoom),updateZoom(!0)}function onClick_ZoomIn(){subEl("zoom-list").selectedIndex++,updateZoom()}function onClick_ZoomOut(){subEl("zoom-list").selectedIndex--,updateZoom()}function updateZoom(e){var t=subEl("zoom-list"),o=t.selectedIndex,n=t.length;console.assert(0<=o&&o10||(ui.zoom=e,ui.render.setZoom(ui.zoom))}function getViewSz(){return new Vec2(ui.render.viewSz)}function setZoomCentered(e,t){if(!t)throw new Error("Center point not specified");e&&setZoomRegular(e),setScrollOffset(0,0);var o=ui.render.obj2view(t).sub(ui.render.viewSz.scaled(.5));setScrollOffset(o.x,o.y)}function setZoomStaticPointInit(e){zspObj=new Vec2(e)}function setZoomStaticPoint(e,t){setZoomRegular(e),setScrollOffset(0,0);var o=ui.render.obj2view(zspObj),n=o.sub(t);setScrollOffset(n.x,n.y)}function setScrollOffset(e,t){var o=clientArea.clientWidth,n=clientArea.clientHeight;ui.render.extendCanvas(e,t,o+e,n+t),clientArea.scrollLeft=e,clientArea.scrollTop=t,scrollLeft=clientArea.scrollLeft,scrollTop=clientArea.scrollTop}function setScrollOffsetRel(e,t){setScrollOffset(clientArea.scrollLeft+e,clientArea.scrollTop+t)}function onClick_CleanUp(){var e=util.array(ui.editor.getSelection(!0).atoms),t=e.length>0;if(t){var o=Set.fromList(e),n=Set.empty();ui.ctab.loops.each(function(e,t){util.findIndex(t.hbs,function(e){return Set.contains(o,ui.ctab.halfBonds.get(e).begin)})>=0&&util.each(t.hbs,function(e){Set.add(n,ui.ctab.halfBonds.get(e).begin)},this)},this),Set.mergeIn(n,o),e=Set.list(n)}ui.editor.deselectAll();try{var r={},i=ui.ctab.clone(null,null,!1,r);t&&util.each(e,function(e){e=r[e];var t=new chem.SGroup("DAT"),o=i.sgroups.add(t);t.id=o,t.pp=new Vec2,t.data.fieldName="_ketcher_selective_layout",t.data.fieldValue="1",i.atomAddToSGroup(o,e)},this);var l=i.addRxnArrowIfNecessary();server.layout({moldata:(new chem.MolfileSaver).saveMolecule(i)},t?{selective:1}:null).then(function(e){var t=parseMayBeCorruptedCTFile(e);l&&t.rxnArrows.clear(),updateMolecule(t)})}catch(e){alert("ERROR: "+e.message)}}function onClick_Aromatize(){try{aromatize(ui.ctab,!0)}catch(e){alert("Molfile: "+e.message)}}function onClick_Dearomatize(){try{aromatize(ui.ctab,!1)}catch(e){alert("Molfile: "+e.message)}}function onClick_Automap(){obsolete.showAutomapProperties({onOk:function(e){var t=ui.ctab,o=t.addRxnArrowIfNecessary();if(0==t.rxnArrows.count())return void echo("Auto-Mapping can only be applied to reactions");var n=(new chem.MolfileSaver).saveMolecule(t,!0);server.automap({moldata:n,mode:e}).then(function(e){var t=parseMayBeCorruptedCTFile(e);o&&t.rxnArrows.clear(),updateMolecule(t)},echo)}})}function loadMolecule(e,t){return getStruct(e,t).then(updateMolecule)}function loadFragment(e,t){return getStruct(e,t).then(function(e){e.rescale(),selectAction("paste",e)})}function guessType(e,t){var o=e.trim(),n=o.match(/^(M END|\$END MOL)$/m);if(n){var r=n.index+n[0].length;if(r==o.length||-1!=o.slice(r,r+20).search(/^\$(MOL|END CTAB)$/m))return"mol"}return"<"==o[0]&&-1!=o.indexOf("=0)throw new Error("The same atom cannot be added to an S-group more than once");if(!n)throw new Error("OpSGroupAtomAdd: Atom "+r+" not found");i.atomAddToSGroup(d,r),e.invalidateAtom(r)},this._invert=function(){var t=new SGroupAtomRemove;return t.data=this.data,t}}function SGroupAtomRemove(t,e){this.type="OpSGroupAtomRemove",this.data={aid:e,sgid:t},this._execute=function(t){var e=this.data.aid,a=this.data.sgid,i=t.render,r=i.ctab,d=r.molecule,n=d.atoms.get(e),s=d.sgroups.get(a);chem.SGroup.removeAtom(s,e),Set.remove(n.sgs,a),i.invalidateAtom(e)},this._invert=function(){var t=new SGroupAtomAdd;return t.data=this.data,t}}function SGroupAttr(t,e,a){this.type="OpSGroupAttr",this.data={sgid:t,attr:e,value:a},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=this.data.sgid,d=i.sgroups.get(r);"DAT"==d.type&&a.sgroupData.has(r)&&(a.clearVisel(a.sgroupData.get(r).visel),a.sgroupData.unset(r)),this.data.value=d.setAttr(this.data.attr,this.data.value)},this._invert=function(){var t=new SGroupAttr;return t.data=this.data,t}}function SGroupCreate(t,e,a){this.type="OpSGroupCreate",this.data={sgid:t,type:e,pp:a},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=new chem.SGroup(this.data.type),d=this.data.sgid;r.id=d,i.sgroups.set(d,r),this.data.pp&&(i.sgroups.get(d).pp=new Vec2(this.data.pp)),a.sgroups.set(d,new rnd.ReSGroup(i.sgroups.get(d))),this.data.sgid=d},this._invert=function(){var t=new SGroupDelete;return t.data=this.data,t}}function SGroupDelete(t){this.type="OpSGroupDelete",this.data={sgid:t},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=this.data.sgid,d=a.sgroups.get(r);if(this.data.type=d.item.type,this.data.pp=d.item.pp,"DAT"==d.item.type&&a.sgroupData.has(r)&&(a.clearVisel(a.sgroupData.get(r).visel),a.sgroupData.unset(r)),a.clearVisel(d.visel),0!=d.item.atoms.length)throw new Error("S-Group not empty!");a.sgroups.unset(r),i.sgroups.remove(r)},this._invert=function(){var t=new SGroupCreate;return t.data=this.data,t}}function SGroupAddToHierarchy(t){this.type="OpSGroupAddToHierarchy",this.data={sgid:t},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=this.data.sgid,d=i.sGroupForest.insert(r,this.data.parent,this.data.children);this.data.parent=d.parent,this.data.children=d.children},this._invert=function(){var t=new SGroupRemoveFromHierarchy;return t.data=this.data,t}}function SGroupRemoveFromHierarchy(t){this.type="OpSGroupRemoveFromHierarchy",this.data={sgid:t},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=this.data.sgid;this.data.parent=i.sGroupForest.parent.get(r),this.data.children=i.sGroupForest.children.get(r),i.sGroupForest.remove(r)},this._invert=function(){var t=new SGroupAddToHierarchy;return t.data=this.data,t}}function BondAdd(t,e,a){this.data={bid:null,bond:a,begin:t,end:e},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;if(this.data.begin==this.data.end)throw new Error("Distinct atoms expected");if(rnd.DEBUG&&this.molecule.checkBondExists(this.data.begin,this.data.end))throw new Error("Bond already exists");e.invalidateAtom(this.data.begin,1),e.invalidateAtom(this.data.end,1);var r={};if(this.data.bond)for(var d in this.data.bond)r[d]=this.data.bond[d];r.type=r.type||chem.Struct.BOND.TYPE.SINGLE,r.begin=this.data.begin,r.end=this.data.end,Object.isNumber(this.data.bid)?i.bonds.set(this.data.bid,new chem.Struct.Bond(r)):this.data.bid=i.bonds.add(new chem.Struct.Bond(r)),i.bondInitHalfBonds(this.data.bid),i.atomAddNeighbor(i.bonds.get(this.data.bid).hb1),i.atomAddNeighbor(i.bonds.get(this.data.bid).hb2),a.notifyBondAdded(this.data.bid)},this._invert=function(){var t=new BondDelete;return t.data=this.data,t}}function BondDelete(t){this.data={bid:t,bond:null,begin:null,end:null},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;this.data.bond||(this.data.bond=i.bonds.get(this.data.bid),this.data.begin=this.data.bond.begin,this.data.end=this.data.bond.end),e.invalidateBond(this.data.bid),a.notifyBondRemoved(this.data.bid);var r=i.bonds.get(this.data.bid);[r.hb1,r.hb2].each(function(t){var e=i.halfBonds.get(t),a=i.atoms.get(e.begin),r=a.neighbors.indexOf(t),d=(r+a.neighbors.length-1)%a.neighbors.length,n=(r+1)%a.neighbors.length;i.setHbNext(a.neighbors[d],a.neighbors[n]),a.neighbors.splice(r,1)},this),i.halfBonds.unset(r.hb1),i.halfBonds.unset(r.hb2),i.bonds.remove(this.data.bid)},this._invert=function(){var t=new BondAdd;return t.data=this.data,t}}function BondAttr(t,e,a){this.data={bid:t,attribute:e,value:a},this.data2=null,this._execute=function(t){var e=t.render.ctab.molecule.bonds.get(this.data.bid);this.data2||(this.data2={bid:this.data.bid,attribute:this.data.attribute,value:e[this.data.attribute]}),e[this.data.attribute]=this.data.value,t.render.invalidateBond(this.data.bid),"type"==this.data.attribute&&t.render.invalidateLoop(this.data.bid)},this._isDummy=function(t){return t.render.ctab.molecule.bonds.get(this.data.bid)[this.data.attribute]==this.data.value},this._invert=function(){var t=new BondAttr;return t.data=this.data2,t.data2=this.data,t}}function FragmentAdd(t){this.frid=Object.isUndefined(t)?null:t,this._execute=function(t){var e=t.render.ctab,a=e.molecule,i=new chem.Struct.Fragment;null==this.frid?this.frid=a.frags.add(i):a.frags.set(this.frid,i),e.frags.set(this.frid,new rnd.ReFrag(i))},this._invert=function(){return new FragmentDelete(this.frid)}}function FragmentDelete(t){this.frid=t,this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;e.invalidateItem("frags",this.frid,1),a.frags.unset(this.frid),i.frags.remove(this.frid)},this._invert=function(){return new FragmentAdd(this.frid)}}function RGroupAttr(t,e,a){this.data={rgid:t,attribute:e,value:a},this.data2=null,this._execute=function(t){var e=t.render.ctab.molecule.rgroups.get(this.data.rgid);this.data2||(this.data2={rgid:this.data.rgid,attribute:this.data.attribute,value:e[this.data.attribute]}),e[this.data.attribute]=this.data.value,t.render.invalidateItem("rgroups",this.data.rgid)},this._isDummy=function(t){return t.render.ctab.molecule.rgroups.get(this.data.rgid)[this.data.attribute]==this.data.value},this._invert=function(){var t=new RGroupAttr;return t.data=this.data2,t.data2=this.data,t}}function RGroupFragment(t,e,a){this.rgid_new=t,this.rg_new=a,this.rgid_old=null,this.rg_old=null,this.frid=e,this._execute=function(t){var e=t.render.ctab,a=e.molecule;if(this.rgid_old=this.rgid_old||chem.Struct.RGroup.findRGroupByFragment(a.rgroups,this.frid),this.rg_old=this.rgid_old?a.rgroups.get(this.rgid_old):null,this.rg_old&&(this.rg_old.frags.remove(this.rg_old.frags.keyOf(this.frid)),e.clearVisel(e.rgroups.get(this.rgid_old).visel),0==this.rg_old.frags.count()?(e.rgroups.unset(this.rgid_old),a.rgroups.unset(this.rgid_old),e.markItemRemoved()):e.markItem("rgroups",this.rgid_old,1)),this.rgid_new){var i=a.rgroups.get(this.rgid_new);i?e.markItem("rgroups",this.rgid_new,1):(i=this.rg_new||new chem.Struct.RGroup,a.rgroups.set(this.rgid_new,i),e.rgroups.set(this.rgid_new,new rnd.ReRGroup(i))),i.frags.add(this.frid)}},this._invert=function(){return new RGroupFragment(this.rgid_old,this.frid,this.rg_old)}}function RxnArrowAdd(t){this.data={arid:null,pos:t},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;Object.isNumber(this.data.arid)?i.rxnArrows.set(this.data.arid,new chem.Struct.RxnArrow):this.data.arid=i.rxnArrows.add(new chem.Struct.RxnArrow),a.notifyRxnArrowAdded(this.data.arid),i._rxnArrowSetPos(this.data.arid,new Vec2(this.data.pos)),e.invalidateItem("rxnArrows",this.data.arid,1)},this._invert=function(){var t=new RxnArrowDelete;return t.data=this.data,t}}function RxnArrowDelete(t){this.data={arid:t,pos:null},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;this.data.pos||(this.data.pos=e.rxnArrowGetPos(this.data.arid)),a.notifyRxnArrowRemoved(this.data.arid),i.rxnArrows.remove(this.data.arid)},this._invert=function(){var t=new RxnArrowAdd;return t.data=this.data,t}}function RxnArrowMove(t,e,a){this.data={id:t,d:e,noinvalidate:a},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=this.data.id,d=this.data.d;i.rxnArrows.get(r).pp.add_(d),a.rxnArrows.get(r).visel.translate(e.ps(d)),this.data.d=d.negated(),this.data.noinvalidate||t.render.invalidateItem("rxnArrows",r,1)},this._invert=function(){var t=new RxnArrowMove;return t.data=this.data,t}}function RxnPlusAdd(t){this.data={plid:null,pos:t},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;Object.isNumber(this.data.plid)?i.rxnPluses.set(this.data.plid,new chem.Struct.RxnPlus):this.data.plid=i.rxnPluses.add(new chem.Struct.RxnPlus),a.notifyRxnPlusAdded(this.data.plid),i._rxnPlusSetPos(this.data.plid,new Vec2(this.data.pos)),e.invalidateItem("rxnPluses",this.data.plid,1)},this._invert=function(){var t=new RxnPlusDelete;return t.data=this.data,t}}function RxnPlusDelete(t){this.data={plid:t,pos:null},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;this.data.pos||(this.data.pos=e.rxnPlusGetPos(this.data.plid)),a.notifyRxnPlusRemoved(this.data.plid),i.rxnPluses.remove(this.data.plid)},this._invert=function(){var t=new RxnPlusAdd;return t.data=this.data,t}}function RxnPlusMove(t,e,a){this.data={id:t,d:e,noinvalidate:a},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=this.data.id,d=this.data.d;i.rxnPluses.get(r).pp.add_(d),a.rxnPluses.get(r).visel.translate(e.ps(d)),this.data.d=d.negated(),this.data.noinvalidate||t.render.invalidateItem("rxnPluses",r,1)},this._invert=function(){var t=new RxnPlusMove;return t.data=this.data,t}}function SGroupDataMove(t,e){this.data={id:t,d:e},this._execute=function(t){ui.ctab.sgroups.get(this.data.id).pp.add_(this.data.d),this.data.d=this.data.d.negated(),t.render.invalidateItem("sgroupData",this.data.id,1)},this._invert=function(){var t=new SGroupDataMove;return t.data=this.data,t}}function CanvasLoad(t){this.data={ctab:t,norescale:!1},this._execute=function(t){var e=t.render;e.ctab.clearVisels();var a=ui.ctab;ui.ctab=this.data.ctab,e.setMolecule(ui.ctab,this.data.norescale),this.data.ctab=a,this.data.norescale=!0},this._invert=function(){var t=new CanvasLoad;return t.data=this.data,t}}function ChiralFlagAdd(t){this.data={pos:t},this._execute=function(e){var a=e.render,i=a.ctab,r=i.molecule;if(i.chiralFlags.count()>0)throw new Error("Cannot add more than one Chiral flag");i.chiralFlags.set(0,new rnd.ReChiralFlag(t)),r.isChiral=!0,a.invalidateItem("chiralFlags",0,1)},this._invert=function(){var t=new ChiralFlagDelete;return t.data=this.data,t}}function ChiralFlagDelete(){this.data={pos:null},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;if(a.chiralFlags.count()<1)throw new Error("Cannot remove chiral flag");a.clearVisel(a.chiralFlags.get(0).visel),this.data.pos=a.chiralFlags.get(0).pp,a.chiralFlags.unset(0),i.isChiral=!1},this._invert=function(){var t=new ChiralFlagAdd(this.data.pos);return t.data=this.data,t}}function ChiralFlagMove(t){this.data={d:t},this._execute=function(t){var e=t.render;e.ctab.chiralFlags.get(0).pp.add_(this.data.d),this.data.d=this.data.d.negated(),e.invalidateItem("chiralFlags",0,1)},this._invert=function(){var t=new ChiralFlagMove;return t.data=this.data,t}}var Vec2=require("../util/vec2"),Set=require("../util/set");require("../chem"),require("../rnd");var ui=global.ui,chem=global.chem,rnd=global.rnd;AtomAdd.prototype=new Base,AtomDelete.prototype=new Base,AtomAttr.prototype=new Base,AtomMove.prototype=new Base,BondMove.prototype=new Base,LoopMove.prototype=new Base,SGroupAtomAdd.prototype=new Base,SGroupAtomRemove.prototype=new Base,SGroupAttr.prototype=new Base,SGroupCreate.prototype=new Base,SGroupDelete.prototype=new Base,SGroupAddToHierarchy.prototype=new Base,SGroupRemoveFromHierarchy.prototype=new Base,BondAdd.prototype=new Base,BondDelete.prototype=new Base,BondAttr.prototype=new Base,FragmentAdd.prototype=new Base,FragmentDelete.prototype=new Base,RGroupAttr.prototype=new Base,RGroupFragment.prototype=new Base,RxnArrowAdd.prototype=new Base,RxnArrowDelete.prototype=new Base,RxnArrowMove.prototype=new Base,RxnPlusAdd.prototype=new Base,RxnPlusDelete.prototype=new Base,RxnPlusMove.prototype=new Base,SGroupDataMove.prototype=new Base,CanvasLoad.prototype=new Base,ChiralFlagAdd.prototype=new Base,ChiralFlagDelete.prototype=new Base,ChiralFlagMove.prototype=new Base,module.exports={AtomAdd:AtomAdd,AtomDelete:AtomDelete,AtomAttr:AtomAttr,AtomMove:AtomMove,BondMove:BondMove,LoopMove:LoopMove,SGroupAtomAdd:SGroupAtomAdd,SGroupAtomRemove:SGroupAtomRemove,SGroupAttr:SGroupAttr,SGroupCreate:SGroupCreate,SGroupDelete:SGroupDelete,SGroupAddToHierarchy:SGroupAddToHierarchy,SGroupRemoveFromHierarchy:SGroupRemoveFromHierarchy,BondAdd:BondAdd,BondDelete:BondDelete,BondAttr:BondAttr,FragmentAdd:FragmentAdd,FragmentDelete:FragmentDelete,RGroupAttr:RGroupAttr,RGroupFragment:RGroupFragment,RxnArrowAdd:RxnArrowAdd,RxnArrowDelete:RxnArrowDelete,RxnArrowMove:RxnArrowMove,RxnPlusAdd:RxnPlusAdd,RxnPlusDelete:RxnPlusDelete,RxnPlusMove:RxnPlusMove,SGroupDataMove:SGroupDataMove,CanvasLoad:CanvasLoad,ChiralFlagAdd:ChiralFlagAdd,ChiralFlagDelete:ChiralFlagDelete,ChiralFlagMove:ChiralFlagMove}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../chem":11,"../rnd":21,"../util/set":42,"../util/vec2":43}],36:[function(require,module,exports){ +module.exports=[{name:"benzene",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 6 6 0 0 0 999 V2000\n 0.8660 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7320 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7320 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.8660 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 2 0 0 0\n 3 4 1 0 0 0\n 4 5 2 0 0 0\n 5 6 1 0 0 0\n 6 1 2 0 0 0\nM END\n",bid:0,aid:0},{name:"cyclopentadiene",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 5 5 0 0 0 999 V2000\n 0.0000 1.4257 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.8090 0.8379 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.5000 -0.1132 0.0000 C 0 0 0 0 0 0 0 0 0\n -0.5000 -0.1132 0.0000 C 0 0 0 0 0 0 0 0 0\n -0.8090 0.8379 0.0000 C 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 2 0 0 0\n 3 4 1 0 0 0\n 4 5 2 0 0 0\n 5 1 1 0 0 0\nM END\n",bid:0,aid:0},{name:"cyclohexane",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 6 6 0 0 0 999 V2000\n 0.8660 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7320 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7320 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.8660 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 6 1 0 0 0\n 6 1 1 0 0 0\nM END\n",bid:0,aid:0},{name:"cyclopentane",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 5 5 0 0 0 999 V2000\n 0.8090 1.5389 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.6180 0.9511 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.3090 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.3090 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 0.9511 0.0000 C 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 1 1 0 0 0\nM END\n",bid:0,aid:0},{name:"cyclopropane",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 3 3 0 0 0 999 V2000\n -3.2250 -0.2750 0.0000 C 0 0 0 0 0 0 0 0 0\n -2.2250 -0.2750 0.0000 C 0 0 0 0 0 0 0 0 0\n -2.7250 0.5910 0.0000 C 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 1 3 1 0 0 0\nM END\n",bid:0,aid:0},{name:"cyclobutane",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 4 4 0 0 0 999 V2000\n -3.8250 1.5500 0.0000 C 0 0 0 0 0 0 0 0 0\n -3.8250 0.5500 0.0000 C 0 0 0 0 0 0 0 0 0\n -2.8250 1.5500 0.0000 C 0 0 0 0 0 0 0 0 0\n -2.8250 0.5500 0.0000 C 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 1 3 1 0 0 0\n 3 4 1 0 0 0\n 4 2 1 0 0 0\nM END\n",bid:0,aid:0},{name:"cycloheptane",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 7 7 0 0 0 999 V2000\n 0.0000 1.6293 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.7835 2.2465 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7559 2.0242 0.0000 C 0 0 0 0 0 0 0 0 0\n 2.1897 1.1289 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 0.6228 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7566 0.2224 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.7835 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 6 7 1 0 0 0\n 5 7 1 0 0 0\n 1 5 1 0 0 0\n 4 6 1 0 0 0\n 3 4 1 0 0 0\n 2 3 1 0 0 0\n 1 2 1 0 0 0\nM END\n",bid:0,aid:0},{name:"cyclooctane",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 8 8 0 0 0 999 V2000\n 0.0000 0.7053 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 1.7078 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.7053 2.4131 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.7056 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7079 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 2.4133 0.7053 0.0000 C 0 0 0 0 0 0 0 0 0\n 2.4133 1.7078 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7079 2.4131 0.0000 C 0 0 0 0 0 0 0 0 0\n 8 3 1 0 0 0\n 7 8 1 0 0 0\n 6 7 1 0 0 0\n 5 6 1 0 0 0\n 4 5 1 0 0 0\n 1 4 1 0 0 0\n 2 3 1 0 0 0\n 1 2 1 0 0 0\nM END\n",bid:0,aid:0}]; + +},{}],37:[function(require,module,exports){ +function ajax(e,t){var r=getXHR(),n=e.headers||{};r.open(e.method,e.url,!!t,e.user,e.password);for(var u in n)n.hasOwnProperty(u)&&r.setRequestHeader(u,n[u]);if("function"==typeof e.config){var a=e.config(r,e);void 0!==a&&(r=a)}return e.timeout>0&&setTimeout(function(){r.status=-1,r.abort()},e.timeout),t&&(r.onreadystatechange=function(){4===r.readyState&&t(r)}),r.send(e.data),r}function successful(e){return e.status>=200&&e.status<300}function queryString(e){var t=[];for(var r in e)e.hasOwnProperty(r)&&t.push(encodeURIComponent(r)+"="+encodeURIComponent(e[r]));return t.join("&")}function request(e){var t=util.extend({method:"GET",headers:{},timeout:6e3},util.isObject(e)?e:{url:e});if(util.isObject(t.data)&&(t.data=JSON.stringify(t.data),t.headers["Content-Type"]="application/json; charset=utf-8"),t.params&&(t.url=t.url+(t.url.indexOf("?")<0?"?":"&")+queryString(t.params)),!t.sync)return new Promise(function(e,r){ajax(t,function(t){(successful(t)?e:r)(t)})});var r=ajax(t);if(!successful(r))throw r;return r}var getXHR=require("xhrpolyfill"),Promise=require("promise-polyfill"),util=require("./index.js");module.exports=request; + +},{"./index.js":39,"promise-polyfill":3,"xhrpolyfill":6}],38:[function(require,module,exports){ +var util=require("./index"),Vec2=require("./vec2"),Box2Abs=function(){1==arguments.length&&"min"in arguments[0]&&"max"in arguments[0]&&(this.p0=arguments[0].min,this.p1=arguments[0].max),2==arguments.length&&arguments[0]instanceof Vec2&&arguments[1]instanceof Vec2?(this.p0=arguments[0],this.p1=arguments[1]):4==arguments.length?(this.p0=new Vec2(arguments[0],arguments[1]),this.p1=new Vec2(arguments[2],arguments[3])):0==arguments.length?(this.p0=new Vec2,this.p1=new Vec2):new Error("Box2Abs constructor only accepts 4 numbers or 2 vectors or no arguments!")};Box2Abs.prototype.toString=function(){return this.p0.toString()+" "+this.p1.toString()},Box2Abs.fromRelBox=function(t){return util.assertDefined(t),new Box2Abs(t.x,t.y,t.x+t.width,t.y+t.height)},Box2Abs.prototype.clone=function(){return new Box2Abs(this.p0,this.p1)},Box2Abs.union=function(t,e){return util.assertDefined(t),util.assertDefined(e),new Box2Abs(Vec2.min(t.p0,e.p0),Vec2.max(t.p1,e.p1))},Box2Abs.prototype.extend=function(t,e){return util.assertDefined(t),e=e||t,new Box2Abs(this.p0.sub(t),this.p1.add(e))},Box2Abs.prototype.include=function(t){return util.assertDefined(t),new Box2Abs(this.p0.min(t),this.p1.max(t))},Box2Abs.prototype.contains=function(t,e){return e=(e||0)-0,util.assertDefined(t),t.x>=this.p0.x-e&&t.x<=this.p1.x+e&&t.y>=this.p0.y-e&&t.y<=this.p1.y+e},Box2Abs.prototype.translate=function(t){return util.assertDefined(t),new Box2Abs(this.p0.add(t),this.p1.add(t))},Box2Abs.prototype.transform=function(t,e){return util.assert(!util.isNullOrUndefined(t)),new Box2Abs(t.call(e,this.p0),t.call(e,this.p1))},Box2Abs.prototype.sz=function(){return this.p1.sub(this.p0)},Box2Abs.prototype.centre=function(){return Vec2.centre(this.p0,this.p1)},Box2Abs.prototype.pos=function(){return this.p0},module.exports=Box2Abs; + +},{"./index":39,"./vec2":43}],39:[function(require,module,exports){ +function find(e,n){for(var t=0;t126||e.charCodeAt(n)<32?t+="\\u"+function(e,n){for(var t=e.toString(16).toUpperCase();t.length=0;)n[t]=e[t];return n},isEmpty=function(e){for(var n in e)if(e.hasOwnProperty(n))return!1;return!0},stopEventPropagation=function(e){if("stopPropagation"in e)e.stopPropagation();else{if(!("cancelBubble"in e))throw Error("Browser unrecognized");e.cancelBubble=!0}},preventDefault=function(e){return"preventDefault"in e&&e.preventDefault(),Prototype.Browser.IE&&(e.returnValue=!1,e.keyCode=0),!1},setElementTextContent=function(e,n){if("textContent"in e)e.textContent=n;else{if(!("innerText"in e))throw Error("Browser unrecognized");e.innerText=n}},getElementTextContent=function(e){if("textContent"in e)return e.textContent;if("innerText"in e)return e.innerText;throw Error("Browser unrecognized")},stringPadded=function(e,n,t){for(var r=e+"",i="";r.length+i.lengthn)throw new Error("number does not fit");return stringPadded(r,n)},paddedInt=function(e,n){var t=e.toFixed(0);if(t.length>n)throw new Error("number does not fit");return stringPadded(t,n)},arrayAddIfMissing=function(e,n){for(var t=0;t=0;)e.splice(t,1),r+=1,t=e.indexOf(n);return r},listNextRotate=function(e,n){return e[(e.indexOf(n)+1)%e.length]},extend=function(e,n){for(var t in n)n.hasOwnProperty(t)&&(e[t]=n[t]);return e},isObject=function(e){return e===Object(e)};module.exports={tfx:tfx,each:each,find:find,findIndex:findIndex,findAll:findAll,array:array,isEmpty:isEmpty,stopEventPropagation:stopEventPropagation,preventDefault:preventDefault,setElementTextContent:setElementTextContent,getElementTextContent:getElementTextContent,stringPadded:stringPadded,normalizeNewlines:normalizeNewlines,splitNewlines:splitNewlines,unicodeLiteral:unicodeLiteral,idList:idList,mapArray:mapArray,arrayMax:arrayMax,arrayMin:arrayMin,map:map,apply:apply,ifDef:ifDef,ifDefList:ifDefList,identityMap:identityMap,strip:strip,stripRight:stripRight,stripQuotes:stripQuotes,paddedFloat:paddedFloat,paddedInt:paddedInt,arrayAddIfMissing:arrayAddIfMissing,assert:assert,assertDefined:assertDefined,isUndefined:isUndefined,isNull:isNull,isNullOrUndefined:isNullOrUndefined,arrayRemoveByValue:arrayRemoveByValue,listNextRotate:listNextRotate,extend:extend,isObject:isObject}; + +},{}],40:[function(require,module,exports){ +var util=require("./index"),Map=function(t){if(void 0!==t&&t.constructor!==Object)throw Error('Passed object is not an instance of "Object"!');this._obj=t||{},this._count=0};Map.prototype.each=function(t,o){var i,r,n;for(i in this._obj)n=parseInt(i,10),r=this._obj[i],isNaN(n)||(i=n),t.call(o,i,r)},Map.prototype.map=function(t,o){var i=new Map;return this.each(function(r,n){i.set(r,t.call(o,r,n))},this),i},Map.prototype.find=function(t,o){var i,r,n;for(i in this._obj)if(r=parseInt(i,10),n=this._obj[i],isNaN(r)||(i=r),t.call(o,i,n))return i},Map.prototype.findAll=function(t,o){var i,r,n,e=[];for(i in this._obj)r=parseInt(i,10),n=this._obj[i],isNaN(r)||(i=r),t.call(o,i,n)&&e.push(i);return e},Map.prototype.keys=function(){var t,o=[];for(t in this._obj)o.push(t);return o},Map.prototype.ikeys=function(){var t=[];for(var o in this._obj)t.push(o-0);return t},Map.prototype.set=function(t,o){var i;return this._count+=(void 0!==o?1:0)-(void 0!==this._obj[t]?1:0),void 0===o?(i=this._obj[t],delete this._obj[t],i):(this._obj[t]=o,o)},Map.prototype.get=function(t){if(this._obj[t]!==Object.prototype[t])return this._obj[t]},Map.prototype.has=function(t){return this._obj[t]!==Object.prototype[t]},Map.prototype.unset=function(t){return this.set(t,void 0)},Map.prototype.update=function(t){for(var o in t)this.set(o,t[o])},Map.prototype.clear=function(){this._obj={},this._count=0},Map.prototype.count=function(){return this._count},Map.prototype.idList=function(){return util.idList(this._obj)},Map.prototype.keyOf=function(t){for(var o in this._obj)if(this._obj[o]===t)return o},module.exports=Map; + +},{"./index":39}],41:[function(require,module,exports){ +var Map=require("./map.js"),Pool=function(){this._map=new Map,this._nextId=0};Pool.prototype.newId=function(){return this._nextId++},Pool.prototype.add=function(t){var o=this._nextId++;return this._map.set(o,t),o},Pool.prototype.set=function(t,o){this._map.set(t,o)},Pool.prototype.get=function(t){return this._map.get(t)},Pool.prototype.has=function(t){return this._map.has(t)},Pool.prototype.remove=function(t){return this._map.unset(t)},Pool.prototype.clear=function(){this._map.clear()},Pool.prototype.keys=function(){return this._map.keys()},Pool.prototype.ikeys=function(){return this._map.ikeys()},Pool.prototype.each=function(t,o){this._map.each(t,o)},Pool.prototype.map=function(t,o){return this._map.map(t,o)},Pool.prototype.find=function(t,o){return this._map.find(t,o)},Pool.prototype.count=function(){return this._map.count()},Pool.prototype.keyOf=function(t){return this._map.keyOf(t)},module.exports=Pool; + +},{"./map.js":40}],42:[function(require,module,exports){ +var Set={empty:function(){return{}},single:function(t){var r={};return Set.add(r,t),r},size:function(t){var r=0;for(var n in t)t[n]!==Object.prototype[n]&&r++;return r},contains:function(t,r){return void 0!==t[r]&&t[r]!==Object.prototype[r]},subset:function(t,r){for(var n in t)if(t[n]!==Object.prototype[n]&&r[n]!==t[n])return!1;return!0},intersection:function(t,r){var n={};for(var e in t)t[e]!==Object.prototype[e]&&r[e]===t[e]&&Set.add(n,e);return n},disjoint:function(t,r){for(var n in t)if(t[n]!==Object.prototype[n]&&r[n]===t[n])return!1;return!0},eq:function(t,r){return Set.subset(t,r)&&Set.subset(r,t)},each:function(t,r,n){for(var e in t)t[e]!==Object.prototype[e]&&r.call(n,t[e])},filter:function(t,r,n){var e={};for(var o in t)t[o]!==Object.prototype[o]&&r.call(n,t[o])&&(e[t[o]]=t[o]);return e},pick:function(t){for(var r in t)if(t[r]!==Object.prototype[r])return t[r];return null},list:function(t){var r=[];for(var n in t)t[n]!==Object.prototype[n]&&r.push(t[n]);return r},add:function(t,r){t[r]=r},mergeIn:function(t,r){Set.each(r,function(r){Set.add(t,r)})},remove:function(t,r){var n=t[r];return delete t[r],n},clone:function(t){var r={};return Set.mergeIn(r,t),r},fromList:function(t){var r={};if(t)for(var n=0;n0?(o<0||c[o]c[u]?(f=u,y=o):(f=o,y=u),c[f]+Math.abs(s[f])*(c[y]-c[f])/(Math.abs(s[f])+Math.abs(s[y]))},module.exports=Vec2; + +},{"./index":39}]},{},[18])(18) +}); \ No newline at end of file diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.py b/public/lib/ketcher-2.0.0-alpha.3/ketcher.py new file mode 100755 index 000000000..66faf64cd --- /dev/null +++ b/public/lib/ketcher-2.0.0-alpha.3/ketcher.py @@ -0,0 +1,330 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import sys +from os import path, getcwd +from mimetypes import guess_type +from cgi import FieldStorage +from wsgiref.util import FileWrapper +from wsgiref.headers import Headers + +from base64 import b64encode + +class application(object): + # don't serve static by default + static_serve = False + static_alias = { '' : 'ketcher.html' } + static_root = None + + indigo = None + indigo_inchi = None + + def __init__(self, environ, start_response): + self.path = environ['PATH_INFO'].strip('/') + self.method = environ['REQUEST_METHOD'] + self.content_type = environ.get('CONTENT_TYPE', '') + self.fields = FieldStorage(fp=environ['wsgi.input'], + environ=environ, keep_blank_values=True) + self.FileWrapper = environ.get('wsgi.file_wrapper', FileWrapper) + self.headers = Headers([]) + + if self.static_serve: + self.headers['Access-Control-Allow-Origin'] = '*' + + route = getattr(self, 'on_' + self.path, None) + if route is None: + route = self.serve_static if self.method == 'GET' and \ + self.static_serve else self.notsupported + + status = "200 OK" + try: + self.response = route() + except self.HttpException as e: + status = e.args[0] + self.response = [e.args[1]] + + self.headers.setdefault('Content-Type', 'text/plain') + start_response(status, self.headers.items()) + + def __iter__(self): + for chunk in self.response: + yield chunk if sys.version_info.major < 3 or \ + not hasattr(chunk, 'encode') else chunk.encode() + + def notsupported(self): + raise self.HttpException("405 Method Not Allowed", + "Request not supported") + + def indigo_required(method): + def wrapper(self, **args): + if not self.indigo: + raise self.HttpException("501 Not Implemented", + "Indigo libraries are not found") + try: + return method(self, **args) + except indigo.IndigoException as e: + message = str(sys.exc_info()[1]) + if 'indigoLoad' in message: # error on load + message = "Cannot load the specified " + \ + "structure: %s " % str(e) + raise self.HttpException("400 Bad Request", + message) + return wrapper + + @indigo_required + def on_knocknock(self): + return ["You are welcome!"] + + @indigo_required + def on_layout(self): + moldata = None + if self.method == 'GET' and 'smiles' in self.fields: + moldata = self.fields.getfirst('smiles') + elif self.is_form_request() and 'moldata' in self.fields: + moldata = self.fields.getfirst('moldata') + selective = 'selective' in self.fields + if moldata: + if '>>' in moldata or moldata.startswith('$RXN'): + rxn = self.indigo.loadQueryReaction(moldata) + if selective: + for mol in rxn.iterateMolecules(): + self.selective_layout(mol) + else: + rxn.layout() + return ["Ok.\n", + rxn.rxnfile()] + elif moldata.startswith('InChI'): + mol = self.indigo_inchi.loadMolecule(moldata) + mol.layout() + return ["Ok.\n", + mol.molfile()] + else: + mol = self.indigo.loadQueryMolecule(moldata) + if selective: + for rg in mol.iterateRGroups(): + for frag in rg.iterateRGroupFragments(): + self.selective_layout(frag) + self.selective_layout(mol) + else: + mol.layout() + return ["Ok.\n", + mol.molfile()] + self.notsupported() + + @indigo_required + def on_smiles(self): + moldata = self.fields.getfirst('moldata') + if moldata: + if '>>' in moldata or moldata.startswith('$RXN'): + rxn = self.indigo.loadQueryReaction(moldata) + return ["Ok.\n", + rxn.smiles()] + elif moldata.startswith('InChI'): + mol = self.indigo_inchi.loadMolecule(moldata) + return ["Ok.\n", + mol.smiles()] + else: + mol = self.indigo.loadQueryMolecule(moldata) + return ["Ok.\n", + mol.smiles()] + self.notsupported() + + @indigo_required + def on_getinchi(self): + md, is_rxn = self.load_moldata() + inchi = self.indigo_inchi.getInchi(md) + return ["Ok.\n", inchi] + + @indigo_required + def on_getmolfile(self): + md, is_rxn = self.load_moldata() + return ["Ok.\n", md.molfile()] + + @indigo_required + def on_automap(self): + moldata = None + if self.method == 'GET' and 'smiles' in self.fields: + moldata = self.fields.getfirst('smiles') + elif self.is_form_request() and 'moldata' in self.fields: + moldata = self.fields.getfirst('moldata') + + if moldata: + mode = self.fields.getfirst('mode', 'discard') + rxn = self.indigo.loadQueryReaction(moldata) + if not moldata.startswith('$RXN'): + rxn.layout() + rxn.automap(mode) + return ["Ok.\n", + rxn.rxnfile()] + self.notsupported() + + @indigo_required + def on_aromatize(self): + try: + md, is_rxn = self.load_moldata() + except: + message = str(sys.exc_info()[1]) + if message.startswith("\"molfile loader:") and \ + message.endswith("queries\""): # hack to avoid user confusion + md, is_rxn = self.load_moldata(True) + else: + raise + md.aromatize() + return ["Ok.\n", + md.rxnfile() if is_rxn else md.molfile()] + + @indigo_required + def on_dearomatize(self): + try: + md, is_rxn = self.load_moldata() + except: # TODO: test for query features presence + raise self.HttpException("400 Bad Request", + "Molecules and reactions " + \ + "containing query features " + \ + "cannot be dearomatized yet.") + md.dearomatize() + return ["Ok.\n", + md.rxnfile() if is_rxn else md.molfile()] + + @indigo_required + def on_calculate_cip(self): + application.indigo.setOption('molfile-saving-add-stereo-desc', True) + try: + md, is_rxn = self.load_moldata() + except: + message = str(sys.exc_info()[1]) + if message.startswith("\"molfile loader:") and \ + message.endswith("queries\""): # hack to avoid user confusion + md, is_rxn = self.load_moldata(True) + else: + raise + result = md.rxnfile() if is_rxn else md.molfile() + application.indigo.setOption('molfile-saving-add-stereo-desc', False) + return ["Ok.\n", + result] + + def on_open(self): + if self.is_form_request(): + self.headers.add_header('Content-Type', 'text/html') + return [''] + self.notsupported() + + def on_save(self): + if self.is_form_request(): + type, data = self.fields.getfirst('filedata').split('\n', 1) + type = type.strip() + if type == 'smi': + self.headers.add_header('Content-Type', + 'chemical/x-daylight-smiles') + elif type == 'mol': + if data.startswith('$RXN'): + type = 'rxn' + self.headers.add_header('Content-Type', + 'chemical/x-mdl-%sfile' % type) + + self.headers.add_header('Content-Length', str(len(data))) + self.headers.add_header('Content-Disposition', 'attachment', + filename='ketcher.%s' % type) + return [data] + self.notsupported() + + class HttpException(Exception): pass + def load_moldata(self, is_query=False): + moldata = self.fields.getfirst('moldata') + is_rxn = False + if moldata.startswith('$RXN'): + if is_query: + md = self.indigo.loadQueryReaction(moldata) + else: + md = self.indigo.loadReaction(moldata) + is_rxn = True + elif moldata.startswith('InChI'): + md = self.indigo_inchi.loadMolecule(moldata) + md.layout() + else: + if is_query: + md = self.indigo.loadQueryMolecule(moldata) + else: + md = self.indigo.loadMolecule(moldata) + return md, is_rxn + + def selective_layout(self, mol): + dsgs = [dsg for dsg in mol.iterateDataSGroups() \ + if dsg.description() == '_ketcher_selective_layout' and \ + dsg.data() == '1'] + atoms = sorted([atom.index() for dsg in dsgs \ + for atom in dsg.iterateAtoms()]) + for dsg in dsgs: + dsg.remove() + mol.getSubmolecule(atoms).layout() + return mol + + def serve_static(self): + root = path.realpath(self.static_root or getcwd()) + fpath = self.static_alias.get(self.path, self.path) + fpath = path.realpath(path.join(root, fpath)) + + if not fpath.startswith(root + path.sep) or not path.isfile(fpath) \ + or fpath == path.realpath(__file__): + raise self.HttpException("404 Not Found", + "Requested file isn't accessible") + + self.headers['Content-Type'] = guess_type(fpath)[0] or 'text/plain' + try: + fd = open(fpath, 'rb') + return self.FileWrapper(fd) if self.method == 'GET' else [''] + except (IOError, OSError): + raise self.HttpException("402 Payment Required", # or 403, hmm.. + "Must get more money for overtime") + + def is_form_request(self): + return self.method == 'POST' and \ + (self.content_type.startswith('application/x-www-form-urlencoded') + or self.content_type.startswith('multipart/form-data')) + +try: + import indigo + import indigo_inchi + application.indigo = indigo.Indigo() + application.indigo_inchi = indigo_inchi.IndigoInchi(application.indigo) + application.indigo.setOption('ignore-stereochemistry-errors', 'true') +except: + pass + +if __name__ == '__main__': + import socket + from wsgiref.simple_server import make_server + + def parse_args(): + dir = sys.argv[1] if len(sys.argv) > 1 else '' + addr = sys.argv[2] if len(sys.argv) > 2 else '' + res = addr.rsplit(':', 1) + return dir, \ + res[0] if len(res) > 1 else '0.0.0.0', \ + int(res[-1] or 8080) + def usage(): + progname = sys.argv[0] + if not progname.startswith('./'): + progname = 'python ' + progname + print( "USAGE:\n %s [static_dir [port|address:port]]\n" % progname) + + if not application.indigo: + print("WARNING: Indigo is not found. Server-side functionality " + \ + "will not be available") + try: + dir, address, port = parse_args() + application.static_serve = True # allow to serve static + application.static_root = dir # in standalone python-server mode + httpd = make_server(address, port, application) + print("Serving on %s:%d..." % (address, port)) + httpd.serve_forever() + except ValueError: + usage() + except (socket.error, socket.gaierror, socket.herror, OSError) as e: + print("Server error: %s" % e.args[1]) + usage() + except KeyboardInterrupt: + pass diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.svg b/public/lib/ketcher-2.0.0-alpha.3/ketcher.svg new file mode 100644 index 000000000..9594ba37b --- /dev/null +++ b/public/lib/ketcher-2.0.0-alpha.3/ketcher.svg @@ -0,0 +1,138 @@ + + + +Copyright (C) 2017 by original authors @ fontello.com + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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b="className",a="for",c=document.createElement("div");c.setAttribute(b,"x");if(c.className!=="x"){c.setAttribute("class","x");if(c.className==="x"){b="class"}}c=null;c=document.createElement("label");c.setAttribute(a,"x");if(c.htmlFor!=="x"){c.setAttribute("htmlFor","x");if(c.htmlFor==="x"){a="htmlFor"}}c=null;return{read:{names:{"class":b,className:b,"for":a,htmlFor:a},values:{_getAttr:function(d,e){return d.getAttribute(e)},_getAttr2:function(d,e){return d.getAttribute(e,2)},_getAttrNode:function(d,f){var e=d.getAttributeNode(f);return e?e.value:""},_getEv:(function(){var d=document.createElement("div"),g;d.onclick=Prototype.emptyFunction;var e=d.getAttribute("onclick");if(String(e).indexOf("{")>-1){g=function(f,h){h=f.getAttribute(h);if(!h){return null}h=h.toString();h=h.split("{")[1];h=h.split("}")[0];return h.strip()}}else{if(e===""){g=function(f,h){h=f.getAttribute(h);if(!h){return null}return h.strip()}}}d=null;return g})(),_flag:function(d,e){return 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Object.isNumber(d)?a(c)[d]:Element.select(c,d)[b||0]}})()}}else{if(Prototype.Browser.Gecko&&/rv:1\.8\.0/.test(navigator.userAgent)){Element.Methods.setOpacity=function(a,b){a=$(a);a.style.opacity=(b==1)?0.999999:(b==="")?"":(b<0.00001)?0:b;return a}}else{if(Prototype.Browser.WebKit){Element.Methods.setOpacity=function(a,b){a=$(a);a.style.opacity=(b==1||b==="")?"":(b<0.00001)?0:b;if(b==1){if(a.tagName.toUpperCase()=="IMG"&&a.width){a.width++;a.width--}else{try{var d=document.createTextNode(" ");a.appendChild(d);a.removeChild(d)}catch(c){}}}return a}}}}}if("outerHTML" in document.documentElement){Element.Methods.replace=function(c,e){c=$(c);if(e&&e.toElement){e=e.toElement()}if(Object.isElement(e)){c.parentNode.replaceChild(e,c);return c}e=Object.toHTML(e);var d=c.parentNode,b=d.tagName.toUpperCase();if(Element._insertionTranslations.tags[b]){var f=c.next(),a=Element._getContentFromAnonymousElement(b,e.stripScripts());d.removeChild(c);if(f){a.each(function(g){d.insertBefore(g,f)})}else{a.each(function(g){d.appendChild(g)})}}else{c.outerHTML=e.stripScripts()}e.evalScripts.bind(e).defer();return c}}Element._returnOffset=function(b,c){var a=[b,c];a.left=b;a.top=c;return a};Element._getContentFromAnonymousElement=function(e,d,f){var g=new Element("div"),c=Element._insertionTranslations.tags[e];var a=false;if(c){a=true}else{if(f){a=true;c=["","",0]}}if(a){g.innerHTML=" "+c[0]+d+c[1];g.removeChild(g.firstChild);for(var b=c[2];b--;){g=g.firstChild}}else{g.innerHTML=d}return $A(g.childNodes)};Element._insertionTranslations={before:function(a,b){a.parentNode.insertBefore(b,a)},top:function(a,b){a.insertBefore(b,a.firstChild)},bottom:function(a,b){a.appendChild(b)},after:function(a,b){a.parentNode.insertBefore(b,a.nextSibling)},tags:{TABLE:["","
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d=c("object");if(Prototype.BrowserFeatures.SpecificElementExtensions){if(d){return function(h){if(h&&typeof h._extendedByPrototype=="undefined"){var g=h.tagName;if(g&&(/^(?:object|applet|embed)$/i.test(g))){b(h,Element.Methods);b(h,Element.Methods.Simulated);b(h,Element.Methods.ByTag[g.toUpperCase()])}}return h}}return Prototype.K}var a={},e=Element.Methods.ByTag;var f=Object.extend(function(i){if(!i||typeof i._extendedByPrototype!="undefined"||i.nodeType!=1||i==window){return i}var g=Object.clone(a),h=i.tagName.toUpperCase();if(e[h]){Object.extend(g,e[h])}b(i,g);i._extendedByPrototype=Prototype.emptyFunction;return i},{refresh:function(){if(!Prototype.BrowserFeatures.ElementExtensions){Object.extend(a,Element.Methods);Object.extend(a,Element.Methods.Simulated)}}});f.refresh();return f})();if(document.documentElement.hasAttribute){Element.hasAttribute=function(a,b){return a.hasAttribute(b)}}else{Element.hasAttribute=Element.Methods.Simulated.hasAttribute}Element.addMethods=function(c){var i=Prototype.BrowserFeatures,d=Element.Methods.ByTag;if(!c){Object.extend(Form,Form.Methods);Object.extend(Form.Element,Form.Element.Methods);Object.extend(Element.Methods.ByTag,{FORM:Object.clone(Form.Methods),INPUT:Object.clone(Form.Element.Methods),SELECT:Object.clone(Form.Element.Methods),TEXTAREA:Object.clone(Form.Element.Methods),BUTTON:Object.clone(Form.Element.Methods)})}if(arguments.length==2){var b=c;c=arguments[1]}if(!b){Object.extend(Element.Methods,c||{})}else{if(Object.isArray(b)){b.each(g)}else{g(b)}}function g(k){k=k.toUpperCase();if(!Element.Methods.ByTag[k]){Element.Methods.ByTag[k]={}}Object.extend(Element.Methods.ByTag[k],c)}function a(m,l,k){k=k||false;for(var o in m){var n=m[o];if(!Object.isFunction(n)){continue}if(!k||!(o in l)){l[o]=n.methodize()}}}function e(n){var k;var m={OPTGROUP:"OptGroup",TEXTAREA:"TextArea",P:"Paragraph",FIELDSET:"FieldSet",UL:"UList",OL:"OList",DL:"DList",DIR:"Directory",H1:"Heading",H2:"Heading",H3:"Heading",H4:"Heading",H5:"Heading",H6:"Heading",Q:"Quote",INS:"Mod",DEL:"Mod",A:"Anchor",IMG:"Image",CAPTION:"TableCaption",COL:"TableCol",COLGROUP:"TableCol",THEAD:"TableSection",TFOOT:"TableSection",TBODY:"TableSection",TR:"TableRow",TH:"TableCell",TD:"TableCell",FRAMESET:"FrameSet",IFRAME:"IFrame"};if(m[n]){k="HTML"+m[n]+"Element"}if(window[k]){return window[k]}k="HTML"+n+"Element";if(window[k]){return window[k]}k="HTML"+n.capitalize()+"Element";if(window[k]){return window[k]}var l=document.createElement(n),o=l.__proto__||l.constructor.prototype;l=null;return o}var h=window.HTMLElement?HTMLElement.prototype:Element.prototype;if(i.ElementExtensions){a(Element.Methods,h);a(Element.Methods.Simulated,h,true)}if(i.SpecificElementExtensions){for(var j in Element.Methods.ByTag){var f=e(j);if(Object.isUndefined(f)){continue}a(d[j],f.prototype)}}Object.extend(Element,Element.Methods);delete Element.ByTag;if(Element.extend.refresh){Element.extend.refresh()}Element.cache={}};document.viewport={getDimensions:function(){return{width:this.getWidth(),height:this.getHeight()}},getScrollOffsets:function(){return Element._returnOffset(window.pageXOffset||document.documentElement.scrollLeft||document.body.scrollLeft,window.pageYOffset||document.documentElement.scrollTop||document.body.scrollTop)}};(function(b){var g=Prototype.Browser,e=document,c,d={};function a(){if(g.WebKit&&!e.evaluate){return document}if(g.Opera&&window.parseFloat(window.opera.version())<9.5){return document.body}return document.documentElement}function f(h){if(!c){c=a()}d[h]="client"+h;b["get"+h]=function(){return c[d[h]]};return b["get"+h]()}b.getWidth=f.curry("Width");b.getHeight=f.curry("Height")})(document.viewport);Element.Storage={UID:1};Element.addMethods({getStorage:function(b){if(!(b=$(b))){return}var a;if(b===window){a=0}else{if(typeof b._prototypeUID==="undefined"){b._prototypeUID=Element.Storage.UID++}a=b._prototypeUID}if(!Element.Storage[a]){Element.Storage[a]=$H()}return Element.Storage[a]},store:function(b,a,c){if(!(b=$(b))){return}if(arguments.length===2){Element.getStorage(b).update(a)}else{Element.getStorage(b).set(a,c)}return b},retrieve:function(c,b,a){if(!(c=$(c))){return}var e=Element.getStorage(c),d=e.get(b);if(Object.isUndefined(d)){e.set(b,a);d=a}return d},clone:function(c,a){if(!(c=$(c))){return}var e=c.cloneNode(a);e._prototypeUID=void 0;if(a){var d=Element.select(e,"*"),b=d.length;while(b--){d[b]._prototypeUID=void 0}}return Element.extend(e)},purge:function(c){if(!(c=$(c))){return}var a=Element._purgeElement;a(c);var d=c.getElementsByTagName("*"),b=d.length;while(b--){a(d[b])}return null}});(function(){function h(v){var u=v.match(/^(\d+)%?$/i);if(!u){return null}return(Number(u[1])/100)}function o(F,G,v){var y=null;if(Object.isElement(F)){y=F;F=y.getStyle(G)}if(F===null){return null}if((/^(?:-)?\d+(\.\d+)?(px)?$/i).test(F)){return window.parseFloat(F)}var A=F.include("%"),w=(v===document.viewport);if(/\d/.test(F)&&y&&y.runtimeStyle&&!(A&&w)){var u=y.style.left,E=y.runtimeStyle.left;y.runtimeStyle.left=y.currentStyle.left;y.style.left=F||0;F=y.style.pixelLeft;y.style.left=u;y.runtimeStyle.left=E;return F}if(y&&A){v=v||y.parentNode;var x=h(F);var B=null;var z=y.getStyle("position");var D=G.include("left")||G.include("right")||G.include("width");var C=G.include("top")||G.include("bottom")||G.include("height");if(v===document.viewport){if(D){B=document.viewport.getWidth()}else{if(C){B=document.viewport.getHeight()}}}else{if(D){B=$(v).measure("width")}else{if(C){B=$(v).measure("height")}}}return(B===null)?0:B*x}return 0}function 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y=this.element;if(j(y)){this._prepared=true;return}var A={position:y.style.position||"",width:y.style.width||"",visibility:y.style.visibility||"",display:y.style.display||""};y.store("prototype_original_styles",A);var B=y.getStyle("position"),u=y.getStyle("width");if(u==="0px"||u===null){y.style.display="block";u=y.getStyle("width")}var v=(B==="fixed")?document.viewport:y.parentNode;y.setStyle({position:"absolute",visibility:"hidden",display:"block"});var w=y.getStyle("width");var x;if(u&&(w===u)){x=o(y,"width",v)}else{if(B==="absolute"||B==="fixed"){x=o(y,"width",v)}else{var C=y.parentNode,z=$(C).getLayout();x=z.get("width")-this.get("margin-left")-this.get("border-left")-this.get("padding-left")-this.get("padding-right")-this.get("border-right")-this.get("margin-right")}}y.setStyle({width:x+"px"});this._prepared=true},_end:function(){var v=this.element;var 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0 0 0 0 0 0 0 0 0 + 7.3145 -9.0650 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 + 7.3145 -8.2400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3145 -9.8900 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4895 -9.0650 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 5 1 0 0 0 0 + 2 3 1 1 0 0 0 + 2 7 1 0 0 0 0 + 3 4 1 1 0 0 0 + 3 6 1 0 0 0 0 + 5 4 1 1 0 0 0 + 5 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 14 9 1 0 0 0 0 + 9 17 1 0 0 0 0 + 10 11 2 0 0 0 0 + 10 16 1 0 0 0 0 + 10 18 1 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 16 14 2 0 0 0 0 + 15 16 1 0 0 0 0 + 15 17 2 0 0 0 0 + 4 19 1 0 0 0 0 + 8 20 1 0 0 0 0 + 20 21 2 0 0 0 0 + 20 22 1 0 0 0 0 + 20 23 1 0 0 0 0 + 23 24 1 0 0 0 0 + 24 25 2 0 0 0 0 + 24 26 1 0 0 0 0 + 24 27 1 0 0 0 0 +M END +> +27 + +> +29 + +$$$$ +Adenosine triphosphate + SMMXDraw10031318252D + + 31 33 0 0 1 0 0 0 0 0999 V2000 + 14.6695 -10.5215 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 14.0020 -10.8431 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 + 14.2570 -11.4643 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 + 15.0820 -11.4643 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + 15.3369 -10.8431 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 + 14.2570 -12.2893 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 14.0020 -10.0181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.1770 -10.0181 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 15.3369 -10.0181 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 + 16.8483 -8.5670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 17.5627 -8.9796 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 17.5627 -9.8046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.8483 -10.2171 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 16.1338 -9.8046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.4068 -8.6851 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 16.1338 -8.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.8876 -9.3262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.8483 -7.7420 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 15.0820 -12.2893 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 12.3520 -10.0181 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 + 12.3520 -9.1931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 12.3520 -10.8431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 11.5270 -10.0181 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 10.7020 -10.0181 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 + 10.7020 -9.1931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 10.7020 -10.8431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 9.8770 -10.0181 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 9.0520 -10.0181 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 + 9.0520 -9.1931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 9.0520 -10.8431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.2270 -10.0181 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 5 1 0 0 0 0 + 2 3 1 1 0 0 0 + 2 7 1 0 0 0 0 + 3 4 1 1 0 0 0 + 3 6 1 0 0 0 0 + 5 4 1 1 0 0 0 + 5 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 14 9 1 0 0 0 0 + 9 17 1 0 0 0 0 + 10 11 2 0 0 0 0 + 10 16 1 0 0 0 0 + 10 18 1 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 16 14 2 0 0 0 0 + 15 16 1 0 0 0 0 + 15 17 2 0 0 0 0 + 4 19 1 0 0 0 0 + 8 20 1 0 0 0 0 + 20 21 2 0 0 0 0 + 20 22 1 0 0 0 0 + 20 23 1 0 0 0 0 + 23 24 1 0 0 0 0 + 24 25 2 0 0 0 0 + 24 26 1 0 0 0 0 + 24 27 1 0 0 0 0 + 27 28 1 0 0 0 0 + 28 29 2 0 0 0 0 + 28 30 1 0 0 0 0 + 28 31 1 0 0 0 0 +M END +> +31 + +> +33 + +$$$$ From 38702f6a596f6d2f81a42f109e8dda1ca7a936a5 Mon Sep 17 00:00:00 2001 From: jmcneil86043 Date: Fri, 30 Jun 2017 10:46:48 -0700 Subject: [PATCH 075/576] Fixes #139. /api/runSystemTest route now returns JSON. Also now accepts grepTerms array of strings to limit mocha tests run to match a list or or'd terms in the array (#140) --- app_template.coffee | 2 +- .../src/server/routes/SystemTestRoutes.coffee | 15 +++++++++------ 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/app_template.coffee b/app_template.coffee index 555355120..64416c403 100644 --- a/app_template.coffee +++ b/app_template.coffee @@ -142,7 +142,7 @@ startApp = -> csUtilities.logUsage("ACAS Node server started", "started", "") if config.all.server.systemTest?.runOnStart? && config.all.server.systemTest.runOnStart - systemTest.runSystemTestInternal false, (status, output) -> + systemTest.runSystemTestInternal true, [], (status, output) -> console.log "system test completed" startApp() diff --git a/modules/SystemTest/src/server/routes/SystemTestRoutes.coffee b/modules/SystemTest/src/server/routes/SystemTestRoutes.coffee index b6d5dde41..0041ac443 100644 --- a/modules/SystemTest/src/server/routes/SystemTestRoutes.coffee +++ b/modules/SystemTest/src/server/routes/SystemTestRoutes.coffee @@ -810,12 +810,13 @@ exports.deleteSELFileInternal = (callback) -> exports.runSystemTest = (req, resp) -> force = req.body.force == true + grepTerms = if req.body.grepTerms? then req.body.grepTerms else [] req.setTimeout 86400000 - exports.runSystemTestInternal force, (statusCode, response) -> + exports.runSystemTestInternal force, grepTerms, (statusCode, response) -> resp.statusCode = statusCode - resp.end response + resp.json response -exports.runSystemTestInternal = (force, callback) -> +exports.runSystemTestInternal = (force, grepTerms, callback) -> fs = require('fs') if !force? force = false @@ -835,7 +836,9 @@ exports.runSystemTestInternal = (force, callback) -> inlineAssets: true unless config.all.server.systemTest.runDestructive - mochaOpts.grep = "-nondestructive" + grepTerms.push "-nondestructive" + if grepTerms.length > 0 + mochaOpts.grep = grepTerms.join '|' mocha = new Mocha mochaOpts @@ -862,9 +865,9 @@ exports.runSystemTestInternal = (force, callback) -> if err throw err console.log "successfully deleted #{systemTestProgressFile}" - fs.readFile path.resolve(path.join(config.all.server.datafiles.relative_path, "systemReport/systemReport.html")), (err, data) => + fs.readFile path.resolve(path.join(config.all.server.datafiles.relative_path, "systemReport/mochawesome.json")), (err, data) => if callback? - callback 200, data + callback 200, JSON.parse(data) return ).on('pass', (test) -> console.debug 'Test passed' From 134e67380a91459101565777dc2ca4bbfac97683 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Wed, 5 Jul 2017 10:46:39 -0700 Subject: [PATCH 076/576] update value is working. still need styling etc --- .../src/client/ACASFormFields.coffee | 6 +- .../client/ACASFormStateDisplayUpdate.coffee | 109 +++++++++++++++++- .../src/client/ACASFormStateDisplayView.html | 56 +++++---- .../ServerAPI/src/client/ExampleThing.coffee | 5 +- 4 files changed, 139 insertions(+), 37 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index de724b2a4..bd5d1a53b 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -33,10 +33,14 @@ class window.ACASFormAbstractFieldController extends Backbone.View @userInputEvent = true getModel: -> - @thingRef.get @modelKey + if @thingRef instanceof Thing + return @thingRef.get @modelKey + else + return @thingRef handleInputChanged: => @checkEmptyAndRequired() + @trigger 'formFieldChanged' checkEmptyAndRequired: -> if @required and @isEmpty() and !@errorSet diff --git a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee index d574bd8e0..8aa18cdba 100644 --- a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee +++ b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee @@ -79,11 +79,13 @@ class window.ACASFormStateDisplayUpdateController extends Backbone.View @callWhenSetupComplete = @completeRenderModelContent completeRenderModelContent: -> - @headerController = new ACASFormStateDisplayUpdateHeaderRowController - tableDef: @options.tableDef - showUnits: @options.showUnits - @$("thead").append @headerController.render().el + unless @headerController? + @headerController = new ACASFormStateDisplayUpdateHeaderRowController + tableDef: @options.tableDef + showUnits: @options.showUnits + @$("thead").append @headerController.render().el + @$("tbody").empty() @getCurrentStates().each (state) => rowController = new ACASFormStateDisplayUpdateRowController collection: state.get 'lsValues' @@ -94,7 +96,10 @@ class window.ACASFormStateDisplayUpdateController extends Backbone.View @currentCellEditor = new ACASFormStateDisplayValueEditController collection: values el: @$('.bv_valueEditor') + tableDef: @tableDef + stateID: state.id @currentCellEditor.render() + @currentCellEditor.on 'saveNewValue', @handleCellUpdate applyOptions: -> if @tableDef?.tableLabel? @@ -136,6 +141,28 @@ class window.ACASFormStateDisplayUpdateController extends Backbone.View states.sort() return states + handleCellUpdate: (valInfo) => + stateToUpdate = @getCurrentStates().findWhere id: valInfo.stateID + if !stateToUpdate? + window.alert "internal problem finding state to update" + return + + oldValue = stateToUpdate.getValuesByTypeAndKind valInfo.newValue.get('lsType'), valInfo.newValue.get('lsKind') + if oldValue.length != 1 + window.alert "internal problem finding value to update" + return + oldValue[0].set + ignored: true + modifiedBy: window.AppLaunchParams.loginUser.username + modifiedDate: new Date().getTime() + isDirty: true + valInfo.newValue.set + recoerdedBy: window.AppLaunchParams.loginUser.username + recordedDate: new Date().getTime() + + stateToUpdate.get('lsValues').add valInfo.newValue + @trigger 'thingSaveRequested', valInfo.comment + class window.ACASFormStateDisplayOldValueController extends Backbone.View tagName: 'tr' template: _.template($("#ACASFormStateDisplayOldValueView").html()) @@ -174,24 +201,94 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View events: -> "keyup .bv_reasonForUpdate": "reasonForUpdateChanged" + "click .bv_cancelBtn": "handleCancelClicked" + "click .bv_saveBtn": "handleSaveClicked" initialize: -> + @tableDef = @options.tableDef + for valDef in @tableDef.values + if valDef.modelDefaults.kind == @collection.at(0).get('lsKind') + @valueDef = valDef + unless @valueDef? + console.log "There is a configuration problem with ACASFormStateDisplayValueEditController. Trying to edit a value whose kind does not have a matching definition" + @moduleName = if @tableDef.moduleName then @tableDef.moduleName else "State Editor" + @commentPrefix = @moduleName+":" + @allowedCommentLength = 250 - @commentPrefix.length render: => $(@el).empty() $(@el).html @template() + @$('.bv_header').html "\"#{@valueDef.fieldSettings.formLabel}\" Value History and Edit" @collection.comparator = 'id' @collection.sort() @collection.each (val) => oldRow = new ACASFormStateDisplayOldValueController model: val @$("tbody").append oldRow.render().el + @setupEditor() + @$('.bv_myPanel').modal + backdrop: "static" + @$('.bv_myPanel').modal "show" + + reasonForUpdateChanged: -> + @comment = @commentPrefix + @$('.bv_reasonForUpdate').val() + labelText = @allowedCommentLength-@comment.length + " characters remaining" + @$('.bv_charactersRemaining').text(labelText) + @formUpdated() + + formUpdated: => + if @comment == @commentPrefix or @newField.isEmpty() + @$('.bv_saveBtn').attr('disabled','disabled') + else + @$('.bv_saveBtn').removeAttr('disabled') + + handleCancelClicked: => + @$('.bv_myPanel').modal "hide" + $(@el).empty() + + handleSaveClicked: => + @trigger 'saveNewValue', + newValue: @newValue + comment: @comment + stateID: @options.stateID + + @$('.bv_myPanel').modal "hide" + $(@el).empty() - @ setupEditor: -> - + currentValue = @collection.findWhere ignored: false + + @newValue = new Value + lsType: @valueDef.modelDefaults.type + lsKind: @valueDef.modelDefaults.kind + unitType: @valueDef.modelDefaults.unitType + unitKind: @valueDef.modelDefaults.unitKind + codeType: @valueDef.modelDefaults.codeType + codeKind: @valueDef.modelDefaults.codeKind + codeOrigin: @valueDef.modelDefaults.codeOrigin + if currentValue? + opts = + modelKey: @valueDef.modelDefaults.kind + inputClass: @valueDef.fieldSettings.inputClass + formLabel: @valueDef.fieldSettings.formLabel + required: true + url: @valueDef.fieldSettings.url + thingRef: @newValue + + switch @valueDef.fieldSettings.fieldType + when 'numericValue' then @newField = new ACASFormLSNumericValueFieldController opts + when 'codeValue' then @newField = new ACASFormLSCodeValueFieldController opts + when 'stringValue' then @newField = new ACASFormLSStringValueFieldController opts + when 'dateValue' then @newField = new ACASFormLSDateValueFieldController opts + + @$('.bv_valueField').append @newField.render().el + @newField.afterRender() + @newField.on 'formFieldChanged', @formUpdated + + + #TODO value editor: # - maybe show transaction creator as modified by and date? diff --git a/modules/Components/src/client/ACASFormStateDisplayView.html b/modules/Components/src/client/ACASFormStateDisplayView.html index 88998b28e..f41cd0bce 100644 --- a/modules/Components/src/client/ACASFormStateDisplayView.html +++ b/modules/Components/src/client/ACASFormStateDisplayView.html @@ -20,37 +20,35 @@
      launching controller must provide or set table label diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index bdfcdb34d..96136bd24 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -359,6 +359,7 @@ ExampleTableAuditConf = tableWrapper: "bv_dataTable" tableLabel: "Example Thing Data Table - Edit Mode" allowEdit: true + moduleName: "ExampleThing" # sortKind: 'media component' values: [ modelDefaults: @@ -441,6 +442,7 @@ class window.ExampleTableAuditController extends AbstractThingFormController $(@el).empty() $(@el).html @template() @setupFormFields(ExampleTableAuditConf.formFieldDefinitions) + @formDisplayTables['exampleThingTable'].on 'thingSaveRequested', @handleUpdateThing @hasRendered = true @ @@ -465,7 +467,8 @@ class window.ExampleTableAuditController extends AbstractThingFormController updateModel: => - handleUpdateThing: => + handleUpdateThing: (transactionComment) => + @model.set 'transactionOptions', comments: transactionComment @model.prepareToSave() @model.reformatBeforeSaving() @model.save() From 13a5b49ff12cfa40b80ad1a9c42018b135f1f515 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Wed, 5 Jul 2017 13:23:06 -0700 Subject: [PATCH 077/576] RC/1.12.0: removed hard-coding width of select2 so that user can set the desired width --- modules/Components/src/client/style.css | 5 ----- 1 file changed, 5 deletions(-) diff --git a/modules/Components/src/client/style.css b/modules/Components/src/client/style.css index 0ed2905fa..c35ddaf3a 100644 --- a/modules/Components/src/client/style.css +++ b/modules/Components/src/client/style.css @@ -30,11 +30,6 @@ margin-bottom: 10px; } -.select2-container { - width: 350px !important; - /* base width matches edit prot and expt */ -} - .select2-container .select2-selection--single { width: 350px; height: 30px; From e933d3517487acdb68365ad4db0ebced4e4aafd4 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 5 Jul 2017 16:49:14 -0700 Subject: [PATCH 078/576] Update gulpfile.coffee --- gulpfile.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gulpfile.coffee b/gulpfile.coffee index c4c318524..6137628b2 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -72,7 +72,7 @@ addREnvironmentCleanUp = (file,contents) -> # file contents are handed # over as buffers if path.extname(file.path) in [".R",".r"] && contents.match('# ROUTE:.*') - cleanFunction = "racas::cleanEnvironment()" + cleanFunction = "racas::cleanEnvironment();gc()" contents = "#{cleanFunction}\n\r#{contents}\r\n#{cleanFunction}\r\n" return contents From e6578ad5cdaafdb3825baff8940b1b901fe065fa Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 6 Jul 2017 16:05:19 -0700 Subject: [PATCH 079/576] Added routes expected by Ketcher API that hit new ACAS Roo structure routes for converting smiles and cleaning molecules. Changed ketcher URI to reference new api routes and take it out of standalone mode. --- .../server/routes/ChemStructureRoutes.coffee | 63 +++++++++++++++++++ .../client/ACASFormChemicalStructure.coffee | 2 +- 2 files changed, 64 insertions(+), 1 deletion(-) diff --git a/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee b/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee index 57aa53247..0e2838e38 100644 --- a/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee +++ b/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee @@ -9,6 +9,9 @@ exports.setupAPIRoutes = (app) -> app.post '/api/chemStructure/renderMolStructureBase64', exports.renderMolStructureBase64 app.post '/api/chemStructure/acasStructureMetaSearch', exports.acasStructureMetaSearch app.post '/api/chemStructure/acasStructureSearch', exports.acasStructureSearch + app.get '/api/chemStructure/ketcher/knocknock', exports.ketcherKnocknock + app.get '/api/chemStructure/ketcher/layout', exports.ketcherConvertSmiles + app.post '/api/chemStructure/ketcher/layout', exports.ketcherLayout exports.setupRoutes = (app, loginRoutes) -> app.get '/api/chemStructure/renderStructureByThingCode', loginRoutes.ensureAuthenticated, exports.renderStructureByThingCode @@ -21,6 +24,9 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/chemStructure/renderMolStructureBase64', loginRoutes.ensureAuthenticated, exports.renderMolStructureBase64 app.post '/api/chemStructure/acasStructureMetaSearch', loginRoutes.ensureAuthenticated, exports.acasStructureMetaSearch app.post '/api/chemStructure/acasStructureSearch', loginRoutes.ensureAuthenticated, exports.acasStructureSearch + app.get '/api/chemStructure/ketcher/knocknock', loginRoutes.ensureAuthenticated, exports.ketcherKnocknock + app.get '/api/chemStructure/ketcher/layout', loginRoutes.ensureAuthenticated, exports.ketcherConvertSmiles + app.post '/api/chemStructure/ketcher/layout', loginRoutes.ensureAuthenticated, exports.ketcherLayout _ = require 'underscore' @@ -253,3 +259,60 @@ exports.acasStructureMetaSearch = (req, resp) -> resp.statusCode = 500 resp.end JSON.stringify "ACAS structure search failed" ) + +exports.ketcherKnocknock = (req, resp) -> + resp.end "You are welcome!" + +exports.ketcherConvertSmiles = (req, resp) -> + if global.specRunnerTestmode + resp.end "Ok.\n\n -INDIGO-06301717442D\n\n 4 3 0 0 0 0 0 0 0 0999 V2000\n -1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.7713 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 1 0 0 0 0\nM END\n" + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"structure/convertSmilesToMol" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: req.query.smiles + json: true + , (error, response, json) => + console.log response + console.log json + if !error && response.statusCode == 200 + statusMessage = "Ok.\n" + resp.end statusMessage+json + else + console.log 'got ajax error trying to convert smiles to MOL' + console.log error + console.log json + console.log response + resp.statusCode = 500 + resp.end JSON.stringify "Smiles to MOL conversion failed" + ) + +exports.ketcherLayout = (req, resp) -> + if global.specRunnerTestmode + resp.end "Ok.\n\n -INDIGO-06301717442D\n\n 4 3 0 0 0 0 0 0 0 0999 V2000\n -1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.7713 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 1 0 0 0 0\nM END\n" + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"structure/cleanMolStructure" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: req.body.moldata + json: true + , (error, response, json) => + console.log response + console.log json + if !error && response.statusCode == 200 + statusMessage = "Ok.\n" + resp.end statusMessage+json + else + console.log 'got ajax error trying to clean MOL' + console.log error + console.log json + console.log response + resp.statusCode = 500 + resp.end JSON.stringify "Cleaning MOL conversion failed" + ) \ No newline at end of file diff --git a/modules/Components/src/client/ACASFormChemicalStructure.coffee b/modules/Components/src/client/ACASFormChemicalStructure.coffee index 54ca2da13..cfe56527b 100644 --- a/modules/Components/src/client/ACASFormChemicalStructure.coffee +++ b/modules/Components/src/client/ACASFormChemicalStructure.coffee @@ -71,7 +71,7 @@ class window.KetcherChemicalStructureController extends Backbone.View $(@el).empty() $(@el).html @template() - searchFrameURL = "/lib/ketcher-2.0.0-alpha.3/ketcher.html" + searchFrameURL = "/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/chemStructure/ketcher/" @$('.bv_sketcherIFrame').attr 'src', searchFrameURL From 915212b0d21005be0e43e0647ea9e88e7aa51b03 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 7 Jul 2017 20:13:05 -0700 Subject: [PATCH 080/576] Added basic logic for changing AbstractForm and Thing behavior for labels based on new "multiple" boolean attribute. If set, allows for multiple labels to function with the same lsType and lsKind, and they are assigned keys of the format "key + number" i.e. alias_0, alias_1, alias_2 when form field definition key is "alias_". Changed logic for "createNewLabel" to just create a new label rather than get or create. --- .../src/client/AbstractFormController.coffee | 3 +- modules/ServerAPI/src/client/Thing.coffee | 38 ++++++++++++++----- 2 files changed, 31 insertions(+), 10 deletions(-) diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 9ac9eaa70..10aef7356 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -103,7 +103,8 @@ class window.AbstractThingFormController extends AbstractFormController url: field.fieldSettings.url thingRef: @model insertUnassigned: field.fieldSettings.insertUnassigned - + if field.multiple? and field.multiple + opts.modelKey = field.key + 0 switch field.fieldSettings.fieldType when 'label' then newField = new ACASFormLSLabelFieldController opts when 'numericValue' then newField = new ACASFormLSNumericValueFieldController opts diff --git a/modules/ServerAPI/src/client/Thing.coffee b/modules/ServerAPI/src/client/Thing.coffee index f39bcf3bc..4cc0a4033 100644 --- a/modules/ServerAPI/src/client/Thing.coffee +++ b/modules/ServerAPI/src/client/Thing.coffee @@ -189,22 +189,42 @@ class window.Thing extends Backbone.Model # add key as attribute of model if @lsProperties.defaultLabels? for dLabel in @lsProperties.defaultLabels - newLabel = @get('lsLabels').getOrCreateLabelByTypeAndKind dLabel.type, dLabel.kind - @listenTo newLabel, 'createNewLabel', @createNewLabel - @set dLabel.key, newLabel - # if newLabel.get('preferred') is undefined - newLabel.set key: dLabel.key - newLabel.set preferred: dLabel.preferred + if dLabel.multiple? and dLabel.multiple + labels = @get('lsLabels').getLabelByTypeAndKind dLabel.type, dLabel.kind + if labels.length > 0 + counter = 0 + _.each labels, (label) => + if !label.has('key') + labelKey = dLabel.key + counter + counter++ + @set labelKey, label + label.set key: labelKey + @listenTo label, 'createNewLabel', @createNewLabel + else + newLabel = @get('lsLabels').getOrCreateLabelByTypeAndKind dLabel.type, dLabel.kind + newKey = dLabel.key + 0 + @set newKey, newLabel + newLabel.set key: newKey + else + newLabel = @get('lsLabels').getOrCreateLabelByTypeAndKind dLabel.type, dLabel.kind + @listenTo newLabel, 'createNewLabel', @createNewLabel + @set dLabel.key, newLabel + # if newLabel.get('preferred') is undefined + newLabel.set key: dLabel.key + newLabel.set preferred: dLabel.preferred createNewLabel: (lKind, newText, key) => - dLabel = _.where(@lsProperties.defaultLabels, {key: key})[0] oldLabel = @get(key) @unset(key) - newLabel = @get('lsLabels').getOrCreateLabelByTypeAndKind dLabel.type, dLabel.kind - newLabel.set + newLabel = new Label + lsType: oldLabel.get 'lsType' + lsKind: oldLabel.get 'lsKind' key: key labelText: newText preferred: oldLabel.get 'preferred' + newLabel.on 'change', => + @trigger('change') + @get('lsLabels').add newLabel @set key, newLabel createDefaultStates: => From 2a3da1acb3c8e279dfaf5669b0ce7f40d43f5f83 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 7 Jul 2017 21:30:18 -0700 Subject: [PATCH 081/576] Working commit - adding MultiLabels to base ACAS Form Fields --- .../src/client/ACASFormMultiLabel.coffee | 67 +++++++++++++++++++ .../src/client/ACASFormMultiLabelView.html | 15 +++++ .../src/client/AbstractFormController.coffee | 9 ++- 3 files changed, 88 insertions(+), 3 deletions(-) create mode 100644 modules/Components/src/client/ACASFormMultiLabel.coffee create mode 100644 modules/Components/src/client/ACASFormMultiLabelView.html diff --git a/modules/Components/src/client/ACASFormMultiLabel.coffee b/modules/Components/src/client/ACASFormMultiLabel.coffee new file mode 100644 index 000000000..232accb36 --- /dev/null +++ b/modules/Components/src/client/ACASFormMultiLabel.coffee @@ -0,0 +1,67 @@ +class window.ACASFormMultiLabelListController extends ACASFormAbstractFieldController + template: _.template($("#ACASFormMultiLabelListView").html()) + #model should be a collection of LSLabels i.e. Labels + #instantiate me with the full conf, not just the fieldDefinition + + initialize: -> + super() + @opts = @options + multiLabels = @thingRef.get('lsLabels').getLabelByTypeAndKind(@opts.modelDefaults.type, @opts.modelDefaults.kind) + _.each multiLabels, (label) => + @addOneLabel(label) + #TODO: initialize the first new label- do I have to? +# opts.modelKey = opts.key + 0 + + events: -> + "click .bv_addLabelButton": "handleAddLabelButtonClicked" + + handleAddLabelButtonClicked: => + @addNewLabel() + + addNewLabel: (skipAmDirtyTrigger) => + keyBase = @modelKey + newModel = new Label + lsType: @opts.modelDefaults.type + lsKind: @opts.modelDefaults.kind + preferred: @opts.modelDefaults.preferred + #count up number of current labels + #TODO: can this be replaced with some get collection?? + currentMultiLabels = @thingRef.get('lsLabels').filter (label) -> + label.has('key') and (label.get('key').indexOf(keyBase) > -1) + console.log currentMultiLabels + newKey = keyBase + currentMultiLabels.length + newModel.set key: newKey + @thingRef.set newKey, newModel + @thingRef.get('lsLabels').add newModel + @addOneLabel(newModel) + unless skipAmDirtyTrigger is true + newModel.trigger 'amDirty' + + addOneLabel: (label) -> + opts = + modelKey: label.get('key') + inputClass: @opts.inputClass + formLabel: @opts.formLabel + placeholder: @opts.placeholder + required: @opts.required + url: @opts.url + thingRef: @thingRef + insertUnassigned:@opts.insertUnassigned + model: label + lc = new ACASFormMultiLabelRowController opts + console.log lc + console.log lc.getModel() + @$('.bv_multiLabels').append lc.render().el + lc.renderModelContent() + lc.on 'updateState', => + @trigger 'updateState' + +class window.ACASFormMultiLabelRowController extends ACASFormLSLabelFieldController + ### + Launching controller must: + - Initialize the model with an LSLabel + Do whatever else is required or optional in ACASFormAbstractFieldController + ### + + template: _.template($("#ACASFormMultiLabelRowView").html()) + diff --git a/modules/Components/src/client/ACASFormMultiLabelView.html b/modules/Components/src/client/ACASFormMultiLabelView.html new file mode 100644 index 000000000..e4fbbf045 --- /dev/null +++ b/modules/Components/src/client/ACASFormMultiLabelView.html @@ -0,0 +1,15 @@ + + + \ No newline at end of file diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 10aef7356..1bd8500a8 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -103,10 +103,13 @@ class window.AbstractThingFormController extends AbstractFormController url: field.fieldSettings.url thingRef: @model insertUnassigned: field.fieldSettings.insertUnassigned - if field.multiple? and field.multiple - opts.modelKey = field.key + 0 + modelDefaults: field.modelDefaults switch field.fieldSettings.fieldType - when 'label' then newField = new ACASFormLSLabelFieldController opts + when 'label' + if field.multiple? and field.multiple + newField = new ACASFormMultiLabelListController opts + else + newField = new ACASFormLSLabelFieldController opts when 'numericValue' then newField = new ACASFormLSNumericValueFieldController opts when 'codeValue' then newField = new ACASFormLSCodeValueFieldController opts when 'htmlClobValue' From e3195bbee2116cf04845e29cc0d074df188a63a8 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 10 Jul 2017 18:44:48 +0000 Subject: [PATCH 082/576] Added init tags to acas.sh needed by Ubuntu --- bin/acas.sh | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/bin/acas.sh b/bin/acas.sh index 7ceee911d..9bdd56231 100755 --- a/bin/acas.sh +++ b/bin/acas.sh @@ -1,4 +1,13 @@ #!/bin/bash +### BEGIN INIT INFO +# Provides: acas +# Required-Start: $local_fs +# Required-Stop: $local_fs +# Default-Start: 2 3 4 5 +# Default-Stop: 0 1 6 +# Short-Description: start and stop the acas app.js, server.js and apache instance +# Description: start and stop the acas app.js, server.js and apache instance +### END INIT INFO # chkconfig: 2345 64 02 # description: start and stop the acas app.js, server.js and apache instance # processname: acas From 2a1eb56a62d9477f1166d1c34ec011b8c6630211 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Mon, 10 Jul 2017 12:46:53 -0600 Subject: [PATCH 083/576] Added dependency: BlockUI.js --- .../routes/RequiredClientScripts_template.js | 3 +- public/lib/blockUI.js | 620 ++++++++++++++++++ 2 files changed, 622 insertions(+), 1 deletion(-) create mode 100644 public/lib/blockUI.js diff --git a/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js b/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js index 58da06749..a47b9a0c9 100644 --- a/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js +++ b/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js @@ -26,7 +26,8 @@ exports.requiredScripts = [ '/lib/spin/js/jquery-spin.js', '/lib/handsontable/dist/handsontable.full.js', '/lib/select2-4.0.2/dist/js/select2.full.js', - '/socket.io/socket.io.js' + '/socket.io/socket.io.js', + '/lib/blockUI.js' ]; exports.applicationScripts = [ diff --git a/public/lib/blockUI.js b/public/lib/blockUI.js new file mode 100644 index 000000000..eadaa6fcc --- /dev/null +++ b/public/lib/blockUI.js @@ -0,0 +1,620 @@ +/*! + * jQuery blockUI plugin + * Version 2.70.0-2014.11.23 + * Requires jQuery v1.7 or later + * + * Examples at: http://malsup.com/jquery/block/ + * Copyright (c) 2007-2013 M. Alsup + * Dual licensed under the MIT and GPL licenses: + * http://www.opensource.org/licenses/mit-license.php + * http://www.gnu.org/licenses/gpl.html + * + * Thanks to Amir-Hossein Sobhi for some excellent contributions! + */ + +;(function() { + /*jshint eqeqeq:false curly:false latedef:false */ + "use strict"; + + function setup($) { + $.fn._fadeIn = $.fn.fadeIn; + + var noOp = $.noop || function() {}; + + // this bit is to ensure we don't call setExpression when we shouldn't (with extra muscle to handle + // confusing userAgent strings on Vista) + var msie = /MSIE/.test(navigator.userAgent); + var ie6 = /MSIE 6.0/.test(navigator.userAgent) && ! /MSIE 8.0/.test(navigator.userAgent); + var mode = document.documentMode || 0; + var setExpr = $.isFunction( document.createElement('div').style.setExpression ); + + // global $ methods for blocking/unblocking the entire page + $.blockUI = function(opts) { install(window, opts); }; + $.unblockUI = function(opts) { remove(window, opts); }; + + // convenience method for quick growl-like notifications (http://www.google.com/search?q=growl) + $.growlUI = function(title, message, timeout, onClose) { + var $m = $('
      '); + if (title) $m.append('

      '+title+'

      '); + if (message) $m.append('

      '+message+'

      '); + if (timeout === undefined) timeout = 3000; + + // Added by konapun: Set timeout to 30 seconds if this growl is moused over, like normal toast notifications + var callBlock = function(opts) { + opts = opts || {}; + + $.blockUI({ + message: $m, + fadeIn : typeof opts.fadeIn !== 'undefined' ? opts.fadeIn : 700, + fadeOut: typeof opts.fadeOut !== 'undefined' ? opts.fadeOut : 1000, + timeout: typeof opts.timeout !== 'undefined' ? opts.timeout : timeout, + centerY: false, + showOverlay: false, + onUnblock: onClose, + css: $.blockUI.defaults.growlCSS + }); + }; + + callBlock(); + var nonmousedOpacity = $m.css('opacity'); + $m.mouseover(function() { + callBlock({ + fadeIn: 0, + timeout: 30000 + }); + + var displayBlock = $('.blockMsg'); + displayBlock.stop(); // cancel fadeout if it has started + displayBlock.fadeTo(300, 1); // make it easier to read the message by removing transparency + }).mouseout(function() { + $('.blockMsg').fadeOut(1000); + }); + // End konapun additions + }; + + // plugin method for blocking element content + $.fn.block = function(opts) { + if ( this[0] === window ) { + $.blockUI( opts ); + return this; + } + var fullOpts = $.extend({}, $.blockUI.defaults, opts || {}); + this.each(function() { + var $el = $(this); + if (fullOpts.ignoreIfBlocked && $el.data('blockUI.isBlocked')) + return; + $el.unblock({ fadeOut: 0 }); + }); + + return this.each(function() { + if ($.css(this,'position') == 'static') { + this.style.position = 'relative'; + $(this).data('blockUI.static', true); + } + this.style.zoom = 1; // force 'hasLayout' in ie + install(this, opts); + }); + }; + + // plugin method for unblocking element content + $.fn.unblock = function(opts) { + if ( this[0] === window ) { + $.unblockUI( opts ); + return this; + } + return this.each(function() { + remove(this, opts); + }); + }; + + $.blockUI.version = 2.70; // 2nd generation blocking at no extra cost! + + // override these in your code to change the default behavior and style + $.blockUI.defaults = { + // message displayed when blocking (use null for no message) + message: '

      Please wait...

      ', + + title: null, // title string; only used when theme == true + draggable: true, // only used when theme == true (requires jquery-ui.js to be loaded) + + theme: false, // set to true to use with jQuery UI themes + + // styles for the message when blocking; if you wish to disable + // these and use an external stylesheet then do this in your code: + // $.blockUI.defaults.css = {}; + css: { + padding: 0, + margin: 0, + width: '30%', + top: '40%', + left: '35%', + textAlign: 'center', + color: '#000', + border: '3px solid #aaa', + backgroundColor:'#fff', + cursor: 'wait' + }, + + // minimal style set used when themes are used + themedCSS: { + width: '30%', + top: '40%', + left: '35%' + }, + + // styles for the overlay + overlayCSS: { + backgroundColor: '#000', + opacity: 0.6, + cursor: 'wait' + }, + + // style to replace wait cursor before unblocking to correct issue + // of lingering wait cursor + cursorReset: 'default', + + // styles applied when using $.growlUI + growlCSS: { + width: '350px', + top: '10px', + left: '', + right: '10px', + border: 'none', + padding: '5px', + opacity: 0.6, + cursor: 'default', + color: '#fff', + backgroundColor: '#000', + '-webkit-border-radius':'10px', + '-moz-border-radius': '10px', + 'border-radius': '10px' + }, + + // IE issues: 'about:blank' fails on HTTPS and javascript:false is s-l-o-w + // (hat tip to Jorge H. N. de Vasconcelos) + /*jshint scripturl:true */ + iframeSrc: /^https/i.test(window.location.href || '') ? 'javascript:false' : 'about:blank', + + // force usage of iframe in non-IE browsers (handy for blocking applets) + forceIframe: false, + + // z-index for the blocking overlay + baseZ: 1000, + + // set these to true to have the message automatically centered + centerX: true, // <-- only effects element blocking (page block controlled via css above) + centerY: true, + + // allow body element to be stetched in ie6; this makes blocking look better + // on "short" pages. disable if you wish to prevent changes to the body height + allowBodyStretch: true, + + // enable if you want key and mouse events to be disabled for content that is blocked + bindEvents: true, + + // be default blockUI will supress tab navigation from leaving blocking content + // (if bindEvents is true) + constrainTabKey: true, + + // fadeIn time in millis; set to 0 to disable fadeIn on block + fadeIn: 200, + + // fadeOut time in millis; set to 0 to disable fadeOut on unblock + fadeOut: 400, + + // time in millis to wait before auto-unblocking; set to 0 to disable auto-unblock + timeout: 0, + + // disable if you don't want to show the overlay + showOverlay: true, + + // if true, focus will be placed in the first available input field when + // page blocking + focusInput: true, + + // elements that can receive focus + focusableElements: ':input:enabled:visible', + + // suppresses the use of overlay styles on FF/Linux (due to performance issues with opacity) + // no longer needed in 2012 + // applyPlatformOpacityRules: true, + + // callback method invoked when fadeIn has completed and blocking message is visible + onBlock: null, + + // callback method invoked when unblocking has completed; the callback is + // passed the element that has been unblocked (which is the window object for page + // blocks) and the options that were passed to the unblock call: + // onUnblock(element, options) + onUnblock: null, + + // callback method invoked when the overlay area is clicked. + // setting this will turn the cursor to a pointer, otherwise cursor defined in overlayCss will be used. + onOverlayClick: null, + + // don't ask; if you really must know: http://groups.google.com/group/jquery-en/browse_thread/thread/36640a8730503595/2f6a79a77a78e493#2f6a79a77a78e493 + quirksmodeOffsetHack: 4, + + // class name of the message block + blockMsgClass: 'blockMsg', + + // if it is already blocked, then ignore it (don't unblock and reblock) + ignoreIfBlocked: false + }; + + // private data and functions follow... + + var pageBlock = null; + var pageBlockEls = []; + + function install(el, opts) { + var css, themedCSS; + var full = (el == window); + var msg = (opts && opts.message !== undefined ? opts.message : undefined); + opts = $.extend({}, $.blockUI.defaults, opts || {}); + + if (opts.ignoreIfBlocked && $(el).data('blockUI.isBlocked')) + return; + + opts.overlayCSS = $.extend({}, $.blockUI.defaults.overlayCSS, opts.overlayCSS || {}); + css = $.extend({}, $.blockUI.defaults.css, opts.css || {}); + if (opts.onOverlayClick) + opts.overlayCSS.cursor = 'pointer'; + + themedCSS = $.extend({}, $.blockUI.defaults.themedCSS, opts.themedCSS || {}); + msg = msg === undefined ? opts.message : msg; + + // remove the current block (if there is one) + if (full && pageBlock) + remove(window, {fadeOut:0}); + + // if an existing element is being used as the blocking content then we capture + // its current place in the DOM (and current display style) so we can restore + // it when we unblock + if (msg && typeof msg != 'string' && (msg.parentNode || msg.jquery)) { + var node = msg.jquery ? msg[0] : msg; + var data = {}; + $(el).data('blockUI.history', data); + data.el = node; + data.parent = node.parentNode; + data.display = node.style.display; + data.position = node.style.position; + if (data.parent) + data.parent.removeChild(node); + } + + $(el).data('blockUI.onUnblock', opts.onUnblock); + var z = opts.baseZ; + + // blockUI uses 3 layers for blocking, for simplicity they are all used on every platform; + // layer1 is the iframe layer which is used to supress bleed through of underlying content + // layer2 is the overlay layer which has opacity and a wait cursor (by default) + // layer3 is the message content that is displayed while blocking + var lyr1, lyr2, lyr3, s; + if (msie || opts.forceIframe) + lyr1 = $(''); + else + lyr1 = $(''); + + if (opts.theme) + lyr2 = $(''); + else + lyr2 = $(''); + + if (opts.theme && full) { + s = ''; + } + else if (opts.theme) { + s = ''; + } + else if (full) { + s = ''; + } + else { + s = ''; + } + lyr3 = $(s); + + // if we have a message, style it + if (msg) { + if (opts.theme) { + lyr3.css(themedCSS); + lyr3.addClass('ui-widget-content'); + } + else + lyr3.css(css); + } + + // style the overlay + if (!opts.theme /*&& (!opts.applyPlatformOpacityRules)*/) + lyr2.css(opts.overlayCSS); + lyr2.css('position', full ? 'fixed' : 'absolute'); + + // make iframe layer transparent in IE + if (msie || opts.forceIframe) + lyr1.css('opacity',0.0); + + //$([lyr1[0],lyr2[0],lyr3[0]]).appendTo(full ? 'body' : el); + var layers = [lyr1,lyr2,lyr3], $par = full ? $('body') : $(el); + $.each(layers, function() { + this.appendTo($par); + }); + + if (opts.theme && opts.draggable && $.fn.draggable) { + lyr3.draggable({ + handle: '.ui-dialog-titlebar', + cancel: 'li' + }); + } + + // ie7 must use absolute positioning in quirks mode and to account for activex issues (when scrolling) + var expr = setExpr && (!$.support.boxModel || $('object,embed', full ? null : el).length > 0); + if (ie6 || expr) { + // give body 100% height + if (full && opts.allowBodyStretch && $.support.boxModel) + $('html,body').css('height','100%'); + + // fix ie6 issue when blocked element has a border width + if ((ie6 || !$.support.boxModel) && !full) { + var t = sz(el,'borderTopWidth'), l = sz(el,'borderLeftWidth'); + var fixT = t ? '(0 - '+t+')' : 0; + var fixL = l ? '(0 - '+l+')' : 0; + } + + // simulate fixed position + $.each(layers, function(i,o) { + var s = o[0].style; + s.position = 'absolute'; + if (i < 2) { + if (full) + s.setExpression('height','Math.max(document.body.scrollHeight, document.body.offsetHeight) - (jQuery.support.boxModel?0:'+opts.quirksmodeOffsetHack+') + "px"'); + else + s.setExpression('height','this.parentNode.offsetHeight + "px"'); + if (full) + s.setExpression('width','jQuery.support.boxModel && document.documentElement.clientWidth || document.body.clientWidth + "px"'); + else + s.setExpression('width','this.parentNode.offsetWidth + "px"'); + if (fixL) s.setExpression('left', fixL); + if (fixT) s.setExpression('top', fixT); + } + else if (opts.centerY) { + if (full) s.setExpression('top','(document.documentElement.clientHeight || document.body.clientHeight) / 2 - (this.offsetHeight / 2) + (blah = document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop) + "px"'); + s.marginTop = 0; + } + else if (!opts.centerY && full) { + var top = (opts.css && opts.css.top) ? parseInt(opts.css.top, 10) : 0; + var expression = '((document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop) + '+top+') + "px"'; + s.setExpression('top',expression); + } + }); + } + + // show the message + if (msg) { + if (opts.theme) + lyr3.find('.ui-widget-content').append(msg); + else + lyr3.append(msg); + if (msg.jquery || msg.nodeType) + $(msg).show(); + } + + if ((msie || opts.forceIframe) && opts.showOverlay) + lyr1.show(); // opacity is zero + if (opts.fadeIn) { + var cb = opts.onBlock ? opts.onBlock : noOp; + var cb1 = (opts.showOverlay && !msg) ? cb : noOp; + var cb2 = msg ? cb : noOp; + if (opts.showOverlay) + lyr2._fadeIn(opts.fadeIn, cb1); + if (msg) + lyr3._fadeIn(opts.fadeIn, cb2); + } + else { + if (opts.showOverlay) + lyr2.show(); + if (msg) + lyr3.show(); + if (opts.onBlock) + opts.onBlock.bind(lyr3)(); + } + + // bind key and mouse events + bind(1, el, opts); + + if (full) { + pageBlock = lyr3[0]; + pageBlockEls = $(opts.focusableElements,pageBlock); + if (opts.focusInput) + setTimeout(focus, 20); + } + else + center(lyr3[0], opts.centerX, opts.centerY); + + if (opts.timeout) { + // auto-unblock + var to = setTimeout(function() { + if (full) + $.unblockUI(opts); + else + $(el).unblock(opts); + }, opts.timeout); + $(el).data('blockUI.timeout', to); + } + } + + // remove the block + function remove(el, opts) { + var count; + var full = (el == window); + var $el = $(el); + var data = $el.data('blockUI.history'); + var to = $el.data('blockUI.timeout'); + if (to) { + clearTimeout(to); + $el.removeData('blockUI.timeout'); + } + opts = $.extend({}, $.blockUI.defaults, opts || {}); + bind(0, el, opts); // unbind events + + if (opts.onUnblock === null) { + opts.onUnblock = $el.data('blockUI.onUnblock'); + $el.removeData('blockUI.onUnblock'); + } + + var els; + if (full) // crazy selector to handle odd field errors in ie6/7 + els = $('body').children().filter('.blockUI').add('body > .blockUI'); + else + els = $el.find('>.blockUI'); + + // fix cursor issue + if ( opts.cursorReset ) { + if ( els.length > 1 ) + els[1].style.cursor = opts.cursorReset; + if ( els.length > 2 ) + els[2].style.cursor = opts.cursorReset; + } + + if (full) + pageBlock = pageBlockEls = null; + + if (opts.fadeOut) { + count = els.length; + els.stop().fadeOut(opts.fadeOut, function() { + if ( --count === 0) + reset(els,data,opts,el); + }); + } + else + reset(els, data, opts, el); + } + + // move blocking element back into the DOM where it started + function reset(els,data,opts,el) { + var $el = $(el); + if ( $el.data('blockUI.isBlocked') ) + return; + + els.each(function(i,o) { + // remove via DOM calls so we don't lose event handlers + if (this.parentNode) + this.parentNode.removeChild(this); + }); + + if (data && data.el) { + data.el.style.display = data.display; + data.el.style.position = data.position; + data.el.style.cursor = 'default'; // #59 + if (data.parent) + data.parent.appendChild(data.el); + $el.removeData('blockUI.history'); + } + + if ($el.data('blockUI.static')) { + $el.css('position', 'static'); // #22 + } + + if (typeof opts.onUnblock == 'function') + opts.onUnblock(el,opts); + + // fix issue in Safari 6 where block artifacts remain until reflow + var body = $(document.body), w = body.width(), cssW = body[0].style.width; + body.width(w-1).width(w); + body[0].style.width = cssW; + } + + // bind/unbind the handler + function bind(b, el, opts) { + var full = el == window, $el = $(el); + + // don't bother unbinding if there is nothing to unbind + if (!b && (full && !pageBlock || !full && !$el.data('blockUI.isBlocked'))) + return; + + $el.data('blockUI.isBlocked', b); + + // don't bind events when overlay is not in use or if bindEvents is false + if (!full || !opts.bindEvents || (b && !opts.showOverlay)) + return; + + // bind anchors and inputs for mouse and key events + var events = 'mousedown mouseup keydown keypress keyup touchstart touchend touchmove'; + if (b) + $(document).bind(events, opts, handler); + else + $(document).unbind(events, handler); + + // former impl... + // var $e = $('a,:input'); + // b ? $e.bind(events, opts, handler) : $e.unbind(events, handler); + } + + // event handler to suppress keyboard/mouse events when blocking + function handler(e) { + // allow tab navigation (conditionally) + if (e.type === 'keydown' && e.keyCode && e.keyCode == 9) { + if (pageBlock && e.data.constrainTabKey) { + var els = pageBlockEls; + var fwd = !e.shiftKey && e.target === els[els.length-1]; + var back = e.shiftKey && e.target === els[0]; + if (fwd || back) { + setTimeout(function(){focus(back);},10); + return false; + } + } + } + var opts = e.data; + var target = $(e.target); + if (target.hasClass('blockOverlay') && opts.onOverlayClick) + opts.onOverlayClick(e); + + // allow events within the message content + if (target.parents('div.' + opts.blockMsgClass).length > 0) + return true; + + // allow events for content that is not being blocked + return target.parents().children().filter('div.blockUI').length === 0; + } + + function focus(back) { + if (!pageBlockEls) + return; + var e = pageBlockEls[back===true ? pageBlockEls.length-1 : 0]; + if (e) + e.focus(); + } + + function center(el, x, y) { + var p = el.parentNode, s = el.style; + var l = ((p.offsetWidth - el.offsetWidth)/2) - sz(p,'borderLeftWidth'); + var t = ((p.offsetHeight - el.offsetHeight)/2) - sz(p,'borderTopWidth'); + if (x) s.left = l > 0 ? (l+'px') : '0'; + if (y) s.top = t > 0 ? (t+'px') : '0'; + } + + function sz(el, p) { + return parseInt($.css(el,p),10)||0; + } + + } + + + /*global define:true */ + if (typeof define === 'function' && define.amd && define.amd.jQuery) { + define(['jquery'], setup); + } else { + setup(jQuery); + } + +})(); \ No newline at end of file From 3ad6ec4c45a2087a78a7f0f6c9e76aa44effccdc Mon Sep 17 00:00:00 2001 From: John McNeil Date: Mon, 10 Jul 2017 13:57:42 -0700 Subject: [PATCH 084/576] fixed styling with Fiona --- .../client/ACASFormStateDisplayUpdate.coffee | 14 +++---- .../src/client/ACASFormStateDisplayView.html | 39 ++++++++++--------- 2 files changed, 27 insertions(+), 26 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee index 8aa18cdba..fafde6332 100644 --- a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee +++ b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee @@ -30,6 +30,8 @@ class window.ACASFormStateDisplayUpdateCellController extends Backbone.View else val = @collection.findWhere ignored: false content = val.get(val.get('lsType')) + if val.get('lsType') == 'dateValue' + content = UtilityFunctions::convertMSToYMDDate val.get('dateValue') $(@el).html content $(@el).addClass if @collection.length > 1 then "valueWasEdited" else "" @@ -227,9 +229,9 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View model: val @$("tbody").append oldRow.render().el @setupEditor() - @$('.bv_myPanel').modal + @$('.bv_aCASFormStateDisplayValueEdit').modal backdrop: "static" - @$('.bv_myPanel').modal "show" + @$('.bv_aCASFormStateDisplayValueEdit').modal "show" reasonForUpdateChanged: -> @comment = @commentPrefix + @$('.bv_reasonForUpdate').val() @@ -244,7 +246,7 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View @$('.bv_saveBtn').removeAttr('disabled') handleCancelClicked: => - @$('.bv_myPanel').modal "hide" + @$('.bv_aCASFormStateDisplayValueEdit').modal "hide" $(@el).empty() handleSaveClicked: => @@ -253,7 +255,7 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View comment: @comment stateID: @options.stateID - @$('.bv_myPanel').modal "hide" + @$('.bv_aCASFormStateDisplayValueEdit').modal "hide" $(@el).empty() @@ -292,8 +294,6 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View #TODO value editor: # - maybe show transaction creator as modified by and date? -# - style value editor so it floats or slides down from top of table or something. It should be modal -# - trigger save at thing level, wait for success to close -# - pass reason to thing to add to transaction # - add new value where none existed? +# show human readable codevalue instead of code diff --git a/modules/Components/src/client/ACASFormStateDisplayView.html b/modules/Components/src/client/ACASFormStateDisplayView.html index f41cd0bce..806516371 100644 --- a/modules/Components/src/client/ACASFormStateDisplayView.html +++ b/modules/Components/src/client/ACASFormStateDisplayView.html @@ -20,30 +20,31 @@
      launching controller must provide or set table label \ No newline at end of file From ca9e66d1ce5e41016900f6334b56076b9026c278 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 11 Jul 2017 13:39:01 -0700 Subject: [PATCH 088/576] Renamed variables for controllers to more descriptive names, and removed unnecessary log statements. --- .../src/client/ACASFormMultiLabel.coffee | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/modules/Components/src/client/ACASFormMultiLabel.coffee b/modules/Components/src/client/ACASFormMultiLabel.coffee index 51726ba61..d44f69e20 100644 --- a/modules/Components/src/client/ACASFormMultiLabel.coffee +++ b/modules/Components/src/client/ACASFormMultiLabel.coffee @@ -18,17 +18,17 @@ class window.ACASFormMultiLabelController extends Backbone.View url: @options.url thingRef: @options.thingRef insertUnassigned: @options.insertUnassigned - @lc = new ACASFormLSLabelFieldController options + @labelController = new ACASFormLSLabelFieldController options render: -> $(@el).empty() $(@el).html @template() - @$('.bv_multiLabel').html @lc.render().el - @lc.renderModelContent() + @$('.bv_multiLabel').html @labelController.render().el + @labelController.renderModelContent() @ handleRemoveLabelButtonClicked: -> - @lc.setEmptyValue() + @labelController.setEmptyValue() $(@el).hide() @@ -79,10 +79,9 @@ class window.ACASFormMultiLabelListController extends ACASFormAbstractFieldContr addOneLabel: (label) -> labelOpts = @opts labelOpts.labelKey = label.get('key') - lc = new ACASFormMultiLabelController labelOpts - console.log label.get('key') - @$('.bv_multiLabels').append lc.render().el - lc.on 'updateState', => + multiLabelController = new ACASFormMultiLabelController labelOpts + @$('.bv_multiLabels').append multiLabelController.render().el + multiLabelController.on 'updateState', => @trigger 'updateState' From c5ddf884c23d47b2a19452c1caddcaededd3e3ca Mon Sep 17 00:00:00 2001 From: John McNeil Date: Tue, 11 Jul 2017 14:03:09 -0700 Subject: [PATCH 089/576] fixes #147 added Thing instance variable to disable this feature by default "noUpdateThingsInInteractions: false" --- modules/ServerAPI/src/client/Thing.coffee | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/modules/ServerAPI/src/client/Thing.coffee b/modules/ServerAPI/src/client/Thing.coffee index 4c1d20cf3..35e2be69a 100644 --- a/modules/ServerAPI/src/client/Thing.coffee +++ b/modules/ServerAPI/src/client/Thing.coffee @@ -2,6 +2,7 @@ class window.Thing extends Backbone.Model lsProperties: {} className: "Thing" deleteEmptyLabelsValsItxsBeforeSave: true + noUpdateThingsInInteractions: false # urlRoot: "/api/things" defaults: () -> @@ -287,10 +288,11 @@ class window.Thing extends Backbone.Model attachFileList reformatBeforeSaving: => - if @get('firstLsThings')? and @get('firstLsThings') instanceof FirstLsThingItxList - @get('firstLsThings').reformatBeforeSaving() - if @get('secondLsThings')? and @get('secondLsThings') instanceof SecondLsThingItxList - @get('secondLsThings').reformatBeforeSaving() + if @noUpdateThingsInInteractions? && @noUpdateThingsInInteractions + if @get('firstLsThings')? and @get('firstLsThings') instanceof FirstLsThingItxList + @get('firstLsThings').reformatBeforeSaving() + if @get('secondLsThings')? and @get('secondLsThings') instanceof SecondLsThingItxList + @get('secondLsThings').reformatBeforeSaving() deleteInteractions : => From 5a5094c9e121bbfa0c8bbb452985b382906de34a Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 11 Jul 2017 19:18:21 -0700 Subject: [PATCH 090/576] Added uniqueness validation to ACASFormStateTable for columns with fieldSettings.unique: true following example from https://github.com/handsontable/handsontable/issues/3102 . Also passed through fieldSettings.format to control numeric formatting. --- .../src/client/ACASFormStateTable.coffee | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 61e413f02..83ececf09 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -128,6 +128,7 @@ class window.ACASFormStateTableController extends Backbone.View colOpts = data: val.modelDefaults.kind if val.modelDefaults.type == 'numericValue' colOpts.type = 'numeric' + colOpts.format = val.fieldSettings.format else if val.modelDefaults.type == 'dateValue' colOpts.type = 'date' colOpts.dateFormat = 'YYYY-MM-DD' @@ -177,6 +178,7 @@ class window.ACASFormStateTableController extends Backbone.View if @tableReadOnly cellProperties.readOnly = true return cellProperties; + @hot.addHook 'afterChange', @validateUniqueness readOnlyRenderer: (instance, td, row, col, prop, value, cellProperties) => Handsontable.renderers.TextRenderer.apply(this, arguments) @@ -384,5 +386,29 @@ class window.ACASFormStateTableController extends Backbone.View # manualRowResize: true # comments: true + validateUniqueness: (changes, source) => + uniqueColumnIndices = @tableDef.values.map (value, idx) -> + if value.fieldSettings.unique? and value.fieldSettings.unique + idx + else + null + uniqueColumnIndices = uniqueColumnIndices.filter (idx) -> + idx? + _.each uniqueColumnIndices, (columnIndex) => + column = @hot.getDataAtCol columnIndex + column.forEach (value, row) => + data = extend [], column + idx = data.indexOf value + data.splice idx, 1 + secondIdx = data.indexOf value + cell = @hot.getCellMeta row, columnIndex + if idx > -1 and secondIdx > -1 and value? and value != '' + cell.valid = false + cell.comment = 'Error: Duplicates not allowed' + else + cell.valid = true + cell.comment = '' + @hot.render() + From 0df201d4f5ed980b6923c6fe6c7be26bc763ca23 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 12 Jul 2017 09:52:22 -0700 Subject: [PATCH 091/576] Enabled comments on StateTable Handsontable to show duplicate comment. Added examples of MultiAlias, unique column, and number formatting to ExampleThing --- .../src/client/ACASFormStateTable.coffee | 1 + modules/ServerAPI/src/client/ExampleThing.coffee | 16 ++++++++++++++++ modules/ServerAPI/src/client/ExampleThing.html | 1 + 3 files changed, 18 insertions(+) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 83ececf09..fa8e516a1 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -164,6 +164,7 @@ class window.ACASFormStateTableController extends Backbone.View minSpareRows: 1, allowInsertRow: true contextMenu: true + comments: true startRows: 1, className: "htCenter", colHeaders: _.pluck @colHeaders, 'displayName' diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index a71e17eb0..3e40e39b8 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -13,6 +13,20 @@ ExampleThingConf = formLabel: "*Name" placeholder: "name" fieldWrapper: "bv_thingName" + , + key: 'alias_' + multiple: true + modelDefaults: + type: 'name' + kind: 'alias' + preferred: false + fieldSettings: + fieldType: 'label' + required: false + inputClass: "" + formLabel: "Alias" + placeholder: "alias" + fieldWrapper: "bv_aliasWrapper" ] values: [ key: 'scientist' @@ -91,6 +105,7 @@ ExampleThingConf = fieldType: 'stringValue' formLabel: "Media Component" required: true + unique: true width: 215 , modelDefaults: @@ -102,6 +117,7 @@ ExampleThingConf = fieldSettings: fieldType: 'numericValue' formLabel: "Volume" + format: "0.00" required: false , modelDefaults: diff --git a/modules/ServerAPI/src/client/ExampleThing.html b/modules/ServerAPI/src/client/ExampleThing.html index 90ebebdb0..2fa223aca 100644 --- a/modules/ServerAPI/src/client/ExampleThing.html +++ b/modules/ServerAPI/src/client/ExampleThing.html @@ -9,6 +9,7 @@
      Thing Registration
      +
      From f12bd97f2049b38672fa37f63cc52f14a7eec763 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 12 Jul 2017 10:29:10 -0700 Subject: [PATCH 092/576] Uncommented options for disabling/enabling comments option as part of State Table disableInput / enableInput. Fixes console error relating to comments when state table is in readOnly mode. --- modules/Components/src/client/ACASFormStateTable.coffee | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index fa8e516a1..2531b4446 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -371,21 +371,21 @@ class window.ACASFormStateTableController extends Backbone.View @hot.updateSettings readOnly: true contextMenu: false + comments: false #Other options I decided not to use # disableVisualSelection: true # manualColumnResize: false # manualRowResize: false -# comments: false enableInput: -> @hot.updateSettings readOnly: false contextMenu: true + comments: true #Other options I decided not to use # disableVisualSelection: false # manualColumnResize: true # manualRowResize: true -# comments: true validateUniqueness: (changes, source) => uniqueColumnIndices = @tableDef.values.map (value, idx) -> From f90ef2e24527c4725b3ee1eb8b2148ca65e50401 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 12 Jul 2017 11:46:42 -0700 Subject: [PATCH 093/576] Update loginRoutes.coffee --- modules/Login/src/server/routes/loginRoutes.coffee | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/modules/Login/src/server/routes/loginRoutes.coffee b/modules/Login/src/server/routes/loginRoutes.coffee index c43f6b97c..5ee25e9b1 100644 --- a/modules/Login/src/server/routes/loginRoutes.coffee +++ b/modules/Login/src/server/routes/loginRoutes.coffee @@ -79,8 +79,6 @@ exports.logout = (req, res) -> exports.ensureAuthenticated = (req, res, next) -> console.log "checking for login for path: "+req.url - console.log "req" - console.log req if req.isAuthenticated() return next() if req.session? @@ -223,4 +221,4 @@ exports.getAuthors = (req, resp) -> baseEntityServiceTestJSON = require '../src/javascripts/spec/testFixtures/BaseEntityServiceTestJSON.js' resp.end JSON.stringify baseEntityServiceTestJSON.authorsList else - csUtilities.getAuthors req, resp \ No newline at end of file + csUtilities.getAuthors req, resp From 63785822a4f3265cb8ce32c001a32318f4c4f7a9 Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Thu, 13 Jul 2017 17:42:00 -0400 Subject: [PATCH 094/576] Issue 153: Implement node route for getContainerStatesByContainerValue with like, rightLike, maxResults and with parameters. --- .../routes/InventoryServiceRoutes.coffee | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index b00256b05..5508ef32d 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -54,6 +54,8 @@ exports.setupAPIRoutes = (app) -> app.post '/api/throwInTrash', exports.throwInTrash app.post '/api/updateContainerHistoryLogs', exports.updateContainerHistoryLogs app.post '/api/getContainerInfoFromBatchCode', exports.getContainerInfoFromBatchCode + app.post '/api/getContainerStatesByContainerValue', exports.getContainerStatesByContainerValue + exports.setupRoutes = (app, loginRoutes) -> app.post '/api/getContainersInLocationWithTypeAndKind', loginRoutes.ensureAuthenticated, exports.getContainersInLocationWithTypeAndKind @@ -103,6 +105,8 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/throwInTrash', loginRoutes.ensureAuthenticated, exports.throwInTrash app.post '/api/updateContainerHistoryLogs', loginRoutes.ensureAuthenticated, exports.updateContainerHistoryLogs app.post '/api/getContainerInfoFromBatchCode', loginRoutes.ensureAuthenticated, exports.getContainerInfoFromBatchCode + app.post '/api/getContainerStatesByContainerValue', loginRoutes.ensureAuthenticated, exports.getContainerStatesByContainerValue + exports.getContainersInLocation = (req, resp) -> req.setTimeout 86400000 @@ -2368,3 +2372,56 @@ exports.getContainerInfoFromBatchCodeInternal = (requestObject, callback) => else return callback {warningMessage: "No results found for #{queryPayload.value}"}, statusCode ) + +exports.getContainerStatesByContainerValue = (req, resp) => + + exports.getContainerStatesByContainerValueInternal(req.body, (json, statusCode) => + resp.statusCode = statusCode + resp.json json + ) + +exports.getContainerStatesByContainerValueInternal = (requestObject, callback) => + + queryParams = [] + if requestObject.like? + queryParams.push "like="+requestObject.like + if requestObject.rightLike? + queryParams.push "rightLike="+requestObject.rightLike + if requestObject.maxResults? + queryParams.push "maxResults="+requestObject.maxResults + if requestObject.with? + queryParams.push "with="+requestObject.with + queryString = queryParams.join "&" + + + queryPayload = + { + containerType: requestObject.containerType + containerKind: requestObject.containerKind + stateType: requestObject.stateType + stateKind: requestObject.stateKind + valueType: requestObject.valueType + valueKind: requestObject.valueKind + value: requestObject.value + } + + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containerstates/getContainerStatesByContainerValue?"+queryString + request = require 'request' + request( + method: 'POST' + url: baseurl + body: queryPayload + json: true + timeout: 86400000 + , (error, response, json) => + if !error && response.statusCode == 200 + callback json, response.statusCode + else + console.error 'got ajax error trying to get getContainerStatesByContainerValue' + console.error error + console.error json + console.error response + callback null, 500 + #resp.end JSON.stringify "getContainerStatesByContainerValue failed" + ) From 3a3f1f9157ec47844b557bc874793429ab3ebb32 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 13 Jul 2017 15:15:37 -0700 Subject: [PATCH 095/576] Added input-append div to allow for proper display of datepicker. icon-th is now wrapped in a box as intended. Fixes #155 --- modules/Components/src/client/ACASFormFieldsView.html | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/modules/Components/src/client/ACASFormFieldsView.html b/modules/Components/src/client/ACASFormFieldsView.html index 86a50c112..004058afe 100644 --- a/modules/Components/src/client/ACASFormFieldsView.html +++ b/modules/Components/src/client/ACASFormFieldsView.html @@ -34,9 +34,11 @@ From a4458202e1a712a1098c816a03a3d73917bca0ea Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Fri, 14 Jul 2017 10:12:04 -0400 Subject: [PATCH 096/576] Issue #158: New service to get container logs from container codes. --- .../routes/InventoryServiceRoutes.coffee | 34 ++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 5508ef32d..9713442f6 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -55,6 +55,7 @@ exports.setupAPIRoutes = (app) -> app.post '/api/updateContainerHistoryLogs', exports.updateContainerHistoryLogs app.post '/api/getContainerInfoFromBatchCode', exports.getContainerInfoFromBatchCode app.post '/api/getContainerStatesByContainerValue', exports.getContainerStatesByContainerValue + app.post '/api/getContainerLogsByContainerCodes', exports.getContainerLogsByContainerCodes exports.setupRoutes = (app, loginRoutes) -> @@ -106,7 +107,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/updateContainerHistoryLogs', loginRoutes.ensureAuthenticated, exports.updateContainerHistoryLogs app.post '/api/getContainerInfoFromBatchCode', loginRoutes.ensureAuthenticated, exports.getContainerInfoFromBatchCode app.post '/api/getContainerStatesByContainerValue', loginRoutes.ensureAuthenticated, exports.getContainerStatesByContainerValue - + app.post '/api/getContainerLogsByContainerCodes', loginRoutes.ensureAuthenticated, exports.getContainerLogsByContainerCodes exports.getContainersInLocation = (req, resp) -> req.setTimeout 86400000 @@ -1855,6 +1856,37 @@ exports.getContainerLogsInternal = (labels, containerType, containerKind, labelT response.push responseObject callback response, 200 +exports.getContainerLogsByContainerCodes = (req, resp) -> + req.setTimeout 86400000 + + exports.getContainerLogsByContainerCodesInternal req.body, (json, statusCode) -> + resp.statusCode = statusCode + resp.json json + +exports.getContainerLogsByContainerCodesInternal = (containerCodes, callback) => + console.log 'containerCodes', containerCodes + if global.specRunnerTestmode + inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' + resp.json inventoryServiceTestJSON.getContainerAndDefinitionContainerByContainerLabelInternalResponse + else + console.debug "incoming getContainerLogsByContainerCodesInternal request: '#{JSON.stringify(containerCodes)}'" + exports.getContainersByCodeNamesInternal(containerCodes, (containersByCodeNamesResponse, statusCode) => + response = [] + for getContainer in containersByCodeNamesResponse + label = getContainer.container.lsLabels[0].labelText + codeName = getContainer.container.codeName + responseObject = + label: label + codeName: codeName + logs: [] + if getContainer.container? + container = getContainerModels([getContainer]) + responseObject.logs = container[0].getLogs() + response.push responseObject + callback response, 200 + ) + + exports.getContainerLocationHistory = (req, resp) -> exports.getContainerLocationHistoryInternal [req.params.label], req.query.containerType, req.query.containerKind, req.query.labelType, req.query.labelKind, (json, statusCode) -> resp.statusCode = statusCode From f7794f5027d947315f4181d9f927291b81bfd2dd Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Fri, 14 Jul 2017 10:14:50 -0400 Subject: [PATCH 097/576] Removed console.log statement. --- .../ServerAPI/src/server/routes/InventoryServiceRoutes.coffee | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 9713442f6..f1cff56b6 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -1864,7 +1864,6 @@ exports.getContainerLogsByContainerCodes = (req, resp) -> resp.json json exports.getContainerLogsByContainerCodesInternal = (containerCodes, callback) => - console.log 'containerCodes', containerCodes if global.specRunnerTestmode inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' resp.json inventoryServiceTestJSON.getContainerAndDefinitionContainerByContainerLabelInternalResponse From fe9ce91da38394c8c0e526738470b1a84ce0bb6c Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Fri, 14 Jul 2017 11:34:59 -0400 Subject: [PATCH 098/576] Implemented the "preferred label" fix. --- .../src/server/routes/InventoryServiceRoutes.coffee | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index f1cff56b6..697b107f6 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -1872,10 +1872,13 @@ exports.getContainerLogsByContainerCodesInternal = (containerCodes, callback) => exports.getContainersByCodeNamesInternal(containerCodes, (containersByCodeNamesResponse, statusCode) => response = [] for getContainer in containersByCodeNamesResponse - label = getContainer.container.lsLabels[0].labelText + lsLabels = getContainer.container.lsLabels + preferredLabelObject = _.filter(lsLabels, (label) -> + label.preferred == true + ) codeName = getContainer.container.codeName responseObject = - label: label + label: preferredLabelObject[0].labelText codeName: codeName logs: [] if getContainer.container? From 5aa8164c9b244cc2f76b8d81c860965d885cbdce Mon Sep 17 00:00:00 2001 From: John McNeil Date: Fri, 14 Jul 2017 09:05:47 -0700 Subject: [PATCH 099/576] Fixes #157 Adds feature for File Form Field. Also small fix to multiple alias form field in Example Thing --- .../src/client/ACASFormFields.coffee | 89 +++++++++++++++++++ .../src/client/ACASFormFieldsView.html | 8 ++ .../src/client/ACASFormMultiLabel.coffee | 2 + .../src/client/AbstractFormController.coffee | 3 + .../ServerAPI/src/client/ExampleThing.coffee | 66 +++----------- .../ServerAPI/src/client/ExampleThing.html | 7 -- .../src/server/ControllerRedirectConf.coffee | 5 ++ 7 files changed, 121 insertions(+), 59 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index de724b2a4..473dd5ab9 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -510,3 +510,92 @@ class window.ACASFormLSDateValueFieldController extends ACASFormAbstractFieldCon handleDateIconClicked: => @$('input').datepicker( "show" ) + + +class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldController + ### + Launching controller must: + - Initialize the model with an LSValue + - Provide allowedFileTypes + Do whatever else is required or optional in ACASFormAbstractFieldController + ### + + template: _.template($("#ACASFormLSFileValueFieldView").html()) + events: -> + "click .bv_deleteSavedFile": "handleDeleteSavedFile" + + applyOptions: -> + super() + if @options.allowedFileTypes? + @allowedFileTypes = @options.allowedFileTypes + else + @allowedFileTypes = ['csv','xlsx','xls','png','jpeg'] + + render: -> + super() + @setupFileController() + + @ + + handleInputChanged: => + @clearError() + @userInputEvent = true + value = UtilityFunctions::convertYMDDateToMs(UtilityFunctions::getTrimmedInput(@$('input'))) + if value == "" || isNaN(value) + @setEmptyValue() + else + @getModel().set + value: value + ignored: false + super() + + setEmptyValue: -> + @getModel().set + value: null + ignored: true + + renderModelContent: => + @setupFileController() + super() + + setupFileController: -> + fileValue = @getModel().get('value') + if @isEmpty() + @createNewFileChooser() + @$('.bv_deleteSavedFile').hide() + else + @$('.bv_File').html ''+@getModel().get('comments')+'' + @$('.bv_deleteSavedFile').show() + + createNewFileChooser: -> + if @fileController? + @fileController.render() + else + @fileController = new LSFileChooserController + el: @$('.bv_File') + formId: 'fieldBlah', + maxNumberOfFiles: 1, + requiresValidation: false + url: UtilityFunctions::getFileServiceURL() + allowedFileTypes: @allowedFileTypes + hideDelete: false + @fileController.on 'amDirty', => + @trigger 'amDirty' + @fileController.on 'amClean', => + @trigger 'amClean' + @fileController.render() + @fileController.on('fileUploader:uploadComplete', @handleFileUpload) #update model with filename + @fileController.on('fileDeleted', @handleFileRemoved) #update model with filename + + handleFileUpload: (nameOnServer) => + @getModel().set + value: nameOnServer + ignored: false + + handleFileRemoved: => + @setEmptyValue() + + handleDeleteSavedFile: => + @handleFileRemoved() + @$('.bv_deleteSavedFile').hide() + @createNewFileChooser() diff --git a/modules/Components/src/client/ACASFormFieldsView.html b/modules/Components/src/client/ACASFormFieldsView.html index 86a50c112..c6ceb1808 100644 --- a/modules/Components/src/client/ACASFormFieldsView.html +++ b/modules/Components/src/client/ACASFormFieldsView.html @@ -56,3 +56,11 @@
      + + diff --git a/modules/Components/src/client/ACASFormMultiLabel.coffee b/modules/Components/src/client/ACASFormMultiLabel.coffee index d44f69e20..c75686fe4 100644 --- a/modules/Components/src/client/ACASFormMultiLabel.coffee +++ b/modules/Components/src/client/ACASFormMultiLabel.coffee @@ -61,6 +61,8 @@ class window.ACASFormMultiLabelListController extends ACASFormAbstractFieldContr @addNewLabel() addNewLabel: (skipAmDirtyTrigger) => + console.log "addNewLabel" + console.log @opts keyBase = @modelKey newModel = new Label lsType: @opts.modelDefaults.type diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 1bd8500a8..f31b2c76d 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -104,6 +104,8 @@ class window.AbstractThingFormController extends AbstractFormController thingRef: @model insertUnassigned: field.fieldSettings.insertUnassigned modelDefaults: field.modelDefaults + allowedFileTypes: field.fieldSettings.allowedFileTypes + switch field.fieldSettings.fieldType when 'label' if field.multiple? and field.multiple @@ -123,6 +125,7 @@ class window.AbstractThingFormController extends AbstractFormController newField = new ACASFormLSThingInteractionFieldController opts when 'stringValue' then newField = new ACASFormLSStringValueFieldController opts when 'dateValue' then newField = new ACASFormLSDateValueFieldController opts + when 'fileValue' then newField = new ACASFormLSFileValueFieldController opts @$("."+field.fieldSettings.fieldWrapper).append newField.render().el newField.afterRender() diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index 3e40e39b8..0f0e04570 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -87,6 +87,19 @@ ExampleThingConf = fieldWrapper: "bv_notebook" placeholder: "notebook and page" required: false + , + key: 'exampleFile' + modelDefaults: + stateType: 'metadata' + stateKind: 'example thing parent' + type: 'fileValue' + kind: 'example file' + value: "" + fieldSettings: + fieldType: 'fileValue' + formLabel: "Example File" + fieldWrapper: "bv_notebook" + required: false ] @@ -159,8 +172,6 @@ ExampleThingConf = firstLsThingItxs: [] secondLsThingItxs: [] - - class window.ExampleThingParent extends Thing urlRoot: "/api/things/parent/example thing" url: -> @@ -176,6 +187,7 @@ class window.ExampleThingParent extends Thing lsKind: "Example Thing" for label in ExampleThingConf.formFieldDefinitions.labels label.modelDefaults.key = label.key + label.modelDefaults.multiple = label.multiple @lsProperties.defaultLabels.push label.modelDefaults for value in ExampleThingConf.formFieldDefinitions.values value.modelDefaults.key = value.key @@ -192,12 +204,6 @@ class window.ExampleThingParent extends Thing defaultLabels: [ ] defaultValues: [ - key: 'structural file' - stateType: 'metadata' - stateKind: 'example thing parent' - type: 'fileValue' - kind: 'structural file' - value: "" ] defaultFirstLsThingItx: [ @@ -226,7 +232,6 @@ class window.ExampleThingController extends AbstractThingFormController events: -> "click .bv_saveThing": "handleUpdateThing" - "click .bv_deleteSavedFile": "handleDeleteSavedStructuralFile" initialize: => @hasRendered = false @@ -253,7 +258,6 @@ class window.ExampleThingController extends AbstractThingFormController $(@el).empty() $(@el).html @template(@model.attributes) @setupFormFields(ExampleThingConf.formFieldDefinitions) - @setupStructuralFileController() @hasRendered = true @ @@ -289,49 +293,8 @@ class window.ExampleThingController extends AbstractThingFormController @trigger 'amDirty' @$('.bv_saveThingComplete').hide() - setupStructuralFileController: => - structuralFileValue = @model.get('structural file').get('value') - if structuralFileValue is null or structuralFileValue is "" or structuralFileValue is undefined - @createNewFileChooser() - @$('.bv_deleteSavedFile').hide() - else - @$('.bv_structuralFile').html ''+@model.get('structural file').get('comments')+'' - @$('.bv_deleteSavedFile').show() - - createNewFileChooser: => - @structuralFileController = new LSFileChooserController - el: @$('.bv_structuralFile') - formId: 'fieldBlah', - maxNumberOfFiles: 1, - requiresValidation: false - url: UtilityFunctions::getFileServiceURL() - allowedFileTypes: ['png', 'jpeg'] - hideDelete: false - @structuralFileController.on 'amDirty', => - @trigger 'amDirty' - @structuralFileController.on 'amClean', => - @trigger 'amClean' - @structuralFileController.render() - @structuralFileController.on('fileUploader:uploadComplete', @handleFileUpload) #update model with filename - @structuralFileController.on('fileDeleted', @handleFileRemoved) #update model with filename - - handleFileUpload: (nameOnServer) => - newFileValue = @model.get('lsStates').getOrCreateValueByTypeAndKind "metadata", "example thing parent", "fileValue", "structural file" - @model.set "structural file", newFileValue - @model.get("structural file").set("value", nameOnServer) - - handleFileRemoved: => - @model.get("structural file").set("ignored", true) - @model.unset "structural file" - - handleDeleteSavedStructuralFile: => - @handleFileRemoved() - @$('.bv_deleteSavedFile').hide() - @createNewFileChooser() - updateModel: => - validationError: => super() @$('.bv_saveThing').attr('disabled', 'disabled') @@ -358,4 +321,3 @@ class window.ExampleThingController extends AbstractThingFormController #TODO add thing interaction to project with field -#TODO file upload is broken diff --git a/modules/ServerAPI/src/client/ExampleThing.html b/modules/ServerAPI/src/client/ExampleThing.html index 2fa223aca..7894fb879 100644 --- a/modules/ServerAPI/src/client/ExampleThing.html +++ b/modules/ServerAPI/src/client/ExampleThing.html @@ -15,13 +15,6 @@
      Thing Registration
      -
      - -
      -
      - -
      -
      diff --git a/modules/ServerAPI/src/server/ControllerRedirectConf.coffee b/modules/ServerAPI/src/server/ControllerRedirectConf.coffee index a5e432b2b..8f51b21b1 100644 --- a/modules/ServerAPI/src/server/ControllerRedirectConf.coffee +++ b/modules/ServerAPI/src/server/ControllerRedirectConf.coffee @@ -29,6 +29,11 @@ "project": deepLink: "project" relatedFilesRelativePath: "entities/projects" + THING: + entityName: "example thing" + "Example Thing": + deepLink: "example_thing" + relatedFilesRelativePath: "entities/exampleThings" PT: entityName: "parent thing" default: From 12db280ece09477420bf2463cefda2b07bfd5468 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Fri, 14 Jul 2017 09:09:12 -0700 Subject: [PATCH 100/576] cleanup log statements --- modules/Components/src/client/ACASFormMultiLabel.coffee | 2 -- 1 file changed, 2 deletions(-) diff --git a/modules/Components/src/client/ACASFormMultiLabel.coffee b/modules/Components/src/client/ACASFormMultiLabel.coffee index c75686fe4..d44f69e20 100644 --- a/modules/Components/src/client/ACASFormMultiLabel.coffee +++ b/modules/Components/src/client/ACASFormMultiLabel.coffee @@ -61,8 +61,6 @@ class window.ACASFormMultiLabelListController extends ACASFormAbstractFieldContr @addNewLabel() addNewLabel: (skipAmDirtyTrigger) => - console.log "addNewLabel" - console.log @opts keyBase = @modelKey newModel = new Label lsType: @opts.modelDefaults.type From 5c36ae1cbdffde3b8f97c2e4017555ea9f149461 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Fri, 14 Jul 2017 09:38:34 -0700 Subject: [PATCH 101/576] cleanup code --- modules/Components/src/client/ACASFormFields.coffee | 7 +++---- modules/Components/src/client/ACASFormFieldsView.html | 2 +- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 473dd5ab9..64ce1cada 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -564,7 +564,7 @@ class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldCon @createNewFileChooser() @$('.bv_deleteSavedFile').hide() else - @$('.bv_File').html ''+@getModel().get('comments')+'' + @$('.bv_file').html ''+@getModel().get('comments')+'' @$('.bv_deleteSavedFile').show() createNewFileChooser: -> @@ -572,9 +572,8 @@ class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldCon @fileController.render() else @fileController = new LSFileChooserController - el: @$('.bv_File') - formId: 'fieldBlah', - maxNumberOfFiles: 1, + el: @$('.bv_file') + maxNumberOfFiles: 1 requiresValidation: false url: UtilityFunctions::getFileServiceURL() allowedFileTypes: @allowedFileTypes diff --git a/modules/Components/src/client/ACASFormFieldsView.html b/modules/Components/src/client/ACASFormFieldsView.html index c6ceb1808..4292def95 100644 --- a/modules/Components/src/client/ACASFormFieldsView.html +++ b/modules/Components/src/client/ACASFormFieldsView.html @@ -59,7 +59,7 @@ From d7b925916641ab978653dba9a654f9b5aafbee78 Mon Sep 17 00:00:00 2001 From: Marjorie Principato Date: Fri, 14 Jul 2017 11:56:39 -0700 Subject: [PATCH 102/576] Fixes #162. Makes it so that moduleMenus looks at a config parameter to tell what the module menus should be --- conf/config.properties.example | 1 + modules/ModuleMenus/src/client/ModuleMenus.coffee | 7 ++++++- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 431a6ad42..f9d39b7d0 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -324,6 +324,7 @@ server.security.authstrategy=database client.moduleMenus.logoText=ACAS client.moduleMenus.homePageMessage=Welcome to ACAS client.moduleMenus.copyrightMessage=© John McNeil & Company 2012-2017 +# client.moduleMenus.menuConfigurationSettings=ModuleMenusConfiguration # If summary statistics is an included feature, set the following to true client.moduleMenus.summaryStats=false # For navigation to external ACAS modules from ACAS homepage diff --git a/modules/ModuleMenus/src/client/ModuleMenus.coffee b/modules/ModuleMenus/src/client/ModuleMenus.coffee index 292709773..c5f2ecdc0 100644 --- a/modules/ModuleMenus/src/client/ModuleMenus.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenus.coffee @@ -17,7 +17,12 @@ class window.ModuleMenusController extends Backbone.View $(@el).html @template() - @moduleLauncherList = new ModuleLauncherList(@options.menuListJSON) + if window.conf.moduleMenus.menuConfigurationSettings? + menuListJSON = window[window.conf.moduleMenus.menuConfigurationSettings] + else + menuListJSON = @options.menuListJSON + + @moduleLauncherList = new ModuleLauncherList(menuListJSON) @moduleLauncherMenuListController = new ModuleLauncherMenuListController el: @$('.bv_modLaunchMenuWrapper') collection: @moduleLauncherList From b58b068f357107056adb225b6531046f0e231bd5 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 14 Jul 2017 13:12:38 -0700 Subject: [PATCH 103/576] Added default value of false for newly required config client.entity.saveInitialsCorpName. Fixes #164 --- conf/config.properties.example | 3 +++ 1 file changed, 3 insertions(+) diff --git a/conf/config.properties.example b/conf/config.properties.example index 95851ae25..390fe3dfd 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -525,3 +525,6 @@ client.projectEditor.restrictedCheckbox.show=true client.projectEditor.isRestricted.default=false client.roles.crossProjectLoaderRole=ROLE_ACAS-CROSS-PROJECT-LOADER + +# For whether protocols and experiments should have sequential user defined corpName labels +client.entity.saveInitialsCorpName=false From a63a7c541085ab256f07780d66f3bbbe01f00442 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Fri, 14 Jul 2017 15:09:04 -0700 Subject: [PATCH 104/576] feature/state_table_display: bug fixes for state display table, add option to configure whether cells in state display table are editable --- .../client/ACASFormStateDisplayUpdate.coffee | 39 ++++++++++++------- .../src/client/ACASFormStateDisplayView.html | 2 +- modules/Components/src/client/style.css | 4 ++ 3 files changed, 29 insertions(+), 16 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee index fafde6332..95c3ead51 100644 --- a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee +++ b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee @@ -30,10 +30,13 @@ class window.ACASFormStateDisplayUpdateCellController extends Backbone.View else val = @collection.findWhere ignored: false content = val.get(val.get('lsType')) - if val.get('lsType') == 'dateValue' - content = UtilityFunctions::convertMSToYMDDate val.get('dateValue') + if val.get('lsType') == 'dateValue' + content = UtilityFunctions::convertMSToYMDDate val.get('dateValue') + $(@el).html content $(@el).addClass if @collection.length > 1 then "valueWasEdited" else "" + if @options.cellDef.editable? and !@options.cellDef.editable + $(@el).addClass 'valueNotEditable' @ @@ -95,6 +98,8 @@ class window.ACASFormStateDisplayUpdateController extends Backbone.View @$("tbody").append rowController.render().el rowController.on 'cellClicked', (values) => + if @currentCellEditor? + @currentCellEditor.undelegateEvents() @currentCellEditor = new ACASFormStateDisplayValueEditController collection: values el: @$('.bv_valueEditor') @@ -159,7 +164,7 @@ class window.ACASFormStateDisplayUpdateController extends Backbone.View modifiedDate: new Date().getTime() isDirty: true valInfo.newValue.set - recoerdedBy: window.AppLaunchParams.loginUser.username + recordedBy: window.AppLaunchParams.loginUser.username recordedDate: new Date().getTime() stateToUpdate.get('lsValues').add valInfo.newValue @@ -219,19 +224,22 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View render: => $(@el).empty() - $(@el).html @template() - @$('.bv_header').html "\"#{@valueDef.fieldSettings.formLabel}\" Value History and Edit" - @collection.comparator = 'id' - @collection.sort() - @collection.each (val) => - oldRow = new ACASFormStateDisplayOldValueController - model: val - @$("tbody").append oldRow.render().el - @setupEditor() - @$('.bv_aCASFormStateDisplayValueEdit').modal - backdrop: "static" - @$('.bv_aCASFormStateDisplayValueEdit').modal "show" + #only display editor if value is editable + if !@valueDef.editable? or (@valueDef.editable? and @valueDef.editable) + $(@el).html @template() + + @$('.bv_header').html "\"#{@valueDef.fieldSettings.formLabel}\" Value History and Edit" + @collection.comparator = 'id' + @collection.sort() + @collection.each (val) => + oldRow = new ACASFormStateDisplayOldValueController + model: val + @$("tbody").append oldRow.render().el + @setupEditor() + @$('.bv_aCASFormStateDisplayValueEdit').modal + backdrop: "static" + @$('.bv_aCASFormStateDisplayValueEdit').modal "show" reasonForUpdateChanged: -> @comment = @commentPrefix + @$('.bv_reasonForUpdate').val() @@ -270,6 +278,7 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View codeType: @valueDef.modelDefaults.codeType codeKind: @valueDef.modelDefaults.codeKind codeOrigin: @valueDef.modelDefaults.codeOrigin + @newValue.set 'value', currentValue.get(currentValue.get('lsType')) if currentValue? opts = modelKey: @valueDef.modelDefaults.kind diff --git a/modules/Components/src/client/ACASFormStateDisplayView.html b/modules/Components/src/client/ACASFormStateDisplayView.html index 806516371..b1f528c54 100644 --- a/modules/Components/src/client/ACASFormStateDisplayView.html +++ b/modules/Components/src/client/ACASFormStateDisplayView.html @@ -30,7 +30,7 @@

      launching controller must provide or set table label

      Value Changed By Changed Date - Reason + Reason For Correction diff --git a/modules/Components/src/client/style.css b/modules/Components/src/client/style.css index 3429cf280..31d237a74 100644 --- a/modules/Components/src/client/style.css +++ b/modules/Components/src/client/style.css @@ -44,4 +44,8 @@ .bv_stateDisplayUpdateTable .valueWasEdited { color: red; +} + +.bv_stateDisplayUpdateTable .valueNotEditable { + color: #9D9D9D; } \ No newline at end of file From b6e973e3214e7370da7ccbb6ee00dd3cea63e350 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 14 Jul 2017 16:48:34 -0700 Subject: [PATCH 105/576] Added clobValue support in StateTable --- modules/Components/src/client/ACASFormStateTable.coffee | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 2531b4446..8d4d2c3eb 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -280,6 +280,8 @@ class window.ACASFormStateTableController extends Backbone.View switch valueDef.modelDefaults.type when 'stringValue' value.set stringValue: if cellContent? then cellContent else "" + when 'clobValue' + value.set clobValue: if cellContent? then cellContent else "" when 'numericValue' numVal = parseFloat(cellContent) if isNaN(numVal) or isNaN(Number(numVal)) From 78ce6578fb01945aecd8d48492b8ce6e19c68d83 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Mon, 17 Jul 2017 09:33:30 -0700 Subject: [PATCH 106/576] feature/state_table_display: added pointer as cursor for editable cells in state display table --- .../Components/src/client/ACASFormStateDisplayUpdate.coffee | 3 ++- modules/Components/src/client/style.css | 4 ++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee index 95c3ead51..4cef35e49 100644 --- a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee +++ b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee @@ -37,7 +37,8 @@ class window.ACASFormStateDisplayUpdateCellController extends Backbone.View $(@el).addClass if @collection.length > 1 then "valueWasEdited" else "" if @options.cellDef.editable? and !@options.cellDef.editable $(@el).addClass 'valueNotEditable' - + else + $(@el).addClass 'valueEditable' @ diff --git a/modules/Components/src/client/style.css b/modules/Components/src/client/style.css index 31d237a74..f84209f93 100644 --- a/modules/Components/src/client/style.css +++ b/modules/Components/src/client/style.css @@ -48,4 +48,8 @@ .bv_stateDisplayUpdateTable .valueNotEditable { color: #9D9D9D; +} + +.bv_stateDisplayUpdateTable .valueEditable { + cursor: pointer; } \ No newline at end of file From bc1db299468180c9dc86baa36556f1c38c4caf9a Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 17 Jul 2017 15:49:23 -0700 Subject: [PATCH 107/576] Fixes #167 --- modules/Components/src/client/PickList.coffee | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/Components/src/client/PickList.coffee b/modules/Components/src/client/PickList.coffee index 13f5a5d6c..17e7f68be 100644 --- a/modules/Components/src/client/PickList.coffee +++ b/modules/Components/src/client/PickList.coffee @@ -261,7 +261,7 @@ class window.PickListSelect2Controller extends PickListSelectController # 'options.propertyMap' is not specified, it defaults to using the # 'acasPropertyMap' initialize: (options) -> - if @options.width? + if @options?.width? @width = @options.width else @width = "100%" @@ -285,7 +285,7 @@ class window.PickListSelect2Controller extends PickListSelectController obj.text = obj[@propertyMap.text] mappedData.push(obj) @placeholder = "" - if @options.placeholder? + if @options?.placeholder? @placeholder = @options.placeholder $(@el).select2 placeholder: @placeholder From eccb9a9c7af432ac6cad4e67789a273841e4f394 Mon Sep 17 00:00:00 2001 From: mprincipato Date: Tue, 18 Jul 2017 11:06:24 -0700 Subject: [PATCH 108/576] Fixes #162. Makes it so that moduleMenus looks at a config parameter to tell what the module menus should be (#163) --- conf/config.properties.example | 1 + modules/ModuleMenus/src/client/ModuleMenus.coffee | 7 ++++++- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 8e2d1d52c..0cb750a17 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -326,6 +326,7 @@ client.moduleMenus.logoText=ACAS client.moduleMenus.logoImageFilePath= client.moduleMenus.homePageMessage=Welcome to ACAS client.moduleMenus.copyrightMessage=© John McNeil & Company 2012-2017 +# client.moduleMenus.menuConfigurationSettings=ModuleMenusConfiguration # If summary statistics is an included feature, set the following to true client.moduleMenus.summaryStats=false # For navigation to external ACAS modules from ACAS homepage diff --git a/modules/ModuleMenus/src/client/ModuleMenus.coffee b/modules/ModuleMenus/src/client/ModuleMenus.coffee index 41118e07e..87d209f5c 100644 --- a/modules/ModuleMenus/src/client/ModuleMenus.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenus.coffee @@ -17,7 +17,12 @@ class window.ModuleMenusController extends Backbone.View $(@el).html @template() - @moduleLauncherList = new ModuleLauncherList(@options.menuListJSON) + if window.conf.moduleMenus.menuConfigurationSettings? + menuListJSON = window[window.conf.moduleMenus.menuConfigurationSettings] + else + menuListJSON = @options.menuListJSON + + @moduleLauncherList = new ModuleLauncherList(menuListJSON) @moduleLauncherMenuListController = new ModuleLauncherMenuListController el: @$('.bv_modLaunchMenuWrapper') collection: @moduleLauncherList From 7cc2808ece53d5b2321d277a6e8f8d6975887e06 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Tue, 18 Jul 2017 15:26:16 -0700 Subject: [PATCH 109/576] feature/state_table_display: added options to state display table to have functions for overriding display of value and for autoupdating other values in the state, and for configuring the text in the GUI, updated getContainer by type/kind service to work for stubs --- .../src/client/ACASFormStateDisplayUpdate.coffee | 14 +++++++++++++- .../src/client/ACASFormStateDisplayView.html | 4 ++-- .../server/routes/InventoryServiceRoutes.coffee | 11 ++++++----- 3 files changed, 21 insertions(+), 8 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee index 4cef35e49..6328d01d1 100644 --- a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee +++ b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee @@ -30,6 +30,8 @@ class window.ACASFormStateDisplayUpdateCellController extends Backbone.View else val = @collection.findWhere ignored: false content = val.get(val.get('lsType')) + if @options.cellDef.displayOverride? + content = @options.cellDef.displayOverride content if val.get('lsType') == 'dateValue' content = UtilityFunctions::convertMSToYMDDate val.get('dateValue') @@ -169,6 +171,8 @@ class window.ACASFormStateDisplayUpdateController extends Backbone.View recordedDate: new Date().getTime() stateToUpdate.get('lsValues').add valInfo.newValue + if valInfo.valueDef?.autoUpdate? + updatedStates = valInfo.valueDef.autoUpdate valInfo, @ @trigger 'thingSaveRequested', valInfo.comment class window.ACASFormStateDisplayOldValueController extends Backbone.View @@ -176,8 +180,12 @@ class window.ACASFormStateDisplayOldValueController extends Backbone.View template: _.template($("#ACASFormStateDisplayOldValueView").html()) render: => + value = @model.get(@model.get('lsType')) + if @options.valueDef.displayOverride? + value = @options.valueDef.displayOverride value + attrs = - value: @model.get(@model.get('lsType')) + value: value attrs.valueClass = if @model.get 'ignored' then "valueWasEdited" else "" if @model.has('modifiedBy') && @model.get('modifiedBy')!="" @@ -236,11 +244,14 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View @collection.each (val) => oldRow = new ACASFormStateDisplayOldValueController model: val + valueDef: @valueDef @$("tbody").append oldRow.render().el @setupEditor() @$('.bv_aCASFormStateDisplayValueEdit').modal backdrop: "static" @$('.bv_aCASFormStateDisplayValueEdit').modal "show" + @$('.bv_valueHeader').html @tableDef.valueHeader + @$('.bv_changeValueHeader').html @tableDef.changeValueHeader reasonForUpdateChanged: -> @comment = @commentPrefix + @$('.bv_reasonForUpdate').val() @@ -263,6 +274,7 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View newValue: @newValue comment: @comment stateID: @options.stateID + valueDef: @valueDef @$('.bv_aCASFormStateDisplayValueEdit').modal "hide" $(@el).empty() diff --git a/modules/Components/src/client/ACASFormStateDisplayView.html b/modules/Components/src/client/ACASFormStateDisplayView.html index b1f528c54..f868f12c0 100644 --- a/modules/Components/src/client/ACASFormStateDisplayView.html +++ b/modules/Components/src/client/ACASFormStateDisplayView.html @@ -27,7 +27,7 @@

      launching controller must provide or set table label

      - + @@ -35,7 +35,7 @@

      launching controller must provide or set table label

      ValueValue Changed By Changed Date Reason For Correction
      -
      Change Value
      +
      Change Value
      diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index b94785c9a..62c368af8 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -723,11 +723,12 @@ exports.containersByTypeKindInternal = (lsType, lsKind, format, stub, testMode, callback JSON.stringify(thingServiceTestJSON.batchList), 200 else baseurl = config.all.client.service.persistence.fullpath+"containers?lsType="+lsType+"&lsKind="+lsKind - stubFlag = "with=stub" - if stub - baseurl += "?#{stubFlag}" - if format? and format=="codetable" - baseurl += "&format=codetable" + if format? + if format=="codetable" + baseurl += "&format=codetable" + else if format == "stub" + baseurl += "&format=stub" + request = require 'request' request( method: 'GET' From 093a92107231dbe70c575c2fa1adaa5830330036 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 19 Jul 2017 09:35:05 -0700 Subject: [PATCH 110/576] Added json2csv npm module (MIT license) for easy csv exporting of JSON objects. --- package.json | 1 + 1 file changed, 1 insertion(+) diff --git a/package.json b/package.json index 31ae5baa9..b6c3679fb 100644 --- a/package.json +++ b/package.json @@ -36,6 +36,7 @@ "jasmine-jquery": "^2.1.1", "jquery": "^2.2.0", "jquery-file-upload-middleware": "https://github.com/mcneilco/jquery-file-upload-middleware.git", + "json2csv": "*", "jszip": "*", "less": "^2.6.0", "lodash": "^4.0.0", From 61e46e57cda2d7aaf7be07a3043df89b06d0aa27 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 19 Jul 2017 09:45:20 -0700 Subject: [PATCH 111/576] Locked down version of json2csv using "npm install --save json2csv" --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index b6c3679fb..e5b9840d0 100644 --- a/package.json +++ b/package.json @@ -36,7 +36,7 @@ "jasmine-jquery": "^2.1.1", "jquery": "^2.2.0", "jquery-file-upload-middleware": "https://github.com/mcneilco/jquery-file-upload-middleware.git", - "json2csv": "*", + "json2csv": "^3.9.1", "jszip": "*", "less": "^2.6.0", "lodash": "^4.0.0", From 8f623a86cd92ab5e874558aa57bc2c261f41600d Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 20 Jul 2017 15:19:33 -0700 Subject: [PATCH 112/576] Removed new comments from ACASFormStateTable.coffee as requested. --- modules/Components/src/client/ACASFormStateTable.coffee | 5 ----- 1 file changed, 5 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 42d51b0f2..61e413f02 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -213,7 +213,6 @@ class window.ACASFormStateTableController extends Backbone.View for valDef in @tableDef.values cellInfo = [] value = state.getOrCreateValueByTypeAndKind valDef.modelDefaults.type, valDef.modelDefaults.kind - #TODO look for ignored values of the same type and kind. Add styling if this was edited if valDef.modelDefaults.type == 'codeValue' if valDef.fieldSettings.fieldType == 'stringValue' displayVal = value.get 'codeValue' @@ -248,10 +247,6 @@ class window.ACASFormStateTableController extends Backbone.View return null handleCellChanged: (changes, source) => - #TODO if audit mode call configured function after change -# that function shoiuld popup a panel to capture a reason, then update the thing -# there should be a cancel option, and this function will have to have undo if cancel pushed -# so I'll have to save the old value ( I have oldValue in a vairable) if changes? for change in changes unless change[2] == change[3] or source == "autofill" From d16f18fcb9d640617b515808e48661f2f0b4499a Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 20 Jul 2017 15:54:14 -0700 Subject: [PATCH 113/576] #176: Listener to server side Thing, Experiment and Container objects --- .../routes/ServerUtilityFunctions.coffee | 37 ++++++++++++++++++- 1 file changed, 35 insertions(+), 2 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee b/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee index ae887c6fd..9e3979f8f 100644 --- a/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee +++ b/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee @@ -511,13 +511,15 @@ class Label extends Backbone.Model handleLabelTextChanged: => unless @isNew() + newText = @get 'labelText' @set ignored: true modifiedBy: AppLaunchParams.loginUser.username modifiedDate: new Date().getTime() isDirty: true - @set labelText: @previous 'labelText' - @trigger 'createNewLabel', @get('lsKind'), @get('labelText') + labelText: @previous 'labelText' + , silent: true + @trigger 'createNewLabel', @get('lsKind'), newText, @get('key') changeLabelText: (options) -> @set labelText: options @@ -836,10 +838,21 @@ class Thing extends Backbone.Model if @lsProperties.defaultLabels? for dLabel in @lsProperties.defaultLabels newLabel = @get('lsLabels').getOrCreateLabelByTypeAndKind dLabel.type, dLabel.kind + @listenTo newLabel, 'createNewLabel', @createNewLabel @set dLabel.key, newLabel # if newLabel.get('preferred') is undefined newLabel.set preferred: dLabel.preferred + createNewLabel: (lKind, newText) => + dLabel = _.where(@lsProperties.defaultLabels, {key: lKind})[0] + oldLabel = @get(lKind) + @unset(lKind) + newLabel = @get('lsLabels').getOrCreateLabelByTypeAndKind dLabel.type, dLabel.kind + newLabel.set + labelText: newText + preferred: oldLabel.get 'preferred' + @set lKind, newLabel + createDefaultStates: => if @lsProperties.defaultValues? for dValue in @lsProperties.defaultValues @@ -1187,10 +1200,20 @@ class Container extends Backbone.Model if @lsProperties.defaultLabels? for dLabel in @lsProperties.defaultLabels newLabel = @get('lsLabels').getOrCreateLabelByTypeAndKind dLabel.type, dLabel.kind + @listenTo newLabel, 'createNewLabel', @createNewLabel @set dLabel.key, newLabel # if newLabel.get('preferred') is undefined newLabel.set preferred: dLabel.preferred + createNewLabel: (lKind, newText) => + dLabel = _.where(@lsProperties.defaultLabels, {key: lKind})[0] + oldLabel = @get(lKind) + @unset(lKind) + newLabel = @get('lsLabels').getOrCreateLabelByTypeAndKind dLabel.type, dLabel.kind + newLabel.set + labelText: newText + preferred: oldLabel.get 'preferred' + @set lKind, newLabel createDefaultStates: => if @lsProperties.defaultValues? @@ -1604,10 +1627,20 @@ class Experiment extends Backbone.Model if @lsProperties.defaultLabels? for dLabel in @lsProperties.defaultLabels newLabel = @get('lsLabels').getOrCreateLabelByTypeAndKind dLabel.type, dLabel.kind + @listenTo newLabel, 'createNewLabel', @createNewLabel @set dLabel.key, newLabel # if newLabel.get('preferred') is undefined newLabel.set preferred: dLabel.preferred + createNewLabel: (lKind, newText) => + dLabel = _.where(@lsProperties.defaultLabels, {key: lKind})[0] + oldLabel = @get(lKind) + @unset(lKind) + newLabel = @get('lsLabels').getOrCreateLabelByTypeAndKind dLabel.type, dLabel.kind + newLabel.set + labelText: newText + preferred: oldLabel.get 'preferred' + @set lKind, newLabel createDefaultStates: => if @lsProperties.defaultValues? From d19d8dc17bda3643f9cf5e8cb9a4fb0c688f46c0 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Thu, 20 Jul 2017 16:23:06 -0700 Subject: [PATCH 114/576] RC/1.12.0 - added review statuses of Reviewed - OK and Reviewed - Not OK, open attached files in new window --- modules/ServerAPI/conf/ExperimentConfJSON.coffee | 11 +++++++++-- modules/ServerAPI/conf/ProtocolConfJSON.coffee | 11 +++++++++-- modules/ServerAPI/src/client/AttachFile.coffee | 2 +- 3 files changed, 19 insertions(+), 5 deletions(-) diff --git a/modules/ServerAPI/conf/ExperimentConfJSON.coffee b/modules/ServerAPI/conf/ExperimentConfJSON.coffee index 4670db836..e13644b15 100644 --- a/modules/ServerAPI/conf/ExperimentConfJSON.coffee +++ b/modules/ServerAPI/conf/ExperimentConfJSON.coffee @@ -319,8 +319,15 @@ codeType: "experiment" codeKind: "review status" codeOrigin: "ACAS DDICT" - code: "reviewed" - name: "Reviewed" + code: "reviewed ok" + name: "Reviewed - OK" + ignored: false + , + codeType: "experiment" + codeKind: "review status" + codeOrigin: "ACAS DDICT" + code: "reviewed not ok" + name: "Reviewed - Not OK" ignored: false , codeType: "analysis" diff --git a/modules/ServerAPI/conf/ProtocolConfJSON.coffee b/modules/ServerAPI/conf/ProtocolConfJSON.coffee index ec7f2eb75..7c9bf1e5e 100644 --- a/modules/ServerAPI/conf/ProtocolConfJSON.coffee +++ b/modules/ServerAPI/conf/ProtocolConfJSON.coffee @@ -296,8 +296,15 @@ codeType: "protocol" codeKind: "review status" codeOrigin: "ACAS DDICT" - code: "reviewed" - name: "Reviewed" + code: "reviewed ok" + name: "Reviewed - OK" + ignored: false + , + codeType: "protocol" + codeKind: "review status" + codeOrigin: "ACAS DDICT" + code: "reviewed not ok" + name: "Reviewed - Not OK" ignored: false , codeType: "assay" diff --git a/modules/ServerAPI/src/client/AttachFile.coffee b/modules/ServerAPI/src/client/AttachFile.coffee index 6205ad3d7..a28155ba6 100644 --- a/modules/ServerAPI/src/client/AttachFile.coffee +++ b/modules/ServerAPI/src/client/AttachFile.coffee @@ -243,7 +243,7 @@ class window.AttachFileController extends BasicFileController if fileValue is null or fileValue is "" or fileValue is undefined @createNewFileChooser() else - @$('.bv_uploadFile').html '' + @$('.bv_uploadFile').html '' uneditableFileTypes = window.conf.experiment.uneditableFileTypes unless uneditableFileTypes? From c7100b3ee14c4ea89db1c38ed7d53a8fa6e34105 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Fri, 21 Jul 2017 10:02:34 -0600 Subject: [PATCH 115/576] #178 Fix realtime device connection issues Fixed issues with realtime device connections when multiple users are connecting / disconnecting. --- .../RealtimeDeviceConnectionController.coffee | 41 +++++------ .../RealtimeDeviceConnectionSockets.coffee | 69 +++++++++---------- 2 files changed, 53 insertions(+), 57 deletions(-) diff --git a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee index 2b5569a34..8fc446c5e 100644 --- a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee +++ b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee @@ -75,7 +75,6 @@ class window.RealtimeDeviceConnectionController extends Backbone.View return instrument.get("lsLabels").pickBestName().get("labelText").toLowerCase() @listenTo @deviceCollection, "sync", @renderSelectListOfExistingInstruments - @connected = false unless @testMode @setupSocketEventHandlers() @@ -96,17 +95,16 @@ class window.RealtimeDeviceConnectionController extends Backbone.View setupSocketEventHandlers: => @socket = io('/deviceChannel') - #@socket.on('connect', @handleDeviceSelectChange) @socket.on('connect_error', @handleConnectError) @socket.on('youShouldTryConnecting', @connectToDevice) @socket.on('disconnectedFromDevice', @disconnectedFromDevice) @socket.on('alertAllDisconnectedFromDevice', @alertAllDisconnectedFromDevice) @socket.on('disconnectedByAnotherUser', @disconnectedByAnotherUser) @socket.on('in_use', @displayUnavailableMessage) + @socket.on('balance_reserved', @balanceReserved) + @socket.on('device_server_offline', @displayServerOfflineMessage) @socket.on('zeroingComplete', => - console.log "zeroingComplete" - if @connected - console.log "zeroingComplete" + if @isConnectedToDevice @resetForm() @enableElement(".bv_disconnect") @enableElement(".bv_zeroBalance") @@ -115,9 +113,8 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @displayInUseMessage() ) - handleZeroBalanceClick: => - if @connected + if @isConnectedToDevice @disableAllFields() @disableElement(".bv_disconnect") @disableElement(".bv_zeroBalance") @@ -126,14 +123,10 @@ class window.RealtimeDeviceConnectionController extends Backbone.View zeroBalanceCallback: (err, data) => - connectToDevice: => - unless @connected - #@selectedDevice = @devicePickList.getSelectedModel() + unless @isConnectedToDevice @selectedInstrumentCode = @$('.bv_deviceSelectContainer').val() @selectedDevice = @deviceCollection.findWhere({"codeName": @selectedInstrumentCode}) - console.log "@selectedDevice.get('url').get('value')" - console.log @selectedDevice.get('url').get('value') @$(".bv_connecting").removeClass "hide" @$(".bv_deviceServerOffline").addClass "hide" @socket.emit('connectToDevice', {deviceName: @selectedDevice.get('description').get('value'), deviceUrl: @selectedDevice.get('url').get('value'), userName: AppLaunchParams.loginUserName}, @connectToDeviceCallback) @@ -143,10 +136,8 @@ class window.RealtimeDeviceConnectionController extends Backbone.View console.info "overide if needed" connectToDeviceCallback: (err, data) => - console.log "err", err - console.log "data", data if err - @connected = false + @isConnectedToDevice = false @setStateToDisconnected() switch err.status when "not_available" @@ -156,20 +147,24 @@ class window.RealtimeDeviceConnectionController extends Backbone.View when "device_not_connected" @displayStatusMessage(".bv_deviceNotConnected") when "device_server_offline" - @displayStatusMessage(".bv_deviceServerOffline") + @displayServerOfflineMessage() when "in_use" @displayStatusMessage(".bv_deviceServerInUse") else - @connected = true + @isConnectedToDevice = true @setStateToConnected() @enableElement(".bv_deviceSelectContainer") @$(".bv_connectionStatusAlert").addClass "hide" displayUnavailableMessage: => - unless @connected + unless @isConnectedToDevice @displayStatusMessage(".bv_deviceServerInUse") + displayServerOfflineMessage: => + @displayStatusMessage(".bv_deviceServerOffline") + @isConnectedToDevice = false + displayStatusMessage: (messageSelector) => @resetStatusMessages() @$(messageSelector).removeClass "hide" @@ -195,7 +190,7 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @disableElement(".bv_deviceSelectContainer") @selectedInstrumentCode = @$('.bv_deviceSelectContainer').val() selectedInstrument = @deviceCollection.findWhere({"codeName": @selectedInstrumentCode}) - @connected = false + @isConnectedToDevice = false @resetStatusMessages() @socket.emit('disconnected') unless selectedInstrument is "" @@ -261,9 +256,11 @@ class window.RealtimeDeviceConnectionController extends Backbone.View unless @isConnectedToDevice @connectToDevice() - disconnectedByAnotherUser: (disconnectingUserName) => - @displayDisconnectedModal(disconnectingUserName) - @setStateToDisconnected() + disconnectedByAnotherUser: (msg) => + @displayDisconnectedModal(msg.username) + + balanceReserved: (msg) => + @connectToDeviceCallback(msg, null) displayDisconnectedModal: (disconnectingUserName) => @$(".bv_disconnectingUserName").html disconnectingUserName diff --git a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee index 5a33a90a9..60c34b866 100644 --- a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee +++ b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee @@ -1,7 +1,5 @@ - request = require 'request' _ = require 'underscore' - Promise = require 'promise' @@ -41,14 +39,20 @@ class BalanceAccess unless @heartBeat? @heartBeat = setInterval( => @getBalanceStatus().then((balanceStatus) => - unless balanceStatus is @status + if balanceStatus is "device_server_offline" and @status is "idle" @status = balanceStatus - switch @status - when "idle" - @room.emit('youShouldTryConnecting') - when "in_use" - @room.emit('in_use') + if @currentConnectedUser? + @currentConnectedUser.socket.emit 'youShouldTryConnecting' + else + unless balanceStatus is @status + @status = balanceStatus + switch @status + when "idle" + @room.emit('youShouldTryConnecting') + when "in_use" + @room.emit('in_use') ).catch((err) => + @status = "device_server_offline" @room.emit("device_server_offline") ) , 1000) @@ -107,19 +111,15 @@ class BalanceAccess @isAvailable = false resolve null else - if _.first(@balanceConnectQueue).clientId is clientId - @currentConnectedUser = {clientId: clientId, userName: userName, socket: socket} - @isAvailable = false - resolve null - else - reject {status: 'not_available', connectedUser: @currentConnectedUser} + unless @currentConnectedUser? + @currentConnectedUser = _.first(@balanceConnectQueue) + reject {status: 'not_available', connectedUser: @currentConnectedUser} when "device_not_connected" reject {status: "device_not_connected"} when "in_use" reject {status: "in_use"} ).catch((err) => - console.log "err" - console.log err + @isAvailable = false reject {status: "device_server_offline"} ) ) @@ -128,13 +128,11 @@ class BalanceAccess clientInQueue = _.findWhere(@balanceConnectQueue, {clientId: userToAdd.clientId}) if clientInQueue @removeUserToAddFromQueue(userToAdd.clientId) - @removeCurrentUser() - @balanceConnectQueue.push {clientId: userToAdd.clientId, userName: userToAdd.userName, socket: socket} @currentConnectedUser = {clientId: userToAdd.clientId, userName: userToAdd.userName, socket: socket} + @balanceConnectQueue.push @currentConnectedUser @isAvailable = false - removeUserToAddFromQueue: (clientId) => @balanceConnectQueue = _.reject(@balanceConnectQueue, (user) -> return user.clientId is clientId @@ -146,12 +144,12 @@ class BalanceAccess @currentConnectedUser = null removeCurrentUser: => - @balanceConnectQueue.shift() + currentUser = @balanceConnectQueue.shift() + @balanceConnectQueue.push currentUser @currentConnectedUser = null zeroBalance: => zeroBalanceURL = @balanceUrl + "api/zeroBalance" - console.log "zeroBalanceURL", zeroBalanceURL return new Promise((resolve, reject) => request( method: 'POST' @@ -203,12 +201,10 @@ class DeviceSocketController balanceAccess = @balances[payload.deviceUrl] balanceAccessPromise = balanceAccess.connectClient(socket.id, payload.userName, socket) balanceAccessPromise.then(() => - console.log "balanceAccessPromise.then" @currentlyConnectedSocket = socket return callback(null, 'Connected to device') ) balanceAccessPromise.catch((err) => - console.log "balanceAccessPromise.catch err" if err.status is "not_available" return callback({status: "not_available", userName: err.connectedUser.userName, clientId: err.connectedUser.clientId}, null) else @@ -223,21 +219,24 @@ class DeviceSocketController handleDisconnected: (socket) -> balanceAccess = @balances[@usersInRoom[socket.id]] - balanceAccess.disconnectCurrentUser() - nextUserInQueue = balanceAccess.getNextUser() - if nextUserInQueue? - socket.broadcast.to(nextUserInQueue.clientId).emit('youShouldTryConnecting') - else - socket.broadcast.emit('alertAllDisconnectedFromDevice') - balanceAccess.clearHeartBeat() - balanceAccess.disconnectFromBalance() + if balanceAccess? + if balanceAccess.getNextUser().clientId is socket.id + balanceAccess.disconnectCurrentUser() + else + balanceAccess.removeUserToAddFromQueue(socket.id) + nextUserInQueue = balanceAccess.getNextUser() + if nextUserInQueue? + socket.broadcast.to(nextUserInQueue.clientId).emit('youShouldTryConnecting') + else + socket.broadcast.emit('alertAllDisconnectedFromDevice') + balanceAccess.clearHeartBeat() + balanceAccess.disconnectFromBalance() socket.leave(@usersInRoom[socket.id]) socket.emit('disconnectedFromDevice') handleDisconnect: (socket) -> balanceAccess = @balances[@usersInRoom[socket.id]] balanceAccess.removeUserFromQueue(socket.id) - nextUserInQueue = balanceAccess.getNextUser() if nextUserInQueue? socket.broadcast.to(nextUserInQueue.clientId).emit('youShouldTryConnecting') @@ -248,10 +247,10 @@ class DeviceSocketController handleBootUser: (socket, payload, callback) -> balanceAccess = @balances[@usersInRoom[socket.id]] - balanceAccess.disconnectCurrentUser() - balanceAccess.swapCurrentUser({userName: payload.userNameToAdd, clientId: socket.id}) + balanceAccess.swapCurrentUser({userName: payload.userNameToAdd, clientId: socket.id}, socket) @currentlyConnectedSocket = socket - socket.broadcast.to(payload.userToBootClientId).emit('disconnectedByAnotherUser', payload.userNameToAdd) + socket.broadcast.to(@usersInRoom[socket.id]).emit('balance_reserved', {status: "not_available", userName: payload.userNameToAdd, clientId: socket.id}) + socket.broadcast.to(payload.userToBootClientId).emit('disconnectedByAnotherUser', {username: payload.userNameToAdd, socketId: socket.id}) callback(null, 'did this connect? ') handleDisconnectAllUsers: (socket, callback) -> From 5038fc14f561d637d62c7bb05a189268f7ed8431 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Fri, 21 Jul 2017 11:55:45 -0600 Subject: [PATCH 116/576] #178 Fix realtime device connection issues Added some checks for edge cases. --- .../RealtimeDeviceConnectionController.coffee | 16 +++++--- .../RealtimeDeviceConnectionSockets.coffee | 41 ++++++++++++------- 2 files changed, 37 insertions(+), 20 deletions(-) diff --git a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee index 8fc446c5e..3f7b432fc 100644 --- a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee +++ b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee @@ -190,11 +190,13 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @disableElement(".bv_deviceSelectContainer") @selectedInstrumentCode = @$('.bv_deviceSelectContainer').val() selectedInstrument = @deviceCollection.findWhere({"codeName": @selectedInstrumentCode}) - @isConnectedToDevice = false + #@isConnectedToDevice = false @resetStatusMessages() - @socket.emit('disconnected') - unless selectedInstrument is "" - @connectToDevice() + if @isConnectedToDevice + @socket.emit('disconnected') + else + unless selectedInstrument is "" + @connectToDevice() handleBootCurrentUserOffDevice: => @socket.emit('bootUser', {userToBootClientId: @clientIdOfConnectedUser, userNameToAdd: AppLaunchParams.loginUserName}, @handleBootCurrentUserOffDeviceCallback) @@ -251,6 +253,9 @@ class window.RealtimeDeviceConnectionController extends Backbone.View disconnectedFromDevice: => @setStateToDisconnected() + selectedInstrument = @deviceCollection.findWhere({"codeName": @selectedInstrumentCode}) + unless selectedInstrument is "" + @connectToDevice() alertAllDisconnectedFromDevice: => unless @isConnectedToDevice @@ -260,7 +265,8 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @displayDisconnectedModal(msg.username) balanceReserved: (msg) => - @connectToDeviceCallback(msg, null) + if msg.balanceUrl is @selectedDevice.get('url').get('value') + @connectToDeviceCallback(msg, null) displayDisconnectedModal: (disconnectingUserName) => @$(".bv_disconnectingUserName").html disconnectingUserName diff --git a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee index 60c34b866..3a2a2bb66 100644 --- a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee +++ b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee @@ -135,7 +135,10 @@ class BalanceAccess removeUserToAddFromQueue: (clientId) => @balanceConnectQueue = _.reject(@balanceConnectQueue, (user) -> - return user.clientId is clientId + if user? + return user.clientId is clientId + else + return false ) clearAllUsers: => @@ -220,37 +223,45 @@ class DeviceSocketController handleDisconnected: (socket) -> balanceAccess = @balances[@usersInRoom[socket.id]] if balanceAccess? - if balanceAccess.getNextUser().clientId is socket.id - balanceAccess.disconnectCurrentUser() - else - balanceAccess.removeUserToAddFromQueue(socket.id) nextUserInQueue = balanceAccess.getNextUser() if nextUserInQueue? + if nextUserInQueue.clientId is socket.id + balanceAccess.disconnectCurrentUser() + else + balanceAccess.removeUserToAddFromQueue(socket.id) + + nextUserInQueue = balanceAccess.getNextUser() + if nextUserInQueue? + balanceAccess.isAvailable = true socket.broadcast.to(nextUserInQueue.clientId).emit('youShouldTryConnecting') else socket.broadcast.emit('alertAllDisconnectedFromDevice') balanceAccess.clearHeartBeat() balanceAccess.disconnectFromBalance() + balanceAccess.isAvailable = true socket.leave(@usersInRoom[socket.id]) socket.emit('disconnectedFromDevice') + handleDisconnect: (socket) -> balanceAccess = @balances[@usersInRoom[socket.id]] - balanceAccess.removeUserFromQueue(socket.id) - nextUserInQueue = balanceAccess.getNextUser() - if nextUserInQueue? - socket.broadcast.to(nextUserInQueue.clientId).emit('youShouldTryConnecting') - else - socket.broadcast.emit('alertAllDisconnectedFromDevice') - balanceAccess.clearHeartBeat() - balanceAccess.disconnectFromBalance() + if balanceAccess? + balanceAccess.removeUserFromQueue(socket.id) + nextUserInQueue = balanceAccess.getNextUser() + if nextUserInQueue? + socket.broadcast.to(nextUserInQueue.clientId).emit('youShouldTryConnecting') + else + socket.broadcast.emit('alertAllDisconnectedFromDevice') + balanceAccess.clearHeartBeat() + balanceAccess.disconnectFromBalance() handleBootUser: (socket, payload, callback) -> balanceAccess = @balances[@usersInRoom[socket.id]] balanceAccess.swapCurrentUser({userName: payload.userNameToAdd, clientId: socket.id}, socket) @currentlyConnectedSocket = socket - socket.broadcast.to(@usersInRoom[socket.id]).emit('balance_reserved', {status: "not_available", userName: payload.userNameToAdd, clientId: socket.id}) - socket.broadcast.to(payload.userToBootClientId).emit('disconnectedByAnotherUser', {username: payload.userNameToAdd, socketId: socket.id}) + socket.broadcast.to(@usersInRoom[socket.id]).emit('balance_reserved', {status: "not_available", userName: payload.userNameToAdd, clientId: socket.id, balanceUrl: @usersInRoom[socket.id]}) + if @usersInRoom[socket.id] is @usersInRoom[payload.userToBootClientId] + socket.broadcast.to(payload.userToBootClientId).emit('disconnectedByAnotherUser', {username: payload.userNameToAdd, socketId: socket.id}) callback(null, 'did this connect? ') handleDisconnectAllUsers: (socket, callback) -> From cd8bdaa08a83eacb9477eda6832a6bc7c5b8939a Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 24 Jul 2017 16:22:00 -0700 Subject: [PATCH 117/576] Added catch to display fileValue itself if comments are not filled out. Fixes #183 --- modules/Components/src/client/ACASFormFields.coffee | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index aa7618332..06949fbb8 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -568,7 +568,10 @@ class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldCon @createNewFileChooser() @$('.bv_deleteSavedFile').hide() else - @$('.bv_file').html ''+@getModel().get('comments')+'' + displayText = @getModel().get('comments') + if !displayText? + displayText = fileValue + @$('.bv_file').html ''+displayText+'' @$('.bv_deleteSavedFile').show() createNewFileChooser: -> From 8ea062f71914ffdbe24207be23316b546f186c7f Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Mon, 24 Jul 2017 16:54:17 -0700 Subject: [PATCH 118/576] RC/1.12.1 - made changes to ACASFormStateDisplayTable --- .../client/ACASFormStateDisplayUpdate.coffee | 33 +++++++++++-------- .../src/client/ACASFormStateDisplayView.html | 8 ++--- 2 files changed, 24 insertions(+), 17 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee index 6328d01d1..128a08a63 100644 --- a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee +++ b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee @@ -183,29 +183,24 @@ class window.ACASFormStateDisplayOldValueController extends Backbone.View value = @model.get(@model.get('lsType')) if @options.valueDef.displayOverride? value = @options.valueDef.displayOverride value + if @options.previousLsTransaction + prevLsTransaction = @options.previousLsTransaction attrs = value: value attrs.valueClass = if @model.get 'ignored' then "valueWasEdited" else "" - if @model.has('modifiedBy') && @model.get('modifiedBy')!="" - attrs.changedBy = @model.get('modifiedBy') - else - attrs.changedBy = @model.get('recordedBy') - - if @model.has('modifiedDate') && !isNaN(@model.get('modifiedBy')) - attrs.changedDate = UtilityFunctions::convertMSToYMDDate @model.get('modifiedDate') - else - attrs.changedDate = UtilityFunctions::convertMSToYMDDate @model.get('recordedDate') - attrs.reason = "current value" + attrs.recordedBy = @model.get('recordedBy') + attrs.recordedDate = UtilityFunctions::convertMSToYMDDate @model.get('recordedDate') + attrs.reason = "initial value" $(@el).empty() $(@el).html @template(attrs) - if @model.get 'ignored' + unless @options.initialVal? and @options.initialVal $.ajax type: 'GET' - url: "/api/transaction/"+@model.get 'lsTransaction' + url: "/api/transaction/"+prevLsTransaction json: true success: (response) => @$('.bv_reason').html response.comments @@ -241,11 +236,23 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View @$('.bv_header').html "\"#{@valueDef.fieldSettings.formLabel}\" Value History and Edit" @collection.comparator = 'id' @collection.sort() - @collection.each (val) => + index = 0 + while index < @collection.length + val = @collection.at(index) + if index is 0 + initialVal = true + else + initialVal = false + previousLsTransaction = @collection.at(index-1).get('lsTransaction') oldRow = new ACASFormStateDisplayOldValueController model: val valueDef: @valueDef + initialVal: initialVal + previousLsTransaction: previousLsTransaction @$("tbody").append oldRow.render().el + + index++ + @setupEditor() @$('.bv_aCASFormStateDisplayValueEdit').modal backdrop: "static" diff --git a/modules/Components/src/client/ACASFormStateDisplayView.html b/modules/Components/src/client/ACASFormStateDisplayView.html index f868f12c0..c6bdffc70 100644 --- a/modules/Components/src/client/ACASFormStateDisplayView.html +++ b/modules/Components/src/client/ACASFormStateDisplayView.html @@ -14,8 +14,8 @@
      launching controller must provide or set table label <%=value%> - <%=changedBy%> - <%=changedDate%> + <%=recordedBy%> + <%=recordedDate%> <%=reason%> @@ -28,8 +28,8 @@

      launching controller must provide or set table label

      - - + + From 749fc5374b22b3ea3e2df91877b7b773e2a3e644 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Tue, 25 Jul 2017 11:15:04 -0600 Subject: [PATCH 119/576] #178 Fix realtime device connection issues Added some checks for edge cases. --- .../RealtimeDeviceConnectionController.coffee | 15 ++++++++++----- .../src/client/RealtimeDeviceConnectionView.html | 5 ++++- .../routes/RealtimeDeviceConnectionSockets.coffee | 13 +++++++++---- 3 files changed, 23 insertions(+), 10 deletions(-) diff --git a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee index 3f7b432fc..f93ca553c 100644 --- a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee +++ b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee @@ -60,6 +60,7 @@ class window.RealtimeDeviceConnectionController extends Backbone.View "click .bv_disconnectedByAnotherUserDismiss": "hideDisconnectedModal" "click .bv_kickUserOff": "displayInUseModal" "click .bv_deviceInUseDismiss": "dismissDeviceInUse" + "click .bv_reconnect": "handleReconnectClicked" "change .bv_deviceSelectContainer": "handleDeviceSelectChange" "click .bv_dismissDisconnectMessage": "handleDismissDisconnectMessage" "click .bv_zeroBalance": "handleZeroBalanceClick" @@ -190,14 +191,21 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @disableElement(".bv_deviceSelectContainer") @selectedInstrumentCode = @$('.bv_deviceSelectContainer').val() selectedInstrument = @deviceCollection.findWhere({"codeName": @selectedInstrumentCode}) - #@isConnectedToDevice = false @resetStatusMessages() if @isConnectedToDevice - @socket.emit('disconnected') + @socket.emit('disconnectFromBalance', @disconnectCallback) else unless selectedInstrument is "" @connectToDevice() + disconnectCallback: => + @isConnectedToDevice = false + @connectToDevice() + + handleReconnectClicked: => + @$(".bv_disconnected").addClass "hide" + @connectToDevice() + handleBootCurrentUserOffDevice: => @socket.emit('bootUser', {userToBootClientId: @clientIdOfConnectedUser, userNameToAdd: AppLaunchParams.loginUserName}, @handleBootCurrentUserOffDeviceCallback) @@ -253,9 +261,6 @@ class window.RealtimeDeviceConnectionController extends Backbone.View disconnectedFromDevice: => @setStateToDisconnected() - selectedInstrument = @deviceCollection.findWhere({"codeName": @selectedInstrumentCode}) - unless selectedInstrument is "" - @connectToDevice() alertAllDisconnectedFromDevice: => unless @isConnectedToDevice diff --git a/modules/Components/src/client/RealtimeDeviceConnectionView.html b/modules/Components/src/client/RealtimeDeviceConnectionView.html index 6977f5908..13bea854c 100644 --- a/modules/Components/src/client/RealtimeDeviceConnectionView.html +++ b/modules/Components/src/client/RealtimeDeviceConnectionView.html @@ -15,7 +15,10 @@

      Tare Single Vial

      Connecting Connected - Disconnected + + Disconnected + Reconnect + Device Not Connected Device Server Offline Currently In Use diff --git a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee index 3a2a2bb66..7004647aa 100644 --- a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee +++ b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee @@ -182,8 +182,8 @@ class DeviceSocketController socket.on('disconnected', => @handleDisconnected(socket) ) - socket.on('disconnect', => - @handleDisconnect(socket) + socket.on('disconnectFromBalance', (callback) => + @handleDisconnect(socket, callback) ) socket.on('bootUser', (payload, callback) => @handleBootUser(socket, payload, callback) @@ -205,6 +205,7 @@ class DeviceSocketController balanceAccessPromise = balanceAccess.connectClient(socket.id, payload.userName, socket) balanceAccessPromise.then(() => @currentlyConnectedSocket = socket + socket.broadcast.to(@usersInRoom[socket.id]).emit('balance_reserved', {status: "not_available", userName: payload.userName, clientId: socket.id, balanceUrl: @usersInRoom[socket.id]}) return callback(null, 'Connected to device') ) balanceAccessPromise.catch((err) => @@ -222,6 +223,7 @@ class DeviceSocketController handleDisconnected: (socket) -> balanceAccess = @balances[@usersInRoom[socket.id]] + if balanceAccess? nextUserInQueue = balanceAccess.getNextUser() if nextUserInQueue? @@ -239,21 +241,24 @@ class DeviceSocketController balanceAccess.clearHeartBeat() balanceAccess.disconnectFromBalance() balanceAccess.isAvailable = true - socket.leave(@usersInRoom[socket.id]) + # socket.emit('disconnectedFromDevice') - handleDisconnect: (socket) -> + handleDisconnect: (socket, callback) -> balanceAccess = @balances[@usersInRoom[socket.id]] if balanceAccess? balanceAccess.removeUserFromQueue(socket.id) nextUserInQueue = balanceAccess.getNextUser() + if nextUserInQueue? socket.broadcast.to(nextUserInQueue.clientId).emit('youShouldTryConnecting') else socket.broadcast.emit('alertAllDisconnectedFromDevice') balanceAccess.clearHeartBeat() balanceAccess.disconnectFromBalance() + socket.leave(@usersInRoom[socket.id]) + callback() handleBootUser: (socket, payload, callback) -> balanceAccess = @balances[@usersInRoom[socket.id]] From a9e882f36731a8b0ebb10bad89445e31ad12cffa Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 26 Jul 2017 13:26:10 -0700 Subject: [PATCH 120/576] Pass placeholder option from form field config to ACASFormLSThingInteractionFieldController. Fixes #82 --- modules/Components/src/client/ACASFormFields.coffee | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 06949fbb8..3f209880b 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -314,6 +314,8 @@ class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractF @labelType = @options.labelType if @options.queryUrl? @queryUrl = @options.queryUrl + if @options.placeholder? + @placeholder = @options.placeholder handleInputChanged: => From 540f59d8b462997c35fab340e31a4e01d7b4719d Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Wed, 26 Jul 2017 13:27:56 -0700 Subject: [PATCH 121/576] RC/1.12.0: fixed bug in experiment browsers (in expt browser and study tracker expt modules) to show protocol corpName initials, fixed bug so that user can deep link to old protocols/expts without corpName initials via '/entity/edit/codeName' --- .../ExperimentBrowser/src/client/ExperimentBrowser.coffee | 5 ++++- .../src/server/routes/ControllerRedirectRoutes.coffee | 6 +++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee b/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee index 3e1f397da..6274f2354 100644 --- a/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee +++ b/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee @@ -243,9 +243,12 @@ class window.ExperimentRowSummaryController extends Backbone.View if @model.get('lsLabels') not instanceof LabelList @model.set 'lsLabels', new LabelList @model.get('lsLabels') subclass = @model.get('subclass') + protocolCode = @model.get('protocol').get('codeName') if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true if @model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 code = @model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') + if @model.get('protocol').get('lsLabels').getLabelByTypeAndKind("corpName", 'protocol corpName').length > 0 + protocolCode = @model.get('protocol').get('lsLabels').getLabelByTypeAndKind('corpName', 'protocol corpName')[0].get('labelText') else code = @model.get("codeName") else if @model.get('lsKind') is "study" and @model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 @@ -256,7 +259,7 @@ class window.ExperimentRowSummaryController extends Backbone.View toDisplay = experimentName: experimentBestName experimentCode: code - protocolCode: @model.get('protocol').get("codeName") + protocolCode: protocolCode protocolName: protocolBestName scientist: @model.getScientist().get('codeValue') status: @model.getStatus().get("codeValue") diff --git a/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee b/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee index efa7f2f1f..7506018fe 100644 --- a/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee @@ -33,7 +33,7 @@ exports.redirectToEditor = (req, resp) -> console.log "getEntityByName" protocolServiceRoutes = require './ProtocolServiceRoutes.js' experimentServiceRoutes = require './ExperimentServiceRoutes.js' - if protOrExpt is 'protocols' + if protOrExpt is 'protocolsWithCorpNames' protocolServiceRoutes.getProtocolByLabelInternal code, (statusCode, json) -> console.log "getEntityByName - getProtocolByLabelInternal " if statusCode is 500 @@ -44,7 +44,7 @@ exports.redirectToEditor = (req, resp) -> console.log "/"+deepLink+"/codeName/"+code resp.redirect "/"+deepLink+"/codeName/"+code - else if protOrExpt is 'experiments' + else if protOrExpt is 'experimentsWithCorpNames' experimentServiceRoutes.getExperimentByLabelInternal code, (statusCode, json) -> console.log "getEntityByName - getExperimentByLabelInternal" if statusCode is 500 @@ -72,7 +72,7 @@ exports.redirectToEditor = (req, resp) -> if config.all.client.entity.saveInitialsCorpName entityName = controllerRedirectConf[queryPrefix]["entityName"] - if entityName is "protocols" or entityName is "experiments" + if entityName is "protocolsWithCorpNames" or entityName is "experimentsWithCorpNames" #get entity by name getEntityByName entityName, resp else From 077269f01b1cc93e3f6577a5c151edee734380ff Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 26 Jul 2017 16:13:44 -0700 Subject: [PATCH 122/576] Fixed simple bug in setEmptyValue function of LsThing Interaction pickers. --- modules/Components/src/client/ACASFormFields.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 3f209880b..a8635a247 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -330,7 +330,7 @@ class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractF setEmptyValue: -> @getModel().set ignored: true - @setItxThing null + @getModel().setItxThing null isEmpty: -> empty = true From f2639d6d224ddd8bc5f403a62d9f5aa04ce05afe Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Thu, 27 Jul 2017 12:04:33 -0700 Subject: [PATCH 123/576] RC/1.12.0: fixed bugs in experiment browser and controller redirect routes for showing/redirecting to study experiments --- .../src/client/ExperimentBrowser.coffee | 32 +++++++------------ .../routes/ControllerRedirectRoutes.coffee | 14 ++++---- 2 files changed, 18 insertions(+), 28 deletions(-) diff --git a/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee b/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee index 6274f2354..9d5889386 100644 --- a/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee +++ b/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee @@ -249,6 +249,8 @@ class window.ExperimentRowSummaryController extends Backbone.View code = @model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') if @model.get('protocol').get('lsLabels').getLabelByTypeAndKind("corpName", 'protocol corpName').length > 0 protocolCode = @model.get('protocol').get('lsLabels').getLabelByTypeAndKind('corpName', 'protocol corpName')[0].get('labelText') + else if @model.get('lsKind') is "study" and @model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 + code = @model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') else code = @model.get("codeName") else if @model.get('lsKind') is "study" and @model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 @@ -497,6 +499,8 @@ class window.ExperimentBrowserController extends Backbone.View if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true if @experimentController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') + else if @model.get('lsKind') is "study" and @model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 + code = @model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') else code = @experimentController.model.get("codeName") else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 @@ -504,15 +508,6 @@ class window.ExperimentBrowserController extends Backbone.View else code = @experimentController.model.get('codeName') -# if @experimentController.model.get('lsKind') is "study" -# if @experimentController.model.get('lsLabels') not instanceof LabelList -# @experimentController.model.set 'lsLabels', new LabelList @model.get('lsLabels') -# if @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 -# code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') -# else -# code = @experimentController.model.get("codeName") -# else -# code = @experimentController.model.get("codeName") @$(".bv_experimentCodeName").html code @$(".bv_deleteButtons").removeClass "hide" @$(".bv_okayButton").addClass "hide" @@ -555,6 +550,8 @@ class window.ExperimentBrowserController extends Backbone.View if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true if @experimentController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') + else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') else code = @experimentController.model.get("codeName") else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 @@ -581,6 +578,8 @@ class window.ExperimentBrowserController extends Backbone.View if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true if @experimentController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') + else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') else code = @experimentController.model.get("codeName") else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 @@ -609,6 +608,8 @@ class window.ExperimentBrowserController extends Backbone.View if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true if @experimentController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') + else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') else code = @experimentController.model.get("codeName") else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 @@ -616,17 +617,6 @@ class window.ExperimentBrowserController extends Backbone.View else code = @experimentController.model.get('codeName') - - # experimentKind = @experimentController.model.get('lsKind') -# if experimentKind is "study" -# if @experimentController.model.get('lsLabels') not instanceof LabelList -# @experimentController.model.set 'lsLabels', new LabelList @experimentController.model.get('lsLabels') -# if @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 -# code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') -# else -# code = @experimentController.model.get("codeName") -# else -# code = @experimentController.model.get("codeName") window.open("/openExptInQueryTool?experiment=#{code}",'_blank') formatOpenInQueryToolButton: => @@ -643,6 +633,8 @@ class window.ExperimentBrowserController extends Backbone.View if window.conf.entity?.saveInitialsCorpName? and window.conf.entity.saveInitialsCorpName is true if @experimentController.model.get('lsLabels').getLabelByTypeAndKind("corpName", subclass + ' corpName').length > 0 code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('corpName', subclass + ' corpName')[0].get('labelText') + else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 + code = @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id')[0].get('labelText') else code = @experimentController.model.get("codeName") else if @experimentController.model.get('lsKind') is "study" and @experimentController.model.get('lsLabels').getLabelByTypeAndKind('id', 'study id').length > 0 diff --git a/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee b/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee index 7506018fe..a30ae37c5 100644 --- a/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ControllerRedirectRoutes.coffee @@ -28,6 +28,7 @@ exports.redirectToEditor = (req, resp) -> console.log "in redirectToEditor" console.log config.all.client.entity.saveInitialsCorpName + console.log queryPrefix getEntityByName = (protOrExpt, resp) => console.log "getEntityByName" @@ -69,14 +70,11 @@ exports.redirectToEditor = (req, resp) -> if queryPrefix != null console.log "url to get entity - in redirectToEditor" - - if config.all.client.entity.saveInitialsCorpName - entityName = controllerRedirectConf[queryPrefix]["entityName"] - if entityName is "protocolsWithCorpNames" or entityName is "experimentsWithCorpNames" - #get entity by name - getEntityByName entityName, resp - else - getEntityByCodeName resp + console.log queryPrefix + entityName = controllerRedirectConf[queryPrefix]["entityName"] + if entityName is "protocolsWithCorpNames" or entityName is "experimentsWithCorpNames" + #get entity by name + getEntityByName entityName, resp else getEntityByCodeName resp else From df587e22d55ee7650c5c9fb7ad6c1e87435499bd Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Thu, 27 Jul 2017 14:02:09 -0700 Subject: [PATCH 124/576] modifty generic_data_parser to save assay_tree_rule if it is a new protocol. Enabled save of 'experiment details' if it is present in the file. Save SEL column order and track if column is marked as a condition. SEL columna attributes are used by downstream query apps such as ACAS dataViewer. --- .../src/server/generic_data_parser.R | 245 ++++++++++++++++-- .../ServerAPI/conf/ExperimentConfJSON.coffee | 18 ++ 2 files changed, 247 insertions(+), 16 deletions(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 87f685609..7758a9756 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -11,6 +11,7 @@ # Parses a "Generic" formatted excel file into an upload file for ACAS ######################################################################### + # How to run: # Before running: # Set your working directory to the ACAS_HOME (RStudio defaults to this) @@ -98,10 +99,10 @@ validateMetaData <- function(metaData, configList, username, formatSettings = li ) } else { expectedDataFormat <- data.frame( - headers = c("Format","Protocol Name","Experiment Name","Scientist","Notebook","In Life Notebook", + headers = c("Format","Protocol Name","Assay Tree Rule","Experiment Name","Experiment Details","Scientist","Notebook","In Life Notebook", "Short Description", "Experiment Keywords", "Page","Assay Date"), - class = c("Text", "Text", "Text", "Text", "Text", "Text", "Text", "Text", "Text", "Date"), - isNullable = c(FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE) + class = c("Text", "Text", "Text", "Text", "Text","Text","Text", "Text", "Text", "Text", "Text", "Date"), + isNullable = c(FALSE, FALSE, TRUE,FALSE, TRUE,FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE) ) projectRequired <- !is.null(configList$client.include.project) && configList$client.include.project shouldSaveProject <- !is.null(configList$client.save.project) && configList$client.save.project @@ -647,9 +648,10 @@ getHiddenColumns <- function(classRow, errorEnv) { dataShown <- gsub(".*\\((.*)\\).*||.*", "\\1",classRow) dataShown[is.na(dataShown)] <- "" hiddenColumns <- grepl("hidden",dataShown,ignore.case=TRUE) + conditionColumns <- grepl("condition",dataShown,ignore.case=TRUE) shownColumns <- grepl("shown",dataShown,ignore.case=TRUE) defaultColumns <- dataShown %in% "" - unknownColumns <- which(!hiddenColumns & !shownColumns & !defaultColumns) + unknownColumns <- which(!hiddenColumns & !shownColumns & !defaultColumns & !conditionColumns) # Error handling for unknown entries rather than 'shown' or 'hidden' if(length(unknownColumns) > 0) { @@ -666,6 +668,39 @@ getHiddenColumns <- function(classRow, errorEnv) { } return(hiddenColumns) } +getConditionColumns <- function(classRow, errorEnv) { + # Get information about which columns to hide (publicData = FALSE) + # + # Args: + # classRow: A character vector of the Datatypes of the calculated results, with (hidden) to mark hidden points + # + # Returns: + # a boolean vector of which results are hidden + + # Pull out info about hidden columns + dataShown <- gsub(".*\\((.*)\\).*||.*", "\\1",classRow) + dataShown[is.na(dataShown)] <- "" + hiddenColumns <- grepl("hidden",dataShown,ignore.case=TRUE) + conditionColumns <- grepl("condition",dataShown,ignore.case=TRUE) + shownColumns <- grepl("shown",dataShown,ignore.case=TRUE) + defaultColumns <- dataShown %in% "" + unknownColumns <- which(!hiddenColumns & !shownColumns & !defaultColumns & !conditionColumns) + + # Error handling for unknown entries rather than 'shown' or 'hidden' + if(length(unknownColumns) > 0) { + if(length(unknownColumns) == 1) { + addError(paste0("In Datatype column ",getExcelColumnFromNumber(unknownColumns),", there is an entry in the parentheses that cannot be understood: '", + dataShown[unknownColumns], + "'. Please enter 'shown' or 'hidden'."), errorEnv) + } else { + addError(paste0("In Datatype columns ",paste0(sapply(unknownColumns,getExcelColumnFromNumber),collapse = ", "), + ", there are unknown entries in the parentheses that cannot be understood: '", + paste0(dataShown[unknownColumns], collapse="', '"), + "'. Please enter 'shown' or 'hidden'."), errorEnv) + } + } + return(conditionColumns) +} getLinkColumns <- function(classRow, errorEnv) { # Get information about which column is a link to lower levels # @@ -944,7 +979,7 @@ getExcelColumnFromNumber <- function(number) { } extractValueKinds <- function(valueKindsVector, ignoreHeaders = NULL, uncertaintyType, uncertaintyCodeWord, commentCol, commentCodeWord, stateAssignments, hiddenColumns, linkColumns, classRow, - stateKindRow, stateTypeRow, codeAssignments = NULL) { + stateKindRow, stateTypeRow, codeAssignments = NULL, conditionColumns = NULL) { # Extracts result types, units, conc, and conc units from a data frame # # Args: @@ -1100,6 +1135,7 @@ organizeCalculatedResults <- function(calculatedResults, inputFormat, formatPara # Check the Datatype row and get information from it hiddenColumns <- getHiddenColumns(as.character(unlist(calculatedResults[1,])), errorEnv) + conditionColumns <- getConditionColumns(as.character(unlist(calculatedResults[1,])), errorEnv) linkColumns <- getLinkColumns(as.character(unlist(calculatedResults[1,])), errorEnv) clobColumns <- vapply(calculatedResults, function(x) any(nchar(as.character(x)) > 255, na.rm = TRUE), c(TRUE)) @@ -1214,10 +1250,15 @@ organizeCalculatedResults <- function(calculatedResults, inputFormat, formatPara } # Call the function that extracts valueKinds, units, conc, concunits from the headers - valueKinds <- extractValueKinds(calculatedResultsValueKindRow, ignoreTheseAsValueKinds, uncertaintyType, + valueKinds <- extractValueKinds(valueKindsVector = calculatedResultsValueKindRow, ignoreHeaders = ignoreTheseAsValueKinds, uncertaintyType = uncertaintyType, uncertaintyCodeWord, commentCol, commentCodeWord, stateAssignments, hiddenColumns, linkColumns, classRow, stateKindRow, stateTypeRow, - codeAssignments = codeAssignments) + codeAssignments = codeAssignments, conditionColumns) + +#(valueKindsVector, ignoreHeaders = NULL, uncertaintyType, uncertaintyCodeWord, +# commentCol, commentCodeWord, stateAssignments, hiddenColumns, linkColumns, classRow, +# stateKindRow, stateTypeRow, codeAssignments = NULL) + if (any(duplicated(valueKinds$reshapeText[!is.na(valueKinds$uncertaintyType)]))) { stopUser("Only one standard deviation may be assigned for a column. Remove the duplicate standard deviation.") @@ -1467,8 +1508,24 @@ organizeCalculatedResults <- function(calculatedResults, inputFormat, formatPara & is.na(organizedData$inlineFileValue) & is.na(organizedData$codeValue) ), ] - - return(organizedData) + + ## modify valueKinds to return + # Add data class and hidden/shown to the valueKinds + if (!is.null(mainCode)) { + notMainCode <- (calculatedResultsValueKindRow != mainCode) & + (is.null(link) | (calculatedResultsValueKindRow != "link")) + } else { + notMainCode <- (is.null(link) | (calculatedResultsValueKindRow != "link")) + } + valueKinds$dataClass <- classRow[notMainCode] + valueKinds$valueType <- translateClassToValueType(valueKinds$dataClass) + hideColumn <- hiddenColumns[2:length(hiddenColumns)] + conditionColumn <- conditionColumns[2:length(conditionColumns)] + valueKinds <- cbind(valueKinds, hideColumn, conditionColumn) + valueKinds$order <- seq(1:nrow(valueKinds)) + valueKinds <- valueKinds[ order(valueKinds$order), ] + + return(list(organizedData, valueKinds)) } addFileValue <- function(imageLocation, calculatedResults) { # Adds a "fileValue" attribute to entries of calculated results that have an inlineFileValue @@ -1734,6 +1791,14 @@ createNewProtocol <- function(metaData, lsTransaction, recordedBy) { codeOrigin = "ACAS DDICT", lsTransaction= lsTransaction) + if (!is.null(metaData$"Assay Tree Rule")) { + protocolValues[[length(protocolValues)+1]] <- createStateValue( + recordedBy = recordedBy, + lsType = "stringValue", + lsKind = "assay tree rule", + stringValue = metaData$"Assay Tree Rule"[1], + lsTransaction= lsTransaction) + } protocolStates[[length(protocolStates)+1]] <- createProtocolState(protocolValues=protocolValues, lsTransaction = lsTransaction, recordedBy=recordedBy, @@ -1757,7 +1822,8 @@ createNewProtocol <- function(metaData, lsTransaction, recordedBy) { protocol <- saveProtocol(protocol) } -createNewExperiment <- function(metaData, protocol, lsTransaction, pathToGenericDataFormatExcelFile, recordedBy, configList, replacedExperimentCodes, additionalStates = NULL, modelFitTransformation = NULL) { +createNewExperiment <- function(metaData, protocol, lsTransaction, pathToGenericDataFormatExcelFile, recordedBy, configList, + replacedExperimentCodes, additionalStates = NULL, modelFitTransformation = NULL, columnOrderStates = NULL) { # creates an experiment using the metaData # # Args: @@ -1794,6 +1860,12 @@ createNewExperiment <- function(metaData, protocol, lsTransaction, pathToGeneric stringValue = metaData$Page[1], lsTransaction= lsTransaction) } + if (!is.null(metaData$"Experiment Details")) { + experimentValues[[length(experimentValues)+1]] <- createStateValue(recordedBy = recordedBy,lsType = "clobValue", + lsKind = "experiment details", + clobValue = metaData$"Experiment Details"[1], + lsTransaction= lsTransaction) + } experimentValues[[length(experimentValues)+1]] <- createStateValue(recordedBy = recordedBy,lsType = "dateValue", lsKind = "completion date", dateValue = as.numeric(format(as.Date(metaData$"Assay Date"[1]), "%s"))*1000, @@ -1864,7 +1936,9 @@ createNewExperiment <- function(metaData, protocol, lsTransaction, pathToGeneric if(!is.null(additionalStates)) { experimentStates <- c(experimentStates, additionalStates) } - + if(!is.null(columnOrderStates)) { + experimentStates <- c(experimentStates, columnOrderStates) + } # Create a label for the experiment name experimentName <- trim(gsub("CREATETHISEXPERIMENT$", "", metaData$"Experiment Name"[1])) experimentLabels <- list() @@ -1898,6 +1972,7 @@ createNewExperiment <- function(metaData, protocol, lsTransaction, pathToGeneric lsTags=lsTags) # Save the experiment to the server + #saveSession('/tmp/experiment.rda') experiment <- saveExperiment(experiment) experiment <- getExperimentById(experiment$id) return(experiment) @@ -1914,6 +1989,7 @@ validateProject <- function(projectName, configList, username, protocolName = NU # The project code if validation was successful, or the empty string if it was not require('RCurl') require('rjson') + tryCatch({ projectList <- getURL(paste0(racas::applicationSettings$server.nodeapi.path, racas::applicationSettings$client.service.project.path, "/", username)) }, error = function(e) { @@ -2662,7 +2738,6 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, # library('RCurl') - fullPathToFile <- racas::getUploadedFilePath(pathToGenericDataFormatExcelFile) if (!is.null(reportFilePath) && reportFilePath != "") { reportFilePath <- racas::getUploadedFilePath(reportFilePath) @@ -2677,6 +2752,17 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, if (!file.exists(fullPathToFile)) { stop("SEL: Cannot find input file") } + +## TEST ### +.libPaths('/opt/acas-dataexplorer/acas/r_libs') +library(racas) +library('RCurl') +source('/opt/acas-dataexplorer/acas/src/r/GenericDataParser/generic_data_parser.R') +fullPathToFile <- '/opt/acas-dataexplorer/acas/privateUploads/Tier1c_SEL_test3 (21).xlsx' +recordedBy <- 'goshiro' +configList <- racas::applicationSettings +lsTransaction <- 1234 +## TEST ### genericDataFileDataFrame <- readExcelOrCsv(fullPathToFile) @@ -2708,10 +2794,14 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, mainCode <- "Corporate Batch ID" } calculateGroupingID <- if (rawOnlyFormat) {calculateTreatmemtGroupID} else {NA} - calculatedResults <- organizeCalculatedResults( + organizedResultsList <- organizeCalculatedResults( calculatedResults, inputFormat, formatParameters, mainCode, lockCorpBatchId = formatParameters$lockCorpBatchId, rawOnlyFormat = rawOnlyFormat, errorEnv = errorEnv, precise = precise, calculateGroupingID = calculateGroupingID) + + calculatedResults <- organizedResultsList[[1]] + selColumnOrderInfo <- organizedResultsList[[2]] + if (!is.null(formatParameters$splitSubjects)) { calculatedResults$subjectID <- calculatedResults$groupingID_2 @@ -2760,6 +2850,7 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, customExperimentMetaDataValues <- NULL } + # Get the protocol and experiment and, when not on a dry run, create them if they do not exist newProtocol <- FALSE if (!useExisting) { @@ -2795,11 +2886,14 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, if(!dryRun && !newExperiment && errorFree) { deletedExperimentCodes <- deleteOldData(experiment, useExistingExperiment) } - + + ## SEL column oder info + columnOrderStates <- createColumnOrderStates(selColumnOrderInfo, errorEnv, recordedBy, lsTransaction) + if (!dryRun && errorFree && !useExistingExperiment) { experiment <- createNewExperiment(metaData = validatedMetaData, protocol, lsTransaction, fullPathToFile, recordedBy, configList, deletedExperimentCodes, validatedCustomMetaDataStates, - modelFitTransformation) + modelFitTransformation, columnOrderStates) # If an error occurs, this allows the experiment to still be accessed assign(x="experiment", value=experiment, envir=parent.frame()) @@ -2822,12 +2916,14 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, } else { calculatedResults$experimentID <- experiment$id calculatedResults$experimentVersion <- experiment$version + saveSession('/tmp/beforeUploadData.rda') uploadData(metaData = validatedMetaData,lsTransaction,calculatedResults,treatmentGroupData, subjectData, xLabel,yLabel,tempIdLabel,testOutputLocation,developmentMode,protocol,experiment, fileStartLocation = pathToGenericDataFormatExcelFile, configList=configList, reportFilePath=reportFilePath, reportFileSummary=reportFileSummary, recordedBy, formatParameters$annotationType, mainCode, appendCodeNameList = list(analysisGroup = "curve id")) } + } if(!dryRun) { @@ -2882,6 +2978,8 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, return(summaryInfo) } + + getStateGroups <- function(formatSettings) { #Gets stateGroups from configuration list @@ -3079,7 +3177,7 @@ organizeSubjectData <- function( lockCorpBatchId= F, errorEnv= errorEnv, precise = precise, link = link, calculateGroupingID = preciseTreatmentGroupID, stateAssignments = stateAssignments, concColumn = concColumn, - codeAssignments = codeAssignments) + codeAssignments = codeAssignments)[[1]] subjectData2 <- as.data.table(subjectData2) subjectData2[, treatmentGroupID := groupingID] @@ -3393,3 +3491,118 @@ external.parseGenericData <- function(request) { racasMessenger$logger <- logger(logName = "com.mcneilco.acas.genericDataParser", reset=TRUE) return(parseGenericData(request)) } +generateExptColStateValues <- function(dataRow, recordedBy, lsTransaction){ + values <- list() + if (!is.null(dataRow$order) && !is.na(dataRow$order)) { + values[[length(values)+1]] <- createStateValue(lsType = "numericValue", + lsKind = "column order", + lsTransaction = lsTransaction, + recordedBy = recordedBy, + numericValue = dataRow$order + )} + if (!is.null(dataRow$valueKind) && !is.na(dataRow$valueKind)) { + values[[length(values)+1]] <- createStateValue(lsType = "stringValue", + lsKind = "column name", + lsTransaction = lsTransaction, + recordedBy = recordedBy, + stringValue = dataRow$valueKind + )} + if (!is.null(dataRow$Conc) && !is.na(dataRow$Conc)) { + values[[length(values)+1]] <- createStateValue(lsType = "numericValue", + lsKind = "column concentration", + lsTransaction = lsTransaction, + recordedBy = recordedBy, + numericValue = as.numeric(dataRow$Conc) + )} + if (!is.null(dataRow$concUnits) && !is.na(dataRow$concUnits)) { + values[[length(values)+1]] <- createStateValue(lsType = "stringValue", + lsKind = "column conc units", + lsTransaction = lsTransaction, + recordedBy = recordedBy, + stringValue = as.character(dataRow$concUnits) + )} + if (!is.null(dataRow$time) && !is.na(dataRow$time)) { + values[[length(values)+1]] <- createStateValue(lsType = "numericValue", + lsKind = "column time", + lsTransaction = lsTransaction, + recordedBy = recordedBy, + numericValue = as.numeric(dataRow$time) + )} + if (!is.null(dataRow$timeUnit) && !is.na(dataRow$timeUnit)) { + values[[length(values)+1]] <- createStateValue(lsType = "stringValue", + lsKind = "column time units", + lsTransaction = lsTransaction, + recordedBy = recordedBy, + stringValue = as.character(dataRow$timeUnit) + )} + if (!is.null(dataRow$Units) && !is.na(dataRow$Units)) { + values[[length(values)+1]] <- createStateValue(lsType = "stringValue", + lsKind = "column units", + lsTransaction = lsTransaction, + recordedBy = recordedBy, + stringValue = as.character(dataRow$Units) + )} + if (!is.null(dataRow$valueType) && !is.na(dataRow$valueType)) { + values[[length(values)+1]] <- createStateValue(lsType = "stringValue", + lsKind = "column type", + lsTransaction = lsTransaction, + recordedBy = recordedBy, + stringValue = dataRow$valueType + )} + if (!is.null(dataRow$hideColumn) && !is.na(dataRow$hideColumn)) { + values[[length(values)+1]] <- createStateValue(lsType = "stringValue", + lsKind = "hide column", + lsTransaction = lsTransaction, + recordedBy = recordedBy, + stringValue = as.character(dataRow$hideColumn) + )} + if (!is.null(dataRow$conditionColumn) && !is.na(dataRow$conditionColumn)) { + values[[length(values)+1]] <- createStateValue(lsType = "stringValue", + lsKind = "condition column", + lsTransaction = lsTransaction, + recordedBy = recordedBy, + stringValue = as.character(dataRow$conditionColumn) + )} +# return(removeEmptyValues_DV(values)) + return(values) +} +createColumnOrderStates <- function(exptDataColumns=selColumnOrderInfo, errorEnv, recordedBy, lsTransaction){ +exptDataColumns=selColumnOrderInfo + experimentStates <- list() + if ((class(exptDataColumns) == 'data.frame') && (nrow(exptDataColumns) > 0)){ + ## create new experiment state to store the column order information (we will have state tuples for each order) + +#saveSession('/tmp/scratchData') + + ## note: save the exptColumns dataframe as a json object for future hydration + ## continue to save the info as a set to state tuples until we refactor the dataviewer code + ## may just need to keep the data condition info +# experimentStates[[length(experimentStates)+1]] <- createExperimentState(experimentValues=list( +# createStateValue(recordedBy = recordedBy, +# lsType = "clobValue", +# lsKind = "data columns json", +# clobValue = jsonlite::toJSON(exptDataColumns), +# lsTransaction= lsTransaction)), +# lsTransaction = lsTransaction, +# recordedBy=recordedBy, +# lsType="metadata", +# lsKind="data column object") + + for (i in 1:nrow(exptDataColumns)){ + experimentStates[[length(experimentStates)+1]] <- createExperimentState(experimentValues = generateExptColStateValues(dataRow=exptDataColumns[i,], + recordedBy = recordedBy, + lsTransaction = lsTransaction + ), + recordedBy = recordedBy, + lsType = "metadata", + lsKind = "data column order", + comments = "", + lsTransaction = lsTransaction + ) + } + } + return(experimentStates) +} + + + diff --git a/modules/ServerAPI/conf/ExperimentConfJSON.coffee b/modules/ServerAPI/conf/ExperimentConfJSON.coffee index 4670db836..db483d75d 100644 --- a/modules/ServerAPI/conf/ExperimentConfJSON.coffee +++ b/modules/ServerAPI/conf/ExperimentConfJSON.coffee @@ -40,6 +40,9 @@ , typeName: "metadata" kindName: "data column order" + , + typeName: "metadata" + kindName: "data column object" ] valuetypes: @@ -158,6 +161,21 @@ , typeName: "stringValue" kindName: "hide column" + , + typeName: "numericValue" + kindName: "column concentration" + , + typeName: "stringValue" + kindName: "column conc units" + , + typeName: "numericValue" + kindName: "column time" + , + typeName: "stringValue" + kindName: "column time units" + , + typeName: "stringValue" + kindName: "condition column" , typeName: "codeValue" kindName: "agonist batch code" From 1774c79280366f490ccb2d4cda0f4f3a86a1ae9d Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Fri, 28 Jul 2017 10:32:09 -0700 Subject: [PATCH 125/576] remove debug saveSession call --- modules/GenericDataParser/src/server/generic_data_parser.R | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 7758a9756..56a7675e2 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -1972,7 +1972,6 @@ createNewExperiment <- function(metaData, protocol, lsTransaction, pathToGeneric lsTags=lsTags) # Save the experiment to the server - #saveSession('/tmp/experiment.rda') experiment <- saveExperiment(experiment) experiment <- getExperimentById(experiment$id) return(experiment) @@ -2916,7 +2915,6 @@ lsTransaction <- 1234 } else { calculatedResults$experimentID <- experiment$id calculatedResults$experimentVersion <- experiment$version - saveSession('/tmp/beforeUploadData.rda') uploadData(metaData = validatedMetaData,lsTransaction,calculatedResults,treatmentGroupData, subjectData, xLabel,yLabel,tempIdLabel,testOutputLocation,developmentMode,protocol,experiment, fileStartLocation = pathToGenericDataFormatExcelFile, configList=configList, @@ -3570,10 +3568,7 @@ createColumnOrderStates <- function(exptDataColumns=selColumnOrderInfo, errorEnv exptDataColumns=selColumnOrderInfo experimentStates <- list() if ((class(exptDataColumns) == 'data.frame') && (nrow(exptDataColumns) > 0)){ - ## create new experiment state to store the column order information (we will have state tuples for each order) - -#saveSession('/tmp/scratchData') - + ## create new experiment state to store the column order information (we will have state tuples for each order) ## note: save the exptColumns dataframe as a json object for future hydration ## continue to save the info as a set to state tuples until we refactor the dataviewer code ## may just need to keep the data condition info From c163f156965037c42b002c69cf1086a429a99468 Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Fri, 28 Jul 2017 10:42:58 -0700 Subject: [PATCH 126/576] clean up code (remove debug artifacts) --- .../src/server/generic_data_parser.R | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 56a7675e2..8184c8641 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -1255,10 +1255,6 @@ organizeCalculatedResults <- function(calculatedResults, inputFormat, formatPara hiddenColumns, linkColumns, classRow, stateKindRow, stateTypeRow, codeAssignments = codeAssignments, conditionColumns) -#(valueKindsVector, ignoreHeaders = NULL, uncertaintyType, uncertaintyCodeWord, -# commentCol, commentCodeWord, stateAssignments, hiddenColumns, linkColumns, classRow, -# stateKindRow, stateTypeRow, codeAssignments = NULL) - if (any(duplicated(valueKinds$reshapeText[!is.na(valueKinds$uncertaintyType)]))) { stopUser("Only one standard deviation may be assigned for a column. Remove the duplicate standard deviation.") @@ -2751,17 +2747,6 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, if (!file.exists(fullPathToFile)) { stop("SEL: Cannot find input file") } - -## TEST ### -.libPaths('/opt/acas-dataexplorer/acas/r_libs') -library(racas) -library('RCurl') -source('/opt/acas-dataexplorer/acas/src/r/GenericDataParser/generic_data_parser.R') -fullPathToFile <- '/opt/acas-dataexplorer/acas/privateUploads/Tier1c_SEL_test3 (21).xlsx' -recordedBy <- 'goshiro' -configList <- racas::applicationSettings -lsTransaction <- 1234 -## TEST ### genericDataFileDataFrame <- readExcelOrCsv(fullPathToFile) @@ -3565,7 +3550,6 @@ generateExptColStateValues <- function(dataRow, recordedBy, lsTransaction){ return(values) } createColumnOrderStates <- function(exptDataColumns=selColumnOrderInfo, errorEnv, recordedBy, lsTransaction){ -exptDataColumns=selColumnOrderInfo experimentStates <- list() if ((class(exptDataColumns) == 'data.frame') && (nrow(exptDataColumns) > 0)){ ## create new experiment state to store the column order information (we will have state tuples for each order) From c00d6c7a1fdbdc465b700e8a3448b08fc6a46c6f Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Tue, 1 Aug 2017 10:01:37 -0700 Subject: [PATCH 127/576] fix valueKind return with DR data. --- .../GenericDataParser/src/server/generic_data_parser.R | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 5c97226ef..1d921f0a3 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -1519,11 +1519,17 @@ organizeCalculatedResults <- function(calculatedResults, inputFormat, formatPara } else { notMainCode <- (is.null(link) | (calculatedResultsValueKindRow != "link")) } - valueKinds$dataClass <- classRow[notMainCode] + + # valueKinds$dataClass <- classRow[notMainCode] valueKinds$valueType <- translateClassToValueType(valueKinds$dataClass) hideColumn <- hiddenColumns[2:length(hiddenColumns)] conditionColumn <- conditionColumns[2:length(conditionColumns)] - valueKinds <- cbind(valueKinds, hideColumn, conditionColumn) + if (is.null(concColumn)){ + valueKinds <- cbind(valueKinds, hideColumn, conditionColumn) + } else { + valueKinds$hideColumn <- !valueKinds$publicData + valueKinds$conditionColumn <- FALSE + } valueKinds$order <- seq(1:nrow(valueKinds)) valueKinds <- valueKinds[ order(valueKinds$order), ] From 1107dd666d85e1382f3331c07eed34b8954a686d Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 1 Aug 2017 10:28:08 -0700 Subject: [PATCH 128/576] Fixed issues with emptying interaction field after it had been filled out, and with re-selecting an interaction after the field had been emptied. Added protecting clause to prevent processing of null "thing" in empty interaction before save. --- modules/Components/src/client/ACASFormFields.coffee | 6 ++++-- modules/ServerAPI/src/client/Thing.coffee | 7 ++++--- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index a8635a247..febb0c582 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -51,6 +51,8 @@ class window.ACASFormAbstractFieldController extends Backbone.View mdl = @getModel() if mdl.has 'labelText' if mdl.get('labelText')=="" then empty = true + else if mdl.has 'itxThing' + if !mdl.get('itxThing').get('id') then empty = true else if mdl.get('value')=="" or !mdl.get('value')? or mdl.get('value')=="unassigned" then empty = true @@ -324,13 +326,13 @@ class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractF thingID = @thingSelectController.getSelectedID() if thingID? @getModel().setItxThing id: thingID + @getModel().set ignored: false else @setEmptyValue() super() setEmptyValue: -> @getModel().set ignored: true - @getModel().setItxThing null isEmpty: -> empty = true @@ -344,7 +346,7 @@ class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractF renderModelContent: => @userInputEvent = false - if @getModel().getItxThing().id? + if @getModel()? and @getModel().getItxThing().id? labels = new LabelList @getModel().getItxThing().lsLabels labelText = labels.pickBestNonEmptyLabel().get('labelText') @thingSelectController.setSelectedCode diff --git a/modules/ServerAPI/src/client/Thing.coffee b/modules/ServerAPI/src/client/Thing.coffee index faf3c1aff..a20aad967 100644 --- a/modules/ServerAPI/src/client/Thing.coffee +++ b/modules/ServerAPI/src/client/Thing.coffee @@ -167,9 +167,10 @@ class window.Thing extends Backbone.Model else thing = itx.get 'secondLsThing' # delete thing['version'] - delete thing['lsLabels'] - delete thing['lsStates'] - delete thing['lsTransaction'] + if thing? + delete thing['lsLabels'] + delete thing['lsStates'] + delete thing['lsTransaction'] setRByAndRDate: (data) -> From f0805b6d08810ade33f8729b87b5c92d6acc5f28 Mon Sep 17 00:00:00 2001 From: Matthew Shaw Date: Tue, 1 Aug 2017 14:05:33 -0600 Subject: [PATCH 129/576] #178 Fixed issue where closing all browser tabs open to module didn't release connection to balance. --- .../src/client/RealtimeDeviceConnectionController.coffee | 8 +++++--- .../server/routes/RealtimeDeviceConnectionSockets.coffee | 9 +++++++-- 2 files changed, 12 insertions(+), 5 deletions(-) diff --git a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee index f93ca553c..84255302f 100644 --- a/modules/Components/src/client/RealtimeDeviceConnectionController.coffee +++ b/modules/Components/src/client/RealtimeDeviceConnectionController.coffee @@ -67,6 +67,7 @@ class window.RealtimeDeviceConnectionController extends Backbone.View initialize: -> @isConnectedToDevice = false + @isConnectingToDevice = false @testMode = @options.testMode if @options.socket? @socket = @options.socket @@ -125,7 +126,8 @@ class window.RealtimeDeviceConnectionController extends Backbone.View zeroBalanceCallback: (err, data) => connectToDevice: => - unless @isConnectedToDevice + unless @isConnectedToDevice or @isConnectingToDevice + @isConnectingToDevice = true @selectedInstrumentCode = @$('.bv_deviceSelectContainer').val() @selectedDevice = @deviceCollection.findWhere({"codeName": @selectedInstrumentCode}) @$(".bv_connecting").removeClass "hide" @@ -137,6 +139,7 @@ class window.RealtimeDeviceConnectionController extends Backbone.View console.info "overide if needed" connectToDeviceCallback: (err, data) => + @isConnectingToDevice = false if err @isConnectedToDevice = false @setStateToDisconnected() @@ -263,8 +266,7 @@ class window.RealtimeDeviceConnectionController extends Backbone.View @setStateToDisconnected() alertAllDisconnectedFromDevice: => - unless @isConnectedToDevice - @connectToDevice() + @connectToDevice() disconnectedByAnotherUser: (msg) => @displayDisconnectedModal(msg.username) diff --git a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee index 7004647aa..3ca192a2d 100644 --- a/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee +++ b/modules/Components/src/server/routes/RealtimeDeviceConnectionSockets.coffee @@ -182,6 +182,9 @@ class DeviceSocketController socket.on('disconnected', => @handleDisconnected(socket) ) + socket.on('disconnect', => + @handleDisconnected(socket) + ) socket.on('disconnectFromBalance', (callback) => @handleDisconnect(socket, callback) ) @@ -237,10 +240,10 @@ class DeviceSocketController balanceAccess.isAvailable = true socket.broadcast.to(nextUserInQueue.clientId).emit('youShouldTryConnecting') else - socket.broadcast.emit('alertAllDisconnectedFromDevice') balanceAccess.clearHeartBeat() balanceAccess.disconnectFromBalance() balanceAccess.isAvailable = true + socket.broadcast.emit('alertAllDisconnectedFromDevice') # socket.emit('disconnectedFromDevice') @@ -252,11 +255,13 @@ class DeviceSocketController nextUserInQueue = balanceAccess.getNextUser() if nextUserInQueue? + balanceAccess.isAvailable = true socket.broadcast.to(nextUserInQueue.clientId).emit('youShouldTryConnecting') else - socket.broadcast.emit('alertAllDisconnectedFromDevice') balanceAccess.clearHeartBeat() balanceAccess.disconnectFromBalance() + balanceAccess.isAvailable = true + socket.broadcast.emit('alertAllDisconnectedFromDevice') socket.leave(@usersInRoom[socket.id]) callback() From cf9cee60940ced8e1e9b06dca563ab9e6587ba75 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 2 Aug 2017 13:32:17 -0700 Subject: [PATCH 130/576] Added simple redirect to curveCurator deeplink for "query tool" "CurveCurator" and added it as a default configured viewer. Resolves #198 --- conf/config.properties.example | 2 +- .../ServerAPI/src/server/routes/OpenExptWithQueryTool.coffee | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 49b6ffd22..7b1e977fd 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -248,7 +248,7 @@ client.fullpath=http://${client.host}:${client.port} # Query tool settings client.service.result.viewer.displayName=Data Viewer -client.service.result.viewer.configuredViewers=DataViewer +client.service.result.viewer.configuredViewers=DataViewer,CurveCurator client.service.result.viewer.defaultViewer=DataViewer client.service.result.viewer.dataViewer.exptTree.showOnlyMatches=false client.service.result.viewer.liveDesign.baseUrl= diff --git a/modules/ServerAPI/src/server/routes/OpenExptWithQueryTool.coffee b/modules/ServerAPI/src/server/routes/OpenExptWithQueryTool.coffee index ef96e46f4..bdf26d119 100644 --- a/modules/ServerAPI/src/server/routes/OpenExptWithQueryTool.coffee +++ b/modules/ServerAPI/src/server/routes/OpenExptWithQueryTool.coffee @@ -32,6 +32,9 @@ exports.redirectToQueryToolForExperiment = (req, resp) -> url = url.replace /(\r\n|\n|\r)/gm,"" console.log "redirecting to #{url}" resp.redirect '/dataViewer/filterByExpt/'+req.query.experiment + else if tool is 'CurveCurator' + url = '/curveCurator/'+encodeURIComponent(req.query.experiment) + resp.redirect url else # Could later add customer specific call here resp.status(500).send('Invalid viewer tool') \ No newline at end of file From 84389f247e7120ccbfb66546760886a408a4521f Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 2 Aug 2017 14:02:23 -0700 Subject: [PATCH 131/576] Fixed typo in error message in Curve Curator when an experiment has not been fit. Fixes #201 --- modules/CurveAnalysis/src/server/CurveStubs.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/CurveAnalysis/src/server/CurveStubs.R b/modules/CurveAnalysis/src/server/CurveStubs.R index c2b3ab3c5..40b69bb69 100644 --- a/modules/CurveAnalysis/src/server/CurveStubs.R +++ b/modules/CurveAnalysis/src/server/CurveStubs.R @@ -26,7 +26,7 @@ get_curve_stubs <- function(myMessenger, GET) { if(myMessenger$errors[[1]]$message == "no experiment results found") { return(handle_response(HTTP_NOT_FOUND , "no experiment results found")) } else if (myMessenger$errors[[1]]$message == "experiment not fit") { - return(handle_response(HTTP_BAD_REQUEST, "Experiment has not been not fit")) + return(handle_response(HTTP_BAD_REQUEST, "Experiment has not been fit")) } else if (myMessenger$errors[[1]]$message == "experiment has been deleted") { return(handle_response(HTTP_BAD_REQUEST, "Experiment has been deleted")) } else { From 226a8d9094a3cf6b779d2104694e2efb96aa8999 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Mon, 7 Aug 2017 10:08:37 -0700 Subject: [PATCH 132/576] Fixed bug in enabling/disabling save button in state display table editor --- .../Components/src/client/ACASFormStateDisplayUpdate.coffee | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee index 128a08a63..59699ca6e 100644 --- a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee +++ b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee @@ -261,13 +261,14 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View @$('.bv_changeValueHeader').html @tableDef.changeValueHeader reasonForUpdateChanged: -> - @comment = @commentPrefix + @$('.bv_reasonForUpdate').val() + reasonForUpdate = UtilityFunctions::getTrimmedInput @$('.bv_reasonForUpdate') + @comment = @commentPrefix + reasonForUpdate labelText = @allowedCommentLength-@comment.length + " characters remaining" @$('.bv_charactersRemaining').text(labelText) @formUpdated() formUpdated: => - if @comment == @commentPrefix or @newField.isEmpty() + if @comment == @commentPrefix or @newField.isEmpty() or !@comment? @$('.bv_saveBtn').attr('disabled','disabled') else @$('.bv_saveBtn').removeAttr('disabled') From 4078069f1524374b4ededa7d69ff35e343101fbc Mon Sep 17 00:00:00 2001 From: John McNeil Date: Mon, 7 Aug 2017 20:16:56 -0700 Subject: [PATCH 133/576] collapsible menus feature complete --- conf/config.properties.example | 46 ++++++++++--------- .../src/client/ModuleLauncher.coffee | 44 ++++++++++++++++-- .../src/client/ModuleLauncherView.html | 5 ++ .../client/ModuleMenusConfiguration.coffee | 2 + modules/ModuleMenus/src/client/style.css | 23 ++++++++++ 5 files changed, 94 insertions(+), 26 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 42bc23aaa..46725fb80 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -179,6 +179,30 @@ client.service.external.structure.url=http://tomcat:8080/cmpdreg/structureimage/ # url to lot details client.service.external.lotDetails.url=/cmpdreg/#lot/ +################################ +# Module Menus ACAS Home Page Options +################################ +# If module is customized and the ACAS header name needs to be replaced, you can set the following options +client.moduleMenus.logoText=ACAS +client.moduleMenus.logoImageFilePath= +client.moduleMenus.homePageMessage=Welcome to ACAS +client.moduleMenus.copyrightMessage=© John McNeil & Company 2012-2017 +# client.moduleMenus.menuConfigurationSettings=ModuleMenusConfiguration +# If summary statistics is an included feature, set the following to true +client.moduleMenus.summaryStats=false +# For navigation to external ACAS modules from ACAS homepage +client.moduleMenus.modules.external=[{"displayName": "Compound Registration", "href": "/cmpdreg/"},\ + {"displayName": "Compound Registration Bulk Loader", "href":"/CmpdRegBulkLoader"}] +client.moduleMenus.dataViewerDeepLink=/dataViewer +# For auto-starting a module when opening up ACAS +client.moduleMenus.moduleAutoLaunchName= + +client.leaveACASMessage=There are no unsaved changes. +#Add user roles that represent groups allowed to fast user switch +#client.moduleMenus.fastUserSwitchingRoles=[{"lsKind":"PROJ-00000001","lsType":"Project","roleName":"User"},{"lsKind":"PROJ-00000002","lsType":"Project","roleName":"User"}] +client.moduleMenus.fastUserSwitchingRoles=[] +client.moduleMenus.fastUserSwitchingChangeUserRoles=false + ################################ # Uncategorized ################################ @@ -319,24 +343,6 @@ server.service.external.inventory.database.password= server.security.authstrategy=database #server.security.properties.path=/opt/seurat/SeuratServer/users.txt - -## ACAS Home Page Options -# If module is customized and the ACAS header name needs to be replaced, you can set the following options -client.moduleMenus.logoText=ACAS -client.moduleMenus.logoImageFilePath= -client.moduleMenus.homePageMessage=Welcome to ACAS -client.moduleMenus.copyrightMessage=© John McNeil & Company 2012-2017 -# client.moduleMenus.menuConfigurationSettings=ModuleMenusConfiguration -# If summary statistics is an included feature, set the following to true -client.moduleMenus.summaryStats=false -# For navigation to external ACAS modules from ACAS homepage -client.moduleMenus.modules.external=[{"displayName": "Compound Registration", "href": "/cmpdreg/"},\ - {"displayName": "Compound Registration Bulk Loader", "href":"/CmpdRegBulkLoader"}] -client.moduleMenus.dataViewerDeepLink=/dataViewer -# For auto-starting a module when opening up ACAS -client.moduleMenus.moduleAutoLaunchName= - -client.leaveACASMessage=There are no unsaved changes. client.scientistCodeOrigin=ACAS authors client.molecularTargetCodeOrigin=ACAS DDICT @@ -531,7 +537,3 @@ client.roles.crossProjectLoaderRole=ROLE_ACAS-CROSS-PROJECT-LOADER # For whether protocols and experiments should have sequential user defined corpName labels client.entity.saveInitialsCorpName=false -#Add user roles that represent groups allowed to fast user switch -client.moduleMenus.fastUserSwitchingRoles=[] -#client.moduleMenus.fastUserSwitchingRoles=[{"lsKind":"PROJ-00000001","lsType":"Project","roleName":"User"},{"lsKind":"PROJ-00000002","lsType":"Project","roleName":"User"}] -client.moduleMenus.fastUserSwitchingChangeUserRoles=false \ No newline at end of file diff --git a/modules/ModuleMenus/src/client/ModuleLauncher.coffee b/modules/ModuleMenus/src/client/ModuleLauncher.coffee index 1afc0c3d6..8c01cbb03 100644 --- a/modules/ModuleMenus/src/client/ModuleLauncher.coffee +++ b/modules/ModuleMenus/src/client/ModuleLauncher.coffee @@ -8,6 +8,7 @@ class window.ModuleLauncher extends Backbone.Model isActive: false isDirty: false autoLaunchName: null + collapsible: false requestActivation: -> if @get('externalLink')? @@ -94,11 +95,37 @@ class window.ModuleLauncherMenuHeaderController extends Backbone.View @ +class window.ModuleLauncherMenuCollapsibleHeaderController extends Backbone.View + template: _.template($("#ModuleLauncherMenuCollapsibleHeaderView").html()) + tagName: 'div' + className: 'bv_collapsibleHeaderController bv_notTopHeader' + + events: + 'click .bv_moduleCategory': "handleClick" + + render: => + if (@model.get('requireUserRoles')? and !UtilityFunctions::testUserHasRole window.AppLaunchParams.loginUser, @model.get('requireUserRoles')) + $(@el).hide() + else + $(@el).empty() + $(@el).html @template() + @$('.bv_moduleCategory').prepend @model.get('menuName') + + @ + + addSubMenu: (el) -> + @$('.bv_modules').append el + + handleClick: => + @$('.bv_modules').slideToggle 200 + @$('.bv_caret').toggle() + class window.ModuleLauncherMenuListController extends Backbone.View template: _.template($("#ModuleLauncherMenuListView").html()) initialize: -> + @lastCollapsibleHeader = null #@collection.bind 'reset', @render() render: => @@ -107,17 +134,27 @@ class window.ModuleLauncherMenuListController extends Backbone.View $(@el).empty() $(@el).html @template() @collection.each @addOne + @$('.bv_collapsibleHeaderController:eq(0)').removeClass "bv_notTopHeader" @ addOne: (menuItem) => menuItemController = @makeMenuItemController(menuItem) - @$('.bv_navList').append menuItemController.render().el + if !menuItem.get('isHeader') and @lastCollapsibleHeader? + @lastCollapsibleHeader.addSubMenu menuItemController.render().el + else + @$('.bv_navList').append menuItemController.render().el makeMenuItemController: (menuItem) -> if menuItem.get('isHeader') - menuItemCont = new ModuleLauncherMenuHeaderController - model: menuItem + if menuItem.get('collapsible') + menuItemCont = new ModuleLauncherMenuCollapsibleHeaderController + model: menuItem + @lastCollapsibleHeader = menuItemCont + else + menuItemCont = new ModuleLauncherMenuHeaderController + model: menuItem + @lastCollapsibleHeader = null else menuItemCont = new ModuleLauncherMenuController model: menuItem @@ -168,7 +205,6 @@ class window.ModuleLauncherController extends Backbone.View @moduleController.render() @model.set isLoaded: true - handleDeactivation: => $(@el).hide() diff --git a/modules/ModuleMenus/src/client/ModuleLauncherView.html b/modules/ModuleMenus/src/client/ModuleLauncherView.html index de72e7290..db6570201 100644 --- a/modules/ModuleMenus/src/client/ModuleLauncherView.html +++ b/modules/ModuleMenus/src/client/ModuleLauncherView.html @@ -12,6 +12,11 @@ + + diff --git a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee index fb75e6b4b..3246c5821 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee @@ -35,6 +35,7 @@ window.ModuleMenusConfiguration = , isHeader: true menuName: "Search and Edit" + collapsible: true , isHeader: false, menuName: "Protocol Browser" mainControllerClassName: "ProtocolBrowserController" @@ -47,6 +48,7 @@ window.ModuleMenusConfiguration = , isHeader: true menuName: "Admin" + collapsible: true , isHeader: false menuName: "Admin Panel" diff --git a/modules/ModuleMenus/src/client/style.css b/modules/ModuleMenus/src/client/style.css index fcc00748a..ff5a22501 100644 --- a/modules/ModuleMenus/src/client/style.css +++ b/modules/ModuleMenus/src/client/style.css @@ -104,3 +104,26 @@ body { margin-top:0px; margin-bottom: 2px; } + +.bv_collapsibleHeaderController .bv_caret { + margin-left: 5px; + /*border-bottom-color: #999999;*/ +} + +.bv_collapsibleHeaderController .bv_modules { + list-style-type: none; + margin-left: 15px; +} +.bv_collapsibleHeaderController .bv_moduleCategory { + cursor: pointer; +} + +.bv_collapsibleHeaderController li { + margin-top: 3px; + + /*margin-bottom: 5px;*/ +} + +.bv_notTopHeader { + margin-top: 5px; +} From fafbf6da68eb41fbbadf23fe9546480bde6b7daf Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 8 Aug 2017 10:13:47 -0700 Subject: [PATCH 134/576] Installed pip, argparse, requests, and psycopg2 required by sync_projects.py and ld_entitlements.py. Fixes #205 --- Dockerfile | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/Dockerfile b/Dockerfile index f08f9e555..9c83f7ff1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -67,6 +67,13 @@ ENV PREPARE_CONFIG_FILES=true ENV RUN_SYSTEM_TEST=true ENV ACAS_HOME=$BUILD_PATH +#Install python dependencies +USER root +RUN curl -SLO dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm && rpm -ivh epel-release-6-8.noarch.rpm && rm epel-release-6-8.noarch.rpm +RUN yum install -y python-pip python-psycopg2 +RUN pip install argparse requests psycopg2 +USER runner + EXPOSE 3000 EXPOSE 3001 From 298d29d60d7528048c73d40cda6ebfbfa8ff9350 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 8 Aug 2017 10:55:37 -0700 Subject: [PATCH 135/576] Add active:{true | false} to projects in groupsJSON, and filter out inactive projects from JSON sent to ld_entitlements.py. Fixes #207 --- .../ServerAPI/src/server/routes/SyncProjectsUsers.coffee | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/ServerAPI/src/server/routes/SyncProjectsUsers.coffee b/modules/ServerAPI/src/server/routes/SyncProjectsUsers.coffee index aceb1a354..adfc3ec29 100644 --- a/modules/ServerAPI/src/server/routes/SyncProjectsUsers.coffee +++ b/modules/ServerAPI/src/server/routes/SyncProjectsUsers.coffee @@ -43,6 +43,7 @@ exports.getGroupsJSON = (callback) -> _.each acasGroupsAndProjects.projects, (project) -> projectGroups = alias: project.code + active: if project.active? then project.active else true groups: project.groups groupsJSON.projects.push projectGroups callback groupsJSON, acasGroupsAndProjects @@ -178,7 +179,12 @@ exports.validateLiveDesignConfigs = (configJSON) -> exports.syncLiveDesignRoles = (caughtPythonErrors, pythonErrors, configJSON, groupsJSON, callback) -> if exports.validateLiveDesignConfigs(configJSON) exec = require('child_process').exec + _ = require "underscore" config = require '../conf/compiled/conf.js' + #Filter out ignored projects + filteredProjects = _.filter groupsJSON.projects, (project) -> + project.active + groupsJSON.projects = filteredProjects #Call ld_entitlements.py to update list of user-project ACLs in LiveDesign command = "python ./src/python/ServerAPI/syncProjectsUsers/ld_entitlements.py " command += "\'"+(JSON.stringify configJSON.ld_server)+"\' "+"\'"+(JSON.stringify groupsJSON)+"\'" From 44b64448e9193227b6bfe49ea02800368c79e651 Mon Sep 17 00:00:00 2001 From: goshiro2013 Date: Tue, 8 Aug 2017 15:37:01 -0700 Subject: [PATCH 136/576] fix vendor and update routes --- .../src/server/routes/CmpdRegAdminRoutes.coffee | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee b/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee index 8167edd6a..d719b85e3 100644 --- a/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee +++ b/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee @@ -4,8 +4,8 @@ exports.setupAPIRoutes = (app, loginRoutes) -> app.get '/api/cmpdRegAdmin/vendors/codeName/:code', exports.getCmpdRegVendorByCode app.post '/api/cmpdRegAdmin/vendors/validateBeforeSave', exports.validateCmpdRegVendorBeforeSave app.post '/api/cmpdRegAdmin/vendors', exports.saveCmpdRegVendor - app.put '/api/cmpdRegAdmin/vendors', exports.updateCmpdRegVendor - app.delete '/api/cmpdRegAdmin/vendors', exports.deleteCmpdRegVendor + app.put '/api/cmpdRegAdmin/vendors/:id', exports.updateCmpdRegVendor + app.delete '/api/cmpdRegAdmin/vendors/:id', exports.deleteCmpdRegVendor exports.setupRoutes = (app, loginRoutes) -> app.get '/api/cmpdRegAdmin/vendors/validate/:code', loginRoutes.ensureAuthenticated, exports.validateCmpdRegVendor @@ -200,7 +200,7 @@ exports.updateCmpdRegVendor = (req, resp) -> config = require '../conf/compiled/conf.js' console.log "exports.updateCmpdRegVendor" - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors/updateVendor' + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors' request( method: 'PUT' url: cmpdRegCall From 3e1e98707ff60c6ce636bdffe96feeb3bc465201 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Tue, 8 Aug 2017 15:53:20 -0700 Subject: [PATCH 137/576] feature/creg-enhancement-101: refactored code for CmpdRegVendor --- .../src/client/CmpdRegVendor.coffee | 204 ++++++------------ .../src/client/CmpdRegVendor.html | 26 ++- .../src/client/CmpdRegVendorBrowser.coffee | 3 +- .../src/client/CmpdRegVendorBrowserView.html | 4 +- 4 files changed, 86 insertions(+), 151 deletions(-) diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee index 119091493..9a668ccf6 100644 --- a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee +++ b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee @@ -8,8 +8,22 @@ class window.Vendor extends Backbone.Model code: null id: null - isEditable: -> - return true + validate: (attrs) -> + errors = [] + if attrs.code? and @isNew() + validChars = attrs.code.match(/[a-zA-Z0-9 _\-+]/g) + unless validChars.length is attrs.code.length + errors.push + attribute: 'vendorCode' + message: "Vendor code can not contain special characters" + if !attrs.name? or attrs.name is "" + errors.push + attribute: 'vendorName' + message: "Vendor name must be set and unique" + if errors.length > 0 + return errors + else + return null ############################################################################ class window.Vendors extends Backbone.Collection @@ -26,8 +40,7 @@ class window.VendorController extends AbstractFormController events: -> "change .bv_vendorCode": "handleVendorCodeNameChanged" - "keyup .bv_vendorName": "attributeChanged" - "keyup .bv_vendorDetails": "attributeChanged" + "keyup .bv_vendorName": "handleVendorNameChanged" "click .bv_save": "handleSaveClicked" "click .bv_newEntity": "handleNewEntityClicked" "click .bv_cancel": "handleCancelClicked" @@ -35,12 +48,29 @@ class window.VendorController extends AbstractFormController "click .bv_confirmClear": "handleConfirmClearClicked" initialize: -> - console.log 'initialize vendorController -- line 38' - template = _.template( $("#VendorView").html()); - $(@el).empty() - $(@el).html template if @model? @completeInitialization() + else + if window.AppLaunchParams.moduleLaunchParams? + if window.AppLaunchParams.moduleLaunchParams.moduleName == @moduleLaunchName + $.ajax + type: 'GET' + url: "/api/cmpdRegAdmin/vendors/codeName/"+window.AppLaunchParams.moduleLaunchParams.code + dataType: 'json' + error: (err) => + alert 'Error getting vendor for code in this URL. Creating a new project' + @completeInitialization() + success: (json) => + if json.id? + @model = new Vendor json + else + alert 'Could not get vendor for code in this URL. Creating a new project' + @completeInitialization() + else + @completeInitialization() + else + @completeInitialization() + completeInitialization: => unless @model? @@ -52,9 +82,10 @@ class window.VendorController extends AbstractFormController else @readOnly = false @listenTo @model, 'saveFailed', @handleSaveFailed + @listenTo @model, 'sync', @modelSaveCallback @listenTo @model, 'change', @modelChangeCallback $(@el).empty() - $(@el).html @template(@model.attributes) + $(@el).html @template() @render() render: => @@ -64,38 +95,20 @@ class window.VendorController extends AbstractFormController @$('.bv_vendorCode').val(code) @$('.bv_vendorCode').html(code) if @model.isNew() - console.log 'new vendor model -- line 67' @$('.bv_vendorCode').removeAttr('disabled') - @$('.bv_save').removeAttr('disabled') - @$('.bv_cancel').removeAttr('disabled') - @$('.VendorView').show() - @$('.bv_vendorCode').show() - @$('.bv_vendorName').show() - else - console.log 'old vendor model -- line 75' - @$('.bv_vendorCode').attr 'disabled', 'disabled' - bestName = @model.get('name') - if bestName? - @$('.bv_vendorName').val bestName - if @model.isNew() - @$('.bv_saveBeforeManagingPermissions').show() - if UtilityFunctions::testUserHasRole window.AppLaunchParams.loginUser, [window.conf.roles.cmpdreg.adminRole] - @$('.bv_saveBeforeManagingPermissions').show() - else - @updateEditable() - if @readOnly is true - @displayInReadOnlyMode() -# @$('.bv_save').attr('disabled','disabled') -# @$('.bv_cancel').attr('disabled','disabled') - @$('.VendorView').show() - @$('.bv_vendorCode').show() - - if @model.isNew() @$('.bv_save').html("Save") @$('.bv_newEntity').hide() else + @$('.bv_vendorCode').attr 'disabled', 'disabled' @$('.bv_save').html("Update") @$('.bv_newEntity').show() + @$('.bv_vendorName').val @model.get('name') + + if @readOnly is true + @displayInReadOnlyMode() + @$('.bv_save').attr('disabled','disabled') + @$('.bv_cancel').attr('disabled','disabled') + @ handleSaveFailed: => @@ -105,10 +118,11 @@ class window.VendorController extends AbstractFormController modelSaveCallback: (method, model) => @$('.bv_save').show() -# @$('.bv_save').attr('disabled', 'disabled') + @$('.bv_save').attr('disabled', 'disabled') unless @$('.bv_saveFailed').is(":visible") @$('.bv_saveComplete').show() @$('.bv_saving').hide() + @$('.bv_cancel').removeAttr 'disabled' @render() @trigger 'amClean' @@ -120,62 +134,20 @@ class window.VendorController extends AbstractFormController @$('.bv_cancel').removeAttr('disabled') @$('.bv_cancelComplete').hide() - updateEditable: => - if @model.isEditable() - if UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, [window.conf.roles.acas.adminRole]) - @enableAllInputs() - @$('.bv_vendorCode').attr 'disabled', 'disabled' - @$('.bv_saveBeforeManagingPermissions').hide() - else - @enableLimitedEditing() - @$('.bv_manageUserPermissions').hide() - else - @disableAllInputs() - @$('.bv_newEntity').removeAttr('disabled') - @$('.bv_status').attr 'disabled', 'disabled' #for now, don't allow status editing - - enableLimitedEditing: -> - @disableAllInputs() - handleVendorCodeNameChanged: => code = UtilityFunctions::getTrimmedInput @$('.bv_vendorCode') - console.log 'here is the codeName change -- line 142' - console.log code + if code is "" - console.log 'deleting the code attribute -- line 145' - delete @model.attributes.code - @model.trigger 'change' + @model.set 'code', null else - #validate codeName - console.log ' 150 -- checking codeName' - console.log code - $.ajax - type: 'GET' - url: "/api/cmpdRegAdmin/vendors/findByCode/"+code - dataType: 'json' - error: (err) => - #codename is new - console.log 'hit error searching for vendor by code -- line 158' - @model.set code: code - console.log JSON.stringify(@model) - @clearValidationErrorStyles - success: (json, status) => - #codeName is not unique - - console.log 'service did not return an error -- but what is the status code' - console.log status - console.log code - @$('.bv_notUniqueModalTitle').html "Error: Vendor code is not unique" - @$('.bv_notUniqueModalBody').html "The entered vendor code is already used by another vendor. Please enter in a new code." - @$('.bv_notUniqueModal').modal('show') - @$('.bv_vendorCode').val @model.get 'code' + @model.set 'code', code + @model.trigger 'change' handleNewEntityClicked: => @$('.bv_confirmClearEntity').modal('show') @$('.bv_confirmClear').removeAttr('disabled') @$('.bv_cancelClear').removeAttr('disabled') @$('.bv_closeModalButton').removeAttr('disabled') - @$('.bv_save').removeAttr('disabled') handleCancelClearClicked: => @$('.bv_confirmClearEntity').modal('hide') @@ -200,14 +172,14 @@ class window.VendorController extends AbstractFormController @$('.bv_canceling').hide() @$('.bv_cancelComplete').show() - updateModel: => - console.log 'line 204 -- updating model' + handleVendorNameChanged: => @model.set("name", UtilityFunctions::getTrimmedInput @$('.bv_vendorName')) - @model.set("code", UtilityFunctions::getTrimmedInput @$('.bv_vendorCode')) handleSaveClicked: => - console.log 'save clicked -- 194' - @callNameValidationService() + if @model.isNew() + @callNameValidationService() + else + @saveVendor() @$('.bv_saving').show() @$('.bv_saveFailed').hide() @@ -215,74 +187,47 @@ class window.VendorController extends AbstractFormController callNameValidationService: => - @updateModel() @$('.bv_saving').show() @$('.bv_save').attr('disabled', 'disabled') validateURL = "/api/cmpdRegAdmin/vendors/validateBeforeSave" dataToPost = data: #dataToPost needs wrapping key, not sure why JSON.stringify(@model) - console.log 'posting data to validate function --- line 225' - console.log validateURL - console.log dataToPost $.ajax type: 'POST' url: validateURL data: dataToPost dataType: 'json' success: (response) => - console.log 'line 234 -- success return from validating vendor' - console.log response @handleValidateReturn(response) error: (err) => - console.log 'line 238 -- error return from validating vendor' - console.log err - @serviceReturn = null + @handleValidateError(JSON.parse err.responseText) + + handleValidateError: (err) => + if err?[0]?.level? and err[0].level is "ERROR" + alert "The requested code has already been used" + @$('.bv_saving').hide() + @$('.bv_saveFailed').show() handleValidateReturn: (validateResp) => - console.log "ValidateResp next line -- 224" - console.log JSON.stringify validateResp if validateResp?[0]?.errorLevel? alert 'The requested vendor name has already been registered. Please choose a new vendor name.' @$('.bv_saving').hide() @$('.bv_saveFailed').show() - else if validateResp is "validate name failed" - alert 'There was an error validating the vendor name. Please try again and/or enter a different name.' - @$('.bv_saving').hide() - @$('.bv_saveFailed').show() else @saveVendor() saveVendor: => - console.log "saveVendor - handle tags changed" if @model.isNew() @$('.bv_saveComplete').html('Save Complete') - newVendor = true else @$('.bv_saveComplete').html('Update Complete') - newVendor = false @$('.bv_save').attr('disabled', 'disabled') - if @model.isNew() #if vendor was new - @model.save null, - success: (model, response) => - console.log 'line 268 -- response from saveVendor' - console.log response - if response is "update vendor failed" - @model.trigger 'saveFailed' - else - if UtilityFunctions::testUserHasRoleTypeKindName(window.AppLaunchParams.loginUser, [@adminRole]) or UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, [window.conf.roles.acas.adminRole]) - @updateVendorRoles() - else - @model.save null, - success: (model, response) => - console.log 'line 271 -- save vendor response' - console.log response - if response is "update lsThing failed" - @model.trigger 'saveFailed' - error: (err) => - console.log 'line 271 -- save vendor err' - console.log err - @model.trigger 'saveFailed' + + @model.save null, + success: (model, response) => + if response is "update vendor failed" + @model.trigger 'saveFailed' validationError: => super() @@ -308,10 +253,3 @@ class window.VendorController extends AbstractFormController @$('.bv_save').removeAttr('disabled') else @$('.bv_save').attr('disabled', 'disabled') - - isValid: => - validCheck = super() - validCheck - - - diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html index 2e869ea44..9a36da1e1 100644 --- a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html +++ b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html @@ -1,18 +1,16 @@ diff --git a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee index 3246c5821..144710936 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee @@ -2,6 +2,7 @@ window.ModuleMenusConfiguration = [ isHeader: true menuName: "Load Data" +# collapsible: true , isHeader: false menuName: "Experiment Loader" diff --git a/modules/ModuleMenus/src/client/style.css b/modules/ModuleMenus/src/client/style.css index ff5a22501..1552dc366 100644 --- a/modules/ModuleMenus/src/client/style.css +++ b/modules/ModuleMenus/src/client/style.css @@ -118,7 +118,10 @@ body { cursor: pointer; } -.bv_collapsibleHeaderController li { +.bv_modLaunchMenuWrapper { + width: 267px; +} +.bv_modLaunchMenuWrapper .bv_menuItem { margin-top: 3px; /*margin-bottom: 5px;*/ @@ -127,3 +130,10 @@ body { .bv_notTopHeader { margin-top: 5px; } + +.bv_expandAll, .bv_collapseAll { + width: 12px; + position: absolute; + top: 75px; + left: 265px; +} \ No newline at end of file diff --git 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HcmV?d00001 From 90b26b7a056a80da4cd080c11f0299ae2d65aaa6 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Wed, 9 Aug 2017 09:53:49 -0700 Subject: [PATCH 139/576] feature/creg-enhancement-101: combining vendor browser and editor into one module --- .../src/client/CmpdRegVendor.coffee | 33 ++-- .../src/client/CmpdRegVendor.html | 6 +- .../src/client/CmpdRegVendorBrowser.coffee | 36 +++- .../src/client/CmpdRegVendorBrowserView.html | 156 +++++++++--------- .../server/routes/CmpdRegAdminRoutes.coffee | 2 +- 5 files changed, 134 insertions(+), 99 deletions(-) diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee index 9a668ccf6..f1014b0cf 100644 --- a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee +++ b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee @@ -39,10 +39,11 @@ class window.VendorController extends AbstractFormController moduleLaunchName: "vendor" events: -> - "change .bv_vendorCode": "handleVendorCodeNameChanged" + "keyup .bv_vendorCode": "handleVendorCodeNameChanged" "keyup .bv_vendorName": "handleVendorNameChanged" "click .bv_save": "handleSaveClicked" - "click .bv_newEntity": "handleNewEntityClicked" + "click .bv_backToVendorBrowserBtn": "handleBackToVendorBrowserClicked" +# "click .bv_newEntity": "handleNewEntityClicked" "click .bv_cancel": "handleCancelClicked" "click .bv_cancelClear": "handleCancelClearClicked" "click .bv_confirmClear": "handleConfirmClearClicked" @@ -95,17 +96,16 @@ class window.VendorController extends AbstractFormController @$('.bv_vendorCode').val(code) @$('.bv_vendorCode').html(code) if @model.isNew() - @$('.bv_vendorCode').removeAttr('disabled') @$('.bv_save').html("Save") - @$('.bv_newEntity').hide() +# @$('.bv_newEntity').hide() else - @$('.bv_vendorCode').attr 'disabled', 'disabled' @$('.bv_save').html("Update") - @$('.bv_newEntity').show() +# @$('.bv_newEntity').show() @$('.bv_vendorName').val @model.get('name') if @readOnly is true @displayInReadOnlyMode() + @$('.bv_backToVendorBrowserBtn').hide() @$('.bv_save').attr('disabled','disabled') @$('.bv_cancel').attr('disabled','disabled') @@ -142,12 +142,16 @@ class window.VendorController extends AbstractFormController else @model.set 'code', code @model.trigger 'change' + + handleBackToVendorBrowserClicked: => + @trigger 'backToBrowser' + - handleNewEntityClicked: => - @$('.bv_confirmClearEntity').modal('show') - @$('.bv_confirmClear').removeAttr('disabled') - @$('.bv_cancelClear').removeAttr('disabled') - @$('.bv_closeModalButton').removeAttr('disabled') +# handleNewEntityClicked: => +# @$('.bv_confirmClearEntity').modal('show') +# @$('.bv_confirmClear').removeAttr('disabled') +# @$('.bv_cancelClear').removeAttr('disabled') +# @$('.bv_closeModalButton').removeAttr('disabled') handleCancelClearClicked: => @$('.bv_confirmClearEntity').modal('hide') @@ -176,10 +180,7 @@ class window.VendorController extends AbstractFormController @model.set("name", UtilityFunctions::getTrimmedInput @$('.bv_vendorName')) handleSaveClicked: => - if @model.isNew() - @callNameValidationService() - else - @saveVendor() + @callNameValidationService() @$('.bv_saving').show() @$('.bv_saveFailed').hide() @@ -244,7 +245,7 @@ class window.VendorController extends AbstractFormController displayInReadOnlyMode: => @$(".bv_save").hide() @$(".bv_cancel").hide() - @$(".bv_newEntity").hide() +# @$(".bv_newEntity").hide() @$('button').attr 'disabled', 'disabled' @disableAllInputs() diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html index 9a36da1e1..98e2c2d85 100644 --- a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html +++ b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html @@ -1,5 +1,4 @@ diff --git a/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee b/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee index d719b85e3..2b7572310 100644 --- a/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee +++ b/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee @@ -16,7 +16,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.get '/api/cmpdRegAdmin/vendors/:id', loginRoutes.ensureAuthenticated, exports.getCmpdRegVendorById app.post '/api/cmpdRegAdmin/vendors', loginRoutes.ensureAuthenticated, exports.saveCmpdRegVendor - app.put '/api/cmpdRegAdmin/vendors', loginRoutes.ensureAuthenticated, exports.updateCmpdRegVendor + app.put '/api/cmpdRegAdmin/vendors/:id', loginRoutes.ensureAuthenticated, exports.updateCmpdRegVendor app.delete '/api/cmpdRegAdmin/vendors/:id', loginRoutes.ensureAuthenticated, exports.deleteCmpdRegVendor exports.validateCmpdRegVendor = (req, resp) -> From e0b7b44ba2cab02243a92c4f0ad45e4a55fa594d Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 16 Aug 2017 13:47:00 -0700 Subject: [PATCH 140/576] #218: add option to moveToLocation to optionally updateMoveToLocation, default for now will be false --- .../routes/InventoryServiceRoutes.coffee | 32 ++++++++++++------- 1 file changed, 20 insertions(+), 12 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 58323145d..d08690b25 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -1333,15 +1333,18 @@ exports.updateAmountInWellInternal = (updateAmountInfo, callback) -> exports.moveToLocation = (req, resp) -> req.setTimeout 86400000 - exports.moveToLocationInternal req.body, req.query.callCustom, (json, statusCode) -> + exports.moveToLocationInternal req.body, req.query.callCustom, req.query.updateLocationHistory, (json, statusCode) -> resp.statusCode = statusCode resp.json json -exports.moveToLocationInternal = (input, callCustom, callback) -> +exports.moveToLocationInternal = (input, callCustom, updateLocationHistory, callback) -> #exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> # console.log 'updated history logs before moving to temp' # ) + # default for callCustom is true callCustom = callCustom != "0" + # default for updateLocationHistory is false + updateLocationHistory = updateLocationHistory == "1" if global.specRunnerTestmode inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' resp.json inventoryServiceTestJSON.moveToLocationResponse @@ -1366,22 +1369,27 @@ exports.moveToLocationInternal = (input, callCustom, callback) -> if !error console.log 'container down here...did it pull through??' console.log input[0].containerCodeName - exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> - if callCustom && csUtilities.moveToLocation? - console.log "running customer specific server function moveToLocation" - csUtilities.moveToLocation input, (customerResponse, statusCode) -> - json = _.extend json, customerResponse - callback json, statusCode - else - console.warn "could not find customer specific server function moveToLocation so not running it" - callback json, response.statusCode + if updateLocationHistory + exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> + callback json, statusCode + # if callCustom && csUtilities.moveToLocation? + # console.log "running customer specific server function moveToLocation" + # csUtilities.moveToLocation input, (customerResponse, statusCode) -> + # json = _.extend json, customerResponse + # callback json, statusCode + # else + # console.warn "could not find customer specific server function moveToLocation so not running it" + # callback json, response.statusCode + # ) ) + else + callback json, response.statusCode else console.error 'got ajax error trying to get moveToLocation' console.error error console.error json console.error response - callback JSON.stringify("updateWellContent failed"), 500 + callback JSON.stringify("moveToLocation failed"), 500 ) #) From ea1d0f847b51631f0c04aba515225eee0cefcadd Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Thu, 17 Aug 2017 14:36:16 -0700 Subject: [PATCH 141/576] RC/1.12.0 updated toPrint route and protocol service routes to get and put protocols in bulk, added webshot and archiver to package.json --- .../routes/ProtocolServiceRoutes.coffee | 71 ++++++++++++++++++- .../ServerAPI/src/server/routes/index.coffee | 18 +++-- package.json | 4 +- 3 files changed, 85 insertions(+), 8 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee index 9f446fd07..0ef46718b 100644 --- a/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee @@ -9,6 +9,8 @@ exports.setupAPIRoutes = (app) -> app.get '/api/protocols/genericSearch/:searchTerm', exports.genericProtocolSearch app.delete '/api/protocols/browser/:id', exports.deleteProtocol app.get '/api/getProtocolByLabel/:protLabel', exports.getProtocolByLabel + app.post '/api/protocols/getByCodeNamesArray', exports.protocolsByCodeNamesArray + app.put '/api/bulkPutProtocols', exports.bulkPutProtocols @@ -23,6 +25,8 @@ exports.setupRoutes = (app, loginRoutes) -> app.get '/api/protocols/genericSearch/:searchTerm', loginRoutes.ensureAuthenticated, exports.genericProtocolSearch app.delete '/api/protocols/browser/:id', loginRoutes.ensureAuthenticated, exports.deleteProtocol app.get '/api/getProtocolByLabel/:protLabel', loginRoutes.ensureAuthenticated, exports.getProtocolByLabel + app.post '/api/protocols/getByCodeNamesArray', loginRoutes.ensureAuthenticated, exports.protocolsByCodeNamesArray + app.put '/api/bulkPutProtocols', loginRoutes.ensureAuthenticated, exports.bulkPutProtocols serverUtilityFunctions = require './ServerUtilityFunctions.js' csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFunctions.js' @@ -511,4 +515,69 @@ exports.getProtocolByLabelInternal = (label, callback) -> else console.log 'got ajax error trying to get protocol by label' callback 500, json.errorMessages - ) \ No newline at end of file + ) + +exports.protocolsByCodeNamesArray = (req, resp) -> + exports.protocolsByCodeNamesArrayInternal req.body.data, req.query.option, req.query.testMode, (returnedProts) -> + if returnedProts.indexOf("Failed") > -1 + resp.statusCode = 500 + resp.json returnedProts + + +exports.protocolsByCodeNamesArrayInternal = (codeNamesArray, returnOption, testMode, callback) -> + if testMode or global.specRunnerTestmode + callback JSON.stringify "stubsMode not implemented" + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"protocols/codename/jsonArray" + #returnOption are stub, fullobject + if returnOption? + baseurl += "?with=#{returnOption}" + console.log "protocolsByCodeNamesArray" + console.log baseurl + request = require 'request' + request( + method: 'POST' + url: baseurl + body: codeNamesArray + json: true + , (error, response, json) => + console.log "protocolsByCodeNamesArray json" + console.log json + console.log "response.statusCode" + console.log response.statusCode + console.log response + if !error && response.statusCode == 200 + callback json + else + console.log "Failed: got error in bulk get of protocols" + callback "Bulk get protocols saveFailed: " + JSON.stringify error + ) + +exports.bulkPutProtocols= (req, resp) -> + exports.bulkPutProtocolsInternal req.body, (response) => + resp.json response + +exports.bulkPutProtocolsInternal = (protsArray, callback) -> + console.log "bulkPutProtocols" + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"/protocols/jsonArray" + console.log "bulkPutProtocolsInternal" + console.log baseurl + console.log protsArray + request = require 'request' + request( + method: 'PUT' + url: baseurl + body: protsArray + json: true + , (error, response, json) => + console.log "bulkPutProtocolsInternal" + console.log response.statusCode + if !error && response.statusCode == 200 + callback json + else + console.log "got error bulk updating protocols" + console.log error + callback JSON.stringify "bulk update protocols saveFailed: " + JSON.stringify error + ) diff --git a/modules/ServerAPI/src/server/routes/index.coffee b/modules/ServerAPI/src/server/routes/index.coffee index ee4c73849..cd6f2777e 100644 --- a/modules/ServerAPI/src/server/routes/index.coffee +++ b/modules/ServerAPI/src/server/routes/index.coffee @@ -1,18 +1,18 @@ scriptPaths = require './RequiredClientScripts.js' exports.setupAPIRoutes = (app) -> - app.get '/toPrint', exports.toPrint + app.get '/toPrint/:code', exports.toPrint exports.setupRoutes = (app, loginRoutes) -> config = require '../conf/compiled/conf.js' if config.all.client.require.login - app.get '/toPrint', loginRoutes.ensureAuthenticated, exports.toPrint + app.get '/toPrint/:code', loginRoutes.ensureAuthenticated, exports.toPrint app.get '/', loginRoutes.ensureAuthenticated, exports.index app.get '/:moduleName/codeName/:code', loginRoutes.ensureAuthenticated, exports.autoLaunchWithCode app.get '/entity/copy/:moduleName/:code', loginRoutes.ensureAuthenticated, exports.copyAndLaunchWithCode app.get '/:moduleName/createFrom/:code', loginRoutes.ensureAuthenticated, exports.autoLaunchCreateFromOtherEntity else - app.get '/toPrint', loginRoutes.ensureAuthenticated, exports.toPrint + app.get '/toPrint/:code', loginRoutes.ensureAuthenticated, exports.toPrint app.get '/:moduleName/codeName/:code', exports.autoLaunchWithCode app.get '/', exports.index @@ -50,14 +50,20 @@ exports.autoLaunchCreateFromOtherEntity = (req, res) -> exports.toPrint = (req, res, moduleLaunchParams) -> #"use strict" + console.log "toPrint" + console.log req.query.moduleName + console.log req.query.controller #TODO: on redirect, pass in moduleName and code. Hardcoded right now. moduleLaunchParams = - moduleName: "primary_screen_protocol" - code: "PROT-00000001" + moduleName: req.query.moduleName + code: req.params.code copy: false createFromOtherEntity: false print: true + console.log "moduleLaunchParams" + console.log moduleLaunchParams + config = require '../conf/compiled/conf.js' global.specRunnerTestmode = if global.stubsMode then true else false @@ -84,7 +90,7 @@ exports.toPrint = (req, res, moduleLaunchParams) -> moduleLaunchParams: if moduleLaunchParams? then moduleLaunchParams else null deployMode: global.deployMode loggingToMongo: config.all.logging.usemongo - controller: "PrimaryScreenProtocolModuleController" + controller: req.query.controller exports.index = (req, res, moduleLaunchParams) -> #"use strict" diff --git a/package.json b/package.json index 31ae5baa9..e26560449 100644 --- a/package.json +++ b/package.json @@ -62,7 +62,9 @@ "url-loader": "*", "yamljs": "*", "request-promise": "*", - "bluebird": "*" + "bluebird": "*", + "webshot": "0.18.0", + "archiver": "2.0.0" }, "devDependencies": { "coffee-script": "^1.12.4", From f8df54f0c58229e9523bce6b25731e2041b1c268 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 24 Aug 2017 11:42:06 -0700 Subject: [PATCH 142/576] Switched out the cmpdRegAdmin "vendors" routes to be generic. Removed extraneous logging. #219 --- .../server/routes/CmpdRegAdminRoutes.coffee | 142 ++++++++---------- 1 file changed, 64 insertions(+), 78 deletions(-) diff --git a/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee b/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee index 2b7572310..566c6c922 100644 --- a/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee +++ b/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee @@ -1,55 +1,51 @@ exports.setupAPIRoutes = (app, loginRoutes) -> - app.get '/api/cmpdRegAdmin/vendors', exports.getCmpdRegVendors - app.get '/api/cmpdRegAdmin/vendors/validate/:code', exports.validateCmpdRegVendor - app.get '/api/cmpdRegAdmin/vendors/codeName/:code', exports.getCmpdRegVendorByCode - app.post '/api/cmpdRegAdmin/vendors/validateBeforeSave', exports.validateCmpdRegVendorBeforeSave - app.post '/api/cmpdRegAdmin/vendors', exports.saveCmpdRegVendor - app.put '/api/cmpdRegAdmin/vendors/:id', exports.updateCmpdRegVendor - app.delete '/api/cmpdRegAdmin/vendors/:id', exports.deleteCmpdRegVendor + app.get '/api/cmpdRegAdmin/:entityType', exports.getCmpdRegEntities + app.get '/api/cmpdRegAdmin/:entityType/validate/:code', exports.validateCmpdRegEntity + app.get '/api/cmpdRegAdmin/:entityType/codeName/:code', exports.getCmpdRegEntityByCode + app.post '/api/cmpdRegAdmin/:entityType/validateBeforeSave', exports.validateCmpdRegEntityBeforeSave + app.post '/api/cmpdRegAdmin/:entityType', exports.saveCmpdRegEntity + app.put '/api/cmpdRegAdmin/:entityType/:id', exports.updateCmpdRegEntity + app.delete '/api/cmpdRegAdmin/:entityType/:id', exports.deleteCmpdRegEntity exports.setupRoutes = (app, loginRoutes) -> - app.get '/api/cmpdRegAdmin/vendors/validate/:code', loginRoutes.ensureAuthenticated, exports.validateCmpdRegVendor - app.get '/api/cmpdRegAdmin/vendors/codeName/:code', loginRoutes.ensureAuthenticated, exports.getCmpdRegVendorByCode - app.get '/api/cmpdRegAdmin/vendors', loginRoutes.ensureAuthenticated, exports.getCmpdRegVendors - app.get '/api/cmpdRegAdmin/vendors/search/:searchTerm', loginRoutes.ensureAuthenticated, exports.searchCmpdRegVendors - app.post '/api/cmpdRegAdmin/vendors/validateBeforeSave', loginRoutes.ensureAuthenticated, exports.validateCmpdRegVendorBeforeSave + app.get '/api/cmpdRegAdmin/:entityType/validate/:code', loginRoutes.ensureAuthenticated, exports.validateCmpdRegEntity + app.get '/api/cmpdRegAdmin/:entityType/codeName/:code', loginRoutes.ensureAuthenticated, exports.getCmpdRegEntityByCode + app.get '/api/cmpdRegAdmin/:entityType', loginRoutes.ensureAuthenticated, exports.getCmpdRegEntities + app.get '/api/cmpdRegAdmin/:entityType/search/:searchTerm', loginRoutes.ensureAuthenticated, exports.searchCmpdRegEntities + app.post '/api/cmpdRegAdmin/:entityType/validateBeforeSave', loginRoutes.ensureAuthenticated, exports.validateCmpdRegEntityBeforeSave - app.get '/api/cmpdRegAdmin/vendors/:id', loginRoutes.ensureAuthenticated, exports.getCmpdRegVendorById - app.post '/api/cmpdRegAdmin/vendors', loginRoutes.ensureAuthenticated, exports.saveCmpdRegVendor - app.put '/api/cmpdRegAdmin/vendors/:id', loginRoutes.ensureAuthenticated, exports.updateCmpdRegVendor - app.delete '/api/cmpdRegAdmin/vendors/:id', loginRoutes.ensureAuthenticated, exports.deleteCmpdRegVendor + app.get '/api/cmpdRegAdmin/:entityType/:id', loginRoutes.ensureAuthenticated, exports.getCmpdRegEntityById + app.post '/api/cmpdRegAdmin/:entityType', loginRoutes.ensureAuthenticated, exports.saveCmpdRegEntity + app.put '/api/cmpdRegAdmin/:entityType/:id', loginRoutes.ensureAuthenticated, exports.updateCmpdRegEntity + app.delete '/api/cmpdRegAdmin/:entityType/:id', loginRoutes.ensureAuthenticated, exports.deleteCmpdRegEntity -exports.validateCmpdRegVendor = (req, resp) -> +exports.validateCmpdRegEntity = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors/validate?code=' + req.params.code - console.log 'attempting vendor call to the following route' - console.log cmpdRegCall + entityType = req.params.entityType + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}/validate?code=' + req.params.code request( method: 'GET' url: cmpdRegCall json: false timeout: 6000000 - , (error, response, validVendor) => + , (error, response, validEntity) => if !error - console.log validVendor resp.statusCode = response.statusCode resp.setHeader('Content-Type', 'application/json') - resp.end validVendor - console.log 'done validating the vendor' + resp.end validEntity + console.log 'done validating the ' + entityType else - console.log 'got ajax error trying to do validate vendor' - console.log validVendor - resp.end JSON.stringify {error: "something went wrong validating the vendor :("} + console.log 'got ajax error trying to do validate #{entityType}' + console.log validEntity + resp.end JSON.stringify {error: "something went wrong validating the #{entityType}"} ) -exports.validateCmpdRegVendorBeforeSave = (req, resp) -> +exports.validateCmpdRegEntityBeforeSave = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors/validateBeforeSave' - console.log 'attempting vendor call to the following route --- line 49' - console.log cmpdRegCall - console.log req.body.data + entityType = req.params.entityType + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}/validateBeforeSave' request( method: 'POST' url: cmpdRegCall @@ -58,27 +54,24 @@ exports.validateCmpdRegVendorBeforeSave = (req, resp) -> timeout: 6000000 headers: "Content-Type": 'application/json' - , (error, response, validVendor) => + , (error, response, validEntity) => if !error - console.log 'line 60 -- is a valid vendor' - console.log validVendor resp.statusCode = response.statusCode resp.setHeader('Content-Type', 'application/json') - resp.end JSON.stringify validVendor + resp.end JSON.stringify validEntity console.log resp.statusCode - console.log 'done validating the vendor' + console.log 'done validating the #{entityType}' else - console.log 'got ajax error trying to do validate vendor' - console.log validVendor - resp.end JSON.stringify {error: "something went wrong validating the vendor :("} + console.log 'got ajax error trying to do validate #{entityType}' + console.log validEntity + resp.end JSON.stringify {error: "something went wrong validating the #{entityType} :("} ) -exports.getCmpdRegVendorById = (req, resp) -> +exports.getCmpdRegEntityById = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors/' + req.params.id - console.log 'attempting vendor call to the following route' - console.log cmpdRegCall + entityType = req.params.entityType + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}/' + req.params.id request( method: 'GET' url: cmpdRegCall @@ -92,17 +85,16 @@ exports.getCmpdRegVendorById = (req, resp) -> resp.json json else resp.statusCode = 404 - console.log 'got ajax error trying to do find vendor' + console.log 'got ajax error trying to do find #{entityType}' console.log json resp.end JSON.stringify {error: "something went wrong :("} ) -exports.getCmpdRegVendorByCode = (req, resp) -> +exports.getCmpdRegEntityByCode = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors/findByCodeEquals?code=' + req.params.code - console.log 'attempting vendor call to the following route' - console.log cmpdRegCall + entityType = req.params.entityType + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}/findByCodeEquals?code=' + req.params.code request( method: 'GET' url: cmpdRegCall @@ -116,17 +108,16 @@ exports.getCmpdRegVendorByCode = (req, resp) -> resp.json json else resp.statusCode = 404 - console.log 'got ajax error trying to do find vendor' + console.log 'got ajax error trying to do find #{entityType}' console.log json resp.end JSON.stringify {error: "something went wrong :("} ) -exports.searchCmpdRegVendors = (req, resp) -> +exports.searchCmpdRegEntities = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors/search/?searchTerm=' + req.params.searchTerm - console.log 'attempting vendor call to the following route' - console.log cmpdRegCall + entityType = req.params.entityType + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}/search/?searchTerm=' + req.params.searchTerm request( method: 'GET' url: cmpdRegCall @@ -140,18 +131,17 @@ exports.searchCmpdRegVendors = (req, resp) -> resp.json json else resp.statusCode = 404 - console.log 'got ajax error trying to do find vendor' + console.log 'got ajax error trying to do find #{entityType}' console.log json resp.end JSON.stringify {error: "something went wrong :("} ) -exports.getCmpdRegVendors = (req, resp) -> +exports.getCmpdRegEntities = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors' - console.log 'attempting vendor call to the following route' - console.log cmpdRegCall + entityType = req.params.entityType + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}' request( method: 'GET' url: cmpdRegCall @@ -164,18 +154,16 @@ exports.getCmpdRegVendors = (req, resp) -> resp.setHeader('Content-Type', 'application/json') resp.json json else - console.log 'got ajax error trying to do get vendors' + console.log 'got ajax error trying to do get #{entityType}s' console.log json resp.end JSON.stringify {error: "something went wrong :("} ) -exports.saveCmpdRegVendor = (req, resp) -> +exports.saveCmpdRegEntity = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' - console.log "line 134 --- exports.saveCmpdRegVendor" - console.log JSON.stringify req.body - - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors' + entityType = req.params.entityType + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}' request( method: 'POST' url: cmpdRegCall @@ -189,18 +177,17 @@ exports.saveCmpdRegVendor = (req, resp) -> resp.setHeader('Content-Type', 'plain/text') resp.json json else - console.log 'got ajax error trying to save the vendor' + console.log 'got ajax error trying to save the #{entityType}' console.log json resp.statusCode = 500 - resp.end "Error trying to save vendor: " + error; + resp.end "Error trying to save #{entityType}: " + error; ) -exports.updateCmpdRegVendor = (req, resp) -> +exports.updateCmpdRegEntity = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' - console.log "exports.updateCmpdRegVendor" - - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors' + entityType = req.params.entityType + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}' request( method: 'PUT' url: cmpdRegCall @@ -214,18 +201,17 @@ exports.updateCmpdRegVendor = (req, resp) -> resp.setHeader('Content-Type', 'plain/text') resp.json json else - console.log 'got ajax error trying to update vendor' + console.log 'got ajax error trying to update #{entityType}' console.log json resp.statusCode = 500 - resp.end "Error trying to update vendor: " + error; + resp.end "Error trying to update #{entityType}: " + error; ) -exports.deleteCmpdRegVendor = (req, resp) -> +exports.deleteCmpdRegEntity = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/vendors/' + req.params.id - console.log 'attempting vendor call to the following route' - console.log cmpdRegCall + entityType = req.params.entityType + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}/' + req.params.id request( method: 'DELETE' url: cmpdRegCall @@ -239,7 +225,7 @@ exports.deleteCmpdRegVendor = (req, resp) -> resp.json json else resp.statusCode = 404 - console.log 'got ajax error trying to delete vendor' + console.log 'got ajax error trying to delete #{entityType}' console.log json resp.end JSON.stringify {error: "something went wrong :("} ) \ No newline at end of file From 35568c0e22432da37a02e4ac835271656fa39249 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 24 Aug 2017 14:07:17 -0700 Subject: [PATCH 143/576] Added new CReg config "disableEditMyLots", default false, which if enabled, disables users being able to edit their own lots. In this case, only admins can edit lots. Also corrected a typo in CReg configuration.json and Lot_Custom.js, and fixed a typo in PickList.html. --- modules/CmpdReg/src/client/custom/Lot_Custom.js | 2 +- modules/CmpdReg/src/client/custom/configuration.json | 5 +++-- modules/CmpdReg/src/client/src/MetaLot.js | 6 ++++-- modules/Components/src/client/PickList.html | 2 +- 4 files changed, 9 insertions(+), 6 deletions(-) diff --git a/modules/CmpdReg/src/client/custom/Lot_Custom.js b/modules/CmpdReg/src/client/custom/Lot_Custom.js index 49d14f16d..52ff3f248 100755 --- a/modules/CmpdReg/src/client/custom/Lot_Custom.js +++ b/modules/CmpdReg/src/client/custom/Lot_Custom.js @@ -229,7 +229,7 @@ $(function() { } else { this.$('.bv_tareWeightContainer').hide(); } - if (window.configuration.metaLot.showTotalAmoundStored) { + if (window.configuration.metaLot.showTotalAmountStored) { this.$('.bv_totalAmountStoredContainer').show(); } else { this.$('.bv_totalAmountStoredContainer').hide(); diff --git a/modules/CmpdReg/src/client/custom/configuration.json b/modules/CmpdReg/src/client/custom/configuration.json index 17ba6861f..3c42ffa3a 100755 --- a/modules/CmpdReg/src/client/custom/configuration.json +++ b/modules/CmpdReg/src/client/custom/configuration.json @@ -40,8 +40,9 @@ "useExactMass": true, "useProjectRolesToRestrictLotDetails": false, "showTareWeight": false, - "showTotalAmoundStored": false, - "disableAliasEdit": false + "showTotalAmountStored": false, + "disableAliasEdit": false, + "disableEditMyLots": false }, "serverSettings": { "corpPrefix": "CMPD", diff --git a/modules/CmpdReg/src/client/src/MetaLot.js b/modules/CmpdReg/src/client/src/MetaLot.js index c9b6f2ee8..c35018ab2 100755 --- a/modules/CmpdReg/src/client/src/MetaLot.js +++ b/modules/CmpdReg/src/client/src/MetaLot.js @@ -406,9 +406,11 @@ $(function() { if (this.user == null || chemist == null || this.model.get('lot').isNew()) return true; // test mode or new - if (this.user.get('isAdmin') || this.user.get('code') == chemist.get('code')) { + if (this.user.get('isAdmin')) { return true; - } else { + }else if (!window.configuration.metaLot.disableEditMyLots && this.user.get('code') == chemist.get('code')){ + return true; + } else { return false; } }, diff --git a/modules/Components/src/client/PickList.html b/modules/Components/src/client/PickList.html index 648ff8684..91dbbe156 100644 --- a/modules/Components/src/client/PickList.html +++ b/modules/Components/src/client/PickList.html @@ -19,7 +19,7 @@

      Add

      - a +
      From 3f9d61c167c84007e3d3f209fb65919eea0faee7 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Thu, 24 Aug 2017 22:11:48 -0400 Subject: [PATCH 144/576] RC/1.12.0: added config to enable/disable editing scientist, config to set protocol/experiment default status. Changed protocol/expt review statuses from reviewed ok/reviewed not ok to read and understood/needs attention --- conf/config.properties.example | 6 ++++++ .../ServerAPI/conf/ExperimentConfJSON.coffee | 8 ++++---- modules/ServerAPI/conf/ProtocolConfJSON.coffee | 8 ++++---- modules/ServerAPI/src/client/BaseEntity.coffee | 18 ++++++++++++++++-- modules/ServerAPI/src/client/Experiment.coffee | 4 ---- 5 files changed, 30 insertions(+), 14 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 390fe3dfd..7995342f3 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -402,6 +402,12 @@ client.entity.notebook.require=true client.entity.notebookPage.save=true client.entity.notebookPage.require=false +#Config for whether scientist is editable for protocols and experiments +client.entity.scientist.editable=true + +#Config for default protocol/experiment status +client.entity.status.default=created + # Protocols and experiments which should be hidden (to non-admin users) in the protocol/expt browser when the status is in the config below client.entity.hideStatuses=["deleted"] diff --git a/modules/ServerAPI/conf/ExperimentConfJSON.coffee b/modules/ServerAPI/conf/ExperimentConfJSON.coffee index e13644b15..df983eb91 100644 --- a/modules/ServerAPI/conf/ExperimentConfJSON.coffee +++ b/modules/ServerAPI/conf/ExperimentConfJSON.coffee @@ -319,15 +319,15 @@ codeType: "experiment" codeKind: "review status" codeOrigin: "ACAS DDICT" - code: "reviewed ok" - name: "Reviewed - OK" + code: "read and understood" + name: "Read and Understood" ignored: false , codeType: "experiment" codeKind: "review status" codeOrigin: "ACAS DDICT" - code: "reviewed not ok" - name: "Reviewed - Not OK" + code: "needs attention" + name: "Needs Attention" ignored: false , codeType: "analysis" diff --git a/modules/ServerAPI/conf/ProtocolConfJSON.coffee b/modules/ServerAPI/conf/ProtocolConfJSON.coffee index 7c9bf1e5e..a9e71b43c 100644 --- a/modules/ServerAPI/conf/ProtocolConfJSON.coffee +++ b/modules/ServerAPI/conf/ProtocolConfJSON.coffee @@ -296,15 +296,15 @@ codeType: "protocol" codeKind: "review status" codeOrigin: "ACAS DDICT" - code: "reviewed ok" - name: "Reviewed - OK" + code: "read and understood" + name: "Read and Understood" ignored: false , codeType: "protocol" codeKind: "review status" codeOrigin: "ACAS DDICT" - code: "reviewed not ok" - name: "Reviewed - Not OK" + code: "needs attention" + name: "Needs Attention" ignored: false , codeType: "assay" diff --git a/modules/ServerAPI/src/client/BaseEntity.coffee b/modules/ServerAPI/src/client/BaseEntity.coffee index 8b842b735..6090a99ee 100644 --- a/modules/ServerAPI/src/client/BaseEntity.coffee +++ b/modules/ServerAPI/src/client/BaseEntity.coffee @@ -74,7 +74,11 @@ class window.BaseEntity extends Backbone.Model valueKind = subclass + " status" status = @.get('lsStates').getOrCreateValueByTypeAndKind "metadata", metadataKind, "codeValue", valueKind if status.get('codeValue') is undefined or status.get('codeValue') is "" - status.set codeValue: "created" + if window.conf.entity?.status?.default? + defaultStatus = window.conf.entity.status.default + else + defaultStatus = "created" + status.set codeValue: defaultStatus status.set codeType: subclass status.set codeKind: "status" status.set codeOrigin: "ACAS DDICT" @@ -238,7 +242,11 @@ class window.BaseEntity extends Backbone.Model recordedBy: window.AppLaunchParams.loginUser.username recordedDate: new Date().getTime() version: 0 - copiedEntity.getStatus().set codeValue: "created" + if window.conf.entity?.status?.default? + defaultStatus = window.conf.entity.status.default + else + defaultStatus = "created" + copiedEntity.getStatus().set codeValue: defaultStatus copiedEntity.getNotebook().set stringValue: "" copiedEntity.getNotebookPage().set stringValue: "" copiedEntity.getScientist().set codeValue: "unassigned" @@ -559,6 +567,12 @@ class window.BaseEntityController extends AbstractThingFormController #TODO: che else unless @model.getStatus().get('codeValue') is "deleted" @$('.bv_status').removeAttr("disabled") + if window.conf.entity?.scientist?.editable? and window.conf.entity.scientist.editable is false + @$('.bv_scientist').attr 'disabled', 'disabled' + else + @$('.bv_scientist').removeAttr 'disabled' + + @model.trigger 'statusChanged' beginSave: => diff --git a/modules/ServerAPI/src/client/Experiment.coffee b/modules/ServerAPI/src/client/Experiment.coffee index 322692c97..678442dc4 100644 --- a/modules/ServerAPI/src/client/Experiment.coffee +++ b/modules/ServerAPI/src/client/Experiment.coffee @@ -710,10 +710,6 @@ class window.ExperimentBaseController extends BaseEntityController handleCompletionDateIconClicked: => @$( ".bv_completionDate" ).datepicker( "show" ) - - updateEditable: => - super() - handleSaveClicked: => @$('.bv_saveFailed').hide() if @model.isNew() and @$('.bv_exptNameChkbx').is(":checked") From c606bbe6ad838cded93572686babc007330f08db Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 28 Aug 2017 10:46:26 -0700 Subject: [PATCH 145/576] Refactored CmpdRegVendor and CmpdRegVendorBrowser into AbstractCmpdRegAdmin and AbstractCmpdRegAdminBrowser. Added in Vendor, StereoCategory, and Scientist as implementations of the new abstract classes. Fixed urls and logging in routes file to properly pull in entityType from url. Resolves #219 Changed routes to properly recognize errors sent back after CmpdReg Roo mods made to send back errors. Fixes #220 --- .../src/client/AbstractCmpdRegAdmin.coffee | 229 ++++++++++++++ .../client/AbstractCmpdRegAdminBrowser.coffee | 284 ++++++++++++++++++ ...l => AbstractCmpdRegAdminBrowserView.html} | 77 +++-- .../src/client/AbstractCmpdRegAdminView.html | 119 ++++++++ .../src/client/CmpdRegScientist.coffee | 64 ++++ .../src/client/CmpdRegScientist.html | 8 + .../src/client/CmpdRegStereoCategory.coffee | 65 ++++ .../src/client/CmpdRegStereoCategory.html | 8 + .../src/client/CmpdRegVendor.coffee | 238 ++------------- .../src/client/CmpdRegVendor.html | 119 +------- .../src/client/CmpdRegVendorBrowser.coffee | 269 ----------------- .../server/routes/CmpdRegAdminRoutes.coffee | 48 +-- .../client/ModuleMenusConfiguration.coffee | 22 ++ 13 files changed, 888 insertions(+), 662 deletions(-) create mode 100644 modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee create mode 100644 modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee rename modules/CmpdRegAdmin/src/client/{CmpdRegVendorBrowserView.html => AbstractCmpdRegAdminBrowserView.html} (54%) create mode 100644 modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminView.html create mode 100644 modules/CmpdRegAdmin/src/client/CmpdRegScientist.coffee create mode 100644 modules/CmpdRegAdmin/src/client/CmpdRegScientist.html create mode 100644 modules/CmpdRegAdmin/src/client/CmpdRegStereoCategory.coffee create mode 100644 modules/CmpdRegAdmin/src/client/CmpdRegStereoCategory.html delete mode 100644 modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowser.coffee diff --git a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee new file mode 100644 index 000000000..9736c1570 --- /dev/null +++ b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee @@ -0,0 +1,229 @@ +class window.AbstractCmpdRegAdminController extends AbstractFormController + ### + Instances of this controller must supply "moduleLaunchName", "entityType", and "modelClass" + entityTypePlural + entityTypeUpper + entityTypeUpperPlural + ### + template: _.template($("#AbstractCmpdRegAdminView").html()) + + events: -> + "keyup .bv_cmpdRegAdminCode": "handleCmpdRegAdminCodeNameChanged" + "keyup .bv_cmpdRegAdminName": "handleCmpdRegAdminNameChanged" + "click .bv_save": "handleSaveClicked" + "click .bv_backToCmpdRegAdminBrowserBtn": "handleBackToCmpdRegAdminBrowserClicked" +# "click .bv_newEntity": "handleNewEntityClicked" + "click .bv_cancel": "handleCancelClicked" + "click .bv_cancelClear": "handleCancelClearClicked" + "click .bv_confirmClear": "handleConfirmClearClicked" + + initialize: -> + console.log "initializing Abstract Controller" + if @model? + @completeInitialization() + else + if window.AppLaunchParams.moduleLaunchParams? + if window.AppLaunchParams.moduleLaunchParams.moduleName == @moduleLaunchName + $.ajax + type: 'GET' + url: @model.urlRoot + '/codeName/'+window.AppLaunchParams.moduleLaunchParams.code + dataType: 'json' + error: (err) => + alert "Error getting #{@entityType} for code in this URL. Creating a new project" + @completeInitialization() + success: (json) => + if json.id? + @model = new window[@modelClass] json + else + alert "Could not get #{@entityType} for code in this URL. Creating a new project" + @completeInitialization() + else + @completeInitialization() + else + @completeInitialization() + + + completeInitialization: => + unless @model? + @model=new window[@modelClass]() + @setBindings() + if @options.readOnly? + @readOnly = @options.readOnly + else + @readOnly = false + @listenTo @model, 'saveFailed', @handleSaveFailed + @listenTo @model, 'sync', @modelSaveCallback + @listenTo @model, 'change', @modelChangeCallback + $(@el).empty() + toDisplay = + entityTypeToDisplay: if @entityTypeToDisplay? then @entityTypeToDisplay else @entityType + entityTypePluralToDisplay: if @entityTypePluralToDisplay? then @entityTypePluralToDisplay else @entityTypePlural + entityTypeUpper: @entityTypeUpper + entityTypeUpperPlural: @entityTypeUpperPlural + $(@el).html(@template(toDisplay)) + @render() + + render: => + unless @model? + @model = new window[@modelClass]() + code = @model.get('code') + @$('.bv_cmpdRegAdminCode').val(code) + @$('.bv_cmpdRegAdminCode').html(code) + if @model.isNew() + @$('.bv_save').html("Save") +# @$('.bv_newEntity').hide() + else + @$('.bv_save').html("Update") + # @$('.bv_newEntity').show() + @$('.bv_cmpdRegAdminName').val @model.get('name') + + if @readOnly is true + @displayInReadOnlyMode() + @$('.bv_backToCmpdRegAdminBrowserBtn').hide() + @$('.bv_save').attr('disabled','disabled') + @$('.bv_cancel').attr('disabled','disabled') + + @ + + handleSaveFailed: => + @$('.bv_saveFailed').show() + @$('.bv_saveComplete').hide() + @$('.bv_saving').hide() + + modelSaveCallback: (method, model) => + @$('.bv_save').show() + @$('.bv_save').attr('disabled', 'disabled') + unless @$('.bv_saveFailed').is(":visible") + @$('.bv_saveComplete').show() + @$('.bv_saving').hide() + @$('.bv_cancel').removeAttr 'disabled' + @render() + @trigger 'amClean' + + modelChangeCallback: (method, model) => + @trigger 'amDirty' + @checkFormValid() + @$('.bv_saveComplete').hide() + @$('.bv_saveFailed').hide() + @$('.bv_cancel').removeAttr('disabled') + @$('.bv_cancelComplete').hide() + + handleCmpdRegAdminCodeNameChanged: => + code = UtilityFunctions::getTrimmedInput @$('.bv_cmpdRegAdminCode') + + if code is "" + @model.set 'code', null + else + @model.set 'code', code + @model.trigger 'change' + + handleBackToCmpdRegAdminBrowserClicked: => + @trigger 'backToBrowser' + + +# handleNewEntityClicked: => +# @$('.bv_confirmClearEntity').modal('show') +# @$('.bv_confirmClear').removeAttr('disabled') +# @$('.bv_cancelClear').removeAttr('disabled') +# @$('.bv_closeModalButton').removeAttr('disabled') + + handleCancelClearClicked: => + @$('.bv_confirmClearEntity').modal('hide') + + handleConfirmClearClicked: => + @$('.bv_confirmClearEntity').modal('hide') + @model = null + @completeInitialization() + @trigger 'amClean' + + handleCancelClicked: => + if @model.isNew() + @model = null + @completeInitialization() + else + @$('.bv_canceling').show() + @model.fetch + success: @handleCancelComplete + @trigger 'amClean' + + handleCancelComplete: => + @$('.bv_canceling').hide() + @$('.bv_cancelComplete').show() + + handleCmpdRegAdminNameChanged: => + @model.set("name", UtilityFunctions::getTrimmedInput @$('.bv_cmpdRegAdminName')) + + handleSaveClicked: => + @callNameValidationService() + + @$('.bv_saving').show() + @$('.bv_saveFailed').hide() + @$('.bv_saveComplete').hide() + + + callNameValidationService: => + @$('.bv_saving').show() + @$('.bv_save').attr('disabled', 'disabled') + validateURL = @model.urlRoot + '/validateBeforeSave' + dataToPost = + data: JSON.stringify(@model) + $.ajax + type: 'POST' + url: validateURL + data: dataToPost + dataType: 'json' + success: (response) => + @handleValidateReturn(response) + error: (err) => + @handleValidateError(JSON.parse err.responseText) + + handleValidateError: (err) => + if err?[0]?.level? and err[0].level is "ERROR" + alert "The requested code has already been used" + @$('.bv_saving').hide() + @$('.bv_saveFailed').show() + + handleValidateReturn: (validateResp) => + if validateResp?[0]?.errorLevel? + alert "The requested #{@entityType} name has already been registered. Please choose a new #{@entityType} name." + @$('.bv_saving').hide() + @$('.bv_saveFailed').show() + else + @saveCmpdRegAdmin() + + saveCmpdRegAdmin: => + if @model.isNew() + @$('.bv_saveComplete').html('Save Complete') + else + @$('.bv_saveComplete').html('Update Complete') + @$('.bv_save').attr('disabled', 'disabled') + + @model.save null, + success: (model, response) => + if response is "update #{@entityType} failed" + @model.trigger 'saveFailed' + + validationError: => + super() + @$('.bv_save').attr('disabled', 'disabled') + + clearValidationErrorStyles: => + super() + @$('.bv_save').removeAttr('disabled') + + checkDisplayMode: => + if @readOnly is true + @displayInReadOnlyMode() + + displayInReadOnlyMode: => + @$(".bv_save").hide() + @$(".bv_cancel").hide() + # @$(".bv_newEntity").hide() + @$('button').attr 'disabled', 'disabled' + @disableAllInputs() + + checkFormValid: => + if @isValid() + @$('.bv_save').removeAttr('disabled') + else + @$('.bv_save').attr('disabled', 'disabled') \ No newline at end of file diff --git a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee new file mode 100644 index 000000000..68901f4f7 --- /dev/null +++ b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee @@ -0,0 +1,284 @@ +############################################################################ +# models +############################################################################ +class window.CmpdRegAdminSearch extends Backbone.Model + defaults: + name: null + code: null + id: null + +############################################################################ +class window.CmpdRegAdminList extends Backbone.Collection + model: CmpdRegAdminSearch + +############################################################################ +# controllers +############################################################################ +class window.CmpdRegAdminSimpleSearchController extends AbstractFormController + ### + Instantiating controller must provide urlRoot and toDisplay in options + ### + + initialize: -> + @searchUrl = "" + @searchUrl = @options.urlRoot + '/search/' + + events: + 'keyup .bv_cmpdRegAdminSearchTerm': 'updateCmpdRegAdminSearchTerm' + 'click .bv_doSearch': 'handleDoSearchClicked' + "click .bv_createNewCmpdRegAdminBtn": "handleCreateNewCmpdRegAdminClicked" + + render: => + console.log "rendering SimpleSearchController" + template = _.template($("#CmpdRegAdminSimpleSearchView").html()) + $(@el).empty() + console.log @options.toDisplay + $(@el).html(template(@options.toDisplay)) + @ + + updateCmpdRegAdminSearchTerm: (e) => + ENTER_KEY = 13 + cmpdRegAdminSearchTerm = $.trim(@$(".bv_cmpdRegAdminSearchTerm").val()) + if cmpdRegAdminSearchTerm isnt "" + @$(".bv_doSearch").attr("disabled", false) + if e.keyCode is ENTER_KEY + $(':focus').blur() + @handleDoSearchClicked() + else + @$(".bv_doSearch").attr("disabled", true) + + handleDoSearchClicked: => + $(".bv_cmpdRegAdminTableController").addClass "hide" + $(".bv_errorOccurredPerformingSearch").addClass "hide" + cmpdRegAdminSearchTerm = $.trim(@$(".bv_cmpdRegAdminSearchTerm").val()) + if cmpdRegAdminSearchTerm isnt "" + $(".bv_noMatchingCmpdRegAdminsFoundMessage").addClass "hide" + $(".bv_cmpdRegAdminBrowserSearchInstructions").addClass "hide" + $(".bv_searchCmpdRegAdminsStatusIndicator").removeClass "hide" + if !window.conf.browser.enableSearchAll and cmpdRegAdminSearchTerm is "*" + $(".bv_moreSpecificCmpdRegAdminSearchNeeded").removeClass "hide" + else + $(".bv_searchingCmpdRegAdminsMessage").removeClass "hide" + $(".bv_cmpdRegAdminSearchTerm").html cmpdRegAdminSearchTerm + $(".bv_moreSpecificCmpdRegAdminSearchNeeded").addClass "hide" + @doSearch cmpdRegAdminSearchTerm + + doSearch: (cmpdRegAdminSearchTerm) => +# disable the search text field while performing a search + @$(".bv_cmpdRegAdminSearchTerm").attr "disabled", true + @$(".bv_doSearch").attr "disabled", true + @trigger 'find' + unless cmpdRegAdminSearchTerm is "" + $.ajax + type: 'GET' + url: @searchUrl + cmpdRegAdminSearchTerm + dataType: "json" + data: + testMode: false + +#fullObject: true + success: (cmpdRegAdmin) => + @trigger "searchReturned", cmpdRegAdmin + error: (result) => + @trigger "searchReturned", null + complete: => +# re-enable the search text field regardless of if any results found + @$(".bv_cmpdRegAdminSearchTerm").attr "disabled", false + @$(".bv_doSearch").attr "disabled", false + + handleCreateNewCmpdRegAdminClicked: => + @trigger 'createNewCmpdRegAdmin' + +############################################################################ +class window.CmpdRegAdminRowSummaryController extends Backbone.View + tagName: 'tr' + className: 'dataTableRow' + events: + "click": "handleClick" + + handleClick: => + @trigger "gotClick", @model + $(@el).closest("table").find("tr").removeClass "info" + $(@el).addClass "info" + + initialize: -> + @template = _.template($('#CmpdRegAdminRowSummaryView').html()) + + render: => + toDisplay = + code: @model.get('code') + name: @model.get('name') + $(@el).html(@template(toDisplay)) + + @ + +############################################################################ +class window.CmpdRegAdminSummaryTableController extends Backbone.View + initialize: -> + + selectedRowChanged: (row) => + @trigger "selectedRowUpdated", row + + render: => + @template = _.template($('#CmpdRegAdminSummaryTableView').html()) + $(@el).html @template(@options.toDisplay) + if @collection.models.length is 0 + $(".bv_noMatchingCmpdRegAdminsFoundMessage").removeClass "hide" + # display message indicating no results were found + else + $(".bv_noMatchingCmpdRegAdminsFoundMessage").addClass "hide" + @collection.each (admin) => + prsc = new CmpdRegAdminRowSummaryController + model: admin + prsc.on "gotClick", @selectedRowChanged + @$("tbody").append prsc.render().el + + @$("table").dataTable oLanguage: + sSearch: "Filter results: " #rename summary table's search bar + + @ + +############################################################################ +class window.AbstractCmpdRegAdminBrowserController extends Backbone.View + ### + Instantiating controller must provide: + entityType + entityClass + entityControllerClass + moduleLaunchName + ### + includeDuplicateAndEdit: false + events: + "click .bv_deleteCmpdRegAdmin": "handleDeleteCmpdRegAdminClicked" + "click .bv_editCmpdRegAdmin": "handleEditCmpdRegAdminClicked" + "click .bv_confirmDeleteCmpdRegAdminButton": "handleConfirmDeleteCmpdRegAdminClicked" + "click .bv_cancelDelete": "handleCancelDeleteClicked" + + + initialize: -> + template = _.template( $("#AbstractCmpdRegAdminBrowserView").html()); + $(@el).empty() + @toDisplay = + entityTypeToDisplay: if @entityTypeToDisplay? then @entityTypeToDisplay else @entityType + entityTypePluralToDisplay: if @entityTypePluralToDisplay? then @entityTypePluralToDisplay else @entityTypePlural + entityTypeUpper: @entityTypeUpper + entityTypeUpperPlural: @entityTypeUpperPlural + $(@el).html(template(@toDisplay)) + @searchController = new CmpdRegAdminSimpleSearchController + model: new CmpdRegAdminSearch() + el: @$('.bv_cmpdRegAdminSearchController') + urlRoot: "/api/CmpdRegAdmin/#{@entityTypePlural}" + toDisplay: @toDisplay + @searchController.render() + @searchController.on "searchReturned", @setupCmpdRegAdminSummaryTable + @searchController.on "createNewCmpdRegAdmin", @handleCreateNewCmpdRegAdminClicked + #@searchController.on "resetSearch", @destroyCmpdRegAdminSummaryTable + + setupCmpdRegAdminSummaryTable: (cmpdRegAdmins) => + @destroyCmpdRegAdminSummaryTable() + + $(".bv_searchingCmpdRegAdminsMessage").addClass "hide" + if cmpdRegAdmins is null + @$(".bv_errorOccurredPerformingSearch").removeClass "hide" + + else if cmpdRegAdmins.length is 0 + @$(".bv_noMatchingCmpdRegAdminsFoundMessage").removeClass "hide" + @$(".bv_cmpdRegAdminTableController").html "" + else + $(".bv_searchCmpdRegAdminsStatusIndicator").addClass "hide" + @$(".bv_cmpdRegAdminTableController").removeClass "hide" + @cmpdRegAdminSummaryTable = new CmpdRegAdminSummaryTableController + collection: new CmpdRegAdminList cmpdRegAdmins + toDisplay: @toDisplay + + @cmpdRegAdminSummaryTable.on "selectedRowUpdated", @selectedCmpdRegAdminUpdated + $(".bv_cmpdRegAdminTableController").html @cmpdRegAdminSummaryTable.render().el + + selectedCmpdRegAdminUpdated: (cmpdRegAdmin) => + @trigger "selectedCmpdRegAdminUpdated" + if @cmpdRegAdminController? + @cmpdRegAdminController.undelegateEvents() + @cmpdRegAdminController = new window[@entityControllerClass] + model: new window[@entityClass] cmpdRegAdmin.attributes + readOnly: true + + $('.bv_cmpdRegAdminController').html @cmpdRegAdminController.render().el + $(".bv_cmpdRegAdminController").removeClass("hide") + $(".bv_cmpdRegAdminControllerContainer").removeClass("hide") + @$('.bv_editCmpdRegAdmin').show() + @$('.bv_deleteCmpdRegAdmin').show() + + handleDeleteCmpdRegAdminClicked: => + @$(".bv_cmpdRegAdminCodeName").html @cmpdRegAdminController.model.get("code") + @$(".bv_deleteButtons").removeClass "hide" + @$(".bv_okayButton").addClass "hide" + @$(".bv_errorDeletingCmpdRegAdminMessage").addClass "hide" + @$(".bv_deleteWarningMessage").removeClass "hide" + @$(".bv_deletingStatusIndicator").addClass "hide" + @$(".bv_cmpdRegAdminDeletedSuccessfullyMessage").addClass "hide" + $(".bv_confirmDeleteCmpdRegAdmin").removeClass "hide" + $('.bv_confirmDeleteCmpdRegAdmin').modal({ + keyboard: false, + backdrop: true + }) + + handleConfirmDeleteCmpdRegAdminClicked: => + @$(".bv_deleteWarningMessage").addClass "hide" + @$(".bv_deletingStatusIndicator").removeClass "hide" + @$(".bv_deleteButtons").addClass "hide" + $.ajax( + url: "/api/cmpdRegAdmin/#{@entityTypePlural}/#{@cmpdRegAdminController.model.get("id")}", + type: 'DELETE', + success: (result) => + @$(".bv_okayButton").removeClass "hide" + @$(".bv_deletingStatusIndicator").addClass "hide" + @$(".bv_cmpdRegAdminDeletedSuccessfullyMessage").removeClass "hide" + @searchController.handleDoSearchClicked() + error: (result) => + @$(".bv_okayButton").removeClass "hide" + @$(".bv_deletingStatusIndicator").addClass "hide" + @$(".bv_errorDeletingCmpdRegAdminMessage").removeClass "hide" + ) + + handleCancelDeleteClicked: => + @$(".bv_confirmDeleteCmpdRegAdmin").modal('hide') + + handleEditCmpdRegAdminClicked: => + @createCmpdRegAdminController @cmpdRegAdminController.model + + destroyCmpdRegAdminSummaryTable: => + if @cmpdRegAdminSummaryTable? + @cmpdRegAdminSummaryTable.remove() + if @cmpdRegAdminController? + @cmpdRegAdminController.remove() + $(".bv_cmpdRegAdminController").addClass("hide") + $(".bv_cmpdRegAdminControllerContainer").addClass("hide") + $(".bv_noMatchingCmpdRegAdminsFoundMessage").addClass("hide") + + render: => + @ + + handleCreateNewCmpdRegAdminClicked: => + @createCmpdRegAdminController new window[@entityClass]() + + createCmpdRegAdminController: (mdl) => + @$('.bv_cmpdRegAdminBrowserWrapper').hide() + @$('.bv_cmpdRegAdminControllerWrapper').show() + if @cmpdRegAdminController? + @cmpdRegAdminController.undelegateEvents() + @$(".bv_cmpdRegAdminControllerWrapper").html "" + @cmpdRegAdminController = new window[@entityControllerClass] + model: mdl + @cmpdRegAdminController.on 'backToBrowser', @handleBackToCmpdRegAdminBrowserClicked + @cmpdRegAdminController.on 'amDirty', => + @trigger 'amDirty' + @cmpdRegAdminController.on 'amClean', => + @trigger 'amClean' + @$(".bv_cmpdRegAdminControllerWrapper").append @cmpdRegAdminController.render().el + @cmpdRegAdminController.$('.bv_backToCmpdRegAdminBrowserBtn').show() + + handleBackToCmpdRegAdminBrowserClicked: => + @$('.bv_cmpdRegAdminBrowserWrapper').show() + @$('.bv_cmpdRegAdminControllerWrapper').hide() + @searchController.handleDoSearchClicked() + @trigger 'amClean' diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowserView.html b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowserView.html similarity index 54% rename from modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowserView.html rename to modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowserView.html index 5eaf87818..fe3d6ddd0 100644 --- a/modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowserView.html +++ b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowserView.html @@ -1,14 +1,14 @@ - - - - diff --git a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminView.html b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminView.html new file mode 100644 index 000000000..e13910de3 --- /dev/null +++ b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminView.html @@ -0,0 +1,119 @@ + + diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegScientist.coffee b/modules/CmpdRegAdmin/src/client/CmpdRegScientist.coffee new file mode 100644 index 000000000..499af880e --- /dev/null +++ b/modules/CmpdRegAdmin/src/client/CmpdRegScientist.coffee @@ -0,0 +1,64 @@ +############################################################################ +# models +############################################################################ +class window.Scientist extends Backbone.Model + urlRoot: "/api/cmpdRegAdmin/scientists" + defaults: + name: null + code: null + id: null + + validate: (attrs) -> + errors = [] + if attrs.code? and @isNew() + validChars = attrs.code.match(/[a-zA-Z0-9 _\-+]/g) + unless validChars.length is attrs.code.length + errors.push + attribute: 'scientistCode' + message: "Scientist code can not contain special characters" + if !attrs.name? or attrs.name is "" + errors.push + attribute: 'scientistName' + message: "Scientist name must be set and unique" + if errors.length > 0 + return errors + else + return null + +############################################################################ +class window.Scientists extends Backbone.Collection + model: Scientist +############################################################################ + +############################################################################ +# controllers +############################################################################ + +class window.ScientistController extends AbstractCmpdRegAdminController + wrapperTemplate: _.template($("#ScientistView").html()) + moduleLaunchName: "scientist" + entityType: "scientist" + entityTypePlural: "scientists" + entityTypeUpper: "Scientist" + entityTypeUpperPlural: "Scientists" + modelClass: "Scientist" + + completeInitialization: => + @errorOwnerName = 'ScientistController' + $(@el).empty() + $(@el).html @wrapperTemplate() +# @$('.bv_scientistControllerDiv').html + console.log @$('.bv_scientistControllerDiv') + console.log "completing initialization of ScientistController" + @$('.bv_scientistControllerDiv').html super() + + +class window.ScientistBrowserController extends AbstractCmpdRegAdminBrowserController + wrapperTemplate: _.template($("#ScientistBrowserView").html()) + entityType: "scientist" + entityTypePlural: "scientists" + entityTypeUpper: "Scientist" + entityTypeUpperPlural: "Scientists" + entityClass: "Scientist" + entityControllerClass: "ScientistController" + moduleLaunchName: "scientist_browser" diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegScientist.html b/modules/CmpdRegAdmin/src/client/CmpdRegScientist.html new file mode 100644 index 000000000..af4f979a0 --- /dev/null +++ b/modules/CmpdRegAdmin/src/client/CmpdRegScientist.html @@ -0,0 +1,8 @@ + + + diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegStereoCategory.coffee b/modules/CmpdRegAdmin/src/client/CmpdRegStereoCategory.coffee new file mode 100644 index 000000000..1017cf077 --- /dev/null +++ b/modules/CmpdRegAdmin/src/client/CmpdRegStereoCategory.coffee @@ -0,0 +1,65 @@ +############################################################################ +# models +############################################################################ +class window.StereoCategory extends Backbone.Model + urlRoot: "/api/cmpdRegAdmin/stereoCategories" + defaults: + name: null + code: null + id: null + + validate: (attrs) -> + errors = [] + if attrs.code? and @isNew() + validChars = attrs.code.match(/[a-zA-Z0-9 _\-+]/g) + unless validChars.length is attrs.code.length + errors.push + attribute: 'code' + message: "Stereo Category code can not contain special characters" + if !attrs.name? or attrs.name is "" + errors.push + attribute: 'name' + message: "Stereo Category name must be set and unique" + if errors.length > 0 + return errors + else + return null + +############################################################################ +class window.StereoCategories extends Backbone.Collection + model: StereoCategory +############################################################################ + +############################################################################ +# controllers +############################################################################ + +class window.StereoCategoryController extends AbstractCmpdRegAdminController + wrapperTemplate: _.template($("#StereoCategoryView").html()) + moduleLaunchName: "stereo_category" + entityType: "stereoCategory" + entityTypePlural: "stereoCategories" + entityTypeToDisplay: "stereo category" + entityTypePluralToDisplay: "stereo categories" + entityTypeUpper: "Stereo Category" + entityTypeUpperPlural: "Stereo Categories" + modelClass: "StereoCategory" + + completeInitialization: => + @errorOwnerName = 'StereoCategoryController' + $(@el).empty() + $(@el).html @wrapperTemplate() + @$('.bv_stereoCategoryControllerDiv').html super() + + +class window.StereoCategoryBrowserController extends AbstractCmpdRegAdminBrowserController + wrapperTemplate: _.template($("#StereoCategoryBrowserView").html()) + entityType: "stereoCategory" + entityTypePlural: "stereoCategories" + entityTypeToDisplay: "stereo category" + entityTypePluralToDisplay: "stereo categories" + entityTypeUpper: "Stereo Category" + entityTypeUpperPlural: "Stereo Categories" + entityClass: "StereoCategory" + entityControllerClass: "StereoCategoryController" + moduleLaunchName: "stereo_category_browser" \ No newline at end of file diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegStereoCategory.html b/modules/CmpdRegAdmin/src/client/CmpdRegStereoCategory.html new file mode 100644 index 000000000..61eaf6494 --- /dev/null +++ b/modules/CmpdRegAdmin/src/client/CmpdRegStereoCategory.html @@ -0,0 +1,8 @@ + + + diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee index f1014b0cf..d66071e44 100644 --- a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee +++ b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.coffee @@ -34,223 +34,31 @@ class window.Vendors extends Backbone.Collection # controllers ############################################################################ -class window.VendorController extends AbstractFormController - template: _.template($("#VendorView").html()) +class window.VendorController extends AbstractCmpdRegAdminController + wrapperTemplate: _.template($("#VendorView").html()) moduleLaunchName: "vendor" - - events: -> - "keyup .bv_vendorCode": "handleVendorCodeNameChanged" - "keyup .bv_vendorName": "handleVendorNameChanged" - "click .bv_save": "handleSaveClicked" - "click .bv_backToVendorBrowserBtn": "handleBackToVendorBrowserClicked" -# "click .bv_newEntity": "handleNewEntityClicked" - "click .bv_cancel": "handleCancelClicked" - "click .bv_cancelClear": "handleCancelClearClicked" - "click .bv_confirmClear": "handleConfirmClearClicked" - - initialize: -> - if @model? - @completeInitialization() - else - if window.AppLaunchParams.moduleLaunchParams? - if window.AppLaunchParams.moduleLaunchParams.moduleName == @moduleLaunchName - $.ajax - type: 'GET' - url: "/api/cmpdRegAdmin/vendors/codeName/"+window.AppLaunchParams.moduleLaunchParams.code - dataType: 'json' - error: (err) => - alert 'Error getting vendor for code in this URL. Creating a new project' - @completeInitialization() - success: (json) => - if json.id? - @model = new Vendor json - else - alert 'Could not get vendor for code in this URL. Creating a new project' - @completeInitialization() - else - @completeInitialization() - else - @completeInitialization() - + entityType: "vendor" + entityTypePlural: "vendors" + entityTypeUpper: "Vendor" + entityTypeUpperPlural: "Vendors" + modelClass: "Vendor" completeInitialization: => - unless @model? - @model=new Vendor() @errorOwnerName = 'VendorController' - @setBindings() - if @options.readOnly? - @readOnly = @options.readOnly - else - @readOnly = false - @listenTo @model, 'saveFailed', @handleSaveFailed - @listenTo @model, 'sync', @modelSaveCallback - @listenTo @model, 'change', @modelChangeCallback $(@el).empty() - $(@el).html @template() - @render() - - render: => - unless @model? - @model = new Vendor() - code = @model.get('code') - @$('.bv_vendorCode').val(code) - @$('.bv_vendorCode').html(code) - if @model.isNew() - @$('.bv_save').html("Save") -# @$('.bv_newEntity').hide() - else - @$('.bv_save').html("Update") -# @$('.bv_newEntity').show() - @$('.bv_vendorName').val @model.get('name') - - if @readOnly is true - @displayInReadOnlyMode() - @$('.bv_backToVendorBrowserBtn').hide() - @$('.bv_save').attr('disabled','disabled') - @$('.bv_cancel').attr('disabled','disabled') - - @ - - handleSaveFailed: => - @$('.bv_saveFailed').show() - @$('.bv_saveComplete').hide() - @$('.bv_saving').hide() - - modelSaveCallback: (method, model) => - @$('.bv_save').show() - @$('.bv_save').attr('disabled', 'disabled') - unless @$('.bv_saveFailed').is(":visible") - @$('.bv_saveComplete').show() - @$('.bv_saving').hide() - @$('.bv_cancel').removeAttr 'disabled' - @render() - @trigger 'amClean' - - modelChangeCallback: (method, model) => - @trigger 'amDirty' - @checkFormValid() - @$('.bv_saveComplete').hide() - @$('.bv_saveFailed').hide() - @$('.bv_cancel').removeAttr('disabled') - @$('.bv_cancelComplete').hide() - - handleVendorCodeNameChanged: => - code = UtilityFunctions::getTrimmedInput @$('.bv_vendorCode') - - if code is "" - @model.set 'code', null - else - @model.set 'code', code - @model.trigger 'change' - - handleBackToVendorBrowserClicked: => - @trigger 'backToBrowser' - - -# handleNewEntityClicked: => -# @$('.bv_confirmClearEntity').modal('show') -# @$('.bv_confirmClear').removeAttr('disabled') -# @$('.bv_cancelClear').removeAttr('disabled') -# @$('.bv_closeModalButton').removeAttr('disabled') - - handleCancelClearClicked: => - @$('.bv_confirmClearEntity').modal('hide') - - handleConfirmClearClicked: => - @$('.bv_confirmClearEntity').modal('hide') - @model = null - @completeInitialization() - @trigger 'amClean' - - handleCancelClicked: => - if @model.isNew() - @model = null - @completeInitialization() - else - @$('.bv_canceling').show() - @model.fetch - success: @handleCancelComplete - @trigger 'amClean' - - handleCancelComplete: => - @$('.bv_canceling').hide() - @$('.bv_cancelComplete').show() - - handleVendorNameChanged: => - @model.set("name", UtilityFunctions::getTrimmedInput @$('.bv_vendorName')) - - handleSaveClicked: => - @callNameValidationService() - - @$('.bv_saving').show() - @$('.bv_saveFailed').hide() - @$('.bv_saveComplete').hide() - - - callNameValidationService: => - @$('.bv_saving').show() - @$('.bv_save').attr('disabled', 'disabled') - validateURL = "/api/cmpdRegAdmin/vendors/validateBeforeSave" - dataToPost = - data: #dataToPost needs wrapping key, not sure why - JSON.stringify(@model) - $.ajax - type: 'POST' - url: validateURL - data: dataToPost - dataType: 'json' - success: (response) => - @handleValidateReturn(response) - error: (err) => - @handleValidateError(JSON.parse err.responseText) - - handleValidateError: (err) => - if err?[0]?.level? and err[0].level is "ERROR" - alert "The requested code has already been used" - @$('.bv_saving').hide() - @$('.bv_saveFailed').show() - - handleValidateReturn: (validateResp) => - if validateResp?[0]?.errorLevel? - alert 'The requested vendor name has already been registered. Please choose a new vendor name.' - @$('.bv_saving').hide() - @$('.bv_saveFailed').show() - else - @saveVendor() - - saveVendor: => - if @model.isNew() - @$('.bv_saveComplete').html('Save Complete') - else - @$('.bv_saveComplete').html('Update Complete') - @$('.bv_save').attr('disabled', 'disabled') - - @model.save null, - success: (model, response) => - if response is "update vendor failed" - @model.trigger 'saveFailed' - - validationError: => - super() - @$('.bv_save').attr('disabled', 'disabled') - - clearValidationErrorStyles: => - super() - @$('.bv_save').removeAttr('disabled') - - checkDisplayMode: => - if @readOnly is true - @displayInReadOnlyMode() - - displayInReadOnlyMode: => - @$(".bv_save").hide() - @$(".bv_cancel").hide() -# @$(".bv_newEntity").hide() - @$('button').attr 'disabled', 'disabled' - @disableAllInputs() - - checkFormValid: => - if @isValid() - @$('.bv_save').removeAttr('disabled') - else - @$('.bv_save').attr('disabled', 'disabled') + $(@el).html @wrapperTemplate() +# @$('.bv_vendorControllerDiv').html + console.log @$('.bv_vendorControllerDiv') + console.log "completing initialization of VendorController" + @$('.bv_vendorControllerDiv').html super() + + +class window.VendorBrowserController extends AbstractCmpdRegAdminBrowserController + wrapperTemplate: _.template($("#VendorBrowserView").html()) + entityType: "vendor" + entityTypePlural: "vendors" + entityTypeUpper: "Vendor" + entityTypeUpperPlural: "Vendors" + entityClass: "Vendor" + entityControllerClass: "VendorController" + moduleLaunchName: "vendor_browser" diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html index 98e2c2d85..251e9825c 100644 --- a/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html +++ b/modules/CmpdRegAdmin/src/client/CmpdRegVendor.html @@ -1,119 +1,8 @@ - + - diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowser.coffee b/modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowser.coffee deleted file mode 100644 index ca35cbc7c..000000000 --- a/modules/CmpdRegAdmin/src/client/CmpdRegVendorBrowser.coffee +++ /dev/null @@ -1,269 +0,0 @@ -############################################################################ -# models -############################################################################ -class window.VendorSearch extends Backbone.Model - defaults: - name: null - code: null - id: null - -############################################################################ -class window.VendorList extends Backbone.Collection - model: VendorSearch - - -############################################################################ -# controllers -############################################################################ - -class window.VendorSimpleSearchController extends AbstractFormController - template: _.template($("#VendorSimpleSearchView").html()) - genericSearchUrl: "/api/CmpdRegAdmin/vendors/search/" - - initialize: -> - @searchUrl = "" - @searchUrl = @genericSearchUrl - - events: - 'keyup .bv_vendorSearchTerm': 'updateVendorSearchTerm' - 'click .bv_doSearch': 'handleDoSearchClicked' - "click .bv_createNewVendorBtn": "handleCreateNewVendorClicked" - - render: => - $(@el).empty() - $(@el).html @template() - - updateVendorSearchTerm: (e) => - ENTER_KEY = 13 - vendorSearchTerm = $.trim(@$(".bv_vendorSearchTerm").val()) - if vendorSearchTerm isnt "" - @$(".bv_doSearch").attr("disabled", false) - if e.keyCode is ENTER_KEY - $(':focus').blur() - @handleDoSearchClicked() - else - @$(".bv_doSearch").attr("disabled", true) - - handleDoSearchClicked: => - $(".bv_vendorTableController").addClass "hide" - $(".bv_errorOccurredPerformingSearch").addClass "hide" - vendorSearchTerm = $.trim(@$(".bv_vendorSearchTerm").val()) - if vendorSearchTerm isnt "" - $(".bv_noMatchingVendorsFoundMessage").addClass "hide" - $(".bv_vendorBrowserSearchInstructions").addClass "hide" - $(".bv_searchVendorsStatusIndicator").removeClass "hide" - if !window.conf.browser.enableSearchAll and vendorSearchTerm is "*" - $(".bv_moreSpecificVendorSearchNeeded").removeClass "hide" - else - $(".bv_searchingVendorsMessage").removeClass "hide" - $(".bv_vendorSearchTerm").html vendorSearchTerm - $(".bv_moreSpecificVendorSearchNeeded").addClass "hide" - @doSearch vendorSearchTerm - - doSearch: (vendorSearchTerm) => -# disable the search text field while performing a search - @$(".bv_vendorSearchTerm").attr "disabled", true - @$(".bv_doSearch").attr "disabled", true - @trigger 'find' - unless vendorSearchTerm is "" - $.ajax - type: 'GET' - url: @searchUrl + vendorSearchTerm - dataType: "json" - data: - testMode: false - -#fullObject: true - success: (vendor) => - @trigger "searchReturned", vendor - error: (result) => - @trigger "searchReturned", null - complete: => -# re-enable the search text field regardless of if any results found - @$(".bv_vendorSearchTerm").attr "disabled", false - @$(".bv_doSearch").attr "disabled", false - - handleCreateNewVendorClicked: => - @trigger 'createNewVendor' - -############################################################################ -class window.VendorRowSummaryController extends Backbone.View - tagName: 'tr' - className: 'dataTableRow' - events: - "click": "handleClick" - - handleClick: => - @trigger "gotClick", @model - $(@el).closest("table").find("tr").removeClass "info" - $(@el).addClass "info" - - initialize: -> - @template = _.template($('#VendorRowSummaryView').html()) - - render: => - toDisplay = - code: @model.get('code') - name: @model.get('name') - $(@el).html(@template(toDisplay)) - - @ - -############################################################################ -class window.VendorSummaryTableController extends Backbone.View - initialize: -> - - selectedRowChanged: (row) => - @trigger "selectedRowUpdated", row - - render: => - @template = _.template($('#VendorSummaryTableView').html()) - $(@el).html @template - if @collection.models.length is 0 - $(".bv_noMatchingVendorsFoundMessage").removeClass "hide" - # display message indicating no results were found - else - $(".bv_noMatchingVendorsFoundMessage").addClass "hide" - @collection.each (vend) => - prsc = new VendorRowSummaryController - model: vend - prsc.on "gotClick", @selectedRowChanged - @$("tbody").append prsc.render().el - - @$("table").dataTable oLanguage: - sSearch: "Filter results: " #rename summary table's search bar - - @ - -############################################################################ -class window.VendorBrowserController extends Backbone.View - #template: _.template($("#VendorBrowserView").html()) - includeDuplicateAndEdit: false - events: - "click .bv_deleteVendor": "handleDeleteVendorClicked" - "click .bv_editVendor": "handleEditVendorClicked" - "click .bv_confirmDeleteVendorButton": "handleConfirmDeleteVendorClicked" - "click .bv_cancelDelete": "handleCancelDeleteClicked" - - moduleLaunchName: "vendor_browser" - - initialize: -> - template = _.template( $("#VendorBrowserView").html()); - $(@el).empty() - $(@el).html template - @searchController = new VendorSimpleSearchController - model: new VendorSearch() - el: @$('.bv_vendorSearchController') - @searchController.render() - @searchController.on "searchReturned", @setupVendorSummaryTable - @searchController.on "createNewVendor", @handleCreateNewVendorClicked - #@searchController.on "resetSearch", @destroyVendorSummaryTable - - setupVendorSummaryTable: (vendors) => - @destroyVendorSummaryTable() - - $(".bv_searchingVendorsMessage").addClass "hide" - if vendors is null - @$(".bv_errorOccurredPerformingSearch").removeClass "hide" - - else if vendors.length is 0 - @$(".bv_noMatchingVendorsFoundMessage").removeClass "hide" - @$(".bv_vendorTableController").html "" - else - $(".bv_searchVendorsStatusIndicator").addClass "hide" - @$(".bv_vendorTableController").removeClass "hide" - @vendorSummaryTable = new VendorSummaryTableController - collection: new VendorList vendors - - @vendorSummaryTable.on "selectedRowUpdated", @selectedVendorUpdated - $(".bv_vendorTableController").html @vendorSummaryTable.render().el - - selectedVendorUpdated: (vendor) => - @trigger "selectedVendorUpdated" - if @vendorController? - @vendorController.undelegateEvents() - @vendorController = new VendorController - model: new Vendor vendor.attributes - readOnly: true - - $('.bv_vendorController').html @vendorController.render().el - $(".bv_vendorController").removeClass("hide") - $(".bv_vendorControllerContainer").removeClass("hide") - @$('.bv_editVendor').show() - @$('.bv_deleteVendor').show() - - handleDeleteVendorClicked: => - @$(".bv_vendorCodeName").html @vendorController.model.get("code") - @$(".bv_deleteButtons").removeClass "hide" - @$(".bv_okayButton").addClass "hide" - @$(".bv_errorDeletingVendorMessage").addClass "hide" - @$(".bv_deleteWarningMessage").removeClass "hide" - @$(".bv_deletingStatusIndicator").addClass "hide" - @$(".bv_vendorDeletedSuccessfullyMessage").addClass "hide" - $(".bv_confirmDeleteVendor").removeClass "hide" - $('.bv_confirmDeleteVendor').modal({ - keyboard: false, - backdrop: true - }) - - handleConfirmDeleteVendorClicked: => - @$(".bv_deleteWarningMessage").addClass "hide" - @$(".bv_deletingStatusIndicator").removeClass "hide" - @$(".bv_deleteButtons").addClass "hide" - $.ajax( - url: "/api/cmpdRegAdmin/vendors/#{@vendorController.model.get("id")}", - type: 'DELETE', - success: (result) => - @$(".bv_okayButton").removeClass "hide" - @$(".bv_deletingStatusIndicator").addClass "hide" - @$(".bv_vendorDeletedSuccessfullyMessage").removeClass "hide" - @searchController.handleDoSearchClicked() - error: (result) => - @$(".bv_okayButton").removeClass "hide" - @$(".bv_deletingStatusIndicator").addClass "hide" - @$(".bv_errorDeletingVendorMessage").removeClass "hide" - ) - - handleCancelDeleteClicked: => - @$(".bv_confirmDeleteVendor").modal('hide') - - handleEditVendorClicked: => - @createVendorController @vendorController.model - - destroyVendorSummaryTable: => - if @vendorSummaryTable? - @vendorSummaryTable.remove() - if @vendorController? - @vendorController.remove() - $(".bv_vendorController").addClass("hide") - $(".bv_vendorControllerContainer").addClass("hide") - $(".bv_noMatchingVendorsFoundMessage").addClass("hide") - - render: => - - @ - - handleCreateNewVendorClicked: => - @createVendorController new Vendor() - - createVendorController: (mdl) => - @$('.bv_vendorBrowserWrapper').hide() - @$('.bv_vendorControllerWrapper').show() - if @vendorController? - @vendorController.undelegateEvents() - @$(".bv_vendorControllerWrapper").html "" - @vendorController = new VendorController - model: mdl - @vendorController.on 'backToBrowser', @handleBackToVendorBrowserClicked - @vendorController.on 'amDirty', => - @trigger 'amDirty' - @vendorController.on 'amClean', => - @trigger 'amClean' - @$(".bv_vendorControllerWrapper").append @vendorController.render().el - @vendorController.$('.bv_backToVendorBrowserBtn').show() - - handleBackToVendorBrowserClicked: => - @$('.bv_vendorBrowserWrapper').show() - @$('.bv_vendorControllerWrapper').hide() - @searchController.handleDoSearchClicked() - @trigger 'amClean' diff --git a/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee b/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee index 566c6c922..f4e83a3f2 100644 --- a/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee +++ b/modules/CmpdRegAdmin/src/server/routes/CmpdRegAdminRoutes.coffee @@ -23,21 +23,21 @@ exports.validateCmpdRegEntity = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' entityType = req.params.entityType - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}/validate?code=' + req.params.code + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + "#{entityType}/validate?code=" + req.params.code request( method: 'GET' url: cmpdRegCall json: false timeout: 6000000 , (error, response, validEntity) => - if !error + if !error and !validEntity.startsWith('<') resp.statusCode = response.statusCode resp.setHeader('Content-Type', 'application/json') resp.end validEntity - console.log 'done validating the ' + entityType + console.log "done validating the #{entityType} testString" else console.log 'got ajax error trying to do validate #{entityType}' - console.log validEntity + resp.statusCode = 500 resp.end JSON.stringify {error: "something went wrong validating the #{entityType}"} ) @@ -45,7 +45,8 @@ exports.validateCmpdRegEntityBeforeSave = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' entityType = req.params.entityType - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}/validateBeforeSave' + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + "#{entityType}/validateBeforeSave" + console.log cmpdRegCall request( method: 'POST' url: cmpdRegCall @@ -55,15 +56,14 @@ exports.validateCmpdRegEntityBeforeSave = (req, resp) -> headers: "Content-Type": 'application/json' , (error, response, validEntity) => - if !error + if !error and !validEntity.toString().startsWith('<') resp.statusCode = response.statusCode resp.setHeader('Content-Type', 'application/json') resp.end JSON.stringify validEntity - console.log resp.statusCode - console.log 'done validating the #{entityType}' else - console.log 'got ajax error trying to do validate #{entityType}' + console.error "got ajax error trying to do validate #{entityType}" console.log validEntity + resp.statusCode = 500 resp.end JSON.stringify {error: "something went wrong validating the #{entityType} :("} ) @@ -71,7 +71,7 @@ exports.getCmpdRegEntityById = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' entityType = req.params.entityType - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}/' + req.params.id + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + "#{entityType}/" + req.params.id request( method: 'GET' url: cmpdRegCall @@ -85,7 +85,7 @@ exports.getCmpdRegEntityById = (req, resp) -> resp.json json else resp.statusCode = 404 - console.log 'got ajax error trying to do find #{entityType}' + console.error "got ajax error trying to do find #{entityType}" console.log json resp.end JSON.stringify {error: "something went wrong :("} ) @@ -94,7 +94,7 @@ exports.getCmpdRegEntityByCode = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' entityType = req.params.entityType - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}/findByCodeEquals?code=' + req.params.code + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + "#{entityType}/findByCodeEquals?code=" + req.params.code request( method: 'GET' url: cmpdRegCall @@ -117,7 +117,8 @@ exports.searchCmpdRegEntities = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' entityType = req.params.entityType - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}/search/?searchTerm=' + req.params.searchTerm + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + "#{entityType}/search/?searchTerm=" + req.params.searchTerm + console.debug cmpdRegCall request( method: 'GET' url: cmpdRegCall @@ -141,7 +142,7 @@ exports.getCmpdRegEntities = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' entityType = req.params.entityType - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}' + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + "#{entityType}" request( method: 'GET' url: cmpdRegCall @@ -154,8 +155,9 @@ exports.getCmpdRegEntities = (req, resp) -> resp.setHeader('Content-Type', 'application/json') resp.json json else - console.log 'got ajax error trying to do get #{entityType}s' + console.log "got ajax error trying to do get #{entityType}" console.log json + resp.statusCode = 404 resp.end JSON.stringify {error: "something went wrong :("} ) @@ -163,7 +165,7 @@ exports.saveCmpdRegEntity = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' entityType = req.params.entityType - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}' + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + "#{entityType}" request( method: 'POST' url: cmpdRegCall @@ -173,11 +175,11 @@ exports.saveCmpdRegEntity = (req, resp) -> headers: "Content-Type": 'application/json' , (error, response, json) => - if !error + if !error and !json.toString().startsWith('<') resp.setHeader('Content-Type', 'plain/text') resp.json json else - console.log 'got ajax error trying to save the #{entityType}' + console.log "got ajax error trying to save the #{entityType}" console.log json resp.statusCode = 500 resp.end "Error trying to save #{entityType}: " + error; @@ -187,7 +189,7 @@ exports.updateCmpdRegEntity = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' entityType = req.params.entityType - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}' + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + "#{entityType}" request( method: 'PUT' url: cmpdRegCall @@ -197,11 +199,11 @@ exports.updateCmpdRegEntity = (req, resp) -> headers: "Content-Type": 'application/json' , (error, response, json) => - if !error + if !error and response.statusCode == 200 resp.setHeader('Content-Type', 'plain/text') resp.json json else - console.log 'got ajax error trying to update #{entityType}' + console.log "got ajax error trying to update #{entityType}" console.log json resp.statusCode = 500 resp.end "Error trying to update #{entityType}: " + error; @@ -211,7 +213,7 @@ exports.deleteCmpdRegEntity = (req, resp) -> request = require 'request' config = require '../conf/compiled/conf.js' entityType = req.params.entityType - cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/#{entityType}/' + req.params.id + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + "#{entityType}/" + req.params.id request( method: 'DELETE' url: cmpdRegCall @@ -225,7 +227,7 @@ exports.deleteCmpdRegEntity = (req, resp) -> resp.json json else resp.statusCode = 404 - console.log 'got ajax error trying to delete #{entityType}' + console.log "got ajax error trying to delete #{entityType}" console.log json resp.end JSON.stringify {error: "something went wrong :("} ) \ No newline at end of file diff --git a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee index 6efb6c6f7..102fbd7bb 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee @@ -63,4 +63,26 @@ window.ModuleMenusConfiguration = mainControllerClassName: "SystemTestController" autoLaunchName:"system_test" requireUserRoles: [] + , + isHeader: true + menuName: "CmpdReg Admin" + requireUserRoles: [] + , + isHeader: false + menuName: "CmpdReg Vendors" + mainControllerClassName: "VendorBrowserController" + autoLaunchName: "vendor_browser" + requireUserRoles: [] + , + isHeader: false + menuName: "CmpdReg Stereo Categories" + mainControllerClassName: "StereoCategoryBrowserController" + autoLaunchName: "stereo_category_browser" + requireUserRoles: [] + , + isHeader: false + menuName: "CmpdReg Scientists" + mainControllerClassName: "ScientistBrowserController" + autoLaunchName: "scientist_browser" + requireUserRoles: [] ] From f729353f4b1c6b00928b5f360b5b9e0a1c3f770b Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Mon, 28 Aug 2017 16:13:05 -0700 Subject: [PATCH 146/576] feature/set-default-year-in-statetable: added beforeChange and beforeValidate functions in state table handsontable so that dates will have default of the current year rather than 2001. Fixes issue #223 --- .../src/client/ACASFormStateTable.coffee | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 61e413f02..03b5acf92 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -158,6 +158,8 @@ class window.ACASFormStateTableController extends Backbone.View setupHot: -> @hot = new Handsontable @$('.bv_tableWrapper')[0], + beforeChange: @handleBeforeChange + beforeValidate: @handleBeforeValidate afterChange: @handleCellChanged afterCreateRow: @handleRowCreated minSpareRows: 1, @@ -246,6 +248,25 @@ class window.ACASFormStateTableController extends Backbone.View else return null + handleBeforeChange: (changes, source) => + prop = changes[0][1] + newVal = changes[0][3] + parsedDate = newVal.split(/([ ,./-])\w/g) + dateDef = _.filter @tableDef.values, (def) -> + def.modelDefaults.type == 'dateValue' and def.modelDefaults.kind == prop + if dateDef.length == 1 and parsedDate.length < 5 + currentYear = new Date().getFullYear() + newVal = currentYear+"-"+newVal + changes[0][3] = newVal + + handleBeforeValidate: (value, row, prop, sources) => + parsedDate = value.split(/([ ,./-])\w/g) + dateDef = _.filter @tableDef.values, (def) -> + def.modelDefaults.type == 'dateValue' and def.modelDefaults.kind == prop + if dateDef.length == 1 and parsedDate.length < 5 + currentYear = new Date().getFullYear() + value = currentYear+"-"+value + handleCellChanged: (changes, source) => if changes? for change in changes From fa934d4bf3de1b24f05c98c6d3b888525f8a0075 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Mon, 28 Aug 2017 20:51:34 -0700 Subject: [PATCH 147/576] edit locking ExmapleThing feature complete --- .../src/client/AbstractFormController.coffee | 21 +++++++ .../AbstractFormControllerRoutes.coffee | 57 +++++++++++++++++++ .../ServerAPI/src/client/ExampleThing.coffee | 4 ++ 3 files changed, 82 insertions(+) create mode 100644 modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index c57bf4fc8..043d7f67f 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -6,6 +6,15 @@ class window.AbstractFormController extends Backbone.View formFieldDefinitions: [] + +# Setup edit lock check for the user session, form and entity identifier +# disable feature if set to null +# Override this in initilize() give model key for entity ID like 'codeName' +# Form subclass must send request to lock when it has the id in hand +# @socket.emit 'editLockEntity', @errorOwnerName, @model.get(@lockEditingForSessionKey) +# This is safe to call repeatedly + lockEditingForSessionKey: null + show: -> $(@el).show() @@ -28,6 +37,9 @@ class window.AbstractFormController extends Backbone.View setBindings: -> @model.on 'invalid', @validationError @model.on 'change', @handleModelChange + if @lockEditingForSessionKey? + @socket = io '/formController:connected' + @socket.on 'editLockRequestResult', @handleEditLockRequestResult validationError: => errors = @model.validationError @@ -54,6 +66,8 @@ class window.AbstractFormController extends Backbone.View @trigger 'valid' else @trigger 'invalid' + if @lockEditingForSessionKey? + @socket.emit 'updateEditLock', @errorOwnerName, @model.get(@lockEditingForSessionKey) disableAllInputs: -> @$('input').not('.dontdisable').attr 'disabled', 'disabled' @@ -80,6 +94,13 @@ class window.AbstractFormController extends Backbone.View @$(".bv_group_tags div.bootstrap-tagsinput").css "background-color", "#ffffff" @$(".bv_group_tags input").css "background-color", "transparent" + handleEditLockRequestResult: (result) => + if !result.okToEdit + updateDate = new Date result.lastActivityDate + alert "This entity is being edited by #{result.currentEditor}. This was last edited #{updateDate}. After they close the form, reload to edit" + @disableAllInputs() + + class window.AbstractThingFormController extends AbstractFormController diff --git a/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee b/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee new file mode 100644 index 000000000..833c992d7 --- /dev/null +++ b/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee @@ -0,0 +1,57 @@ +_ = require 'underscore' + +exports.setupChannels = (io, sessionStore, loginRoutes) -> + nsp = io.of('/formController:connected') + connectedUsers = {} + global.editLockedEntities = {} + nsp.on('connection', (socket) => + + socket.on('disconnect', => + console.log "got disconnect" + sessionLocks = _.where global.editLockedEntities, socketID: socket.id + for lockKey, lock of global.editLockedEntities + if lock.socketID==socket.id + console.log "clearing lock on #{lock}" + delete global.editLockedEntities[lockKey] + ) + + socket.on('editLockEntity', (entityType, codeName) => + console.log "got editLockEntity #{entityType}, #{codeName}" + + parsedCookie = JSON.parse(sessionStore.sessions[socket.request.sessionID]) + lockKey = entityType+"_"+codeName + console.log "trying to lock #{lockKey} for session #{socket.id}" + + lockedEntity = global.editLockedEntities[lockKey] + if lockedEntity? and lockedEntity.socketID!=socket.id + result = + okToEdit: false + currentEditor: lockedEntity.currentEditor + lastActivityDate: lockedEntity.lastActivityDate + lockCreatedDate: lockedEntity.lockCreatedDate + else + now = new Date().getTime() + global.editLockedEntities[lockKey] = + currentEditor: parsedCookie.passport.user.username + lastActivityDate: now + lockCreatedDate: now + socketID: socket.id + result = + okToEdit: true + currentEditor: parsedCookie.passport.user.username + lastActivityDate: now + lockCreatedDate: now + + socket.emit('editLockRequestResult', result) + ) + socket.on('updateEditLock', (entityType, codeName) => + console.log "got updateEditLock #{entityType}, #{codeName}" + lockKey = entityType+"_"+codeName + lockedEntity = global.editLockedEntities[lockKey] + if lockedEntity? and lockedEntity.socketID==socket.id + now = new Date().getTime() + lockedEntity.lastActivityDate = now + ) + ) + + diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index 662d074dd..267e00e00 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -234,6 +234,8 @@ class window.ExampleThingController extends AbstractThingFormController "click .bv_saveThing": "handleUpdateThing" initialize: => + @lockEditingForSessionKey = 'codeName' + @hasRendered = false if window.AppLaunchParams.moduleLaunchParams? if window.AppLaunchParams.moduleLaunchParams.moduleName == @moduleLaunchName @@ -263,6 +265,8 @@ class window.ExampleThingController extends AbstractThingFormController @ renderModelContent: -> + @socket.emit 'editLockEntity', @errorOwnerName, @model.get(@lockEditingForSessionKey) + codeName = @model.get('codeName') @$('.bv_thingCode').val(codeName) @$('.bv_thingCode').html(codeName) From 993e9ebf7260c746106dd307c986caa5ca33fdf4 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 29 Aug 2017 10:38:54 -0700 Subject: [PATCH 148/576] Removed unnecessary code containing underscore usage that was missing an import. --- modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee | 3 --- 1 file changed, 3 deletions(-) diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index b00d30f8a..0fbf56733 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -645,9 +645,6 @@ exports.updateParent = (req, resp) -> exports.updateLotMetadata = (req, resp) -> - grantedRoles = _.map req.user.roles, (role) -> - role.roleEntry.roleName - console.log grantedRoles request = require 'request' config = require '../conf/compiled/conf.js' console.log 'in update lot metaData' From e770b8bb665ff3e6df41a8a2c142bc9965dd057f Mon Sep 17 00:00:00 2001 From: John McNeil Date: Tue, 29 Aug 2017 14:00:35 -0700 Subject: [PATCH 149/576] Fixes #226 Show Menu Item as disabled text when mainControllerClassName set to null --- .../src/client/ModuleLauncher.coffee | 56 +++++++++++-------- 1 file changed, 32 insertions(+), 24 deletions(-) diff --git a/modules/ModuleMenus/src/client/ModuleLauncher.coffee b/modules/ModuleMenus/src/client/ModuleLauncher.coffee index 1afc0c3d6..ebfcbdf54 100644 --- a/modules/ModuleMenus/src/client/ModuleLauncher.coffee +++ b/modules/ModuleMenus/src/client/ModuleLauncher.coffee @@ -3,7 +3,7 @@ class window.ModuleLauncher extends Backbone.Model defaults: isHeader: false menuName: "Menu Name Replace Me" - mainControllerClassName: "controllerClassNameReplaceMe" + mainControllerClassName: null isLoaded: false isActive: false isDirty: false @@ -43,31 +43,39 @@ class window.ModuleLauncherMenuController extends Backbone.View render: => $(@el).empty() $(@el).html(@template(@model.toJSON())) - @$('.bv_menuName').addClass 'bv_launch_'+@model.get('autoLaunchName') - if @model.get('isActive') then $(@el).addClass "active" - else $(@el).removeClass "active" - - @$('.bv_isLoaded').hide() - if @model.get('isDirty') - @$('.bv_isDirty').show() - window.conf.leaveACASMessage = "WARNING: There are unsaved changes." + if @model.get('mainControllerClassName')? + @$('.bv_menuName').addClass 'bv_launch_'+@model.get('autoLaunchName') + if @model.get('isActive') then $(@el).addClass "active" + else $(@el).removeClass "active" + + @$('.bv_isLoaded').hide() + if @model.get('isDirty') + @$('.bv_isDirty').show() + window.conf.leaveACASMessage = "WARNING: There are unsaved changes." + else + @$('.bv_isDirty').hide() + window.conf.leaveACASMessage = "There are no unsaved changes." + + if @model.has 'requireUserRoles' + userRoles = [] + _.each @model.get('requireUserRoles'), (role) => + if role.indexOf(',') + roles = role.split(',') + _.each roles, (r) => + userRoles.push $.trim(r) + else + userRoles.push r + if !UtilityFunctions::testUserHasRole window.AppLaunchParams.loginUser, userRoles + $(@el).attr 'title', "User is not authorized to use this feature" + @$('.bv_menuName').hide() + # @$('.bv_menuName_disabled').show() + else + @$('.bv_menuName').hide() + @$('.bv_menuName_disabled').show() + @$('.bv_isLoaded').hide() @$('.bv_isDirty').hide() - window.conf.leaveACASMessage = "There are no unsaved changes." - - if @model.has 'requireUserRoles' - userRoles = [] - _.each @model.get('requireUserRoles'), (role) => - if role.indexOf(',') - roles = role.split(',') - _.each roles, (r) => - userRoles.push $.trim(r) - else - userRoles.push r - if !UtilityFunctions::testUserHasRole window.AppLaunchParams.loginUser, userRoles - $(@el).attr 'title', "User is not authorized to use this feature" - @$('.bv_menuName').hide() - # @$('.bv_menuName_disabled').show() + @ From 0fe51449c5c3985fa1ba1b6fdeb53724d5bfb98a Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 29 Aug 2017 16:03:54 -0700 Subject: [PATCH 150/576] Added code to PickList to set mouseover/title attribute to the selected name. Applies to all picklists in CReg. --- modules/CmpdReg/src/client/src/PickList.js | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/CmpdReg/src/client/src/PickList.js b/modules/CmpdReg/src/client/src/PickList.js index 380e03297..90066a8d6 100755 --- a/modules/CmpdReg/src/client/src/PickList.js +++ b/modules/CmpdReg/src/client/src/PickList.js @@ -120,7 +120,8 @@ $(function() { $(this.el).hide(); $(this.el).show(); this.rendered = true; - + var selectedText = this.getSelectedModel().get('name'); + $(this.el).prop('title', selectedText); return this; }, From c2790b15160aea391f5f68dfc98f6b75ca32ec07 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Tue, 29 Aug 2017 20:41:36 -0700 Subject: [PATCH 151/576] Fixes #227 AbstractFormController entity edit locking --- .../src/client/AbstractFormController.coffee | 20 +++++++++---- .../AbstractFormControllerRoutes.coffee | 30 ++++++++++++++++--- .../src/client/ModuleLauncher.coffee | 12 ++++++++ .../src/client/ModuleLauncherView.html | 1 + .../ServerAPI/src/client/ExampleThing.coffee | 10 ++++++- 5 files changed, 63 insertions(+), 10 deletions(-) diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 043d7f67f..800554108 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -10,6 +10,8 @@ class window.AbstractFormController extends Backbone.View # Setup edit lock check for the user session, form and entity identifier # disable feature if set to null # Override this in initilize() give model key for entity ID like 'codeName' +# Form must open socket, probably during initialize +# @openFormControllerSocket() # Form subclass must send request to lock when it has the id in hand # @socket.emit 'editLockEntity', @errorOwnerName, @model.get(@lockEditingForSessionKey) # This is safe to call repeatedly @@ -37,9 +39,6 @@ class window.AbstractFormController extends Backbone.View setBindings: -> @model.on 'invalid', @validationError @model.on 'change', @handleModelChange - if @lockEditingForSessionKey? - @socket = io '/formController:connected' - @socket.on 'editLockRequestResult', @handleEditLockRequestResult validationError: => errors = @model.validationError @@ -94,13 +93,24 @@ class window.AbstractFormController extends Backbone.View @$(".bv_group_tags div.bootstrap-tagsinput").css "background-color", "#ffffff" @$(".bv_group_tags input").css "background-color", "transparent" + openFormControllerSocket: -> + if @lockEditingForSessionKey? + @socket = io '/formController:connected' + @socket.on 'editLockRequestResult', @handleEditLockRequestResult + @socket.on 'editLockAvailable', @handleEditLockAvailable + handleEditLockRequestResult: (result) => if !result.okToEdit updateDate = new Date result.lastActivityDate - alert "This entity is being edited by #{result.currentEditor}. This was last edited #{updateDate}. After they close the form, reload to edit" + alert "This entity is being edited by #{result.currentEditor}. This was last edited #{updateDate}. After they close the form, reload to edit. The form will be displayed read-only." @disableAllInputs() + @trigger 'editLocked' + else + @trigger 'editUnLocked' - + handleEditLockAvailable: => + @trigger 'editUnLocked' + #you should extend this class window.AbstractThingFormController extends AbstractFormController diff --git a/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee b/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee index 833c992d7..fb321e5e8 100644 --- a/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee +++ b/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee @@ -1,10 +1,15 @@ _ = require 'underscore' +exports.setupRoutes = (app, loginRoutes) -> + app.get '/api/formController/clearAllLocks', exports.clearAllLocks + +global.editLockedEntities = {} + exports.setupChannels = (io, sessionStore, loginRoutes) -> nsp = io.of('/formController:connected') connectedUsers = {} - global.editLockedEntities = {} nsp.on('connection', (socket) => + console.log "Opened new connection #{socket.id}" socket.on('disconnect', => console.log "got disconnect" @@ -12,11 +17,13 @@ exports.setupChannels = (io, sessionStore, loginRoutes) -> for lockKey, lock of global.editLockedEntities if lock.socketID==socket.id console.log "clearing lock on #{lock}" + for quid in lock.rejectedRequestSocketIDs + socket.broadcast.to(quid).emit('editLockAvailable') delete global.editLockedEntities[lockKey] ) socket.on('editLockEntity', (entityType, codeName) => - console.log "got editLockEntity #{entityType}, #{codeName}" + console.log "got editLockEntity request #{entityType}, #{codeName}" parsedCookie = JSON.parse(sessionStore.sessions[socket.request.sessionID]) lockKey = entityType+"_"+codeName @@ -24,11 +31,18 @@ exports.setupChannels = (io, sessionStore, loginRoutes) -> lockedEntity = global.editLockedEntities[lockKey] if lockedEntity? and lockedEntity.socketID!=socket.id + lockedEntity.rejectedRequestSocketIDs.push socket.id result = okToEdit: false currentEditor: lockedEntity.currentEditor lastActivityDate: lockedEntity.lastActivityDate lockCreatedDate: lockedEntity.lockCreatedDate + else if lockedEntity? and lockedEntity.socketID==socket.id + result = + okToEdit: true + currentEditor: lockedEntity.currentEditor + lastActivityDate: lockedEntity.lastActivityDate + lockCreatedDate: lockedEntity.lockCreatedDate else now = new Date().getTime() global.editLockedEntities[lockKey] = @@ -36,6 +50,9 @@ exports.setupChannels = (io, sessionStore, loginRoutes) -> lastActivityDate: now lockCreatedDate: now socketID: socket.id + entityType: entityType + codeName: codeName + rejectedRequestSocketIDs: [] result = okToEdit: true currentEditor: parsedCookie.passport.user.username @@ -45,7 +62,7 @@ exports.setupChannels = (io, sessionStore, loginRoutes) -> socket.emit('editLockRequestResult', result) ) socket.on('updateEditLock', (entityType, codeName) => - console.log "got updateEditLock #{entityType}, #{codeName}" +# console.log "got updateEditLock #{entityType}, #{codeName}" lockKey = entityType+"_"+codeName lockedEntity = global.editLockedEntities[lockKey] if lockedEntity? and lockedEntity.socketID==socket.id @@ -54,4 +71,9 @@ exports.setupChannels = (io, sessionStore, loginRoutes) -> ) ) - +exports.clearAllLocks = (req, resp) -> + console.log "clearing edit locks. Users will have to reload to get access" + console.dir global.editLockedEntities, depth: 3 + global.editLockedEntities = {} + console.dir global.editLockedEntities, depth: 3 + resp.end() diff --git a/modules/ModuleMenus/src/client/ModuleLauncher.coffee b/modules/ModuleMenus/src/client/ModuleLauncher.coffee index 1afc0c3d6..077e964ab 100644 --- a/modules/ModuleMenus/src/client/ModuleLauncher.coffee +++ b/modules/ModuleMenus/src/client/ModuleLauncher.coffee @@ -7,6 +7,7 @@ class window.ModuleLauncher extends Backbone.Model isLoaded: false isActive: false isDirty: false + isLocked: false autoLaunchName: null requestActivation: -> @@ -55,6 +56,11 @@ class window.ModuleLauncherMenuController extends Backbone.View @$('.bv_isDirty').hide() window.conf.leaveACASMessage = "There are no unsaved changes." + if @model.get('isLocked') + @$('.bv_isLocked').show() + else + @$('.bv_isLocked').hide() + if @model.has 'requireUserRoles' userRoles = [] _.each @model.get('requireUserRoles'), (role) => @@ -165,6 +171,12 @@ class window.ModuleLauncherController extends Backbone.View @model.set isDirty: true @moduleController.bind 'amClean', => @model.set isDirty: false + @moduleController.bind 'editLocked', => + console.log "got editLocked trigger" + @model.set isLocked: true + @moduleController.bind 'editUnLocked', => + console.log "got editUnLocked trigger" + @model.set isLocked: false @moduleController.render() @model.set isLoaded: true diff --git a/modules/ModuleMenus/src/client/ModuleLauncherView.html b/modules/ModuleMenus/src/client/ModuleLauncherView.html index de72e7290..bada18b8e 100644 --- a/modules/ModuleMenus/src/client/ModuleLauncherView.html +++ b/modules/ModuleMenus/src/client/ModuleLauncherView.html @@ -4,6 +4,7 @@ <%= menuName %> + diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index 267e00e00..c7e2289cf 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -235,6 +235,7 @@ class window.ExampleThingController extends AbstractThingFormController initialize: => @lockEditingForSessionKey = 'codeName' + @openFormControllerSocket() @hasRendered = false if window.AppLaunchParams.moduleLaunchParams? @@ -272,6 +273,8 @@ class window.ExampleThingController extends AbstractThingFormController @$('.bv_thingCode').html(codeName) if @readOnly is true @displayInReadOnlyMode() + else + @enableAllInputs() @$('.bv_saveThing').attr('disabled','disabled') if @model.isNew() @$('.bv_saveThing').html("Save") @@ -329,8 +332,13 @@ class window.ExampleThingController extends AbstractThingFormController @disableAllInputs() -#TODO add thing interaction to project with field + handleEditLockAvailable: => + super() + alert("Document is avaialble to edit. Push OK to attempt to edit (you may not the first requestor)") + @model.fetch() + +#TODO add thing interaction to project with field ExampleTableAuditConf = formFieldDefinitions: From d4dd3ed01dad9aef8a488e6e2ae13f5ee76662e2 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Wed, 30 Aug 2017 05:58:53 -0700 Subject: [PATCH 152/576] added clear locks login check --- .../src/server/routes/AbstractFormControllerRoutes.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee b/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee index fb321e5e8..2c4b5f729 100644 --- a/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee +++ b/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee @@ -1,7 +1,7 @@ _ = require 'underscore' exports.setupRoutes = (app, loginRoutes) -> - app.get '/api/formController/clearAllLocks', exports.clearAllLocks + app.get '/api/formController/clearAllLocks', loginRoutes.ensureAuthenticated, exports.clearAllLocks global.editLockedEntities = {} From 4f71871b93a9db5a899c6cf25854f56ee256cc9a Mon Sep 17 00:00:00 2001 From: John McNeil Date: Wed, 30 Aug 2017 08:05:56 -0700 Subject: [PATCH 153/576] fix module menus merge issue --- .../src/client/ModuleLauncher.coffee | 30 +++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/modules/ModuleMenus/src/client/ModuleLauncher.coffee b/modules/ModuleMenus/src/client/ModuleLauncher.coffee index 7331b4155..a21b8bfb5 100644 --- a/modules/ModuleMenus/src/client/ModuleLauncher.coffee +++ b/modules/ModuleMenus/src/client/ModuleLauncher.coffee @@ -62,21 +62,6 @@ class window.ModuleLauncherMenuController extends Backbone.View @$('.bv_isLocked').show() else @$('.bv_isLocked').hide() - - if @model.has 'requireUserRoles' - userRoles = [] - _.each @model.get('requireUserRoles'), (role) => - if role.indexOf(',') - roles = role.split(',') - _.each roles, (r) => - userRoles.push $.trim(r) - else - userRoles.push r - if !UtilityFunctions::testUserHasRole window.AppLaunchParams.loginUser, userRoles - $(@el).attr 'title', "User is not authorized to use this feature" - @$('.bv_menuName').hide() - # @$('.bv_menuName_disabled').show() - else @$('.bv_menuName').hide() @$('.bv_menuName_disabled').show() @@ -84,6 +69,21 @@ class window.ModuleLauncherMenuController extends Backbone.View @$('.bv_isDirty').hide() @$('.bv_isLocked').hide() + if @model.has 'requireUserRoles' + userRoles = [] + _.each @model.get('requireUserRoles'), (role) => + if role.indexOf(',') + roles = role.split(',') + _.each roles, (r) => + userRoles.push $.trim(r) + else + userRoles.push r + if !UtilityFunctions::testUserHasRole window.AppLaunchParams.loginUser, userRoles + $(@el).attr 'title', "User is not authorized to use this feature" + @$('.bv_menuName').hide() + @$('.bv_menuName_disabled').hide() + + @ handleSelect: => From 68def82a1fc86335ad20bced3ac5766292033951 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 30 Aug 2017 08:14:54 -0700 Subject: [PATCH 154/576] removing extra console log login --- .../ServerAPI/src/server/routes/InventoryServiceRoutes.coffee | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index d08690b25..644e9a0f8 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -1367,7 +1367,6 @@ exports.moveToLocationInternal = (input, callCustom, updateLocationHistory, call #add the call to updateContainerHistoryLogs here... console.debug "response statusCode: #{response.statusCode}" if !error - console.log 'container down here...did it pull through??' console.log input[0].containerCodeName if updateLocationHistory exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> From 21f580871f9d022369ebce7225e89546e95bff91 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Wed, 30 Aug 2017 14:26:55 -0700 Subject: [PATCH 155/576] Fixing edit lock alert language --- modules/Components/src/client/AbstractFormController.coffee | 2 +- modules/ServerAPI/src/client/ExampleThing.coffee | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 800554108..008cc5bad 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -102,7 +102,7 @@ class window.AbstractFormController extends Backbone.View handleEditLockRequestResult: (result) => if !result.okToEdit updateDate = new Date result.lastActivityDate - alert "This entity is being edited by #{result.currentEditor}. This was last edited #{updateDate}. After they close the form, reload to edit. The form will be displayed read-only." + alert "This is being edited by #{result.currentEditor}. It was last edited at #{updateDate}. If you leave this tab open, you will be notified when it becomes available. For now, the form will be displayed as read-only." @disableAllInputs() @trigger 'editLocked' else diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index c7e2289cf..f9e9baba6 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -334,7 +334,7 @@ class window.ExampleThingController extends AbstractThingFormController handleEditLockAvailable: => super() - alert("Document is avaialble to edit. Push OK to attempt to edit (you may not the first requestor)") + alert("Document is available to edit. Click OK to attempt to edit (you may be not the first requestor)") @model.fetch() From d96ad004b342e8cc8d4f30413c310355c0c0dc13 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Wed, 30 Aug 2017 14:55:23 -0700 Subject: [PATCH 156/576] menu dimming was breaking the externalLink feature --- modules/ModuleMenus/src/client/ModuleLauncher.coffee | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/ModuleMenus/src/client/ModuleLauncher.coffee b/modules/ModuleMenus/src/client/ModuleLauncher.coffee index a21b8bfb5..9406510ba 100644 --- a/modules/ModuleMenus/src/client/ModuleLauncher.coffee +++ b/modules/ModuleMenus/src/client/ModuleLauncher.coffee @@ -10,6 +10,7 @@ class window.ModuleLauncher extends Backbone.Model isLocked: false autoLaunchName: null collapsible: false + externalLink: null requestActivation: -> if @get('externalLink')? @@ -46,7 +47,7 @@ class window.ModuleLauncherMenuController extends Backbone.View render: => $(@el).empty() $(@el).html(@template(@model.toJSON())) - if @model.get('mainControllerClassName')? + if @model.get('mainControllerClassName')? or @model.get('externalLink')? @$('.bv_menuName').addClass 'bv_launch_'+@model.get('autoLaunchName') if @model.get('isActive') then $(@el).addClass "active" else $(@el).removeClass "active" From bb876d1e9e0ee22efb9c38441bc4da5583b47751 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 30 Aug 2017 15:02:55 -0700 Subject: [PATCH 157/576] set node_modules path for gulp when running coffeeify --- gulpfile.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gulpfile.coffee b/gulpfile.coffee index 85d798cd8..008eb654e 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -449,7 +449,7 @@ createTask = (options, type) -> .pipe(plumber({errorHandler: onError})) .pipe(gulpif(shouldFlatten,flatten())) .pipe(gulpif(modifyFunction?, modify(fileModifier: modifyFunction))) - .pipe(gulpif(shouldCoffeify, coffeeify({options:{paths:[build]}}))) + .pipe(gulpif(shouldCoffeify, coffeeify({options:{paths:[build+ '/node_modules']}}))) .pipe(gulpif(shouldCoffee,coffee(bare: true))) .pipe(gulpif(renameFunction?,rename(renameFunction))) .pipe gulp.dest(dest) From 15df43c0d39583fd9db88a668208e8fad8332158 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Wed, 30 Aug 2017 15:10:52 -0700 Subject: [PATCH 158/576] RC/1.12.0: fixing bug in set default year in statetable to parse value only if it's a dateValue. Fixes issue #223 --- .../src/client/ACASFormStateTable.coffee | 20 ++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 03b5acf92..00410b954 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -251,21 +251,23 @@ class window.ACASFormStateTableController extends Backbone.View handleBeforeChange: (changes, source) => prop = changes[0][1] newVal = changes[0][3] - parsedDate = newVal.split(/([ ,./-])\w/g) dateDef = _.filter @tableDef.values, (def) -> def.modelDefaults.type == 'dateValue' and def.modelDefaults.kind == prop - if dateDef.length == 1 and parsedDate.length < 5 - currentYear = new Date().getFullYear() - newVal = currentYear+"-"+newVal - changes[0][3] = newVal + if dateDef.length == 1 + parsedDate = newVal.split(/([ ,./-])\w/g) + if parsedDate.length < 5 + currentYear = new Date().getFullYear() + newVal = currentYear+"-"+newVal + changes[0][3] = newVal handleBeforeValidate: (value, row, prop, sources) => - parsedDate = value.split(/([ ,./-])\w/g) dateDef = _.filter @tableDef.values, (def) -> def.modelDefaults.type == 'dateValue' and def.modelDefaults.kind == prop - if dateDef.length == 1 and parsedDate.length < 5 - currentYear = new Date().getFullYear() - value = currentYear+"-"+value + if dateDef.length == 1 + parsedDate = value.split(/([ ,./-])\w/g) + if parsedDate.length < 5 + currentYear = new Date().getFullYear() + value = currentYear+"-"+value handleCellChanged: (changes, source) => if changes? From b06c064f5fd7ce6aea25ac728b411cc9d165fde3 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 30 Aug 2017 19:23:50 -0400 Subject: [PATCH 159/576] Added checks for whether editor has loaded, and if it has not, delay setting content and enable/disable until after editor has loaded. Fixes #231 --- .../src/client/ACASFormFields.coffee | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index febb0c582..5480e35b3 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -415,7 +415,10 @@ class window.ACASFormLSHTMLClobValueFieldController extends ACASFormAbstractFiel ignored: true renderModelContent: => - @editor.setContent @getModel().get('value') + if @editor? + @editor.setContent @getModel().get('value') + else + @contentToLoad = @getModel().get('value') super() setupTinyMCE: -> @@ -429,14 +432,24 @@ class window.ACASFormLSHTMLClobValueFieldController extends ACASFormAbstractFiel setup: (editor) => editor.on 'init', (e) => @editor = editor + if @contentToLoad? + @editor.setContent @contentToLoad + if @disableEditor? + @editor.getBody().setAttribute('contenteditable', @disableEditor) editor.on 'change', (e) => @textChanged editor.getContent() disableInput: -> - @editor.getBody().setAttribute('contenteditable', false) + if @editor? + @editor.getBody().setAttribute('contenteditable', false) + else + @disableEditor = true enableInput: -> - @editor.getBody().setAttribute('contenteditable', true) + if @editor? + @editor.getBody().setAttribute('contenteditable', true) + else + @disableEditor = false class window.ACASFormLSStringValueFieldController extends ACASFormAbstractFieldController ### From b93d4dba47de550ec52cc4b1f42d0025f73348f7 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 30 Aug 2017 16:44:49 -0700 Subject: [PATCH 160/576] set node_modules path for gulp when running coffeeify (#230) --- gulpfile.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gulpfile.coffee b/gulpfile.coffee index 85d798cd8..008eb654e 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -449,7 +449,7 @@ createTask = (options, type) -> .pipe(plumber({errorHandler: onError})) .pipe(gulpif(shouldFlatten,flatten())) .pipe(gulpif(modifyFunction?, modify(fileModifier: modifyFunction))) - .pipe(gulpif(shouldCoffeify, coffeeify({options:{paths:[build]}}))) + .pipe(gulpif(shouldCoffeify, coffeeify({options:{paths:[build+ '/node_modules']}}))) .pipe(gulpif(shouldCoffee,coffee(bare: true))) .pipe(gulpif(renameFunction?,rename(renameFunction))) .pipe gulp.dest(dest) From 0e52dcb5be564056cb83de6afaa59c0e515b78be Mon Sep 17 00:00:00 2001 From: John McNeil Date: Thu, 31 Aug 2017 11:32:01 -0700 Subject: [PATCH 161/576] Fixes #233 ExampleThing modified to prevent locking empty/new form. Also snuck in a fix to state table date validation --- modules/Components/src/client/ACASFormStateTable.coffee | 4 ++-- modules/ServerAPI/src/client/ExampleThing.coffee | 5 +++-- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index ce7bbfea0..7d0ded6ed 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -256,7 +256,7 @@ class window.ACASFormStateTableController extends Backbone.View newVal = changes[0][3] dateDef = _.filter @tableDef.values, (def) -> def.modelDefaults.type == 'dateValue' and def.modelDefaults.kind == prop - if dateDef.length == 1 + if dateDef.length == 1 and value? parsedDate = newVal.split(/([ ,./-])\w/g) if parsedDate.length < 5 currentYear = new Date().getFullYear() @@ -266,7 +266,7 @@ class window.ACASFormStateTableController extends Backbone.View handleBeforeValidate: (value, row, prop, sources) => dateDef = _.filter @tableDef.values, (def) -> def.modelDefaults.type == 'dateValue' and def.modelDefaults.kind == prop - if dateDef.length == 1 + if dateDef.length == 1 and value? parsedDate = value.split(/([ ,./-])\w/g) if parsedDate.length < 5 currentYear = new Date().getFullYear() diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index f9e9baba6..1bc326f2e 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -234,6 +234,7 @@ class window.ExampleThingController extends AbstractThingFormController "click .bv_saveThing": "handleUpdateThing" initialize: => + @errorOwnerName = 'ExampleThingController' @lockEditingForSessionKey = 'codeName' @openFormControllerSocket() @@ -248,7 +249,6 @@ class window.ExampleThingController extends AbstractThingFormController @model = new ExampleThingParent() @modelSaveCallback() - @errorOwnerName = 'ExampleThingController' @setBindings() if @options.readOnly? @readOnly = @options.readOnly @@ -266,7 +266,8 @@ class window.ExampleThingController extends AbstractThingFormController @ renderModelContent: -> - @socket.emit 'editLockEntity', @errorOwnerName, @model.get(@lockEditingForSessionKey) + if !@model.isNew() + @socket.emit 'editLockEntity', @errorOwnerName, @model.get(@lockEditingForSessionKey) codeName = @model.get('codeName') @$('.bv_thingCode').val(codeName) From c270ed4c471e3fdbc00e893f1ec33c5c3ef87635 Mon Sep 17 00:00:00 2001 From: jmcneil86043 Date: Thu, 31 Aug 2017 11:39:28 -0700 Subject: [PATCH 162/576] Fixes #233 ExampleThing modified to prevent locking empty/new form. Also snuck in a fix to state table date validation (#234) --- modules/Components/src/client/ACASFormStateTable.coffee | 4 ++-- modules/ServerAPI/src/client/ExampleThing.coffee | 5 +++-- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index ce7bbfea0..7d0ded6ed 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -256,7 +256,7 @@ class window.ACASFormStateTableController extends Backbone.View newVal = changes[0][3] dateDef = _.filter @tableDef.values, (def) -> def.modelDefaults.type == 'dateValue' and def.modelDefaults.kind == prop - if dateDef.length == 1 + if dateDef.length == 1 and value? parsedDate = newVal.split(/([ ,./-])\w/g) if parsedDate.length < 5 currentYear = new Date().getFullYear() @@ -266,7 +266,7 @@ class window.ACASFormStateTableController extends Backbone.View handleBeforeValidate: (value, row, prop, sources) => dateDef = _.filter @tableDef.values, (def) -> def.modelDefaults.type == 'dateValue' and def.modelDefaults.kind == prop - if dateDef.length == 1 + if dateDef.length == 1 and value? parsedDate = value.split(/([ ,./-])\w/g) if parsedDate.length < 5 currentYear = new Date().getFullYear() diff --git a/modules/ServerAPI/src/client/ExampleThing.coffee b/modules/ServerAPI/src/client/ExampleThing.coffee index f9e9baba6..1bc326f2e 100644 --- a/modules/ServerAPI/src/client/ExampleThing.coffee +++ b/modules/ServerAPI/src/client/ExampleThing.coffee @@ -234,6 +234,7 @@ class window.ExampleThingController extends AbstractThingFormController "click .bv_saveThing": "handleUpdateThing" initialize: => + @errorOwnerName = 'ExampleThingController' @lockEditingForSessionKey = 'codeName' @openFormControllerSocket() @@ -248,7 +249,6 @@ class window.ExampleThingController extends AbstractThingFormController @model = new ExampleThingParent() @modelSaveCallback() - @errorOwnerName = 'ExampleThingController' @setBindings() if @options.readOnly? @readOnly = @options.readOnly @@ -266,7 +266,8 @@ class window.ExampleThingController extends AbstractThingFormController @ renderModelContent: -> - @socket.emit 'editLockEntity', @errorOwnerName, @model.get(@lockEditingForSessionKey) + if !@model.isNew() + @socket.emit 'editLockEntity', @errorOwnerName, @model.get(@lockEditingForSessionKey) codeName = @model.get('codeName') @$('.bv_thingCode').val(codeName) From 0c2547932c5a96cd85e4b6bd84d3ea0a642ca0a8 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Fri, 1 Sep 2017 11:46:31 -0700 Subject: [PATCH 163/576] RC/1.12.0: - for ACASFormStateTable: added options to set readOnly, wordWrap, format for numeric cell types, handleAfterValidate function - Alphabetized all returns of codetable values unless there is a displayOrder already or no name attribute - Protocol/Experiment ConfJSONs: set displayOrder for status and review status ddict values --- .../Components/src/client/ACASFormStateTable.coffee | 10 ++++++++++ .../src/server/routes/CodeTableServiceRoutes.coffee | 7 +++++++ modules/ServerAPI/conf/ExperimentConfJSON.coffee | 10 ++++++++++ modules/ServerAPI/conf/ProtocolConfJSON.coffee | 10 ++++++++++ 4 files changed, 37 insertions(+) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 00410b954..e44418cd1 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -126,8 +126,14 @@ class window.ACASFormStateTableController extends Backbone.View width: if val.fieldSettings.width? then val.fieldSettings.width else 75 colOpts = data: val.modelDefaults.kind + colOpts.readOnly = if val.fieldSettings.readOnly? then val.fieldSettings.readOnly else false + colOpts.wordWrap = true if val.modelDefaults.type == 'numericValue' colOpts.type = 'numeric' + if val.fieldSettings.fieldFormat? + colOpts.format = val.fieldSettings.fieldFormat + else + colOpts.format = '0.[00]' else if val.modelDefaults.type == 'dateValue' colOpts.type = 'date' colOpts.dateFormat = 'YYYY-MM-DD' @@ -156,11 +162,15 @@ class window.ACASFormStateTableController extends Backbone.View @unitKeyValueMap[val.fieldSettings.unitColumnKey] = val.modelDefaults.kind + if @tableDef.handleAfterValidate? + @handleAfterValidate = @tableDef.handleAfterValidate + setupHot: -> @hot = new Handsontable @$('.bv_tableWrapper')[0], beforeChange: @handleBeforeChange beforeValidate: @handleBeforeValidate afterChange: @handleCellChanged + afterValidate: @handleAfterValidate afterCreateRow: @handleRowCreated minSpareRows: 1, allowInsertRow: true diff --git a/modules/Components/src/server/routes/CodeTableServiceRoutes.coffee b/modules/Components/src/server/routes/CodeTableServiceRoutes.coffee index c7823bc20..422d307f0 100644 --- a/modules/Components/src/server/routes/CodeTableServiceRoutes.coffee +++ b/modules/Components/src/server/routes/CodeTableServiceRoutes.coffee @@ -51,6 +51,13 @@ exports.getCodeTableValues = (req, resp) -> json: true , (error, response, json) => if !error && response.statusCode == 200 + if json.length > 0 and !json[0].displayOrder? and json[0].name? + json = json.sort (a, b) -> + if a.name.toUpperCase() < b.name.toUpperCase() + return -1 + if a.name.toUpperCase() > b.name.toUpperCase() + return 1 + return 0 resp.json json else console.log 'got ajax error trying to get code table entries' diff --git a/modules/ServerAPI/conf/ExperimentConfJSON.coffee b/modules/ServerAPI/conf/ExperimentConfJSON.coffee index df983eb91..64e7e0af3 100644 --- a/modules/ServerAPI/conf/ExperimentConfJSON.coffee +++ b/modules/ServerAPI/conf/ExperimentConfJSON.coffee @@ -265,6 +265,7 @@ codeOrigin: "ACAS DDICT" code: "created" name: "Created" + displayOrder: 10 ignored: false , codeType: "experiment" @@ -272,6 +273,7 @@ codeOrigin: "ACAS DDICT" code: "in process" name: "In Process" + displayOrder: 20 ignored: false , codeType: "experiment" @@ -279,6 +281,7 @@ codeOrigin: "ACAS DDICT" code: "complete" name: "Complete" + displayOrder: 30 ignored: false , codeType: "experiment" @@ -286,6 +289,7 @@ codeOrigin: "ACAS DDICT" code: "approved" name: "Approved" + displayOrder: 40 ignored: false , codeType: "experiment" @@ -293,6 +297,7 @@ codeOrigin: "ACAS DDICT" code: "rejected" name: "Rejected" + displayOrder: 50 ignored: false , codeType: "experiment" @@ -300,6 +305,7 @@ codeOrigin: "ACAS DDICT" code: "deleted" name: "Deleted" + displayOrder: 60 ignored: false , codeType: "experiment" @@ -307,6 +313,7 @@ codeOrigin: "ACAS DDICT" code: "in progress" name: "In Progress" + displayOrder: 10 ignored: false , codeType: "experiment" @@ -314,6 +321,7 @@ codeOrigin: "ACAS DDICT" code: "ready for review" name: "Ready for Review" + displayOrder: 20 ignored: false , codeType: "experiment" @@ -321,6 +329,7 @@ codeOrigin: "ACAS DDICT" code: "read and understood" name: "Read and Understood" + displayOrder: 30 ignored: false , codeType: "experiment" @@ -328,6 +337,7 @@ codeOrigin: "ACAS DDICT" code: "needs attention" name: "Needs Attention" + displayOrder: 40 ignored: false , codeType: "analysis" diff --git a/modules/ServerAPI/conf/ProtocolConfJSON.coffee b/modules/ServerAPI/conf/ProtocolConfJSON.coffee index a9e71b43c..3f65708ad 100644 --- a/modules/ServerAPI/conf/ProtocolConfJSON.coffee +++ b/modules/ServerAPI/conf/ProtocolConfJSON.coffee @@ -242,6 +242,7 @@ codeOrigin: "ACAS DDICT" code: "created" name: "Created" + displayOrder: 10 ignored: false , codeType: "protocol" @@ -249,6 +250,7 @@ codeOrigin: "ACAS DDICT" code: "in process" name: "In Process" + displayOrder: 20 ignored: false , codeType: "protocol" @@ -256,6 +258,7 @@ codeOrigin: "ACAS DDICT" code: "complete" name: "Complete" + displayOrder: 30 ignored: false , codeType: "protocol" @@ -263,6 +266,7 @@ codeOrigin: "ACAS DDICT" code: "approved" name: "Approved" + displayOrder: 40 ignored: false , codeType: "protocol" @@ -270,6 +274,7 @@ codeOrigin: "ACAS DDICT" code: "rejected" name: "Rejected" + displayOrder: 50 ignored: false , codeType: "protocol" @@ -277,6 +282,7 @@ codeOrigin: "ACAS DDICT" code: "deleted" name: "Deleted" + displayOrder: 60 ignored: false , codeType: "protocol" @@ -284,6 +290,7 @@ codeOrigin: "ACAS DDICT" code: "in progress" name: "In Progress" + displayOrder: 10 ignored: false , codeType: "protocol" @@ -291,6 +298,7 @@ codeOrigin: "ACAS DDICT" code: "ready for review" name: "Ready for Review" + displayOrder: 20 ignored: false , codeType: "protocol" @@ -298,6 +306,7 @@ codeOrigin: "ACAS DDICT" code: "read and understood" name: "Read and Understood" + displayOrder: 30 ignored: false , codeType: "protocol" @@ -305,6 +314,7 @@ codeOrigin: "ACAS DDICT" code: "needs attention" name: "Needs Attention" + displayOrder: 40 ignored: false , codeType: "assay" From 73f6c59da73a5ae4e23458125f1d69792191f4c1 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Fri, 1 Sep 2017 14:58:44 -0700 Subject: [PATCH 164/576] Fixes #235 File Form Field does not handle required styling correctly --- .../Components/src/client/ACASFormFields.coffee | 14 ++------------ 1 file changed, 2 insertions(+), 12 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 5480e35b3..2a226451c 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -558,18 +558,6 @@ class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldCon @ - handleInputChanged: => - @clearError() - @userInputEvent = true - value = UtilityFunctions::convertYMDDateToMs(UtilityFunctions::getTrimmedInput(@$('input'))) - if value == "" || isNaN(value) - @setEmptyValue() - else - @getModel().set - value: value - ignored: false - super() - setEmptyValue: -> @getModel().set value: null @@ -611,12 +599,14 @@ class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldCon @fileController.on('fileDeleted', @handleFileRemoved) #update model with filename handleFileUpload: (nameOnServer) => + @clearError() @getModel().set value: nameOnServer ignored: false handleFileRemoved: => @setEmptyValue() + @checkEmptyAndRequired() handleDeleteSavedFile: => @handleFileRemoved() From 5503be23f0a0f329f17c48cf78e63a66eed5e2bf Mon Sep 17 00:00:00 2001 From: jmcneil86043 Date: Fri, 1 Sep 2017 15:07:06 -0700 Subject: [PATCH 165/576] Fixes #235 File Form Field does not handle required styling correctly (#236) --- .../Components/src/client/ACASFormFields.coffee | 14 ++------------ 1 file changed, 2 insertions(+), 12 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 5480e35b3..2a226451c 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -558,18 +558,6 @@ class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldCon @ - handleInputChanged: => - @clearError() - @userInputEvent = true - value = UtilityFunctions::convertYMDDateToMs(UtilityFunctions::getTrimmedInput(@$('input'))) - if value == "" || isNaN(value) - @setEmptyValue() - else - @getModel().set - value: value - ignored: false - super() - setEmptyValue: -> @getModel().set value: null @@ -611,12 +599,14 @@ class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldCon @fileController.on('fileDeleted', @handleFileRemoved) #update model with filename handleFileUpload: (nameOnServer) => + @clearError() @getModel().set value: nameOnServer ignored: false handleFileRemoved: => @setEmptyValue() + @checkEmptyAndRequired() handleDeleteSavedFile: => @handleFileRemoved() From 52f41cfed2cff444e55d1bc4a07abe03370fb7f6 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Fri, 1 Sep 2017 16:14:25 -0700 Subject: [PATCH 166/576] Fixes #237 Add feature to interaction form fields to show corpName : name --- .../Components/src/client/ACASFormFields.coffee | 7 ++++++- .../src/client/AbstractFormController.coffee | 1 + modules/ServerAPI/src/client/Label.coffee | 15 +++++++++++++++ 3 files changed, 22 insertions(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 2a226451c..f2544030f 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -318,6 +318,8 @@ class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractF @queryUrl = @options.queryUrl if @options.placeholder? @placeholder = @options.placeholder + if @options.extendedLabel? + @extendedLabel = @options.extendedLabel handleInputChanged: => @@ -348,7 +350,10 @@ class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractF @userInputEvent = false if @getModel()? and @getModel().getItxThing().id? labels = new LabelList @getModel().getItxThing().lsLabels - labelText = labels.pickBestNonEmptyLabel().get('labelText') + if @extendedLabel? and @extendedLabel + labelText = labels.getExtendedNameText() + else + labelText = labels.pickBestNonEmptyLabel().get('labelText') @thingSelectController.setSelectedCode code: @getModel().getItxThing().codeName label: labelText diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 008cc5bad..b881f513d 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -136,6 +136,7 @@ class window.AbstractThingFormController extends AbstractFormController insertUnassigned: field.fieldSettings.insertUnassigned modelDefaults: field.modelDefaults allowedFileTypes: field.fieldSettings.allowedFileTypes + extendedLabel: field.fieldSettings.extendedLabel switch field.fieldSettings.fieldType when 'label' diff --git a/modules/ServerAPI/src/client/Label.coffee b/modules/ServerAPI/src/client/Label.coffee index 81890ed63..2f50c94a8 100644 --- a/modules/ServerAPI/src/client/Label.coffee +++ b/modules/ServerAPI/src/client/Label.coffee @@ -105,6 +105,21 @@ class window.LabelList extends Backbone.Collection (lab.get('preferred') is false) && (lab.get('lsType') == "name") nonPreferredName[0] + getExtendedNameText: -> + corpNames = @filter (lab) -> + !lab.get('ignored') && (lab.get('labelText') != "") && lab.get('lsType').toLowerCase() == "corpname" + if corpNames.length > 0 + bestCorpName = _.max corpNames, (lab) -> + rd = lab.get 'recordedDate' + (if (rd is "") then rd else -1) + names = @filter (lab) -> + !lab.get('ignored') && (lab.get('labelText') != "") && lab.get('lsType').toLowerCase() == "name" + if names.length > 0 + bestName = _.max names, (lab) -> + rd = lab.get 'recordedDate' + (if (rd is "") then rd else -1) + return bestCorpName?.get('labelText')+" : "+bestName?.get('labelText') + setName: (label, currentName) -> if currentName? if currentName.isNew() From 3d9fd389e8e08c3eb3b0c59d04549ab2f4bd37b2 Mon Sep 17 00:00:00 2001 From: jmcneil86043 Date: Fri, 1 Sep 2017 16:20:06 -0700 Subject: [PATCH 167/576] Fixes #237 Add feature to interaction form fields to show corpName : name (#238) --- .../Components/src/client/ACASFormFields.coffee | 7 ++++++- .../src/client/AbstractFormController.coffee | 1 + modules/ServerAPI/src/client/Label.coffee | 15 +++++++++++++++ 3 files changed, 22 insertions(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 2a226451c..f2544030f 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -318,6 +318,8 @@ class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractF @queryUrl = @options.queryUrl if @options.placeholder? @placeholder = @options.placeholder + if @options.extendedLabel? + @extendedLabel = @options.extendedLabel handleInputChanged: => @@ -348,7 +350,10 @@ class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractF @userInputEvent = false if @getModel()? and @getModel().getItxThing().id? labels = new LabelList @getModel().getItxThing().lsLabels - labelText = labels.pickBestNonEmptyLabel().get('labelText') + if @extendedLabel? and @extendedLabel + labelText = labels.getExtendedNameText() + else + labelText = labels.pickBestNonEmptyLabel().get('labelText') @thingSelectController.setSelectedCode code: @getModel().getItxThing().codeName label: labelText diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 008cc5bad..b881f513d 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -136,6 +136,7 @@ class window.AbstractThingFormController extends AbstractFormController insertUnassigned: field.fieldSettings.insertUnassigned modelDefaults: field.modelDefaults allowedFileTypes: field.fieldSettings.allowedFileTypes + extendedLabel: field.fieldSettings.extendedLabel switch field.fieldSettings.fieldType when 'label' diff --git a/modules/ServerAPI/src/client/Label.coffee b/modules/ServerAPI/src/client/Label.coffee index 81890ed63..2f50c94a8 100644 --- a/modules/ServerAPI/src/client/Label.coffee +++ b/modules/ServerAPI/src/client/Label.coffee @@ -105,6 +105,21 @@ class window.LabelList extends Backbone.Collection (lab.get('preferred') is false) && (lab.get('lsType') == "name") nonPreferredName[0] + getExtendedNameText: -> + corpNames = @filter (lab) -> + !lab.get('ignored') && (lab.get('labelText') != "") && lab.get('lsType').toLowerCase() == "corpname" + if corpNames.length > 0 + bestCorpName = _.max corpNames, (lab) -> + rd = lab.get 'recordedDate' + (if (rd is "") then rd else -1) + names = @filter (lab) -> + !lab.get('ignored') && (lab.get('labelText') != "") && lab.get('lsType').toLowerCase() == "name" + if names.length > 0 + bestName = _.max names, (lab) -> + rd = lab.get 'recordedDate' + (if (rd is "") then rd else -1) + return bestCorpName?.get('labelText')+" : "+bestName?.get('labelText') + setName: (label, currentName) -> if currentName? if currentName.isNew() From b2af893d96e8f3d53988e0f448f4adb7d889e282 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Mon, 4 Sep 2017 15:11:11 -0700 Subject: [PATCH 168/576] Fixes #239 Create MarvinJS Sketcher widget --- .../routes/RequiredClientScripts_template.js | 5 + modules/CmpdReg/src/client/src/SearchForm.js | 1 + .../client/ACASFormChemicalStructure.coffee | 106 +++++++++++++++++- .../client/ACASFormChemicalStructureView.html | 4 + .../{ExcelApp.coffee => ExcelApp.coffee_hide} | 0 .../client/ModuleMenusConfiguration.coffee | 4 + 6 files changed, 115 insertions(+), 5 deletions(-) rename modules/ExcelApp/src/client/{ExcelApp.coffee => ExcelApp.coffee_hide} (100%) diff --git a/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js b/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js index a47b9a0c9..ee36e787c 100644 --- a/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js +++ b/modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js @@ -26,6 +26,11 @@ exports.requiredScripts = [ '/lib/spin/js/jquery-spin.js', '/lib/handsontable/dist/handsontable.full.js', '/lib/select2-4.0.2/dist/js/select2.full.js', + // Add the following four lines to use MarvinJSChemicalStructureController + // '/CmpdReg/marvinjs/js/lib/rainbow/rainbow-custom.min.js', + // '/CmpdReg/marvinjs/gui/lib/promise-1.0.0.min.js', + // '/CmpdReg/marvinjs/js/marvinjslauncher.js', + // '/CmpdReg/client/custom/marvinStructureTemplate.js', '/socket.io/socket.io.js', '/lib/blockUI.js' ]; diff --git a/modules/CmpdReg/src/client/src/SearchForm.js b/modules/CmpdReg/src/client/src/SearchForm.js index 73a910b94..25b88da3b 100755 --- a/modules/CmpdReg/src/client/src/SearchForm.js +++ b/modules/CmpdReg/src/client/src/SearchForm.js @@ -51,6 +51,7 @@ $(function() { this.valid = false; this.marvinLoaded = false; this.exportFormat = "mol"; + this.exportFormat = "mol"; if(window.configuration.marvin) { if (window.configuration.marvin.exportFormat) { this.exportFormat = window.configuration.marvin.exportFormat; diff --git a/modules/Components/src/client/ACASFormChemicalStructure.coffee b/modules/Components/src/client/ACASFormChemicalStructure.coffee index cfe56527b..8226acd98 100644 --- a/modules/Components/src/client/ACASFormChemicalStructure.coffee +++ b/modules/Components/src/client/ACASFormChemicalStructure.coffee @@ -1,6 +1,39 @@ class window.ACASFormChemicalStructureExampleController extends Backbone.View template: _.template($("#ACASFormChemicalStructureExampleControllerView").html()) + molToSet: "\n\n\n"+ + " 14 15 0 0 0 0 0 0 0 0999 V2000\n"+ + " 0.5089 7.8316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " 1.2234 6.5941 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " 1.2234 7.4191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " -0.2055 6.5941 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " -0.9200 7.8316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " 0.5089 5.3566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " -0.2055 7.4191 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " 0.5089 6.1816 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " -0.9200 6.1816 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " 0.5089 8.6566 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " 2.4929 7.0066 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " 2.0080 7.6740 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " 2.0080 6.3391 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " 2.2630 8.4586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"+ + " 1 7 1 0 0 0 0\n"+ + " 8 2 1 0 0 0 0\n"+ + " 1 3 1 0 0 0 0\n"+ + " 2 3 2 0 0 0 0\n"+ + " 7 4 1 0 0 0 0\n"+ + " 4 8 1 0 0 0 0\n"+ + " 4 9 2 0 0 0 0\n"+ + " 7 5 1 0 0 0 0\n"+ + " 8 6 1 0 0 0 0\n"+ + " 1 10 2 0 0 0 0\n"+ + " 3 12 1 0 0 0 0\n"+ + " 2 13 1 0 0 0 0\n"+ + " 13 11 2 0 0 0 0\n"+ + " 12 11 1 0 0 0 0\n"+ + " 12 14 1 0 0 0 0\n"+ + "M END\n" + events: -> "click .bv_getMolButton": "getMol" "click .bv_setMolButton": "setMol" @@ -8,18 +41,24 @@ class window.ACASFormChemicalStructureExampleController extends Backbone.View render: => $(@el).empty() $(@el).html @template() - @sketcher = new ACASFormChemicalStructureController +# @sketcher = new ACASFormChemicalStructureController + @sketcher = new KetcherChemicalStructureController +# @sketcher = new MarvinJSChemicalStructureController searchMode: false @$('.bv_sketcher').append @sketcher.render().el @ getMol: => - mol = @sketcher.getMol() - alert mol + if @sketcher.getMol? + mol = @sketcher.getMol() + alert mol + else + @sketcher.getMolAsync (mol) => + alert mol - setMol: (molStr) => - @sketcher.setMol molStr + setMol: => + @sketcher.setMol @molToSet getChemDoodleJSON: => mol = @sketcher.getChemDoodleJSON() @@ -88,3 +127,60 @@ class window.KetcherChemicalStructureController extends Backbone.View setMol: (molStr) -> molStruct = @windowObj.ketcher.setMolecule molStr + + + +# To use This MarvinJS sketcher you must uncomment four lines in +# modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js + +class window.MarvinJSChemicalStructureController extends Backbone.View + tagName: "DIV" + template: _.template($("#MarvinJSChemicalStructureControllerView").html()) + + + initialize: -> + @exportFormat = "mol"; + if window.configuration?.marvin?.exportFormat? + @exportFormat = window.configuration.marvin.exportFormat + + render: => + $(@el).empty() + $(@el).html @template() + + searchFrameURL = "/CmpdReg/marvinjs/editorws.html" + + @marvinIFrameID = "marvinSketcher_" + new Date().getMilliseconds() + @$('.bv_sketcherIFrame').attr 'id', @marvinIFrameID + @$('.bv_sketcherIFrame').attr 'src', searchFrameURL + + @$('.bv_sketcherIFrame').on 'load', @startSketcher + + @ + + startSketcher: => + MarvinJSUtil.getEditor(@marvinIFrameID).then (sketcherInstance) => + @marvinSketcherInstance = sketcherInstance; + if typeof window.marvinStructureTemplates != 'undefined' + for msTempl in window.marvinStructureTemplates + sketcherInstance.addTemplate msTempl + @trigger 'sketcherLoaded' + , (error) => + alert("Cannot retrieve MarvinSketch sketcher instance from iframe:"+error); + + getMolAsync: (callback) -> + @marvinSketcherInstance.exportStructure(@exportFormat).then (molecule) => + console.dir molecule, depth: 3 + if molecule.indexOf("0 0 0 0 0 0 0 0 0 0999")>-1 + mol = '' + else if molecule.indexOf("M V30 COUNTS 0 0 0 0 0")>-1 + mol = '' + else + mol = molecule + callback mol + ,(error) => + alert("Molecule export failed from search sketcher:"+error) + callback null + + + setMol: (molStr) -> + @marvinSketcherInstance.importStructure("mol", molStr) diff --git a/modules/Components/src/client/ACASFormChemicalStructureView.html b/modules/Components/src/client/ACASFormChemicalStructureView.html index 269c44ff3..ba9cccdb4 100644 --- a/modules/Components/src/client/ACASFormChemicalStructureView.html +++ b/modules/Components/src/client/ACASFormChemicalStructureView.html @@ -13,3 +13,7 @@

      Test sketcher thingy

      + + diff --git a/modules/ExcelApp/src/client/ExcelApp.coffee b/modules/ExcelApp/src/client/ExcelApp.coffee_hide similarity index 100% rename from modules/ExcelApp/src/client/ExcelApp.coffee rename to modules/ExcelApp/src/client/ExcelApp.coffee_hide diff --git a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee index 144710936..66a6a5933 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee @@ -4,6 +4,10 @@ window.ModuleMenusConfiguration = menuName: "Load Data" # collapsible: true , +# isHeader: false +# menuName: "Chem Struct" +# mainControllerClassName: "ACASFormChemicalStructureExampleController" +# , isHeader: false menuName: "Experiment Loader" mainControllerClassName: "GenericDataParserController" From 1e676c3b34fc26e17dcbff6fbdf21b8c7ce61eee Mon Sep 17 00:00:00 2001 From: John McNeil Date: Mon, 4 Sep 2017 18:06:42 -0700 Subject: [PATCH 169/576] Fixes #240 Allow systems to be configured to use Ketcher for drawing molecular structures in Compound Registration. New code only tested in search and reg search. Need to test on New Salt, Edit Parent, and Salt Form --- modules/CmpdReg/spec/SaltSpec.js | 8 +- .../src/client/custom/configuration.json | 7 +- modules/CmpdReg/src/client/spec/SaltSpec.js | 8 +- modules/CmpdReg/src/client/src/EditParent.js | 113 +++++++++++------- .../src/client/src/RegSearchResults.js | 4 +- .../src/client/src/RegistrationSearch.js | 90 +++++++++----- modules/CmpdReg/src/client/src/Salt.js | 88 ++++++++++---- modules/CmpdReg/src/client/src/SaltForm.js | 67 +++++++---- modules/CmpdReg/src/client/src/SearchForm.js | 84 ++++++++----- .../client/templates/EditParentSearchView.inc | 2 +- .../client/templates/LotForm/NewSaltView.inc | 2 +- .../client/templates/LotForm/SaltFormView.inc | 2 +- .../templates/RegistrationSearchView.inc | 2 +- .../templates/Search/SearchFormView.inc | 2 +- .../client/ACASFormChemicalStructure.coffee | 3 +- 15 files changed, 313 insertions(+), 169 deletions(-) diff --git a/modules/CmpdReg/spec/SaltSpec.js b/modules/CmpdReg/spec/SaltSpec.js index 48d46f510..db1b7d281 100755 --- a/modules/CmpdReg/spec/SaltSpec.js +++ b/modules/CmpdReg/spec/SaltSpec.js @@ -251,7 +251,7 @@ $(function () { this.newSaltController.render(); }); waitsFor( function (){ - return this.newSaltController.marvinLoaded; + return this.newSaltController.sketcherLoaded; }); }); @@ -289,7 +289,7 @@ $(function () { this.newSaltController.$('.salt_abbrev').val('saltAbbrev1'); }); waitsFor( function (){ - return this.newSaltController.marvinLoaded; + return this.newSaltController.sketcherLoaded; }); runs(function() { this.newSaltController.marvinSketcherInstance.importStructure("mrv", testMrv).catch(function(error) { @@ -337,7 +337,7 @@ $(function () { this.newSaltController.$('.salt_abbrev').val('saltAbbrev1'); }); waitsFor( function (){ - return this.newSaltController.marvinLoaded; + return this.newSaltController.sketcherLoaded; }); runs(function() { this.newSaltController.marvinSketcherInstance.importStructure("mrv", testMrv).catch(function(error) { @@ -395,7 +395,7 @@ $(function () { this.newSaltController.$('.salt_abbrev').val(' saltAbbrev1 '); }); waitsFor( function (){ - return this.newSaltController.marvinLoaded; + return this.newSaltController.sketcherLoaded; }); runs(function() { this.newSaltController.marvinSketcherInstance.importStructure("mrv", testMrv).catch(function(error) { diff --git a/modules/CmpdReg/src/client/custom/configuration.json b/modules/CmpdReg/src/client/custom/configuration.json index 17ba6861f..dbc4a0acc 100755 --- a/modules/CmpdReg/src/client/custom/configuration.json +++ b/modules/CmpdReg/src/client/custom/configuration.json @@ -10,12 +10,7 @@ "applicationNameForTitleBar": "ACAS Compound Registration", "commonNameLabel": "Original ID:" }, - "marvin": { - "marvinImplicitH": "heteroterm", - "sketchBondLength": 20, - "delayShowStep2Next": 750, - "exportFormat": "mol" - }, + "ketcher": true, "regSearchResults": { "hideVirtualOption": false }, diff --git a/modules/CmpdReg/src/client/spec/SaltSpec.js b/modules/CmpdReg/src/client/spec/SaltSpec.js index 77cf137d7..27c45f0ba 100755 --- a/modules/CmpdReg/src/client/spec/SaltSpec.js +++ b/modules/CmpdReg/src/client/spec/SaltSpec.js @@ -251,7 +251,7 @@ $(function () { this.newSaltController.render(); }); waitsFor( function (){ - return this.newSaltController.marvinLoaded; + return this.newSaltController.sketcherLoaded; }); }); @@ -289,7 +289,7 @@ $(function () { this.newSaltController.$('.salt_abbrev').val('saltAbbrev1'); }); waitsFor( function (){ - return this.newSaltController.marvinLoaded; + return this.newSaltController.sketcherLoaded; }); runs(function() { this.newSaltController.marvinSketcherInstance.importStructure("mrv", testMrv).catch(function(error) { @@ -337,7 +337,7 @@ $(function () { this.newSaltController.$('.salt_abbrev').val('saltAbbrev1'); }); waitsFor( function (){ - return this.newSaltController.marvinLoaded; + return this.newSaltController.sketcherLoaded; }); runs(function() { this.newSaltController.marvinSketcherInstance.importStructure("mrv", testMrv).catch(function(error) { @@ -395,7 +395,7 @@ $(function () { this.newSaltController.$('.salt_abbrev').val(' saltAbbrev1 '); }); waitsFor( function (){ - return this.newSaltController.marvinLoaded; + return this.newSaltController.sketcherLoaded; }); runs(function() { this.newSaltController.marvinSketcherInstance.importStructure("mrv", testMrv).catch(function(error) { diff --git a/modules/CmpdReg/src/client/src/EditParent.js b/modules/CmpdReg/src/client/src/EditParent.js index 7d78e3558..95c7e7dae 100644 --- a/modules/CmpdReg/src/client/src/EditParent.js +++ b/modules/CmpdReg/src/client/src/EditParent.js @@ -22,18 +22,21 @@ $(function () { initialize: function(){ _.bindAll(this, 'next', 'cancel', 'render', 'validationError'); this.valid = false; - this.marvinLoaded = false; + this.sketcherLoaded = false; this.exportFormat = "mol"; - if(window.configuration.marvin) { - if (window.configuration.marvin.exportFormat) { - this.exportFormat = window.configuration.marvin.exportFormat; - } - } + if(window.configuration.marvin) { + this.useMarvin = true; + if (window.configuration.marvin.exportFormat) { + this.exportFormat = window.configuration.marvin.exportFormat; + } + } else if(window.configuration.ketcher) { + this.useKetcher = true; + } this.hide(); }, render: function() { - if (!this.marvinLoaded) { // only load template once so we don't wipe out marvin + if (!this.sketcherLoaded) { // only load template once so we don't wipe out marvin $(this.el).html(this.template()); if(this.options.corpName){ this.$('.corpName').val(this.options.corpName); @@ -42,22 +45,29 @@ $(function () { this.hide(); var self = this; - MarvinJSUtil.getEditor("#editParentMarvinSketch").then(function (sketcherInstance) { - self.marvinSketcherInstance = sketcherInstance; - if (typeof window.marvinStructureTemplates !== 'undefined') { - for (i=0 ; i-1) - mol = null; + if (this.useMarvin) { + this.marvinSketcherInstance.exportStructure(this.exportFormat).then(function (molecule) { + if (molecule.indexOf("0 0 0 0 0 0 0 0 0 0999") > -1) + mol = null; + else + mol = molecule; + editParentSearch.set({ + molStructure: mol, + corpName: jQuery.trim(self.$('.corpName').val()) + }); + + if ( self.isValid() ) { + self.trigger('editParentSearchNext', editParentSearch); + self.hide(); + } + }, function(error) { + alert("Molecule export failed from search sketcher:"+error); + }); + + } else if (this.useKetcher) { + mol = this.ketcher.getMolfile(); + if (mol=="") + mol = null; else - mol = molecule; - editParentSearch.set({ - molStructure: mol, - corpName: jQuery.trim(self.$('.corpName').val()) - }); - - if ( self.isValid() ) { - self.trigger('editParentSearchNext', editParentSearch); - self.hide(); - } - }, function(error) { - alert("Molecule export failed from search sketcher:"+error); - }); - + mol = molecule; + editParentSearch.set({ + molStructure: mol, + corpName: jQuery.trim(self.$('.corpName').val()) + }); + + if ( self.isValid() ) { + self.trigger('editParentSearchNext', editParentSearch); + self.hide(); + } + } else { + alert("No edit parent sketcher configured in search action"); + } }, isValid: function() { @@ -141,13 +170,13 @@ $(function () { initialize: function(){ _.bindAll(this, 'toggleParentsVisible', 'next'); - this.marvinLoaded = false; + this.sketcherLoaded = false; this.hide(); this.parentModel = this.options.parentModel; }, render: function () { - if (!this.marvinLoaded) { // only load template once so we don't wipe out marvin + if (!this.sketcherLoaded) { // only load template once so we don't wipe out marvin $(this.el).html(this.template()); } diff --git a/modules/CmpdReg/src/client/src/RegSearchResults.js b/modules/CmpdReg/src/client/src/RegSearchResults.js index 96caf4531..3279a0069 100755 --- a/modules/CmpdReg/src/client/src/RegSearchResults.js +++ b/modules/CmpdReg/src/client/src/RegSearchResults.js @@ -12,12 +12,12 @@ $(function() { initialize: function(){ _.bindAll(this, 'toggleParentsVisible', 'next'); - this.marvinLoaded = false; + this.sketcherLoaded = false; this.hide(); }, render: function () { - if (!this.marvinLoaded) { // only load template once so we don't wipe out marvin + if (!this.sketcherLoaded) { // only load template once so we don't wipe out marvin $(this.el).html(this.template()); } diff --git a/modules/CmpdReg/src/client/src/RegistrationSearch.js b/modules/CmpdReg/src/client/src/RegistrationSearch.js index b966ef86b..aac7ae23c 100755 --- a/modules/CmpdReg/src/client/src/RegistrationSearch.js +++ b/modules/CmpdReg/src/client/src/RegistrationSearch.js @@ -26,19 +26,22 @@ $(function() { initialize: function(){ _.bindAll(this, 'next', 'cancel', 'render', 'validationError'); this.valid = false; - this.marvinLoaded = false; + this.sketcherLoaded = false; this.exportFormat = "mol"; if(window.configuration.marvin) { + this.useMarvin = true; if (window.configuration.marvin.exportFormat) { this.exportFormat = window.configuration.marvin.exportFormat; } + } else if(window.configuration.ketcher) { + this.useKetcher = true; } this.hide(); }, render: function () { - if (!this.marvinLoaded) { // only load template once so we don't wipe out marvin + if (!this.sketcherLoaded) { // only load template once so we don't wipe out marvin $(this.el).html(this.template()); if(this.options.corpName){ this.$('.corpName').val(this.options.corpName); @@ -47,18 +50,30 @@ $(function() { this.hide(); var self = this; - MarvinJSUtil.getEditor("#registrationSearchMarvinSketch").then(function (sketcherInstance) { - self.marvinSketcherInstance = sketcherInstance; - if (typeof window.marvinStructureTemplates !== 'undefined') { - for (i=0 ; i-1) - mol = null; - else if ( molecule.indexOf("M V30 COUNTS 0 0 0 0 0")>-1) - mol = null; - else - mol = molecule; + + if (this.useMarvin) { + this.marvinSketcherInstance.exportStructure(this.exportFormat).then(function (molecule) { + if (molecule.indexOf("0 0 0 0 0 0 0 0 0 0999") > -1) + mol = ''; + else if (molecule.indexOf("M V30 COUNTS 0 0 0 0 0") > -1) + mol = ''; + else + mol = molecule; + regSearch.set({ + molStructure: mol, + corpName: jQuery.trim(self.$('.corpName').val()) + }); + + if ( self.isValid() ) { + self.trigger('registrationSearchNext', regSearch); + self.hide(); + } + }, function (error) { + alert("Molecule export failed from search sketcher:" + error); + }); + } else if (this.useKetcher) { + mol = this.ketcher.getMolfile(); regSearch.set({ molStructure: mol, corpName: jQuery.trim(self.$('.corpName').val()) }); - if ( self.isValid() ) { - self.trigger('registrationSearchNext', regSearch); - self.hide(); + if ( this.isValid() ) { + this.trigger('registrationSearchNext', regSearch); + this.hide(); } - }, function(error) { - alert("Molecule export failed from search sketcher:"+error); - }); - + } else { + alert("No registration sketcher configured in search action"); + } }, isValid: function() { diff --git a/modules/CmpdReg/src/client/src/Salt.js b/modules/CmpdReg/src/client/src/Salt.js index 8b7cd83d6..173754c09 100755 --- a/modules/CmpdReg/src/client/src/Salt.js +++ b/modules/CmpdReg/src/client/src/Salt.js @@ -155,35 +155,55 @@ $(function() { $(this.el).html(this.template()); this.exportFormat = "mol"; if(window.configuration.marvin) { + this.useMarvin = true; if (window.configuration.marvin.exportFormat) { this.exportFormat = window.configuration.marvin.exportFormat; } + } else if(window.configuration.ketcher) { + this.useKetcher = true; } - this.marvinLoaded = false; + this.sketcherLoaded = false; }, render: function () { var self = this; - MarvinJSUtil.getEditor("#newSaltMarvinSketch").then(function (sketcherInstance) { - self.marvinSketcherInstance = sketcherInstance; - if (typeof window.marvinStructureTemplates !== 'undefined') { - for (i=0 ; i-1) + + var gotMol = function (molecule) { + + if (molecule.indexOf("0 0 0 0 0 0 0 0 0 0999") > -1) mol = ''; else mol = molecule; @@ -226,28 +249,43 @@ $(function() { self.delegateEvents({}); // stop listening to buttons self.collection.create(salt, { - success: function() { + success: function () { self.clearValidationErrorStyles(); self.clearInputFields(); self.delegateEvents(); // start listening to events self.hide(); }, - error: function(model, error) { + error: function (model, error) { self.clearValidationErrorStyles(); var resp = $.parseJSON(error.responseText); - _.each(resp, function(err) { - self.trigger('notifyError', {owner: "NewSaltController", errorLevel: err.level, message: err.message}); + _.each(resp, function (err) { + self.trigger('notifyError', { + owner: "NewSaltController", + errorLevel: err.level, + message: err.message + }); }); self.delegateEvents(); // start listening to events } }); } + } + if (this.useMarvin) { + this.marvinSketcherInstance.exportStructure(this.exportFormat).then( + gotMol, + function (error) { + alert("Molecule export failed from search sketcher:"+error); + } + ); + + } else if (this.useKetcher) { + mol = this.ketcher.getMolfile(); + gotMol(mol); + } else { + alert("No new salt sketcher configured"); + } - - }, function(error) { - alert("Molecule export failed from search sketcher:"+error); - }); } }, diff --git a/modules/CmpdReg/src/client/src/SaltForm.js b/modules/CmpdReg/src/client/src/SaltForm.js index aa4a29d3f..ba00fb573 100755 --- a/modules/CmpdReg/src/client/src/SaltForm.js +++ b/modules/CmpdReg/src/client/src/SaltForm.js @@ -83,12 +83,15 @@ $(function() { this.valid = true; this.isEditable = this.options.isEditable; - this.marvinLoaded = false; // load on demand, not default, to make testing more reliable and fast + this.sketcherLoaded = false; // load on demand, not default, to make testing more reliable and fast this.exportFormat = "mol"; if(window.configuration.marvin) { + this.useMarvin = true; if (window.configuration.marvin.exportFormat) { this.exportFormat = window.configuration.marvin.exportFormat; } + } else if(window.configuration.ketcher) { + this.useKetcher = true; } if ( this.isEditable ) { @@ -158,7 +161,7 @@ $(function() { this.isosaltEquivListController.updateModel(); var mol = ''; - if(this.marvinLoaded && this.$('.structureWrapper').is(':visible')) { + if(this.sketcherLoaded && this.$('.structureWrapper').is(':visible')) { self = this; this.marvinSketcherInstance.exportStructure(this.exportFormat).then(function(molecule) { if ( molecule.indexOf("0 0 0 0 0 0 0 0 0 0999")>-1) @@ -273,27 +276,49 @@ $(function() { if( this.isEditable) { var self = this; self.$('.saltFormImage').hide(); - MarvinJSUtil.getEditor("#saltFormMarvinSketch").then(function (sketcherInstance) { - self.marvinSketcherInstance = sketcherInstance; - if (typeof window.marvinStructureTemplates !== 'undefined') { - for (i=0 ; i-1) - mol = ''; - else if ( molecule.indexOf("M V30 COUNTS 0 0 0 0 0")>-1) - mol = ''; - else - mol = molecule; - var sf = self.makeSearchFormModel(mol); - if ( self.isValid() ) { - self.trigger('searchNext', sf); - self.hide(); + if (this.useMarvin) { + this.marvinSketcherInstance.exportStructure(this.exportFormat).then(function (molecule) { + if (molecule.indexOf("0 0 0 0 0 0 0 0 0 0999") > -1) + mol = ''; + else if (molecule.indexOf("M V30 COUNTS 0 0 0 0 0") > -1) + mol = ''; + else + mol = molecule; + var sf = self.makeSearchFormModel(mol); + if (self.isValid()) { + self.trigger('searchNext', sf); + self.hide(); + } + }, function (error) { + alert("Molecule export failed from search sketcher:" + error); + }); + } else if (this.useKetcher) { + mol = this.ketcher.getMolfile(); + var sf = this.makeSearchFormModel(mol); + if (this.isValid()) { + this.trigger('searchNext', sf); + this.hide(); } - }, function(error) { - alert("Molecule export failed from search sketcher:"+error); - }); + } else { + alert("No search sketcher configured in search action"); + } }, makeSearchFormModel: function(molecule) { this.clearValidationErrors(); diff --git a/modules/CmpdReg/src/client/templates/EditParentSearchView.inc b/modules/CmpdReg/src/client/templates/EditParentSearchView.inc index b4b77a2c3..4060c8292 100644 --- a/modules/CmpdReg/src/client/templates/EditParentSearchView.inc +++ b/modules/CmpdReg/src/client/templates/EditParentSearchView.inc @@ -3,7 +3,7 @@

      Edit Parent Step 1: Draw Structure

      - +
      diff --git a/modules/CmpdReg/src/client/templates/LotForm/NewSaltView.inc b/modules/CmpdReg/src/client/templates/LotForm/NewSaltView.inc index 2205f01ae..73a795fc2 100755 --- a/modules/CmpdReg/src/client/templates/LotForm/NewSaltView.inc +++ b/modules/CmpdReg/src/client/templates/LotForm/NewSaltView.inc @@ -2,7 +2,7 @@

      Register New Salt:

      - +
      diff --git a/modules/CmpdReg/src/client/templates/LotForm/SaltFormView.inc b/modules/CmpdReg/src/client/templates/LotForm/SaltFormView.inc index 37f778a05..e7b1cce98 100755 --- a/modules/CmpdReg/src/client/templates/LotForm/SaltFormView.inc +++ b/modules/CmpdReg/src/client/templates/LotForm/SaltFormView.inc @@ -8,7 +8,7 @@ Isotope/salt Structure:
      - +
      diff --git a/modules/CmpdReg/src/client/templates/RegistrationSearchView.inc b/modules/CmpdReg/src/client/templates/RegistrationSearchView.inc index 9550614cf..ca6cf5dcd 100755 --- a/modules/CmpdReg/src/client/templates/RegistrationSearchView.inc +++ b/modules/CmpdReg/src/client/templates/RegistrationSearchView.inc @@ -3,7 +3,7 @@

      Registration Step 1: Draw Structure

      - +
      diff --git a/modules/CmpdReg/src/client/templates/Search/SearchFormView.inc b/modules/CmpdReg/src/client/templates/Search/SearchFormView.inc index bcf61d235..45d6dc96c 100755 --- a/modules/CmpdReg/src/client/templates/Search/SearchFormView.inc +++ b/modules/CmpdReg/src/client/templates/Search/SearchFormView.inc @@ -3,7 +3,7 @@

      - +
      diff --git a/modules/Components/src/client/ACASFormChemicalStructure.coffee b/modules/Components/src/client/ACASFormChemicalStructure.coffee index 8226acd98..0cd3cf35f 100644 --- a/modules/Components/src/client/ACASFormChemicalStructure.coffee +++ b/modules/Components/src/client/ACASFormChemicalStructure.coffee @@ -131,8 +131,7 @@ class window.KetcherChemicalStructureController extends Backbone.View # To use This MarvinJS sketcher you must uncomment four lines in -# modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js - +# class window.MarvinJSChemicalStructureController extends Backbone.View tagName: "DIV" template: _.template($("#MarvinJSChemicalStructureControllerView").html()) From 2bf18229f019e995c74777fd2cd99f2a8e8c2a8f Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Wed, 6 Sep 2017 15:18:46 -0700 Subject: [PATCH 170/576] RC/1.12.0 - updated experiment browser to read from different attr in ControllerRedirectConf, fixed updating notebook page for protocols/expts --- .../src/client/ExperimentBrowser.coffee | 4 +-- .../ServerAPI/src/client/BaseEntity.coffee | 29 ++++++++++--------- 2 files changed, 17 insertions(+), 16 deletions(-) diff --git a/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee b/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee index 9d5889386..bc8b8aa74 100644 --- a/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee +++ b/modules/ExperimentBrowser/src/client/ExperimentBrowser.coffee @@ -397,10 +397,10 @@ class window.ExperimentBrowserController extends Backbone.View setupExperimentController: (experiment) => lsKind = experiment.get('lsKind') - if @controllerRedirectConf['EXPT']?[lsKind]?['modelClass']? and @controllerRedirectConf['EXPT']?[lsKind]?['controllerClass']? + if @controllerRedirectConf['EXPT']?[lsKind]?['modelClass']? and @controllerRedirectConf['EXPT']?[lsKind]?['browserControllerClass']? if @controllerRedirectConf['EXPT']?[lsKind]?['protocolKindFilter']? protocolKindFilter = @controllerRedirectConf['EXPT'][lsKind]['protocolKindFilter'] - @experimentController = new window[@controllerRedirectConf['EXPT'][lsKind]['controllerClass']] + @experimentController = new window[@controllerRedirectConf['EXPT'][lsKind]['browserControllerClass']] protocolKindFilter: protocolKindFilter model: new window[@controllerRedirectConf['EXPT'][lsKind]['modelClass']] JSON.parse(JSON.stringify(experiment)) readOnly: true diff --git a/modules/ServerAPI/src/client/BaseEntity.coffee b/modules/ServerAPI/src/client/BaseEntity.coffee index 6090a99ee..c3e6191ac 100644 --- a/modules/ServerAPI/src/client/BaseEntity.coffee +++ b/modules/ServerAPI/src/client/BaseEntity.coffee @@ -318,22 +318,23 @@ class window.BaseEntityController extends AbstractThingFormController #TODO: che if requireNotebook console.log "require notebook" @$('.bv_notebookLabel').html "*Notebook" - saveNotebookPage = true #default - if window.conf.entity?.notebookPage?.save? - saveNotebookPage = window.conf.entity.notebookPage.save - requireNotebookPage = false #default - if window.conf.entity?.notebookPage?.require? - requireNotebookPage= window.conf.entity.notebookPage.require - if saveNotebookPage - @$('.bv_notebookPage').val @model.getNotebookPage().get('stringValue') - if requireNotebookPage - @$('.bv_notebookPageLabel').html "*Notebook Page" - else - @$('.bv_notebookPageLabel').html "Notebook Page" - else - @$('.bv_group_notebookPage').hide() else @$('.bv_notebookLabel').html "Notebook" + saveNotebookPage = true #default + if window.conf.entity?.notebookPage?.save? + saveNotebookPage = window.conf.entity.notebookPage.save + requireNotebookPage = false #default + if window.conf.entity?.notebookPage?.require? + requireNotebookPage= window.conf.entity.notebookPage.require + if saveNotebookPage + @$('.bv_notebookPage').val @model.getNotebookPage().get('stringValue') + if requireNotebookPage + @$('.bv_notebookPageLabel').html "*Notebook Page" + else + @$('.bv_notebookPageLabel').html "Notebook Page" + else + @$('.bv_group_notebookPage').hide() + else @$('.bv_group_notebook').hide() From 14baf0d6dfdb669f42c8b864bfd34548e5347e13 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 12 Sep 2017 08:19:38 -0700 Subject: [PATCH 171/576] Made minor fix for Edit Parent to populate mol of parent being edited. Switched service routes for all CReg ketcher instances to point at new CReg-backed structure services to enable ketcher utility buttons like clean, and SMILES conversion. Changed docker environment to work with indigo/bingo CReg. --- conf/docker/cmpdreg/environment/cmpdreg.env | 2 +- docker-compose.yml | 8 +- modules/CmpdReg/src/client/src/EditParent.js | 12 ++- .../src/client/src/RegistrationSearch.js | 3 +- modules/CmpdReg/src/client/src/Salt.js | 3 +- modules/CmpdReg/src/client/src/SaltForm.js | 2 +- modules/CmpdReg/src/client/src/SearchForm.js | 3 +- .../src/server/routes/CmpdRegRoutes.coffee | 98 ++++++++++++++++++- 8 files changed, 116 insertions(+), 15 deletions(-) diff --git a/conf/docker/cmpdreg/environment/cmpdreg.env b/conf/docker/cmpdreg/environment/cmpdreg.env index 02b33be58..c4fa753f5 100644 --- a/conf/docker/cmpdreg/environment/cmpdreg.env +++ b/conf/docker/cmpdreg/environment/cmpdreg.env @@ -8,5 +8,5 @@ CMPDREG_USER_PASSWORD=compound CMPDREG_DATABASE_DRIVER=org.postgresql.Driver CMPDREG_DATABASE_URL=jdbc:postgresql://db:5432/${CMPDREG_DB_NAME}?searchpath=${CMPDREG_SCHEMA} CMPDREG_VALIDATION_QUERY=select version() -CMPDREG_FLYWAY_LOCATION=com.labsynch.cmpdreg.db.migration.postgres,db/migration/postgres +CMPDREG_FLYWAY_LOCATION=com.labsynch.cmpdreg.db.migration.postgres,db/migration/postgres,db/migration/indigo/postgres CMPDREG_HIBERNATE_DIALECT=org.hibernate.dialect.PostgreSQLDialect diff --git a/docker-compose.yml b/docker-compose.yml index 3ba809351..738122fa7 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -47,7 +47,7 @@ services: - logs:/home/runner/logs command: ["bin/acas.sh", "run", "rservices"] db: - image: mcneilco/acas-postgres:${ACAS_TAG} + image: mcneilco/acas-postgres:bingo restart: always volumes: - dbstore:/var/lib/postgresql/data @@ -86,12 +86,12 @@ services: - /usr/local/tomcat/webapps/acas command: /bin/true cmpdreg: - image: mcneilco/acas-cmpdreg-roo-server-oss:${ACAS_TAG} + image: mcneilco/acas-cmpdreg-roo-server-oss:indigo volumes: - /usr/local/tomcat/webapps/cmpdreg # Add chemaxon license files here - - ./chemaxon/licenses/marvin4js-license.cxl:/usr/local/tomcat/webapps/ROOT/marvin4js-license.cxl - - ./chemaxon/licenses/license.cxl:/root/.chemaxon/license.cxl + # - ./chemaxon/licenses/marvin4js-license.cxl:/usr/local/tomcat/webapps/ROOT/marvin4js-license.cxl + # - ./chemaxon/licenses/license.cxl:/root/.chemaxon/license.cxl command: /bin/true volumes: dbstore: diff --git a/modules/CmpdReg/src/client/src/EditParent.js b/modules/CmpdReg/src/client/src/EditParent.js index 95c7e7dae..e172079f4 100644 --- a/modules/CmpdReg/src/client/src/EditParent.js +++ b/modules/CmpdReg/src/client/src/EditParent.js @@ -53,6 +53,10 @@ $(function () { for (i = 0; i < window.marvinStructureTemplates.length; i++) { sketcherInstance.addTemplate(window.marvinStructureTemplates[i]); } + var pastePromise = sketcherInstance.importStructure(null, self.options.parentModel.get('molStructure')); + pastePromise.then(function() {}, function(error) { + alert(error); + }); } self.show(); self.sketcherLoaded = true; @@ -61,9 +65,10 @@ $(function () { }); } else if (this.useKetcher) { - this.$('#editParentMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/chemStructure/ketcher/"); + this.$('#editParentMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/cmpdReg/ketcher/"); this.$('#editParentMarvinSketch').on('load', function () { self.ketcher = self.$('#editParentMarvinSketch')[0].contentWindow.ketcher; + self.ketcher.setMolecule(self.options.parentModel.get('molStructure')); }); } else { alert("No edit parent sketcher configured"); @@ -113,10 +118,7 @@ $(function () { } else if (this.useKetcher) { mol = this.ketcher.getMolfile(); - if (mol=="") - mol = null; - else - mol = molecule; + if (mol.indexOf(" 0 0 0 0 0 999") > -1) mol = null; editParentSearch.set({ molStructure: mol, corpName: jQuery.trim(self.$('.corpName').val()) diff --git a/modules/CmpdReg/src/client/src/RegistrationSearch.js b/modules/CmpdReg/src/client/src/RegistrationSearch.js index aac7ae23c..7c9b92783 100755 --- a/modules/CmpdReg/src/client/src/RegistrationSearch.js +++ b/modules/CmpdReg/src/client/src/RegistrationSearch.js @@ -67,7 +67,7 @@ $(function() { }); } else if (this.useKetcher) { - this.$('#registrationSearchMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/chemStructure/ketcher/"); + this.$('#registrationSearchMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/cmpdReg/ketcher/"); this.$('#registrationSearchMarvinSketch').on('load', function () { self.ketcher = self.$('#registrationSearchMarvinSketch')[0].contentWindow.ketcher; }); @@ -127,6 +127,7 @@ $(function() { }); } else if (this.useKetcher) { mol = this.ketcher.getMolfile(); + if (mol.indexOf(" 0 0 0 0 0 999") > -1) mol = null; regSearch.set({ molStructure: mol, corpName: jQuery.trim(self.$('.corpName').val()) diff --git a/modules/CmpdReg/src/client/src/Salt.js b/modules/CmpdReg/src/client/src/Salt.js index 173754c09..6bce90060 100755 --- a/modules/CmpdReg/src/client/src/Salt.js +++ b/modules/CmpdReg/src/client/src/Salt.js @@ -184,7 +184,7 @@ $(function() { }); } else if (this.useKetcher) { - this.$('#newSaltMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/chemStructure/ketcher/"); + this.$('#newSaltMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/cmpdReg/ketcher/"); this.$('#newSaltMarvinSketch').on('load', function () { self.ketcher = self.$('#newSaltMarvinSketch')[0].contentWindow.ketcher; self.sketcherLoaded = true; @@ -281,6 +281,7 @@ $(function() { } else if (this.useKetcher) { mol = this.ketcher.getMolfile(); + if (mol.indexOf(" 0 0 0 0 0 999") > -1) mol = ''; gotMol(mol); } else { alert("No new salt sketcher configured"); diff --git a/modules/CmpdReg/src/client/src/SaltForm.js b/modules/CmpdReg/src/client/src/SaltForm.js index ba00fb573..c13080c71 100755 --- a/modules/CmpdReg/src/client/src/SaltForm.js +++ b/modules/CmpdReg/src/client/src/SaltForm.js @@ -302,7 +302,7 @@ $(function() { }); } else if (this.useKetcher) { - this.$('#saltFormMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/chemStructure/ketcher/"); + this.$('#saltFormMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/cmpdReg/ketcher/"); this.$('#saltFormMarvinSketch').on('load', function () { self.ketcher = self.$('#saltFormMarvinSketch')[0].contentWindow.ketcher; if (!self.sketcherLoaded) { diff --git a/modules/CmpdReg/src/client/src/SearchForm.js b/modules/CmpdReg/src/client/src/SearchForm.js index 4ad755312..67049e173 100755 --- a/modules/CmpdReg/src/client/src/SearchForm.js +++ b/modules/CmpdReg/src/client/src/SearchForm.js @@ -106,7 +106,7 @@ $(function() { }); } else if (this.useKetcher) { - this.$('#searchMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/chemStructure/ketcher/"); + this.$('#searchMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/cmpdReg/ketcher/"); this.$('#searchMarvinSketch').on('load', function () { self.ketcher = self.$('#searchMarvinSketch')[0].contentWindow.ketcher; }); @@ -159,6 +159,7 @@ $(function() { }); } else if (this.useKetcher) { mol = this.ketcher.getMolfile(); + if (mol.indexOf(" 0 0 0 0 0 999") > -1) mol = ''; var sf = this.makeSearchFormModel(mol); if (this.isValid()) { this.trigger('searchNext', sf); diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index b00d30f8a..6e952bb35 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -43,6 +43,10 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/cmpdReg/api/v1/parentServices/update/parent/metadata/jsonArray', loginRoutes.ensureAuthenticated, exports.updateParentsMetadata app.post '/cmpdReg/api/v1/lotServices/reparent/lot', loginRoutes.ensureAuthenticated, exports.reparentLot app.post '/cmpdReg/api/v1/lotServices/reparent/lot/jsonArray', loginRoutes.ensureAuthenticated, exports.reparentLots + app.get '/api/cmpdReg/ketcher/knocknock', loginRoutes.ensureAuthenticated, exports.ketcherKnocknock + app.get '/api/cmpdReg/ketcher/layout', loginRoutes.ensureAuthenticated, exports.ketcherConvertSmiles + app.post '/api/cmpdReg/ketcher/layout', loginRoutes.ensureAuthenticated, exports.ketcherLayout + app.post '/api/cmpdReg/ketcher/calculate_cip', loginRoutes.ensureAuthenticated, exports.ketcherCalculateCip exports.cmpdRegIndex = (req, res) -> scriptPaths = require './RequiredClientScripts.js' @@ -803,5 +807,97 @@ exports.reparentLots = (req, resp) -> resp.end "Error trying to reparent lot array: " + error; ) +exports.ketcherKnocknock = (req, resp) -> + resp.end "You are welcome!" - \ No newline at end of file +exports.ketcherConvertSmiles = (req, resp) -> + if global.specRunnerTestmode + resp.end "Ok.\n\n -INDIGO-06301717442D\n\n 4 3 0 0 0 0 0 0 0 0999 V2000\n -1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.7713 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 1 0 0 0 0\nM END\n" + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.cmpdReg.persistence.fullpath+"/structureServices/molconvert" + request = require 'request' + data = + structure: req.query.smiles + inputFormat: 'smiles' + request( + method: 'POST' + url: baseurl + body: data + json: true + , (error, response, json) => + console.log response + console.log json + if !error && response.statusCode == 200 + statusMessage = "Ok.\n" + resp.end statusMessage+json.structure + else + console.log 'got ajax error trying to convert smiles to MOL' + console.log error + console.log json + console.log response + resp.statusCode = 500 + resp.end JSON.stringify "Smiles to MOL conversion failed" + ) + +exports.ketcherLayout = (req, resp) -> + if global.specRunnerTestmode + resp.end "Ok.\n\n -INDIGO-06301717442D\n\n 4 3 0 0 0 0 0 0 0 0999 V2000\n -1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.7713 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 1 0 0 0 0\nM END\n" + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.cmpdReg.persistence.fullpath+"/structureServices/clean" + request = require 'request' + data = + structure: req.body.moldata + parameters: + dim: 2 + opts: "" + console.log data + request( + method: 'POST' + url: baseurl + body: data + json: true + , (error, response, json) => + console.log response + console.log json + if !error && response.statusCode == 200 + statusMessage = "Ok.\n" + resp.end statusMessage+json + else + console.log 'got ajax error trying to clean MOL' + console.log error + console.log json + console.log response + resp.statusCode = 500 + resp.end JSON.stringify "Cleaning MOL conversion failed" + ) + +exports.ketcherCalculateCip = (req, resp) -> + if global.specRunnerTestmode + resp.end "Ok.\n\n -INDIGO-06301717442D\n\n 4 3 0 0 0 0 0 0 0 0999 V2000\n -1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.7713 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 1 0 0 0 0\nM END\n" + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.cmpdReg.persistence.fullpath+"/structureServices/cipStereoInfo" + request = require 'request' + data = + structure: req.body.moldata + request( + method: 'POST' + url: baseurl + body: data + json: true + , (error, response, json) => + console.log response + console.log json + if !error && response.statusCode == 200 + statusMessage = "Ok.\n" + resp.end statusMessage+json + else + console.log 'got ajax error trying to calculate CIP stereo descriptors' + console.log error + console.log json + console.log response + resp.statusCode = 500 + resp.end JSON.stringify "CIP stereo descriptor calculation failed" + ) \ No newline at end of file From c8f7a1279e38f4d0ca649143ac88d78f98478495 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 12 Sep 2017 08:21:55 -0700 Subject: [PATCH 172/576] Minor bugfix to catch Roo error pages and throw an error from node rather than passing through error HTML page with 200 status code. --- modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index 6e952bb35..6c472b538 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -826,9 +826,7 @@ exports.ketcherConvertSmiles = (req, resp) -> body: data json: true , (error, response, json) => - console.log response - console.log json - if !error && response.statusCode == 200 + if !error && response.statusCode == 200 and json.indexOf('<') != 0 statusMessage = "Ok.\n" resp.end statusMessage+json.structure else @@ -859,9 +857,7 @@ exports.ketcherLayout = (req, resp) -> body: data json: true , (error, response, json) => - console.log response - console.log json - if !error && response.statusCode == 200 + if !error && response.statusCode == 200 and json.indexOf('<') != 0 statusMessage = "Ok.\n" resp.end statusMessage+json else @@ -890,7 +886,7 @@ exports.ketcherCalculateCip = (req, resp) -> , (error, response, json) => console.log response console.log json - if !error && response.statusCode == 200 + if !error && response.statusCode == 200 and json.indexOf('<') != 0 statusMessage = "Ok.\n" resp.end statusMessage+json else From 5fd7b453b6ec7d2e7b2a67b2e9f329d204034517 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Thu, 14 Sep 2017 11:20:25 -0700 Subject: [PATCH 173/576] bugfix/styling-RealTimeDeviceConnectionView: fix styling for RealTimeDeviceConnectionView --- .../Components/src/client/RealtimeDeviceConnectionView.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/Components/src/client/RealtimeDeviceConnectionView.html b/modules/Components/src/client/RealtimeDeviceConnectionView.html index 13bea854c..3c0273b07 100644 --- a/modules/Components/src/client/RealtimeDeviceConnectionView.html +++ b/modules/Components/src/client/RealtimeDeviceConnectionView.html @@ -3,10 +3,10 @@ Not connected to the server....
      -

      Tare Single Vial

      +

      Tare Single Vial

      -
      +
      -
      +
      From 7afc5c7dba4b7f53923c08b213ed3cd07d6c2b0c Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 15 Sep 2017 17:38:55 -0700 Subject: [PATCH 174/576] ACASLabelSequences: Added whole new module with successful saving of LabelSequences to ACAS Roo, along with attached roles. Much code copied from Project, still needs cleanup. Added many associated routes for CRUD, and routes for getting LsRoles, labelTypeAndKinds, and thingTypeAndKinds as codetables. Also added route for getting available labelSequences authorized for request user, which can be further filtered by labelTypeAndKind and thingTypeAndKind. CmpdReg Node Server: Added ConfJSON with default thing types and thing kinds for CmpdReg Label Sequences. Refactored require statements in CmpdRegRoutes. Added getAuthorizedPrefixes route which gets authorized labelSequences and then reformats into codetable format to be fed to a picklist. CmpdReg client: Added "Prefix" to the MetaLot page, controlled by the corpParentFormat config. Added corresponding "labelPrefix" attribute to the Parent client object, which is now understood by the Roo server. Prefix field is only visible when creating new parent. Otherwise, should be apparent from the corporate ID. --- .../ACASLabelSequencesTestJSON.coffee | 67 +++ .../src/client/ACASLabelSequences.coffee | 493 ++++++++++++++++++ .../src/client/ACASLabelSequences.css | 4 + .../src/client/ACASLabelSequencesView.html | 71 +++ .../routes/ACASLabelSequencesRoutes.coffee | 220 ++++++++ modules/CmpdReg/conf/CmpdRegConfJSON.coffee | 25 + .../src/client/css/NewCmpdReg_nocompile.css | 4 + modules/CmpdReg/src/client/src/Parent.js | 15 +- .../client/templates/LotForm/ParentView.inc | 5 + .../src/server/routes/CmpdRegRoutes.coffee | 86 +-- .../client/ModuleMenusConfiguration.coffee | 5 + 11 files changed, 931 insertions(+), 64 deletions(-) create mode 100644 modules/ACASLabelSequences/spec/testFixtures/ACASLabelSequencesTestJSON.coffee create mode 100644 modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee create mode 100644 modules/ACASLabelSequences/src/client/ACASLabelSequences.css create mode 100644 modules/ACASLabelSequences/src/client/ACASLabelSequencesView.html create mode 100644 modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee create mode 100644 modules/CmpdReg/conf/CmpdRegConfJSON.coffee diff --git a/modules/ACASLabelSequences/spec/testFixtures/ACASLabelSequencesTestJSON.coffee b/modules/ACASLabelSequences/spec/testFixtures/ACASLabelSequencesTestJSON.coffee new file mode 100644 index 000000000..58e7d7bf9 --- /dev/null +++ b/modules/ACASLabelSequences/spec/testFixtures/ACASLabelSequencesTestJSON.coffee @@ -0,0 +1,67 @@ +((exports) -> + exports.labelSequence = + dbSequence: "labelseq_PROJ_id_codeName_project_project" + digits: 8 + groupDigits: false + id: 10 + ignored: false + labelPrefix: "PROJ" + labelSeparator: "-" + labelSequenceRoles: [ + id: 1 + roleEntry: + id: 2 + lsKind: "ACAS" + lsType: "System" + lsTypeAndKind: "System_ACAS" + roleDescription: "ROLE_ACAS-ADMINS autocreated by ACAS" + roleName: "ROLE_ACAS-ADMINS" + version: 0 + version: 0 + + ] + labelTypeAndKind: "id_codeName" + startingNumber: 0 + thingTypeAndKind: "project_project" + version: 0 + + exports.labelSequenceArray = [ + dbSequence: "labelseq_PROJ_id_codeName_project_project" + digits: 8 + groupDigits: false + id: 10 + ignored: false + labelPrefix: "PROJ" + labelSeparator: "-" + labelSequenceRoles: [ + id: 1 + roleEntry: + id: 2 + lsKind: "ACAS" + lsType: "System" + lsTypeAndKind: "System_ACAS" + roleDescription: "ROLE_ACAS-ADMINS autocreated by ACAS" + roleName: "ROLE_ACAS-ADMINS" + version: 0 + version: 0 + ] + labelTypeAndKind: "id_codeName" + startingNumber: 0 + thingTypeAndKind: "project_project" + version: 0 + , + dbSequence: "labelseq_PROT_id_codeName_document_protocol" + digits: 8 + groupDigits: false + id: 11 + ignored: false + labelPrefix: "PROT" + labelSeparator: "-" + labelSequenceRoles: [] + labelTypeAndKind: "id_codeName" + startingNumber: 0 + thingTypeAndKind: "document_protocol" + version: 0 + ] + +) (if (typeof process is "undefined" or not process.versions) then window.labelSequenceTestJSON = window.labelSequenceTestJSON or {} else exports) diff --git a/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee new file mode 100644 index 000000000..5e6b4155e --- /dev/null +++ b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee @@ -0,0 +1,493 @@ +#MODELS +class window.ACASLabelSequenceRole extends Backbone.Model + +class window.ACASLabelSequenceRoleList extends Backbone.Collection + model: ACASLabelSequenceRole + + validateCollection: => + modelErrors = [] + usedRoles={} + if @.length != 0 + for index in [0..@.length-1] + model = @.at(index) + if model.get('lsRole')? and model.get('lsRole').get('id')? + currentRole = model.get('lsRole').get('id') + else + currentRole = null + if currentRole of usedRoles + modelErrors.push + attribute: 'role:eq('+index+')' + message: "The same lsRole can not be chosen more than once" + modelErrors.push + attribute: 'role:eq('+usedRoles[currentRole]+')' + message: "The same lsRole can not be chosen more than once" + else + usedRoles[currentRole] = index + modelErrors + +class window.ACASLabelSequence extends Backbone.Model + url: "/api/labelsequences/" + defaults: + labelPrefix: "" + startingNumber: null + digits: null + labelSeparator: null + labelTypeAndKind: null + thingTypeAndKind: null + labelSequenceRoles: [] + + validate: (attrs) -> + errors = [] + if attrs.labelPrefix is "" or attrs.labelPrefix is undefined + errors.push + attribute: 'labelPrefix' + message: "Label prefix must be set" + if isNaN(attrs.startingNumber) or attrs.startingNumber is undefined + errors.push + attribute: 'startingNumber' + message: "Starting Number must set and be a number" + if isNaN(attrs.digits) or attrs.digits is undefined + errors.push + attribute: 'digits' + message: "Number of digits must set and be a number" + #TODO: Add more validation + if errors.length > 0 + return errors + else + return null + + getLsRoles: => + @get('labelSequenceRoles') + + isEditable: -> + return false + +class window.ACASLabelSequenceList extends Backbone.Collection + model: ACASLabelSequence + +#CONTROLLERS +class window.ACASLabelSequenceRoleController extends AbstractFormController + template: _.template($("#ACASLabelSequenceRoleView").html()) + tagName: "div" + + events: -> + "change .bv_role": "updateModel" + "click .bv_deleteLabelSequenceRole": "clear" + + initialize: -> + @errorOwnerName = 'ProjectLeaderController' + @setBindings() + @model.on "destroy", @remove, @ + + render: => + $(@el).empty() + $(@el).html @template(@model.attributes) + @setupRoleSelect() + + @ + + setupRoleSelect: -> + @roleList = new PickListList() + @roleList.url = "/api/lsRoles/codeTable" + @roleListController = new PickListSelectController + el: @$('.bv_role') + collection: @roleList + insertFirstOption: new PickList + code: "unassigned" + name: "Select Role" + selectedCode: @model.get('lsRole') + + updateModel: => + role = @roleListController.getSelectedModel() + if @model.get('id')? + newModel = new ACASLabelSequenceRole + lsRole: role + @model.set "ignored", true + @$('.bv_labelSequenceRoleWrapper').hide() + @trigger 'addNewModel', newModel + else + @model.set + lsRole: role + @trigger 'amDirty' + + clear: => + if @model.get('id')? + @model.set "ignored", true + @$('.bv_labelSequenceRoleWrapper').hide() + else + @model.destroy() + @trigger 'amDirty' + +class window.ACASLabelSequenceRoleListController extends Backbone.View + template: _.template($("#ACASLabelSequenceRoleListView").html()) + + events: + "click .bv_addLabelSequenceRoleButton": "addNewLabelSequenceRole" + + initialize: -> + unless @collection? + @collection = new ACASLabelSequenceRoleList() + newModel = new ACASLabelSequenceRole + @collection.add newModel + + render: => + $(@el).empty() + $(@el).html @template() + + @collection.each (leaderInfo) => + @addProjectLeader(leaderInfo) + if @collection.length == 0 + @addNewLabelSequenceRole() + @trigger 'renderComplete' + @ + + addNewLabelSequenceRole: => + newModel = new ACASLabelSequenceRole + @collection.add newModel + @addLabelSequenceRole(newModel) + @trigger 'amDirty' + + addLabelSequenceRole: (roleInfo) => + labelSeqRoleController = new ACASLabelSequenceRoleController + model: roleInfo + labelSeqRoleController.on 'addNewModel', (newModel) => + @collection.add newModel + @addLabelSequenceRole newModel + labelSeqRoleController.on 'amDirty', => + @trigger 'amDirty' + @$('.bv_labelSequenceRoleInfo').append labelSeqRoleController.render().el + + isValid: => + validCheck = true + errors = @collection.validateCollection() + if errors.length > 0 + validCheck = false + @validationError(errors) + validCheck + + validationError: (errors) => + @clearValidationErrorStyles() + _.each errors, (err) => + unless @$('.bv_'+err.attribute).attr('disabled') is 'disabled' + @$('.bv_group_'+err.attribute).attr('data-toggle', 'tooltip') + @$('.bv_group_'+err.attribute).attr('data-placement', 'bottom') + @$('.bv_group_'+err.attribute).attr('data-original-title', err.message) + # @$('.bv_group_'+err.attribute).tooltip(); + @$("[data-toggle=tooltip]").tooltip(); + @$("body").tooltip selector: '.bv_group_'+err.attribute + @$('.bv_group_'+err.attribute).addClass 'input_error error' + @trigger 'notifyError', owner: this.errorOwnerName, errorLevel: 'error', message: err.message + + clearValidationErrorStyles: => + errorElms = @$('.input_error') + _.each errorElms, (ee) => + $(ee).removeAttr('data-toggle') + $(ee).removeAttr('data-placement') + $(ee).removeAttr('title') + $(ee).removeAttr('data-original-title') + $(ee).removeClass 'input_error error' + +class window.ACASLabelSequenceController extends AbstractFormController + template: _.template($("#ACASLabelSequenceView").html()) + moduleLaunchName: "acasLabelSequence" + + events: -> + "keyup .bv_labelPrefix": "attributeChanged" + "keyup .bv_startingNumber": "attributeChanged" + "keyup .bv_digits": "attributeChanged" + "keyup .bv_labelSeparator": "attributeChanged" + "change .bv_labelTypeAndKind": "attributeChanged" + "change .bv_thingTypeAndKind": "attributeChanged" + "click .bv_save": "handleSaveClicked" + "click .bv_cancel": "handleCancelClicked" + + initialize: -> + if @model? + @completeInitialization() + else + if window.AppLaunchParams.moduleLaunchParams? + if window.AppLaunchParams.moduleLaunchParams.moduleName == @moduleLaunchName + $.ajax + type: 'GET' + url: "/api/projects" + dataType: 'json' + error: (err) => + alert 'Could not get projects for this user. Creating a new project' + @completeInitialization() + success: (projectsList) => + if _.where(projectsList, {code: window.AppLaunchParams.moduleLaunchParams.code}).length > 0 + @getACASLabelSequence() + else + alert 'Could not get project for code in this URL, creating new one' + @completeInitialization() + else + @completeInitialization() + else + @completeInitialization() + + attributeChanged: => + super() + @updatePreview() + + updatePreview: => + prefix = @model.get('labelPrefix') + firstNum = @model.get('startingNumber') + numDigits = @model.get('digits') + labelSep = @model.get('labelSeparator') + previewLabel = prefix + labelSep + firstNum.toString().padStart(numDigits, '0') + $('.bv_labelPreview').val previewLabel + + getACASLabelSequence: => + $.ajax + type: 'GET' + url: "/api/labelsequences/"+window.AppLaunchParams.moduleLaunchParams.code + dataType: 'json' + error: (err) => + alert 'Could not get project for code in this URL, creating new one' + @completeInitialization() + success: (json) => + if json.length == 0 + alert 'Could not get project for code in this URL, creating new one' + else + proj = new ACASLabelSequence json + proj.set proj.parse(proj.attributes) + @model = proj + @completeInitialization() + + + completeInitialization: => + unless @model? + @model=new ACASLabelSequence() + @errorOwnerName = 'ACASLabelSequenceController' + @setBindings() + if @options.readOnly? + @readOnly = @options.readOnly + else + @readOnly = false + @listenTo @model, 'saveFailed', @handleSaveFailed + @listenTo @model, 'sync', @modelSaveCallback + @listenTo @model, 'change', @modelChangeCallback + $(@el).empty() + $(@el).html @template(@model.attributes) + @setupACASLabelSequenceRoleListController() + @setupLabelTypeAndKindSelect() + @setupThingTypeAndKindSelect() + @render() + + render: => + unless @model? + @model = new ACASLabelSequence() + #TODO + #@$('.bv_shortDescription').val @model.get('short description').get('value') + if @readOnly is true + @displayInReadOnlyMode() + @$('.bv_save').attr('disabled','disabled') + @$('.bv_cancel').attr('disabled','disabled') + if @model.isNew() + @$('.bv_save').html("Save") + @$('.bv_newEntity').hide() + else + @$('.bv_save').html("Update") + @$('.bv_newEntity').show() + @ + + handleSaveFailed: => + @$('.bv_saveFailed').show() + @$('.bv_saveComplete').hide() + @$('.bv_saving').hide() + + modelSaveCallback: (method, model) => + @$('.bv_save').show() + @$('.bv_save').attr('disabled', 'disabled') + unless @$('.bv_saveFailed').is(":visible") + @$('.bv_saveComplete').show() + @$('.bv_saving').hide() + @setupACASLabelSequenceRoleListController() + @render() + @trigger 'amClean' + + modelChangeCallback: (method, model) => + @trigger 'amDirty' + @checkFormValid() + @$('.bv_saveComplete').hide() + @$('.bv_saveFailed').hide() + @$('.bv_cancel').removeAttr('disabled') + @$('.bv_cancelComplete').hide() + + setupACASLabelSequenceRoleListController: -> + if @acasLabelSequenceRoleListController? + @acasLabelSequenceRoleListController.undelegateEvents() + + rolesList = new ACASLabelSequenceRoleList() + roles = @model.getLsRoles() + _.each roles, (role) => + newModel = new ACASLabelSequenceRole role.attributes + newModel.set 'lsRole', role + rolesList.add newModel + + @acasLabelSequenceRoleListController= new ACASLabelSequenceRoleListController + el: @$('.bv_acasLabelSequenceRoleList') + collection: rolesList + @acasLabelSequenceRoleListController.on 'amClean', => + @trigger 'amClean' + @acasLabelSequenceRoleListController.on 'renderComplete', => + @checkDisplayMode() + @acasLabelSequenceRoleListController.render() + @acasLabelSequenceRoleListController.on 'amDirty', => + @trigger 'amDirty' + @$('.bv_saveComplete').hide() + @$('.bv_saveFailed').hide() + @checkFormValid() + + setupLabelTypeAndKindSelect: -> + @labelTypeAndKindList = new PickListList() + @labelTypeAndKindList.url = "/api/labelTypeAndKinds/codetable" + @labelTypeAndKindListController = new PickListSelectController + el: @$('.bv_labelTypeAndKind') + collection: @labelTypeAndKindList + insertFirstOption: new PickList + code: "unassigned" + name: "Select Label Type And Kind" + selectedCode: @model.get('labelTypeAndKind') + + setupThingTypeAndKindSelect: -> + @thingTypeAndKindList = new PickListList() + @thingTypeAndKindList.url = "/api/thingTypeAndKinds/codetable" + @thingTypeAndKindListController = new PickListSelectController + el: @$('.bv_thingTypeAndKind') + collection: @thingTypeAndKindList + insertFirstOption: new PickList + code: "unassigned" + name: "Select Thing Type And Kind" + selectedCode: @model.get('thingTypeAndKind') + + updateEditable: => + if @model.isEditable() + if UtilityFunctions::testUserHasRoleTypeKindName(window.AppLaunchParams.loginUser, [@adminRole]) or UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, [window.conf.roles.acas.adminRole]) + @enableAllInputs() + @$('.bv_projectCode').attr 'disabled', 'disabled' + @$('.bv_manageUserPermissions').show() + @$('.bv_saveBeforeManagingPermissions').hide() + else + @enableLimitedEditing() + @$('.bv_manageUserPermissions').hide() + else + @disableAllInputs() + @$('.bv_newEntity').removeAttr('disabled') + if UtilityFunctions::testUserHasRoleTypeKindName(window.AppLaunchParams.loginUser, [@adminRole]) or UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, [window.conf.roles.acas.adminRole]) + @$('.bv_manageUserPermissions').show() + else + @$('.bv_manageUserPermissions').hide() + @$('.bv_status').attr 'disabled', 'disabled' #for now, don't allow status editing + + enableLimitedEditing: -> + @disableAllInputs() + @$('.bv_shortDescription').removeAttr 'disabled' + @$('.bv_projectDetails').removeAttr 'disabled' + @$('.bv_fileType').removeAttr 'disabled' + @$('button').removeAttr 'disabled' + @$('.bv_deleteProjectLeader').attr 'disabled', 'disabled' + @$('.bv_addProjectLeaderButton').attr 'disabled', 'disabled' + + handleCancelClicked: => + if @model.isNew() + @model = null + @completeInitialization() + else + @$('.bv_canceling').show() + @model.fetch + success: @handleCancelComplete + @trigger 'amClean' + + handleCancelComplete: => + @$('.bv_canceling').hide() + @$('.bv_cancelComplete').show() + + updateModel: => + @model.set("labelPrefix", UtilityFunctions::getTrimmedInput @$('.bv_labelPrefix')) + @model.set("startingNumber", UtilityFunctions::getTrimmedInput @$('.bv_startingNumber')) + @model.set("digits", UtilityFunctions::getTrimmedInput @$('.bv_digits')) + @model.set("labelSeparator", UtilityFunctions::getTrimmedInput @$('.bv_labelSeparator')) + @model.set("labelTypeAndKind", UtilityFunctions::getTrimmedInput @$('.bv_labelTypeAndKind')) + @model.set("thingTypeAndKind", UtilityFunctions::getTrimmedInput @$('.bv_thingTypeAndKind')) + + prepareToSaveLabelSequenceRoles: => + reformattedLabelSequenceRoles = [] + @acasLabelSequenceRoleListController.collection.each (labelSequenceRoleModel) => + console.log labelSequenceRoleModel + if labelSequenceRoleModel.get('lsRole')?.get('id')? + labelSequenceRole = + roleEntry: {id: labelSequenceRoleModel.get('lsRole').get('id')} + reformattedLabelSequenceRoles.push labelSequenceRole + @model.set('labelSequenceRoles', reformattedLabelSequenceRoles) + + handleSaveClicked: => + @saveLabelSequence() + @$('.bv_saving').show() + @$('.bv_saveFailed').hide() + @$('.bv_saveComplete').hide() + + saveLabelSequence: => +# @model.prepareToSave() + @prepareToSaveLabelSequenceRoles() + console.log @model + if @model.isNew() + @$('.bv_saveComplete').html('Save Complete') + else + @$('.bv_saveComplete').html('Update Complete') + @$('.bv_save').attr('disabled', 'disabled') + if @model.isNew() + @model.save null, + success: (model, response) => + if response is "update lsThing failed" + @model.trigger 'saveFailed' + else + @modelSaveCallback + + else + if UtilityFunctions::testUserHasRoleTypeKindName(window.AppLaunchParams.loginUser, [@adminRole]) or UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, [window.conf.roles.acas.adminRole]) + @updateProjectRoles() + else + @model.save null, + success: (model, response) => + if response is "update lsThing failed" + @model.trigger 'saveFailed' + else + @modelSaveCallback + error: (err) => + @model.trigger 'saveFailed' + + validationError: => + super() + @$('.bv_save').attr('disabled', 'disabled') + + clearValidationErrorStyles: => + super() + @$('.bv_save').removeAttr('disabled') + + checkDisplayMode: => + if @readOnly is true + @displayInReadOnlyMode() + + displayInReadOnlyMode: => + @$(".bv_save").hide() + @$(".bv_cancel").hide() + @$(".bv_newEntity").hide() + @$('button').attr 'disabled', 'disabled' + @$(".bv_startDateIcon").addClass "uneditable-input" + @$(".bv_startDateIcon").on "click", -> + return false + @disableAllInputs() + + checkFormValid: => + if @isValid() + @$('.bv_save').removeAttr('disabled') + else + @$('.bv_save').attr('disabled', 'disabled') + + isValid: => + validCheck = super() + if @acasLabelSequenceRoleListController? + if @acasLabelSequenceRoleListController.isValid() is false + validCheck = false + validCheck diff --git a/modules/ACASLabelSequences/src/client/ACASLabelSequences.css b/modules/ACASLabelSequences/src/client/ACASLabelSequences.css new file mode 100644 index 000000000..c2e818edc --- /dev/null +++ b/modules/ACASLabelSequences/src/client/ACASLabelSequences.css @@ -0,0 +1,4 @@ +.bv_acasLabelSequenceForm .form-control{ + width: 330px; + margin-left: 20px; +} \ No newline at end of file diff --git a/modules/ACASLabelSequences/src/client/ACASLabelSequencesView.html b/modules/ACASLabelSequences/src/client/ACASLabelSequencesView.html new file mode 100644 index 000000000..9f309f874 --- /dev/null +++ b/modules/ACASLabelSequences/src/client/ACASLabelSequencesView.html @@ -0,0 +1,71 @@ + + + + + + \ No newline at end of file diff --git a/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee b/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee new file mode 100644 index 000000000..5c18d75c3 --- /dev/null +++ b/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee @@ -0,0 +1,220 @@ +exports.setupAPIRoutes = (app) -> + app.get '/api/labelSequences', exports.getAllLabelSequences + app.get '/api/labelSequences/reagents/codename', exports.getReagentByCodename + +exports.setupRoutes = (app, loginRoutes) -> + app.get '/api/labelSequences', loginRoutes.ensureAuthenticated, exports.getAllLabelSequences + app.get '/api/labelSequences/getAuthorizedLabelSequences', loginRoutes.ensureAuthenticated, exports.getAuthorizedLabelSequences + app.get '/api/labelSequences/:id', loginRoutes.ensureAuthenticated, exports.getLabelSequenceById + app.post '/api/labelSequences', loginRoutes.ensureAuthenticated, exports.saveLabelSequence + app.post '/api/labelSequences/jsonArray', loginRoutes.ensureAuthenticated, exports.saveLabelSequenceArray + app.put '/api/labelSequences/:id', loginRoutes.ensureAuthenticated, exports.updateLabelSequence + app.put '/api/labelSequences/jsonArray', loginRoutes.ensureAuthenticated, exports.updateLabelSequenceArray + app.delete '/api/labelSequences/:id', loginRoutes.ensureAuthenticated, exports.deleteLabelSequence + app.get '/api/lsRoles/codeTable', loginRoutes.ensureAuthenticated, exports.getLsRoleCodeTables + app.get '/api/labelTypeAndKinds/codeTable', loginRoutes.ensureAuthenticated, exports.getLabelTypeAndKindCodeTables + app.get '/api/thingTypeAndKinds/codeTable', loginRoutes.ensureAuthenticated, exports.getThingTypeAndKindCodeTables + +config = require '../conf/compiled/conf.js' +request = require 'request' +serverUtilityFunctions = require './ServerUtilityFunctions.js' +_ = require 'underscore' + +exports.getAllLabelSequences = (req, resp) -> + exports.getAllLabelSequencesInternal req, (statusCode, json) -> + resp.json json + +exports.getAllLabelSequencesInternal = (req, callback) -> + if global.specRunnerTestmode + labelSequenceTestJSON = require '../public/javascripts/spec/testFixtures/ACASLabelSequenceTestJSON.js' + callback labelSequenceTestJSON.labelSequenceArray + else + baseurl = config.all.client.service.persistence.fullpath+"labelsequences" + if req.query?.thingTypeAndKind? and req.query?.labelTypeAndKind? + baseurl += "?thingTypeAndKind=#{req.query.thingTypeAndKind}&labelTypeAndKind=#{req.query.labelTypeAndKind}" + else if req.query?.thingTypeAndKind? + baseurl += "?thingTypeAndKind=#{req.query.thingTypeAndKind}" + else if req.query?.labelTypeAndKind? + baseurl += "?labelTypeAndKind=#{req.query.labelTypeAndKind}" + serverUtilityFunctions.getFromACASServerInternal(baseurl, callback) + +exports.getAuthorizedLabelSequences = (req, resp) -> + exports.getAuthorizedLabelSequencesInternal req, (statusCode, json) -> + resp.json json + +exports.getAuthorizedLabelSequencesInternal = (req, callback) -> + if global.specRunnerTestmode + labelSequenceTestJSON = require '../public/javascripts/spec/testFixtures/ACASLabelSequenceTestJSON.js' + callback labelSequenceTestJSON.labelSequenceArray + else + username = req.session.passport.user.username + baseurl = config.all.client.service.persistence.fullpath+"labelsequences/getAuthorizedLabelSequences?userName=#{username}" + if req.query?.thingTypeAndKind? + baseurl += "&thingTypeAndKind=#{req.query.thingTypeAndKind}" + if req.query?.labelTypeAndKind? + baseurl += "&labelTypeAndKind=#{req.query.labelTypeAndKind}" + serverUtilityFunctions.getFromACASServerInternal(baseurl, callback) + +exports.getLabelSequenceById = (req, resp) -> + if global.specRunnerTestmode + labelSequenceTestJSON = require '../public/javascripts/spec/testFixtures/ACASLabelSequenceTestJSON.js' + resp.json labelSequenceTestJSON.labelSequence + else + baseurl = config.all.client.service.persistence.fullpath+"labelsequences/#{req.params.id}" + serverUtilityFunctions.getFromACASServer(baseurl, resp) + +exports.saveLabelSequence = (req, resp) -> + if global.specRunnerTestmode + labelSequenceTestJSON = require '../public/javascripts/spec/testFixtures/ACASLabelSequenceTestJSON.js' + resp.json labelSequenceTestJSON.labelSequence + else + console.log req.body + baseurl = config.all.client.service.persistence.fullpath+"labelsequences" + request( + method: 'POST' + url: baseurl + body: req.body + json: true + , (error, response, json) => + console.log json + if !error && response.statusCode == 201 + resp.json json + else + console.error 'got ajax error trying to save label sequence' + resp.statusCode = 500 + resp.end "saveFailed" + ) + +exports.saveLabelSequenceArray = (req, resp) -> + if global.specRunnerTestmode + labelSequenceTestJSON = require '../public/javascripts/spec/testFixtures/ACASLabelSequenceTestJSON.js' + resp.json labelSequenceTestJSON.labelSequenceArray + else + baseurl = config.all.client.service.persistence.fullpath+"labelsequences/jsonArray" + request( + method: 'POST' + url: baseurl + body: req.body + json: true + , (error, response, json) => + if !error && response.statusCode == 201 + resp.json json + else + console.error 'got ajax error trying to save label sequence array' + resp.end "saveFailed" + ) + +exports.updateLabelSequence = (req, resp) -> + if global.specRunnerTestmode + labelSequenceTestJSON = require '../public/javascripts/spec/testFixtures/ACASLabelSequenceTestJSON.js' + resp.json labelSequenceTestJSON.labelSequence + else + baseurl = config.all.client.service.persistence.fullpath+"labelsequences" + request( + method: 'PUT' + url: baseurl + body: req.body + json: true + , (error, response, json) => + if !error && response.statusCode == 200 + resp.json json + else + console.error 'got ajax error trying to update label sequence' + resp.end "updateFailed" + ) + +exports.updateLabelSequenceArray = (req, resp) -> + if global.specRunnerTestmode + labelSequenceTestJSON = require '../public/javascripts/spec/testFixtures/ACASLabelSequenceTestJSON.js' + resp.json labelSequenceTestJSON.labelSequenceArray + else + baseurl = config.all.client.service.persistence.fullpath+"labelsequences/jsonArray" + request( + method: 'PUT' + url: baseurl + body: req.body + json: true + , (error, response, json) => + if !error && response.statusCode == 200 + resp.json json + else + console.error 'got ajax error trying to update label sequence array' + resp.end "updateFailed" + ) + +exports.deleteLabelSequence = (req, resp) -> + if global.specRunnerTestmode + resp.end 'stub delete complete' + else + baseurl = config.all.client.service.persistence.fullpath+"labelsequences/#{req.params.id}" + request( + method: 'DELETE' + url: baseurl + json: true + , (error, response, json) => + if !error && response.statusCode == 200 + resp.end 'delete successful' + else + console.error 'Unable to delete label sequence' + resp.statusCode = 404 + resp.end "deleted failed" + ) + +exports.getLsRoleCodeTables = (req, resp) -> + if global.specRunnerTestmode + resp.end 'TODO' + else + baseurl = config.all.client.service.persistence.fullpath+"lsRoles?format=codeTable" + if req.query.lsType? + baseurl += "&lsType=#{lsType}" + if req.query.lsKind? + baseurl += "&lsKind=#{lsKind}" + serverUtilityFunctions.getFromACASServer(baseurl, resp) + +exports.getLabelTypeAndKindCodeTables = (req, resp) -> + if global.specRunnerTestmode + resp.end 'TODO' + else + baseurl = config.all.client.service.persistence.fullpath+"labelkinds" + request( + url: baseurl + json: true + , (error, response, json) -> + if !error && response.statusCode == 200 + codeTables = [] + _.each json, (kind) -> + codeTable = + id: kind.id + code: kind.lsTypeAndKind + name: kind.lsTypeAndKind + codeTables.push codeTable + resp.json codeTables + else + console.error 'error getting labelKinds' + resp.statusCode = 404 + resp.end 'could not get labelKinds' + ) + +exports.getThingTypeAndKindCodeTables = (req, resp) -> + if global.specRunnerTestmode + resp.end 'TODO' + else + baseurl = config.all.client.service.persistence.fullpath+"thingkinds" + request( + url: baseurl + json: true + , (error, response, json) -> + if !error && response.statusCode == 200 + codeTables = [] + _.each json, (kind) -> + codeTable = + id: kind.id + code: kind.lsTypeAndKind + name: kind.lsTypeAndKind + codeTables.push codeTable + resp.json codeTables + else + console.error 'error getting thingKinds' + resp.statusCode = 404 + resp.end 'could not get thingKinds' + ) \ No newline at end of file diff --git a/modules/CmpdReg/conf/CmpdRegConfJSON.coffee b/modules/CmpdReg/conf/CmpdRegConfJSON.coffee new file mode 100644 index 000000000..e71bb94f4 --- /dev/null +++ b/modules/CmpdReg/conf/CmpdRegConfJSON.coffee @@ -0,0 +1,25 @@ +((exports) -> + exports.typeKindList = + thingtypes: + [ + typeName: "parent" + ] + + thingkinds: + [ + typeName: "parent" + kindName: "compound" + ] + + labeltypes: + [ + typeName: "id" + ] + + labelkinds: + [ + typeName: "id" + kindName: "corpName" + ] + +) (if (typeof process is "undefined" or not process.versions) then window.cmpdRegConfJSON = window.cmpdRegConfJSON or {} else exports) diff --git a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css index 0715a7810..c6a1cb43d 100755 --- a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css +++ b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css @@ -832,6 +832,10 @@ div { margin-left: 30px !important; } +.LotForm_ParentView .parentStructureForm .bv_labelPrefix { + font-size: 18 !important; +} + .LotForm_ParentView .parentComments { width:800px; } diff --git a/modules/CmpdReg/src/client/src/Parent.js b/modules/CmpdReg/src/client/src/Parent.js index 43d88753e..c9590f5c3 100755 --- a/modules/CmpdReg/src/client/src/Parent.js +++ b/modules/CmpdReg/src/client/src/Parent.js @@ -11,7 +11,8 @@ $(function() { comment: '', corpName: '', chemist: null, - isMixture: false + isMixture: false, + labelPrefix: null }, initialize: function() { @@ -188,6 +189,15 @@ $(function() { this.$('.bv_parentAnnotationContainer').hide(); } + if (this.model.isNew() && window.configuration.serverSettings.corpParentFormat != null && window.configuration.serverSettings.corpParentFormat == 'ACASLabelSequence') { + var optionToInsert = null; + this.labelPrefixCodeController = + this.setupCodeController('labelPrefix', 'labelPrefixes', 'labelPrefix', optionToInsert); + + } else { + this.$('.bv_labelPrefix').hide(); + } + this.$('.stereoComment').val(this.model.get('stereoComment')); this.$('.comment').val(this.model.get('comment')); //this.$('.commonName').val(this.model.get('commonName')); @@ -279,6 +289,9 @@ $(function() { if(this.parentAnnotationCodeController != null){ this.model.set({parentAnnotation: this.parentAnnotationCodeController.getSelectedModel()}) }; + if (this.labelPrefixCodeController != null){ + this.model.set({labelPrefix: this.labelPrefixCodeController.getSelectedModel()}) + }; }, editParent: function() { var self = this; diff --git a/modules/CmpdReg/src/client/templates/LotForm/ParentView.inc b/modules/CmpdReg/src/client/templates/LotForm/ParentView.inc index 759db4c55..4a712e54b 100755 --- a/modules/CmpdReg/src/client/templates/LotForm/ParentView.inc +++ b/modules/CmpdReg/src/client/templates/LotForm/ParentView.inc @@ -28,6 +28,11 @@ Is Mixture
      +
      + + +
      +
      diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index 0fbf56733..228f27eb9 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -43,12 +43,15 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/cmpdReg/api/v1/parentServices/update/parent/metadata/jsonArray', loginRoutes.ensureAuthenticated, exports.updateParentsMetadata app.post '/cmpdReg/api/v1/lotServices/reparent/lot', loginRoutes.ensureAuthenticated, exports.reparentLot app.post '/cmpdReg/api/v1/lotServices/reparent/lot/jsonArray', loginRoutes.ensureAuthenticated, exports.reparentLots - + app.get '/cmpdReg/labelPrefixes', loginRoutes.ensureAuthenticated, exports.getAuthorizedPrefixes + +_ = require 'underscore' +request = require 'request' +config = require '../conf/compiled/conf.js' + exports.cmpdRegIndex = (req, res) -> scriptPaths = require './RequiredClientScripts.js' - config = require '../conf/compiled/conf.js' cmpdRegConfig = require '../public/CmpdReg/client/custom/configuration.json' - _ = require 'underscore' grantedRoles = _.map req.user.roles, (role) -> role.roleEntry.roleName console.log grantedRoles @@ -94,9 +97,6 @@ exports.cmpdRegIndex = (req, res) -> cmpdRegConfig: cmpdRegConfig syncCmpdRegUser = (req, cmpdRegUser) -> - request = require 'request' - config = require '../conf/compiled/conf.js' - _ = require "underscore" exports.getScientists req, (scientistResponse) -> foundScientists = JSON.parse scientistResponse if (_.findWhere foundScientists, {code: cmpdRegUser.code})? @@ -118,8 +118,6 @@ syncCmpdRegUser = (req, cmpdRegUser) -> exports.saveScientists [cmpdRegUser], (saveScientistsResponse) -> exports.getBasicCmpdReg = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' console.log 'in getBasicCmpdReg' console.log req.originalUrl endOfUrl = (req.originalUrl).replace /\/cmpdreg\//, "" @@ -133,7 +131,6 @@ exports.getAuthorizedCmpdRegProjects = (req, resp) -> resp.end JSON.stringify response exports.getAuthorizedCmpdRegProjectsInternal = (req, callback) -> - _ = require "underscore" exports.getACASProjects req, (statusCode, acasProjectsResponse)-> acasProjects = acasProjectsResponse exports.getProjects req, (cmpdRegProjectsResponse)-> @@ -155,8 +152,6 @@ exports.getACASProjects = (req, callback) -> csUtilities.getProjectsInternal req, callback exports.getProjects = (req, callback) -> - request = require 'request' - config = require '../conf/compiled/conf.js' console.log 'in getProjects' cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + "/projects" request( @@ -176,8 +171,7 @@ exports.getProjects = (req, callback) -> ) exports.saveProjects = (jsonBody, callback) -> - request = require 'request' - config = require '../conf/compiled/conf.js' + console.log 'in saveProjects' cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + "/projects/jsonArray" request( @@ -198,8 +192,6 @@ exports.saveProjects = (jsonBody, callback) -> ) exports.updateProjects = (jsonBody, callback) -> - request = require 'request' - config = require '../conf/compiled/conf.js' console.log 'in updateProjects' cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + "/projects/jsonArray" request( @@ -220,8 +212,6 @@ exports.updateProjects = (jsonBody, callback) -> ) exports.getScientists = (req, callback) -> - request = require 'request' - config = require '../conf/compiled/conf.js' console.log 'in getScientists' cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + "/scientists" request( @@ -241,8 +231,6 @@ exports.getScientists = (req, callback) -> ) exports.saveScientists = (jsonBody, callback) -> - request = require 'request' - config = require '../conf/compiled/conf.js' console.log 'in saveScientists' cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + "/scientists/jsonArray" request( @@ -263,8 +251,6 @@ exports.saveScientists = (jsonBody, callback) -> ) exports.updateScientists = (jsonBody, callback) -> - request = require 'request' - config = require '../conf/compiled/conf.js' console.log 'in updateScientists' cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + "/scientists/jsonArray" request( @@ -285,8 +271,6 @@ exports.updateScientists = (jsonBody, callback) -> ) exports.searchCmpds = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + '/search/cmpds' request( method: 'POST' @@ -308,16 +292,11 @@ exports.searchCmpds = (req, resp) -> ) exports.getStructureImage = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' imagePath = (req.originalUrl).replace /\/cmpdreg\/structureimage/, "" cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + '/structureimage' + imagePath req.pipe(request(cmpdRegCall)).pipe(resp) exports.getMetaLot = (req, resp) -> - request = require 'request' - _ = require 'underscore' - config = require '../conf/compiled/conf.js' endOfUrl = (req.originalUrl).replace /\/cmpdreg\/metalots/, "" cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + '/metalots' + endOfUrl console.log cmpdRegCall @@ -369,8 +348,6 @@ exports.getMetaLot = (req, resp) -> ) exports.regSearch = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + '/regsearches/parent' console.log cmpdRegCall request( @@ -394,16 +371,12 @@ exports.regSearch = (req, resp) -> ) exports.getMarvinJSLicense = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' cmpdRegCall = (config.all.client.service.cmpdReg.persistence.basepath).replace '\/cmpdreg', "/" licensePath = cmpdRegCall + 'marvin4js-license.cxl' console.log licensePath req.pipe(request(licensePath)).pipe(resp) exports.getMultipleFilePicker = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' endOfUrl = (req.originalUrl).replace /\/cmpdreg\//, "" cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + "/" +endOfUrl cmpdRegCall = cmpdRegCall.replace /\\/g, "%5C" @@ -411,14 +384,10 @@ exports.getMultipleFilePicker = (req, resp) -> req.pipe(request(cmpdRegCall)).pipe(resp) exports.fileSave = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + '/filesave' req.pipe(request[req.method.toLowerCase()](cmpdRegCall)).pipe(resp) exports.metaLots = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + '/metalots' request( method: 'POST' @@ -441,8 +410,6 @@ exports.metaLots = (req, resp) -> ) exports.saveSalts = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + '/salts' request( method: 'POST' @@ -465,8 +432,6 @@ exports.saveSalts = (req, resp) -> ) exports.saveIsotopes = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + '/isotopes' request( method: 'POST' @@ -489,8 +454,6 @@ exports.saveIsotopes = (req, resp) -> ) exports.molConvert = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' endOfUrl = (req.originalUrl).replace /\/cmpdreg\//, "" cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + "/" +endOfUrl # cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + '/api/v1/structureServices/molconvert' @@ -515,8 +478,6 @@ exports.molConvert = (req, resp) -> ) exports.genericStructureService = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' endOfUrl = (req.originalUrl).replace /\/cmpdreg\//, "" cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + "/" +endOfUrl request( @@ -541,8 +502,6 @@ exports.genericStructureService = (req, resp) -> exports.exportSearchResults = (req, resp) -> path = require 'path' - request = require 'request' - config = require '../conf/compiled/conf.js' serverUtilityFunctions = require './ServerUtilityFunctions.js' cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/export/searchResults' @@ -594,8 +553,6 @@ exports.exportSearchResults = (req, resp) -> ) exports.validateParent = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' console.log "exports.validateParent" cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/parents/validateParent' @@ -619,8 +576,6 @@ exports.validateParent = (req, resp) -> ) exports.updateParent = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' console.log "exports.updateParent" cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/parents/updateParent' @@ -671,8 +626,6 @@ exports.updateLotMetadata = (req, resp) -> ) exports.updateLotsMetadata = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' console.log 'in update lot array metaData' cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/parentLot/updateLot/metadata/jsonArray' console.log cmpdRegCall @@ -697,8 +650,6 @@ exports.updateLotsMetadata = (req, resp) -> ) exports.updateParentMetadata = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' console.log 'in update parent metaData' cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/parents/updateParent/metadata' console.log cmpdRegCall @@ -723,8 +674,6 @@ exports.updateParentMetadata = (req, resp) -> ) exports.updateParentsMetadata = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' console.log 'in update parent array metaData' cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/parents/updateParent/metadata/jsonArray' console.log cmpdRegCall @@ -749,8 +698,6 @@ exports.updateParentsMetadata = (req, resp) -> ) exports.reparentLot = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' console.log 'in reparent lot' cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/parentLot/reparentLot' console.log cmpdRegCall @@ -775,8 +722,6 @@ exports.reparentLot = (req, resp) -> ) exports.reparentLots = (req, resp) -> - request = require 'request' - config = require '../conf/compiled/conf.js' console.log 'in reparent lot' cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/parentLot/reparentLot/jsonArray' console.log cmpdRegCall @@ -801,4 +746,19 @@ exports.reparentLots = (req, resp) -> ) - \ No newline at end of file +exports.getAuthorizedPrefixes = (req, resp) -> + labelSeqRoutes = require './ACASLabelSequencesRoutes.js' + req.query = + labelTypeAndKind: 'id_corpName' + thingTypeAndKind: 'parent_compound' + labelSeqRoutes.getAuthorizedLabelSequencesInternal req, (statusCode, json) -> + codeTables = [] + _.each json, (labelSeq) -> + codeTable = + id: labelSeq.id + name: labelSeq.labelPrefix + code: "#{labelSeq.labelPrefix}_#{labelSeq.labelTypeAndKind}_#{labelSeq.thingTypeAndKind}" + labelTypeAndKind: labelSeq.labelTypeAndKind + thingTypeAndKind: labelSeq.thingTypeAndKind + codeTables.push codeTable + resp.json codeTables \ No newline at end of file diff --git a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee index 6efb6c6f7..f9f951d4c 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee @@ -63,4 +63,9 @@ window.ModuleMenusConfiguration = mainControllerClassName: "SystemTestController" autoLaunchName:"system_test" requireUserRoles: [] + , + isHeader: false + menuName: "Label Sequence" + mainControllerClassName: "ACASLabelSequenceController" + autoLaunchName: "acasLabelSequence" ] From 951b106472f07a726a887cdfa507623ba96a1386 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 18 Sep 2017 13:50:39 -0700 Subject: [PATCH 175/576] CmpdRegBulkLoader: Added corp prefix selector that will display based on CmpdReg config. Updated bulk loader index route to pass CmpdReg configs through. If Prefix is visible, it is a required field and passes the selected label sequence to the server. ACASLabelSequences: Cleaned up extraneous references to "project" PrepareModuleConfJSON: The LabelSequence property "latestNumber" was renamed/repurposed to "startingNumber". Added catch/translation for this in PrepareModuleConfJSON so existing confJSON can work as-is, or with the new property name. Random Issues: Removed duplicate copy of client.cmpdReg.showProjectSelect in default configs. Added missing default labelSequence for DDICTs that Roo was auto-creating. --- conf/config.properties.example | 3 - .../src/client/ACASLabelSequences.coffee | 74 ++++++------------- .../src/server/PrepareModuleConfJSON.coffee | 5 ++ .../src/client/CmpdRegBulkLoader.coffee | 40 +++++++++- .../src/client/CmpdRegBulkLoader.html | 9 +++ .../routes/CmpdRegBulkLoaderRoutes.coffee | 2 + .../ServerAPI/conf/ExperimentConfJSON.coffee | 8 ++ 7 files changed, 82 insertions(+), 59 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 6cf0491d3..5f81bf189 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -409,9 +409,6 @@ client.protocol.showAssayTreeRule=false client.protocol.showCurveDisplayParams=true client.experiment.uneditableFileTypes=["source file", "annotation file"] -# If project select is shown separately in the Configuration part of the GUI -client.cmpdReg.showProjectSelect=true - # Default status for experiments loaded thorugh experiment loader server.sel.experimentStatus=approved server.sel.protocolStatus=created diff --git a/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee index 5e6b4155e..4b0ada077 100644 --- a/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee +++ b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee @@ -75,7 +75,7 @@ class window.ACASLabelSequenceRoleController extends AbstractFormController "click .bv_deleteLabelSequenceRole": "clear" initialize: -> - @errorOwnerName = 'ProjectLeaderController' + @errorOwnerName = 'ACASLabelSequenceRoleController' @setBindings() @model.on "destroy", @remove, @ @@ -134,8 +134,8 @@ class window.ACASLabelSequenceRoleListController extends Backbone.View $(@el).empty() $(@el).html @template() - @collection.each (leaderInfo) => - @addProjectLeader(leaderInfo) + @collection.each (roleInfo) => + @addLabelSequenceRole(roleInfo) if @collection.length == 0 @addNewLabelSequenceRole() @trigger 'renderComplete' @@ -209,16 +209,16 @@ class window.ACASLabelSequenceController extends AbstractFormController if window.AppLaunchParams.moduleLaunchParams.moduleName == @moduleLaunchName $.ajax type: 'GET' - url: "/api/projects" + url: "/api/labelsequences/getAuthorizedLabelSequences" dataType: 'json' error: (err) => - alert 'Could not get projects for this user. Creating a new project' + alert 'Could not get label sequences for this user. Creating a new label sequence' @completeInitialization() - success: (projectsList) => - if _.where(projectsList, {code: window.AppLaunchParams.moduleLaunchParams.code}).length > 0 + success: (labelSequencesList) => + if _.where(labelSequencesList, {code: window.AppLaunchParams.moduleLaunchParams.code}).length > 0 @getACASLabelSequence() else - alert 'Could not get project for code in this URL, creating new one' + alert 'Could not get label sequence for code in this URL, creating new one' @completeInitialization() else @completeInitialization() @@ -243,15 +243,15 @@ class window.ACASLabelSequenceController extends AbstractFormController url: "/api/labelsequences/"+window.AppLaunchParams.moduleLaunchParams.code dataType: 'json' error: (err) => - alert 'Could not get project for code in this URL, creating new one' + alert 'Could not get label sequence for code in this URL, creating new one' @completeInitialization() success: (json) => if json.length == 0 - alert 'Could not get project for code in this URL, creating new one' + alert 'Could not get label sequence for code in this URL, creating new one' else - proj = new ACASLabelSequence json - proj.set proj.parse(proj.attributes) - @model = proj + labelSeq = new ACASLabelSequence json + labelSeq.set labelSeq.parse(labelSeq.attributes) + @model = labelSeq @completeInitialization() @@ -361,34 +361,6 @@ class window.ACASLabelSequenceController extends AbstractFormController name: "Select Thing Type And Kind" selectedCode: @model.get('thingTypeAndKind') - updateEditable: => - if @model.isEditable() - if UtilityFunctions::testUserHasRoleTypeKindName(window.AppLaunchParams.loginUser, [@adminRole]) or UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, [window.conf.roles.acas.adminRole]) - @enableAllInputs() - @$('.bv_projectCode').attr 'disabled', 'disabled' - @$('.bv_manageUserPermissions').show() - @$('.bv_saveBeforeManagingPermissions').hide() - else - @enableLimitedEditing() - @$('.bv_manageUserPermissions').hide() - else - @disableAllInputs() - @$('.bv_newEntity').removeAttr('disabled') - if UtilityFunctions::testUserHasRoleTypeKindName(window.AppLaunchParams.loginUser, [@adminRole]) or UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, [window.conf.roles.acas.adminRole]) - @$('.bv_manageUserPermissions').show() - else - @$('.bv_manageUserPermissions').hide() - @$('.bv_status').attr 'disabled', 'disabled' #for now, don't allow status editing - - enableLimitedEditing: -> - @disableAllInputs() - @$('.bv_shortDescription').removeAttr 'disabled' - @$('.bv_projectDetails').removeAttr 'disabled' - @$('.bv_fileType').removeAttr 'disabled' - @$('button').removeAttr 'disabled' - @$('.bv_deleteProjectLeader').attr 'disabled', 'disabled' - @$('.bv_addProjectLeaderButton').attr 'disabled', 'disabled' - handleCancelClicked: => if @model.isNew() @model = null @@ -428,7 +400,6 @@ class window.ACASLabelSequenceController extends AbstractFormController @$('.bv_saveComplete').hide() saveLabelSequence: => -# @model.prepareToSave() @prepareToSaveLabelSequenceRoles() console.log @model if @model.isNew() @@ -439,23 +410,20 @@ class window.ACASLabelSequenceController extends AbstractFormController if @model.isNew() @model.save null, success: (model, response) => - if response is "update lsThing failed" + if response is "save label sequence failed" @model.trigger 'saveFailed' else @modelSaveCallback else - if UtilityFunctions::testUserHasRoleTypeKindName(window.AppLaunchParams.loginUser, [@adminRole]) or UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, [window.conf.roles.acas.adminRole]) - @updateProjectRoles() - else - @model.save null, - success: (model, response) => - if response is "update lsThing failed" - @model.trigger 'saveFailed' - else - @modelSaveCallback - error: (err) => + @model.save null, + success: (model, response) => + if response is "update label sequence failed" @model.trigger 'saveFailed' + else + @modelSaveCallback + error: (err) => + @model.trigger 'saveFailed' validationError: => super() diff --git a/modules/BuildUtilities/src/server/PrepareModuleConfJSON.coffee b/modules/BuildUtilities/src/server/PrepareModuleConfJSON.coffee index 970d0677c..d97d1e297 100644 --- a/modules/BuildUtilities/src/server/PrepareModuleConfJSON.coffee +++ b/modules/BuildUtilities/src/server/PrepareModuleConfJSON.coffee @@ -92,6 +92,11 @@ data = require "#{ACAS_HOME}/public/javascripts/conf/confJSON/CompiledModuleConf config = require "#{ACAS_HOME}/conf/compiled/conf.js" async.forEachSeries typeKinds, ((typeOrKind, callback) -> + if typeOrKind == 'labelsequences' + _.each data[typeOrKind], (labelSeq) -> + if labelSeq.latestNumber? + labelSeq.startingNumber = labelSeq.latestNumber + delete labelSeq.latestNumber baseurl = config.all.client.service.persistence.fullpath+"setup/"+typeOrKind if data[typeOrKind]? console.log "trying to save " + typeOrKind diff --git a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee index b04196824..ab9a3f2db 100644 --- a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee +++ b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee @@ -340,6 +340,7 @@ class window.AssignSdfPropertiesController extends Backbone.View events: "change .bv_dbProject": "handleDbProjectChanged" + "change .bv_labelPrefix": "handleLabelPrefixChanged" "keyup .bv_fileDate": "handleFileDateChanged" "change .bv_fileDate": "handleFileDateChanged" #have this here too for when you set date using date icon "click .bv_fileDateIcon": "handleFileDateIconClicked" @@ -364,9 +365,14 @@ class window.AssignSdfPropertiesController extends Backbone.View @$('.bv_group_fileDate').hide() if window.conf.cmpdReg.showProjectSelect @setupProjectSelect() - @isValid() else @$('.bv_group_dbProject').hide() + if window.AppLaunchParams.cmpdRegConfig.serverSettings.corpParentFormat? and window.AppLaunchParams.cmpdRegConfig.serverSettings.corpParentFormat == 'ACASLabelSequence' + @setupPrefixSelect() + else + @$('.bv_group_labelPrefix').hide() + @isValid() + @setupAssignedPropertiesListController() getAndFormatTemplateOptions: -> @@ -413,6 +419,17 @@ class window.AssignSdfPropertiesController extends Backbone.View name: "Select Project" selectedCode: "unassigned" + setupPrefixSelect: -> + @prefixList = new PickListList() + @prefixList.url = "/cmpdreg/labelPrefixes" + @prefixListController = new PickListSelectController + el: @$('.bv_labelPrefix') + collection: @prefixList + insertFirstOption: new PickList + code: "unassigned" + name: "Select Prefix" + selectedCode: "unassigned" + setupAssignedPropertiesListController: -> @assignedPropertiesListController= new AssignedPropertiesListController el: @$('.bv_assignedPropertiesList') @@ -455,6 +472,12 @@ class window.AssignSdfPropertiesController extends Backbone.View @isValid() @trigger 'projectChanged', project + handleLabelPrefixChanged: -> + labelPrefix = @prefixListController.getSelectedModel() + @labelPrefix = labelPrefix.attributes + @labelPrefix.labelPrefix = labelPrefix.get('name') + @isValid() + handleFileDateChanged: -> if UtilityFunctions::getTrimmedInput(@$('.bv_fileDate')) is "" @fileDate = null @@ -533,6 +556,8 @@ class window.AssignSdfPropertiesController extends Backbone.View otherErrors.push @getProjectErrors()... if window.conf.cmpdReg.showFileDate otherErrors.push @getFileDateErrors()... + if window.AppLaunchParams.cmpdRegConfig.serverSettings.corpParentFormat? and window.AppLaunchParams.cmpdRegConfig.serverSettings.corpParentFormat == 'ACASLabelSequence' + otherErrors.push @getPrefixErrors() if @assignedPropertiesList? otherErrors.push @assignedPropertiesList.checkDuplicates()... otherErrors.push @assignedPropertiesList.checkSaltProperties()... @@ -540,9 +565,8 @@ class window.AssignSdfPropertiesController extends Backbone.View @showValidationErrors(otherErrors) unless @$('.bv_unassignedProperties').html() == "" validCheck = false - if otherErrors.length > 0 + if (_.flatten otherErrors).length > 0 validCheck = false - if validCheck @$('.bv_regCmpds').removeAttr('disabled') else @@ -558,6 +582,14 @@ class window.AssignSdfPropertiesController extends Backbone.View message: 'Project must be selected' projectError + getPrefixErrors: -> + prefixError = [] + if @prefixListController.getSelectedCode() is "unassigned" or @prefixListController.getSelectedCode() is null + prefixError = + attribute: 'labelPrefix' + message: 'Prefix must be selected' + prefixError + validateAssignedProperties: -> validCheck = true if @assignedPropertiesList? @@ -666,6 +698,8 @@ class window.AssignSdfPropertiesController extends Backbone.View fileName: @fileName mappings: JSON.parse(JSON.stringify(@assignedPropertiesListController.collection.models)) userName: window.AppLaunchParams.loginUser.username + if window.AppLaunchParams.cmpdRegConfig.serverSettings.corpParentFormat? and window.AppLaunchParams.cmpdRegConfig.serverSettings.corpParentFormat == 'ACASLabelSequence' + dataToPost.labelPrefix = @labelPrefix if window.conf.cmpdReg.showFileDate dataToPost.fileDate = @fileDate $.ajax diff --git a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.html b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.html index 69407066e..d21260026 100644 --- a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.html +++ b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.html @@ -92,6 +92,15 @@

      Bulk Compound Registration

      Configuration

      +
      +
      + +
      + +
      +
      +
      diff --git a/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee b/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee index 5b9ff543c..7231130a1 100644 --- a/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee +++ b/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee @@ -21,6 +21,7 @@ exports.setupRoutes = (app, loginRoutes) -> exports.cmpdRegBulkLoaderIndex = (req, res) -> scriptPaths = require './RequiredClientScripts.js' config = require '../conf/compiled/conf.js' + cmpdRegConfig = require '../public/CmpdReg/client/custom/configuration.json' global.specRunnerTestmode = if global.stubsMode then true else false scriptsToLoad = scriptPaths.requiredScripts.concat(scriptPaths.applicationScripts) @@ -45,6 +46,7 @@ exports.cmpdRegBulkLoaderIndex = (req, res) -> testMode: false moduleLaunchParams: if moduleLaunchParams? then moduleLaunchParams else null deployMode: global.deployMode + cmpdRegConfig: cmpdRegConfig exports.getCmpdRegBulkLoaderTemplates = (req, resp) -> if req.query.testMode or global.specRunnerTestmode diff --git a/modules/ServerAPI/conf/ExperimentConfJSON.coffee b/modules/ServerAPI/conf/ExperimentConfJSON.coffee index 4670db836..4700f1a77 100644 --- a/modules/ServerAPI/conf/ExperimentConfJSON.coffee +++ b/modules/ServerAPI/conf/ExperimentConfJSON.coffee @@ -697,6 +697,14 @@ labelTypeAndKind: "id_codeName" thingTypeAndKind: "document_experiment" latestNumber:0 + , + digits: 8 + groupDigits: false + labelPrefix: "DDICT" + labelSeparator: "-" + labelTypeAndKind: "id_codeName" + thingTypeAndKind: "document_datadictionary" + startingNumber: 1 ] ) (if (typeof process is "undefined" or not process.versions) then window.experimentConfJSON = window.experimentConfJSON or {} else exports) From 6429fa20fd8e7a8b3faf6e2305f00ddb724ced67 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 18 Sep 2017 17:26:39 -0700 Subject: [PATCH 176/576] Fixed getPrefixErrors to use ... operator which removes the need for _.flatten --- modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee index ab9a3f2db..01df35c0e 100644 --- a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee +++ b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee @@ -557,7 +557,7 @@ class window.AssignSdfPropertiesController extends Backbone.View if window.conf.cmpdReg.showFileDate otherErrors.push @getFileDateErrors()... if window.AppLaunchParams.cmpdRegConfig.serverSettings.corpParentFormat? and window.AppLaunchParams.cmpdRegConfig.serverSettings.corpParentFormat == 'ACASLabelSequence' - otherErrors.push @getPrefixErrors() + otherErrors.push @getPrefixErrors()... if @assignedPropertiesList? otherErrors.push @assignedPropertiesList.checkDuplicates()... otherErrors.push @assignedPropertiesList.checkSaltProperties()... @@ -565,7 +565,7 @@ class window.AssignSdfPropertiesController extends Backbone.View @showValidationErrors(otherErrors) unless @$('.bv_unassignedProperties').html() == "" validCheck = false - if (_.flatten otherErrors).length > 0 + if otherErrors.length > 0 validCheck = false if validCheck @$('.bv_regCmpds').removeAttr('disabled') From 0874825ad4d99d95c344fccbb8fa91a976582968 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 19 Sep 2017 08:14:24 -0700 Subject: [PATCH 177/576] adding preprocessorhtmlsummary div for pre processor summary information --- .../src/client/BasicFileValidateAndSave.coffee | 12 ++++++++++++ .../src/client/BasicFileValidateAndSaveView.html | 1 + 2 files changed, 13 insertions(+) diff --git a/modules/Components/src/client/BasicFileValidateAndSave.coffee b/modules/Components/src/client/BasicFileValidateAndSave.coffee index 44f65841f..890f27c37 100644 --- a/modules/Components/src/client/BasicFileValidateAndSave.coffee +++ b/modules/Components/src/client/BasicFileValidateAndSave.coffee @@ -174,6 +174,8 @@ class window.BasicFileValidateAndSaveController extends Backbone.View @notificationController.addNotifications(@errorOwnerName, json.errorMessages) if json.results?.htmlSummary? @$('.bv_htmlSummary').html(json.results.htmlSummary) + if json.results?.preProcessorHTMLSummary? + @showPreProcessorHTMLSUmmary json.results.preProcessorHTMLSummary @$('.bv_validateStatusDropDown').modal("hide") if json.results?.csvDataPreview? @showCSVPreview json.results.csvDataPreview @@ -188,6 +190,8 @@ class window.BasicFileValidateAndSaveController extends Backbone.View @$('.bv_htmlSummary').html(json.results.htmlSummary) @newExperimentCode = json.results.experimentCode @showFileUploadCompletePhase() + if json.results?.preProcessorHTMLSummary? + @showPreProcessorHTMLSUmmary json.results.preProcessorHTMLSummary @$('.bv_resultStatus').html(summaryStr) @$('.bv_saveStatusDropDown').modal("hide") @trigger 'amClean' @@ -214,6 +218,8 @@ class window.BasicFileValidateAndSaveController extends Backbone.View @$('.bv_completeControlContainer').hide() @$('.bv_notifications').hide() @$('.bv_csvPreviewContainer').hide() + @$('.bv_preProcessorHTMLSummary').hide() + @$('.bv_preProcessorHTMLSummary').hide('') handleAttachReportFileChanged: -> attachReportFile = @$('.bv_attachReportFile').is(":checked") @@ -247,6 +253,7 @@ class window.BasicFileValidateAndSaveController extends Backbone.View @$('.bv_resultStatus').show() @$('.bv_htmlSummary').show() @$('.bv_csvPreviewContainer').hide() + @$('.bv_preProcessorHTMLSummary').hide() @$('.bv_fileUploadWrapper').hide() @$('.bv_nextControlContainer').hide() @$('.bv_saveControlContainer').hide() @@ -262,6 +269,11 @@ class window.BasicFileValidateAndSaveController extends Backbone.View @$(".bv_next").removeAttr 'disabled' @$(".bv_save").removeAttr 'disabled' + showPreProcessorHTMLSUmmary: (preProcessorSummaryHTML) -> + console.log "showing here" + @$('.bv_preProcessorHTMLSummary').html(preProcessorSummaryHTML) + @$('.bv_preProcessorHTMLSummary').show() + showCSVPreview: (csv) -> @$('.csvPreviewTHead').empty() @$('.csvPreviewTBody').empty() diff --git a/modules/Components/src/client/BasicFileValidateAndSaveView.html b/modules/Components/src/client/BasicFileValidateAndSaveView.html index 65cd7576b..83a15461f 100644 --- a/modules/Components/src/client/BasicFileValidateAndSaveView.html +++ b/modules/Components/src/client/BasicFileValidateAndSaveView.html @@ -38,6 +38,7 @@
      +

      Data Preview:

      From 5edd00fbd44e057d6acaf116098a871a3dc2b5fd Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 19 Sep 2017 08:14:53 -0700 Subject: [PATCH 178/576] adding a post things internal route to post multiple ls things at once --- .../server/routes/ThingServiceRoutes.coffee | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee index 4f6da8896..2ad2bab7e 100644 --- a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee @@ -20,6 +20,7 @@ exports.setupAPIRoutes = (app, loginRoutes) -> app.get '/api/getThingCodeTablesByLabelText/:lsType/:lsKind/:labelText', exports.getThingsByTypeAndKindAndLabelTypeAndLabelText app.post '/api/things/:lsType/:lsKind/codeNames/jsonArray', exports.getThingsByCodeNames app.get '/api/thingKinds', exports.getThingKinds + app.post '/api/things/jsonArray', exports.postThings exports.setupRoutes = (app, loginRoutes) -> app.get '/api/things/:lsType/:lsKind', loginRoutes.ensureAuthenticated, exports.thingsByTypeKind @@ -44,6 +45,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/things/:lsType/:lsKind/codeNames/jsonArray', loginRoutes.ensureAuthenticated, exports.getThingsByCodeNames app.get '/api/thingKinds', loginRoutes.ensureAuthenticated, exports.getThingKinds app.get '/api/transaction/:id', loginRoutes.ensureAuthenticated, exports.getTransaction + app.post '/api/things/jsonArray', loginRoutes.ensureAuthenticated, exports.postThings exports.thingsByTypeKind = (req, resp) -> @@ -645,3 +647,38 @@ exports.getTransaction = (req, resp) -> baseurl = config.all.client.service.persistence.fullpath+"lstransactions/"+req.params.id serverUtilityFunctions.getFromACASServer baseurl, resp +exports.postThings = (req, resp) -> + exports.postThingsInternal {things: req.body.things}, (output, err) -> + if err? + resp.statusCode = 500 + resp.json err + +exports.postThingsInternal = (input, callback) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + serverUtilityFunctions = require './ServerUtilityFunctions.js' + baseurl = config.all.client.service.persistence.fullpath+"lsthings/jsonArray" + requestOptions = + method: 'POST' + url: baseurl + body: input.things + json: true + request requestOptions, (error, response, object) -> + if !error + if response.statusCode == 500 + callback object, response + else + callback object, null + else + console.log 'got ajax error trying to save validate thing name' + console.log error + console.log json + console.log response + callback object, error + + + + + + + \ No newline at end of file From 011fe358849c8e6925b66211148d4630b98f44e4 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 19 Sep 2017 12:22:53 -0700 Subject: [PATCH 179/576] Fixed prefixError construction to be an array now that I am using the splats "..." operator when combining it into the errors array. Added more validation to Label Sequence creator --- .../src/client/ACASLabelSequences.coffee | 16 +++++++++++++--- .../src/client/CmpdRegBulkLoader.coffee | 2 +- 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee index 4b0ada077..77d5b0125 100644 --- a/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee +++ b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee @@ -42,15 +42,24 @@ class window.ACASLabelSequence extends Backbone.Model errors.push attribute: 'labelPrefix' message: "Label prefix must be set" - if isNaN(attrs.startingNumber) or attrs.startingNumber is undefined + if isNaN(attrs.startingNumber) or attrs.startingNumber is undefined or attrs.startingNumber is null or attrs.startingNumber.length < 1 errors.push attribute: 'startingNumber' message: "Starting Number must set and be a number" - if isNaN(attrs.digits) or attrs.digits is undefined + if isNaN(attrs.digits) or attrs.digits is undefined or attrs.digits is null or attrs.digits.length < 1 errors.push attribute: 'digits' message: "Number of digits must set and be a number" - #TODO: Add more validation + labelTypeAndKind = @get('labelTypeAndKind') + if labelTypeAndKind is "unassigned" or labelTypeAndKind is undefined or labelTypeAndKind is "" or labelTypeAndKind is null + errors.push + attribute: 'labelTypeAndKind' + message: "Label Type and Kind must be set" + thingTypeAndKind = @get('thingTypeAndKind') + if thingTypeAndKind is "unassigned" or thingTypeAndKind is undefined or thingTypeAndKind is "" or thingTypeAndKind is null + errors.push + attribute: 'thingTypeAndKind' + message: "Thing Type and Kind must be set" if errors.length > 0 return errors else @@ -228,6 +237,7 @@ class window.ACASLabelSequenceController extends AbstractFormController attributeChanged: => super() @updatePreview() + @isValid() updatePreview: => prefix = @model.get('labelPrefix') diff --git a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee index 01df35c0e..342e65475 100644 --- a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee +++ b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee @@ -585,7 +585,7 @@ class window.AssignSdfPropertiesController extends Backbone.View getPrefixErrors: -> prefixError = [] if @prefixListController.getSelectedCode() is "unassigned" or @prefixListController.getSelectedCode() is null - prefixError = + prefixError.push attribute: 'labelPrefix' message: 'Prefix must be selected' prefixError From 2279ccb4701e64807544b14709f1e4929100ab66 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 19 Sep 2017 13:25:00 -0700 Subject: [PATCH 180/576] adding preprocessor result html value --- modules/ServerAPI/conf/ExperimentConfJSON.coffee | 3 +++ 1 file changed, 3 insertions(+) diff --git a/modules/ServerAPI/conf/ExperimentConfJSON.coffee b/modules/ServerAPI/conf/ExperimentConfJSON.coffee index 5553d9461..c546bd4be 100644 --- a/modules/ServerAPI/conf/ExperimentConfJSON.coffee +++ b/modules/ServerAPI/conf/ExperimentConfJSON.coffee @@ -107,6 +107,9 @@ , typeName: "clobValue" kindName: "analysis result html" + , + typeName: "clobValue" + kindName: "preprocessor result html" , typeName: "clobValue" kindName: "model fit result html" From f1d1de8e4be0b8b9574b257435a73c3e26302236 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 19 Sep 2017 13:46:29 -0700 Subject: [PATCH 181/576] ACASLabelSequences: Improved styling by separating preview from the inputs. Fixed widths. CmpdReg: Restyled Prefix so it has an unselected firstOption, has an asterisk, and throws a validation error if not set. Prefix now acts exactly like stereo category. --- .../src/client/ACASLabelSequences.css | 2 +- .../src/client/ACASLabelSequencesView.html | 1 + .../CmpdReg/src/client/css/NewCmpdReg_nocompile.css | 4 ---- modules/CmpdReg/src/client/src/Parent.js | 12 +++++++++++- .../src/client/templates/LotForm/ParentView.inc | 2 +- 5 files changed, 14 insertions(+), 7 deletions(-) diff --git a/modules/ACASLabelSequences/src/client/ACASLabelSequences.css b/modules/ACASLabelSequences/src/client/ACASLabelSequences.css index c2e818edc..f4c1cb6c4 100644 --- a/modules/ACASLabelSequences/src/client/ACASLabelSequences.css +++ b/modules/ACASLabelSequences/src/client/ACASLabelSequences.css @@ -1,4 +1,4 @@ .bv_acasLabelSequenceForm .form-control{ - width: 330px; + width: 335px; margin-left: 20px; } \ No newline at end of file diff --git a/modules/ACASLabelSequences/src/client/ACASLabelSequencesView.html b/modules/ACASLabelSequences/src/client/ACASLabelSequencesView.html index 9f309f874..3523b0fac 100644 --- a/modules/ACASLabelSequences/src/client/ACASLabelSequencesView.html +++ b/modules/ACASLabelSequences/src/client/ACASLabelSequencesView.html @@ -6,6 +6,7 @@

      Create Entity Prefix

      +
      diff --git a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css index c6a1cb43d..0715a7810 100755 --- a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css +++ b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css @@ -832,10 +832,6 @@ div { margin-left: 30px !important; } -.LotForm_ParentView .parentStructureForm .bv_labelPrefix { - font-size: 18 !important; -} - .LotForm_ParentView .parentComments { width:800px; } diff --git a/modules/CmpdReg/src/client/src/Parent.js b/modules/CmpdReg/src/client/src/Parent.js index c9590f5c3..39a6e2b83 100755 --- a/modules/CmpdReg/src/client/src/Parent.js +++ b/modules/CmpdReg/src/client/src/Parent.js @@ -88,6 +88,11 @@ $(function() { errors.push({attribute: 'compoundTypeCode', message: "Compound type must be supplied"}); } } + if (this.isNew() && window.configuration.serverSettings.corpParentFormat != null && window.configuration.serverSettings.corpParentFormat == 'ACASLabelSequence' && attr.labelPrefix != null) { + if (attr.labelPrefix.get('code')=='not_set') { + errors.push({attribute: 'labelPrefix', message: "Prefix must be supplied"}); + } + } if (errors.length > 0) {return errors;} }, @@ -190,7 +195,12 @@ $(function() { } if (this.model.isNew() && window.configuration.serverSettings.corpParentFormat != null && window.configuration.serverSettings.corpParentFormat == 'ACASLabelSequence') { - var optionToInsert = null; + var optionToInsert = new PickList({ + "code": "not_set", + "id": 0, + "name": "Select Prefix", + "version": 0 + }); this.labelPrefixCodeController = this.setupCodeController('labelPrefix', 'labelPrefixes', 'labelPrefix', optionToInsert); diff --git a/modules/CmpdReg/src/client/templates/LotForm/ParentView.inc b/modules/CmpdReg/src/client/templates/LotForm/ParentView.inc index 4a712e54b..49fe9124d 100755 --- a/modules/CmpdReg/src/client/templates/LotForm/ParentView.inc +++ b/modules/CmpdReg/src/client/templates/LotForm/ParentView.inc @@ -29,7 +29,7 @@
      - +
      From 574eb3ba339fe66003dfe7734de25d66a2562705 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 20 Sep 2017 11:00:14 -0700 Subject: [PATCH 182/576] Tweaked dockerfile to use different tomcat build and not try to map marvin --- docker-compose.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 738122fa7..5243463b5 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -22,7 +22,7 @@ services: - /home/runner/build/src/r - /home/runner/build/conf/compiled # Add chemaxon marvinjs here - - ./chemaxon/marvinjs:/home/runner/build/public/CmpdReg/marvinjs + # - ./chemaxon/marvinjs:/home/runner/build/public/CmpdReg/marvinjs # Please add any dev volumes below this line - ./:/home/runner/acas # - ./modules/BuildUtilities/:/home/runner/acas/modules/BuildUtilities @@ -60,7 +60,7 @@ services: ports: - "5432:5432" tomcat: - image: mcneilco/tomcat-maven + image: mcneilco/tomcat-maven:openjdk7 restart: always depends_on: - db From 6fa131214e01272f76707183556babfedaae9a95 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 20 Sep 2017 14:49:57 -0700 Subject: [PATCH 183/576] Don't show expandAll of there is less than 2 collapsible menus --- modules/ModuleMenus/src/client/ModuleLauncher.coffee | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/modules/ModuleMenus/src/client/ModuleLauncher.coffee b/modules/ModuleMenus/src/client/ModuleLauncher.coffee index 9406510ba..951c5d4f4 100644 --- a/modules/ModuleMenus/src/client/ModuleLauncher.coffee +++ b/modules/ModuleMenus/src/client/ModuleLauncher.coffee @@ -163,8 +163,10 @@ class window.ModuleLauncherMenuListController extends Backbone.View $(@el).empty() $(@el).html @template() @collection.each @addOne + if @collapsibleHeaders.length < 2 + @$('.bv_expandAll').hide() @$('.bv_notTopHeader:eq(0)').removeClass "bv_notTopHeader" - + @ addOne: (menuItem) => From 6de69eb066e0bf6ba44ca4252874001a3ce52cff Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Fri, 22 Sep 2017 10:22:28 -0700 Subject: [PATCH 184/576] RC/1.12.0: disable protocol date icon, allow form state table context menu to be configurable, refactored canEdit, updateEditable, checkDisplayMode --- .../src/client/ACASFormStateTable.coffee | 13 +++-- .../src/client/AbstractFormController.coffee | 3 ++ .../ServerAPI/src/client/BaseEntity.coffee | 50 +++++++++++-------- 3 files changed, 41 insertions(+), 25 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index e44418cd1..9f94b6f16 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -166,6 +166,10 @@ class window.ACASFormStateTableController extends Backbone.View @handleAfterValidate = @tableDef.handleAfterValidate setupHot: -> + if @tableDef.contextMenu? + contextMenu = @tableDef.contextMenu + else + contextMenu = true @hot = new Handsontable @$('.bv_tableWrapper')[0], beforeChange: @handleBeforeChange beforeValidate: @handleBeforeValidate @@ -173,8 +177,7 @@ class window.ACASFormStateTableController extends Backbone.View afterValidate: @handleAfterValidate afterCreateRow: @handleRowCreated minSpareRows: 1, - allowInsertRow: true - contextMenu: true + contextMenu: contextMenu startRows: 1, className: "htCenter", colHeaders: _.pluck @colHeaders, 'displayName' @@ -408,9 +411,13 @@ class window.ACASFormStateTableController extends Backbone.View # comments: false enableInput: -> + if @tableDef.contextMenu? + contextMenu = @tableDef.contextMenu + else + contextMenu = true @hot.updateSettings readOnly: false - contextMenu: true + contextMenu: contextMenu #Other options I decided not to use # disableVisualSelection: false # manualColumnResize: true diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 9ac9eaa70..ddd842223 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -62,6 +62,9 @@ class window.AbstractFormController extends Backbone.View @$("textarea").not('.dontdisable').attr 'disabled', 'disabled' @$(".bv_experimentCode").not('.dontdisable').css "background-color", "#eeeeee" @$(".bv_experimentCode").not('.dontdisable').css "color", "#333333" + @$(".bv_creationDateIcon").not('.dontdisable').addClass "uneditable-input" + @$(".bv_creationDateIcon").not('.dontdisable').on "click", -> + return false @$(".bv_completionDateIcon").not('.dontdisable').addClass "uneditable-input" @$(".bv_completionDateIcon").not('.dontdisable').on "click", -> return false diff --git a/modules/ServerAPI/src/client/BaseEntity.coffee b/modules/ServerAPI/src/client/BaseEntity.coffee index c3e6191ac..7f983e3c7 100644 --- a/modules/ServerAPI/src/client/BaseEntity.coffee +++ b/modules/ServerAPI/src/client/BaseEntity.coffee @@ -373,7 +373,7 @@ class window.BaseEntityController extends AbstractThingFormController #TODO: che if @model.isNew() or @model.getScientist().get('codeValue') is "unassigned" return true else - if window.conf.entity?.editingRoles? + if window.conf.entity?.editingRoles? and $.trim(window.conf.entity.editingRoles).length > 0 rolesToTest = [] for role in window.conf.entity.editingRoles.split(",") role = $.trim(role) @@ -391,9 +391,12 @@ class window.BaseEntityController extends AbstractThingFormController #TODO: che rolesToTest.push role if rolesToTest.length is 0 return false - unless UtilityFunctions::testUserHasRole window.AppLaunchParams.loginUser, rolesToTest + if UtilityFunctions::testUserHasRole window.AppLaunchParams.loginUser, rolesToTest + return true + else return false - return true + else + return true canDelete: -> if window.conf.entity?.deletingRoles? @@ -553,25 +556,28 @@ class window.BaseEntityController extends AbstractThingFormController #TODO: che @model.trigger 'change' updateEditable: => - if @model.isEditable() - @enableAllInputs() - @$('.bv_lock').hide() - else - @disableAllInputs() - @$('.bv_status').removeAttr('disabled') - @$('.bv_lock').show() - @$('.bv_newEntity').removeAttr('disabled') - if @model.getStatus().get('codeValue') is "deleted" - @$('.bv_status').attr 'disabled', 'disabled' - if @model.isNew() - @$('.bv_status').attr("disabled", "disabled") - else - unless @model.getStatus().get('codeValue') is "deleted" - @$('.bv_status').removeAttr("disabled") - if window.conf.entity?.scientist?.editable? and window.conf.entity.scientist.editable is false - @$('.bv_scientist').attr 'disabled', 'disabled' + if @readOnly + @displayInReadOnlyMode() else - @$('.bv_scientist').removeAttr 'disabled' + if @model.isEditable() + @enableAllInputs() + @$('.bv_lock').hide() + else + @disableAllInputs() + @$('.bv_status').removeAttr('disabled') + @$('.bv_lock').show() + @$('.bv_newEntity').removeAttr('disabled') + if @model.getStatus().get('codeValue') is "deleted" + @$('.bv_status').attr 'disabled', 'disabled' + if @model.isNew() + @$('.bv_status').attr("disabled", "disabled") + else + unless @model.getStatus().get('codeValue') is "deleted" + @$('.bv_status').removeAttr("disabled") + if window.conf.entity?.scientist?.editable? and window.conf.entity.scientist.editable is false + @$('.bv_scientist').attr 'disabled', 'disabled' + else + @$('.bv_scientist').removeAttr 'disabled' @model.trigger 'statusChanged' @@ -659,7 +665,7 @@ class window.BaseEntityController extends AbstractThingFormController #TODO: che @displayInReadOnlyMode() else if status is "deleted" or status is "approved" or status is "rejected" @disableAllInputs() - unless @model.getStatus().get('codeValue') is "deleted" + if @model.getStatus().get('codeValue') != "deleted" and @canEdit() @$('.bv_status').removeAttr 'disabled' @$('.bv_newEntity').removeAttr('disabled') @$('.bv_newEntity').removeAttr('disabled') From fb506bf64cfa9116a092373f539fbf7669d532e7 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Fri, 22 Sep 2017 10:54:56 -0700 Subject: [PATCH 185/576] RC/1.12.3: fix bug in hiding curve display params in protocol editor --- modules/ServerAPI/src/client/Protocol.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/client/Protocol.coffee b/modules/ServerAPI/src/client/Protocol.coffee index 527cd5a54..5340ba8d2 100644 --- a/modules/ServerAPI/src/client/Protocol.coffee +++ b/modules/ServerAPI/src/client/Protocol.coffee @@ -260,7 +260,7 @@ class window.ProtocolBaseController extends BaseEntityController @$('.bv_maxY').val(@model.getCurveDisplayMax().get('numericValue')) @$('.bv_minY').val(@model.getCurveDisplayMin().get('numericValue')) else - @$('.bv_group_assayStageWrapper').hide() + @$('.bv_group_curveDisplayWrapper').hide() super() @ From c05e3de563cd219589f621efcfc48b01615c70d9 Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Fri, 22 Sep 2017 16:42:27 -0400 Subject: [PATCH 186/576] Created node route using newly exposed avancedSearchContainers Roo route to get tubes from batch code. --- .../routes/InventoryServiceRoutes.coffee | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 644e9a0f8..6bc9aa2b4 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -55,6 +55,7 @@ exports.setupAPIRoutes = (app) -> app.post '/api/getContainerInfoFromBatchCode', exports.getContainerInfoFromBatchCode app.post '/api/getContainerStatesByContainerValue', exports.getContainerStatesByContainerValue app.post '/api/getContainerLogsByContainerCodes', exports.getContainerLogsByContainerCodes + app.post '/api/getTubesFromBatchCode', exports.getTubesFromBatchCode exports.setupRoutes = (app, loginRoutes) -> @@ -104,6 +105,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/createTubes', loginRoutes.ensureAuthenticated, exports.createTubes app.post '/api/throwInTrash', loginRoutes.ensureAuthenticated, exports.throwInTrash app.post '/api/updateContainerHistoryLogs', loginRoutes.ensureAuthenticated, exports.updateContainerHistoryLogs + app.post '/api/getTubesFromBatchCode', loginRoutes.ensureAuthenticated, exports.getTubesFromBatchCode exports.getContainersInLocation = (req, resp) -> @@ -2464,3 +2466,70 @@ exports.getContainerStatesByContainerValueInternal = (requestObject, callback) = callback null, 500 #resp.end JSON.stringify "getContainerStatesByContainerValue failed" ) + +exports.getTubesFromBatchCode = (req, resp) => + + exports.getTubesFromBatchCodeInternal(req.body, (json, statusCode) => + resp.statusCode = statusCode + resp.json json + ) + +exports.getTubesFromBatchCodeInternal = (input, callback) => + batchCode = input.batchCode + + queryPayload = + { + "lsType": "container" , + "lsKind": "tube", + "values":[ + { + "stateType":"metadata", + "stateKind":"information", + "valueType": "codeValue", + "valueKind": "status", + "operator": "!=", + "value":"expired" + } + ], + "secondInteractions":[ + { + "interactionType": "has member", + "interactionKind": "container_well", + "thingType": "well", + "thingKind": "default", + "thingValues":[ + { + "stateType":"status", + "stateKind":"content", + "valueType": "codeValue", + "valueKind": "batch code", + "operator": "=", + "value":batchCode + } + ] + } + ] + } + + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containers/advancedSearchContainers?with=codeTable&labelType=barcode" + console.log 'baseurl', baseurl + request = require 'request' + request( + method: 'POST' + url: baseurl + body: queryPayload + json: true + timeout: 86400000 + , (error, response, json) => + if !error && response.statusCode == 200 + tubes = _.pluck(json.results, 'name') + callback tubes, response.statusCode + else + console.error 'got ajax error trying to getTubesFromBatchCode' + console.error error + console.error json + console.error response + callback null, 500 + #resp.end JSON.stringify "getContainerStatesByContainerValue failed" + ) From d0d6694c0e64d9d5caa6fc8cf203353c575edac5 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 22 Sep 2017 16:50:23 -0700 Subject: [PATCH 187/576] Added incomplete version of bulk Parent Vial csv loading route. Response JSON is incorrect for non-dryrun, and it is missing an html summary, but the loading and saving of vials works. --- .../routes/InventoryServiceRoutes.coffee | 309 ++++++++++++++++++ 1 file changed, 309 insertions(+) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 644e9a0f8..57652fb4f 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -4,6 +4,8 @@ _ = require 'underscore' preferredEntityCodeService = require '../routes/PreferredEntityCodeService.js' config = require '../conf/compiled/conf.js' RUN_CUSTOM_FLAG = "0" +fs = require('fs') +parse = require('csv-parse') exports.setupAPIRoutes = (app) -> @@ -55,6 +57,7 @@ exports.setupAPIRoutes = (app) -> app.post '/api/getContainerInfoFromBatchCode', exports.getContainerInfoFromBatchCode app.post '/api/getContainerStatesByContainerValue', exports.getContainerStatesByContainerValue app.post '/api/getContainerLogsByContainerCodes', exports.getContainerLogsByContainerCodes + app.post '/api/loadParentVialsFromCSV', exports.loadParentVialsFromCSV exports.setupRoutes = (app, loginRoutes) -> @@ -1226,6 +1229,38 @@ getContainerCodesFromLabels = (req, callback) -> callback json ) +getContainerCodesFromLabelsInternal = (barcodes, containerType, containerKind, callback) -> + if global.specRunnerTestmode + response = + codeName: 'CONT-0000001' + label: 'test label' + callback response + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containers/getContainerCodesByLabels?" + url = baseurl+"containerType=#{containerType}&containerKind=#{containerKind}" + postBody = barcodes + console.debug postBody + console.debug url + request = require 'request' + request( + method: 'POST' + url: url + body: postBody + json: true + timeout: 86400000 + , (error, response, json) => + console.debug response.statusCode + console.debug json + if !error and !json.error + callback json + else + console.error 'got ajax error trying to lookup lsContainer name' + console.error error + console.error response + callback json + ) + exports.getContainerCodesFromLabels = (req, resp) -> req.setTimeout 86400000 getContainerCodesFromLabels req, (json) -> @@ -2464,3 +2499,277 @@ exports.getContainerStatesByContainerValueInternal = (requestObject, callback) = callback null, 500 #resp.end JSON.stringify "getContainerStatesByContainerValue failed" ) + +PARENT_COMPOUND_LOT_INDEX = 0 +PARENT_DESTINATION_VIAL_INDEX = 1 +PARENT_AMOUNT_INDEX = 2 +PARENT_AMOUNT_UNITS_INDEX = 3 +PARENT_PREPARED_BY_INDEX = 4 +PARENT_PREPARED_DATE_INDEX = 5 +PARENT_PHYSICAL_STATE_INDEX = 6 +PARENT_CONCENTRATION_INDEX = 7 +PARENT_CONC_UNITS_INDEX = 8 +PARENT_SOLVENT_INDEX = 9 + +DAUGHTER_SOURCE_VIAL_INDEX = 0 +DAUGHTER_DESTINATION_VIAL_INDEX = 1 +DAUGHTER_AMOUNT_INDEX = 2 +DAUGHTER_AMOUNT_UNITS_INDEX = 3 +DAUGHTER_PREPARED_BY_INDEX = 4 +DAUGHTER_PREPARED_DATE_INDEX = 5 +DAUGHTER_PHYSICAL_STATE_INDEX = 6 +DAUGHTER_CONCENTRATION_INDEX = 7 +DAUGHTER_CONC_UNITS_INDEX = 8 +DAUGHTER_SOLVENT_INDEX = 9 + +exports.loadParentVialsFromCSV = (req, resp) -> + exports.loadParentVialsFromCSVInternal req.body.fileToParse, req.body.dryRunMode, req.body.user, (response) -> + resp.json response + +exports.loadParentVialsFromCSVInternal = (csvFileName, dryRun, user, callback) -> + if dryRun + exports.validateParentVialsFromCSVInternal csvFileName, (validationResponse) -> + callback validationResponse + else + exports.createParentVialsFromCSVInternal csvFileName, user, (createVialsResponse) -> + callback createVialsResponse + +exports.validateParentVialsFromCSV = (req, resp) -> + exports.validateParentVialsFromCSVInternal req.body.csvFileName, (validationResponse) -> + resp.json validationResponse + +exports.validateParentVialsFromCSVInternal = (csvFileName, callback) -> + getFileExists csvFileName, (exists, path) -> + validationResponse = + results: + dryRun: true + fileToParse: csvFileName + htmlSummary: '' + hasError: true + hasWarning: false + errorMessages: [] + transactionId: null + if exists + validationResponse.results.path = path + createParentVialFileEntryArray csvFileName, (fileEntryArray) -> + console.log fileEntryArray + checkRequiredAttributes fileEntryArray, (requiredAttributeErrors) -> + if requiredAttributeErrors? + validationResponse.errorMessages.push requiredAttributeErrors... + checkDataTypeErrors fileEntryArray, (dataTypeErrors) -> + if dataTypeErrors? + validationResponse.errorMessages.push dataTypeErrors... + checkBatchCodesExist fileEntryArray, (missingBatchCodeErrors) -> + if missingBatchCodeErrors? and missingBatchCodeErrors.length > 1 + error = + level: 'error' + message: "The following batches do not exist: "+ missingBatchCodeErrors.join ', ' + validationResponse.errorMessages.push error + barcodes = _.pluck fileEntryArray, 'destinationVialBarcode' + checkBarcodesExist barcodes, (existingBarcodes, newBarcodes) -> + if existingBarcodes? and existingBarcodes.length > 1 + error = + level: 'error' + message: "The following barcodes already exist: " + existingBarcodes.join ', ' + validationResponse.errorMessages.push error + if validationResponse.errorMessages.length < 1 + validationResponse.hasError = false + validationResponse.results.htmlSummary = prepareValidationHTMLSummary validationResponse.hasError, validationResponse.errorMessages + callback validationResponse + else + error = + level: 'error' + message: "File cannot be found" + validationResponse.errorMessages.push error + callback validationResponse + +getFileExists = (csvFileName, callback) => + exists = false + path = config.all.server.file.server.path + '/' + fileName = csvFileName + fs.stat path+fileName, (err, stats) -> + console.log 'path+fileName', path+fileName + console.log stats + console.log err + if stats?.isFile() + exists = true + callback exists, path+fileName + else + callback exists, path+fileName + +createParentVialFileEntryArray = (csvFileName, callback) => + csvFileEntries = [] + path = config.all.server.file.server.path + '/' + fileName = csvFileName + rowCount = 0 + fs.createReadStream(path + fileName) + .pipe(parse({delimiter: ','})) + .on('data', (csvrow) -> + fileEntry = + batchCode: csvrow[PARENT_COMPOUND_LOT_INDEX].trim() + destinationVialBarcode: csvrow[PARENT_DESTINATION_VIAL_INDEX].trim() + amount: csvrow[PARENT_AMOUNT_INDEX].trim() + amountUnits: csvrow[PARENT_AMOUNT_UNITS_INDEX].trim() + preparedBy: csvrow[PARENT_PREPARED_BY_INDEX].trim() + preparedDate: csvrow[PARENT_PREPARED_DATE_INDEX].trim() + physicalState: csvrow[PARENT_PHYSICAL_STATE_INDEX].trim() + concentration: csvrow[PARENT_CONCENTRATION_INDEX].trim() + concUnits:csvrow[PARENT_CONC_UNITS_INDEX].trim() + solvent: csvrow[PARENT_SOLVENT_INDEX].trim() + rowNumber: rowCount + if rowCount? and rowCount > 0 + csvFileEntries.push(fileEntry) + rowCount++ + ) + .on('end', () -> + return callback csvFileEntries, 200 + ) + +createDaughterVialFileEntryArray = (csvFileName, callback) => + csvFileEntries = [] + path = config.all.server.file.server.path + '/' + fileName = csvFileName + rowCount = 0 + fs.createReadStream(path + fileName) + .pipe(parse({delimiter: ','})) + .on('data', (csvrow) -> + fileEntry = + sourceVialBarcode: csvrow[DAUGHTER_SOURCE_VIAL_INDEX].trim() + destinationVialBarcode: csvrow[DAUGHTER_DESTINATION_VIAL_INDEX].trim() + amount: csvrow[DAUGHTER_AMOUNT_INDEX].trim() + amountUnits: csvrow[DAUGHTER_AMOUNT_UNITS_INDEX].trim() + preparedBy: csvrow[DAUGHTER_PREPARED_BY_INDEX].trim() + preparedDate: csvrow[DAUGHTER_PREPARED_DATE_INDEX].trim() + physicalState: csvrow[DAUGHTER_PHYSICAL_STATE_INDEX].trim() + concentration: csvrow[DAUGHTER_CONCENTRATION_INDEX].trim() + concUnits: csvrow[DAUGHTER_CONC_UNITS_INDEX].trim() + solvent: csvrow[DAUGHTER_SOLVENT_INDEX].trim() + rowNumber: rowCount + if rowCount? and rowCount > 0 + csvFileEntries.push(fileEntry) + rowCount++ + ) + .on('end', () -> + return callback csvFileEntries, 200 + ) + +checkRequiredAttributes = (fileEntryArray, callback) -> + requiredAttributeErrors = [] + _.each fileEntryArray, (entry) -> + missingAttributes = [] + for attr in ['batchCode', 'destinationVialBarcode', 'sourceVialBarcode', 'amount', 'amountUnits', 'preparedBy', 'preparedDate', 'physicalState', 'concentration', 'concUnits', 'solvent'] + if entry[attr]? + if attr in ['concentration', 'concUnits', 'solvent'] + if entry.physicalState == 'solution' + if entry[attr] == "" + missingAttributes.push attr + else + if entry[attr] == "" + missingAttributes.push attr + if missingAttributes.length > 0 + error = + level: 'error' + message: "Row #{entry.rowNumber} is missing the required attributes: " + missingAttributes.join ', ' + requiredAttributeErrors.push error + callback requiredAttributeErrors + +checkDataTypeErrors = (fileEntryArray, callback) -> + dataTypeErrors = [] + _.each fileEntryArray, (entry) -> + if entry.amount? and entry.amount.length > 0 and isNaN(parseFloat(entry.amount)) + error = + level: 'error' + message: "Row #{entry.rowNumber} contains the invalid amount: #{entry.amount}" + dataTypeErrors.push error + if entry.concentration? and entry.concentration.length > 0 and isNaN(parseFloat(entry.concentration)) + error = + level: 'error' + message: "Row #{entry.rowNumber} contains the invalid concentration: #{entry.concentration}" + dataTypeErrors.push error + callback dataTypeErrors + +checkBatchCodesExist = (fileEntryArray, callback) -> + requests = [] + _.each fileEntryArray, (entry) -> + request = + requestName: entry.batchCode + requests.push request + csUtilities.getPreferredBatchIds requests, (batchIdResponse) -> + missingBatchCodes = [] + _.each batchIdResponse, (batchCodeRequest) -> + if batchCodeRequest.preferredName.length < 1 + missingBatchCodes.push batchCodeRequest.requestName + callback missingBatchCodes + +checkBarcodesExist = (barcodes, callback) -> + getContainerCodesFromLabelsInternal barcodes, 'container', 'tube', (containerCodes) -> + existingBarcodes = [] + newBarcodes = [] + _.each containerCodes, (containerCodeEntry) -> + if containerCodeEntry.foundCodeNames? and containerCodeEntry.foundCodeNames.length > 0 + existingBarcodes.push containerCodeEntry.requestLabel + else + newBarcodes.push containerCodeEntry.requestLabel + callback existingBarcodes, newBarcodes + +prepareValidationHTMLSummary = (hasError, errorMessages) -> + + 'html summary goes here' + +exports.createParentVialsFromCSVInternal = (csvFileName, user, callback) -> + getFileExists csvFileName, (exists, path) -> + createResponse = + results: + dryRun: true + fileToParse: csvFileName + htmlSummary: '' + hasError: true + hasWarning: false + errorMessages: [] + transactionId: null + if exists + createResponse.results.path = path + createParentVialFileEntryArray csvFileName, (fileEntryArray) -> + getContainerTubeDefinitionCode (definitionCode) -> + if !definitionCode? + error = + level: 'error' + message: 'Could not find definition container for tube' + createResponse.errorMessages.push error + tubesToCreate = [] + _.each fileEntryArray, (entry) -> + tube = + barcode: entry.destinationVialBarcode + definition: definitionCode + recordedBy: user + createdUser: entry.preparedBy + createdDate: entry.createdDate + physicalState: entry.physicalState + wells: [ + wellName: "A001" + batchCode: entry.batchCode + amount: parseFloat(entry.amount) + amountUnits: entry.amountUnits + physicalState: entry.physicalState + recordedBy: user + recordedDate: (new Date()).getTime() + ] + if entry.physicalState == 'solution' + tube.wells[0].batchConcentration = parseFloat(entry.concentration) + tube.wells[0].batchConcUnits = entry.concUnits + tube.wells[0].solventCode = entry.solvent + tubesToCreate.push tube + console.log JSON.stringify tubesToCreate + exports.createTubesInternal tubesToCreate, 0, (json, statusCode) -> + console.log json + callback json + else + error = + level: 'error' + message: "File cannot be found" + createResponse.errorMessages.push error + callback createResponse + +getContainerTubeDefinitionCode = (callback) -> + exports.containersByTypeKindInternal 'definition container', 'tube', 'codetable', false, false, (definitionContainers) -> + callback definitionContainers[0].code \ No newline at end of file From a0f43bb3577d6b4f1bd22f39423b217f51106128 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 22 Sep 2017 17:11:59 -0700 Subject: [PATCH 188/576] Added missing config --- conf/config.properties.example | 2 ++ 1 file changed, 2 insertions(+) diff --git a/conf/config.properties.example b/conf/config.properties.example index 25c3ba2c3..ac9ccce09 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -339,6 +339,8 @@ server.service.external.inventory.database.name= server.service.external.inventory.database.username= server.service.external.inventory.database.password= +client.compoundInventory.enforceUppercaseBarcodes=false + ## options for auth. strategy are: properties, database, ldap server.security.authstrategy=database #server.security.properties.path=/opt/seurat/SeuratServer/users.txt From 51e8bebc83b9981438c33a2faef03c0fe10511cc Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 26 Sep 2017 12:33:33 -0700 Subject: [PATCH 189/576] Added daughter aliquot loading route and completed html summary for both csv loader routes. Also exposed getWellCodesByPlateBarcodesInternal properly so it can be used in vial loading routes. --- .gitignore | 1 + .../routes/InventoryServiceRoutes.coffee | 488 +++++++++++++++--- 2 files changed, 423 insertions(+), 66 deletions(-) diff --git a/.gitignore b/.gitignore index fb38cfb25..fbc19bffb 100644 --- a/.gitignore +++ b/.gitignore @@ -26,3 +26,4 @@ build licenses #this is for the soft link in .dockerfile (git ignore .git by default) .git +chemaxon diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 57652fb4f..ddea9e109 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -58,6 +58,7 @@ exports.setupAPIRoutes = (app) -> app.post '/api/getContainerStatesByContainerValue', exports.getContainerStatesByContainerValue app.post '/api/getContainerLogsByContainerCodes', exports.getContainerLogsByContainerCodes app.post '/api/loadParentVialsFromCSV', exports.loadParentVialsFromCSV + app.post '/api/loadDaughterVialsFromCSV', exports.loadDaughterVialsFromCSV exports.setupRoutes = (app, loginRoutes) -> @@ -107,6 +108,8 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/createTubes', loginRoutes.ensureAuthenticated, exports.createTubes app.post '/api/throwInTrash', loginRoutes.ensureAuthenticated, exports.throwInTrash app.post '/api/updateContainerHistoryLogs', loginRoutes.ensureAuthenticated, exports.updateContainerHistoryLogs + app.post '/api/loadParentVialsFromCSV', loginRoutes.ensureAuthenticated, exports.loadParentVialsFromCSV + app.post '/api/loadDaughterVialsFromCSV', loginRoutes.ensureAuthenticated, exports.loadDaughterVialsFromCSV exports.getContainersInLocation = (req, resp) -> @@ -407,6 +410,31 @@ exports.getWellCodesByPlateBarcodes = (req, resp) -> resp.end JSON.stringify "getWellCodesByPlateBarcodes failed" ) +exports.getWellCodesByPlateBarcodesInternal = (plateBarcodes, callback) -> + if global.specRunnerTestmode + inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' + callback inventoryServiceTestJSON.getWellCodesByPlateBarcodesResponse + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containers/getWellCodesByPlateBarcodes" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: plateBarcodes + json: true + timeout: 86400000 + , (error, response, json) => + if !error && response.statusCode == 200 + callback json + else + console.error 'got ajax error trying to get getWellCodesByPlateBarcodes' + console.error error + console.error json + console.error response + callback "getWellCodesByPlateBarcodes failed" + ) + exports.getWellContent = (req, resp) -> req.setTimeout 86400000 exports.getWellContentInternal req.body, (json) -> @@ -2528,21 +2556,25 @@ exports.loadParentVialsFromCSV = (req, resp) -> exports.loadParentVialsFromCSVInternal = (csvFileName, dryRun, user, callback) -> if dryRun - exports.validateParentVialsFromCSVInternal csvFileName, (validationResponse) -> + exports.validateParentVialsFromCSVInternal csvFileName, dryRun, (validationResponse) -> callback validationResponse else - exports.createParentVialsFromCSVInternal csvFileName, user, (createVialsResponse) -> - callback createVialsResponse + exports.validateParentVialsFromCSVInternal csvFileName, dryRun, (validationResponse) -> + if validationResponse.hasError + callback validationResponse + else + exports.createParentVialsFromCSVInternal csvFileName, dryRun, user, (createVialsResponse) -> + callback createVialsResponse exports.validateParentVialsFromCSV = (req, resp) -> exports.validateParentVialsFromCSVInternal req.body.csvFileName, (validationResponse) -> resp.json validationResponse -exports.validateParentVialsFromCSVInternal = (csvFileName, callback) -> +exports.validateParentVialsFromCSVInternal = (csvFileName, dryRun, callback) -> getFileExists csvFileName, (exists, path) -> validationResponse = results: - dryRun: true + dryRun: dryRun fileToParse: csvFileName htmlSummary: '' hasError: true @@ -2552,7 +2584,7 @@ exports.validateParentVialsFromCSVInternal = (csvFileName, callback) -> if exists validationResponse.results.path = path createParentVialFileEntryArray csvFileName, (fileEntryArray) -> - console.log fileEntryArray + summaryInfo = prepareSummaryInfo fileEntryArray checkRequiredAttributes fileEntryArray, (requiredAttributeErrors) -> if requiredAttributeErrors? validationResponse.errorMessages.push requiredAttributeErrors... @@ -2560,21 +2592,21 @@ exports.validateParentVialsFromCSVInternal = (csvFileName, callback) -> if dataTypeErrors? validationResponse.errorMessages.push dataTypeErrors... checkBatchCodesExist fileEntryArray, (missingBatchCodeErrors) -> - if missingBatchCodeErrors? and missingBatchCodeErrors.length > 1 + if missingBatchCodeErrors? and missingBatchCodeErrors.length > 0 error = level: 'error' message: "The following batches do not exist: "+ missingBatchCodeErrors.join ', ' validationResponse.errorMessages.push error barcodes = _.pluck fileEntryArray, 'destinationVialBarcode' checkBarcodesExist barcodes, (existingBarcodes, newBarcodes) -> - if existingBarcodes? and existingBarcodes.length > 1 + if existingBarcodes? and existingBarcodes.length > 0 error = level: 'error' message: "The following barcodes already exist: " + existingBarcodes.join ', ' validationResponse.errorMessages.push error if validationResponse.errorMessages.length < 1 validationResponse.hasError = false - validationResponse.results.htmlSummary = prepareValidationHTMLSummary validationResponse.hasError, validationResponse.errorMessages + validationResponse.results.htmlSummary = prepareValidationHTMLSummary validationResponse.hasError, validationResponse.hasWarning, validationResponse.errorMessages, summaryInfo callback validationResponse else error = @@ -2583,6 +2615,234 @@ exports.validateParentVialsFromCSVInternal = (csvFileName, callback) -> validationResponse.errorMessages.push error callback validationResponse +exports.createParentVialsFromCSVInternal = (csvFileName, dryRun, user, callback) -> + getFileExists csvFileName, (exists, path) -> + createResponse = + results: + dryRun: dryRun + fileToParse: csvFileName + htmlSummary: '' + hasError: true + hasWarning: false + errorMessages: [] + transactionId: null + commit: false + if exists + createResponse.results.path = path + createParentVialFileEntryArray csvFileName, (fileEntryArray) -> + summaryInfo = prepareSummaryInfo fileEntryArray + getContainerTubeDefinitionCode (definitionCode) -> + if !definitionCode? + error = + level: 'error' + message: 'Could not find definition container for tube' + createResponse.errorMessages.push error + tubesToCreate = [] + _.each fileEntryArray, (entry) -> + tube = + barcode: entry.destinationVialBarcode + definition: definitionCode + recordedBy: user + createdUser: entry.preparedBy + createdDate: entry.createdDate + physicalState: entry.physicalState + wells: [ + wellName: "A001" + batchCode: entry.batchCode + amount: parseFloat(entry.amount) + amountUnits: entry.amountUnits + physicalState: entry.physicalState + recordedBy: user + recordedDate: (new Date()).getTime() + ] + if entry.physicalState == 'solution' + tube.wells[0].batchConcentration = parseFloat(entry.concentration) + tube.wells[0].batchConcUnits = entry.concUnits + tube.wells[0].solventCode = entry.solvent + tubesToCreate.push tube + console.log JSON.stringify tubesToCreate + exports.createTubesInternal tubesToCreate, 0, (json, statusCode) -> + console.log statusCode + console.log json + if statusCode != 200 + createResponse.hasError = true + console.error json + error = + level: 'error' + message: json + createResponse.errorMessages.push error + else + createResponse.hasError = false + createResponse.commit = true + createResponse.results.htmlSummary = prepareCreateParentVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo + callback createResponse + else + error = + level: 'error' + message: "File cannot be found" + createResponse.errorMessages.push error + callback createResponse + +exports.loadDaughterVialsFromCSV = (req, resp) -> + exports.loadDaughterVialsFromCSVInternal req.body.fileToParse, req.body.dryRunMode, req.body.user, (response) -> + resp.json response + +exports.loadDaughterVialsFromCSVInternal = (csvFileName, dryRun, user, callback) -> + if dryRun + exports.validateDaughterVialsFromCSVInternal csvFileName, dryRun, (validationResponse) -> + callback validationResponse + else + exports.validateDaughterVialsFromCSVInternal csvFileName, dryRun, (validationResponse) -> + if validationResponse.hasError + callback validationResponse + else + exports.createDaughterVialsFromCSVInternal csvFileName, dryRun, user, (createVialsResponse) -> + callback createVialsResponse + +exports.validateDaughterVialsFromCSV = (req, resp) -> + exports.validateDaughterVialsFromCSVInternal req.body.csvFileName, (validationResponse) -> + resp.json validationResponse + +exports.validateDaughterVialsFromCSVInternal = (csvFileName, dryRun, callback) -> + getFileExists csvFileName, (exists, path) -> + validationResponse = + results: + dryRun: dryRun + fileToParse: csvFileName + htmlSummary: '' + hasError: true + hasWarning: false + errorMessages: [] + transactionId: null + if exists + validationResponse.results.path = path + createDaughterVialFileEntryArray csvFileName, (fileEntryArray) -> + summaryInfo = prepareSummaryInfo fileEntryArray + checkRequiredAttributes fileEntryArray, (requiredAttributeErrors) -> + if requiredAttributeErrors? + validationResponse.errorMessages.push requiredAttributeErrors... + checkDataTypeErrors fileEntryArray, (dataTypeErrors) -> + if dataTypeErrors? + validationResponse.errorMessages.push dataTypeErrors... + sourceBarcodes = _.pluck fileEntryArray, 'sourceVialBarcode' + checkBarcodesExist sourceBarcodes, (existingBarcodes, newBarcodes) -> + console.log 'checking source vial barcodes which should exist' + console.log existingBarcodes + console.log newBarcodes + if newBarcodes? and newBarcodes.length > 0 + error = + level: 'error' + message: "The following source barcodes do not exist: " + newBarcodes.join ', ' + validationResponse.errorMessages.push error + destinationBarcodes = _.pluck fileEntryArray, 'destinationVialBarcode' + checkBarcodesExist destinationBarcodes, (existingBarcodes, newBarcodes) -> + if existingBarcodes? and existingBarcodes.length > 0 + error = + level: 'error' + message: "The following destination barcodes already exist: " + existingBarcodes.join ', ' + validationResponse.errorMessages.push error + checkParentWellContent fileEntryArray, (parentWellContentErrors) -> + if parentWellContentErrors? + validationResponse.errorMessages.push parentWellContentErrors... + if validationResponse.errorMessages.length < 1 + validationResponse.hasError = false + validationResponse.results.htmlSummary = prepareValidationHTMLSummary validationResponse.hasError, validationResponse.hasWarning, validationResponse.errorMessages, summaryInfo + callback validationResponse + else + error = + level: 'error' + message: "File cannot be found" + validationResponse.errorMessages.push error + callback validationResponse + +exports.createDaughterVialsFromCSVInternal = (csvFileName, dryRun, user, callback) -> + getFileExists csvFileName, (exists, path) -> + createResponse = + results: + dryRun: dryRun + fileToParse: csvFileName + htmlSummary: '' + hasError: true + hasWarning: false + errorMessages: [] + transactionId: null + commit: false + if exists + createResponse.results.path = path + createDaughterVialFileEntryArray csvFileName, (fileEntryArray) -> + summaryInfo = prepareSummaryInfo fileEntryArray + getContainerTubeDefinitionCode (definitionCode) -> + if !definitionCode? + error = + level: 'error' + message: 'Could not find definition container for tube' + createResponse.errorMessages.push error + tubesToCreate = [] + _.each fileEntryArray, (entry) -> + tube = + barcode: entry.destinationVialBarcode + definition: definitionCode + recordedBy: user + createdUser: entry.preparedBy + createdDate: entry.createdDate + physicalState: entry.physicalState + wells: [ + wellName: "A001" + batchCode: entry.batchCode + amount: parseFloat(entry.amount) + amountUnits: entry.amountUnits + physicalState: entry.physicalState + recordedBy: user + recordedDate: (new Date()).getTime() + ] + if entry.physicalState == 'solution' + tube.wells[0].batchConcentration = parseFloat(entry.concentration) + tube.wells[0].batchConcUnits = entry.concUnits + tube.wells[0].solventCode = entry.solvent + tubesToCreate.push tube + console.log JSON.stringify tubesToCreate + exports.createTubesInternal tubesToCreate, 0, (json, statusCode) -> + console.log statusCode + console.log json + if statusCode != 200 + createResponse.hasError = true + console.error json + error = + level: 'error' + message: json + createResponse.errorMessages.push error + else + createResponse.hasError = false + createResponse.commit = true + if !createResponse.hasError + #TODO: create interactions or values of daughter to parent relation + parentVialsToDecrement = [] + _.each fileEntryArray, (entry) -> + toDecrement = + barcode: entry.sourceVialBarcode + amountToDecrement: parseFloat(entry.amount) + amountToDecrementUnits: entry.amountUnits + parentVialsToDecrement.push toDecrement + decrementAmountsFromVials parentVialsToDecrement, user, (decrementVialsResponse, decrementVialsStatusCode) -> + if decrementVialsStatusCode != 200 + error = + level: 'error' + message: decrementVialsResponse + createResponse.errorMessages.push error + createResponse.hasError = true + createResponse.results.htmlSummary = prepareCreateDaughterVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo + callback createResponse + else + createResponse.results.htmlSummary = prepareCreateDaughterVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo + callback createResponse + else + error = + level: 'error' + message: "File cannot be found" + createResponse.errorMessages.push error + callback createResponse + + getFileExists = (csvFileName, callback) => exists = false path = config.all.server.file.server.path + '/' @@ -2712,64 +2972,160 @@ checkBarcodesExist = (barcodes, callback) -> newBarcodes.push containerCodeEntry.requestLabel callback existingBarcodes, newBarcodes -prepareValidationHTMLSummary = (hasError, errorMessages) -> - - 'html summary goes here' +checkParentWellContent = (fileEntryArray, callback) -> + #The purpose of this function is to check that the source vial content is compatible with the daughter content being loaded in, including + #physical state must match + #amount in parent vial would be negative if the daughter amount is removed + #amount units match + #concentration and concentration units match if solution + errorMessages = [] + vialBarcodes = _.pluck fileEntryArray, 'sourceVialBarcode' + exports.getWellContentByContainerLabelsInternal vialBarcodes, 'container', 'tube', 'barcode', 'barcode', (wellContentList, statusCode) -> + _.each fileEntryArray, (fileEntry) -> + parentVialAndWellContent = _.findWhere wellContentList, {label: fileEntry.sourceVialBarcode} + if parentVialAndWellContent.wellContent? + parentWellContent = parentVialAndWellContent.wellContent[0] + if parentWellContent.physicalState != fileEntry.physicalState + error = + level: 'error' + message: "Daughter vial #{fileEntry.destinationVialBarcode} must be of the same physical state as parent vial #{fileEntry.sourceVialBarcode}, which is #{parentWellContent.physicalState}." + errorMessages.push error + if fileEntry.physicalState == 'solution' and (Math.abs(parseFloat(fileEntry.concentration) - parentWellContent.batchConcentration) > 0.0001 or fileEntry.concUnits != parentWellContent.batchConcUnits) + error = + level: 'error' + message: "Daughter vial #{fileEntry.destinationVialBarcode} must have the same concentration as parent vial #{fileEntry.sourceVialBarcode}, which is #{parentWellContent.batchConcentration} #{parentWellContent.batchConcUnits}." + errorMessages.push error + if parentWellContent.amountUnits != fileEntry.amountUnits + error = + level: 'error' + message: "Daughter vial #{fileEntry.destinationVialBarcode} must use the same amount units as parent vial #{fileEntry.sourceVialBarcode}, which is in #{parentWellContent.amountUnits}." + errorMessages.push error + else if parentWellContent.amount < parseFloat(fileEntry.amount) + error = + level: 'warning' + message: "Creating daughter vial #{fileEntry.destinationVialBarcode} will remove more than the total amount currently in parent vial #{fileEntry.sourceVialBarcode}, leaving a negative amount in the parent vial." + errorMessages.push error + else + error = + level: 'error' + message: "Could not find a well for barcode #{fileEntry.sourceVialBarcode}" + errorMessages.push error + console.log errorMessages + callback errorMessages + -exports.createParentVialsFromCSVInternal = (csvFileName, user, callback) -> - getFileExists csvFileName, (exists, path) -> - createResponse = - results: - dryRun: true - fileToParse: csvFileName - htmlSummary: '' - hasError: true - hasWarning: false - errorMessages: [] - transactionId: null - if exists - createResponse.results.path = path - createParentVialFileEntryArray csvFileName, (fileEntryArray) -> - getContainerTubeDefinitionCode (definitionCode) -> - if !definitionCode? - error = - level: 'error' - message: 'Could not find definition container for tube' - createResponse.errorMessages.push error - tubesToCreate = [] - _.each fileEntryArray, (entry) -> - tube = - barcode: entry.destinationVialBarcode - definition: definitionCode - recordedBy: user - createdUser: entry.preparedBy - createdDate: entry.createdDate - physicalState: entry.physicalState - wells: [ - wellName: "A001" - batchCode: entry.batchCode - amount: parseFloat(entry.amount) - amountUnits: entry.amountUnits - physicalState: entry.physicalState - recordedBy: user - recordedDate: (new Date()).getTime() - ] - if entry.physicalState == 'solution' - tube.wells[0].batchConcentration = parseFloat(entry.concentration) - tube.wells[0].batchConcUnits = entry.concUnits - tube.wells[0].solventCode = entry.solvent - tubesToCreate.push tube - console.log JSON.stringify tubesToCreate - exports.createTubesInternal tubesToCreate, 0, (json, statusCode) -> - console.log json - callback json - else - error = - level: 'error' - message: "File cannot be found" - createResponse.errorMessages.push error - callback createResponse + + +prepareValidationHTMLSummary = (hasError, hasWarning, errorMessages, summaryInfo) -> + errors = _.where errorMessages, {level: 'error'} + warnings = _.where errorMessages, {level: 'warning'} + errorHeader = "

      Please fix the following errors and use the 'Back' button at the bottom of this screen to upload a new version of the file.

      " + if hasWarning + successHeader = "

      Please review the warnings and summary before uploading.

      " + else + successHeader = "

      Please review the summary before uploading.

      " + errorsBlock = "\n

      Errors: #{errors.length}

      \n
        " + _.each errors, (error) -> + errorsBlock += "
      • #{error.message}
        • " + errorsBlock += "
      " + warningsBlock = "\n

      Warnings: #{warnings.length}

      \n

      Warnings provide information on issues found in the upload file. You can proceed with warnings; however, it is recommended that, if possible, you make the changes suggested by the warnings and upload a new version of the file by using the 'Back' button at the bottom of this screen.

      \n
        " + _.each warnings, (warning) -> + warningsBlock += "
      • #{warning.message}
        • " + warningsBlock += "
      " + htmlSummaryInfo = "

      Summary

      Information:

      \n
        \n " + htmlSummaryInfo += "
      • Total Vials: #{summaryInfo.totalNumberOfVials}
        • " + htmlSummaryInfo += "
      • Solid Vials: #{summaryInfo.numSolidVials}
        • " + htmlSummaryInfo += "
      • Liquid Vials: #{summaryInfo.numLiquidVials}
        • " + if summaryInfo.totalBatchCodes? + htmlSummaryInfo += "
      • Unique Corporate Batch ID's: #{summaryInfo.totalBatchCodes}
        • " + htmlSummaryInfo += "\n
      " + htmlSummary = "" + if hasError + htmlSummary += errorHeader + errorsBlock + else + htmlSummary += successHeader + if hasWarning + htmlSummary += warningsBlock + if !hasError + htmlSummary += htmlSummaryInfo + htmlSummary + +prepareCreateParentVialsHTMLSummary = (hasError, hasWarning, errorMessages, summaryInfo) -> + errors = _.where errorMessages, {level: 'error'} + warnings = _.where errorMessages, {level: 'warning'} + errorHeader = "

      An error occurred during uploading. If the messages below are unhelpful, you will need to contact your system administrator.

      " + #TODO implement HTML summary for successful upload + successHeader = "

      Upload completed.

      " + errorsBlock = "\n

      Errors: #{errors.length}

      \n
        " + _.each errors, (error) -> + errorsBlock += "
      • #{error.message}
        • " + errorsBlock += "
      " + warningsBlock = "\n

      Warnings: #{warnings.length}

      \n

      Warnings provide information on issues found in the upload file. You can proceed with warnings; however, it is recommended that, if possible, you make the changes suggested by the warnings and upload a new version of the file by using the 'Back' button at the bottom of this screen.

      \n
        " + _.each warnings, (warning) -> + warningsBlock += "
      • #{warning.message}
        • " + warningsBlock += "
      " + htmlSummary = "" + if hasError + htmlSummary += errorHeader + errorsBlock + else + htmlSummary += successHeader + if hasWarning + htmlSummary += warningsBlock + htmlSummary getContainerTubeDefinitionCode = (callback) -> exports.containersByTypeKindInternal 'definition container', 'tube', 'codetable', false, false, (definitionContainers) -> - callback definitionContainers[0].code \ No newline at end of file + callback definitionContainers[0].code + +decrementAmountsFromVials = (parentVialsToDecrement, user, callback) -> + vialBarcodes = _.pluck parentVialsToDecrement, 'barcode' + exports.getWellContentByContainerLabelsInternal vialBarcodes, 'container', 'tube', 'barcode', 'barcode', (wellContentList, statusCode) -> + wellsToUpdate = [] + _.each parentVialsToDecrement, (toDecrement) -> + wellCode = (_.findWhere plateWellCodes, {plateBarcode: toDecrement.barcode}).wellCodeName + oldContainerWellContent = _.findWhere wellContentList, {containerCodeName: wellCode} + oldWellContent = oldContainerWellContent.wellContent[0] + newWellContent = + containerCodeName: wellCode + amount: oldWellContent.amount - toDecrement.amountToDecrement + recordedBy: user + wellsToUpdate.push newWellContent + console.log wellsToUpdate + exports.updateWellContentInternal wellsToUpdate, true, false, (updateWellsResponse, updateWellsStatusCode) -> + console.log updateWellsStatusCode + if updateWellsStatusCode != 204 + callback "Error: #{updateWellsResponse}" + else + callback updateWellsResponse, 200 + +prepareCreateDaughterVialsHTMLSummary = (hasError, hasWarning, errorMessages, summaryInfo) -> + errors = _.where errorMessages, {level: 'error'} + warnings = _.where errorMessages, {level: 'warning'} + errorHeader = "

      An error occurred during uploading. If the messages below are unhelpful, you will need to contact your system administrator.

      " + successHeader = "

      Upload completed.

      " + errorsBlock = "\n

      Errors: #{errors.length}

      \n
        " + _.each errors, (error) -> + errorsBlock += "
      • #{error.message}
        • " + errorsBlock += "
      " + warningsBlock = "\n

      Warnings: #{warnings.length}

      \n

      Warnings provide information on issues found in the upload file. You can proceed with warnings; however, it is recommended that, if possible, you make the changes suggested by the warnings and upload a new version of the file by using the 'Back' button at the bottom of this screen.

      \n
        " + _.each warnings, (warning) -> + warningsBlock += "
      • #{warning.message}
        • " + warningsBlock += "
      " + htmlSummary = "" + if hasError + htmlSummary += errorHeader + errorsBlock + else + htmlSummary += successHeader + if hasWarning + htmlSummary += warningsBlock + htmlSummary + +prepareSummaryInfo = (fileEntryArray) -> + summaryInfo = + totalNumberOfVials: fileEntryArray.length + numSolidVials: (_.where fileEntryArray, {physicalState: 'solid'}).length + numLiquidVials: (_.where fileEntryArray, {physicalState: 'solution'}).length + batchCodes = _.pluck fileEntryArray, 'batchCode' + if batchCodes? + summaryInfo.totalBatchCodes = (_.uniq batchCodes).length + summaryInfo \ No newline at end of file From 4a2a85bdc4cdd5c08821a6002f6db62607f5246d Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 29 Jun 2017 15:16:10 -0700 Subject: [PATCH 190/576] Imported Ketcher from EPAM (GNU Affero GPL) and created new basic controller and view for it. --- .../client/ACASFormChemicalStructure.coffee | 25 + .../client/ACASFormChemicalStructureView.html | 4 + public/lib/ketcher-2.0.0-alpha.3/LICENSE | 632 ++++++++ public/lib/ketcher-2.0.0-alpha.3/demo.html | 126 ++ public/lib/ketcher-2.0.0-alpha.3/favicon.ico | Bin 0 -> 1078 bytes public/lib/ketcher-2.0.0-alpha.3/ketcher.css | 1 + public/lib/ketcher-2.0.0-alpha.3/ketcher.eot | Bin 0 -> 26576 bytes public/lib/ketcher-2.0.0-alpha.3/ketcher.html | 1322 +++++++++++++++++ public/lib/ketcher-2.0.0-alpha.3/ketcher.js | 1068 +++++++++++++ public/lib/ketcher-2.0.0-alpha.3/ketcher.py | 330 ++++ public/lib/ketcher-2.0.0-alpha.3/ketcher.svg | 138 ++ public/lib/ketcher-2.0.0-alpha.3/ketcher.ttf | Bin 0 -> 17072 bytes public/lib/ketcher-2.0.0-alpha.3/ketcher.woff | Bin 0 -> 16164 bytes public/lib/ketcher-2.0.0-alpha.3/logo.jpg | Bin 0 -> 5816 bytes .../ketcher-2.0.0-alpha.3/prototype-min.js | 8 + .../lib/ketcher-2.0.0-alpha.3/raphael.min.js | 3 + .../lib/ketcher-2.0.0-alpha.3/templates.sdf | 368 +++++ 17 files changed, 4025 insertions(+) create mode 100644 public/lib/ketcher-2.0.0-alpha.3/LICENSE create mode 100644 public/lib/ketcher-2.0.0-alpha.3/demo.html create mode 100644 public/lib/ketcher-2.0.0-alpha.3/favicon.ico create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.css create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.eot create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.html create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.js create mode 100755 public/lib/ketcher-2.0.0-alpha.3/ketcher.py create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.svg create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.ttf create mode 100644 public/lib/ketcher-2.0.0-alpha.3/ketcher.woff create mode 100644 public/lib/ketcher-2.0.0-alpha.3/logo.jpg create mode 100644 public/lib/ketcher-2.0.0-alpha.3/prototype-min.js create mode 100644 public/lib/ketcher-2.0.0-alpha.3/raphael.min.js create mode 100644 public/lib/ketcher-2.0.0-alpha.3/templates.sdf diff --git a/modules/Components/src/client/ACASFormChemicalStructure.coffee b/modules/Components/src/client/ACASFormChemicalStructure.coffee index b523b3667..54ca2da13 100644 --- a/modules/Components/src/client/ACASFormChemicalStructure.coffee +++ b/modules/Components/src/client/ACASFormChemicalStructure.coffee @@ -63,3 +63,28 @@ class window.ACASFormChemicalStructureController extends Backbone.View #TODO Why is it making a call to WebHQ outside our server, and make it stop +class window.KetcherChemicalStructureController extends Backbone.View + tagName: "DIV" + template: _.template($("#KetcherChemicalStructureControllerView").html()) + + render: => + $(@el).empty() + $(@el).html @template() + + searchFrameURL = "/lib/ketcher-2.0.0-alpha.3/ketcher.html" + + @$('.bv_sketcherIFrame').attr 'src', searchFrameURL + + @$('.bv_sketcherIFrame').on 'load', @startSketcher + + @ + + startSketcher: => + @windowObj = @$('.bv_sketcherIFrame')[0].contentWindow + @trigger 'sketcherLoaded' + + getMol: -> + @windowObj.ketcher.getMolfile(); + + setMol: (molStr) -> + molStruct = @windowObj.ketcher.setMolecule molStr diff --git a/modules/Components/src/client/ACASFormChemicalStructureView.html b/modules/Components/src/client/ACASFormChemicalStructureView.html index 94e7147f1..269c44ff3 100644 --- a/modules/Components/src/client/ACASFormChemicalStructureView.html +++ b/modules/Components/src/client/ACASFormChemicalStructureView.html @@ -9,3 +9,7 @@

      Test sketcher thingy

      + + diff --git a/public/lib/ketcher-2.0.0-alpha.3/LICENSE b/public/lib/ketcher-2.0.0-alpha.3/LICENSE new file mode 100644 index 000000000..677c7cd75 --- /dev/null +++ b/public/lib/ketcher-2.0.0-alpha.3/LICENSE @@ -0,0 +1,632 @@ + Ketcher is Copyright (C) of EPAM Systems 2009-2015. + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published + by the Free Software Foundation, version 3 of the License. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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If the Program does not specify a version number of the +GNU Affero General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU Affero General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS diff --git a/public/lib/ketcher-2.0.0-alpha.3/demo.html b/public/lib/ketcher-2.0.0-alpha.3/demo.html new file mode 100644 index 000000000..b72332b6a --- /dev/null +++ b/public/lib/ketcher-2.0.0-alpha.3/demo.html @@ -0,0 +1,126 @@ + + + + + + Ketcher demo + + + + + + + +

      Ketcher example

      + + +

      Ketcher interaction example

      +
      + +
        + + + + + + + +
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.save{font-size:1.1em;height:2em;width:2.5em;line-height:1;vertical-align:middle;padding:.15em;background:inherit}#generics-table button:hover,#generics-table #open-file .open:hover,#generics-table #save-file .save:hover{-webkit-transition:-webkit-transform .2s ease-out;-moz-transition:-moz-transform .2s ease-out;-o-transition:-o-transform .2s ease-out;transition:-webkit-transform .2s ease-out,-moz-transform .2s ease-out,-o-transform .2s ease-out,transform .2s ease-out;-webkit-transform:scale(1.25);-moz-transform:scale(1.25);-o-transform:scale(1.25);-ms-transform:scale(1.25);transform:scale(1.25);-webkit-box-shadow:inset 0 0 1px 1px rgba(0,0,0,.12);-moz-box-shadow:inset 0 0 1px 1px rgba(0,0,0,.12);box-shadow:inset 0 0 1px 1px rgba(0,0,0,.12)}#generics-table button:active,#generics-table #open-file .open:active,#generics-table #save-file .save:active{-webkit-transform:scale(1);-moz-transform:scale(1);-o-transform:scale(1);-ms-transform:scale(1);transform:scale(1);-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none}#generics-table button.selected,#generics-table #open-file .open.selected,#generics-table #save-file .save.selected{background:#444;color:#fff}#open-file label{display:block}#open-file textarea{width:32em;height:23em;overflow:auto;white-space:pre;resize:both}#open-file .open{float:left}#open-file input[type=file]{left:-9999px;position:absolute}#save-file label{display:block;text-align:right}#save-file select{width:16em}#save-file textarea{width:32em;height:23em;overflow:auto;white-space:pre;resize:both}#save-file .save{float:left}li,ul,menu{list-style:none;margin:0;padding:0}html{height:100%;width:100%}body{min-height:100%;position:relative;font:14px FreeSans,Arimo,"Droid Sans",Helvetica,"Helvetica Neue",Arial,sans-serif;background-color:#fff;color:#333}main{position:absolute;border:#ccc 1px solid;-webkit-border-radius:5px;-webkit-background-clip:padding-box;-moz-border-radius:5px;-moz-background-clip:padding;border-radius:5px;background-clip:padding-box;overflow:auto;top:45px;left:45px;right:45px;bottom:45px}#mainmenu{position:absolute;top:3px;left:45px;right:45px;height:40px}#mainmenu>menu{width:100%}#elements{position:absolute;right:3px;top:45px;bottom:45px;width:40px}#elements>menu{height:100%}#template{position:absolute;bottom:3px;left:45px;right:45px;height:40px}#template>menu{width:100%}#toolbox{position:absolute;left:3px;top:45px;bottom:45px;width:40px}#toolbox>menu{height:100%}#meta{position:absolute;right:0}#generic-groups{position:absolute;bottom:0;left:0}[role=toolbar]{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;user-select:none}[role=toolbar] menu{font-size:0;-webkit-text-size-adjust:none}[role=toolbar] li{display:inline-block;vertical-align:top}[role=toolbar] button,[role=toolbar] #open-file .open,[role=toolbar] #save-file .save{-webkit-border-radius:4px;-webkit-background-clip:padding-box;-moz-border-radius:4px;-moz-background-clip:padding;border-radius:4px;background-clip:padding-box;display:block;border:0;padding:0;position:relative;background:inherit;background-color:#fff;width:32px;height:32px;margin:4px}[role=toolbar] button:active,[role=toolbar] button:focus,[role=toolbar] #open-file .open:active,[role=toolbar] #open-file .open:focus,[role=toolbar] #save-file .save:active,[role=toolbar] #save-file .save:focus{outline:0}[role=toolbar] button:before,[role=toolbar] button:after,[role=toolbar] #open-file .open:before,[role=toolbar] #open-file .open:after,[role=toolbar] #save-file .save:before,[role=toolbar] #save-file .save:after{display:inline-block;vertical-align:middle;font-family:ketcher}[role=toolbar] button:after,[role=toolbar] #open-file .open:after,[role=toolbar] #save-file .save:after{position:absolute;left:0}[role=toolbar] button:hover,[role=toolbar] #open-file .open:hover,[role=toolbar] #save-file .save:hover{-webkit-transition:-webkit-transform .2s ease-out;-moz-transition:-moz-transform .2s ease-out;-o-transition:-o-transform .2s ease-out;transition:-webkit-transform .2s ease-out,-moz-transform .2s ease-out,-o-transform .2s ease-out,transform .2s ease-out;-webkit-transform:scale(1.25);-moz-transform:scale(1.25);-o-transform:scale(1.25);-ms-transform:scale(1.25);transform:scale(1.25);-webkit-box-shadow:inset 0 0 1px 1px rgba(0,0,0,.12);-moz-box-shadow:inset 0 0 1px 1px rgba(0,0,0,.12);box-shadow:inset 0 0 1px 1px rgba(0,0,0,.12)}[role=toolbar] button:active,[role=toolbar] button[disabled],[role=toolbar] #open-file .open:active,[role=toolbar] #open-file .open[disabled],[role=toolbar] #save-file .save:active,[role=toolbar] #save-file .save[disabled]{-webkit-transform:scale(1);-moz-transform:scale(1);-o-transform:scale(1);-ms-transform:scale(1);transform:scale(1);-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none}[role=toolbar] button:before,[role=toolbar] button:after,[role=toolbar] #open-file .open:before,[role=toolbar] #open-file .open:after,[role=toolbar] #save-file .save:before,[role=toolbar] #save-file .save:after{font-size:26px}[role=toolbar] .selected button,[role=toolbar] .selected #open-file .open,[role=toolbar] .selected #save-file .save{background:#444;color:#fff}[role=toolbar] kbd{display:none;font:.8em monospace;color:#ccc}input.cliparea{position:absolute;bottom:0;left:0;width:10px;height:10px;display:block;font-size:1;z-index:-1;color:transparent;background:0 0;overflow:hidden;border:none;padding:0;resize:none;outline:0;-webkit-user-select:text;user-select:text}li.opened>menu{margin:0!important;position:absolute;left:47px;z-index:20;white-space:nowrap;word-break:keep-all;padding:2px;background:#fff;border:1px solid #ccc;-webkit-border-radius:5px;-webkit-background-clip:padding-box;-moz-border-radius:5px;-moz-background-clip:padding;border-radius:5px;background-clip:padding-box;-webkit-box-shadow:0 6px 12px rgba(0,0,0,.175);-moz-box-shadow:0 6px 12px rgba(0,0,0,.175);box-shadow:0 6px 12px rgba(0,0,0,.175)}li.opened>menu li+li>menu{margin-top:3px;border-top:1px solid #ccc;padding-top:2px}#atom button,#atom #open-file .open,#atom #save-file .save{font-size:19px}#atom kbd{display:none}select{font-size:14px}#select,#bond-common,#bond-stereo,#bond-query,#reaction{position:relative;overflow:hidden;height:40px;width:100%}#select:after,#bond-common:after,#bond-stereo:after,#bond-query:after,#reaction:after{font-size:7px;width:7px;height:7px;display:block;font-family:ketcher;content:'\e818';position:absolute;z-index:10;right:0;bottom:0}#select:hover:after,#bond-common:hover:after,#bond-stereo:hover:after,#bond-query:hover:after,#reaction:hover:after{color:#1a7090}#select.opened,#bond-common.opened,#bond-stereo.opened,#bond-query.opened,#reaction.opened{overflow:visible}@media (max-width:850px){#bond-common,#bond-stereo,#bond-query{height:32px;width:100%}}@media (max-height:850px){#rgroup{position:relative;overflow:hidden;height:40px;width:100%}#rgroup:after{font-size:7px;width:7px;height:7px;display:block;font-family:ketcher;content:'\e818';position:absolute;z-index:10;right:0;bottom:0}#rgroup:hover:after{color:#1a7090}#rgroup.opened{overflow:visible}}@media (max-height:850px) and (max-width:850px){#rgroup{height:32px;width:100%}}@media (max-height:800px){#transform{position:relative;overflow:hidden;height:40px;width:100%}#transform:after{font-size:7px;width:7px;height:7px;display:block;font-family:ketcher;content:'\e818';position:absolute;z-index:10;right:0;bottom:0}#transform:hover:after{color:#1a7090}#transform.opened{overflow:visible}}@media (max-height:800px) and (max-width:850px){#transform{height:32px;width:100%}}@media (max-height:700px){li.opened li{display:block}li.opened button,li.opened #open-file .open,li.opened #save-file .save{display:block;width:100%;margin:1px 0;padding:.3em 4.5em .3em .3em;height:1.7em;font-size:14px;text-align:left}li.opened button:before,li.opened button:after,li.opened #open-file .open:before,li.opened #open-file .open:after,li.opened #save-file .save:before,li.opened #save-file .save:after{padding-right:.4em;font-size:18px}li.opened button[disabled],li.opened #open-file .open[disabled],li.opened #save-file .save[disabled]{background:inherit;color:#baa}li.opened button:hover,li.opened .selected button,li.opened #open-file .open:hover,li.opened .selected #open-file .open,li.opened #save-file .save:hover,li.opened .selected #save-file .save{-webkit-transform:scale(1);-moz-transform:scale(1);-o-transform:scale(1);-ms-transform:scale(1);transform:scale(1);-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none;background:#444;color:#fff}li.opened kbd{display:inline-block;position:absolute;right:.5em}#bond-common,#bond-stereo,#bond-query{position:static;overflow:visible;height:auto;width:auto}#bond-common:after,#bond-stereo:after,#bond-query:after{content:none}#bond{position:relative;overflow:hidden;height:40px;width:100%}#bond:after{font-size:7px;width:7px;height:7px;display:block;font-family:ketcher;content:'\e818';position:absolute;z-index:10;right:0;bottom:0}#bond:hover:after{color:#1a7090}#bond.opened{overflow:visible}}@media (max-height:700px) and (max-width:850px){li.opened button,li.opened #open-file .open,li.opened #save-file .save{font-size:12px}li.opened button:before,li.opened button:after,li.opened #open-file .open:before,li.opened #open-file .open:after,li.opened #save-file .save:before,li.opened #save-file .save:after{font-size:16px}#bond{height:32px;width:100%}}@media (max-height:600px){#rgroup,#transform,#bond{height:32px;width:100%}}@media (min-width:650px){#document+li,#edit+li,#zoom+li{margin-left:15px;border-left:1px solid #ccc;padding-left:14px}}@media (min-height:800px){#sgroup+li{margin-top:10px;border-top:1px solid #ccc;padding-top:9px}}@media (min-height:650px){#erase+li,#chain+li,#charge+li,#transform+li,#atom+li{margin-top:10px;border-top:1px solid #ccc;padding-top:9px}}@media (max-height:600px),(max-width:850px){body,select{font-size:11px}main{top:37px;left:37px;right:37px;bottom:37px}#mainmenu,#template{left:37px;right:37px;height:32px}#elements,#toolbox{top:37px;bottom:37px;width:32px}[role=toolbar] button,[role=toolbar] #open-file .open,[role=toolbar] #save-file .save{width:24px;height:24px;margin:4px}[role=toolbar] button:before,[role=toolbar] button:after,[role=toolbar] #open-file .open:before,[role=toolbar] #open-file .open:after,[role=toolbar] #save-file .save:before,[role=toolbar] #save-file .save:after{font-size:20px}#select,#reaction{height:32px;width:100%}li.opened>menu{left:37px}#atom button,#atom #open-file .open,#atom #save-file .save{font-size:16px}}@media (max-width:720px){#meta{display:none}#mainmenu{right:0}body{min-width:520px}}#arom button:before,#arom #open-file .open:before,#arom #save-file .save:before{content:'\e804'}#bond-any button:before,#bond-any #open-file .open:before,#bond-any #save-file .save:before{content:'\e805'}#bond-aromatic button:before,#bond-aromatic #open-file .open:before,#bond-aromatic #save-file .save:before{content:'\e806'}#bond-crossed button:before,#bond-crossed #open-file .open:before,#bond-crossed #save-file .save:before{content:'\e807'}#bond-double button:before,#bond-double #open-file .open:before,#bond-double #save-file .save:before{content:'\e808'}#bond-doublearomatic button:before,#bond-doublearomatic #open-file .open:before,#bond-doublearomatic #save-file .save:before{content:'\e809'}#bond-down button:before,#bond-down #open-file .open:before,#bond-down #save-file .save:before{content:'\e80a'}#bond-single button:before,#bond-single #open-file .open:before,#bond-single #save-file .save:before{content:'\e80b'}#bond-singlearomatic button:before,#bond-singlearomatic #open-file .open:before,#bond-singlearomatic #save-file .save:before{content:'\e80c'}#bond-singledouble button:before,#bond-singledouble #open-file .open:before,#bond-singledouble #save-file .save:before{content:'\e80d'}#bond-triple button:before,#bond-triple #open-file .open:before,#bond-triple #save-file .save:before{content:'\e80e'}#bond-up button:before,#bond-up #open-file .open:before,#bond-up #save-file .save:before{content:'\e80f'}#bond-updown button:before,#bond-updown #open-file .open:before,#bond-updown #save-file .save:before{content:'\e810'}#chain button:before,#chain #open-file .open:before,#chain #save-file .save:before{content:'\e811'}#charge-minus button:before,#charge-minus #open-file .open:before,#charge-minus #save-file .save:before{content:'\e812'}#charge-plus button:before,#charge-plus #open-file .open:before,#charge-plus #save-file .save:before{content:'\e813'}#cleanup button:before,#cleanup #open-file .open:before,#cleanup #save-file .save:before{content:'\e814'}#copy button:before,#copy #open-file .open:before,#copy #save-file .save:before{content:'\e815'}#cut button:before,#cut #open-file .open:before,#cut #save-file .save:before{content:'\e816'}#dearom button:before,#dearom #open-file .open:before,#dearom #save-file .save:before{content:'\e817'}#dropdown button:before,#dropdown #open-file .open:before,#dropdown #save-file .save:before{content:'\e818'}#erase button:before,#erase #open-file .open:before,#erase #save-file .save:before{content:'\e819'}#generic-groups button:before,#generic-groups #open-file .open:before,#generic-groups #save-file .save:before{content:'\e81a'}#info button:before,#info #open-file .open:before,#info #save-file .save:before{content:'\e81b'}#new button:before,#new #open-file .open:before,#new #save-file .save:before{content:'\e81d'}#open button:before,#open #open-file .open:before,#open #save-file .save:before{content:'\e81e'}#paste button:before,#paste #open-file .open:before,#paste #save-file .save:before{content:'\e81f'}#period-table button:before,#period-table #open-file .open:before,#period-table #save-file .save:before{content:'\e820'}#reaction-arrow button:before,#reaction-arrow #open-file .open:before,#reaction-arrow #save-file .save:before{content:'\e821'}#reaction-automap button:before,#reaction-automap #open-file .open:before,#reaction-automap #save-file .save:before{content:'\e822'}#reaction-map button:before,#reaction-map #open-file .open:before,#reaction-map #save-file .save:before{content:'\e823'}#reaction-plus button:before,#reaction-plus #open-file .open:before,#reaction-plus #save-file .save:before{content:'\e824'}#reaction-unmap button:before,#reaction-unmap #open-file .open:before,#reaction-unmap #save-file .save:before{content:'\e825'}#redo button:before,#redo #open-file .open:before,#redo #save-file .save:before{content:'\e826'}#rgroup-attpoints button:before,#rgroup-attpoints #open-file .open:before,#rgroup-attpoints #save-file .save:before{content:'\e827'}#rgroup-fragment button:before,#rgroup-fragment #open-file .open:before,#rgroup-fragment #save-file .save:before{content:'\e828'}#save button:before,#save #open-file .open:before,#save #save-file .save:before{content:'\e82b'}#select-fragment button:before,#select-fragment #open-file .open:before,#select-fragment #save-file .save:before{content:'\e82c'}#select-lasso button:before,#select-lasso #open-file .open:before,#select-lasso #save-file .save:before{content:'\e82d'}#select-rectangle button:before,#select-rectangle #open-file .open:before,#select-rectangle #save-file .save:before{content:'\e82e'}#settings button:before,#settings #open-file .open:before,#settings #save-file .save:before{content:'\e82f'}#sgroup button:before,#sgroup #open-file .open:before,#sgroup #save-file .save:before{content:'\e830'}#template-0 button:before,#template-0 #open-file .open:before,#template-0 #save-file .save:before{content:'\e831'}#template-1 button:before,#template-1 #open-file .open:before,#template-1 #save-file .save:before{content:'\e832'}#template-2 button:before,#template-2 #open-file .open:before,#template-2 #save-file .save:before{content:'\e833'}#template-3 button:before,#template-3 #open-file .open:before,#template-3 #save-file .save:before{content:'\e834'}#template-4 button:before,#template-4 #open-file .open:before,#template-4 #save-file .save:before{content:'\e835'}#template-5 button:before,#template-5 #open-file .open:before,#template-5 #save-file .save:before{content:'\e836'}#template-6 button:before,#template-6 #open-file .open:before,#template-6 #save-file .save:before{content:'\e837'}#template-7 button:before,#template-7 #open-file .open:before,#template-7 #save-file .save:before{content:'\e838'}#template-custom button:before,#template-custom #open-file .open:before,#template-custom #save-file 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        + + + + + + +
        + + + + diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.js b/public/lib/ketcher-2.0.0-alpha.3/ketcher.js new file mode 100644 index 000000000..2c9589f28 --- /dev/null +++ b/public/lib/ketcher-2.0.0-alpha.3/ketcher.js @@ -0,0 +1,1068 @@ +/**************************************************************************** + * Copyright (C) 2009-2017. EPAM Systems. + * + * This file may be distributed and/or modified under the terms of the + * GNU Affero General Public License version 3 as published by the Free + * Software Foundation and appearing in the file LICENSE included in + * the packaging of this file. + * + * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE + * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. + ***************************************************************************/ + +(function(f){if(typeof exports==="object"&&typeof module!=="undefined"){module.exports=f()}else if(typeof define==="function"&&define.amd){define([],f)}else{var g;if(typeof window!=="undefined"){g=window}else if(typeof global!=="undefined"){g=global}else if(typeof self!=="undefined"){g=self}else{g=this}g.ketcher = f()}})(function(){var define,module,exports;return (function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o= 0; i--) { + chains = getNestedChains(allChains, scope.slice(0, i)); + if (!chains) { + continue; + } + matched = true; + for (var j = 0; j < seq.length; j++) { + key = seq[j]; + if (!chains[key]) { + matched = false; + break; + } + chains = chains[key]; + } + + if (matched) { + break; + } + } + + var definitionScope = scope.slice(0, i).join('.'); + var preventDefault = chains.preventDefault; + + // partial match, save the sequence + if (matched && !chains.handlers) { + sequence = seq; + if (preventDefault) { + e.preventDefault(); + } + return; + } + + if (matched) { + for (i = 0; i < chains.handlers.length; i++) { + var handler = chains.handlers[i]; + var options = handler._keymage; + + var res = handler.call(options.context, e, { + shortcut: options.original, + scope: currentScope, + definitionScope: definitionScope + }); + + if (res === false || preventDefault) { + e.preventDefault(); + } + } + } + + // either matched or not, drop the sequence + sequence = []; + } + + function getHandlers(scope, keychain, fn) { + var bits = scope.split('.'); + var chains = allChains; + bits = bits.concat(keychain); + + for (var i = 0, l = bits.length; i < l; i++) { + var bit = bits[i]; + if (!bit) continue; + + chains = chains[bit] || (chains[bit] = {}); + if (fn && fn._keymage.preventDefault) { + chains.preventDefault = true; + } + + if (i === l - 1) { + var handlers = chains.handlers || (chains.handlers = []); + return handlers; + } + } + } + + function assignKey(scope, keychain, fn) { + var handlers = getHandlers(scope, keychain, fn); + handlers.push(fn); + } + + function unassignKey(scope, keychain, fn) { + var handlers = getHandlers(scope, keychain); + var idx = handlers.indexOf(fn); + if (~idx) { + handlers.splice(idx, 1); + } + } + + function parsed(scope, keychain, fn, options) { + if (keychain === undefined && fn === undefined) { + return function(keychain, fn) { + return keymage(scope, keychain, fn); + }; + } + + if (typeof keychain === 'function') { + options = fn; + fn = keychain; + keychain = scope; + scope = ''; + } + + var normalized = normalizeKeyChain(keychain); + + return [scope, normalized, fn, options]; + } + + // optional arguments: scope, options. + function keymage(scope, keychain, fn, options) { + var args = parsed(scope, keychain, fn, options); + fn = args[2]; + options = args[3]; + fn._keymage = options || {}; + fn._keymage.original = keychain; + assignKey.apply(null, args); + + return function () { + unassignKey.apply(null, args); + }; + } + + keymage.unbind = function(scope, keychain, fn) { + var args = parsed(scope, keychain, fn); + unassignKey.apply(null, args); + }; + + keymage.parse = parseKeyString; + keymage.stringify = stringifyKey; + + keymage.bindings = allChains; + + keymage.setScope = function(scope) { + currentScope = scope ? scope : ''; + }; + + keymage.getScope = function() { return currentScope; }; + + keymage.pushScope = function(scope) { + currentScope = (currentScope ? currentScope + '.' : '') + scope; + return currentScope; + }; + + keymage.popScope = function(scope) { + var i; + + if (!scope) { + i = currentScope.lastIndexOf('.'); + scope = currentScope.slice(i + 1); + currentScope = i == -1 ? '' : currentScope.slice(0, i); + return scope; + } + + currentScope = currentScope.replace( + new RegExp('(^|\\.)' + scope + '(\\.|$).*'), ''); + return scope; + }; + + keymage.version = VERSION; + + window.addEventListener('keydown', dispatch, false); + + return keymage; +}); +})(typeof define !== 'undefined' ? define : function(factory) { + if (typeof module !== 'undefined') { + module.exports = factory(); + } else { + window.keymage = factory(); + } +}); + +},{}],3:[function(require,module,exports){ +(function(root) { + + // Use polyfill for setImmediate for performance gains + var asap = (typeof setImmediate === 'function' && setImmediate) || + function(fn) { setTimeout(fn, 1); }; + + // Polyfill for Function.prototype.bind + function bind(fn, thisArg) { + return function() { + fn.apply(thisArg, arguments); + } + } + + var isArray = Array.isArray || function(value) { return Object.prototype.toString.call(value) === "[object Array]" }; + + function Promise(fn) { + if (typeof this !== 'object') throw new TypeError('Promises must be constructed via new'); + if (typeof fn !== 'function') throw new TypeError('not a function'); + this._state = null; + this._value = null; + this._deferreds = [] + + doResolve(fn, bind(resolve, this), bind(reject, this)) + } + + function handle(deferred) { + var me = this; + if (this._state === null) { + this._deferreds.push(deferred); + return + } + asap(function() { + var cb = me._state ? deferred.onFulfilled : deferred.onRejected + if (cb === null) { + (me._state ? deferred.resolve : deferred.reject)(me._value); + return; + } + var ret; + try { + ret = cb(me._value); + } + catch (e) { + deferred.reject(e); + return; + } + deferred.resolve(ret); + }) + } + + function resolve(newValue) { + try { //Promise Resolution Procedure: https://github.com/promises-aplus/promises-spec#the-promise-resolution-procedure + if (newValue === this) throw new TypeError('A promise cannot be resolved with itself.'); + if (newValue && (typeof newValue === 'object' || typeof newValue === 'function')) { + var then = newValue.then; + if (typeof then === 'function') { + doResolve(bind(then, newValue), bind(resolve, this), bind(reject, this)); + return; + } + } + this._state = true; + this._value = newValue; + finale.call(this); + } catch (e) { reject.call(this, e); } + } + + function reject(newValue) { + this._state = false; + this._value = newValue; + finale.call(this); + } + + function finale() { + for (var i = 0, len = this._deferreds.length; i < len; i++) { + handle.call(this, this._deferreds[i]); + } + this._deferreds = null; + } + + function Handler(onFulfilled, onRejected, resolve, reject){ + this.onFulfilled = typeof onFulfilled === 'function' ? onFulfilled : null; + this.onRejected = typeof onRejected === 'function' ? onRejected : null; + this.resolve = resolve; + this.reject = reject; + } + + /** + * Take a potentially misbehaving resolver function and make sure + * onFulfilled and onRejected are only called once. + * + * Makes no guarantees about asynchrony. + */ + function doResolve(fn, onFulfilled, onRejected) { + var done = false; + try { + fn(function (value) { + if (done) return; + done = true; + onFulfilled(value); + }, function (reason) { + if (done) return; + done = true; + onRejected(reason); + }) + } catch (ex) { + if (done) return; + done = true; + onRejected(ex); + } + } + + Promise.prototype['catch'] = function (onRejected) { + return this.then(null, onRejected); + }; + + Promise.prototype.then = function(onFulfilled, onRejected) { + var me = this; + return new Promise(function(resolve, reject) { + handle.call(me, new Handler(onFulfilled, onRejected, resolve, reject)); + }) + }; + + Promise.all = function () { + var args = Array.prototype.slice.call(arguments.length === 1 && isArray(arguments[0]) ? arguments[0] : arguments); + + return new Promise(function (resolve, reject) { + if (args.length === 0) return resolve([]); + var remaining = args.length; + function res(i, val) { + try { + if (val && (typeof val === 'object' || typeof val === 'function')) { + var then = val.then; + if (typeof then === 'function') { + then.call(val, function (val) { res(i, val) }, reject); + return; + } + } + args[i] = val; + if (--remaining === 0) { + resolve(args); + } + } catch (ex) { + reject(ex); + } + } + for (var i = 0; i < args.length; i++) { + res(i, args[i]); + } + }); + }; + + Promise.resolve = function (value) { + if (value && typeof value === 'object' && value.constructor === Promise) { + return value; + } + + return new Promise(function (resolve) { + resolve(value); + }); + }; + + Promise.reject = function (value) { + return new Promise(function (resolve, reject) { + reject(value); + }); + }; + + Promise.race = function (values) { + return new Promise(function (resolve, reject) { + for(var i = 0, len = values.length; i < len; i++) { + values[i].then(resolve, reject); + } + }); + }; + + /** + * Set the immediate function to execute callbacks + * @param fn {function} Function to execute + * @private + */ + Promise._setImmediateFn = function _setImmediateFn(fn) { + asap = fn; + }; + + if (typeof module !== 'undefined' && module.exports) { + module.exports = Promise; + } else if (!root.Promise) { + root.Promise = Promise; + } + +})(this); +},{}],4:[function(require,module,exports){ +'use strict'; +var strictUriEncode = require('strict-uri-encode'); + +exports.extract = function (str) { + return str.split('?')[1] || ''; +}; + +exports.parse = function (str) { + if (typeof str !== 'string') { + return {}; + } + + str = str.trim().replace(/^(\?|#|&)/, ''); + + if (!str) { + return {}; + } + + return str.split('&').reduce(function (ret, param) { + var parts = param.replace(/\+/g, ' ').split('='); + // Firefox (pre 40) decodes `%3D` to `=` + // https://github.com/sindresorhus/query-string/pull/37 + var key = parts.shift(); + var val = parts.length > 0 ? parts.join('=') : undefined; + + key = decodeURIComponent(key); + + // missing `=` should be `null`: + // http://w3.org/TR/2012/WD-url-20120524/#collect-url-parameters + val = val === undefined ? null : decodeURIComponent(val); + + if (!ret.hasOwnProperty(key)) { + ret[key] = val; + } else if (Array.isArray(ret[key])) { + ret[key].push(val); + } else { + ret[key] = [ret[key], val]; + } + + return ret; + }, {}); +}; + +exports.stringify = function (obj) { + return obj ? Object.keys(obj).sort().map(function (key) { + var val = obj[key]; + + if (Array.isArray(val)) { + return val.sort().map(function (val2) { + return strictUriEncode(key) + '=' + strictUriEncode(val2); + }).join('&'); + } + + return strictUriEncode(key) + '=' + strictUriEncode(val); + }).filter(function (x) { + return x.length > 0; + }).join('&') : ''; +}; + +},{"strict-uri-encode":5}],5:[function(require,module,exports){ +'use strict'; +module.exports = function (str) { + return encodeURIComponent(str).replace(/[!'()*]/g, function (c) { + return '%' + c.charCodeAt(0).toString(16).toUpperCase(); + }); +}; + +},{}],6:[function(require,module,exports){ +var xhrFactory = (function getXHRfactory (factories) { + for (var i=0, xhr, X, len=factories.length; i0?1:-1},chem.CisTrans.prototype._sameside=function(e,t,s,i){return this.sameside(this.molecule.atoms.get(e).pp,this.molecule.atoms.get(t).pp,this.molecule.atoms.get(s).pp,this.molecule.atoms.get(i).pp)},chem.CisTrans.prototype._sortSubstituents=function(e){var t=this.molecule.atoms.get(e[0]).pureHydrogen(),s=e[1]<0||this.molecule.atoms.get(e[1]).pureHydrogen(),i=this.molecule.atoms.get(e[2]).pureHydrogen(),r=e[3]<0||this.molecule.atoms.get(e[3]).pureHydrogen();return(!t||!s)&&((!i||!r)&&(s?e[1]=-1:t?(e[0]=e[1],e[1]=-1):e[0]>e[1]&&e.swap(0,1),r?e[3]=-1:i?(e[2]=e[3],e[3]=-1):e[2]>e[3]&&e.swap(2,3),!0))},chem.CisTrans.prototype.isGeomStereoBond=function(e,t){var s=this.molecule.bonds.get(e);if(s.type!=chem.Struct.BOND.TYPE.DOUBLE)return!1;var i=this.molecule.atoms.get(s.begin).label,r=this.molecule.atoms.get(s.end).label;if("C"!=i&&"N"!=i&&"Si"!=i&&"Ge"!=i)return!1;if("C"!=r&&"N"!=r&&"Si"!=r&&"Ge"!=r)return!1;var n=this.getNeighbors.call(this.context,s.begin),o=this.getNeighbors.call(this.context,s.end);if(n.length<2||n.length>3||o.length<2||o.length>3)return!1;t[0]=-1,t[1]=-1,t[2]=-1,t[3]=-1;var u,a;for(u=0;u=0&&this.vertices[v].branches--}this.vertices[h].branches++,this.vertices[f].parent_vertex=h,this.vertices[f].parent_edge=u,this.vertices[f].dfs_state=1,s.push(f)}}}},chem.Dfs.prototype.edgeClosingCycle=function(e){return 0!=this.edges[e].closing_cycle},chem.Dfs.prototype.numBranches=function(e){return this.vertices[e].branches},chem.Dfs.prototype.numOpeningCycles=function(e){return this.edges[e].opening_cycles},chem.Dfs.prototype.toString=function(){var e="";return this.v_seq.each(function(t){e+=t.idx+" -> "}),e+="*"}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../util/":39,"../util/set":42,"./element":10}],10:[function(require,module,exports){ +function el(e,l,f,a,b){return{label:e,period:l,group:f,putHydrogenOnTheLeft:a,color:b||"#000000"}}var Map=require("../util/map"),element=new Map({1:el("H",1,1,!1,"#000000"),2:el("He",1,8,!1,"#d9ffff"),3:el("Li",2,1,!1,"#cc80ff"),4:el("Be",2,2,!1,"#c2ff00"),5:el("B",2,3,!1,"#ffb5b5"),6:el("C",2,4,!1,"#000000"),7:el("N",2,5,!1,"#304ff7"),8:el("O",2,6,!0,"#ff0d0d"),9:el("F",2,7,!0,"#8fe04f"),10:el("Ne",2,8,!1,"#b3e3f5"),11:el("Na",3,1,!1,"#ab5cf2"),12:el("Mg",3,2,!1,"#8aff00"),13:el("Al",3,3,!1,"#bfa6a6"),14:el("Si",3,4,!1,"#f0c7a1"),15:el("P",3,5,!1,"#ff8000"),16:el("S",3,6,!0,"#d9a61a"),17:el("Cl",3,7,!0,"#1fd01f"),18:el("Ar",3,8,!1,"#80d1e3"),19:el("K",4,1,!1,"#8f40d4"),20:el("Ca",4,2,!1,"#3dff00"),21:el("Sc",4,3,!1,"#e6e6e6"),22:el("Ti",4,4,!1,"#bfc2c7"),23:el("V",4,5,!1,"#a6a6ab"),24:el("Cr",4,6,!1,"#8a99c7"),25:el("Mn",4,7,!1,"#9c7ac7"),26:el("Fe",4,8,!1,"#e06633"),27:el("Co",4,8,!1,"#f08fa1"),28:el("Ni",4,8,!1,"#4fd14f"),29:el("Cu",4,1,!1,"#c78033"),30:el("Zn",4,2,!1,"#7d80b0"),31:el("Ga",4,3,!1,"#c28f8f"),32:el("Ge",4,4,!1,"#668f8f"),33:el("As",4,5,!1,"#bd80e3"),34:el("Se",4,6,!0,"#ffa100"),35:el("Br",4,7,!0,"#a62929"),36:el("Kr",4,8,!1,"#5cb8d1"),37:el("Rb",5,1,!1,"#702eb0"),38:el("Sr",5,2,!1,"#00ff00"),39:el("Y",5,3,!1,"#94ffff"),40:el("Zr",5,4,!1,"#94e0e0"),41:el("Nb",5,5,!1,"#73c2c9"),42:el("Mo",5,6,!1,"#54b5b5"),43:el("Tc",5,7,!1,"#3b9e9e"),44:el("Ru",5,8,!1,"#248f8f"),45:el("Rh",5,8,!1,"#0a7d8c"),46:el("Pd",5,8,!1,"#006985"),47:el("Ag",5,1,!1,"#bfbfbf"),48:el("Cd",5,2,!1,"#ffd98f"),49:el("In",5,3,!1,"#a67573"),50:el("Sn",5,4,!1,"#668080"),51:el("Sb",5,5,!1,"#9e63b5"),52:el("Te",5,6,!1,"#d47a00"),53:el("I",5,7,!0,"#940094"),54:el("Xe",5,8,!1,"#429eb0"),55:el("Cs",6,1,!1,"#57178f"),56:el("Ba",6,2,!1,"#00c900"),57:el("La",6,3,!1,"#70d4ff"),58:el("Ce",6,3,!1,"#ffffc7"),59:el("Pr",6,3,!1,"#d9ffc7"),60:el("Nd",6,3,!1,"#c7ffc7"),61:el("Pm",6,3,!1,"#a3ffc7"),62:el("Sm",6,3,!1,"#8fffc7"),63:el("Eu",6,3,!1,"#61ffc7"),64:el("Gd",6,3,!1,"#45ffc7"),65:el("Tb",6,3,!1,"#30ffc7"),66:el("Dy",6,3,!1,"#1fffc7"),67:el("Ho",6,3,!1,"#00ff9c"),68:el("Er",6,3,!1,"#00e675"),69:el("Tm",6,3,!1,"#00d452"),70:el("Yb",6,3,!1,"#00bf38"),71:el("Lu",6,3,!1,"#00ab24"),72:el("Hf",6,4,!1,"#4dc2ff"),73:el("Ta",6,5,!1,"#4da6ff"),74:el("W",6,6,!1,"#2194d6"),75:el("Re",6,7,!1,"#267dab"),76:el("Os",6,8,!1,"#266696"),77:el("Ir",6,8,!1,"#175487"),78:el("Pt",6,8,!1,"#d1d1e0"),79:el("Au",6,1,!1,"#ffd124"),80:el("Hg",6,2,!1,"#b8b8d1"),81:el("Tl",6,3,!1,"#a6544d"),82:el("Pb",6,4,!1,"#575961"),83:el("Bi",6,5,!1,"#9e4fb5"),84:el("Po",6,6,!1,"#ab5c00"),85:el("At",6,7,!1,"#754f45"),86:el("Rn",6,8,!1,"#428296"),87:el("Fr",7,1,!1,"#420066"),88:el("Ra",7,2,!1,"#007d00"),89:el("Ac",7,3,!1,"#70abfa"),90:el("Th",7,3,!1,"#00baff"),91:el("Pa",7,3,!1,"#00a1ff"),92:el("U",7,3,!1,"#008fff"),93:el("Np",7,3,!1,"#0080ff"),94:el("Pu",7,3,!1,"#006bff"),95:el("Am",7,3,!1,"#545cf2"),96:el("Cm",7,3,!1,"#785ce3"),97:el("Bk",7,3,!1,"#8a4fe3"),98:el("Cf",7,3,!1,"#a136d4"),99:el("Es",7,3,!1,"#b31fd4"),100:el("Fm",7,3,!1,"#000000"),101:el("Md",7,3,!1,"#000000"),102:el("No",7,3,!1,"#000000"),103:el("Lr",7,3,!1,"#000000"),104:el("Rf",7,4,!1,"#4dc2ff"),105:el("Db",7,5,!1,"#4da6ff"),106:el("Sg",7,6,!1,"#2194d6"),107:el("Bh",7,7,!1,"#267dab"),108:el("Hs",7,8,!1,"#266696"),109:el("Mt",7,8,!1,"#175487"),110:el("Ds",7,8,!1,"#d1d1e0"),111:el("Rg",7,1,!1,"#ffd124"),112:el("Cn",7,2,!1,"#b8b8d1"),113:el("Uut",7,3,!1),114:el("Fl",7,4,!1),115:el("Uup",7,5,!1),116:el("Lv",7,6,!1),117:el("Uus",7,7,!1),118:el("Uuo",7,8,!1)}),labelMap=null;element.getElementByLabel=function(e){return labelMap||(labelMap={},element.each(function(e,l){labelMap[l.label]=e-0})),labelMap[e]||null},module.exports=element; + +},{"../util/map":40}],11:[function(require,module,exports){ +(function (global){ +require("./struct"),require("./cis_trans"),require("./dfs"),require("./molfile"),require("./sgroup"),require("./smiles"),require("./stereocenters"),require("./struct_valence"),global.chem=global.chem||{}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"./cis_trans":8,"./dfs":9,"./molfile":12,"./sgroup":13,"./smiles":14,"./stereocenters":15,"./struct":16,"./struct_valence":17}],12:[function(require,module,exports){ +(function (global){ +var Map=require("../util/map"),Set=require("../util/set"),Vec2=require("../util/vec2"),element=require("./element"),util=require("../util"),chem=global.chem=global.chem||{};chem.Molfile=function(){},chem.Molfile.loadRGroupFragments=!0,chem.Molfile.parseDecimalInt=function(e){var t=parseInt(e,10);return isNaN(t)?0:t},chem.Molfile.partitionLine=function(e,t,r){for(var i=[],a=0,n=0;a0&&(M.ifthen=g),M.resth=1==w,M.range=S,n[d]=M}else if("APO"==c)o.get("attpnt")||o.set("attpnt",new Map),o.get("attpnt").update(l.readKeyValuePairs(p));else if("ALS"==c){o.get("atomList")||o.set("atomList",new Map);var v=l.parsePropertyLineAtomList(l.partitionLine(p,[1,3,3,1,1,1]),l.partitionLineFixed(p.slice(10),4,!1));o.get("atomList").update(v),o.get("label")||o.set("label",new Map);for(var D in v)o.get("label").set(D,"L#")}else if("STY"==c)l.initSGroup(a,p);else if("SST"==c)l.applySGroupProp(a,"subtype",p);else if("SLB"==c)l.applySGroupProp(a,"label",p,!0);else if("SPL"==c)l.applySGroupProp(a,"parent",p,!0,!0);else if("SCN"==c)l.applySGroupProp(a,"connectivity",p);else if("SAL"==c)l.applySGroupArrayProp(a,"atoms",p,-1);else if("SBL"==c)l.applySGroupArrayProp(a,"bonds",p,-1);else if("SPA"==c)l.applySGroupArrayProp(a,"patoms",p,-1);else if("SMT"==c){var b=l.parseDecimalInt(p.slice(0,4))-1;a[b].data.subscript=p.slice(4).strip()}else"SDT"==c?l.applyDataSGroupDesc(a,p):"SDD"==c?l.applyDataSGroupInfoLine(a,p):"SCD"==c?l.applyDataSGroupDataLine(a,p,!1):"SED"==c&&l.applyDataSGroupDataLine(a,p,!0)}++r}return o},chem.Molfile.applyAtomProp=function(e,t,r,i){t.each(function(t,i){e.get(t)[r]=i})},chem.Molfile.parseCTabV2000=function(e,t){var r,i=new chem.Struct,a=chem.Molfile,n=a.parseDecimalInt(t[0]),l=a.parseDecimalInt(t[1]),o=a.parseDecimalInt(t[2]);i.isChiral=0!=a.parseDecimalInt(t[4]);var s=a.parseDecimalInt(t[5]),c=a.parseDecimalInt(t[10]),p=0,h=e.slice(p,p+n);p+=n;var u=e.slice(p,p+l);p+=l;var m=e.slice(p,p+o);p+=o+s;var f=h.map(a.parseAtomLine);for(r=0;r=0){var b=g[D-1];"GEN"===b.type&&(v.atoms=util.array(b.atoms))}}}for(S in g)chem.SGroup.addGroup(i,g[S],M);var N=[];for(S in g)chem.SGroup.filter(i,g[S],M),0!=g[S].atoms.length||g[S].allAtoms||N.push(S);for(r=0;rn+1&&i.push(e.slice(n+1,r)),n=r);return r>n+1&&i.push(e.slice(n+1,r)),n=r,i},chem.Molfile.splitonce=function(e,t){var r=e.indexOf(t);return[e.slice(0,r),e.slice(r+1)]},chem.Molfile.splitSGroupDef=function(e){for(var t=[],r=0,i=!1,a=0;a0&&t.push(e.strip()),t},chem.Molfile.parseBracedNumberList=function(e,t){if(!e)return null;var r=[];e=e.strip(),e=e.substr(1,e.length-2);var i=e.split(" ");t=t||0;for(var a=1;a0&&(d.ifthen=u),d.resth=1==m,d.range=f,i[l]=d,a++}}}for(var g in r)for(var w=0;wr[s];)++s;n[s]=n[s]||{},Set.mergeIn(n[s],t[a])}var c=[],p=[],h=[];for(a=0;a0,e.rxnArrows.count()>1)throw new Error("Reaction may not contain more than one arrow");if(this.molfile="",this.reaction){if(e.rgroups.count()>0)throw new Error("Unable to save the structure - reactions with r-groups are not supported at the moment");var a=chem.MolfileSaver.getComponents(e),n=a.reactants,l=a.products,o=n.concat(l);this.molfile="$RXN\n\n\n\n"+util.paddedInt(n.length,3)+util.paddedInt(l.length,3)+util.paddedInt(0,3)+"\n";for(var s=0;s0){if(!r){var u=new chem.MolfileSaver(!1).getCTab(e.getScaffold(),e.rgroups);return this.molfile="$MDL REV 1\n$MOL\n$HDR\n\n\n\n$END HDR\n",this.molfile+="$CTAB\n"+u+"$END CTAB\n",e.rgroups.each(function(t,r){this.molfile+="$RGP\n",this.writePaddedNumber(t,3),this.molfile+="\n",r.frags.each(function(t,r){var i=new chem.MolfileSaver(!1).getCTab(e.getFragment(r));this.molfile+="$CTAB\n"+i+"$END CTAB\n"},this),this.molfile+="$END RGP\n"},this),this.molfile+="$END MOL\n",this.molfile}e=e.getScaffold()}return this.molecule=e.clone(),this.prepareSGroups(t,i),this.writeHeader(),this.writeCTab2000(),this.molfile},chem.MolfileSaver.prototype.writeHeader=function(){var e=new Date;this.writeCR(),this.writeWhiteSpace(2),this.write("Ketcher"),this.writeWhiteSpace(),this.writeCR((e.getMonth()+1).toPaddedString(2)+e.getDate().toPaddedString(2)+(e.getFullYear()%100).toPaddedString(2)+e.getHours().toPaddedString(2)+e.getMinutes().toPaddedString(2)+"2D 1 1.00000 0.00000 0"),this.writeCR()},chem.MolfileSaver.prototype.write=function(e){this.molfile+=e},chem.MolfileSaver.prototype.writeCR=function(e){0==arguments.length&&(e=""),this.molfile+=e+"\n"},chem.MolfileSaver.prototype.writeWhiteSpace=function(e){0==arguments.length&&(e=1),e.times(function(){this.write(" ")},this)},chem.MolfileSaver.prototype.writePadded=function(e,t){this.write(e),this.writeWhiteSpace(t-e.length)},chem.MolfileSaver.prototype.writePaddedNumber=function(e,t){var r=(e-0).toString();this.writeWhiteSpace(t-r.length),this.write(r)},chem.MolfileSaver.prototype.writePaddedFloat=function(e,t,r){this.write(util.paddedFloat(e,t,r))},chem.MolfileSaver.prototype.writeCTab2000Header=function(){this.writePaddedNumber(this.molecule.atoms.count(),3),this.writePaddedNumber(this.molecule.bonds.count(),3),this.writePaddedNumber(0,3),this.writeWhiteSpace(3),this.writePaddedNumber(this.molecule.isChiral?1:0,3),this.writePaddedNumber(0,3),this.writeWhiteSpace(12),this.writePaddedNumber(999,3),this.writeCR(" V2000")},chem.MolfileSaver.prototype.writeCTab2000=function(e){this.writeCTab2000Header(),this.mapping={};var t=1,r=[],i=[];for(this.molecule.atoms.each(function(e,a){this.writePaddedFloat(a.pp.x,10,4),this.writePaddedFloat(-a.pp.y,10,4),this.writePaddedFloat(0,10,4),this.writeWhiteSpace();var n=a.label;null!=a.atomList?(n="L",r.push(e)):null==element.getElementByLabel(n)&&-1==["A","Q","X","*","R#"].indexOf(n)&&(n="C",i.push(e)),this.writePadded(n,3),this.writePaddedNumber(0,2),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),Object.isUndefined(a.hCount)&&(a.hCount=0),this.writePaddedNumber(a.hCount,3),Object.isUndefined(a.stereoCare)&&(a.stereoCare=0),this.writePaddedNumber(a.stereoCare,3),this.writePaddedNumber(a.explicitValence<0?0:0==a.explicitValence?15:a.explicitValence,3),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),Object.isUndefined(a.aam)&&(a.aam=0),this.writePaddedNumber(a.aam,3),Object.isUndefined(a.invRet)&&(a.invRet=0),this.writePaddedNumber(a.invRet,3),Object.isUndefined(a.exactChangeFlag)&&(a.exactChangeFlag=0),this.writePaddedNumber(a.exactChangeFlag,3),this.writeCR(),this.mapping[e]=t,t++},this),this.bondMapping={},t=1,this.molecule.bonds.each(function(e,r){this.bondMapping[e]=t++,this.writePaddedNumber(this.mapping[r.begin],3),this.writePaddedNumber(this.mapping[r.end],3),this.writePaddedNumber(r.type,3),Object.isUndefined(r.stereo)&&(r.stereo=0),this.writePaddedNumber(r.stereo,3),this.writeWhiteSpace(3),Object.isUndefined(r.topology)&&(r.topology=0),this.writePaddedNumber(r.topology,3),Object.isUndefined(r.reactingCenterStatus)&&(r.reactingCenterStatus=0),this.writePaddedNumber(r.reactingCenterStatus,3),this.writeCR()},this);i.length>0;)this.write("A "),this.writePaddedNumber(i[0]+1,3),this.writeCR(),this.writeCR(this.molecule.atoms.get(i[0]).label),i.splice(0,1);var a=new Array,n=new Array,l=new Array,o=new Array,s=new Array,c=new Array,p=new Array,h=new Array,u=new Array;this.molecule.atoms.each(function(e,t){if(0!=t.charge&&a.push([e,t.charge]),0!=t.isotope&&n.push([e,t.isotope]),0!=t.radical&&l.push([e,t.radical]),null!=t.rglabel&&"R#"==t.label)for(var r=0;r<32;r++)t.rglabel&1<0||t.range.length>0){var r=" 1 "+util.paddedInt(e,3)+" "+util.paddedInt(t.ifthen,3)+" "+util.paddedInt(t.resth?1:0,3)+" "+t.range;s.push(r)}});var m=function(e,t){for(;t.length>0;){for(var r=new Array;t.length>0&&r.length<8;)r.push(t[0]),t.splice(0,1);this.write(e),this.writePaddedNumber(r.length,3),r.each(function(e){this.writeWhiteSpace(),this.writePaddedNumber(this.mapping[e[0]],3),this.writeWhiteSpace(),this.writePaddedNumber(e[1],3)},this),this.writeCR()}};m.call(this,"M CHG",a),m.call(this,"M ISO",n),m.call(this,"M RAD",l),m.call(this,"M RGP",o);for(var f=0;f0)for(f=0;f=0&&(this.write("M SPL"),this.writePaddedNumber(1,3),this.writeWhiteSpace(1),this.writePaddedNumber(N,3),this.writeWhiteSpace(1),this.writePaddedNumber(M[T],3),this.writeCR()),"SRU"==A.type&&A.data.connectivity){var C="";C+=" ",C+=util.stringPadded(N.toString(),3),C+=" ",C+=util.stringPadded(A.data.connectivity,3,!0),this.write("M SCN"),this.writePaddedNumber(1,3),this.write(C.toUpperCase()),this.writeCR()}"SRU"==A.type&&(this.write("M SMT "),this.writePaddedNumber(N,3),this.writeWhiteSpace(),this.write(A.data.subscript||"n"),this.writeCR()),this.writeCR(A.saveToMolfile(this.molecule,M,this.mapping,this.bondMapping))}this.writeCR("M END")},chem.Molfile.parseRxn=function(e){var t=chem.Molfile,r=e[0].strip().split(" ");return r.length>1&&"V3000"==r[1]?t.parseRxn3000(e):t.parseRxn2000(e)},chem.Molfile.parseRxn2000=function(e){var t=chem.Molfile;e=e.slice(4);var r=t.partitionLine(e[0],t.fmtInfo.rxnItemsPartition),i=r[0]-0,a=r[1]-0,n=r[2]-0;e=e.slice(1);for(var l=[];e.length>0&&"$MOL"==e[0].substr(0,4);){e=e.slice(1);for(var o=0;o2?r[2]-0:0,l=function(e){util.assert(e,"CTab format invalid")},o=[],s=[],c=null,p=[],h=0;h=0?s.push(e[o]):s.push(-1)}return s},chem.SGroup.removeNegative=function(t){for(var e=[],s=0;s=0&&e.push(t[s]);return e},chem.SGroup.filter=function(t,e,s){e.atoms=chem.SGroup.removeNegative(chem.SGroup.filterAtoms(e.atoms,s))},chem.SGroup.clone=function(t,e,s){var r=new chem.SGroup(t.type);for(var o in t.data)r.data[o]=t.data[o];return r.atoms=util.mapArray(t.atoms,e),r.pp=t.pp,r.bracketBox=t.bracketBox,r.patoms=null,r.bonds=null,r.allAtoms=t.allAtoms,r},chem.SGroup.addAtom=function(t,e){t.atoms.push(e)},chem.SGroup.removeAtom=function(t,e){for(var s=0;sm.d.y)&&(l=p)}var f=d[l],S=function(s,r){var o=e.ps(f.c.addScaled(f.n,r*f.h)),i=e.paper.text(o.x,o.y,s).attr({font:e.settings.font,"font-size":e.settings.fontszsub});c&&i.attr(c);var n=Box2Abs.fromRelBox(rnd.relBox(i.getBBox())),a=Math.max(Vec2.shiftRayBox(o,f.d.negated(),n),3)+2;i.translateAbs(a*f.d.x,a*f.d.y),t.push(i)};h&&S(h,.5),u&&S(u,-.5)},chem.SGroup.drawBracket=function(t,e,s,r,o,i,n,a){n=n||.25,a=a||1;var h=i.addScaled(o,-.5*a),u=i.addScaled(o,.5*a),c=h.addScaled(r,-n),d=u.addScaled(r,-n);return h=t.obj2scaled(h),u=t.obj2scaled(u),c=t.obj2scaled(c),d=t.obj2scaled(d),e.path("M {0}, {1} L {2} , {3} L {4} , {5} L {6} , {7}",c.x,c.y,h.x,h.y,u.x,u.y,d.x,d.y).attr(s.sgroupBracketStyle)},chem.SGroup.getBracketParameters=function(t,e,s,r,o,i,n,a){var h=function(t,e,s,r){this.c=t,this.d=e,this.n=e.rotateSC(1,0),this.w=s,this.h=r},u=[];return e.length<2?function(){o=o||new Vec2(1,0),i=i||o.rotateSC(1,0);var t=Math.min(.25,.3*r.sz().x),e=Vec2.lc2(o,r.p0.x,i,.5*(r.p0.y+r.p1.y)),s=Vec2.lc2(o,r.p1.x,i,.5*(r.p0.y+r.p1.y)),n=r.sz().y;u.push(new h(e,o.negated(),t,n),new h(s,o,t,n))}():2===e.length?function(){var s=t.bonds.get(e[0]),r=t.bonds.get(e[1]),o=s.getCenter(t),i=r.getCenter(t),c=-1,d=-1,l=-1,p=-1,m=Vec2.centre(o,i),g=Vec2.diff(i,o).normalized(),f=g.negated(),S=g.rotateSC(1,0),v=S.negated();util.each(t.sGroupForest.children.get(a),function(t){var e=n?n.ctab.sgroups.get(t).visel.boundingBox:null;util.isNull(e)||(e=e.translate((n.offset||new Vec2).negated()).transform(n.scaled2obj,n),c=Math.max(c,Vec2.shiftRayBox(o,f,e)),d=Math.max(d,Vec2.shiftRayBox(i,g,e)),l=Math.max(l,Vec2.shiftRayBox(m,S,e)),p=Math.max(p,Vec2.shiftRayBox(m,v,e)))},this),c=Math.max(c+.2,0),d=Math.max(d+.2,0),l=Math.max(Math.max(l,p)+.1,0);var b=1.5+l;u.push(new h(o.addScaled(f,c),f,.25,b),new h(i.addScaled(g,d),g,.25,b))}():function(){for(var r=0;r=0&&s.indexOf(e.end)>=0&&r.push(t)}),r},chem.SGroup.GroupMul={draw:function(t){var e=t.render,s=e.paper.set(),r=[],o=[],i=Set.fromList(this.atoms);chem.SGroup.getCrossBonds(r,o,t.molecule,i),chem.SGroup.bracketPos(this,e,t.molecule,o);var n=this.bracketBox,a=this.bracketDir,h=a.rotateSC(1,0);return this.areas=[n],chem.SGroup.drawBrackets(s,e,this,o,i,n,a,h,this.data.mul),s},saveToMolfile:function(t,e,s,r){var o=util.stringPadded(e[this.id],3),i=[];i=i.concat(chem.SGroup.makeAtomBondLines("SAL",o,util.idList(this.atomSet),s)),i=i.concat(chem.SGroup.makeAtomBondLines("SPA",o,util.idList(this.parentAtomSet),s)),i=i.concat(chem.SGroup.makeAtomBondLines("SBL",o,this.bonds,r));var n="M SMT "+o+" "+this.data.mul;return i.push(n),i=i.concat(chem.SGroup.bracketsToMolfile(t,this,o)),i.join("\n")},prepareForSaving:function(t){var e;this.atoms.sort(),this.atomSet=Set.fromList(this.atoms),this.parentAtomSet=Set.clone(this.atomSet);var s=[],r=[];if(t.bonds.each(function(t,e){Set.contains(this.parentAtomSet,e.begin)&&Set.contains(this.parentAtomSet,e.end)?s.push(t):(Set.contains(this.parentAtomSet,e.begin)||Set.contains(this.parentAtomSet,e.end))&&r.push(t)},this),0!=r.length&&2!=r.length)throw{id:this.id,"error-type":"cross-bond-number",message:"Unsupported cross-bonds number"};var o=-1,i=-1,n=null;if(2==r.length){var a=t.bonds.get(r[0]);o=Set.contains(this.parentAtomSet,a.begin)?a.begin:a.end;var h=t.bonds.get(r[1]);i=Set.contains(this.parentAtomSet,h.begin)?h.begin:h.end,n=h}var u=null,c=o,d=[];for(e=0;e=0){var p=t.bonds.get(r[0]);p.begin==o?p.begin=c:p.end=c}this.bonds=r},postLoad:function(t,e){this.data.mul=this.data.subscript-0;var s={};this.atoms=chem.SGroup.filterAtoms(this.atoms,e),this.patoms=chem.SGroup.filterAtoms(this.patoms,e);for(var r=1;r=0?util.paddedInt(i.nCharnCharsToDisplay,3):"ALL")+" 1 "+util.stringPadded(i.tagChar,1)+" "+util.paddedInt(i.daspPos,1)+" ";a.push(u);var c=util.normalizeNewlines(i.fieldValue).replace(/\n*$/,"");return c.split("\n").each(function(t){for(;t.length>69;)a.push("M SCD "+o+" "+t.slice(0,69)),t=t.slice(69);a.push("M SED "+o+" "+t)}),a.join("\n")},prepareForSaving:function(t){this.atoms=chem.SGroup.getAtoms(t,this)},postLoad:function(t,e){this.data.absolute||(this.pp=this.pp.add(chem.SGroup.getMassCentre(t,this.atoms)))}},chem.SGroup.TYPES={MUL:chem.SGroup.GroupMul,SRU:chem.SGroup.GroupSru,SUP:chem.SGroup.GroupSup,DAT:chem.SGroup.GroupDat,GEN:chem.SGroup.GroupGen},chem.SGroupForest=function(t){this.parent=new Map,this.children=new Map,this.children.set(-1,[]),this.molecule=t},chem.SGroupForest.prototype.getSGroupsBFS=function(){var t=[],e=[],s=-1;for(e=util.array(this.children.get(-1));e.length>0;){var s=e.shift();e=e.concat(this.children.get(s)),t.push(s)}return t},chem.SGroupForest.prototype.getAtomSets=function(){return this.molecule.sgroups.map(function(t,e){return Set.fromList(e.atoms)})},chem.SGroupForest.prototype.getAtomSetRelations=function(t,e,s){var r=new Map,o=new Map,s=this.getAtomSets();s.unset(t),s.each(function(t,s){o.set(t,Set.subset(e,s)),r.set(t,Set.subset(s,e)&&!Set.eq(s,e))},this);var i=s.findAll(function(t){return!!o.get(t)&&!(util.findIndex(this.children.get(t),function(t){return o.get(t)},this)>=0)},this);return util.assert(i.length<=1),{children:s.findAll(function(t,e){return r.get(t)&&!r.get(this.parent.get(t))},this),parent:0===i.length?-1:i[0]}},chem.SGroupForest.prototype.getPathToRoot=function(t){for(var e=[],s=t;s>=0;s=this.parent.get(s))util.assert(e.indexOf(s)<0,"SGroupForest: loop detected"),e.push(s);return e},chem.SGroupForest.prototype.validate=function(){var t=this.getAtomSets();this.molecule.sgroups.each(function(t){this.getPathToRoot(t)},this);var e=!0;return this.parent.each(function(s,r){r>=0&&!Set.subset(t.get(s),t.get(r))&&(e=!1)},this),this.children.each(function(s){for(var r=this.children.get(s),o=0;o=0){var l=this.atoms[c],g=h.numOpeningCycles(b);for(i=0;i=4)throw new Error("internal: pyramid overflow");o[r++]=n;break}if(4==r)r=o[0],o[0]=o[1],o[1]=o[2],o[2]=o[3],o[3]=r;else if(3!=r)throw new Error("cannot calculate chirality");chem.Stereocenters.isPyramidMappingRigid(o)?this.atoms[t].chirality=1:this.atoms[t].chirality=2},this)}catch(t){alert("Warning: "+t.message)}var _=[];_.push(0);var p=!0;for(s=0;s=0){for(h.numBranches(m)>1&&this.atoms[m].branch_cnt>0&&this.atoms[m].paren_written&&(this.smiles+=")"),g=h.numOpeningCycles(b),i=0;i=0){var v=h.numBranches(m);if(v>1&&this.atoms[m].branch_cntv)throw new Error("unexpected branch")}var S=t.bonds.get(b),w=0;if(S.type==chem.Struct.BOND.TYPE.SINGLE&&(w=this._calcBondDirection(t,b,m)),1==w&&c==S.end||2==w&&c==S.begin?this.smiles+="/":2==w&&c==S.end||1==w&&c==S.begin?this.smiles+="\\":S.type==chem.Struct.BOND.TYPE.ANY?this.smiles+="~":S.type==chem.Struct.BOND.TYPE.DOUBLE?this.smiles+="=":S.type==chem.Struct.BOND.TYPE.TRIPLE?this.smiles+="#":S.type!=chem.Struct.BOND.TYPE.AROMATIC||this.atoms[S.begin].lowercase&&this.atoms[S.end].lowercase&&this.isBondInRing(b)?S.type==chem.Struct.BOND.TYPE.SINGLE&&this.atoms[S.begin].aromatic&&this.atoms[S.end].aromatic?this.smiles+="-":!1:this.smiles+=":",h.edgeClosingCycle(b)){for(i=1;i<_.length&&_[i]!=c;i++);if(i==_.length)throw new Error("cycle number not found");this._writeCycleNumber(i),_[i]=-1,f=!1}}else p||(this.smiles+=this._written_components==h.nComponentsInReactants?">>":"."),p=!1,this._written_components++;f&&(this._writeAtom(t,c,this.atoms[c].aromatic,this.atoms[c].lowercase,this.atoms[c].chirality),this._written_atoms.push(d.idx))}return this.comma=!1,this._writeRadicals(t),this.comma&&(this.smiles+="|"),this.smiles},chem.SmilesSaver.prototype._writeCycleNumber=function(t){if(t>0&&t<10)this.smiles+=t;else if(t>=10&&t<100)this.smiles+="%"+t;else{if(!(t>=100&&t<1e3))throw new Error("bad cycle number: "+t);this.smiles+="%%"+t}},chem.SmilesSaver.prototype._writeAtom=function(t,e,s,i,n){var o=t.atoms.get(e),r=!1,a=-1,h=0;if("A"==o.label)return void(this.smiles+="*");if("R"==o.label||"R#"==o.label)return void(this.smiles+="[*]");h=o.aam,"C"!=o.label&&"P"!=o.label&&"N"!=o.label&&"S"!=o.label&&"O"!=o.label&&"Cl"!=o.label&&"F"!=o.label&&"Br"!=o.label&&"B"!=o.label&&"I"!=o.label&&(r=!0),(o.explicitValence>=0||0!=o.radical||n>0||s&&"C"!=o.label&&"O"!=o.label||s&&"C"==o.label&&this.atoms[e].neighbours.length<3&&0==this.atoms[e].h_count)&&(a=this.atoms[e].h_count);var d=o.label;if(o.atomList&&!o.atomList.notList?(d=o.atomList.label(),r=!1):o.isPseudo()||o.atomList&&o.atomList.notList?(d="*",r=!0):(n||0!=o.charge||o.isotope>0||a>=0||h>0)&&(r=!0),r&&(-1==a&&(a=this.atoms[e].h_count),this.smiles+="["),o.isotope>0&&(this.smiles+=o.isotope),this.smiles+=i?d.toLowerCase():d,n>0&&(this.smiles+=1==n?"@":"@@",o.implicitH>1))throw new Error(o.implicitH+" implicit H near stereocenter");"H"!=o.label&&(a>1||0==a&&!r?this.smiles+="H"+a:1==a&&(this.smiles+="H")),o.charge>1?this.smiles+="+"+o.charge:o.charge<-1?this.smiles+=o.charge:1==o.charge?this.smiles+="+":-1==o.charge&&(this.smiles+="-"),h>0&&(this.smiles+=":"+h),r&&(this.smiles+="]")},chem.SmilesSaver.prototype._markCisTrans=function(t){this.cis_trans=new chem.CisTrans(t,function(t){return this.atoms[t].neighbours},this),this.cis_trans.build(),this._dbonds=new Array(t.bonds.count()),t.bonds.each(function(t){this._dbonds[t]={ctbond_beg:-1,ctbond_end:-1,saved:0}},this),this.cis_trans.each(function(e,s){var i=t.bonds.get(e);if(0!=s.parity&&!this.isBondInRing(e)){var n=this.atoms[i.begin].neighbours,o=this.atoms[i.end].neighbours,r=!0,a=!0;if(n.each(function(s){s.bid!=e&&t.bonds.get(s.bid).type==chem.Struct.BOND.TYPE.SINGLE&&(r=!1)},this),o.each(function(s){s.bid!=e&&t.bonds.get(s.bid).type==chem.Struct.BOND.TYPE.SINGLE&&(a=!1)},this),r||a)return;n.each(function(s){s.bid!=e&&(t.bonds.get(s.bid).begin==i.begin?this._dbonds[s.bid].ctbond_beg=e:this._dbonds[s.bid].ctbond_end=e)},this),o.each(function(s){s.bid!=e&&(t.bonds.get(s.bid).begin==i.end?this._dbonds[s.bid].ctbond_beg=e:this._dbonds[s.bid].ctbond_end=e)},this)}},this)},chem.SmilesSaver.prototype._updateSideBonds=function(t,e){var s=t.bonds.get(e),i=this.cis_trans.getSubstituents(e),n=this.cis_trans.getParity(e),o=[-1,-1,-1,-1];o[0]=t.findBondId(i[0],s.begin),-1!=i[1]&&(o[1]=t.findBondId(i[1],s.begin)),o[2]=t.findBondId(i[2],s.end),-1!=i[3]&&(o[3]=t.findBondId(i[3],s.end));var r=0,a=0,h=0,d=0;if(0!=this._dbonds[o[0]].saved&&(1==this._dbonds[o[0]].saved&&t.bonds.get(o[0]).begin==s.begin||2==this._dbonds[o[0]].saved&&t.bonds.get(o[0]).end==s.begin?r++:a++),-1!=o[1]&&0!=this._dbonds[o[1]].saved&&(2==this._dbonds[o[1]].saved&&t.bonds.get(o[1]).begin==s.begin||1==this._dbonds[o[1]].saved&&t.bonds.get(o[1]).end==s.begin?r++:a++),0!=this._dbonds[o[2]].saved&&(1==this._dbonds[o[2]].saved&&t.bonds.get(o[2]).begin==s.end||2==this._dbonds[o[2]].saved&&t.bonds.get(o[2]).end==s.end?h++:d++),-1!=o[3]&&0!=this._dbonds[o[3]].saved&&(2==this._dbonds[o[3]].saved&&t.bonds.get(o[3]).begin==s.end||1==this._dbonds[o[3]].saved&&t.bonds.get(o[3]).end==s.end?h++:d++),n==chem.CisTrans.PARITY.CIS?(r+=h,a+=d):(r+=d,a+=h),r>0&&a>0)throw new Error("incompatible cis-trans configuration");return(0!=r||0!=a)&&(r>0&&(this._dbonds[o[0]].saved=t.bonds.get(o[0]).begin==s.begin?1:2,-1!=o[1]&&(this._dbonds[o[1]].saved=t.bonds.get(o[1]).begin==s.begin?2:1),this._dbonds[o[2]].saved=t.bonds.get(o[2]).begin==s.end==(n==chem.CisTrans.PARITY.CIS)?1:2,-1!=o[3]&&(this._dbonds[o[3]].saved=t.bonds.get(o[3]).begin==s.end==(n==chem.CisTrans.PARITY.CIS)?2:1)),a>0&&(this._dbonds[o[0]].saved=t.bonds.get(o[0]).begin==s.begin?2:1,-1!=o[1]&&(this._dbonds[o[1]].saved=t.bonds.get(o[1]).begin==s.begin?1:2),this._dbonds[o[2]].saved=t.bonds.get(o[2]).begin==s.end==(n==chem.CisTrans.PARITY.CIS)?2:1,-1!=o[3]&&(this._dbonds[o[3]].saved=t.bonds.get(o[3]).begin==s.end==(n==chem.CisTrans.PARITY.CIS)?1:2)),!0)},chem.SmilesSaver.prototype._calcBondDirection=function(t,e,s){var i;if(-1==this._dbonds[e].ctbond_beg&&-1==this._dbonds[e].ctbond_end)return 0;if(t.bonds.get(e).type!=chem.Struct.BOND.TYPE.SINGLE)throw new Error("internal: directed bond type "+t.bonds.get(e).type);for(;;){if(i=0,this.cis_trans.each(function(e,s){0==s.parity||this.isBondInRing(e)||this._updateSideBonds(t,e)&&i++},this),i==this._touched_cistransbonds)break;this._touched_cistransbonds=i}return 0==this._dbonds[e].saved&&(s==t.bonds.get(e).begin?this._dbonds[e].saved=1:this._dbonds[e].saved=2),this._dbonds[e].saved},chem.SmilesSaver.prototype._writeRadicals=function(t){var e,s,i=new Array(this._written_atoms.length);for(e=0;e=0)return!1;if(util.findIndex([c.bid,d.bid],function(e){return t.get(e).type!=chem.Struct.BOND.TYPE.DOUBLE},this)>=0)return!1;var a=util.findAll(this.getNeighbors.call(this.context,c.aid),function(r){return r.aid!=e},this),s=util.findAll(this.getNeighbors.call(this.context,d.aid),function(r){return r.aid!=e},this);return!(a.length<1||a.length>2||s.length<1||s.length>2)&&(!(util.findIndex(a.concat(s),function(e){return t.get(e.bid).type!=chem.Struct.BOND.TYPE.SINGLE},this)>=0)&&(!(util.findIndex(a.concat(s),function(e){return t.get(e.bid).stereo==chem.Struct.BOND.STEREO.EITHER},this)>=0)&&(Set.add(n,c.aid),void Set.add(n,d.aid))))},this),Set.size(n)>0&&alert("This structure may contain allenes, which cannot be represented in the SMILES notation. Relevant stereo-information will be discarded."),r.each(function(e){if(!Set.contains(n,e)){var r=this.getNeighbors.call(this.context,e),t=!1;r.find(function(r){var n=this.molecule.bonds.get(r.bid);return n.type==chem.Struct.BOND.TYPE.SINGLE&&n.begin==e&&(n.stereo==chem.Struct.BOND.STEREO.UP||n.stereo==chem.Struct.BOND.STEREO.DOWN)&&(t=!0,!0)},this),t&&this._buildOneCenter(e)}},this)},chem.Stereocenters.allowed_stereocenters=[{elem:"C",charge:0,degree:3,n_double_bonds:0,implicit_degree:4},{elem:"C",charge:0,degree:4,n_double_bonds:0,implicit_degree:4},{elem:"Si",charge:0,degree:3,n_double_bonds:0,implicit_degree:4},{elem:"Si",charge:0,degree:4,n_double_bonds:0,implicit_degree:4},{elem:"N",charge:1,degree:3,n_double_bonds:0,implicit_degree:4},{elem:"N",charge:1,degree:4,n_double_bonds:0,implicit_degree:4},{elem:"N",charge:0,degree:3,n_double_bonds:0,implicit_degree:3},{elem:"S",charge:0,degree:4,n_double_bonds:2,implicit_degree:4},{elem:"S",charge:1,degree:3,n_double_bonds:0,implicit_degree:3},{elem:"S",charge:0,degree:3,n_double_bonds:1,implicit_degree:3},{elem:"P",charge:0,degree:3,n_double_bonds:0,implicit_degree:3},{elem:"P",charge:1,degree:4,n_double_bonds:0,implicit_degree:4},{elem:"P",charge:0,degree:4,n_double_bonds:1,implicit_degree:4}],chem.Stereocenters.prototype._buildOneCenter=function(e){var r=this.molecule.atoms.get(e),t=this.getNeighbors.call(this.context,e),n=t.length,i=-1,o={group:0,type:0,pyramid:new Array(4)},c=0,d=new Array(4),a=0,s=0;o.pyramid[0]=-1,o.pyramid[1]=-1,o.pyramid[2]=-1,o.pyramid[3]=-1;var h=0;if(n>4)throw new Error("stereocenter with %d bonds are not supported"+n);if(t.each(function(e){var t=this.molecule.atoms.get(e.aid),n=this.molecule.bonds.get(e.bid);if(d[c]={edge_idx:e.bid,nei_idx:e.aid,rank:e.aid,vec:Vec2.diff(t.pp,r.pp).yComplement()},t.pureHydrogen()?(h++,d[c].rank=1e4):"H"==t.label&&(d[c].rank=5e3),!d[c].vec.normalize())throw new Error("zero bond length");if(n.type==chem.Struct.BOND.TYPE.TRIPLE)throw new Error("non-single bonds not allowed near stereocenter");if(n.type==chem.Struct.BOND.TYPE.AROMATIC)throw new Error("aromatic bonds not allowed near stereocenter");n.type==chem.Struct.BOND.TYPE.DOUBLE&&s++,c++},this),chem.Stereocenters.allowed_stereocenters.find(function(e){return e.elem==r.label&&e.charge==r.charge&&e.degree==n&&e.n_double_bonds==s&&(i=e.implicit_degree,!0)},this),-1==i)throw new Error("unknown stereocenter configuration: "+r.label+", charge "+r.charge+", "+n+" bonds ("+s+" double)");if(4==n&&h>1)throw new Error(h+" hydrogens near stereocenter");if(3==n&&4==i&&h>0)throw new Error("have hydrogen(s) besides implicit hydrogen near stereocenter");if(4==n){d[0].rank>d[1].rank&&d.swap(0,1),d[1].rank>d[2].rank&&d.swap(1,2),d[2].rank>d[3].rank&&d.swap(2,3),d[1].rank>d[2].rank&&d.swap(1,2),d[0].rank>d[1].rank&&d.swap(0,1),d[1].rank>d[2].rank&&d.swap(1,2);var m=-1,l=-1,u=-1,g=-1,S=0;for(c=0;c<4;c++){var p=this._getBondStereo(e,d[c].edge_idx);if(p==chem.Struct.BOND.STEREO.UP||p==chem.Struct.BOND.STEREO.DOWN){m=c,S=p;break}}if(-1==m)throw new Error("none of 4 bonds going from stereocenter is stereobond");var _,E;if(-1==l&&(_=chem.Stereocenters._xyzzy(d[m].vec,d[(m+1)%4].vec,d[(m+2)%4].vec),E=chem.Stereocenters._xyzzy(d[m].vec,d[(m+1)%4].vec,d[(m+3)%4].vec),_+E!=3&&_+E!=12||(l=(m+1)%4,u=(m+2)%4,g=(m+3)%4)),-1==l&&(_=chem.Stereocenters._xyzzy(d[m].vec,d[(m+2)%4].vec,d[(m+1)%4].vec),E=chem.Stereocenters._xyzzy(d[m].vec,d[(m+2)%4].vec,d[(m+3)%4].vec),_+E!=3&&_+E!=12||(l=(m+2)%4,u=(m+1)%4,g=(m+3)%4)),-1==l&&(_=chem.Stereocenters._xyzzy(d[m].vec,d[(m+3)%4].vec,d[(m+1)%4].vec),E=chem.Stereocenters._xyzzy(d[m].vec,d[(m+3)%4].vec,d[(m+2)%4].vec),_+E!=3&&_+E!=12||(l=(m+3)%4,u=(m+2)%4,g=(m+1)%4)),-1==l)throw new Error("internal error: can not find opposite bond");if(S==chem.Struct.BOND.STEREO.UP&&this._getBondStereo(e,d[l].edge_idx)==chem.Struct.BOND.STEREO.DOWN)throw new Error("stereo types of the opposite bonds mismatch");if(S==chem.Struct.BOND.STEREO.DOWN&&this._getBondStereo(e,d[l].edge_idx)==chem.Struct.BOND.STEREO.UP)throw new Error("stereo types of the opposite bonds mismatch");if(S==this._getBondStereo(e,d[u].edge_idx))throw new Error("stereo types of non-opposite bonds match");if(S==this._getBondStereo(e,d[g].edge_idx))throw new Error("stereo types of non-opposite bonds match");a=3==m||3==l?S:S==chem.Struct.BOND.STEREO.UP?chem.Struct.BOND.STEREO.DOWN:chem.Struct.BOND.STEREO.UP,N=chem.Stereocenters._sign(d[0].vec,d[1].vec,d[2].vec),a==chem.Struct.BOND.STEREO.UP&&N>0||a==chem.Struct.BOND.STEREO.DOWN&&N<0?(o.pyramid[0]=d[0].nei_idx,o.pyramid[1]=d[1].nei_idx,o.pyramid[2]=d[2].nei_idx):(o.pyramid[0]=d[0].nei_idx,o.pyramid[1]=d[2].nei_idx,o.pyramid[2]=d[1].nei_idx),o.pyramid[3]=d[3].nei_idx}else if(3==n){d[0].rank>d[1].rank&&d.swap(0,1),d[1].rank>d[2].rank&&d.swap(1,2),d[0].rank>d[1].rank&&d.swap(0,1);var b=this._getBondStereo(e,d[0].edge_idx),O=this._getBondStereo(e,d[1].edge_idx),f=this._getBondStereo(e,d[2].edge_idx),w=0,y=0;if(w+=b==chem.Struct.BOND.STEREO.UP?1:0,w+=O==chem.Struct.BOND.STEREO.UP?1:0,w+=f==chem.Struct.BOND.STEREO.UP?1:0,y+=b==chem.Struct.BOND.STEREO.DOWN?1:0,y+=O==chem.Struct.BOND.STEREO.DOWN?1:0,y+=f==chem.Struct.BOND.STEREO.DOWN?1:0,4==i){if(3==w)throw new Error("all 3 bonds up near stereoatom");if(3==y)throw new Error("all 3 bonds down near stereoatom");if(0==w&&0==y)throw new Error("no up/down bonds near stereoatom -- indefinite case");if(1==w&&1==y)throw new Error("one bond up, one bond down -- indefinite case");if(S=0,2==w)a=chem.Struct.BOND.STEREO.DOWN;else if(2==y)a=chem.Struct.BOND.STEREO.UP;else{for(m=-1,u=-1,g=-1,c=0;c<3;c++)if((x=this._getBondStereo(e,d[c].edge_idx))==chem.Struct.BOND.STEREO.UP||x==chem.Struct.BOND.STEREO.DOWN){m=c,S=x,u=(c+1)%3,g=(c+2)%3;break}if(-1==m)throw new Error("internal error: can not find up or down bond");var v=chem.Stereocenters._xyzzy(d[u].vec,d[g].vec,d[m].vec);if(3==v||4==v)throw new Error("degenerate case for 3 bonds near stereoatom");a=1==v?S:S==chem.Struct.BOND.STEREO.UP?chem.Struct.BOND.STEREO.DOWN:chem.Struct.BOND.STEREO.UP}var N=chem.Stereocenters._sign(d[0].vec,d[1].vec,d[2].vec);a==chem.Struct.BOND.STEREO.UP&&N>0||a==chem.Struct.BOND.STEREO.DOWN&&N<0?(o.pyramid[0]=d[0].nei_idx,o.pyramid[1]=d[1].nei_idx,o.pyramid[2]=d[2].nei_idx):(o.pyramid[0]=d[0].nei_idx,o.pyramid[1]=d[2].nei_idx,o.pyramid[2]=d[1].nei_idx),o.pyramid[3]=-1}else{var x;if(y>0&&w>0)throw new Error("one bond up, one bond down -- indefinite case");if(0==y&&0==w)throw new Error("no up-down bonds attached to stereocenter");x=w>0?1:-1,1!=chem.Stereocenters._xyzzy(d[0].vec,d[1].vec,d[2].vec)&&1!=chem.Stereocenters._xyzzy(d[0].vec,d[2].vec,d[1].vec)&&1!=chem.Stereocenters._xyzzy(d[2].vec,d[1].vec,d[0].vec)||(x=-x),N=chem.Stereocenters._sign(d[0].vec,d[1].vec,d[2].vec),N==x?(o.pyramid[0]=d[0].nei_idx,o.pyramid[1]=d[2].nei_idx,o.pyramid[2]=d[1].nei_idx):(o.pyramid[0]=d[0].nei_idx,o.pyramid[1]=d[1].nei_idx,o.pyramid[2]=d[2].nei_idx),o.pyramid[3]=-1}}this.atoms.set(e,o)},chem.Stereocenters.prototype._getBondStereo=function(e,r){var t=this.molecule.bonds.get(r);return e!=t.begin?0:t.stereo},chem.Stereocenters._xyzzy=function(e,r,t){var n=Vec2.cross(e,r),i=Vec2.dot(e,r),o=Vec2.cross(e,t),c=Vec2.dot(e,t);if(Math.abs(n)<.001){if(Math.abs(o)<.001)throw new Error("degenerate case -- bonds overlap");return o>0?4:8}return n*o<-1e-6?2:c.001)return 1;if(n<-.001)return-1;throw new Error("degenerate triangle")},chem.Stereocenters.isPyramidMappingRigid=function(e){var r=e.clone(),t=!0;return r[0]>r[1]&&(r.swap(0,1),t=!t),r[1]>r[2]&&(r.swap(1,2),t=!t),r[2]>r[3]&&(r.swap(2,3),t=!t),r[1]>r[2]&&(r.swap(1,2),t=!t),r[0]>r[1]&&(r.swap(0,1),t=!t),r[1]>r[2]&&(r.swap(1,2),t=!t),t}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../util":39,"../util/map":40,"../util/set":42,"../util/vec2":43,"./struct":16}],16:[function(require,module,exports){ +(function (global){ +var Map=require("../util/map"),Pool=require("../util/pool"),Set=require("../util/set"),Vec2=require("../util/vec2"),util=require("../util"),element=require("./element"),chem=global.chem=global.chem||{};chem.Struct=function(){this.atoms=new Pool,this.bonds=new Pool,this.sgroups=new Pool,this.halfBonds=new Map,this.loops=new Pool,this.isChiral=!1,this.isReaction=!1,this.rxnArrows=new Pool,this.rxnPluses=new Pool,this.frags=new Pool,this.rgroups=new Map,this.name="",this.sGroupForest=new chem.SGroupForest(this)},chem.Struct.prototype.hasRxnProps=function(){return this.atoms.find(function(t,e){return e.hasRxnProps()},this)>=0||this.bonds.find(function(t,e){return e.hasRxnProps()},this)>=0},chem.Struct.prototype.hasRxnArrow=function(){return this.rxnArrows.count()>0},chem.Struct.prototype.addRxnArrowIfNecessary=function(){var t=!this.hasRxnArrow()&&this.hasRxnProps();return t&&this.rxnArrows.add(new chem.Struct.RxnArrow),t},chem.Struct.prototype.getSGroupsInAtomSet=function(t){var e=new Hash;util.each(t,function(t){Set.list(this.atoms.get(t).sgs).each(function(t){var n=e.get(t);Object.isUndefined(n)?n=1:n++,e.set(t,n)},this)},this);var n=[];return e.each(function(t){var e=parseInt(t.key,10),i=this.sgroups.get(e),o=chem.SGroup.getAtoms(this,i);t.value==o.length&&n.push(e)},this),n},chem.Struct.prototype.isBlank=function(){return 0===this.atoms.count()&&0===this.rxnArrows.count()&&0===this.rxnPluses.count()&&!this.isChiral},chem.Struct.prototype.toLists=function(){var t={},e=[];this.atoms.each(function(n,i){t[n]=e.length,e.push(i)});var n=[];return this.bonds.each(function(e,i){var o=new chem.Struct.Bond(i);o.begin=t[i.begin],o.end=t[i.end],n.push(o)}),{atoms:e,bonds:n}},chem.Struct.prototype.clone=function(t,e,n,i){var o=new chem.Struct;return this.mergeInto(o,t,e,n,!1,i)},chem.Struct.prototype.getScaffold=function(){var t=Set.empty();return this.atoms.each(function(e){Set.add(t,e)},this),this.rgroups.each(function(e,n){n.frags.each(function(e,n){this.atoms.each(function(e,i){i.fragment==n&&Set.remove(t,e)},this)},this)},this),this.clone(t)},chem.Struct.prototype.getFragmentIds=function(t){var e=Set.empty();return this.atoms.each(function(n,i){i.fragment==t&&Set.add(e,n)},this),e},chem.Struct.prototype.getFragment=function(t){return this.clone(this.getFragmentIds(t))},chem.Struct.prototype.mergeInto=function(t,e,n,i,o,s){e=e||Set.keySetInt(this.atoms),n=n||Set.keySetInt(this.bonds),n=Set.filter(n,function(t){var n=this.bonds.get(t);return Set.contains(e,n.begin)&&Set.contains(e,n.end)},this);var r={};this.atoms.each(function(t,n){Set.contains(e,t)&&(r[n.fragment]=1)});var h={};this.frags.each(function(e,n){r[e]&&(h[e]=t.frags.add(n.clone()))}),this.rgroups.each(function(e,n){var i=o;if(i||(n.frags.each(function(t,e){r[e]&&(i=!0)}),i)){var s=t.rgroups.get(e);s?n.frags.each(function(t,e){r[e]&&s.frags.add(h[e])}):t.rgroups.set(e,n.clone(h))}}),void 0!==s&&null!==s||(s={}),this.atoms.each(function(n,i){Set.contains(e,n)&&(s[n]=t.atoms.add(i.clone(h)))});var c={};return this.bonds.each(function(e,i){Set.contains(n,e)&&(c[e]=t.bonds.add(i.clone(s)))}),this.sgroups.each(function(n,i){var o;for(o=0;o1e-4?o:new Vec2(1,0),e.norm=e.dir.turnLeft(),e.ang=e.dir.oxAngle(),e.loop<0&&(e.loop=-1)},chem.Struct.prototype.initHalfBonds=function(){this.halfBonds.clear(),this.bonds.each(this.bondInitHalfBonds,this)},chem.Struct.prototype.setHbNext=function(t,e){this.halfBonds.get(this.halfBonds.get(t).contra).next=e},chem.Struct.prototype.halfBondSetAngle=function(t,e){var n=this.halfBonds.get(t),i=this.halfBonds.get(e);i.rightCos=n.leftCos=Vec2.dot(i.dir,n.dir),i.rightSin=n.leftSin=Vec2.cross(i.dir,n.dir),n.leftNeighbor=e,i.rightNeighbor=t},chem.Struct.prototype.atomAddNeighbor=function(t){var e=this.halfBonds.get(t),n=this.atoms.get(e.begin),i=0;for(i=0;ie.ang);++i);n.neighbors.splice(i,0,t);var o=n.neighbors[(i+1)%n.neighbors.length],s=n.neighbors[(i+n.neighbors.length-1)%n.neighbors.length];this.setHbNext(s,t),this.setHbNext(t,o),this.halfBondSetAngle(t,s),this.halfBondSetAngle(o,t)},chem.Struct.prototype.atomSortNeighbors=function(t){var e=this.atoms.get(t);e.neighbors=e.neighbors.sortBy(function(t){return this.halfBonds.get(t).ang},this);var n;for(n=0;n0?t.totalLength/t.cnt:-1},chem.Struct.prototype.getAvgClosestAtomDistance=function(){var t,e,n,i=0,o=0,s=this.atoms.keys();for(e=0;eo)&&(t=o));i+=t}return s.length>0?i/s.length:-1},chem.Struct.prototype.checkBondExists=function(t,e){var n=!1;return this.bonds.each(function(i,o){(o.begin==t&&o.end==e||o.end==t&&o.begin==e)&&(n=!0)},this),n},chem.Loop=function(t,e,n){this.hbs=t,this.dblBonds=0,this.aromatic=!0,this.convex=n||!1,t.each(function(t){var n=e.bonds.get(e.halfBonds.get(t).bid);n.type!=chem.Struct.BOND.TYPE.AROMATIC&&(this.aromatic=!1),n.type==chem.Struct.BOND.TYPE.DOUBLE&&this.dblBonds++},this)},chem.Struct.RxnPlus=function(t){t=t||{},this.pp=t.pp?new Vec2(t.pp):new Vec2},chem.Struct.RxnPlus.prototype.clone=function(){return new chem.Struct.RxnPlus(this)},chem.Struct.RxnArrow=function(t){t=t||{},this.pp=t.pp?new Vec2(t.pp):new Vec2},chem.Struct.RxnArrow.prototype.clone=function(){return new chem.Struct.RxnArrow(this)},chem.Struct.prototype.findConnectedComponent=function(t){for(var e={},n=[t],i=Set.empty();n.length>0;)(function(){var t=n.pop();e[t]=1,Set.add(i,t);for(var o=this.atoms.get(t),s=0;s0)return!1}return!0},chem.Struct.prototype.loopIsInner=function(t){for(var e=2*Math.PI,n=0;n0&&t==r){var c=this.partitionLoop(n);util.each(c,function(t){this.loopIsInner(t)&&!this.loopHasSelfIntersections(t)?(i=util.arrayMin(t),this.loops.set(i,new chem.Loop(t,this,this.loopIsConvex(t)))):i=-2,t.each(function(t){this.halfBonds.get(t).loop=i,Set.add(s,this.halfBonds.get(t).bid)},this),i>=0&&o.push(i)},this);break}n.push(t)}},this),{newLoops:o,bondsToMark:Set.list(s)}},chem.Struct.prototype.prepareLoopStructure=function(){this.initHalfBonds(),this.initNeighbors(),this.updateHalfBonds(this.atoms.keys()),this.sortNeighbors(this.atoms.keys()),this.findLoops()},chem.Struct.prototype.atomAddToSGroup=function(t,e){chem.SGroup.addAtom(this.sgroups.get(t),e),Set.add(this.atoms.get(e).sgs,t)}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../util":39,"../util/map":40,"../util/pool":41,"../util/set":42,"../util/vec2":43,"./element":10}],17:[function(require,module,exports){ +(function (global){ +var util=require("../util"),element=require("./element");require("./struct");var chem=global.chem=global.chem||{};chem.Struct.prototype.calcConn=function(e){for(var t=0,i=this.atoms.get(e),r=!1,l=0;l=1?(a=3,u=3-n-e):(a=2,u=2-n-e-s):"S"==r||"Se"==r||"Po"==r?1==i?e<=3?(a=3,u=3-n-e):(a=5,u=5-n-e):e+n+s<=2?(a=2,u=2-n-e-s):e+n+s<=4?(a=4,u=4-n-e-s):(a=6,u=6-n-e-s):"Te"==r&&(-1==i?e<=2&&(a=2,u=2-n-e-s):0!=i&&2!=i||(e<=2?(a=2,u=2-n-e-s):e<=4?(a=4,u=4-n-e-s):0==i&&e<=6?(a=6,u=6-n-e-s):u=-1)):7==c&&("F"==r?(a=1,u=1-n-e-s):"Cl"!=r&&"Br"!=r&&"I"!=r&&"At"!=r||(1==i?e<=2?(a=2,u=2-n-e):(3==e||5==e||e>=7)&&(u=-1):0==i&&(e<=1?(a=1,u=1-n-e):2==e||4==e||6==e?1==n?(a=e,u=0):u=-1:e>7&&(u=-1)))),this.valence=a,this.implicitH=u,!(this.implicitH<0)||(this.valence=e,this.implicitH=0,this.badConn=!0,!1)},chem.Struct.Atom.prototype.calcValenceMinusHyd=function(e){var t=this,i=t.charge,r=t.label,l=element.getElementByLabel(r);if(null==l)throw new Error("Element "+r+" unknown");if(l<0)return this.implicitH=0,null;var c=element.get(l).group,n=chem.Struct.radicalElectrons(t.radical);if(3==c){if(("B"==r||"Al"==r||"Ga"==r||"In"==r)&&-1==i&&n+e<=4)return n+e}else if(5==c){if("N"==r||"P"==r){if(1==i)return n+e;if(2==i)return n+e}else if("Sb"==r||"Bi"==r||"As"==r){if(1==i)return n+e;if(2==i)return n+e}}else if(6==c){if("O"==r){if(i>=1)return n+e}else if(("S"==r||"Se"==r||"Po"==r)&&1==i)return n+e}else if(7==c&&("Cl"==r||"Br"==r||"I"==r||"At"==r)&&1==i)return n+e;return n+e+Math.abs(i)},chem.Struct.prototype.calcImplicitHydrogen=function(e){var t=this.calcConn(e),i=this.atoms.get(e);if(i.badConn=!1,t<0||i.isQuery())return void(i.implicitH=0);if(i.explicitValence>=0){var r=element.getElementByLabel(i.label);i.implicitH=0,null!=r&&(i.implicitH=i.explicitValence-i.calcValenceMinusHyd(t),i.implicitH<0&&(i.implicitH=0,i.badConn=!0))}else i.calcValence(t)},chem.Struct.prototype.setImplicitHydrogen=function(e){var t=function(e){this.calcImplicitHydrogen(e)};util.isNullOrUndefined(e)?this.atoms.each(t,this):util.each(e,t,this)}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../util":39,"./element":10,"./struct":16}],18:[function(require,module,exports){ +(function (global){ +function getSmiles(e){var t=ui.standalone||e,i=t?new chem.SmilesSaver:new chem.MolfileSaver,r=i.saveMolecule(ui.ctab,!0);return t?r:ketcher.server.smiles.sync({moldata:r})}function getMolfile(){return(new chem.MolfileSaver).saveMolecule(ui.ctab,!0)}function setMolecule(e){Object.isString(e)&&ui.loadMolecule(e)}function addFragment(e){Object.isString(e)&&ui.loadFragment(e)}function showMolfile(e,t,i){var r=util.extend({bondLength:75,showSelectionRegions:!1,showBondIds:!1,showHalfBondIds:!1,showLoopIds:!1,showAtomIds:!1,autoScale:!1,autoScaleMargin:4,hideImplicitHydrogen:!1},i),l=new rnd.Render(e,r.bondLength,r);if(t){var n=chem.Molfile.parseCTFile(t);l.setMolecule(n)}return l.update(),l}function onStructChange(e){util.assert(e),ui.render.addStructChangeHandler(e)}var queryString=require("query-string"),util=require("./util"),api=require("./api.js");require("./ui"),require("./chem"),require("./rnd");var ui=global.ui,chem=global.chem,rnd=global.rnd;window.onload=function(){var e=queryString.parse(document.location.search);e.api_path&&(ketcher.api_path=e.api_path),ketcher.server=api(ketcher.api_path),ui.init(util.extend({},e),ketcher.server)};var ketcher=module.exports={version:"2.0.0-alpha.3",api_path:"",build_date:"2017-06-28 16-34-14",build_number:null,build_options:"__BUILD_NUMBER__",getSmiles:getSmiles,getMolfile:getMolfile,setMolecule:setMolecule,addFragment:addFragment,showMolfile:showMolfile,onStructChange:onStructChange}; +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"./api.js":7,"./chem":11,"./rnd":21,"./ui":34,"./util":39,"query-string":4}],19:[function(require,module,exports){ +(function (global){ +var Raphael=(typeof window !== "undefined" ? window['Raphael'] : typeof global !== "undefined" ? global['Raphael'] : null),Vec2=require("./util/vec2");Raphael.el.translateAbs=function(t,a){this.delta=this.delta||new Vec2,this.delta.x+=t-0,this.delta.y+=a-0,this.transform("t"+this.delta.x.toString()+","+this.delta.y.toString())},Raphael.st.translateAbs=function(t,a){this.forEach(function(e){e.translateAbs(t,a)})},module.exports=Raphael; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"./util/vec2":43}],20:[function(require,module,exports){ +(function (global){ +function bondFlipRequired(t,e){return e.type==chem.Struct.BOND.TYPE.SINGLE&&t.stereo==chem.Struct.BOND.STEREO.NONE&&e.stereo!=chem.Struct.BOND.STEREO.NONE&&ui.ctab.atoms.get(t.begin).neighbors.length0&&(!t||"sgroupData"!==e))return!0;return!1},rnd.Editor.prototype.getSelection=function(t){var e={};if("selection"in this._selectionHelper)for(var o in this._selectionHelper.selection)e[o]=this._selectionHelper.selection[o].slice(0);if(t){var i=this.render.ctab.molecule;"bonds"in e&&e.bonds.each(function(t){var o=i.bonds.get(t);e.atoms=e.atoms||[],e.atoms.indexOf(o.begin)<0&&e.atoms.push(o.begin),e.atoms.indexOf(o.end)<0&&e.atoms.push(o.end)},this),"atoms"in e&&"bonds"in e&&i.bonds.each(function(t){if(!("bonds"in e)||e.bonds.indexOf(t)<0){var o=i.bonds.get(t);e.atoms.indexOf(o.begin)>=0&&e.atoms.indexOf(o.end)>=0&&(e.bonds=e.bonds||[],e.bonds.push(t))}},this)}return e},rnd.Editor.prototype.getSelectionStruct=function(){console.assert(ui.ctab==this.render.ctab.molecule,"Another ctab");var t=ui.ctab,e=this.getSelection(!0),o=t.clone(Set.fromList(e.atoms),Set.fromList(e.bonds),!0);return t.rxnArrows.each(function(t,i){-1!=e.rxnArrows.indexOf(t)&&o.rxnArrows.add(i.clone())}),t.rxnPluses.each(function(t,i){-1!=e.rxnPluses.indexOf(t)&&o.rxnPluses.add(i.clone())}),o.isReaction=t.isReaction&&(o.rxnArrows.count()||o.rxnPluses.count()),o},rnd.Editor.SelectionHelper=function(t){this.editor=t},rnd.Editor.SelectionHelper.prototype.setSelection=function(t,e){if(!("selection"in this&&e)){this.selection={};for(var o in rnd.ReStruct.maps)this.selection[o]=[]}if(t&&"id"in t&&"map"in t&&(t[t.map]=t[t.map]||[]).push(t.id),t)for(var i in this.selection)if(i in t)for(var r=0;r-1},rnd.Editor.EditorTool=function(t){this.editor=t},rnd.Editor.EditorTool.prototype.processEvent=function(t,e,o){if("touches"in e&&1!=e.touches.length){if("lastEvent"in this.OnMouseDown0)return this.OnMouseUp0(e,o)}else{if(t+"0"in this)return this[t+"0"](e,o);if(t in this)return this[t](e,o);console.log("EditorTool.dispatchEvent: event '"+t+"' is not handled.")}},rnd.Editor.EditorTool.prototype.OnMouseDown=function(){},rnd.Editor.EditorTool.prototype.OnMouseMove=function(){},rnd.Editor.EditorTool.prototype.OnMouseUp=function(){},rnd.Editor.EditorTool.prototype.OnClick=function(){},rnd.Editor.EditorTool.prototype.OnDblClick=function(){},rnd.Editor.EditorTool.prototype.OnMouseLeave=function(){this.OnCancel()},rnd.Editor.EditorTool.prototype.OnKeyPress=function(){},rnd.Editor.EditorTool.prototype.OnCancel=function(){},rnd.Editor.EditorTool.prototype.OnMouseDown0=function(t){return!!ui.hideBlurredControls()||(this.OnMouseDown0.lastEvent=t,this.OnMouseMove0.lastEvent=t,"OnMouseDown"in this?this.OnMouseDown(t):void 0)},rnd.Editor.EditorTool.prototype.OnMouseMove0=function(t){if(this.OnMouseMove0.lastEvent=t,"OnMouseMove"in this)return this.OnMouseMove(t)},rnd.Editor.EditorTool.prototype.OnMouseUp0=function(t){if(!("lastEvent"in this.OnMouseDown0))return!0;"lastEvent"in this.OnMouseMove0&&(t=Object.clone(t),t.pageX=this.OnMouseMove0.lastEvent.pageX,t.pageY=this.OnMouseMove0.lastEvent.pageY);try{if("OnMouseUp"in this)return this.OnMouseUp(t)}finally{delete this.OnMouseDown0.lastEvent}},rnd.Editor.EditorTool.atom_label_map={atom_tool_any:"A",atom_tool_h:"H",atom_tool_c:"C",atom_tool_n:"N",atom_tool_o:"O",atom_tool_s:"S",atom_tool_p:"P",atom_tool_f:"F",atom_tool_br:"Br",atom_tool_cl:"Cl",atom_tool_i:"I"},rnd.Editor.EditorTool.prototype.OnKeyPress0=function(t,e){if("rgroup_tool_label"===e&&"lastEvent"in this.OnMouseMove0)return rnd.Editor.RGroupAtomTool.prototype.OnMouseUp.call(this,this.OnMouseMove0.lastEvent);if(e in rnd.Editor.EditorTool.atom_label_map){var o=rnd.Editor.EditorTool.atom_label_map[e],i=this.editor.getSelection();if(i&&"atoms"in i&&i.atoms.length>0)return ui.addUndoAction(Action.fromAtomsAttrs(i.atoms,{label:o},!0),!0),ui.render.update(),!0;var r=this.editor.render.findItem(this.OnMouseMove0.lastEvent);if(r)return r.label={label:o},"atoms"===r.map?ui.addUndoAction(Action.fromAtomsAttrs(r.id,r.label,!0),!0):-1==r.id&&ui.addUndoAction(Action.fromAtomAddition(ui.page2obj(this.OnMouseMove0.lastEvent),r.label),!0),ui.render.update(),!0}return"OnKeyPress"in this&&this.OnKeyPress(t)},rnd.Editor.EditorTool.prototype._calcAngle=function(t,e){var o=Vec2.diff(e,t),i=Math.atan2(o.y,o.x),r=i<0?-1:1,n=Math.floor(Math.abs(i)/(Math.PI/12))*(Math.PI/12);return i=r*(n+(Math.abs(i)-n=0){var e=this.editor.render.findItem(t,[this.dragCtx.item.map],this.dragCtx.item);this._hoverHelper.hover(e.map==this.dragCtx.item.map?e:null)}this.editor.render.update()}else this._lassoHelper.running()?this.editor._selectionHelper.setSelection(this._lassoHelper.addPoint(t),t.shiftKey):this._hoverHelper.hover(this.editor.render.findItem(t,this._lassoHelper.fragment||t.ctrlKey?["frags","sgroups","sgroupData","rgroups","rxnArrows","rxnPluses","chiralFlags"]:["atoms","bonds","sgroups","sgroupData","rgroups","rxnArrows","rxnPluses","chiralFlags"]));return!0},rnd.Editor.LassoTool.prototype.OnMouseUp=function(t){if("dragCtx"in this){if("stopTapping"in this.dragCtx&&this.dragCtx.stopTapping(),["atoms"].indexOf(this.dragCtx.item.map)>=0){var e=this.editor.render.findItem(t,[this.dragCtx.item.map],this.dragCtx.item);e.map==this.dragCtx.item.map&&(this._hoverHelper.hover(null),this.editor._selectionHelper.setSelection(),this.dragCtx.action=this.dragCtx.action?Action.fromAtomMerge(this.dragCtx.item.id,e.id).mergeWith(this.dragCtx.action):Action.fromAtomMerge(this.dragCtx.item.id,e.id))}ui.addUndoAction(this.dragCtx.action,!0),this.editor.render.update(),delete this.dragCtx}else this._lassoHelper.running()?this.editor._selectionHelper.setSelection(this._lassoHelper.end(),t.shiftKey):this._lassoHelper.fragment&&this.editor._selectionHelper.setSelection();return!0},rnd.Editor.LassoTool.prototype.OnDblClick=function(t){var e=this.editor.render.findItem(t);if("atoms"==e.map){this.editor._selectionHelper.setSelection(e);var o=ui.ctab.atoms.get(e.id);"R#"==o.label?rnd.Editor.RGroupAtomTool.prototype.OnMouseUp.call(this,t):"L#"==o.label?ui.showElemTable({selection:o,onOk:function(t){return o.label==t.label&&o.atomList.equals(t.atomList)||(ui.addUndoAction(Action.fromAtomsAttrs(e.id,t)),ui.render.update()),!0}.bind(this)}):(element.getElementByLabel(o.label)||121)<120?ui.showAtomProperties(e.id):ui.showReaGenericsTable({values:[o.label],onOk:function(t){var i=t.values[0];return o.label!=i&&(ui.addUndoAction(Action.fromAtomsAttrs(e.id,{label:i})),ui.render.update()),!0}.bind(this)})}else"bonds"==e.map?(this.editor._selectionHelper.setSelection(e),ui.showBondProperties(e.id)):"sgroups"==e.map&&(this.editor._selectionHelper.setSelection(e),this._sGroupHelper.showPropertiesDialog(e.id));return!0},rnd.Editor.LassoTool.prototype.OnCancel=function(){"dragCtx"in this?("stopTapping"in this.dragCtx&&this.dragCtx.stopTapping(),ui.addUndoAction(this.dragCtx.action,!0),this.editor.render.update(),delete this.dragCtx):this._lassoHelper.running()&&this.editor._selectionHelper.setSelection(this._lassoHelper.end()),this._hoverHelper.hover(null)},rnd.Editor.LassoTool.LassoHelper=function(t,e,o){this.mode=t,this.fragment=o,this.editor=e},rnd.Editor.LassoTool.LassoHelper.prototype.getSelection=function(){if(0==this.mode)return ui.render.getElementsInPolygon(this.points);if(1==this.mode)return ui.render.getElementsInRectangle(this.points[0],this.points[1]);throw new Error("Selector mode unknown")},rnd.Editor.LassoTool.LassoHelper.prototype.begin=function(t){this.points=[ui.page2obj(t)],1==this.mode&&this.points.push(this.points[0])},rnd.Editor.LassoTool.LassoHelper.prototype.running=function(){return"points"in this},rnd.Editor.LassoTool.LassoHelper.prototype.addPoint=function(t){return!!this.running()&&(0==this.mode?(this.points.push(ui.page2obj(t)),this.editor.render.drawSelectionPolygon(this.points)):1==this.mode&&(this.points=[this.points[0],ui.page2obj(t)],this.editor.render.drawSelectionRectangle(this.points[0],this.points[1])),this.getSelection())},rnd.Editor.LassoTool.LassoHelper.prototype.end=function(){var t=this.getSelection();return"points"in this&&(this.editor.render.drawSelectionPolygon(null),delete this.points),t},rnd.Editor.EraserTool=function(t,e){this.editor=t,this.maps=["atoms","bonds","rxnArrows","rxnPluses","sgroups","sgroupData","chiralFlags"],this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this),this._lassoHelper=new rnd.Editor.LassoTool.LassoHelper(e||0,t)},rnd.Editor.EraserTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.EraserTool.prototype.OnMouseDown=function(t){var e=this.editor.render.findItem(t,this.maps);e&&"Canvas"!=e.type||this._lassoHelper.begin(t)},rnd.Editor.EraserTool.prototype.OnMouseMove=function(t){this._lassoHelper.running()?this.editor._selectionHelper.setSelection(this._lassoHelper.addPoint(t)):this._hoverHelper.hover(this.editor.render.findItem(t,this.maps))},rnd.Editor.EraserTool.prototype.OnMouseUp=function(t){if(this._lassoHelper.running())ui.addUndoAction(Action.fromFragmentDeletion(this._lassoHelper.end(t))),this.editor.deselectAll(),ui.render.update();else{var e=this.editor.render.findItem(t,this.maps);if(e&&"Canvas"!=e.type){if(this._hoverHelper.hover(null),"atoms"==e.map)ui.addUndoAction(Action.fromAtomDeletion(e.id));else if("bonds"==e.map)ui.addUndoAction(Action.fromBondDeletion(e.id));else if("sgroups"==e.map||"sgroupData"==e.map)ui.addUndoAction(Action.fromSgroupDeletion(e.id));else if("rxnArrows"==e.map)ui.addUndoAction(Action.fromArrowDeletion(e.id));else if("rxnPluses"==e.map)ui.addUndoAction(Action.fromPlusDeletion(e.id));else{if("chiralFlags"!=e.map)return void console.log("EraserTool: unable to delete the object "+e.map+"["+e.id+"]");ui.addUndoAction(Action.fromChiralFlagDeletion())}this.editor.deselectAll(),ui.render.update()}}},rnd.Editor.AtomTool=function(t,e){this.editor=t,this.atomProps=e,this.bondProps={type:1,stereo:chem.Struct.BOND.STEREO.NONE},this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.AtomTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.AtomTool.prototype.OnMouseDown=function(t){this._hoverHelper.hover(null);var e=this.editor.render.findItem(t,["atoms"]);e&&"Canvas"!=e.type?"atoms"==e.map&&(this.dragCtx={item:e,xy0:ui.page2obj(t)}):this.dragCtx={xy0:ui.page2obj(t)}},rnd.Editor.AtomTool.prototype.OnMouseMove=function(t){var e=this.editor,o=e.render;if("dragCtx"in this&&"item"in this.dragCtx){var i=this.dragCtx,r=this._calcNewAtomPos(o.atomGetPos(i.item.id),ui.page2obj(t));"action"in i&&i.action.perform();var n=Action.fromBondAddition(this.bondProps,i.item.id,Object.clone(this.atomProps),r,r);i.action=n[0],i.aid2=n[2],o.update()}else this._hoverHelper.hover(o.findItem(t,["atoms"]))},rnd.Editor.AtomTool.prototype.OnMouseUp=function(t){if("dragCtx"in this){var e=this.dragCtx;ui.addUndoAction("action"in e?e.action:"item"in e?Action.fromAtomsAttrs(e.item.id,this.atomProps,!0):Action.fromAtomAddition(ui.page2obj(t),this.atomProps),!0),this.editor.render.update(),delete this.dragCtx}},rnd.Editor.BondTool=function(t,e){this.editor=t,this.atomProps={label:"C"},this.bondProps=e,this.plainBondTypes=[chem.Struct.BOND.TYPE.SINGLE,chem.Struct.BOND.TYPE.DOUBLE,chem.Struct.BOND.TYPE.TRIPLE],this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.BondTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.BondTool.prototype.OnMouseDown=function(t){return this._hoverHelper.hover(null),this.dragCtx={xy0:ui.page2obj(t),item:this.editor.render.findItem(t,["atoms","bonds"])},this.dragCtx.item&&"Canvas"!=this.dragCtx.item.type||delete this.dragCtx.item,!0},rnd.Editor.BondTool.prototype.OnMouseMove=function(t){var e=this.editor,o=e.render;if("dragCtx"in this){var i=this.dragCtx;if(!("item"in i)||"atoms"==i.item.map){"action"in i&&i.action.perform();var r,n,s,d;"item"in i&&"atoms"==i.item.map?(r=i.item.id,n=o.findItem(t,["atoms"],i.item)):(r=this.atomProps,s=i.xy0,n=o.findItem(t,["atoms"]));var a=Number.MAX_VALUE;if(n&&"atoms"==n.map)n=n.id;else{n=this.atomProps;var l=ui.page2obj(t);a=Vec2.dist(i.xy0,l),s?d=this._calcNewAtomPos(s,l):s=this._calcNewAtomPos(o.atomGetPos(r),l)}return a>.3?i.action=Action.fromBondAddition(this.bondProps,r,n,s,d)[0]:delete i.action,o.update(),!0}}return this._hoverHelper.hover(o.findItem(t,["atoms","bonds"])),!0},rnd.Editor.BondTool.prototype.OnMouseUp=function(t){if("dragCtx"in this){var e=this.dragCtx;if("action"in e)ui.addUndoAction(e.action);else if("item"in e){if("atoms"==e.item.map)ui.addUndoAction(Action.fromBondAddition(this.bondProps,e.item.id)[0]);else if("bonds"==e.item.map){var o=Object.clone(this.bondProps),i=ui.ctab.bonds.get(e.item.id);if(o.stereo!=chem.Struct.BOND.STEREO.NONE&&i.type==chem.Struct.BOND.TYPE.SINGLE&&o.type==chem.Struct.BOND.TYPE.SINGLE&&i.stereo==o.stereo)ui.addUndoAction(Action.fromBondFlipping(e.item.id));else{if(o.type===chem.Struct.BOND.TYPE.SINGLE&&i.stereo===chem.Struct.BOND.STEREO.NONE&&o.stereo===chem.Struct.BOND.STEREO.NONE){var r=this.plainBondTypes.indexOf(o.type)>=0?this.plainBondTypes:null;r&&(o.type=r[(r.indexOf(i.type)+1)%r.length])}ui.addUndoAction(Action.fromBondAttrs(e.item.id,o,bondFlipRequired(i,o)),!0)}}}else{var n=ui.page2obj(t),s=new Vec2(.5,0).rotate(this.bondProps.type==chem.Struct.BOND.TYPE.SINGLE?-Math.PI/6:0),d=Action.fromBondAddition(this.bondProps,{label:"C"},{label:"C"},{x:n.x-s.x,y:n.y-s.y},{x:n.x+s.x,y:n.y+s.y});ui.addUndoAction(d[0])}this.editor.render.update(),delete this.dragCtx}return!0},rnd.Editor.ChainTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.ChainTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.ChainTool.prototype.OnMouseDown=function(t){return this._hoverHelper.hover(null),this.dragCtx={xy0:ui.page2obj(t),item:this.editor.render.findItem(t,["atoms"])},this.dragCtx.item&&"Canvas"!=this.dragCtx.item.type||delete this.dragCtx.item,!0},rnd.Editor.ChainTool.prototype.OnMouseMove=function(t){var e=this.editor,o=e.render;if("dragCtx"in this){var i=this.dragCtx;"action"in i&&i.action.perform();var r="item"in i?o.atomGetPos(i.item.id):i.xy0,n=ui.page2obj(t);return i.action=Action.fromChain(r,this._calcAngle(r,n),Math.ceil(Vec2.diff(n,r).length()),"item"in i?i.item.id:null),o.update(),!0}return this._hoverHelper.hover(o.findItem(t,["atoms"])),!0},rnd.Editor.ChainTool.prototype.OnMouseUp=function(){return"dragCtx"in this&&("action"in this.dragCtx&&ui.addUndoAction(this.dragCtx.action),delete this.dragCtx),!0},rnd.Editor.ChainTool.prototype.OnCancel=function(){this.OnMouseUp()},rnd.Editor.TemplateTool=function(t,e){if(this.editor=t,this.template=e,!this.template.molecule){var o=chem.Molfile.parseCTFile(this.template.molfile);o.rescale();var i=new Vec2;o.atoms.each(function(t,e){i.add_(e.pp)}),this.template.molecule=o,this.template.xy0=i.scaled(1/o.atoms.count()),this.template.angle0=this._calcAngle(o.atoms.get(this.template.aid).pp,this.template.xy0);var r=o.bonds.get(this.template.bid);this.template.sign=this._getSign(o,r,this.template.xy0)}this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.TemplateTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.TemplateTool.prototype._getSign=function(t,e,o){var i=t.atoms.get(e.begin).pp,r=t.atoms.get(e.end).pp,n=Vec2.cross(Vec2.diff(i,r),Vec2.diff(o,r));return n>0?1:n<0?-1:0},rnd.Editor.TemplateTool.prototype.OnMouseDown=function(t){var e=this.editor,o=e.render;this._hoverHelper.hover(null),this.dragCtx={xy0:ui.page2obj(t),item:o.findItem(t,["atoms","bonds"])};var i=this.dragCtx,r=i.item;if(r&&"Canvas"!=r.type){if("bonds"==r.map){var n=o.ctab.molecule,s=new Vec2,d=n.bonds.get(r.id),a=o.atomGetAttr(d.begin,"fragment"),l=n.getFragmentIds(a),h=0,p=n.halfBonds.get(d.hb1).loop;if(p<0&&(p=n.halfBonds.get(d.hb2).loop),p>=0){var u=n.loops.get(p).hbs;u.each(function(t){s.add_(n.atoms.get(n.halfBonds.get(t).begin).pp),h++})}else Set.each(l,function(t){s.add_(n.atoms.get(t).pp),h++});i.v0=s.scaled(1/h);var c=this._getSign(n,d,i.v0);i.sign1=c||1,i.sign2=this.template.sign}}else delete i.item;return!0},rnd.Editor.TemplateTool.prototype.OnMouseMove=function(t){var e=this.editor,o=e.render;if("dragCtx"in this){var i,r,n,s=this.dragCtx,d=s.item,a=ui.page2obj(t);if(s.mouse_moved=!0,d&&"Canvas"!=d.type){if("atoms"==d.map)i=o.atomGetPos(d.id),n=Vec2.dist(i,a)>1;else if("bonds"==d.map){var l=o.ctab.molecule,h=l.bonds.get(d.id),p=this._getSign(l,h,a);return s.sign1*this.template.sign>0&&(p=-p),p==s.sign2&&s.action||("action"in s&&s.action.perform(),s.sign2=p,s.action=Action.fromTemplateOnBond(d.id,this.template,this._calcAngle,s.sign1*s.sign2>0),o.update()),!0}}else i=s.xy0;r=this._calcAngle(i,a);var u=Math.round(180/Math.PI*r);if("angle"in s&&s.angle==u){if(!("extra_bond"in s))return!0;if(s.extra_bond==n)return!0}return"action"in s&&s.action.perform(),s.angle=u,d&&"Canvas"!=d.type?"atoms"==d.map&&(s.action=Action.fromTemplateOnAtom(d.id,r,n,this.template,this._calcAngle),s.extra_bond=n):s.action=Action.fromTemplateOnCanvas(i,r,this.template),o.update(),!0}return this._hoverHelper.hover(o.findItem(t,["atoms","bonds"])),!0},rnd.Editor.TemplateTool.prototype.OnMouseUp=function(t){var e=this.editor,o=e.render;if("dragCtx"in this){var i=this.dragCtx,r=i.item;if(!i.action){if(r&&"Canvas"!=r.type)if("atoms"==r.map){var n=o.atomGetDegree(r.id);if(n>1)i.action=Action.fromTemplateOnAtom(r.id,null,!0,this.template,this._calcAngle);else if(1==n){var s=o.ctab.molecule,d=s.halfBonds.get(s.atoms.get(r.id).neighbors[0]).end,a=s.atoms.get(r.id),l=s.atoms.get(d);i.action=Action.fromTemplateOnAtom(r.id,this._calcAngle(l.pp,a.pp),!1,this.template,this._calcAngle)}else i.action=Action.fromTemplateOnAtom(r.id,0,!1,this.template,this._calcAngle)}else"bonds"==r.map&&(i.action=Action.fromTemplateOnBond(r.id,this.template,this._calcAngle,i.sign1*i.sign2>0));else i.action=Action.fromTemplateOnCanvas(i.xy0,0,this.template);o.update()}"action"in this.dragCtx&&(this.dragCtx.action.isDummy()||ui.addUndoAction(this.dragCtx.action)),delete this.dragCtx}},rnd.Editor.TemplateTool.prototype.OnCancel=function(){this.OnMouseUp()},rnd.Editor.ChargeTool=function(t,e){this.editor=t,this.charge=e,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.ChargeTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.ChargeTool.prototype.OnMouseMove=function(t){var e=this.editor.render.findItem(t,["atoms"]);return e&&"atoms"==e.map&&null!=element.getElementByLabel(ui.ctab.atoms.get(e.id).label)?this._hoverHelper.hover(e):this._hoverHelper.hover(null),!0},rnd.Editor.ChargeTool.prototype.OnMouseUp=function(t){var e=this.editor,o=e.render,i=o.findItem(t,["atoms"]);return i&&"atoms"==i.map&&null!=element.getElementByLabel(ui.ctab.atoms.get(i.id).label)&&(this._hoverHelper.hover(null),ui.addUndoAction(Action.fromAtomsAttrs(i.id,{charge:o.ctab.molecule.atoms.get(i.id).charge+this.charge})),o.update()),!0},rnd.Editor.RGroupAtomTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.RGroupAtomTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.RGroupAtomTool.prototype.OnMouseMove=function(t){this._hoverHelper.hover(this.editor.render.findItem(t,["atoms"]))},rnd.Editor.RGroupAtomTool.prototype.OnMouseUp=function(t){function e(t){var e=0;return t.values.forEach(function(t){var o=t.substr(1)-1;e|=1<,<,=]?[0-9]+$/g)||t.match(/^[0-9]+\-[0-9]+$/g)}))return alert("Bad occurrence value"),!1;o.range=t.occurrence}return n.resth!=t.resth&&(o.resth=t.resth),n.ifthen!=t.ifthen&&(o.ifthen=t.ifthen),("range"in o||"resth"in o||"ifthen"in o)&&(ui.addUndoAction(Action.fromRGroupAttrs(e.id,o)),this.editor.render.update()),!0}.bind(this)}),!0}},rnd.Editor.APointTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.APointTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.APointTool.prototype.OnMouseMove=function(t){this._hoverHelper.hover(this.editor.render.findItem(t,["atoms"]))},rnd.Editor.APointTool.prototype.OnMouseUp=function(t){var e=this.editor.render.findItem(t,["atoms"]);if(e&&"atoms"==e.map){this._hoverHelper.hover(null);var o=this.editor.render.ctab.molecule.atoms.get(e.id).attpnt;return ui.showAtomAttachmentPoints({selection:o,onOk:function(t){o!=t&&(ui.addUndoAction(Action.fromAtomsAttrs(e.id,{attpnt:t}),!0),ui.render.update())}.bind(this)}),!0}},rnd.Editor.ReactionArrowTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.ReactionArrowTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.ReactionArrowTool.prototype.OnMouseDown=function(t){var e=this.editor.render.findItem(t,["rxnArrows"]);e&&"rxnArrows"==e.map&&(this._hoverHelper.hover(null),this.editor._selectionHelper.setSelection(e),this.dragCtx={xy0:ui.page2obj(t)})},rnd.Editor.ReactionArrowTool.prototype.OnMouseMove=function(t){"dragCtx"in this?(this.dragCtx.action&&this.dragCtx.action.perform(),this.dragCtx.action=Action.fromMultipleMove(this.editor._selectionHelper.selection,ui.page2obj(t).sub(this.dragCtx.xy0)),ui.render.update()):this._hoverHelper.hover(this.editor.render.findItem(t,["rxnArrows"]))},rnd.Editor.ReactionArrowTool.prototype.OnMouseUp=function(t){"dragCtx"in this?(ui.addUndoAction(this.dragCtx.action,!1),this.editor.render.update(),delete this.dragCtx):this.editor.render.ctab.molecule.rxnArrows.count()<1&&(ui.addUndoAction(Action.fromArrowAddition(ui.page2obj(t))),this.editor.render.update())},rnd.Editor.ReactionPlusTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this)},rnd.Editor.ReactionPlusTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.ReactionPlusTool.prototype.OnMouseDown=function(t){var e=this.editor.render.findItem(t,["rxnPluses"]);e&&"rxnPluses"==e.map&&(this._hoverHelper.hover(null),this.editor._selectionHelper.setSelection(e),this.dragCtx={xy0:ui.page2obj(t)})},rnd.Editor.ReactionPlusTool.prototype.OnMouseMove=function(t){"dragCtx"in this?(this.dragCtx.action&&this.dragCtx.action.perform(),this.dragCtx.action=Action.fromMultipleMove(this.editor._selectionHelper.selection,ui.page2obj(t).sub(this.dragCtx.xy0)),ui.render.update()):this._hoverHelper.hover(this.editor.render.findItem(t,["rxnPluses"]))},rnd.Editor.ReactionPlusTool.prototype.OnMouseUp=function(t){"dragCtx"in this?(ui.addUndoAction(this.dragCtx.action,!1),this.editor.render.update(),delete this.dragCtx):(ui.addUndoAction(Action.fromPlusAddition(ui.page2obj(t))),this.editor.render.update())},rnd.Editor.ReactionMapTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this),this.editor._selectionHelper.setSelection(null),this.rcs=chem.MolfileSaver.getComponents(this.editor.render.ctab.molecule)},rnd.Editor.ReactionMapTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.ReactionMapTool.prototype.OnMouseDown=function(t){var e=this.editor.render.findItem(t,["atoms"]);e&&"atoms"==e.map&&(this._hoverHelper.hover(null),this.dragCtx={item:e,xy0:ui.page2obj(t)})},rnd.Editor.ReactionMapTool.prototype.OnMouseMove=function(t){var e=this.editor.render;if("dragCtx"in this){var o=e.findItem(t,["atoms"],this.dragCtx.item);o&&"atoms"==o.map&&this._isValidMap(this.dragCtx.item.id,o.id)?(this._hoverHelper.hover(o),e.drawSelectionLine(e.atomGetPos(this.dragCtx.item.id),e.atomGetPos(o.id))):(this._hoverHelper.hover(null),e.drawSelectionLine(e.atomGetPos(this.dragCtx.item.id),ui.page2obj(t)))}else this._hoverHelper.hover(e.findItem(t,["atoms"]))},rnd.Editor.ReactionMapTool.prototype.OnMouseUp=function(t){if("dragCtx"in this){var e=this.editor.render,o=e.findItem(t,["atoms"],this.dragCtx.item);if(o&&"atoms"==o.map&&this._isValidMap(this.dragCtx.item.id,o.id)){var i=new Action,r=e.ctab.molecule.atoms,n=r.get(this.dragCtx.item.id),s=r.get(o.id),d=n.aam,a=s.aam;if(!d||d!=a){if((d&&d!=a||!d&&a)&&r.each(function(t,e){t!=this.dragCtx.item.id&&(d&&e.aam==d||a&&e.aam==a)&&i.mergeWith(Action.fromAtomsAttrs(t,{aam:0}))},this),d)i.mergeWith(Action.fromAtomsAttrs(o.id,{aam:d}));else{var l=0;r.each(function(t,e){l=Math.max(l,e.aam||0)}),i.mergeWith(Action.fromAtomsAttrs(this.dragCtx.item.id,{aam:l+1})),i.mergeWith(Action.fromAtomsAttrs(o.id,{aam:l+1}))}ui.addUndoAction(i,!0),e.update()}}e.drawSelectionLine(null),delete this.dragCtx}this._hoverHelper.hover(null)},rnd.Editor.ReactionMapTool.prototype._isValidMap=function(t,e){for(var o,i,r=0;(!o||!i)&&r=0&&(o="r"),!i&&n.indexOf(e)>=0&&(i="r")}for(var s=0;(!o||!i)&&s=0&&(o="p"),!i&&d.indexOf(e)>=0&&(i="p")}return o&&i&&o!=i},rnd.Editor.ReactionUnmapTool=function(t){this.editor=t,this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this),this.editor._selectionHelper.setSelection(null)},rnd.Editor.ReactionUnmapTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.ReactionUnmapTool.prototype.OnMouseMove=function(t){var e=this.editor.render.findItem(t,["atoms"]);e&&"atoms"==e.map?this._hoverHelper.hover(this.editor.render.ctab.molecule.atoms.get(e.id).aam?e:null):this._hoverHelper.hover(null)},rnd.Editor.ReactionUnmapTool.prototype.OnMouseUp=function(t){var e=this.editor.render.findItem(t,["atoms"]),o=this.editor.render.ctab.molecule.atoms;if(e&&"atoms"==e.map&&o.get(e.id).aam){var i=new Action,r=o.get(e.id).aam;o.each(function(t,e){e.aam==r&&i.mergeWith(Action.fromAtomsAttrs(t,{aam:0}))},this),ui.addUndoAction(i,!0),this.editor.render.update()}this._hoverHelper.hover(null)},rnd.Editor.SGroupTool=function(t){this.editor=t,this.maps=["atoms","bonds","sgroups","sgroupData"],this._hoverHelper=new rnd.Editor.EditorTool.HoverHelper(this),this._lassoHelper=new rnd.Editor.LassoTool.LassoHelper(1,t),this._sGroupHelper=new rnd.Editor.SGroupTool.SGroupHelper(t) +;var e=this.editor.getSelection();e.atoms&&e.atoms.length>0?this._sGroupHelper.showPropertiesDialog(null,e):this.editor.deselectAll()},rnd.Editor.SGroupTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.SGroupTool.prototype.OnMouseDown=function(t){var e=this.editor.render.findItem(t,this.maps);e&&"Canvas"!=e.type||this._lassoHelper.begin(t)},rnd.Editor.SGroupTool.prototype.OnMouseMove=function(t){this._lassoHelper.running()?this.editor._selectionHelper.setSelection(this._lassoHelper.addPoint(t)):this._hoverHelper.hover(this.editor.render.findItem(t,this.maps))},rnd.Editor.SGroupTool.SGroupHelper=function(t){this.editor=t,this.selection=null},rnd.Editor.SGroupTool.SGroupHelper.prototype.showPropertiesDialog=function(t,e){this.selection=e;var o=this.editor.render;if(null==t){var i={},r={};if(e.atoms.each(function(t){r[t]=!0},this),!Object.isUndefined(e.atoms.detect(function(t){var n=o.atomGetSGroups(t);return!Object.isUndefined(n.detect(function(t){if(t in i)return!1;var n=o.sGroupGetAtoms(t);if(n.length0)&&this._sGroupHelper.showPropertiesDialog(e,o)},rnd.Editor.PasteTool=function(t,e){this.editor=t,this.struct=e,this.action=Action.fromPaste(this.struct,"lastEvent"in this.OnMouseMove0?ui.page2obj(this.OnMouseMove0.lastEvent):void 0),this.editor.render.update()},rnd.Editor.PasteTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.PasteTool.prototype.OnMouseMove=function(t){"action"in this&&this.action.perform(this.editor),this.action=Action.fromPaste(this.struct,ui.page2obj(t)),this.editor.render.update()},rnd.Editor.PasteTool.prototype.OnMouseUp=function(){ui.addUndoAction(this.action),delete this.action,ui.selectAction(null)},rnd.Editor.PasteTool.prototype.OnCancel=function(){"action"in this&&(this.action.perform(this.editor),delete this.action)},rnd.Editor.RotateTool=function(t){this.editor=t,this._lassoHelper=new rnd.Editor.LassoTool.LassoHelper(1,t);var e=this.editor._selectionHelper.selection;e.atoms&&e.atoms.length||this.editor._selectionHelper.setSelection(null)},rnd.Editor.RotateTool.prototype=new rnd.Editor.EditorTool,rnd.Editor.RotateTool.prototype.OnMouseDown=function(t){var e=this.editor._selectionHelper.selection;if(e.atoms&&e.atoms.length){var o=this.editor.render.ctab.molecule,i=new Vec2;if(!e.atoms||!e.atoms.length)return!0;var r=null,n=!1;e.atoms.each(function(t){var s=o.atoms.get(t);i.add_(s.pp),n||s.neighbors.find(function(i){var s=o.halfBonds.get(i);if(-1==e.atoms.indexOf(s.end)){if(s.loop>=0){var d=o.atoms.get(t);if(!Object.isUndefined(d.neighbors.find(function(t){var i=o.halfBonds.get(t);return i.loop>=0&&-1!=e.atoms.indexOf(i.end)})))return n=!0,!0}if(null==r)r=t;else if(r!=t)return n=!0,!0}return!1})}),i=n||null==r?i.scaled(1/e.atoms.length):o.atoms.get(r).pp,this.dragCtx={xy0:i,angle1:this._calcAngle(i,ui.page2obj(t)),all:n}}else this._lassoHelper.begin(t);return!0},rnd.Editor.RotateTool.prototype.OnMouseMove=function(t){if(this._lassoHelper.running())this.editor._selectionHelper.setSelection(this._lassoHelper.addPoint(t));else if("dragCtx"in this){var e=this.editor,o=e.render,i=this.dragCtx,r=ui.page2obj(t),n=this._calcAngle(i.xy0,r)-i.angle1,s=Math.round(n/Math.PI*180);if(s>180?s-=360:s<=-180&&(s+=360),"angle"in i&&i.angle==s)return!0;"action"in i&&i.action.perform(),i.angle=s,i.action=Action.fromRotate(i.all?o.ctab.molecule:this.editor.getSelection(),i.xy0,n),$("toolText").update(s+"º"),o.update()}return!0},rnd.Editor.RotateTool.prototype.OnMouseUp=function(t){return this._lassoHelper.running()?this._lassoHelper.end(t):"dragCtx"in this&&("action"in this.dragCtx?(ui.addUndoAction(this.dragCtx.action,!0),$("toolText").update("")):this.editor._selectionHelper.setSelection(),delete this.dragCtx),!0},rnd.Editor.RotateTool.prototype.OnCancel=function(){"dragCtx"in this&&("action"in this.dragCtx&&(ui.addUndoAction(this.dragCtx.action,!0),$("toolText").update("")),delete this.dragCtx)}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../chem":11,"../chem/element":10,"../ui":34,"../ui/action":26,"../util":39,"../util/set":42,"../util/vec2":43,"./restruct":23}],21:[function(require,module,exports){ +(function (global){ +require("./visel"),require("./restruct"),require("./editor"),require("./render"),require("./restruct_rendering"),global.rnd=global.rnd||{}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"./editor":20,"./render":22,"./restruct":23,"./restruct_rendering":24,"./visel":25}],22:[function(require,module,exports){ +(function (global){ +var Raphael=require("../raphael-ext.js"),Box2Abs=require("../util/box2abs"),Set=require("../util/set"),Vec2=require("../util/vec2"),util=require("../util");require("./restruct"),require("../ui"),require("../chem"),require("./restruct_rendering");var rnd=global.rnd=global.rnd||{},chem=global.chem=global.chem||{},ui=global.ui,tfx=util.tfx;rnd.DEBUG=!1,rnd.logcnt=0,rnd.logmouse=!1,rnd.hl=!1;var EventMap={mousemove:"mousemove",mousedown:"mousedown",mouseup:"mouseup"};rnd.logMethod=function(){},rnd.RenderDummy=function(t,e,o,s){this.clientArea=t=$(t),t.innerHTML="",this.paper=new Raphael(t),this.paper.rect(0,0,100,100).attr({fill:"#0F0",stroke:"none"}),this.setMolecule=function(){},this.update=function(){}},rnd.RenderOptions=function(t){t=t||{},this.showSelectionRegions=t.showSelectionRegions||!1,this.showAtomIds=t.showAtomIds||!1,this.showBondIds=t.showBondIds||!1,this.showHalfBondIds=t.showHalfBondIds||!1,this.showLoopIds=t.showLoopIds||!1,this.hideChiralFlag=t.hideChiralFlag||!1,this.showValenceWarnings=!!Object.isUndefined(t.showValenceWarnings)||t.showValenceWarnings,this.autoScale=t.autoScale||!1,this.autoScaleMargin=t.autoScaleMargin||0,this.maxBondLength=t.maxBondLength||0,this.atomColoring=t.atomColoring||0,this.hideImplicitHydrogen=t.hideImplicitHydrogen||!1,this.hideTerminalLabels=t.hideTerminalLabels||!1,this.ignoreMouseEvents=t.ignoreMouseEvents||!1,this.selectionDistanceCoefficient=(t.selectionDistanceCoefficient||.4)-0},rnd.Render=function(t,e,o,s){this.opt=new rnd.RenderOptions(o),this.useOldZoom=Prototype.Browser.IE,this.scale=e||100,this.baseScale=this.scale,this.offset=new Vec2,this.clientArea=t=$(t),t.innerHTML="",this.paper=new Raphael(t),this.size=new Vec2,this.viewSz=s||new Vec2(t.clientWidth||100,t.clientHeight||100),this.bb=new Box2Abs(new Vec2,this.viewSz),this.dirty=!0,this.selectionRect=null,this.rxnArrow=null,this.rxnMode=!1,this.zoom=1,this.structChangeHandlers=[];var n=this,i=0,r=0,a=t;do{i+=a.offsetTop||0,r+=a.offsetLeft||0,a=a.offsetParent}while(a);this.clientAreaPos=new Vec2(r,i);var h=this;h.longTapFlag=!1,h.longTapTimeout=null,h.longTapTouchstart=null,h.setLongTapTimeout=function(t){h.longTapFlag=!1,h.longTapTouchstart=t,h.longTapTimeout=setTimeout(function(){h.longTapFlag=!0,h.longTapTimeout=null},500)},h.resetLongTapTimeout=function(t){clearTimeout(h.longTapTimeout),h.longTapTimeout=null,t&&(h.longTapTouchstart=null,h.longTapFlag=!1)},"hiddenPaths"in rnd.ReStruct.prototype&&t.observe("touchend",function(t){if(0==t.touches.length)for(;rnd.ReStruct.prototype.hiddenPaths.length>0;)rnd.ReStruct.prototype.hiddenPaths.pop().remove()}),this.opt.ignoreMouseEvents||(t.observe("selectstart",function(t){return util.stopEventPropagation(t),util.preventDefault(t)}),t.observe("touchstart",function(t){h.resetLongTapTimeout(!0),2==t.touches.length?(this._tui=this._tui||{},this._tui.center={pageX:(t.touches[0].pageX+t.touches[1].pageX)/2,pageY:(t.touches[0].pageY+t.touches[1].pageY)/2},ui.setZoomStaticPointInit(ui.page2obj(this._tui.center))):1==t.touches.length&&h.setLongTapTimeout(t)}),t.observe("touchmove",function(t){h.resetLongTapTimeout(!0),"_tui"in this&&2==t.touches.length&&(this._tui.center={pageX:(t.touches[0].pageX+t.touches[1].pageX)/2,pageY:(t.touches[0].pageY+t.touches[1].pageY)/2})}),t.observe("gesturestart",function(t){this._tui=this._tui||{},this._tui.scale0=ui.render.zoom,t.preventDefault()}),t.observe("gesturechange",function(t){ui.setZoomStaticPoint(this._tui.scale0*t.scale,ui.page2canvas2(this._tui.center)),ui.render.update(),t.preventDefault()}),t.observe("gestureend",function(t){delete this._tui,t.preventDefault()}),t.observe("onresize",function(t){n.onResize()}),["Click","DblClick","MouseDown","MouseMove","MouseUp","MouseLeave"].each(function(e){var o=e.toLowerCase();o=EventMap[o]||o,t.observe(o,function(s){if(!("MouseLeave"==e||ui&&ui.is_touch)){var n=t.cumulativeOffset();n=new Vec2(n[0],n[1]);var i=new Vec2(s.clientX,s.clientY).sub(n),r=new Vec2(t.clientWidth,t.clientHeight);if(!(i.x>0&&i.y>0&&i.x=0&&this.ctab.loopRemove(o),s>=0&&this.ctab.loopRemove(s)},rnd.Render.prototype.invalidateBond=function(t){var e=this.ctab.bonds.get(t);this.invalidateLoop(t),this.invalidateAtom(e.b.begin,0),this.invalidateAtom(e.b.end,0)},rnd.Render.prototype.invalidateItem=function(t,e,o){"atoms"==t?this.invalidateAtom(e,o):"bonds"==t?(this.invalidateBond(e),o>0&&this.invalidateLoop(e)):this.ctab.markItem(t,e,o)},rnd.Render.prototype.atomGetDegree=function(t){return rnd.logMethod("atomGetDegree"),this.ctab.atoms.get(t).a.neighbors.length},rnd.Render.prototype.isBondInRing=function(t){var e=this.ctab.bonds.get(t);return this.ctab.molecule.halfBonds.get(e.b.hb1).loop>=0||this.ctab.molecule.halfBonds.get(e.b.hb2).loop>=0},rnd.Render.prototype.atomGetNeighbors=function(t){for(var e=this.ctab.atoms.get(t),o=[],s=0;s-1))return!1;var o=this.ctab[t.map].get(t.id);if(null==o)return!0;if("sgroups"==t.map&&"DAT"==o.item.type||"sgroupData"==t.map){var s=this.ctab.sgroups.get(t.id),n=this.ctab.sgroupData.get(t.id);null!=s&&s.setHighlight(e,this),null!=n&&n.setHighlight(e,this)}else o.setHighlight(e,this);return!0},rnd.Render.prototype.itemGetPos=function(t,e){return this.ctab.molecule[t].get(e).pp},rnd.Render.prototype.atomGetPos=function(t){return rnd.logMethod("atomGetPos"),this.itemGetPos("atoms",t)},rnd.Render.prototype.rxnArrowGetPos=function(t){return rnd.logMethod("rxnArrowGetPos"),this.itemGetPos("rxnArrows",t)},rnd.Render.prototype.rxnPlusGetPos=function(t){return rnd.logMethod("rxnPlusGetPos"),this.itemGetPos("rxnPluses",t)},rnd.Render.prototype.getAdjacentBonds=function(t){for(var e=Set.fromList(t),o=Set.empty(),s=Set.empty(),n=0;nn&&s.xr&&s.yn&&e.a.pp.xr&&e.a.pp.yn&&e.item.pp.xr&&e.item.pp.yn&&e.item.pp.xr&&e.item.pp.yn&&e.pp.xr&&e.pp.yn&&e.sgroup.pp.xr&&e.sgroup.pp.y1){for(var e=this.obj2scaled(t[t.length-1]).add(this.offset),o="M"+tfx(e.x)+","+tfx(e.y),s=0;s-1e-5?r>-1e-5&&(l=!0):(Math.abs(i)*Math.abs(f)-Math.abs(g)*Math.abs(r))*f>0&&(l=!0)),l&&d&&Vec2.dot(p,s)*Vec2(a,s)>=0&&(l=!1),l&&h++,n=u,i=g,r=f,a=p,d=l}return h%2!=0},rnd.Render.prototype.ps=function(t){return t.scaled(this.settings.scaleFactor)},rnd.Render.prototype.getElementsInPolygon=function(t){rnd.logMethod("getElementsInPolygon");for(var e=[],o=[],s=[],n=0;n0?.8*this.viewSz.y/(e.max.y-e.min.y):100,s=e.max.x-e.min.x>0?.8*this.viewSz.x/(e.max.x-e.min.x):100;this.scale=Math.min(o,s),this.opt.maxBondLength>0&&this.scale>this.opt.maxBondLength&&(this.scale=this.opt.maxBondLength)}this.initSettings(),this.initStyles(),this.dirty=!1,t=!0}var n=(new Date).getTime(),i=this.ctab.update(t);this.setSelection(null);var r=(new Date).getTime()-n;if(t&&$("log")&&($("log").innerHTML=r.toString()+"\n"),i){var a=this.settings.scaleFactor,h=this.ctab.getVBoxObj().transform(this.obj2scaled,this).translate(this.offset||new Vec2);if(this.opt.autoScale){var l=h.sz(),d=this.opt.autoScaleMargin,c=new Vec2(d,d),u=this.viewSz;if(u.x<2*d+1||u.y<2*d+1)throw new Error("View box too small for the given margin");var p=Math.max(l.x/(u.x-2*d),l.y/(u.y-2*d));this.opt.maxBondLength/p>1&&(p=1);var g=l.add(c.scaled(2*p));this.paper.setViewBox(h.pos().x-d*p-(u.x*p-g.x)/2,h.pos().y-d*p-(u.y*p-g.y)/2,u.x*p,u.y*p)}else{var f=Vec2.UNIT.scaled(a),m=h.sz().length()>0?h.extend(f,f):h;console.assert(ui.zoom==this.zoom);var b=new Box2Abs(ui.scrollPos(),this.viewSz.scaled(1/ui.zoom).sub(Vec2.UNIT.scaled(20))),y=Box2Abs.union(b,m);this.oldCb||(this.oldCb=new Box2Abs);var v=y.sz().floor(),x=this.oldCb.p0.sub(y.p0).ceil();this.oldBb=h,this.sz&&v.x==this.sz.x&&v.y==this.sz.y||this.setPaperSize(v),this.offset=this.offset||new Vec2,0==x.x&&0==x.y||(this.setOffset(this.offset.add(x)),this.ctab.translate(x))}}},rnd.Render.prototype.checkBondExists=function(t,e){return this.ctab.molecule.checkBondExists(t,e)},rnd.Render.prototype.findClosestAtom=function(t,e,o){var s=null,n=this.opt.selectionDistanceCoefficient;return e=e||n,e=Math.min(e,n),this.ctab.atoms.each(function(n,i){if(n!=o){var r=Vec2.dist(t,i.a.pp);re.dist||o)&&(s={type:t,id:e.id,dist:e.dist})};if(!e||e.indexOf("atoms")>=0){n("Atom",this.findClosestAtom(t,void 0,Object.isUndefined(o)||"atoms"!=o.map?void 0:o.id))}if(!e||e.indexOf("bonds")>=0){var i=this.findClosestBond(t);i&&(null!==i.cid&&n("Bond",{id:i.cid,dist:i.cdist}),(null==s||s.dist>.4*this.scale)&&n("Bond",i))}if(!e||e.indexOf("chiralFlags")>=0){n("ChiralFlag",rnd.ReChiralFlag.findClosest(this,t))}if(!e||e.indexOf("sgroupData")>=0){n("DataSGroupData",rnd.ReDataSGroupData.findClosest(this,t))}if(!e||e.indexOf("sgroups")>=0){n("SGroup",rnd.ReSGroup.findClosest(this,t))}if(!e||e.indexOf("rxnArrows")>=0){n("RxnArrow",rnd.ReRxnArrow.findClosest(this,t))}if(!e||e.indexOf("rxnPluses")>=0){n("RxnPlus",rnd.ReRxnPlus.findClosest(this,t))}if(!e||e.indexOf("frags")>=0){n("Fragment",rnd.ReFrag.findClosest(this,t,o&&"atoms"==o.map?o.id:void 0))}if(!e||e.indexOf("rgroups")>=0){n("RGroup",rnd.ReRGroup.findClosest(this,t))}return s=s||{type:"Canvas",id:-1}},rnd.Render.prototype.setZoom=function(t){this.zoom=t,this._setPaperSize(this.sz)},rnd.Render.prototype.extendCanvas=function(t,e,o,s){var n=0,i=0,r=0,a=0;t-=0,o-=0,e-=0,s-=0,t<0&&(n+=-t,r+=-t),e<0&&(i+=-e,a+=-e);var h=this.sz.x*this.zoom,l=this.sz.y*this.zoom;h0||n>0){var c=new Vec2(n,i).scaled(1/this.zoom),u=this.sz.add(c);this.setPaperSize(u),(d.x>0||d.y>0)&&(this.ctab.translate(d),this.setOffset(this.offset.add(d)))}return d},rnd.Render.prototype.setScale=function(t){this.offset&&(this.offset=this.offset.scaled(1/t).scaled(this.zoom)),this.scale=this.baseScale*this.zoom,this.settings=null,this.update(!0)},rnd.Render.prototype.setViewBox=function(t){this.useOldZoom?this.setScale(t):this.paper.canvas.setAttribute("viewBox","0 0 "+this.sz.x+" "+this.sz.y)}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../chem":11,"../raphael-ext.js":19,"../ui":34,"../util":39,"../util/box2abs":38,"../util/set":42,"../util/vec2":43,"./restruct":23,"./restruct_rendering":24}],23:[function(require,module,exports){ +(function (global){ +var Box2Abs=require("../util/box2abs"),Map=require("../util/map"),Pool=require("../util/pool"),Set=require("../util/set"),Vec2=require("../util/vec2"),util=require("../util"),element=require("../chem/element");require("../chem");var rnd=global.rnd=global.rnd||{},chem=global.chem,tfx=util.tfx;rnd.ReObject=function(){this.__ext=new Vec2(.05*3,.05*3)},rnd.ReObject.prototype.init=function(t){this.visel=new rnd.Visel(t),this.highlight=!1,this.highlighting=null,this.selected=!1,this.selectionPlate=null},rnd.ReObject.prototype.getVBoxObj=function(t){var e=this.visel.boundingBox;return util.isNull(e)?null:(t.offset&&(e=e.translate(t.offset.negated())),e.transform(t.scaled2obj,t))},rnd.ReObject.prototype.drawHighlight=function(t){console.log("ReObject.drawHighlight is not overridden")},rnd.ReObject.prototype.setHighlight=function(t,e){if(t){var n="highlighting"in this&&null!=this.highlighting;n&&(n="set"==this.highlighting.type?!this.highlighting[0].removed:!this.highlighting.removed),n=n&&(!("hiddenPaths"in rnd.ReStruct.prototype)||rnd.ReStruct.prototype.hiddenPaths.indexOf(this.highlighting)<0),n?this.highlighting.show():(e.paper.setStart(),this.drawHighlight(e),this.highlighting=e.paper.setFinish())}else this.highlighting&&this.highlighting.hide();this.highlight=t},rnd.ReObject.prototype.makeSelectionPlate=function(t){console.log("ReObject.makeSelectionPlate is not overridden")},rnd.ReAtom=function(t){this.init(rnd.Visel.TYPE.ATOM),this.a=t,this.showLabel=!1,this.hydrogenOnTheLeft=!1,this.component=-1},rnd.ReAtom.prototype=new rnd.ReObject,rnd.ReAtom.isSelectable=function(){return!0},rnd.ReAtom.prototype.getVBoxObj=function(t){return this.visel.boundingBox?rnd.ReObject.prototype.getVBoxObj.call(this,t):new Box2Abs(this.a.pp,this.a.pp)},rnd.ReAtom.prototype.drawHighlight=function(t){var e=this.makeHighlightPlate(t);return t.ctab.addReObjectPath("highlighting",this.visel,e),e},rnd.ReAtom.prototype.makeHighlightPlate=function(t){var e=t.paper,n=t.styles,r=t.ps(this.a.pp);return e.circle(r.x,r.y,n.atomSelectionPlateRadius).attr(n.highlightStyle)},rnd.ReAtom.prototype.makeSelectionPlate=function(t,e,n){var r=t.render.ps(this.a.pp);return e.circle(r.x,r.y,n.atomSelectionPlateRadius).attr(n.selectionStyle)},rnd.ReBond=function(t){this.init(rnd.Visel.TYPE.BOND),this.b=t,this.doubleBondShift=0},rnd.ReBond.prototype=new rnd.ReObject,rnd.ReBond.isSelectable=function(){return!0},rnd.ReBond.prototype.drawHighlight=function(t){var e=this.makeHighlightPlate(t);return t.ctab.addReObjectPath("highlighting",this.visel,e),e},rnd.ReBond.prototype.makeHighlightPlate=function(t){t.ctab.bondRecalc(t.settings,this);var e=t.ps(this.b.center);return t.paper.circle(e.x,e.y,.8*t.styles.atomSelectionPlateRadius).attr(t.styles.highlightStyle)},rnd.ReBond.prototype.makeSelectionPlate=function(t,e,n){t.bondRecalc(t.render.settings,this);var r=t.render.ps(this.b.center);return e.circle(r.x,r.y,.8*n.atomSelectionPlateRadius).attr(n.selectionStyle)},rnd.ReStruct=function(t,e,n){this.render=e,this.atoms=new Map,this.bonds=new Map,this.reloops=new Map,this.rxnPluses=new Map,this.rxnArrows=new Map,this.frags=new Map,this.rgroups=new Map,this.sgroups=new Map,this.sgroupData=new Map,this.chiralFlags=new Map,this.molecule=t||new chem.Struct,this.initialized=!1,this.layers=[],this.initLayers(),this.connectedComponents=new Pool,this.ccFragmentType=new Map;for(var r in rnd.ReStruct.maps)this[r+"Changed"]={};if(this.structChanged=!1,t.atoms.each(function(t,e){this.atoms.set(t,new rnd.ReAtom(e))},this),t.bonds.each(function(t,e){this.bonds.set(t,new rnd.ReBond(e))},this),t.loops.each(function(t,e){this.reloops.set(t,new rnd.ReLoop(e))},this),t.rxnPluses.each(function(t,e){this.rxnPluses.set(t,new rnd.ReRxnPlus(e))},this),t.rxnArrows.each(function(t,e){this.rxnArrows.set(t,new rnd.ReRxnArrow(e))},this),t.frags.each(function(t,e){this.frags.set(t,new rnd.ReFrag(e))},this),t.rgroups.each(function(t,e){this.rgroups.set(t,new rnd.ReRGroup(e))},this),t.sgroups.each(function(t,e){this.sgroups.set(t,new rnd.ReSGroup(e)),"DAT"!=e.type||e.data.attached||this.sgroupData.set(t,new rnd.ReDataSGroupData(e))},this),t.isChiral&&!this.render.opt.hideChiralFlag){var i=t.getCoordBoundingBox();this.chiralFlags.set(0,new rnd.ReChiralFlag(new Vec2(i.max.x,i.min.y-1)))}this.coordProcess(n)},rnd.ReStruct.prototype.connectedComponentRemoveAtom=function(t,e){if(e=e||this.atoms.get(t),!(e.component<0)){var n=this.connectedComponents.get(e.component);Set.remove(n,t),Set.size(n)<1&&this.connectedComponents.remove(e.component),e.component=-1}},rnd.ReStruct.prototype.printConnectedComponents=function(){var t=[];this.connectedComponents.each(function(e,n){t.push(" "+e+":["+Set.list(n).toString()+"]."+Set.size(n).toString())},this),console.log(t.toString())},rnd.ReStruct.prototype.clearConnectedComponents=function(){this.connectedComponents.clear(),this.atoms.each(function(t,e){e.component=-1})},rnd.ReStruct.prototype.getConnectedComponent=function(t,e){for(var n="number"==typeof t.length?util.array(t):[t],r=Set.empty();n.length>0;)(function(){var t=n.pop();Set.add(r,t);var i=this.atoms.get(t);i.component>=0&&Set.add(e,i.component);for(var o=0;o=0)){var n=Set.empty(),r=this.getConnectedComponent(t,n);Set.each(n,function(t){this.removeConnectedComponent(t)},this),this.addConnectedComponent(r)}},this)},rnd.ReStruct.prototype.connectedComponentGetBoundingBox=function(t,e,n){return e=e||this.connectedComponents.get(t),n=n||{min:null,max:null},Set.each(e,function(t){var e=this.render.ps(this.atoms.get(t).a.pp);null==n.min?n.min=n.max=e:(n.min=n.min.min(e),n.max=n.max.max(e))},this),n},rnd.ReStruct.prototype.initLayers=function(){for(var t in rnd.ReStruct.layerMap)this.layers[rnd.ReStruct.layerMap[t]]=this.render.paper.rect(0,0,10,10).attr({fill:"#000",opacity:"0.0"}).toFront()},rnd.ReStruct.prototype.insertInLayer=function(t,e){e.insertBefore(this.layers[t])},rnd.ReStruct.prototype.clearMarks=function(){for(var t in rnd.ReStruct.maps)this[t+"Changed"]={};this.structChanged=!1},rnd.ReStruct.prototype.markItemRemoved=function(){this.structChanged=!0},rnd.ReStruct.prototype.markBond=function(t,e){this.markItem("bonds",t,e)},rnd.ReStruct.prototype.markAtom=function(t,e){this.markItem("atoms",t,e)},rnd.ReStruct.prototype.markItem=function(t,e,n){var r=this[t+"Changed"];r[e]=void 0!==r[e]?Math.max(n,r[e]):n,this[t].has(e)&&this.clearVisel(this[t].get(e).visel)},rnd.ReStruct.prototype.eachVisel=function(t,e){for(var n in rnd.ReStruct.maps)this[n].each(function(n,r){t.call(e,r.visel)},this)},rnd.ReStruct.prototype.getVBoxObj=function(t){if(t=t||{},this.selectionIsEmpty(t))for(var e in rnd.ReStruct.maps)t[e]=this[e].keys();var n=null;for(var e in rnd.ReStruct.maps)t[e]&&util.each(t[e],function(t){var r=this[e].get(t).getVBoxObj(this.render);r&&(n=n?Box2Abs.union(n,r):r.clone())},this);return n=n||new Box2Abs(0,0,0,0)},rnd.ReStruct.prototype.selectionIsEmpty=function(t){if(util.assert(!util.isUndefined(t),"'selection' is not defined"),util.isNull(t))return!0;for(var e in rnd.ReStruct.maps)if(t[e]&&t[e].length>0)return!1;return!0},rnd.ReStruct.prototype.translate=function(t){this.eachVisel(function(e){e.translate(t)},this)},rnd.ReStruct.prototype.scale=function(t){this.eachVisel(function(e){this.scaleVisel(e,t)},this)},rnd.ReStruct.prototype.scaleRPath=function(t,e){if("set"==t.type)for(var n=0;n=0&&n[1]>=0},rnd.ReStruct.prototype.findIncomingUpBonds=function(t,e){var n=util.map([e.b.begin,e.b.end],function(e){var n=this.molecule.atoms.get(e),r=this.findIncomingStereoUpBond(n,t,!0);return r<0?-1:n.neighbors[r]},this);util.assert(2===n.length),e.neihbid1=this.atoms.get(e.b.begin).showLabel?-1:n[0],e.neihbid2=this.atoms.get(e.b.end).showLabel?-1:n[1]},rnd.ReStruct.prototype.checkStereoBoldBonds=function(){this.bonds.each(this.checkStereoBold,this)},rnd.ReStruct.prototype.update=function(t){t=t||!this.initialized;var e;t?function(){for(var t in rnd.ReStruct.maps){var e=this[t+"Changed"];this[t].each(function(t){e[t]=1},this)}}.call(this):function(){for(var t in rnd.ReStruct.maps){var n=this[t+"Changed"];for(e in n)this[t].has(e)||delete n[e]}}.call(this);for(e in this.atomsChanged)this.connectedComponentRemoveAtom(e);for(var n=this.frags.findAll(function(t,e){return!e.calcBBox(this.render,t)},this),r=0;r0}}).call(this),this.structChanged&&util.each(this.render.structChangeHandlers,function(t){t.call()}),this.sgroups.each(function(t,e){this.clearVisel(e.visel),e.highlighting=null,e.selectionPlate=null},this),this.frags.each(function(t,e){this.clearVisel(e.visel)},this),this.rgroups.each(function(t,e){this.clearVisel(e.visel)},this),t&&(this.clearConnectedComponents(),this.molecule.initHalfBonds(),this.molecule.initNeighbors()),this.molecule.updateHalfBonds(new Map(this.atomsChanged).findAll(function(t,e){return e>=0},this)),this.molecule.sortNeighbors(new Map(this.atomsChanged).findAll(function(t,e){return e>=1},this)),this.assignConnectedComponents(),this.setImplicitHydrogen(),this.setHydrogenPos(),this.initialized=!0,this.verifyLoops();var o=t||this.structChanged;return o&&this.updateLoops(),this.setDoubleBondShift(),this.checkLabelsToShow(),this.checkStereoBoldBonds(),this.showLabels(),this.showBonds(),o&&this.renderLoops(),this.drawReactionSymbols(),this.drawSGroups(),this.drawFragments(),this.drawRGroups(),this.chiralFlags.each(function(t,e){this.chiralFlagsChanged[t]>0&&e.draw(this.render)},this),this.clearMarks(),!0},rnd.ReStruct.prototype.drawReactionSymbols=function(){var t,e;for(e in this.rxnArrowsChanged)t=this.rxnArrows.get(e),this.drawReactionArrow(e,t);for(e in this.rxnPlusesChanged)t=this.rxnPluses.get(e),this.drawReactionPlus(e,t)},rnd.ReStruct.prototype.drawReactionArrow=function(t,e){var n=this.render.ps(e.item.pp),r=this.drawArrow(new Vec2(n.x-this.render.scale,n.y),new Vec2(n.x+this.render.scale,n.y));e.visel.add(r,Box2Abs.fromRelBox(rnd.relBox(r.getBBox())));var i=this.render.offset;null!=i&&r.translateAbs(i.x,i.y)},rnd.ReStruct.prototype.drawReactionPlus=function(t,e){var n=this.render.ps(e.item.pp),r=this.drawPlus(n);e.visel.add(r,Box2Abs.fromRelBox(rnd.relBox(r.getBBox())));var i=this.render.offset;null!=i&&r.translateAbs(i.x,i.y)},rnd.ReStruct.prototype.drawSGroups=function(){util.each(this.molecule.sGroupForest.getSGroupsBFS().reverse(),function(t){var e=this.sgroups.get(t),n=e.draw(this.render);this.addReObjectPath("data",e.visel,n,null,!0),e.setHighlight(e.highlight,this.render)},this)},rnd.ReStruct.prototype.drawFragments=function(){this.frags.each(function(t,e){var n=e.draw(this.render,t);n&&this.addReObjectPath("data",e.visel,n,null,!0)},this)},rnd.ReStruct.prototype.drawRGroups=function(){this.rgroups.each(function(t,e){var n=e.draw(this.render);for(var r in n)for(;n[r].length>0;)this.addReObjectPath(r,e.visel,n[r].shift(),null,!0)},this)},rnd.ReStruct.prototype.eachCC=function(t,e,n){this.connectedComponents.each(function(r,i){e&&this.ccFragmentType.get(r)!=e||t.call(n||this,r,i)},this)},rnd.ReStruct.prototype.getGroupBB=function(t){var e={min:null,max:null};return this.eachCC(function(t,n){e=this.connectedComponentGetBoundingBox(t,n,e)},t,this),e},rnd.ReStruct.prototype.setHydrogenPos=function(){for(var t in this.atomsChanged){var e=this.atoms.get(t);if(0!=e.a.neighbors.length){for(var n=1,r=1,i=0,o=0,s=0;si}else{var h=element.getElementByLabel(e.a.label);null!=h&&(e.hydrogenOnTheLeft=element.get(h).putHydrogenOnTheLeft)}}},rnd.ReStruct.prototype.setImplicitHydrogen=function(){this.molecule.setImplicitHydrogen(util.idList(this.atomsChanged))},rnd.ReLoop=function(t){this.loop=t,this.visel=new rnd.Visel(rnd.Visel.TYPE.LOOP),this.centre=new Vec2,this.radius=new Vec2},rnd.ReLoop.prototype=new rnd.ReObject,rnd.ReLoop.isSelectable=function(){return!1},rnd.ReStruct.prototype.coordProcess=function(t){t||this.molecule.rescale()},rnd.ReStruct.prototype.notifyAtomAdded=function(t){var e=new rnd.ReAtom(this.molecule.atoms.get(t));e.component=this.connectedComponents.add(Set.single(t)),this.atoms.set(t,e),this.markAtom(t,1)},rnd.ReStruct.prototype.notifyRxnPlusAdded=function(t){this.rxnPluses.set(t,new rnd.ReRxnPlus(this.molecule.rxnPluses.get(t)))},rnd.ReStruct.prototype.notifyRxnArrowAdded=function(t){this.rxnArrows.set(t,new rnd.ReRxnArrow(this.molecule.rxnArrows.get(t)))},rnd.ReStruct.prototype.notifyRxnArrowRemoved=function(t){this.markItemRemoved(),this.clearVisel(this.rxnArrows.get(t).visel),this.rxnArrows.unset(t)},rnd.ReStruct.prototype.notifyRxnPlusRemoved=function(t){this.markItemRemoved(),this.clearVisel(this.rxnPluses.get(t).visel),this.rxnPluses.unset(t)},rnd.ReStruct.prototype.notifyBondAdded=function(t){this.bonds.set(t,new rnd.ReBond(this.molecule.bonds.get(t))),this.markBond(t,1)},rnd.ReStruct.prototype.notifyAtomRemoved=function(t){var e=this.atoms.get(t),n=this.connectedComponents.get(e.component);Set.remove(n,t),0==Set.size(n)&&this.connectedComponents.remove(e.component),this.clearVisel(e.visel),this.atoms.unset(t),this.markItemRemoved()},rnd.ReStruct.prototype.notifyBondRemoved=function(t){var e=this.bonds.get(t);[e.b.hb1,e.b.hb2].each(function(t){var e=this.molecule.halfBonds.get(t);e.loop>=0&&this.loopRemove(e.loop)},this),this.clearVisel(e.visel),this.bonds.unset(t),this.markItemRemoved()},rnd.ReStruct.prototype.loopRemove=function(t){if(this.reloops.has(t)){var e=this.reloops.get(t);this.clearVisel(e.visel);for(var n=[],r=0;r0;){var o=r.shift();t.call(n,o);for(var s=this.atoms.get(o),a=0;ae.y&&a.p0.xe.x){var h=Math.min(Math.abs(a.p0.x-e.x),Math.abs(a.p1.x-e.x));(!i||h0?"IF ":"")+"R"+a.toString()+(this.item.range.length>0?this.item.range.startsWith(">")||this.item.range.startsWith("<")||this.item.range.startsWith("=")?this.item.range:"="+this.item.range:">0")+(this.item.resth?" (RestH)":"")+(this.item.ifthen>0?"\nTHEN R"+this.item.ifthen.toString():""));for(var u=l.height/2+n.lineWidth/2,g=0;ga.y&&c.p0.xa.x,d=Math.min(Math.abs(c.p0.x-a.x),Math.abs(c.p1.x-a.x));l&&(null==n||de.y&&o.p0.xe.x,a=Math.min(Math.abs(o.p0.x-e.x),Math.abs(o.p1.x-e.x));s&&(null==r||a=0){var p=this.stereoUpBondGetCoordinates(e,r.neihbid2);l=p[0],c=p[1]}return o.path("M{0},{1}L{2},{3}L{4},{5}Z",tfx(a.x),tfx(a.y),tfx(l.x),tfx(l.y),tfx(c.x),tfx(c.y)).attr(s.lineattr).attr({fill:"#000"})},rnd.ReStruct.prototype.drawVec=function(t,e,r,a){var n=this.render.settings,d=this.render.paper,i=this.render.styles,o=n.bondSpace,s=t.addScaled(e,a||3*o);return d.path("M{0},{1}L{2},{3}",tfx(t.x),tfx(t.y),tfx(s.x),tfx(s.y)).attr(i.lineattr).attr({stroke:r||"#0F0"})},rnd.ReStruct.prototype.stereoUpBondGetCoordinates=function(t,e){var r=this.render.settings.bondSpace,a=this.molecule.halfBonds.get(e),n=Vec2.dot(t.dir,a.dir),d=Vec2.cross(t.dir,a.dir),i=Math.sqrt(.5*(1-n)),o=a.dir.rotateSC((d>=0?-1:1)*i,Math.sqrt(.5*(1+n))),s=t.p.addScaled(o,.7*r/(i+.3)),h=t.p.addScaled(o.negated(),.7*r/(i+.3));return d>0?[s,h]:[h,s]},rnd.ReStruct.prototype.drawBondSingleStereoBold=function(t,e,r,a){var n=this.render.paper,d=this.render.settings,i=this.render.styles,o=this.stereoUpBondGetCoordinates(t,r.neihbid1),s=this.stereoUpBondGetCoordinates(e,r.neihbid2),h=o[0],l=o[1],c=s[0],p=s[1],b=n.path("M{0},{1}L{2},{3}L{4},{5}L{6},{7}Z",tfx(h.x),tfx(h.y),tfx(l.x),tfx(l.y),tfx(c.x),tfx(c.y),tfx(p.x),tfx(p.y)).attr(i.lineattr).attr({stroke:"#000",fill:"#000"});if(a){var u=t.p,f=e.p,S=t.norm,x=r.doubleBondShift,g=1.5*d.bondSpace,B=u.addScaled(S,g*x),v=f.addScaled(S,g*x),R=!this.atoms.get(t.begin).showLabel,y=!this.atoms.get(e.begin).showLabel;return x>0?(R&&(B=B.addScaled(t.dir,g*this.getBondLineShift(t.rightCos,t.rightSin))),y&&(v=v.addScaled(t.dir,-g*this.getBondLineShift(e.leftCos,e.leftSin)))):x<0&&(R&&(B=B.addScaled(t.dir,g*this.getBondLineShift(t.leftCos,t.leftSin))),y&&(v=v.addScaled(t.dir,-g*this.getBondLineShift(e.rightCos,e.rightSin)))),n.set([b,n.path("M{0},{1}L{2},{3}",tfx(B.x),tfx(B.y),tfx(v.x),tfx(v.y)).attr(i.lineattr)])}return b},rnd.ReStruct.prototype.drawBondSingleDown=function(t,e){var r=t.p,a=e.p,n=t.norm,d=this.render.settings,i=this.render.paper,o=this.render.styles,s=.7*d.bondSpace,h=a.sub(r),l=h.length()+.2;h=h.normalized();for(var c,p,b=1.2*d.lineWidth,u=Math.max(Math.floor((l-d.lineWidth)/(d.lineWidth+b)),0)+2,f=l/(u-1),S="",x=r,g=0;g.9?0:e/(1-t)},rnd.ReStruct.prototype.drawBondDouble=function(t,e,r,a){var n=t.p,d=e.p,i=t.norm,o=a?0:r.doubleBondShift,s=this.render.settings,h=this.render.paper,l=this.render.styles,c=s.bondSpace/2,p=c,b=-c;p+=o*c,b+=o*c;var u=n.addScaled(i,p),f=d.addScaled(i,p),S=n.addScaled(i,b),x=d.addScaled(i,b),g=!this.atoms.get(t.begin).showLabel,B=!this.atoms.get(e.begin).showLabel;return o>0?(g&&(u=u.addScaled(t.dir,s.bondSpace*this.getBondLineShift(t.rightCos,t.rightSin))),B&&(f=f.addScaled(t.dir,-s.bondSpace*this.getBondLineShift(e.leftCos,e.leftSin)))):o<0&&(g&&(S=S.addScaled(t.dir,s.bondSpace*this.getBondLineShift(t.leftCos,t.leftSin))),B&&(x=x.addScaled(t.dir,-s.bondSpace*this.getBondLineShift(e.rightCos,e.rightSin)))),h.path(a?"M{0},{1}L{6},{7}M{4},{5}L{2},{3}":"M{0},{1}L{2},{3}M{4},{5}L{6},{7}",tfx(u.x),tfx(u.y),tfx(f.x),tfx(f.y),tfx(S.x),tfx(S.y),tfx(x.x),tfx(x.y)).attr(l.lineattr)},rnd.ReStruct.makeStroke=function(t,e){return"M"+tfx(t.x)+","+tfx(t.y)+"L"+tfx(e.x)+","+tfx(e.y)+"\t"},rnd.ReStruct.prototype.drawBondSingleOrDouble=function(t,e){var r=t.p,a=e.p,n=t.norm,d=this.render,i=d.settings,o=d.paper,s=d.styles,h=i.bondSpace/2,l=(Vec2.dist(r,a)/(i.bondSpace+i.lineWidth)).toFixed()-0;1&l||(l+=1);for(var c="",p=r,b=1;b<=l;++b){var u=Vec2.lc2(r,(l-b)/l,a,b/l);1&b?c+=rnd.ReStruct.makeStroke(p,u):(c+=rnd.ReStruct.makeStroke(p.addScaled(n,h),u.addScaled(n,h)),c+=rnd.ReStruct.makeStroke(p.addScaled(n,-h),u.addScaled(n,-h))),p=u}return o.path(c).attr(s.lineattr)},rnd.ReStruct.prototype.drawBondTriple=function(t,e){var r=t.p,a=e.p,n=t.norm,d=this.render,i=d.settings,o=d.paper,s=d.styles,h=r.addScaled(n,i.bondSpace),l=a.addScaled(n,i.bondSpace),c=r.addScaled(n,-i.bondSpace),p=a.addScaled(n,-i.bondSpace);return o.path(rnd.ReStruct.makeStroke(r,a)+rnd.ReStruct.makeStroke(h,l)+rnd.ReStruct.makeStroke(c,p)).attr(s.lineattr)},rnd.dashedPath=function(t,e,r){for(var a=0,n=Vec2.dist(t,e),d=Vec2.diff(e,t).normalized(),i=!0,o="",s=0;a0?o:s).attr({"stroke-dasharray":"- "}),d.set([o,s])},rnd.dashdotPattern=[.125,.125,.005,.125],rnd.ReStruct.prototype.drawBondSingleOrAromatic=function(t,e,r){var a=r.doubleBondShift,n=this.render.paper,d=this.render.settings.scaleFactor,i=util.map(rnd.dashdotPattern,function(t){return t*d}),o=this.preparePathsForAromaticBond(t,e,a,a>0?1:2,i),s=o[0],h=o[1];return n.set([s,h])},rnd.ReStruct.prototype.preparePathsForAromaticBond=function(t,e,r,a,n){var d=this.render.settings,i=this.render.paper,o=this.render.styles,s=t.p,h=e.p,l=t.norm,c=d.bondSpace/2,p=c,b=-c;p+=r*c,b+=r*c;var u=s.addScaled(l,p),f=h.addScaled(l,p),S=s.addScaled(l,b),x=h.addScaled(l,b),g=!this.atoms.get(t.begin).showLabel,B=!this.atoms.get(e.begin).showLabel;return r>0?(g&&(u=u.addScaled(t.dir,d.bondSpace*this.getBondLineShift(t.rightCos,t.rightSin))),B&&(f=f.addScaled(t.dir,-d.bondSpace*this.getBondLineShift(e.leftCos,e.leftSin)))):r<0&&(g&&(S=S.addScaled(t.dir,d.bondSpace*this.getBondLineShift(t.leftCos,t.leftSin))),B&&(x=x.addScaled(t.dir,-d.bondSpace*this.getBondLineShift(e.rightCos,e.rightSin)))),[i.path(n&&1&a?rnd.dashedPath(u,f,n):rnd.ReStruct.makeStroke(u,f)).attr(o.lineattr),i.path(n&&2&a?rnd.dashedPath(S,x,n):rnd.ReStruct.makeStroke(S,x)).attr(o.lineattr)]},rnd.ReStruct.prototype.drawBondDoubleOrAromatic=function(t,e,r){var a=r.doubleBondShift,n=this.render.paper,d=this.render.settings.scaleFactor,i=util.map(rnd.dashdotPattern,function(t){return t*d}),o=this.preparePathsForAromaticBond(t,e,a,3,i),s=o[0],h=o[1];return n.set([s,h])},rnd.ReStruct.prototype.drawBondAny=function(t,e){var r=t.p,a=e.p,n=this.render.paper,d=this.render.styles;return n.path(rnd.ReStruct.makeStroke(r,a)).attr(d.lineattr).attr({"stroke-dasharray":"- "})},rnd.ReStruct.prototype.drawReactingCenter=function(t,e,r){var a=e.p,n=r.p,d=n.add(a).scaled(.5),i=n.sub(a).normalized(),o=i.rotateSC(1,0),s=this.render.paper,h=this.render.styles,l=this.render.settings,c=[],p=l.lineWidth,b=l.bondSpace/2,u=p,f=2*p,S=1.5*b,x=1.5*b,g=3*b;switch(t.b.reactingCenterStatus){case chem.Struct.BOND.REACTING_CENTER.NOT_CENTER:c.push(d.addScaled(o,g).addScaled(i,.2*g)),c.push(d.addScaled(o,-g).addScaled(i,-.2*g)),c.push(d.addScaled(o,g).addScaled(i,-.2*g)),c.push(d.addScaled(o,-g).addScaled(i,.2*g));break;case chem.Struct.BOND.REACTING_CENTER.CENTER:c.push(d.addScaled(o,g).addScaled(i,.2*g).addScaled(i,u)),c.push(d.addScaled(o,-g).addScaled(i,-.2*g).addScaled(i,u)),c.push(d.addScaled(o,g).addScaled(i,.2*g).addScaled(i,-u)),c.push(d.addScaled(o,-g).addScaled(i,-.2*g).addScaled(i,-u)),c.push(d.addScaled(i,S).addScaled(o,x)),c.push(d.addScaled(i,-S).addScaled(o,x)),c.push(d.addScaled(i,S).addScaled(o,-x)),c.push(d.addScaled(i,-S).addScaled(o,-x));break;case chem.Struct.BOND.REACTING_CENTER.MADE_OR_BROKEN:c.push(d.addScaled(o,g).addScaled(i,f)),c.push(d.addScaled(o,-g).addScaled(i,f)),c.push(d.addScaled(o,g).addScaled(i,-f)),c.push(d.addScaled(o,-g).addScaled(i,-f));break;case chem.Struct.BOND.REACTING_CENTER.ORDER_CHANGED:c.push(d.addScaled(o,g)),c.push(d.addScaled(o,-g));break;case chem.Struct.BOND.REACTING_CENTER.MADE_OR_BROKEN_AND_CHANGED:c.push(d.addScaled(o,g).addScaled(i,f)),c.push(d.addScaled(o,-g).addScaled(i,f)),c.push(d.addScaled(o,g).addScaled(i,-f)),c.push(d.addScaled(o,-g).addScaled(i,-f)),c.push(d.addScaled(o,g)),c.push(d.addScaled(o,-g));break;default:return null}for(var B="",v=0;v0?l=l.scaled(-t.doubleBondShift):0==t.doubleBondShift&&(c+=d.bondSpace/2);var p=new Vec2(2,1).scaled(d.bondSpace);t.b.type==chem.Struct.BOND.TYPE.TRIPLE&&(c+=d.bondSpace);var b=s.add(new Vec2(l.x*(p.x+c),l.y*(p.y+c))),u=n.text(b.x,b.y,a).attr({font:d.font,"font-size":d.fontszsub,fill:"#000"}),f=rnd.relBox(u.getBBox());return this.centerText(u,f),u},rnd.ReStruct.prototype.drawBond=function(t,e,r){var a=null,n=this.molecule;switch(t.b.type){case chem.Struct.BOND.TYPE.SINGLE:switch(t.b.stereo){case chem.Struct.BOND.STEREO.UP:this.findIncomingUpBonds(e.bid,t),a=t.boldStereo&&t.neihbid1>=0&&t.neihbid2>=0?this.drawBondSingleStereoBold(e,r,t):this.drawBondSingleUp(e,r,t);break;case chem.Struct.BOND.STEREO.DOWN:a=this.drawBondSingleDown(e,r,t);break;case chem.Struct.BOND.STEREO.EITHER:a=this.drawBondSingleEither(e,r,t);break;default:a=this.drawBondSingle(e,r)}break;case chem.Struct.BOND.TYPE.DOUBLE:this.findIncomingUpBonds(e.bid,t),a=t.b.stereo===chem.Struct.BOND.STEREO.NONE&&t.boldStereo&&t.neihbid1>=0&&t.neihbid2>=0?this.drawBondSingleStereoBold(e,r,t,!0):this.drawBondDouble(e,r,t,t.b.stereo===chem.Struct.BOND.STEREO.CIS_TRANS);break;case chem.Struct.BOND.TYPE.TRIPLE:a=this.drawBondTriple(e,r,t);break;case chem.Struct.BOND.TYPE.AROMATIC:var d=e.loop>=0&&n.loops.get(e.loop).aromatic||r.loop>=0&&n.loops.get(r.loop).aromatic;a=this.drawBondAromatic(e,r,t,!d);break;case chem.Struct.BOND.TYPE.SINGLE_OR_DOUBLE:a=this.drawBondSingleOrDouble(e,r,t);break;case chem.Struct.BOND.TYPE.SINGLE_OR_AROMATIC:a=this.drawBondSingleOrAromatic(e,r,t);break;case chem.Struct.BOND.TYPE.DOUBLE_OR_AROMATIC:a=this.drawBondDoubleOrAromatic(e,r,t);break;case chem.Struct.BOND.TYPE.ANY:a=this.drawBondAny(e,r,t);break;default:throw new Error("Bond type "+t.b.type+" not supported")}return a},rnd.ReStruct.prototype.radicalCap=function(t){var e=this.render.settings,r=this.render.paper,a=.9*e.lineWidth,n=a,d=2*a;return r.path("M{0},{1}L{2},{3}L{4},{5}",tfx(t.x-n),tfx(t.y+d),tfx(t.x),tfx(t.y),tfx(t.x+n),tfx(t.y+d)).attr({stroke:"#000","stroke-width":.7*e.lineWidth,"stroke-linecap":"square","stroke-linejoin":"miter"})},rnd.ReStruct.prototype.radicalBullet=function(t){var e=this.render.settings;return this.render.paper.circle(t.x,t.y,e.lineWidth).attr({stroke:null,fill:"#000"})},rnd.ReStruct.prototype.centerText=function(t,e){this.render.paper.raphael.vml&&this.pathAndRBoxTranslate(t,e,0,.16*e.height)},rnd.ReStruct.prototype.showItemSelection=function(t,e,r){var a=null!=e.selectionPlate&&!e.selectionPlate.removed;if(a=a&&(!("hiddenPaths"in rnd.ReStruct.prototype)||rnd.ReStruct.prototype.hiddenPaths.indexOf(e.selectionPlate)<0),r){if(!a){var n=this.render,d=n.styles,i=n.paper;e.selectionPlate=e.makeSelectionPlate(this,i,d),this.addReObjectPath("selection-plate",e.visel,e.selectionPlate)}e.selectionPlate&&e.selectionPlate.show()}else a&&e.selectionPlate&&e.selectionPlate.hide()},rnd.ReStruct.prototype.pathAndRBoxTranslate=function(t,e,r,a){t.translateAbs(r,a),e.x+=r,e.y+=a};var markerColors=["black","cyan","magenta","red","green","blue","green"];rnd.ReStruct.prototype.showLabels=function(){var t=this.render,e=t.settings,r=t.styles,a=t.opt,n=t.paper,d=.5*e.lineWidth;for(var i in this.atomsChanged){var o=this.atoms.get(i),s=t.ps(o.a.pp),h=null;a.showAtomIds&&(h={},h.text=i.toString(),h.path=n.text(s.x,s.y,h.text).attr({font:e.font,"font-size":e.fontszsub,fill:"#070"}),h.rbb=rnd.relBox(h.path.getBBox()),this.centerText(h.path,h.rbb),this.addReObjectPath("indices",o.visel,h.path,s)),o.setHighlight(o.highlight,t);var l="#000000";if(o.showLabel){var c=0,p=0,b={};if(null!=o.a.atomList)b.text=o.a.atomList.label();else if("R#"==o.a.label&&null!=o.a.rglabel){b.text="";for(var u=0;u<32;u++)o.a.rglabel&1<0&&(B={},B.text=(S+1).toString(),B.path=n.text(s.x,s.y,B.text).attr({font:e.font,"font-size":e.fontszsub,fill:l}),B.rbb=rnd.relBox(B.path.getBBox()),this.centerText(B.path,B.rbb),this.pathAndRBoxTranslate(B.path,B.rbb,c+.5*B.rbb.width+d,.2*b.rbb.height),c+=B.rbb.width+d,this.addReObjectPath("data",o.visel,B.path,s,!0));var R={};if(0!=o.a.radical){var y;switch(o.a.radical){case 1:R.path=n.set(),y=1.6*e.lineWidth,R.path.push(this.radicalBullet(s.add(new Vec2(-y,0))),this.radicalBullet(s.add(new Vec2(y,0)))),R.path.attr("fill",l);break;case 2:R.path=this.radicalBullet(s).attr("fill",l);break;case 3:R.path=n.set(),y=1.6*e.lineWidth,R.path.push(this.radicalCap(s.add(new Vec2(-y,0))),this.radicalCap(s.add(new Vec2(y,0)))),R.path.attr("stroke",l)}R.rbb=rnd.relBox(R.path.getBBox());var m=-.5*(b.rbb.height+R.rbb.height);3==o.a.radical&&(m-=e.lineWidth/2),this.pathAndRBoxTranslate(R.path,R.rbb,0,m),this.addReObjectPath("data",o.visel,R.path,s,!0)}var w={};0!=o.a.isotope&&(w.text=o.a.isotope.toString(),w.path=n.text(s.x,s.y,w.text).attr({font:e.font,"font-size":e.fontszsub,fill:l}),w.rbb=rnd.relBox(w.path.getBBox()),this.centerText(w.path,w.rbb),this.pathAndRBoxTranslate(w.path,w.rbb,p-.5*w.rbb.width-d,-.3*b.rbb.height),p-=w.rbb.width+d,this.addReObjectPath("data",o.visel,w.path,s,!0)),!x&&S>0&&!t.opt.hideImplicitHydrogen&&(g.text="H",g.path=n.text(s.x,s.y,g.text).attr({font:e.font,"font-size":e.fontsz,fill:l}),g.rbb=rnd.relBox(g.path.getBBox()),this.centerText(g.path,g.rbb),v||(this.pathAndRBoxTranslate(g.path,g.rbb,c+.5*g.rbb.width+d,0),c+=g.rbb.width+d),S>1&&(B={},B.text=S.toString(),B.path=n.text(s.x,s.y,B.text).attr({font:e.font,"font-size":e.fontszsub,fill:l}),B.rbb=rnd.relBox(B.path.getBBox()),this.centerText(B.path,B.rbb),v||(this.pathAndRBoxTranslate(B.path,B.rbb,c+.5*B.rbb.width+d,.2*b.rbb.height),c+=B.rbb.width+d)),v&&(null!=B&&(this.pathAndRBoxTranslate(B.path,B.rbb,p-.5*B.rbb.width-d,.2*b.rbb.height),p-=B.rbb.width+d),this.pathAndRBoxTranslate(g.path,g.rbb,p-.5*g.rbb.width-d,0),p-=g.rbb.width+d),this.addReObjectPath("data",o.visel,g.path,s,!0),null!=B&&this.addReObjectPath("data",o.visel,B.path,s,!0));var O={};if(0!=o.a.charge){O.text="";var T=Math.abs(o.a.charge);1!=T&&(O.text=T.toString()),o.a.charge<0?O.text+="–":O.text+="+",O.path=n.text(s.x,s.y,O.text).attr({font:e.font,"font-size":e.fontszsub,fill:l}),O.rbb=rnd.relBox(O.path.getBBox()),this.centerText(O.path,O.rbb),this.pathAndRBoxTranslate(O.path,O.rbb,c+.5*O.rbb.width+d,-.3*b.rbb.height),c+=O.rbb.width+d,this.addReObjectPath("data",o.visel,O.path,s,!0)}var E={},L={0:"0",1:"I",2:"II",3:"III",4:"IV",5:"V",6:"VI",7:"VII",8:"VIII",9:"IX",10:"X",11:"XI",12:"XII",13:"XIII",14:"XIV"};if(o.a.explicitValence>=0){if(E.text=L[o.a.explicitValence],!E.text)throw new Error("invalid valence "+o.a.explicitValence.toString());E.text="("+E.text+")",E.path=n.text(s.x,s.y,E.text).attr({font:e.font,"font-size":e.fontszsub,fill:l}),E.rbb=rnd.relBox(E.path.getBBox()),this.centerText(E.path,E.rbb),this.pathAndRBoxTranslate(E.path,E.rbb,c+.5*E.rbb.width+d,-.3*b.rbb.height),c+=E.rbb.width+d,this.addReObjectPath("data",o.visel,E.path,s,!0)}if(o.a.badConn&&a.showValenceWarnings){var C={},k=s.y+b.rbb.height/2+d;C.path=n.path("M{0},{1}L{2},{3}",tfx(s.x+p),tfx(k),tfx(s.x+c),tfx(k)).attr(this.render.styles.lineattr).attr({stroke:"#F00"}),C.rbb=rnd.relBox(C.path.getBBox()),this.addReObjectPath("warnings",o.visel,C.path,s,!0)}h&&this.pathAndRBoxTranslate(h.path,h.rbb,-.5*b.rbb.width-.5*h.rbb.width-d,.3*b.rbb.height)}var P=this.bisectLargestSector(o),I=Prototype.Browser.IE?"*":"∗";if(o.a.attpnt){var M,A;for(M=0,0;M<4;++M){var N="";if(o.a.attpnt&1<0&&(N+=" "),N+=I,A=0;A<(0==M?0:M+1);++A)N+="'";var V=new Vec2(s),D=s.addScaled(P,.7*e.scaleFactor),z=n.text(D.x,D.y,N).attr({font:e.font,"font-size":e.fontsz,fill:l}),W=rnd.relBox(z.getBBox());this.centerText(z,W);var j=P.negated();D=D.addScaled(j,Vec2.shiftRayBox(D,j,Box2Abs.fromRelBox(W))+e.lineWidth/2),V=this.shiftBondEnd(o,V,P,e.lineWidth);var _=P.rotateSC(1,0),F=D.addScaled(_,.05*e.scaleFactor).addScaled(j,.09*e.scaleFactor),G=D.addScaled(_,-.05*e.scaleFactor).addScaled(j,.09*e.scaleFactor),U=n.set();U.push(z,n.path("M{0},{1}L{2},{3}M{4},{5}L{2},{3}L{6},{7}",tfx(V.x),tfx(V.y),tfx(D.x),tfx(D.y),tfx(F.x),tfx(F.y),tfx(G.x),tfx(G.y)).attr(r.lineattr).attr({"stroke-width":e.lineWidth/2})),this.addReObjectPath("indices",o.visel,U,s),P=P.rotate(Math.PI/6)}}}var Y="";if(o.a.aam>0&&(Y+=o.a.aam),o.a.invRet>0)if(Y.length>0&&(Y+=","),1==o.a.invRet)Y+="Inv";else{if(2!=o.a.invRet)throw new Error("Invalid value for the invert/retain flag");Y+="Ret"}var H="";if(0!=o.a.ringBondCount)if(o.a.ringBondCount>0)H+="rb"+o.a.ringBondCount.toString();else if(-1==o.a.ringBondCount)H+="rb0";else{if(-2!=o.a.ringBondCount)throw new Error("Ring bond count invalid");H+="rb*"}if(0!=o.a.substitutionCount)if(H.length>0&&(H+=","),o.a.substitutionCount>0)H+="s"+o.a.substitutionCount.toString();else if(-1==o.a.substitutionCount)H+="s0";else{if(-2!=o.a.substitutionCount)throw new Error("Substitution count invalid");H+="s*"}if(o.a.unsaturatedAtom>0){if(H.length>0&&(H+=","),1!=o.a.unsaturatedAtom)throw new Error("Unsaturated atom invalid value");H+="u"}if(o.a.hCount>0&&(H.length>0&&(H+=","),H+="H"+(o.a.hCount-1).toString()),o.a.exactChangeFlag>0){if(Y.length>0&&(Y+=","),1!=o.a.exactChangeFlag)throw new Error("Invalid value for the exact change flag");Y+="ext"}if(Y=(H.length>0?H+"\n":"")+(Y.length>0?"."+Y+".":""),Y.length>0){var q=n.text(s.x,s.y,Y).attr({font:e.font,"font-size":e.fontszsub,fill:l}),X=rnd.relBox(q.getBBox());this.centerText(q,X);var Z=this.bisectLargestSector(o),K=o.visel,J=3;for(M=0;M0&&(e=e.addScaled(r,n+a)),e},rnd.ReStruct.prototype.bisectLargestSector=function(t){var e=[];t.a.neighbors.each(function(t){var r=this.molecule.halfBonds.get(t);e.push(r.ang)},this),e=e.sort(function(t,e){return t-e});for(var r=[],a=0;an&&(n=r[a],d=e[a]+r[a]/2);return new Vec2(Math.cos(d),Math.sin(d))},rnd.ReStruct.prototype.bondRecalc=function(t,e){var r=this.render,a=this.atoms.get(e.b.begin),n=this.atoms.get(e.b.end),d=r.ps(a.a.pp),i=r.ps(n.a.pp),o=this.molecule.halfBonds.get(e.b.hb1),s=this.molecule.halfBonds.get(e.b.hb2);o.p=this.shiftBondEnd(a,d,o.dir,2*t.lineWidth),s.p=this.shiftBondEnd(n,i,s.dir,2*t.lineWidth),e.b.center=Vec2.lc2(a.a.pp,.5,n.a.pp,.5),e.b.len=Vec2.dist(d,i),e.b.sb=5*t.lineWidth,e.b.sa=Math.max(e.b.sb,e.b.len/2-2*t.lineWidth),e.b.angle=180*Math.atan2(o.dir.y,o.dir.x)/Math.PI},rnd.ReStruct.prototype.showBonds=function(){var t=this.render,e=t.settings,r=t.paper,a=t.opt;for(var n in this.bondsChanged){var d=this.bonds.get(n),i=this.molecule.halfBonds.get(d.b.hb1),o=this.molecule.halfBonds.get(d.b.hb2);this.bondRecalc(e,d),d.path=this.drawBond(d,i,o),d.rbb=rnd.relBox(d.path.getBBox()),this.addReObjectPath("data",d.visel,d.path,null,!0);var s={};s.path=this.drawReactingCenter(d,i,o),s.path&&(s.rbb=rnd.relBox(s.path.getBBox()),this.addReObjectPath("data",d.visel,s.path,null,!0));var h={};h.path=this.drawTopologyMark(d,i,o),h.path&&(h.rbb=rnd.relBox(h.path.getBBox()),this.addReObjectPath("data",d.visel,h.path,null,!0)),d.setHighlight(d.highlight,t);var l=.6*e.subFontSize,c=null,p=null;if(a.showBondIds){var b=Vec2.lc(i.p,.5,o.p,.5,i.norm,l);c=r.text(b.x,b.y,n.toString()),p=rnd.relBox(c.getBBox()),this.centerText(c,p),this.addReObjectPath("indices",d.visel,c)}if(a.showHalfBondIds){var u=Vec2.lc(i.p,.8,o.p,.2,i.norm,l);c=r.text(u.x,u.y,d.b.hb1.toString()),p=rnd.relBox(c.getBBox()),this.centerText(c,p),this.addReObjectPath("indices",d.visel,c);var f=Vec2.lc(i.p,.2,o.p,.8,o.norm,l);c=r.text(f.x,f.y,d.b.hb2.toString()),p=rnd.relBox(c.getBBox()),this.centerText(c,p),this.addReObjectPath("indices",d.visel,c)}if(a.showLoopIds&&!a.showBondIds){var S=Vec2.lc(i.p,.5,o.p,.5,o.norm,l);c=r.text(S.x,S.y,i.loop.toString()),p=rnd.relBox(c.getBBox()),this.centerText(c,p),this.addReObjectPath("indices",d.visel,c);var x=Vec2.lc(i.p,.5,o.p,.5,i.norm,l);c=r.text(x.x,x.y,o.loop.toString()),p=rnd.relBox(c.getBBox()),this.centerText(c,p),this.addReObjectPath("indices",d.visel,c)}}},rnd.ReStruct.prototype.labelIsVisible=function(t,e){if(0==e.a.neighbors.length||e.a.neighbors.length<2&&!this.render.opt.hideTerminalLabels||"c"!=e.a.label.toLowerCase()||e.a.badConn&&this.render.opt.showValenceWarnings||0!=e.a.isotope||0!=e.a.radical||0!=e.a.charge||e.a.explicitValence>=0||null!=e.a.atomList||null!=e.a.rglabel)return!0;if(2==e.a.neighbors.length){var r=e.a.neighbors[0],a=e.a.neighbors[1],n=this.molecule.halfBonds.get(r),d=this.molecule.halfBonds.get(a),i=this.bonds.get(n.bid),o=this.bonds.get(d.bid);if(i.b.type==o.b.type&&i.b.stereo==chem.Struct.BOND.STEREO.NONE&&o.b.stereo==chem.Struct.BOND.STEREO.NONE&&Math.abs(Vec2.cross(n.dir,d.dir))<.2)return!0}return!1},rnd.ReStruct.prototype.checkLabelsToShow=function(){for(var t in this.atomsChanged){var e=this.atoms.get(t);e.showLabel=this.labelIsVisible(t,e)}},rnd.ReStruct.layerMap={background:0,"selection-plate":1,highlighting:2,warnings:3,data:4,indices:5},rnd.ReStruct.prototype.addReObjectPath=function(t,e,r,a,n){if(r){var d=this.render.offset,i=n?Box2Abs.fromRelBox(rnd.relBox(r.getBBox())):null,o=a&&i?i.translate(a.negated()):null;null!==d&&(r.translateAbs(d.x,d.y),i=i?i.translate(d):null),e.add(r,i,o),this.insertInLayer(rnd.ReStruct.layerMap[t],r)}},rnd.ReStruct.prototype.clearVisel=function(t){for(var e=0;e1||1==a)?-1:6==e&&6!=t&&(a>1||1==r)?1:e*r>t*a?-1:e*rt?-1:1},rnd.ReStruct.prototype.selectDoubleBondShift_Chain=function(t){var e=this.molecule,r=e.halfBonds.get(t.b.hb1),a=e.halfBonds.get(t.b.hb2),n=(r.leftSin>.3?1:0)+(a.rightSin>.3?1:0),d=(a.leftSin>.3?1:0)+(r.rightSin>.3?1:0);return n>d?-1:n.3?1:0)+(r.rightSin>.3?1:0)==1?1:0},rnd.ReStruct.prototype.setDoubleBondShift=function(){var t=this.molecule;for(var e in this.bondsChanged){var r,a,n=this.bonds.get(e);if(r=t.halfBonds.get(n.b.hb1).loop,a=t.halfBonds.get(n.b.hb2).loop,r>=0&&a>=0){var d=t.loops.get(r).dblBonds,i=t.loops.get(a).dblBonds,o=t.loops.get(r).hbs.length,s=t.loops.get(a).hbs.length;n.doubleBondShift=this.selectDoubleBondShift(o,s,d,i)}else n.doubleBondShift=r>=0?-1:a>=0?1:this.selectDoubleBondShift_Chain(n)}},rnd.ReStruct.prototype.updateLoops=function(){this.reloops.each(function(t,e){this.clearVisel(e.visel)},this);var t=this.molecule.findLoops();util.each(t.bondsToMark,function(t){this.markBond(t,1)},this),util.each(t.newLoops,function(t){this.reloops.set(t,new rnd.ReLoop(this.molecule.loops.get(t)))},this)},rnd.ReStruct.prototype.renderLoops=function(){var t=this.render,e=t.settings,r=t.paper,a=this.molecule;this.reloops.each(function(n,d){var i=d.loop;d.centre=new Vec2,i.hbs.each(function(e){var r=a.halfBonds.get(e),n=this.bonds.get(r.bid),o=t.ps(this.atoms.get(r.begin).a.pp);n.b.type!=chem.Struct.BOND.TYPE.AROMATIC&&(i.aromatic=!1),d.centre.add_(o)},this),i.convex=!0;for(var o=0;o0&&(i.convex=!1)}if(d.centre=d.centre.scaled(1/i.hbs.length),d.radius=-1,i.hbs.each(function(e){var r=a.halfBonds.get(e),n=t.ps(this.atoms.get(r.begin).a.pp),i=t.ps(this.atoms.get(r.end).a.pp),o=Vec2.diff(i,n).rotateSC(1,0).normalized(),s=Vec2.dot(Vec2.diff(n,d.centre),o);d.radius<0?d.radius=s:d.radius=Math.min(d.radius,s)},this),d.radius*=.7,i.aromatic){var c=null;if(i.convex)c=r.circle(d.centre.x,d.centre.y,d.radius).attr({stroke:"#000","stroke-width":e.lineWidth});else{var p="";for(o=0;o2)throw new Error("One vector or two scalar arguments expected");if(void 0===s)this.translate(t.x,t.y);else{for(var n=new Vec2(t,s),i=0;i=0&&Set.add(p,r)},this)):Set.contains(u,t.b.begin)?Set.add(m,t.b.begin):Set.contains(u,t.b.end)&&Set.add(m,t.b.end)},this),r=0;ri&&(a=o,i=n);var d=new Vec2(1,0);if(t.length>0){if(1==t.length){i=-4*Math.PI/3;var p=ui.render.atomGetNeighbors(e)[0];if(ui.render.atomGetDegree(p.aid)>1){var m=[],u=ui.render.atomGetPos(p.aid),s=Vec2.diff(r,u),f=Math.atan2(s.y,s.x);ui.render.atomGetNeighbors(p.aid).each(function(e){var t=ui.render.atomGetPos(e.aid);if(!(e.bid==p.bid||Vec2.dist(u,t)<.1)){var r=Vec2.diff(t,u),o=Math.atan2(r.y,r.x)-f;o<0&&(o+=2*Math.PI),m.push(o)}}),m.sort(function(e,t){return e-t}),m[0]<=1.01*Math.PI&&m[m.length-1]<=1.01*Math.PI&&(i*=-1)}}n=i/2+Math.atan2(t[a].v.y,t[a].v.x),d=d.rotate(n)}d.add_(r);var c=ui.render.findClosestAtom(d,.1);return c=null==c?{label:"C"}:c.id,{atom:c,pos:d}}function fromBondAddition(e,t,r,o,n){if(void 0===r){var a=atomForNewBond(t);r=a.atom,o=a.pos}var i=new Action,d=null;if(Object.isNumber(t)){if(d=ui.render.atomGetAttr(t,"fragment"),Object.isNumber(r)){var p=ui.render.atomGetAttr(r,"fragment");mergeFragments(i,d,p)}}else Object.isNumber(r)&&(d=ui.render.atomGetAttr(r,"fragment"));null==d&&(d=i.addOp((new op.FragmentAdd).perform(ui.editor)).frid),Object.isNumber(t)?"*"==ui.render.atomGetAttr(t,"label")&&i.addOp(new op.AtomAttr(t,"label","C").perform(ui.editor)):(t.fragment=d,t=i.addOp(new op.AtomAdd(t,o).perform(ui.editor)).data.aid,o=n),Object.isNumber(r)?"*"==ui.render.atomGetAttr(r,"label")&&i.addOp(new op.AtomAttr(r,"label","C").perform(ui.editor)):(r.fragment=d,r=i.addOp(new op.AtomAdd(r,o).perform(ui.editor)).data.aid,Object.isNumber(t)&&ui.render.atomGetSGroups(t).each(function(e){i.addOp(new op.SGroupAtomAdd(e,r).perform(ui.editor))},this));var m=i.addOp(new op.BondAdd(t,r,e).perform(ui.editor)).data.bid;return i.operations.reverse(),[i,t,r,m]}function fromArrowAddition(e){var t=new Action;return ui.ctab.rxnArrows.count()<1&&t.addOp(new op.RxnArrowAdd(e).perform(ui.editor)),t}function fromArrowDeletion(e){var t=new Action;return t.addOp(new op.RxnArrowDelete(e)),t.perform()}function fromChiralFlagAddition(e){var t=new Action;return ui.render.ctab.chiralFlags.count()<1&&t.addOp(new op.ChiralFlagAdd(e).perform(ui.editor)),t}function fromChiralFlagDeletion(){var e=new Action;return e.addOp(new op.ChiralFlagDelete),e.perform()}function fromPlusAddition(e){var t=new Action;return t.addOp(new op.RxnPlusAdd(e).perform(ui.editor)),t}function fromPlusDeletion(e){var t=new Action;return t.addOp(new op.RxnPlusDelete(e)),t.perform()}function fromAtomDeletion(e){var t=new Action,r=new Array,o=ui.ctab.atoms.get(e).fragment;return ui.render.atomGetNeighbors(e).each(function(e){t.addOp(new op.BondDelete(e.bid)),1==ui.render.atomGetDegree(e.aid)&&(t.removeAtomFromSgroupIfNeeded(e.aid)&&r.push(e.aid),t.addOp(new op.AtomDelete(e.aid)))},this),t.removeAtomFromSgroupIfNeeded(e)&&r.push(e),t.addOp(new op.AtomDelete(e)),t.removeSgroupIfNeeded(r),t=t.perform(),t.mergeWith(fromFragmentSplit(o)),t}function fromBondDeletion(e){var t=new Action,r=ui.ctab.bonds.get(e),o=ui.ctab.atoms.get(r.begin).fragment,n=new Array;return t.addOp(new op.BondDelete(e)),1==ui.render.atomGetDegree(r.begin)&&(t.removeAtomFromSgroupIfNeeded(r.begin)&&n.push(r.begin),t.addOp(new op.AtomDelete(r.begin))),1==ui.render.atomGetDegree(r.end)&&(t.removeAtomFromSgroupIfNeeded(r.end)&&n.push(r.end),t.addOp(new op.AtomDelete(r.end))),t.removeSgroupIfNeeded(n),t=t.perform(),t.mergeWith(fromFragmentSplit(o)),t}function fromFragmentSplit(e){var t=new Action,r=chem.Struct.RGroup.findRGroupByFragment(ui.ctab.rgroups,e);return ui.ctab.atoms.each(function(o,n){if(n.fragment==e){var a=t.addOp((new op.FragmentAdd).perform(ui.editor)).frid,i=function(r){t.addOp(new op.AtomAttr(r,"fragment",a).perform(ui.editor)),ui.render.atomGetNeighbors(r).each(function(t){ui.ctab.atoms.get(t.aid).fragment==e&&i(t.aid)})};i(o),r&&t.mergeWith(fromRGroupFragment(r,a))}}),-1!=e&&(t.mergeWith(fromRGroupFragment(0,e)),t.addOp(new op.FragmentDelete(e).perform(ui.editor))),t}function fromFragmentAddition(e,t,r,o,n){var a=new Action;return r.each(function(e){a.addOp(new op.SGroupRemoveFromHierarchy(e)),a.addOp(new op.SGroupDelete(e))},this),t.each(function(e){a.addOp(new op.BondDelete(e))},this),e.each(function(e){a.addOp(new op.AtomDelete(e))},this),o.each(function(e){a.addOp(new op.RxnArrowDelete(e))},this),n.each(function(e){a.addOp(new op.RxnPlusDelete(e))},this),a.mergeWith(new fromFragmentSplit(-1)),a}function fromFragmentDeletion(e){e=e||ui.editor.getSelection();var t=new Action,r=new Array,o=[],n=new Action;for(e.sgroupData&&e.sgroupData.each(function(e){n.mergeWith(fromSgroupDeletion(e))},this),e.atoms.each(function(t){ui.render.atomGetNeighbors(t).each(function(t){-1==e.bonds.indexOf(t.bid)&&(e.bonds=e.bonds.concat([t.bid]))},this)},this),e.bonds.each(function(n){t.addOp(new op.BondDelete(n));var a=ui.ctab.bonds.get(n);if(-1==e.atoms.indexOf(a.begin)&&1==ui.render.atomGetDegree(a.begin)){var i=ui.ctab.atoms.get(a.begin).fragment;o.indexOf(i)<0&&o.push(i),t.removeAtomFromSgroupIfNeeded(a.begin)&&r.push(a.begin),t.addOp(new op.AtomDelete(a.begin))}if(-1==e.atoms.indexOf(a.end)&&1==ui.render.atomGetDegree(a.end)){var d=ui.ctab.atoms.get(a.end).fragment;o.indexOf(d)<0&&o.push(d),t.removeAtomFromSgroupIfNeeded(a.end)&&r.push(a.end),t.addOp(new op.AtomDelete(a.end))}},this),e.atoms.each(function(e){var n=ui.ctab.atoms.get(e).fragment;o.indexOf(n)<0&&o.push(n),t.removeAtomFromSgroupIfNeeded(e)&&r.push(e),t.addOp(new op.AtomDelete(e))},this),t.removeSgroupIfNeeded(r),e.rxnArrows.each(function(e){t.addOp(new op.RxnArrowDelete(e))},this),e.rxnPluses.each(function(e){t.addOp(new op.RxnPlusDelete(e))},this),e.chiralFlags.each(function(e){t.addOp(new op.ChiralFlagDelete(e))},this),t=t.perform();o.length>0;)t.mergeWith(new fromFragmentSplit(o.pop()));return t.mergeWith(n),t}function fromAtomMerge(e,t){var r=new Action,o=ui.render.atomGetAttr(e,"fragment"),n=ui.render.atomGetAttr(t,"fragment");o!=n&&mergeFragments(r,o,n);var a=new Action;ui.render.atomGetNeighbors(e).each(function(e){var r,o,n=ui.ctab.bonds.get(e.bid);n.begin==e.aid?(r=e.aid,o=t):(r=t,o=e.aid),t!=n.begin&&t!=n.end&&-1==ui.ctab.findBondId(r,o)&&a.addOp(new op.BondAdd(r,o,n)),a.addOp(new op.BondDelete(e.bid))},this);var i=chem.Struct.Atom.getAttrHash(ui.ctab.atoms.get(e));1==ui.render.atomGetDegree(e)&&"*"==i.get("label")&&i.set("label","C"),i.each(function(e){a.addOp(new op.AtomAttr(t,e.key,e.value))},this);var d=a.removeAtomFromSgroupIfNeeded(e);return a.addOp(new op.AtomDelete(e)),d&&a.removeSgroupIfNeeded([e]),a.perform().mergeWith(r)}function toBondFlipping(e){var t=ui.ctab.bonds.get(e),r=new Action;return r.addOp(new op.BondDelete(e)),r.addOp(new op.BondAdd(t.end,t.begin,t)).data.bid=e,r}function fromBondFlipping(e){return toBondFlipping(e).perform()}function fromTemplateOnCanvas(e,t,r){var o=new Action,n=r.molecule,a=(new op.FragmentAdd).perform(ui.editor),i={};return n.atoms.each(function(n,d){var p,m=chem.Struct.Atom.getAttrHash(d).toObject();m.fragment=a.frid,o.addOp(p=new op.AtomAdd(m,Vec2.diff(d.pp,r.xy0).rotate(t).add(e)).perform(ui.editor)),i[n]=p.data.aid}),n.bonds.each(function(e,t){o.addOp(new op.BondAdd(i[t.begin],i[t.end],t).perform(ui.editor))}),o.operations.reverse(),o.addOp(a),o}function atomAddToSGroups(e,t){var r=new Action;return util.each(e,function(e){r.addOp(new op.SGroupAtomAdd(e,t).perform(ui.editor))},this),r}function fromTemplateOnAtom(e,t,r,o,n){var a=new Action,i=o.molecule,d=ui.render,p=d.ctab,m=p.molecule,u=m.atoms.get(e),s=e,f=null,c=ui.render.atomGetSGroups(e),g=d.atomGetAttr(e,"fragment"),l={},h=i.atoms.get(o.aid).pp;if(r){if(null==t){var A=atomForNewBond(e),w=fromBondAddition({type:1},e,A.atom,A.pos);a=w[0],a.operations.reverse(),f=e=w[2]}else{var v;a.addOp(v=new op.AtomAdd({label:"C",fragment:g},new Vec2(1,0).rotate(t).add(u.pp)).perform(ui.editor)),a.addOp(new op.BondAdd(e,v.data.aid,{type:1}).perform(ui.editor)),f=e=v.data.aid,a.mergeWith(atomAddToSGroups(c,e))}var b=u;u=m.atoms.get(e);var O=n(b.pp,u.pp)-o.angle0}else null==t&&(A=atomForNewBond(e),t=n(u.pp,A.pos)),O=t-o.angle0;return i.atoms.each(function(t,r){var n=chem.Struct.Atom.getAttrHash(r).toObject();if(n.fragment=g,t==o.aid)a.mergeWith(fromAtomsAttrs(e,n,!0)),l[t]=e;else{var i;i=Vec2.diff(r.pp,h).rotate(O).add(u.pp),a.addOp(v=new op.AtomAdd(n,i).perform(ui.editor)),l[t]=v.data.aid}l[t]-0!=s-0&&l[t]-0!=f-0&&a.mergeWith(atomAddToSGroups(c,l[t]))}),i.bonds.each(function(e,t){a.addOp(new op.BondAdd(l[t.begin],l[t.end],t).perform(ui.editor))}),a.operations.reverse(),a}function fromTemplateOnBond(e,t,r,o){var n,a,i=new Action,d=t.molecule,p=ui.render,m=p.ctab,u=m.molecule,s=u.bonds.get(e),f=u.atoms.get(s.begin),c=u.atoms.get(s.end),g=Set.list(Set.intersection(Set.fromList(ui.render.atomGetSGroups(s.begin)),Set.fromList(ui.render.atomGetSGroups(s.end)))),l=d.bonds.get(t.bid),h=p.atomGetAttr(s.begin,"fragment"),A={};o?(n=d.atoms.get(l.end),a=d.atoms.get(l.begin),A[l.end]=s.begin,A[l.begin]=s.end):(n=d.atoms.get(l.begin),a=d.atoms.get(l.end),A[l.begin]=s.begin,A[l.end]=s.end);var w=r(f.pp,c.pp)-r(n.pp,a.pp),v=Vec2.dist(f.pp,c.pp)/Vec2.dist(n.pp,a.pp);n.pp;return d.atoms.each(function(e,t){var r=chem.Struct.Atom.getAttrHash(t).toObject();if(r.fragment=h,e==l.begin||e==l.end)return void i.mergeWith(fromAtomsAttrs(A[e],r,!0));var o;o=Vec2.diff(t.pp,n.pp).rotate(w).scaled(v).add(f.pp);var a=p.findClosestAtom(o,.1);if(null==a){var d;i.addOp(d=new op.AtomAdd(r,o).perform(ui.editor)),A[e]=d.data.aid,i.mergeWith(atomAddToSGroups(g,A[e]))}else A[e]=a.id,i.mergeWith(fromAtomsAttrs(A[e],r,!0))}),d.bonds.each(function(e,t){var r=u.findBondId(A[t.begin],A[t.end]);-1==r?i.addOp(new op.BondAdd(A[t.begin],A[t.end],t).perform(ui.editor)):i.mergeWith(fromBondAttrs(r,l,!1,!0))}),i.operations.reverse(),i}function fromChain(e,t,r,o){var n,a=Math.PI/6,i=Math.cos(a),d=Math.sin(a),p=new Action;n=null!=o?ui.render.atomGetAttr(o,"fragment"):p.addOp((new op.FragmentAdd).perform(ui.editor)).frid;var m=-1;return m=null!=o?o:p.addOp(new op.AtomAdd({label:"C",fragment:n},e).perform(ui.editor)).data.aid,p.operations.reverse(),r.times(function(r){var o=new Vec2(i*(r+1),1&r?0:d).rotate(t).add(e),n=ui.render.findClosestAtom(o,.1),a=fromBondAddition({},m,n?n.id:{},o);p=a[0].mergeWith(p),m=a[2]},this),p}function fromNewCanvas(e){var t=new Action;return t.addOp(new op.CanvasLoad(e)),t.perform()}function fromSgroupType(e,t){var r=ui.render,o=r.sGroupGetType(e);if(t&&t!=o){var n=util.array(r.sGroupGetAtoms(e)),a=r.sGroupGetAttrs(e),i=fromSgroupDeletion(e);return fromSgroupAddition(t,n,a,e).mergeWith(i)}return new Action}function fromSgroupAttrs(e,t){var r=new Action,o=ui.render,n=o.ctab;n.sgroups.get(e).item;return new Hash(t).each(function(t){r.addOp(new op.SGroupAttr(e,t.key,t.value))},this),r.perform()}function sGroupAttributeAction(e,t){var r=new Action;return new Hash(t).each(function(t){r.addOp(new op.SGroupAttr(e,t.key,t.value))},this),r}function fromSgroupDeletion(e){var t=new Action,r=ui.render,o=r.ctab,n=o.molecule;if("SRU"==ui.render.sGroupGetType(e)){ui.render.sGroupsFindCrossBonds();ui.render.sGroupGetNeighborAtoms(e).each(function(e){"*"==ui.render.atomGetAttr(e,"label")&&t.addOp(new op.AtomAttr(e,"label","C"))},this)}var a=n.sgroups.get(e),i=chem.SGroup.getAtoms(n,a),d=a.getAttrs();t.addOp(new op.SGroupRemoveFromHierarchy(e));for(var p=0;p=0;S--)n.addOp(O.operations[S])}if(ui.editor.render.ctab.rxnArrows.count()<1)for(var G=0;G0&&(t.each(function(t){this.addOp(new op.SGroupAtomRemove(t,e))},this),!0)},Action.prototype.removeSgroupIfNeeded=function(e){var t=ui.render,r=t.ctab,o=r.molecule,n=new Hash;e.each(function(e){ui.render.atomGetSGroups(e).each(function(e){var t=n.get(e);Object.isUndefined(t)?t=1:t++,n.set(e,t)},this)},this),n.each(function(e){var t=parseInt(e.key);if(ui.render.sGroupGetAtoms(t).length==e.value){var r=o.sgroups.get(t);this.mergeWith(sGroupAttributeAction(t,r.getAttrs())),this.addOp(new op.SGroupRemoveFromHierarchy(t)),this.addOp(new op.SGroupDelete(t))}},this)},module.exports=util.extend(Action,{fromMultipleMove:fromMultipleMove,fromAtomAddition:fromAtomAddition,fromArrowAddition:fromArrowAddition,fromArrowDeletion:fromArrowDeletion,fromChiralFlagDeletion:fromChiralFlagDeletion,fromPlusAddition:fromPlusAddition,fromPlusDeletion:fromPlusDeletion,fromAtomDeletion:fromAtomDeletion,fromBondDeletion:fromBondDeletion,fromFragmentDeletion:fromFragmentDeletion,fromAtomMerge:fromAtomMerge,fromBondFlipping:fromBondFlipping,fromTemplateOnCanvas:fromTemplateOnCanvas,fromTemplateOnAtom:fromTemplateOnAtom,fromTemplateOnBond:fromTemplateOnBond,fromAtomsAttrs:fromAtomsAttrs,fromBondAttrs:fromBondAttrs,fromChain:fromChain,fromBondAddition:fromBondAddition,fromNewCanvas:fromNewCanvas,fromSgroupType:fromSgroupType,fromSgroupDeletion:fromSgroupDeletion,fromSgroupAttrs:fromSgroupAttrs,fromRGroupFragment:fromRGroupFragment,fromPaste:fromPaste,fromRGroupAttrs:fromRGroupAttrs,fromSgroupAddition:fromSgroupAddition,fromFlip:fromFlip,fromRotate:fromRotate}); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../chem":11,"../util":39,"../util/set":42,"../util/vec2":43,"./op":35}],27:[function(require,module,exports){ +(function (global){ +function initDialogs(){$("input_label").observe("blur",function(){keymage.setScope("editor"),this.hide()}),$("input_label").observe("keypress",onKeyPress_InputLabel),$("input_label").observe("keyup",onKeyUp_InputLabel),$("atom_label").observe("change",onChange_AtomLabel),$("atom_charge").observe("change",onChange_AtomCharge),$("atom_isotope").observe("change",onChange_AtomIsotope),$("atom_valence").observe("change",onChange_AtomValence),$("atom_prop_cancel").observe("click",function(){ui.hideDialog("atom_properties")}),$("atom_prop_ok").observe("click",function(){applyAtomProperties()}),$("bond_prop_cancel").observe("click",function(){ui.hideDialog("bond_properties")}),$("bond_prop_ok").observe("click",function(){applyBondProperties()})}function showAtomAttachmentPoints(e){$("atom_ap1").checked=(1&(e.selection||0))>0,$("atom_ap2").checked=(2&(e.selection||0))>0,ui.showDialog("atom_attpoints");var t=new Event.Handler("atom_attpoints_ok","click",void 0,function(){t.stop(),o.stop(),ui.hideDialog("atom_attpoints"),"onOk"in e&&e.onOk(($("atom_ap1").checked?1:0)+($("atom_ap2").checked?2:0))}).start(),o=new Event.Handler("atom_attpoints_cancel","click",void 0,function(){t.stop(),o.stop(),ui.hideDialog("atom_attpoints"),"onCancel"in e&&e.onCancel()}).start();$("atom_attpoints_ok").focus()}function showAtomProperties(e){$("atom_properties").atom_id=e,$("atom_label").value=ui.render.atomGetAttr(e,"label"),onChange_AtomLabel.call($("atom_label"));var t=ui.render.atomGetAttr(e,"charge")-0;$("atom_charge").value=0==t?"":t,t=ui.render.atomGetAttr(e,"isotope")-0,$("atom_isotope").value=0==t?"":t,t=ui.render.atomGetAttr(e,"explicitValence")-0,$("atom_valence").value=t<0?"":t,$("atom_radical").value=ui.render.atomGetAttr(e,"radical"),$("atom_inversion").value=ui.render.atomGetAttr(e,"invRet"),$("atom_exactchange").value=ui.render.atomGetAttr(e,"exactChangeFlag")?1:0,$("atom_ringcount").value=ui.render.atomGetAttr(e,"ringBondCount"),$("atom_substitution").value=ui.render.atomGetAttr(e,"substitutionCount"),$("atom_unsaturation").value=ui.render.atomGetAttr(e,"unsaturatedAtom"),$("atom_hcount").value=ui.render.atomGetAttr(e,"hCount"),ui.showDialog("atom_properties"),$("atom_label").activate()}function applyAtomProperties(){ui.hideDialog("atom_properties");var e=$("atom_properties").atom_id;ui.addUndoAction(Action.fromAtomsAttrs(e,{label:$("atom_label").value,charge:""==$("atom_charge").value?0:parseInt($("atom_charge").value,10),isotope:""==$("atom_isotope").value?0:parseInt($("atom_isotope").value,10),explicitValence:""==$("atom_valence").value?-1:parseInt($("atom_valence").value,10),radical:parseInt($("atom_radical").value,10),invRet:parseInt($("atom_inversion").value,10),exactChangeFlag:!!parseInt($("atom_exactchange").value,10),ringBondCount:parseInt($("atom_ringcount").value,10),substitutionCount:parseInt($("atom_substitution").value,10),unsaturatedAtom:parseInt($("atom_unsaturation").value,10),hCount:parseInt($("atom_hcount").value,10)}),!0),ui.render.update()}function onChange_AtomLabel(){this.value=this.value.strip().capitalize();var e=element.getElementByLabel(this.value);null==e&&"A"!==this.value&&"*"!==this.value&&"Q"!==this.value&&"X"!==this.value&&"R"!==this.value&&(this.value=ui.render.atomGetAttr($("atom_properties").atom_id,"label"),"A"!==this.value&&"*"!==this.value&&(e=element.getElementByLabel(this.value))),"A"==this.value||"*"==this.value?$("atom_number").value="any":$("atom_number").value=e?e.toString():""}function onChange_AtomCharge(){""===this.value.strip()||"0"==this.value?this.value="":this.value.match(/^[1-9][0-9]{0,1}[-+]$/)?this.value=(this.value.endsWith("-")?"-":"")+this.value.substr(0,this.value.length-1):this.value.match(/^[+-]?[1-9][0-9]{0,1}$/)||(this.value=ui.render.atomGetAttr($("atom_properties").atom_id,"charge"))}function onChange_AtomIsotope(){this.value==util.getElementTextContent($("atom_number"))||""==this.value.strip()||"0"==this.value?this.value="":this.value.match(/^[1-9][0-9]{0,2}$/)||(this.value=ui.render.atomGetAttr($("atom_properties").atom_id,"isotope"))}function onChange_AtomValence(){}function showBondProperties(e){var t;$("bond_properties").bond_id=e;var o=ui.render.bondGetAttr(e,"type"),a=ui.render.bondGetAttr(e,"stereo");for(t in ui.bondTypeMap)if(ui.bondTypeMap[t].type==o&&ui.bondTypeMap[t].stereo==a)break;$("bond_type").value=t,$("bond_topology").value=ui.render.bondGetAttr(e,"topology")||0,$("bond_center").value=ui.render.bondGetAttr(e,"reactingCenterStatus")||0,ui.showDialog("bond_properties"),$("bond_type").activate()}function applyBondProperties(){ui.hideDialog("bond_properties");var e=$("bond_properties").bond_id,t=Object.clone(ui.bondTypeMap[$("bond_type").value]);t.topology=parseInt($("bond_topology").value,10),t.reactingCenterStatus=parseInt($("bond_center").value,10),ui.addUndoAction(Action.fromBondAttrs(e,t),!0),ui.render.update()}function showAutomapProperties(e){ui.showDialog("automap_properties");var t,o;t=new Event.Handler("automap_ok","click",void 0,function(){t.stop(),o.stop(),e&&"onOk"in e&&e.onOk($("automap_mode").value),ui.hideDialog("automap_properties")}).start(),o=new Event.Handler("automap_cancel","click",void 0,function(){t.stop(),o.stop(),ui.hideDialog("automap_properties"),e&&"onCancel"in e&&e.onCancel()}).start(),$("automap_mode").activate()}function showRLogicTable(e){var t=e||{};t.rlogic=t.rlogic||{},$("rlogic_occurrence").value=t.rlogic.occurrence||">0",$("rlogic_resth").value=t.rlogic.resth?"1":"0";for(var o='',a=1;a<=32;a++)a!=t.rgid&&0!=(t.rgmask&1<IF R'+t.rgid+" THEN R"+a+"");$("rlogic_if").outerHTML='",$("rlogic_if").value=t.rlogic.ifthen,ui.showDialog("rlogic_table");var i=new Event.Handler("rlogic_ok","click",void 0,function(){var e={occurrence:$("rlogic_occurrence").value.replace(/\s*/g,"").replace(/,+/g,",").replace(/^,/,"").replace(/,$/,""),resth:"1"==$("rlogic_resth").value,ifthen:parseInt($("rlogic_if").value,10)};t&&"onOk"in t&&!t.onOk(e)||(i.stop(),n.stop(),ui.hideDialog("rlogic_table"))}).start(),n=new Event.Handler("rlogic_cancel","click",void 0,function(){i.stop(),n.stop(),ui.hideDialog("rlogic_table"),t&&"onCancel"in t&&t.onCancel()}).start();$("rlogic_occurrence").activate()}function onKeyPress_Dialog(e){if(util.stopEventPropagation(e),27===e.keyCode)return ui.hideDialog(this.id),util.preventDefault(e)}function onKeyPress_InputLabel(e){if(util.stopEventPropagation(e),13==e.keyCode){keymage.setScope("editor"),this.hide();var t="",o=0,a=this.value.toArray();if("*"==this.value)t="A";else if(this.value.match(/^[*][1-9]?[+-]$/i))t="A",o=2==this.value.length?1:parseInt(a[1]),"-"==a[2]&&(o*=-1);else if(this.value.match(/^[A-Z]{1,2}$/i))t=this.value.capitalize();else if(this.value.match(/^[A-Z]{1,2}[0][+-]?$/i))t=this.value.match(/^[A-Z]{2}/i)?this.value.substr(0,2).capitalize():a[0].capitalize();else if(this.value.match(/^[A-Z]{1,2}[1-9]?[+-]$/i)){t=this.value.match(/^[A-Z]{2}/i)?this.value.substr(0,2).capitalize():a[0].capitalize();var i=this.value.match(/[0-9]/i);o=null!=i?parseInt(i[0]):1,"-"==a[this.value.length-1]&&(o*=-1)}return"A"!=t&&"Q"!=t&&"X"!=t&&"R"!=t&&null==element.getElementByLabel(t)||(ui.addUndoAction(Action.fromAtomsAttrs(this.atom_id,{label:t,charge:o}),!0),ui.render.update()),util.preventDefault(e)}if(27==e.keyCode)return this.hide(),keymage.setScope("editor"),util.preventDefault(e)}function onKeyUp_InputLabel(e){if(util.stopEventPropagation(e),27==e.keyCode)return this.hide(),keymage.setScope("editor"),util.preventDefault(e)}function showLabelEditor(e){var t=$("input_label");keymage.setScope("label");var o=Math.min(7*ui.render.zoom,16);t.atom_id=e,t.value=ui.render.atomGetAttr(e,"label"),t.style.fontSize=2*o+"px",t.show();var a=ui.render.obj2view(ui.render.atomGetPos(e)),i={left:0,top:0},n=Element.cumulativeOffset(t.offsetParent);t.style.left=a.x+i.left-n.left-o-0+"px",t.style.top=a.y+i.top-n.top-o-0+"px",t.activate()}var keymage=require("keymage"),element=require("../../chem/element"),util=require("../../util"),Action=require("../action"),ui=global.ui;module.exports={initDialogs:initDialogs,showAtomAttachmentPoints:showAtomAttachmentPoints,showAtomProperties:showAtomProperties,showBondProperties:showBondProperties,showAutomapProperties:showAutomapProperties,showRLogicTable:showRLogicTable,showLabelEditor:showLabelEditor}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../../chem/element":10,"../../util":39,"../action":26,"keymage":2}],28:[function(require,module,exports){ +(function (global){ +function dialog(e){var n,i=ui.showDialog("open-file"),t=i.select("input[value=OK]")[0],o=i.select("textarea")[0],l=i.select("input[type=file]")[0],a=i.select("input[name=fragment]")[0],r=[];r[0]=i.on("click","input[type=button]",function(n,i){r.forEach(function(e){e.stop()}),ui.hideDialog("open-file");var t="on"+i.value.capitalize();e&&t in e&&e[t]({fragment:a.checked,value:o.value})}),r[1]=l.on("change",function(e,t){console.assert(n,"No valid file opener"),t.files.length&&(i.select("input").each(function(e){e.disabled=!0}),n(t.files[0]).then(function(e){o.value=e,i.select("input").each(function(e){e.disabled=!1})},ui.echo))}),r[2]=o.on("input",function(e,n){var i=o.value.trim();t.disabled=!i}),o.value="",a.checked=!1,t.disabled=!0,l.disabled=!0,l.parentNode.addClassName("disabled"),fileOpener().then(function(e){n=e,l.disabled=!1,l.parentNode.removeClassName("disabled")})}function fileOpener(){function e(e){return new Promise(function(n,i){var t=new FileReader;t.onload=function(e){n(e.target.result)},t.onerror=function(e){i(e)},t.readAsText(e,"UTF-8")})}function n(e,n){var i=e.OpenTextFile(n.name,1),t=i.ReadAll();return i.Close(),t}function i(e){}return new Promise(function(t,o){if(global.FileReader)return t(e);if(global.ActiveXObject)try{var l=new global.ActiveXObject("Scripting.FileSystemObject");return t(function(e){return Promise.resolve(n(l,e))})}catch(e){}return ui.standalone?o("Standalone mode!"):t(i)})}function loadHook(){}var Promise=require("promise-polyfill"),ui=global.ui;dialog.loadHook=loadHook,module.exports=dialog; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"promise-polyfill":3}],29:[function(require,module,exports){ +(function (global){ +function saveDialog(e,l){function i(e,l){l=l||"mol",n.value=e,n.className=l,n.activate()}var a,o=ui.showDialog("save-file"),n=o.select("textarea")[0],t=o.select("select")[0],c=o.select(".save")[0],s=[];s[0]=o.on("click","input[type=button]",function(l,i){s.forEach(function(e){e.stop()}),ui.hideDialog("save-file");var a="on"+i.value.capitalize();e&&a in e&&e[a]({})}),s[1]=t.on("change",function(a,o){var n=t.value;convertMolecule(l,e.molecule,n).then(function(e){i(e,n)},ui.echo)}),s[2]=c.on("click",function(e){a&&(a(n.value,t.value),o.select("input[type=button]")[0].click()),e.preventDefault()}),i((new chem.MolfileSaver).saveMolecule(e.molecule)),c.addClassName("disabled"),fileSaver(l).then(function(e){a=e,c.removeClassName("disabled")}),t.select("[value=inchi]")[0].disabled=ui.standalone}function fileSaver(e){var l={smi:"chemical/x-daylight-smiles",mol:"chemical/x-mdl-molfile",rxn:"chemical/x-mdl-rxnfile",inchi:"chemical/x-inchi"};return new Promise(function(i,a){global.Blob&&fs.saveAs?i(function(e,i){"mol"==i&&0==e.indexOf("$RXN")&&(i="rxn"),console.assert(l[i],"Unknown chemical file type");var a=new Blob([e],{type:l[i]});fs.saveAs(a,"ketcher."+i)}):ui.standalone?a("Standalone mode!"):i(function(l,i){e.save({filedata:[i,l].join("\n")})})})}function convertMolecule(e,l,i){return new Promise(function(a,o){var n=(new chem.MolfileSaver).saveMolecule(l);if("mol"==i)a(n);else if("smi"==i)a(ui.standalone?(new chem.SmilesSaver).saveMolecule(l):e.smiles({moldata:n}));else if("inchi"==i){if(ui.standalone)throw Error("InChI is not supported in the standalone mode");0!==l.rgroups.count()&&ui.echo("R-group fragments are not supported and will be discarded"),l=l.getScaffold(),0===l.atoms.count()?a(""):(l=l.clone(),l.sgroups.each(function(e,l){if("MUL"!=l.type&&!/^INDIGO_.+_DESC$/i.test(l.data.fieldName))throw Error("InChi data format doesn't support s-groups")}),a(e.inchi({moldata:n})))}})}var Promise=require("promise-polyfill"),fs=require("filesaver.js");require("../../chem");var chem=global.chem,ui=global.ui;module.exports=saveDialog; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../../chem":11,"filesaver.js":1,"promise-polyfill":3}],30:[function(require,module,exports){ +(function (global){ +function dialog(e,n){function t(e){a.select(".selected").each(function(e){e.removeClassName("selected")}),e?a.select("button").each(function(n){var t=n.value||n.textContent||n.innerText;e.indexOf(t)>=0&&n.addClassName("selected")}):n.required&&(i.disabled=!0)}function l(){var e=[];return a.select(".selected").each(function(n){var t=n.value||n.textContent||n.innerText;e.push(t)}),e}var a=ui.showDialog(e),i=a.select("input[value=OK]")[0],c=n.mode||"single",o=[];o[0]=a.on("click","input[type=button]",function(t,a){o.forEach(function(e){e.stop()}),ui.hideDialog(e);var i="on"+a.value.capitalize();console.assert("onOk"!=i||!n.required||0!=l().length,"No elements selected"),n&&i in n&&n[i]({mode:c,values:l()})}),o[1]=a.on("click","button",function(e,l){"single"===c&&(l.hasClassName("selected")?n.required&&i.click():t(null)),l.toggleClassName("selected"),n.required&&(i.disabled=0===a.select(".selected").length),e.stop()}),o[2]=a.on("click","input[name=mode]",function(e,n){n.value!=c&&("single"==n.value&&t(null),c=n.value)}),t(n.values),a.select("input[name=mode]").each(function(e){e.value==c&&(e.checked=!0)})}var ui=global.ui;module.exports=dialog; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{}],31:[function(require,module,exports){ +(function (global){ +function dialog(e){var t=ui.showDialog("sgroup_special"),a={},l=[];console.assert(!e.type||"DAT"==e.type),console.assert(!e.type||e.attrs.fieldName),setContext(e.type&&matchContext(e.attrs.fieldName,e.attrs.fieldValue)||e.context||"Fragment",a,!0),e.attrs.fieldName&&setField(e.attrs.fieldName,a,!0),$("sgroup_special_value").value=e.attrs.fieldValue,e.attrs.attached?$("sgroup_special_attached").checked=!0:e.attrs.absolute?$("sgroup_special_absolute").checked=!0:$("sgroup_special_relative").checked=!0,l[0]=t.on("click","input[type=button]",function(t,a){var n="on"+a.value.capitalize(),i="onOk"!=n||getValidateAttrs();i&&(l.forEach(function(e){e.stop()}),ui.hideDialog("sgroup_special"),n in e&&i&&e[n](i))}),l[1]=t.on("change","select",function(e,t){"sgroup_context"==t.id&&setContext($("sgroup_context").value,a),"sgroup_special_name"==t.id&&setField($("sgroup_special_name").value,a)})}function getValidateAttrs(){var e={mul:null,connectivity:"",name:"",subscript:""};return e.fieldName=$("sgroup_special_name").value.strip(),e.fieldValue=$("sgroup_special_value").value.strip(),e.absolute=$("sgroup_special_absolute").checked,e.attached=$("sgroup_special_attached").checked,""==e.fieldValue?(alert("Please, specify data field value."),null):{type:"DAT",attrs:e}}function setContext(e,t,a){if(console.info("set context:",e,t),console.assert(t.context||a,"Field setup should be forced"),a||e!=t.context.name){t.context=util.find(special_choices,function(t){return t.name==e}),console.assert(t.context,"Can't find such context");var l=t.context.value.reduce(function(e,t){return e+'"},"");$("sgroup_special_name").update(l),setField(t.context.value[0].name,t,!0),a&&($("sgroup_context").value=e)}}function setField(e,t,a){if(console.info("set field:",e,t),console.assert(t.field||a,"Field setup should be forced"),e||e!=t.field.name){if(t.field=util.find(t.context.value,function(t){return t.name==e}),console.assert(t.field,"Can't find such field"),t.field.value){var l=t.field.value.reduce(function(e,t){return e+'"},"");$("sgroup_special_value").outerHTML='"}else $("sgroup_special_value").outerHTML='';$("sgroup_special_name").value=e}}function matchContext(e,t){console.info("search:",util.unicodeLiteral(e),util.unicodeLiteral(t));var a=util.find(special_choices,function(a){var l=util.find(a.value,function(t){return t.name==e});return!!l&&(!t||!l.value||!!util.find(l.value,function(e){return e==t}))});return a&&a.name}var util=require("../../util"),ui=global.ui,special_choices=[{name:"Fragment",value:[{name:"MDLBG_FRAGMENT_STEREO",value:["abs","(+)-enantiomer","(-)-enantiomer","steric","rel","R(a)","S(a)","R(p)","S(p)"]},{name:"MDLBG_FRAGMENT_COEFFICIENT",value:null},{name:"MDLBG_FRAGMENT_CHARGE",value:null},{name:"MDLBG_FRAGMENT_RADICALS",value:null}]},{name:"Single Bond",value:[{name:"MDLBG_STEREO_KEY",value:["erythro","threo","alpha","beta","endo","exo","anti","syn","ECL","STG"]},{name:"MDLBG_BOND_KEY",value:["Value=4"]}]},{name:"Atom",value:[{name:"MDLBG_STEREO_KEY",value:["RS","SR","P-3","P-3-PI","SP-4","SP-4-PI","T-4","T-4-PI","SP-5","SP-5-PI","TB-5","TB-5-PI","OC-6","TB-5-PI","TP-6","PB-7","CU-8","SA-8","DD-8","HB-9","TPS-9","HB-9"]}]},{name:"Group",value:[{name:"MDLBG_STEREO_KEY",value:["cis","trans"]}]}];dialog.match=function(e){return!e.type||"DAT"==e.type&&!!matchContext(e.attrs.fieldName,e.attrs.fieldValue)},module.exports=dialog; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../../util":39}],32:[function(require,module,exports){ +(function (global){ +function dialog(e){var a=ui.showDialog("sgroup_properties"),t=e.type||"GEN";switch($("sgroup_type").value=t,$("sgroup_type").activate(),onChange_SGroupType.call($("sgroup_type")),t){case"SRU":$("sgroup_connection").value=e.attrs.connectivity,$("sgroup_label").value=e.attrs.subscript;break;case"MUL":$("sgroup_label").value=e.attrs.mul;break;case"SUP":$("sgroup_label").value=e.attrs.name;break;case"DAT":$("sgroup_field_name").value=e.attrs.fieldName,$("sgroup_field_value").value=e.attrs.fieldValue,e.attrs.attached?$("sgroup_pos_attached").checked=!0:e.attrs.absolute?$("sgroup_pos_absolute").checked=!0:$("sgroup_pos_relative").checked=!0}"DAT"!=t&&($("sgroup_field_name").value="",$("sgroup_field_value").value="");var s=[];s[0]=a.on("click","input[type=button]",function(a,t){var l="on"+t.value.capitalize(),u="onOk"!=l||getValidateAttrs();u&&(s.forEach(function(e){e.stop()}),ui.hideDialog("sgroup_properties"),l in e&&u&&e[l](u))}),s[1]=$("sgroup_type").on("change",onChange_SGroupType),s[2]=$("sgroup_label").on("change",onChange_SGroupLabel)}function getValidateAttrs(){var e=$("sgroup_type").value,a={mul:null,connectivity:"",name:"",subscript:"",fieldName:"",fieldValue:"",attached:!1,absolute:!1};switch(e){case"SRU":if(a.connectivity=$("sgroup_connection").value.strip(),a.subscript=$("sgroup_label").value.strip(),1!=a.subscript.length||!a.subscript.match(/^[a-zA-Z]$/))return alert(a.subscript.length?"SRU subscript should consist of a single letter.":"Please provide an SRU subscript."),null;break;case"MUL":a.mul=parseInt($("sgroup_label").value);break;case"SUP":if(a.name=$("sgroup_label").value.strip(),!a.name)return alert("Please provide a name for the superatom."),null;break;case"DAT":if(a.fieldName=$("sgroup_field_name").value.strip(),a.fieldValue=$("sgroup_field_value").value.strip(),a.absolute=$("sgroup_pos_absolute").checked,a.attached=$("sgroup_pos_attached").checked,""==a.fieldName||""==a.fieldValue)return alert("Please, specify data field name and value."),null}return{type:e,attrs:a}}function onChange_SGroupLabel(){"MUL"!=$("sgroup_type").value||this.value.match(/^[1-9][0-9]{0,2}$/)||(this.value="1")}function onChange_SGroupType(){var e=$("sgroup_type").value;if("DAT"==e)return $$("#sgroup_properties .base")[0].hide(),void $$("#sgroup_properties .data")[0].show();$$("#sgroup_properties .base")[0].show(),$$("#sgroup_properties .data")[0].hide(),$("sgroup_label").disabled="SRU"!=e&&"MUL"!=e&&"SUP"!=e,$("sgroup_connection").disabled="SRU"!=e,"MUL"!=e||$("sgroup_label").value.match(/^[1-9][0-9]{0,2}$/)?"SRU"==e?$("sgroup_label").value="n":"GEN"!=e&&"SUP"!=e||($("sgroup_label").value=""):$("sgroup_label").value="1"}var ui=global.ui;module.exports=dialog; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{}],33:[function(require,module,exports){ +(function (global){ +function parseSdf(e){var t=e.split(/^[$][$][$][$]$/m),i=[];return t.each(function(e){e=e.replace(/\r/g,""),e=e.strip();var t=e.indexOf("M END");if(-1!=t){var n={};n.molfile=e.substring(0,t+6),n.name=e.substring(0,e.indexOf("\n")).strip(),e=e.substr(t+7).strip();e.split(/^$/m).each(function(e){if(e=e.strip(),e.startsWith("> <")){var t=e.split("\n"),i=t[0].strip().substring(3,t[0].lastIndexOf(">")).strip();n[i]=parseInt(t[1].strip())||t[1].strip()}}),i.push(n)}}),i}function fetchTemplateCustom(e){return ajax(e+"templates.sdf").then(function(e){var t=parseSdf(e.responseText),i=[],n=0;return t.each(function(e){i.push({name:(e.name||"customtemplate "+ ++n).capitalize(),molfile:e.molfile,aid:(e.atomid||1)-1,bid:(e.bondid||1)-1})}),i})}function initTemplateCustom(e,t){return fetchTemplateCustom(t).then(function(t){return custom_templates=t,eachAsync(t,function(t,i){var n=new Element("li");n.title=t.name,e.insert({bottom:n});var a=chem.Molfile.parseCTFile(t.molfile),l=new rnd.Render(n,0,{autoScale:!0,autoScaleMargin:0,ignoreMouseEvents:!0,hideChiralFlag:!0,maxBondLength:30});l.setMolecule(a),l.update()},50)})}function eachAsync(e,t,i,n){return new Promise(function(a){function l(){s",r.forEach(function(e){var t=e.toLowerCase();Array.isArray(o[t])?o[t].push(l):o[t]=[l]})}else e.title=e.title||t}),o=util.extend(o,{a:["atom-any"],"defmod-a":["select-all"],"defmod-shift-a":["deselect-all"],"ctrl-alt-r":["force-update"]}),Object.keys(o).forEach(function(e){keymage("editor",e,1==o[e].length?function(t){var n=o[e][0];-1==clipActions.indexOf(n)&&(selectAction(o[e][0]),t.preventDefault())}:function(){console.info("actions",o[e])})}),keymage.setScope("editor"),toolbar.select("li").each(function(e){e.on("click",function(e){"BUTTON"==e.target.tagName&&e.target.parentNode==this&&(this.hasClassName("selected")||e.stop(),selectAction(this.id)),hideBlurredControls()?e.stop():"hidden"==this.getStyle("overflow")&&(this.addClassName("opened"),dropdownOpened=this,e.stop())})}),initCliparea(ketcherWindow),initZoom(),updateHistoryButtons(),clientArea.on("scroll",onScroll_ClientArea),clientArea.on("mousedown",function(){keymage.setScope("editor")});var n=new rnd.RenderOptions(e);n.atomColoring=!0,ui.render=new rnd.Render(clientArea,SCALE,n),ui.editor=new rnd.Editor(ui.render),ui.render.onCanvasOffsetChanged=onOffsetChanged,selectAction("select-lasso"),setScrollOffset(0,0),ui.render.setMolecule(ui.ctab),ui.render.update()}function shortcutStr(e){var t=navigator.platform.toUpperCase().indexOf("MAC")>=0;return e.replace(/Defmod/g,t?"⌘":"Ctrl").replace(/-(?!$)/g,"+")}function subEl(e){return $(e).children[0]}function hideBlurredControls(){if(!dropdownOpened)return!1;dropdownOpened.removeClassName("opened");var e=dropdownOpened.select(".selected");if(1==e.length){var t=subEl(dropdownOpened);t.style.marginTop=-e[0].offsetTop+t.offsetTop+"px"}return clientArea.style.visibility="hidden",setTimeout(function(){clientArea.style.visibility="visible"},0),dropdownOpened=null,!0}function selectAction(e){e=e||lastSelected;var t=$(e),o=[].slice.call(arguments,1);if(console.assert(e.startsWith,"id is not a string",e),-1!=clipActions.indexOf(e)&&0==o.length)return delegateCliparea(e);if(!t||!subEl(t).disabled){o.unshift(e);var n=mapTool.apply(null,o);if(n instanceof rnd.Editor.EditorTool){var r=toolbar.select(".selected")[0];t==r&&t||(ui.render.current_tool&&ui.render.current_tool.OnCancel(),ui.render.current_tool=n,e.startsWith("select-")&&(lastSelected=e),t&&t.addClassName("selected"),r&&r.removeClassName("selected"))}return n}return null}function delegateCliparea(e){var t=document.queryCommandSupported(e);if(t)try{document.execCommand(e)}catch(e){t=!1}if(!t){var o=subEl(e);echo("These action is unavailble via menu.\nInstead, use "+shortcutStr(o.dataset?o.dataset.keys:o.getAttribute("data-keys"))+" to "+e+".")}return null}function initCliparea(e){var t=new Element("input",{type:"text",class:"cliparea",autofocus:!0}),o=window.clipboardData,n=["chemical/x-mdl-molfile","chemical/x-mdl-rxnfile","chemical/x-cml","text/plain","chemical/x-daylight-smiles","chemical/x-inchi"],r=function(){return"editor"==keymage.getScope()&&(t.value=" ",t.focus(),t.select(),!0)},i=function(e,t){var n=(new chem.MolfileSaver).saveMolecule(e);if(!t&&o)o.setData("text",n);else{t.setData("text/plain",n);try{t.setData(e.isReaction?"chemical/x-mdl-rxnfile":"chemical/x-mdl-molfile",n),t.setData("chemical/x-daylight-smiles",(new chem.SmilesSaver).saveMolecule(e))}catch(e){console.info("Could not write exact type",e)}}},l=function(e){var t="";if(!e&&o)t=o.getData("text");else for(var r=0;r=0&&n[r],t.slice(0,50),".."),t};e.insert(t),e.on("mouseup",r),["copy","cut"].forEach(function(t){e.on(t,function(e){if(r()){var o=selectAction(t,!0);o&&i(o,e.clipboardData),e.preventDefault()}})}),e.on("paste",function(e){if(r()){var t=l(e.clipboardData);t&&loadFragment(t),e.preventDefault()}})}function updateClipboardButtons(){subEl("copy").disabled=subEl("cut").disabled=!ui.editor.hasSelection(!0)}function updateHistoryButtons(){subEl("undo").disabled=0==undoStack.length,subEl("redo").disabled=0==redoStack.length}function updateServerButtons(){serverActions.forEach(function(e){subEl(e).disabled=ui.standalone})}function transitionEndEvent(){var e,t=document.createElement("transitionTest"),o={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"};for(e in o)if(void 0!==t.style[e])return o[e];return!1}function animateToggle(e,t){ketcherWindow.addClassName("animate");var o=transitionEndEvent(),n=function(e){setTimeout(function(){e&&e(),ketcherWindow.removeClassName("animate")},0)};if(t&&o){var r=function(){n(t),e.removeEventListener(o,r,!1)};e.addEventListener(o,r,!1)}else n(t),t||e()}function showDialog(e){var t=$(e);return keymage.setScope("dialog"),animateToggle(function(){$$(".overlay")[0].show(),t.style.display=""}),t}function hideDialog(e){var t=$$(".overlay")[0];animateToggle(t,function(){$(e).style.display="none",t.hide(),keymage.setScope("editor")})}function showElemTable(e){e.required=!0,selectDialog("elem-table",e)}function showRGroupTable(e){selectDialog("rgroup-table",e)}function showReaGenericsTable(e){e.required=!0,selectDialog("generics-table",e)}function echo(e){alert(e)}function updateMolecule(e){if(void 0!==e&&null!=e){ui.editor.deselectAll(),addUndoAction(Action.fromNewCanvas(e)),showDialog("loading");try{ui.render.onResize(),ui.render.update(),setZoomCentered(null,ui.render.getStructCenter())}catch(e){alert(e.message)}finally{hideDialog("loading")}}}function addUndoAction(e,t){null!=e&&(1==t&&e.isDummy()||(undoStack.push(e),redoStack.clear(),undoStack.length>HISTORY_LENGTH&&undoStack.splice(0,1),updateHistoryButtons()))}function onClick_NewFile(){selectAction(null),ui.ctab.isBlank()||(addUndoAction(Action.fromNewCanvas(new chem.Struct)),ui.render.update())}function onClick_OpenFile(){openDialog({onOk:function(e){e.fragment?loadFragment(e.value,!0):loadMolecule(e.value,!0)}})}function onClick_SaveFile(){saveDialog({molecule:ui.ctab},server)}function aromatize(e,t){e=e.clone();var o=e.addRxnArrowIfNecessary(),n=(new chem.MolfileSaver).saveMolecule(e);if(ui.standalone)throw new Error("Aromatization and dearomatization are not supported in the standalone mode.");server[t?"aromatize":"dearomatize"]({moldata:n}).then(function(e){var t=parseMayBeCorruptedCTFile(e);o&&t.rxnArrows.clear(),updateMolecule(t)},echo)}function calculateCip(){util.assert(!ui.standalone,"Can't calculate in standalone mode!");var e=ui.ctab.clone(),t=e.addRxnArrowIfNecessary(),o=(new chem.MolfileSaver).saveMolecule(e);server.calculateCip({moldata:o}).then(function(e){var o=parseMayBeCorruptedCTFile(e);t&&o.rxnArrows.clear(),updateMolecule(o)},echo)}function initZoom(){var e=subEl("zoom-list");e.on("focus",function(){keymage.pushScope("zoom")}),e.on("blur",function(){keymage.popScope("zoom")}),e.on("change",updateZoom),updateZoom(!0)}function onClick_ZoomIn(){subEl("zoom-list").selectedIndex++,updateZoom()}function onClick_ZoomOut(){subEl("zoom-list").selectedIndex--,updateZoom()}function updateZoom(e){var t=subEl("zoom-list"),o=t.selectedIndex,n=t.length;console.assert(0<=o&&o10||(ui.zoom=e,ui.render.setZoom(ui.zoom))}function getViewSz(){return new Vec2(ui.render.viewSz)}function setZoomCentered(e,t){if(!t)throw new Error("Center point not specified");e&&setZoomRegular(e),setScrollOffset(0,0);var o=ui.render.obj2view(t).sub(ui.render.viewSz.scaled(.5));setScrollOffset(o.x,o.y)}function setZoomStaticPointInit(e){zspObj=new Vec2(e)}function setZoomStaticPoint(e,t){setZoomRegular(e),setScrollOffset(0,0);var o=ui.render.obj2view(zspObj),n=o.sub(t);setScrollOffset(n.x,n.y)}function setScrollOffset(e,t){var o=clientArea.clientWidth,n=clientArea.clientHeight;ui.render.extendCanvas(e,t,o+e,n+t),clientArea.scrollLeft=e,clientArea.scrollTop=t,scrollLeft=clientArea.scrollLeft,scrollTop=clientArea.scrollTop}function setScrollOffsetRel(e,t){setScrollOffset(clientArea.scrollLeft+e,clientArea.scrollTop+t)}function onClick_CleanUp(){var e=util.array(ui.editor.getSelection(!0).atoms),t=e.length>0;if(t){var o=Set.fromList(e),n=Set.empty();ui.ctab.loops.each(function(e,t){util.findIndex(t.hbs,function(e){return Set.contains(o,ui.ctab.halfBonds.get(e).begin)})>=0&&util.each(t.hbs,function(e){Set.add(n,ui.ctab.halfBonds.get(e).begin)},this)},this),Set.mergeIn(n,o),e=Set.list(n)}ui.editor.deselectAll();try{var r={},i=ui.ctab.clone(null,null,!1,r);t&&util.each(e,function(e){e=r[e];var t=new chem.SGroup("DAT"),o=i.sgroups.add(t);t.id=o,t.pp=new Vec2,t.data.fieldName="_ketcher_selective_layout",t.data.fieldValue="1",i.atomAddToSGroup(o,e)},this);var l=i.addRxnArrowIfNecessary();server.layout({moldata:(new chem.MolfileSaver).saveMolecule(i)},t?{selective:1}:null).then(function(e){var t=parseMayBeCorruptedCTFile(e);l&&t.rxnArrows.clear(),updateMolecule(t)})}catch(e){alert("ERROR: "+e.message)}}function onClick_Aromatize(){try{aromatize(ui.ctab,!0)}catch(e){alert("Molfile: "+e.message)}}function onClick_Dearomatize(){try{aromatize(ui.ctab,!1)}catch(e){alert("Molfile: "+e.message)}}function onClick_Automap(){obsolete.showAutomapProperties({onOk:function(e){var t=ui.ctab,o=t.addRxnArrowIfNecessary();if(0==t.rxnArrows.count())return void echo("Auto-Mapping can only be applied to reactions");var n=(new chem.MolfileSaver).saveMolecule(t,!0);server.automap({moldata:n,mode:e}).then(function(e){var t=parseMayBeCorruptedCTFile(e);o&&t.rxnArrows.clear(),updateMolecule(t)},echo)}})}function loadMolecule(e,t){return getStruct(e,t).then(updateMolecule)}function loadFragment(e,t){return getStruct(e,t).then(function(e){e.rescale(),selectAction("paste",e)})}function guessType(e,t){var o=e.trim(),n=o.match(/^(M END|\$END MOL)$/m);if(n){var r=n.index+n[0].length;if(r==o.length||-1!=o.slice(r,r+20).search(/^\$(MOL|END CTAB)$/m))return"mol"}return"<"==o[0]&&-1!=o.indexOf("=0)throw new Error("The same atom cannot be added to an S-group more than once");if(!n)throw new Error("OpSGroupAtomAdd: Atom "+r+" not found");i.atomAddToSGroup(d,r),e.invalidateAtom(r)},this._invert=function(){var t=new SGroupAtomRemove;return t.data=this.data,t}}function SGroupAtomRemove(t,e){this.type="OpSGroupAtomRemove",this.data={aid:e,sgid:t},this._execute=function(t){var e=this.data.aid,a=this.data.sgid,i=t.render,r=i.ctab,d=r.molecule,n=d.atoms.get(e),s=d.sgroups.get(a);chem.SGroup.removeAtom(s,e),Set.remove(n.sgs,a),i.invalidateAtom(e)},this._invert=function(){var t=new SGroupAtomAdd;return t.data=this.data,t}}function SGroupAttr(t,e,a){this.type="OpSGroupAttr",this.data={sgid:t,attr:e,value:a},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=this.data.sgid,d=i.sgroups.get(r);"DAT"==d.type&&a.sgroupData.has(r)&&(a.clearVisel(a.sgroupData.get(r).visel),a.sgroupData.unset(r)),this.data.value=d.setAttr(this.data.attr,this.data.value)},this._invert=function(){var t=new SGroupAttr;return t.data=this.data,t}}function SGroupCreate(t,e,a){this.type="OpSGroupCreate",this.data={sgid:t,type:e,pp:a},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=new chem.SGroup(this.data.type),d=this.data.sgid;r.id=d,i.sgroups.set(d,r),this.data.pp&&(i.sgroups.get(d).pp=new Vec2(this.data.pp)),a.sgroups.set(d,new rnd.ReSGroup(i.sgroups.get(d))),this.data.sgid=d},this._invert=function(){var t=new SGroupDelete;return t.data=this.data,t}}function SGroupDelete(t){this.type="OpSGroupDelete",this.data={sgid:t},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=this.data.sgid,d=a.sgroups.get(r);if(this.data.type=d.item.type,this.data.pp=d.item.pp,"DAT"==d.item.type&&a.sgroupData.has(r)&&(a.clearVisel(a.sgroupData.get(r).visel),a.sgroupData.unset(r)),a.clearVisel(d.visel),0!=d.item.atoms.length)throw new Error("S-Group not empty!");a.sgroups.unset(r),i.sgroups.remove(r)},this._invert=function(){var t=new SGroupCreate;return t.data=this.data,t}}function SGroupAddToHierarchy(t){this.type="OpSGroupAddToHierarchy",this.data={sgid:t},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=this.data.sgid,d=i.sGroupForest.insert(r,this.data.parent,this.data.children);this.data.parent=d.parent,this.data.children=d.children},this._invert=function(){var t=new SGroupRemoveFromHierarchy;return t.data=this.data,t}}function SGroupRemoveFromHierarchy(t){this.type="OpSGroupRemoveFromHierarchy",this.data={sgid:t},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=this.data.sgid;this.data.parent=i.sGroupForest.parent.get(r),this.data.children=i.sGroupForest.children.get(r),i.sGroupForest.remove(r)},this._invert=function(){var t=new SGroupAddToHierarchy;return t.data=this.data,t}}function BondAdd(t,e,a){this.data={bid:null,bond:a,begin:t,end:e},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;if(this.data.begin==this.data.end)throw new Error("Distinct atoms expected");if(rnd.DEBUG&&this.molecule.checkBondExists(this.data.begin,this.data.end))throw new Error("Bond already exists");e.invalidateAtom(this.data.begin,1),e.invalidateAtom(this.data.end,1);var r={};if(this.data.bond)for(var d in this.data.bond)r[d]=this.data.bond[d];r.type=r.type||chem.Struct.BOND.TYPE.SINGLE,r.begin=this.data.begin,r.end=this.data.end,Object.isNumber(this.data.bid)?i.bonds.set(this.data.bid,new chem.Struct.Bond(r)):this.data.bid=i.bonds.add(new chem.Struct.Bond(r)),i.bondInitHalfBonds(this.data.bid),i.atomAddNeighbor(i.bonds.get(this.data.bid).hb1),i.atomAddNeighbor(i.bonds.get(this.data.bid).hb2),a.notifyBondAdded(this.data.bid)},this._invert=function(){var t=new BondDelete;return t.data=this.data,t}}function BondDelete(t){this.data={bid:t,bond:null,begin:null,end:null},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;this.data.bond||(this.data.bond=i.bonds.get(this.data.bid),this.data.begin=this.data.bond.begin,this.data.end=this.data.bond.end),e.invalidateBond(this.data.bid),a.notifyBondRemoved(this.data.bid);var r=i.bonds.get(this.data.bid);[r.hb1,r.hb2].each(function(t){var e=i.halfBonds.get(t),a=i.atoms.get(e.begin),r=a.neighbors.indexOf(t),d=(r+a.neighbors.length-1)%a.neighbors.length,n=(r+1)%a.neighbors.length;i.setHbNext(a.neighbors[d],a.neighbors[n]),a.neighbors.splice(r,1)},this),i.halfBonds.unset(r.hb1),i.halfBonds.unset(r.hb2),i.bonds.remove(this.data.bid)},this._invert=function(){var t=new BondAdd;return t.data=this.data,t}}function BondAttr(t,e,a){this.data={bid:t,attribute:e,value:a},this.data2=null,this._execute=function(t){var e=t.render.ctab.molecule.bonds.get(this.data.bid);this.data2||(this.data2={bid:this.data.bid,attribute:this.data.attribute,value:e[this.data.attribute]}),e[this.data.attribute]=this.data.value,t.render.invalidateBond(this.data.bid),"type"==this.data.attribute&&t.render.invalidateLoop(this.data.bid)},this._isDummy=function(t){return t.render.ctab.molecule.bonds.get(this.data.bid)[this.data.attribute]==this.data.value},this._invert=function(){var t=new BondAttr;return t.data=this.data2,t.data2=this.data,t}}function FragmentAdd(t){this.frid=Object.isUndefined(t)?null:t,this._execute=function(t){var e=t.render.ctab,a=e.molecule,i=new chem.Struct.Fragment;null==this.frid?this.frid=a.frags.add(i):a.frags.set(this.frid,i),e.frags.set(this.frid,new rnd.ReFrag(i))},this._invert=function(){return new FragmentDelete(this.frid)}}function FragmentDelete(t){this.frid=t,this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;e.invalidateItem("frags",this.frid,1),a.frags.unset(this.frid),i.frags.remove(this.frid)},this._invert=function(){return new FragmentAdd(this.frid)}}function RGroupAttr(t,e,a){this.data={rgid:t,attribute:e,value:a},this.data2=null,this._execute=function(t){var e=t.render.ctab.molecule.rgroups.get(this.data.rgid);this.data2||(this.data2={rgid:this.data.rgid,attribute:this.data.attribute,value:e[this.data.attribute]}),e[this.data.attribute]=this.data.value,t.render.invalidateItem("rgroups",this.data.rgid)},this._isDummy=function(t){return t.render.ctab.molecule.rgroups.get(this.data.rgid)[this.data.attribute]==this.data.value},this._invert=function(){var t=new RGroupAttr;return t.data=this.data2,t.data2=this.data,t}}function RGroupFragment(t,e,a){this.rgid_new=t,this.rg_new=a,this.rgid_old=null,this.rg_old=null,this.frid=e,this._execute=function(t){var e=t.render.ctab,a=e.molecule;if(this.rgid_old=this.rgid_old||chem.Struct.RGroup.findRGroupByFragment(a.rgroups,this.frid),this.rg_old=this.rgid_old?a.rgroups.get(this.rgid_old):null,this.rg_old&&(this.rg_old.frags.remove(this.rg_old.frags.keyOf(this.frid)),e.clearVisel(e.rgroups.get(this.rgid_old).visel),0==this.rg_old.frags.count()?(e.rgroups.unset(this.rgid_old),a.rgroups.unset(this.rgid_old),e.markItemRemoved()):e.markItem("rgroups",this.rgid_old,1)),this.rgid_new){var i=a.rgroups.get(this.rgid_new);i?e.markItem("rgroups",this.rgid_new,1):(i=this.rg_new||new chem.Struct.RGroup,a.rgroups.set(this.rgid_new,i),e.rgroups.set(this.rgid_new,new rnd.ReRGroup(i))),i.frags.add(this.frid)}},this._invert=function(){return new RGroupFragment(this.rgid_old,this.frid,this.rg_old)}}function RxnArrowAdd(t){this.data={arid:null,pos:t},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;Object.isNumber(this.data.arid)?i.rxnArrows.set(this.data.arid,new chem.Struct.RxnArrow):this.data.arid=i.rxnArrows.add(new chem.Struct.RxnArrow),a.notifyRxnArrowAdded(this.data.arid),i._rxnArrowSetPos(this.data.arid,new Vec2(this.data.pos)),e.invalidateItem("rxnArrows",this.data.arid,1)},this._invert=function(){var t=new RxnArrowDelete;return t.data=this.data,t}}function RxnArrowDelete(t){this.data={arid:t,pos:null},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;this.data.pos||(this.data.pos=e.rxnArrowGetPos(this.data.arid)),a.notifyRxnArrowRemoved(this.data.arid),i.rxnArrows.remove(this.data.arid)},this._invert=function(){var t=new RxnArrowAdd;return t.data=this.data,t}}function RxnArrowMove(t,e,a){this.data={id:t,d:e,noinvalidate:a},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=this.data.id,d=this.data.d;i.rxnArrows.get(r).pp.add_(d),a.rxnArrows.get(r).visel.translate(e.ps(d)),this.data.d=d.negated(),this.data.noinvalidate||t.render.invalidateItem("rxnArrows",r,1)},this._invert=function(){var t=new RxnArrowMove;return t.data=this.data,t}}function RxnPlusAdd(t){this.data={plid:null,pos:t},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;Object.isNumber(this.data.plid)?i.rxnPluses.set(this.data.plid,new chem.Struct.RxnPlus):this.data.plid=i.rxnPluses.add(new chem.Struct.RxnPlus),a.notifyRxnPlusAdded(this.data.plid),i._rxnPlusSetPos(this.data.plid,new Vec2(this.data.pos)),e.invalidateItem("rxnPluses",this.data.plid,1)},this._invert=function(){var t=new RxnPlusDelete;return t.data=this.data,t}}function RxnPlusDelete(t){this.data={plid:t,pos:null},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;this.data.pos||(this.data.pos=e.rxnPlusGetPos(this.data.plid)),a.notifyRxnPlusRemoved(this.data.plid),i.rxnPluses.remove(this.data.plid)},this._invert=function(){var t=new RxnPlusAdd;return t.data=this.data,t}}function RxnPlusMove(t,e,a){this.data={id:t,d:e,noinvalidate:a},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule,r=this.data.id,d=this.data.d;i.rxnPluses.get(r).pp.add_(d),a.rxnPluses.get(r).visel.translate(e.ps(d)),this.data.d=d.negated(),this.data.noinvalidate||t.render.invalidateItem("rxnPluses",r,1)},this._invert=function(){var t=new RxnPlusMove;return t.data=this.data,t}}function SGroupDataMove(t,e){this.data={id:t,d:e},this._execute=function(t){ui.ctab.sgroups.get(this.data.id).pp.add_(this.data.d),this.data.d=this.data.d.negated(),t.render.invalidateItem("sgroupData",this.data.id,1)},this._invert=function(){var t=new SGroupDataMove;return t.data=this.data,t}}function CanvasLoad(t){this.data={ctab:t,norescale:!1},this._execute=function(t){var e=t.render;e.ctab.clearVisels();var a=ui.ctab;ui.ctab=this.data.ctab,e.setMolecule(ui.ctab,this.data.norescale),this.data.ctab=a,this.data.norescale=!0},this._invert=function(){var t=new CanvasLoad;return t.data=this.data,t}}function ChiralFlagAdd(t){this.data={pos:t},this._execute=function(e){var a=e.render,i=a.ctab,r=i.molecule;if(i.chiralFlags.count()>0)throw new Error("Cannot add more than one Chiral flag");i.chiralFlags.set(0,new rnd.ReChiralFlag(t)),r.isChiral=!0,a.invalidateItem("chiralFlags",0,1)},this._invert=function(){var t=new ChiralFlagDelete;return t.data=this.data,t}}function ChiralFlagDelete(){this.data={pos:null},this._execute=function(t){var e=t.render,a=e.ctab,i=a.molecule;if(a.chiralFlags.count()<1)throw new Error("Cannot remove chiral flag");a.clearVisel(a.chiralFlags.get(0).visel),this.data.pos=a.chiralFlags.get(0).pp,a.chiralFlags.unset(0),i.isChiral=!1},this._invert=function(){var t=new ChiralFlagAdd(this.data.pos);return t.data=this.data,t}}function ChiralFlagMove(t){this.data={d:t},this._execute=function(t){var e=t.render;e.ctab.chiralFlags.get(0).pp.add_(this.data.d),this.data.d=this.data.d.negated(),e.invalidateItem("chiralFlags",0,1)},this._invert=function(){var t=new ChiralFlagMove;return t.data=this.data,t}}var Vec2=require("../util/vec2"),Set=require("../util/set");require("../chem"),require("../rnd");var ui=global.ui,chem=global.chem,rnd=global.rnd;AtomAdd.prototype=new Base,AtomDelete.prototype=new Base,AtomAttr.prototype=new Base,AtomMove.prototype=new Base,BondMove.prototype=new Base,LoopMove.prototype=new Base,SGroupAtomAdd.prototype=new Base,SGroupAtomRemove.prototype=new Base,SGroupAttr.prototype=new Base,SGroupCreate.prototype=new Base,SGroupDelete.prototype=new Base,SGroupAddToHierarchy.prototype=new Base,SGroupRemoveFromHierarchy.prototype=new Base,BondAdd.prototype=new Base,BondDelete.prototype=new Base,BondAttr.prototype=new Base,FragmentAdd.prototype=new Base,FragmentDelete.prototype=new Base,RGroupAttr.prototype=new Base,RGroupFragment.prototype=new Base,RxnArrowAdd.prototype=new Base,RxnArrowDelete.prototype=new Base,RxnArrowMove.prototype=new Base,RxnPlusAdd.prototype=new Base,RxnPlusDelete.prototype=new Base,RxnPlusMove.prototype=new Base,SGroupDataMove.prototype=new Base,CanvasLoad.prototype=new Base,ChiralFlagAdd.prototype=new Base,ChiralFlagDelete.prototype=new Base,ChiralFlagMove.prototype=new Base,module.exports={AtomAdd:AtomAdd,AtomDelete:AtomDelete,AtomAttr:AtomAttr,AtomMove:AtomMove,BondMove:BondMove,LoopMove:LoopMove,SGroupAtomAdd:SGroupAtomAdd,SGroupAtomRemove:SGroupAtomRemove,SGroupAttr:SGroupAttr,SGroupCreate:SGroupCreate,SGroupDelete:SGroupDelete,SGroupAddToHierarchy:SGroupAddToHierarchy,SGroupRemoveFromHierarchy:SGroupRemoveFromHierarchy,BondAdd:BondAdd,BondDelete:BondDelete,BondAttr:BondAttr,FragmentAdd:FragmentAdd,FragmentDelete:FragmentDelete,RGroupAttr:RGroupAttr,RGroupFragment:RGroupFragment,RxnArrowAdd:RxnArrowAdd,RxnArrowDelete:RxnArrowDelete,RxnArrowMove:RxnArrowMove,RxnPlusAdd:RxnPlusAdd,RxnPlusDelete:RxnPlusDelete,RxnPlusMove:RxnPlusMove,SGroupDataMove:SGroupDataMove,CanvasLoad:CanvasLoad,ChiralFlagAdd:ChiralFlagAdd,ChiralFlagDelete:ChiralFlagDelete,ChiralFlagMove:ChiralFlagMove}; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"../chem":11,"../rnd":21,"../util/set":42,"../util/vec2":43}],36:[function(require,module,exports){ +module.exports=[{name:"benzene",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 6 6 0 0 0 999 V2000\n 0.8660 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7320 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7320 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.8660 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 2 0 0 0\n 3 4 1 0 0 0\n 4 5 2 0 0 0\n 5 6 1 0 0 0\n 6 1 2 0 0 0\nM END\n",bid:0,aid:0},{name:"cyclopentadiene",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 5 5 0 0 0 999 V2000\n 0.0000 1.4257 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.8090 0.8379 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.5000 -0.1132 0.0000 C 0 0 0 0 0 0 0 0 0\n -0.5000 -0.1132 0.0000 C 0 0 0 0 0 0 0 0 0\n -0.8090 0.8379 0.0000 C 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 2 0 0 0\n 3 4 1 0 0 0\n 4 5 2 0 0 0\n 5 1 1 0 0 0\nM END\n",bid:0,aid:0},{name:"cyclohexane",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 6 6 0 0 0 999 V2000\n 0.8660 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7320 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7320 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.8660 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 6 1 0 0 0\n 6 1 1 0 0 0\nM END\n",bid:0,aid:0},{name:"cyclopentane",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 5 5 0 0 0 999 V2000\n 0.8090 1.5389 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.6180 0.9511 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.3090 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.3090 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 0.9511 0.0000 C 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 3 4 1 0 0 0\n 4 5 1 0 0 0\n 5 1 1 0 0 0\nM END\n",bid:0,aid:0},{name:"cyclopropane",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 3 3 0 0 0 999 V2000\n -3.2250 -0.2750 0.0000 C 0 0 0 0 0 0 0 0 0\n -2.2250 -0.2750 0.0000 C 0 0 0 0 0 0 0 0 0\n -2.7250 0.5910 0.0000 C 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 2 3 1 0 0 0\n 1 3 1 0 0 0\nM END\n",bid:0,aid:0},{name:"cyclobutane",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 4 4 0 0 0 999 V2000\n -3.8250 1.5500 0.0000 C 0 0 0 0 0 0 0 0 0\n -3.8250 0.5500 0.0000 C 0 0 0 0 0 0 0 0 0\n -2.8250 1.5500 0.0000 C 0 0 0 0 0 0 0 0 0\n -2.8250 0.5500 0.0000 C 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0\n 1 3 1 0 0 0\n 3 4 1 0 0 0\n 4 2 1 0 0 0\nM END\n",bid:0,aid:0},{name:"cycloheptane",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 7 7 0 0 0 999 V2000\n 0.0000 1.6293 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.7835 2.2465 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7559 2.0242 0.0000 C 0 0 0 0 0 0 0 0 0\n 2.1897 1.1289 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 0.6228 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7566 0.2224 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.7835 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 6 7 1 0 0 0\n 5 7 1 0 0 0\n 1 5 1 0 0 0\n 4 6 1 0 0 0\n 3 4 1 0 0 0\n 2 3 1 0 0 0\n 1 2 1 0 0 0\nM END\n",bid:0,aid:0},{name:"cyclooctane",molfile:"\n Ketcher 11161218352D 1 1.00000 0.00000 0\n\n 8 8 0 0 0 999 V2000\n 0.0000 0.7053 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.0000 1.7078 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.7053 2.4131 0.0000 C 0 0 0 0 0 0 0 0 0\n 0.7056 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7079 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0\n 2.4133 0.7053 0.0000 C 0 0 0 0 0 0 0 0 0\n 2.4133 1.7078 0.0000 C 0 0 0 0 0 0 0 0 0\n 1.7079 2.4131 0.0000 C 0 0 0 0 0 0 0 0 0\n 8 3 1 0 0 0\n 7 8 1 0 0 0\n 6 7 1 0 0 0\n 5 6 1 0 0 0\n 4 5 1 0 0 0\n 1 4 1 0 0 0\n 2 3 1 0 0 0\n 1 2 1 0 0 0\nM END\n",bid:0,aid:0}]; + +},{}],37:[function(require,module,exports){ +function ajax(e,t){var r=getXHR(),n=e.headers||{};r.open(e.method,e.url,!!t,e.user,e.password);for(var u in n)n.hasOwnProperty(u)&&r.setRequestHeader(u,n[u]);if("function"==typeof e.config){var a=e.config(r,e);void 0!==a&&(r=a)}return e.timeout>0&&setTimeout(function(){r.status=-1,r.abort()},e.timeout),t&&(r.onreadystatechange=function(){4===r.readyState&&t(r)}),r.send(e.data),r}function successful(e){return e.status>=200&&e.status<300}function queryString(e){var t=[];for(var r in e)e.hasOwnProperty(r)&&t.push(encodeURIComponent(r)+"="+encodeURIComponent(e[r]));return t.join("&")}function request(e){var t=util.extend({method:"GET",headers:{},timeout:6e3},util.isObject(e)?e:{url:e});if(util.isObject(t.data)&&(t.data=JSON.stringify(t.data),t.headers["Content-Type"]="application/json; charset=utf-8"),t.params&&(t.url=t.url+(t.url.indexOf("?")<0?"?":"&")+queryString(t.params)),!t.sync)return new Promise(function(e,r){ajax(t,function(t){(successful(t)?e:r)(t)})});var r=ajax(t);if(!successful(r))throw r;return r}var getXHR=require("xhrpolyfill"),Promise=require("promise-polyfill"),util=require("./index.js");module.exports=request; + +},{"./index.js":39,"promise-polyfill":3,"xhrpolyfill":6}],38:[function(require,module,exports){ +var util=require("./index"),Vec2=require("./vec2"),Box2Abs=function(){1==arguments.length&&"min"in arguments[0]&&"max"in arguments[0]&&(this.p0=arguments[0].min,this.p1=arguments[0].max),2==arguments.length&&arguments[0]instanceof Vec2&&arguments[1]instanceof Vec2?(this.p0=arguments[0],this.p1=arguments[1]):4==arguments.length?(this.p0=new Vec2(arguments[0],arguments[1]),this.p1=new Vec2(arguments[2],arguments[3])):0==arguments.length?(this.p0=new Vec2,this.p1=new Vec2):new Error("Box2Abs constructor only accepts 4 numbers or 2 vectors or no arguments!")};Box2Abs.prototype.toString=function(){return this.p0.toString()+" "+this.p1.toString()},Box2Abs.fromRelBox=function(t){return util.assertDefined(t),new Box2Abs(t.x,t.y,t.x+t.width,t.y+t.height)},Box2Abs.prototype.clone=function(){return new Box2Abs(this.p0,this.p1)},Box2Abs.union=function(t,e){return util.assertDefined(t),util.assertDefined(e),new Box2Abs(Vec2.min(t.p0,e.p0),Vec2.max(t.p1,e.p1))},Box2Abs.prototype.extend=function(t,e){return util.assertDefined(t),e=e||t,new Box2Abs(this.p0.sub(t),this.p1.add(e))},Box2Abs.prototype.include=function(t){return util.assertDefined(t),new Box2Abs(this.p0.min(t),this.p1.max(t))},Box2Abs.prototype.contains=function(t,e){return e=(e||0)-0,util.assertDefined(t),t.x>=this.p0.x-e&&t.x<=this.p1.x+e&&t.y>=this.p0.y-e&&t.y<=this.p1.y+e},Box2Abs.prototype.translate=function(t){return util.assertDefined(t),new Box2Abs(this.p0.add(t),this.p1.add(t))},Box2Abs.prototype.transform=function(t,e){return util.assert(!util.isNullOrUndefined(t)),new Box2Abs(t.call(e,this.p0),t.call(e,this.p1))},Box2Abs.prototype.sz=function(){return this.p1.sub(this.p0)},Box2Abs.prototype.centre=function(){return Vec2.centre(this.p0,this.p1)},Box2Abs.prototype.pos=function(){return this.p0},module.exports=Box2Abs; + +},{"./index":39,"./vec2":43}],39:[function(require,module,exports){ +function find(e,n){for(var t=0;t126||e.charCodeAt(n)<32?t+="\\u"+function(e,n){for(var t=e.toString(16).toUpperCase();t.length=0;)n[t]=e[t];return n},isEmpty=function(e){for(var n in e)if(e.hasOwnProperty(n))return!1;return!0},stopEventPropagation=function(e){if("stopPropagation"in e)e.stopPropagation();else{if(!("cancelBubble"in e))throw Error("Browser unrecognized");e.cancelBubble=!0}},preventDefault=function(e){return"preventDefault"in e&&e.preventDefault(),Prototype.Browser.IE&&(e.returnValue=!1,e.keyCode=0),!1},setElementTextContent=function(e,n){if("textContent"in e)e.textContent=n;else{if(!("innerText"in e))throw Error("Browser unrecognized");e.innerText=n}},getElementTextContent=function(e){if("textContent"in e)return e.textContent;if("innerText"in e)return e.innerText;throw Error("Browser unrecognized")},stringPadded=function(e,n,t){for(var r=e+"",i="";r.length+i.lengthn)throw new Error("number does not fit");return stringPadded(r,n)},paddedInt=function(e,n){var t=e.toFixed(0);if(t.length>n)throw new Error("number does not fit");return stringPadded(t,n)},arrayAddIfMissing=function(e,n){for(var t=0;t=0;)e.splice(t,1),r+=1,t=e.indexOf(n);return r},listNextRotate=function(e,n){return e[(e.indexOf(n)+1)%e.length]},extend=function(e,n){for(var t in n)n.hasOwnProperty(t)&&(e[t]=n[t]);return e},isObject=function(e){return e===Object(e)};module.exports={tfx:tfx,each:each,find:find,findIndex:findIndex,findAll:findAll,array:array,isEmpty:isEmpty,stopEventPropagation:stopEventPropagation,preventDefault:preventDefault,setElementTextContent:setElementTextContent,getElementTextContent:getElementTextContent,stringPadded:stringPadded,normalizeNewlines:normalizeNewlines,splitNewlines:splitNewlines,unicodeLiteral:unicodeLiteral,idList:idList,mapArray:mapArray,arrayMax:arrayMax,arrayMin:arrayMin,map:map,apply:apply,ifDef:ifDef,ifDefList:ifDefList,identityMap:identityMap,strip:strip,stripRight:stripRight,stripQuotes:stripQuotes,paddedFloat:paddedFloat,paddedInt:paddedInt,arrayAddIfMissing:arrayAddIfMissing,assert:assert,assertDefined:assertDefined,isUndefined:isUndefined,isNull:isNull,isNullOrUndefined:isNullOrUndefined,arrayRemoveByValue:arrayRemoveByValue,listNextRotate:listNextRotate,extend:extend,isObject:isObject}; + +},{}],40:[function(require,module,exports){ +var util=require("./index"),Map=function(t){if(void 0!==t&&t.constructor!==Object)throw Error('Passed object is not an instance of "Object"!');this._obj=t||{},this._count=0};Map.prototype.each=function(t,o){var i,r,n;for(i in this._obj)n=parseInt(i,10),r=this._obj[i],isNaN(n)||(i=n),t.call(o,i,r)},Map.prototype.map=function(t,o){var i=new Map;return this.each(function(r,n){i.set(r,t.call(o,r,n))},this),i},Map.prototype.find=function(t,o){var i,r,n;for(i in this._obj)if(r=parseInt(i,10),n=this._obj[i],isNaN(r)||(i=r),t.call(o,i,n))return i},Map.prototype.findAll=function(t,o){var i,r,n,e=[];for(i in this._obj)r=parseInt(i,10),n=this._obj[i],isNaN(r)||(i=r),t.call(o,i,n)&&e.push(i);return e},Map.prototype.keys=function(){var t,o=[];for(t in this._obj)o.push(t);return o},Map.prototype.ikeys=function(){var t=[];for(var o in this._obj)t.push(o-0);return t},Map.prototype.set=function(t,o){var i;return this._count+=(void 0!==o?1:0)-(void 0!==this._obj[t]?1:0),void 0===o?(i=this._obj[t],delete this._obj[t],i):(this._obj[t]=o,o)},Map.prototype.get=function(t){if(this._obj[t]!==Object.prototype[t])return this._obj[t]},Map.prototype.has=function(t){return this._obj[t]!==Object.prototype[t]},Map.prototype.unset=function(t){return this.set(t,void 0)},Map.prototype.update=function(t){for(var o in t)this.set(o,t[o])},Map.prototype.clear=function(){this._obj={},this._count=0},Map.prototype.count=function(){return this._count},Map.prototype.idList=function(){return util.idList(this._obj)},Map.prototype.keyOf=function(t){for(var o in this._obj)if(this._obj[o]===t)return o},module.exports=Map; + +},{"./index":39}],41:[function(require,module,exports){ +var Map=require("./map.js"),Pool=function(){this._map=new Map,this._nextId=0};Pool.prototype.newId=function(){return this._nextId++},Pool.prototype.add=function(t){var o=this._nextId++;return this._map.set(o,t),o},Pool.prototype.set=function(t,o){this._map.set(t,o)},Pool.prototype.get=function(t){return this._map.get(t)},Pool.prototype.has=function(t){return this._map.has(t)},Pool.prototype.remove=function(t){return this._map.unset(t)},Pool.prototype.clear=function(){this._map.clear()},Pool.prototype.keys=function(){return this._map.keys()},Pool.prototype.ikeys=function(){return this._map.ikeys()},Pool.prototype.each=function(t,o){this._map.each(t,o)},Pool.prototype.map=function(t,o){return this._map.map(t,o)},Pool.prototype.find=function(t,o){return this._map.find(t,o)},Pool.prototype.count=function(){return this._map.count()},Pool.prototype.keyOf=function(t){return this._map.keyOf(t)},module.exports=Pool; + +},{"./map.js":40}],42:[function(require,module,exports){ +var Set={empty:function(){return{}},single:function(t){var r={};return Set.add(r,t),r},size:function(t){var r=0;for(var n in t)t[n]!==Object.prototype[n]&&r++;return r},contains:function(t,r){return void 0!==t[r]&&t[r]!==Object.prototype[r]},subset:function(t,r){for(var n in t)if(t[n]!==Object.prototype[n]&&r[n]!==t[n])return!1;return!0},intersection:function(t,r){var n={};for(var e in t)t[e]!==Object.prototype[e]&&r[e]===t[e]&&Set.add(n,e);return n},disjoint:function(t,r){for(var n in t)if(t[n]!==Object.prototype[n]&&r[n]===t[n])return!1;return!0},eq:function(t,r){return Set.subset(t,r)&&Set.subset(r,t)},each:function(t,r,n){for(var e in t)t[e]!==Object.prototype[e]&&r.call(n,t[e])},filter:function(t,r,n){var e={};for(var o in t)t[o]!==Object.prototype[o]&&r.call(n,t[o])&&(e[t[o]]=t[o]);return e},pick:function(t){for(var r in t)if(t[r]!==Object.prototype[r])return t[r];return null},list:function(t){var r=[];for(var n in t)t[n]!==Object.prototype[n]&&r.push(t[n]);return r},add:function(t,r){t[r]=r},mergeIn:function(t,r){Set.each(r,function(r){Set.add(t,r)})},remove:function(t,r){var n=t[r];return delete t[r],n},clone:function(t){var r={};return Set.mergeIn(r,t),r},fromList:function(t){var r={};if(t)for(var n=0;n0?(o<0||c[o]c[u]?(f=u,y=o):(f=o,y=u),c[f]+Math.abs(s[f])*(c[y]-c[f])/(Math.abs(s[f])+Math.abs(s[y]))},module.exports=Vec2; + +},{"./index":39}]},{},[18])(18) +}); \ No newline at end of file diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.py b/public/lib/ketcher-2.0.0-alpha.3/ketcher.py new file mode 100755 index 000000000..66faf64cd --- /dev/null +++ b/public/lib/ketcher-2.0.0-alpha.3/ketcher.py @@ -0,0 +1,330 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import sys +from os import path, getcwd +from mimetypes import guess_type +from cgi import FieldStorage +from wsgiref.util import FileWrapper +from wsgiref.headers import Headers + +from base64 import b64encode + +class application(object): + # don't serve static by default + static_serve = False + static_alias = { '' : 'ketcher.html' } + static_root = None + + indigo = None + indigo_inchi = None + + def __init__(self, environ, start_response): + self.path = environ['PATH_INFO'].strip('/') + self.method = environ['REQUEST_METHOD'] + self.content_type = environ.get('CONTENT_TYPE', '') + self.fields = FieldStorage(fp=environ['wsgi.input'], + environ=environ, keep_blank_values=True) + self.FileWrapper = environ.get('wsgi.file_wrapper', FileWrapper) + self.headers = Headers([]) + + if self.static_serve: + self.headers['Access-Control-Allow-Origin'] = '*' + + route = getattr(self, 'on_' + self.path, None) + if route is None: + route = self.serve_static if self.method == 'GET' and \ + self.static_serve else self.notsupported + + status = "200 OK" + try: + self.response = route() + except self.HttpException as e: + status = e.args[0] + self.response = [e.args[1]] + + self.headers.setdefault('Content-Type', 'text/plain') + start_response(status, self.headers.items()) + + def __iter__(self): + for chunk in self.response: + yield chunk if sys.version_info.major < 3 or \ + not hasattr(chunk, 'encode') else chunk.encode() + + def notsupported(self): + raise self.HttpException("405 Method Not Allowed", + "Request not supported") + + def indigo_required(method): + def wrapper(self, **args): + if not self.indigo: + raise self.HttpException("501 Not Implemented", + "Indigo libraries are not found") + try: + return method(self, **args) + except indigo.IndigoException as e: + message = str(sys.exc_info()[1]) + if 'indigoLoad' in message: # error on load + message = "Cannot load the specified " + \ + "structure: %s " % str(e) + raise self.HttpException("400 Bad Request", + message) + return wrapper + + @indigo_required + def on_knocknock(self): + return ["You are welcome!"] + + @indigo_required + def on_layout(self): + moldata = None + if self.method == 'GET' and 'smiles' in self.fields: + moldata = self.fields.getfirst('smiles') + elif self.is_form_request() and 'moldata' in self.fields: + moldata = self.fields.getfirst('moldata') + selective = 'selective' in self.fields + if moldata: + if '>>' in moldata or moldata.startswith('$RXN'): + rxn = self.indigo.loadQueryReaction(moldata) + if selective: + for mol in rxn.iterateMolecules(): + self.selective_layout(mol) + else: + rxn.layout() + return ["Ok.\n", + rxn.rxnfile()] + elif moldata.startswith('InChI'): + mol = self.indigo_inchi.loadMolecule(moldata) + mol.layout() + return ["Ok.\n", + mol.molfile()] + else: + mol = self.indigo.loadQueryMolecule(moldata) + if selective: + for rg in mol.iterateRGroups(): + for frag in rg.iterateRGroupFragments(): + self.selective_layout(frag) + self.selective_layout(mol) + else: + mol.layout() + return ["Ok.\n", + mol.molfile()] + self.notsupported() + + @indigo_required + def on_smiles(self): + moldata = self.fields.getfirst('moldata') + if moldata: + if '>>' in moldata or moldata.startswith('$RXN'): + rxn = self.indigo.loadQueryReaction(moldata) + return ["Ok.\n", + rxn.smiles()] + elif moldata.startswith('InChI'): + mol = self.indigo_inchi.loadMolecule(moldata) + return ["Ok.\n", + mol.smiles()] + else: + mol = self.indigo.loadQueryMolecule(moldata) + return ["Ok.\n", + mol.smiles()] + self.notsupported() + + @indigo_required + def on_getinchi(self): + md, is_rxn = self.load_moldata() + inchi = self.indigo_inchi.getInchi(md) + return ["Ok.\n", inchi] + + @indigo_required + def on_getmolfile(self): + md, is_rxn = self.load_moldata() + return ["Ok.\n", md.molfile()] + + @indigo_required + def on_automap(self): + moldata = None + if self.method == 'GET' and 'smiles' in self.fields: + moldata = self.fields.getfirst('smiles') + elif self.is_form_request() and 'moldata' in self.fields: + moldata = self.fields.getfirst('moldata') + + if moldata: + mode = self.fields.getfirst('mode', 'discard') + rxn = self.indigo.loadQueryReaction(moldata) + if not moldata.startswith('$RXN'): + rxn.layout() + rxn.automap(mode) + return ["Ok.\n", + rxn.rxnfile()] + self.notsupported() + + @indigo_required + def on_aromatize(self): + try: + md, is_rxn = self.load_moldata() + except: + message = str(sys.exc_info()[1]) + if message.startswith("\"molfile loader:") and \ + message.endswith("queries\""): # hack to avoid user confusion + md, is_rxn = self.load_moldata(True) + else: + raise + md.aromatize() + return ["Ok.\n", + md.rxnfile() if is_rxn else md.molfile()] + + @indigo_required + def on_dearomatize(self): + try: + md, is_rxn = self.load_moldata() + except: # TODO: test for query features presence + raise self.HttpException("400 Bad Request", + "Molecules and reactions " + \ + "containing query features " + \ + "cannot be dearomatized yet.") + md.dearomatize() + return ["Ok.\n", + md.rxnfile() if is_rxn else md.molfile()] + + @indigo_required + def on_calculate_cip(self): + application.indigo.setOption('molfile-saving-add-stereo-desc', True) + try: + md, is_rxn = self.load_moldata() + except: + message = str(sys.exc_info()[1]) + if message.startswith("\"molfile loader:") and \ + message.endswith("queries\""): # hack to avoid user confusion + md, is_rxn = self.load_moldata(True) + else: + raise + result = md.rxnfile() if is_rxn else md.molfile() + application.indigo.setOption('molfile-saving-add-stereo-desc', False) + return ["Ok.\n", + result] + + def on_open(self): + if self.is_form_request(): + self.headers.add_header('Content-Type', 'text/html') + return [''] + self.notsupported() + + def on_save(self): + if self.is_form_request(): + type, data = self.fields.getfirst('filedata').split('\n', 1) + type = type.strip() + if type == 'smi': + self.headers.add_header('Content-Type', + 'chemical/x-daylight-smiles') + elif type == 'mol': + if data.startswith('$RXN'): + type = 'rxn' + self.headers.add_header('Content-Type', + 'chemical/x-mdl-%sfile' % type) + + self.headers.add_header('Content-Length', str(len(data))) + self.headers.add_header('Content-Disposition', 'attachment', + filename='ketcher.%s' % type) + return [data] + self.notsupported() + + class HttpException(Exception): pass + def load_moldata(self, is_query=False): + moldata = self.fields.getfirst('moldata') + is_rxn = False + if moldata.startswith('$RXN'): + if is_query: + md = self.indigo.loadQueryReaction(moldata) + else: + md = self.indigo.loadReaction(moldata) + is_rxn = True + elif moldata.startswith('InChI'): + md = self.indigo_inchi.loadMolecule(moldata) + md.layout() + else: + if is_query: + md = self.indigo.loadQueryMolecule(moldata) + else: + md = self.indigo.loadMolecule(moldata) + return md, is_rxn + + def selective_layout(self, mol): + dsgs = [dsg for dsg in mol.iterateDataSGroups() \ + if dsg.description() == '_ketcher_selective_layout' and \ + dsg.data() == '1'] + atoms = sorted([atom.index() for dsg in dsgs \ + for atom in dsg.iterateAtoms()]) + for dsg in dsgs: + dsg.remove() + mol.getSubmolecule(atoms).layout() + return mol + + def serve_static(self): + root = path.realpath(self.static_root or getcwd()) + fpath = self.static_alias.get(self.path, self.path) + fpath = path.realpath(path.join(root, fpath)) + + if not fpath.startswith(root + path.sep) or not path.isfile(fpath) \ + or fpath == path.realpath(__file__): + raise self.HttpException("404 Not Found", + "Requested file isn't accessible") + + self.headers['Content-Type'] = guess_type(fpath)[0] or 'text/plain' + try: + fd = open(fpath, 'rb') + return self.FileWrapper(fd) if self.method == 'GET' else [''] + except (IOError, OSError): + raise self.HttpException("402 Payment Required", # or 403, hmm.. + "Must get more money for overtime") + + def is_form_request(self): + return self.method == 'POST' and \ + (self.content_type.startswith('application/x-www-form-urlencoded') + or self.content_type.startswith('multipart/form-data')) + +try: + import indigo + import indigo_inchi + application.indigo = indigo.Indigo() + application.indigo_inchi = indigo_inchi.IndigoInchi(application.indigo) + application.indigo.setOption('ignore-stereochemistry-errors', 'true') +except: + pass + +if __name__ == '__main__': + import socket + from wsgiref.simple_server import make_server + + def parse_args(): + dir = sys.argv[1] if len(sys.argv) > 1 else '' + addr = sys.argv[2] if len(sys.argv) > 2 else '' + res = addr.rsplit(':', 1) + return dir, \ + res[0] if len(res) > 1 else '0.0.0.0', \ + int(res[-1] or 8080) + def usage(): + progname = sys.argv[0] + if not progname.startswith('./'): + progname = 'python ' + progname + print( "USAGE:\n %s [static_dir [port|address:port]]\n" % progname) + + if not application.indigo: + print("WARNING: Indigo is not found. Server-side functionality " + \ + "will not be available") + try: + dir, address, port = parse_args() + application.static_serve = True # allow to serve static + application.static_root = dir # in standalone python-server mode + httpd = make_server(address, port, application) + print("Serving on %s:%d..." % (address, port)) + httpd.serve_forever() + except ValueError: + usage() + except (socket.error, socket.gaierror, socket.herror, OSError) as e: + print("Server error: %s" % e.args[1]) + usage() + except KeyboardInterrupt: + pass diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.svg b/public/lib/ketcher-2.0.0-alpha.3/ketcher.svg new file mode 100644 index 000000000..9594ba37b --- /dev/null +++ b/public/lib/ketcher-2.0.0-alpha.3/ketcher.svg @@ -0,0 +1,138 @@ + + + +Copyright (C) 2017 by original authors @ fontello.com + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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b="className",a="for",c=document.createElement("div");c.setAttribute(b,"x");if(c.className!=="x"){c.setAttribute("class","x");if(c.className==="x"){b="class"}}c=null;c=document.createElement("label");c.setAttribute(a,"x");if(c.htmlFor!=="x"){c.setAttribute("htmlFor","x");if(c.htmlFor==="x"){a="htmlFor"}}c=null;return{read:{names:{"class":b,className:b,"for":a,htmlFor:a},values:{_getAttr:function(d,e){return d.getAttribute(e)},_getAttr2:function(d,e){return d.getAttribute(e,2)},_getAttrNode:function(d,f){var e=d.getAttributeNode(f);return e?e.value:""},_getEv:(function(){var d=document.createElement("div"),g;d.onclick=Prototype.emptyFunction;var e=d.getAttribute("onclick");if(String(e).indexOf("{")>-1){g=function(f,h){h=f.getAttribute(h);if(!h){return null}h=h.toString();h=h.split("{")[1];h=h.split("}")[0];return h.strip()}}else{if(e===""){g=function(f,h){h=f.getAttribute(h);if(!h){return null}return h.strip()}}}d=null;return g})(),_flag:function(d,e){return 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f=c.next(),a=Element._getContentFromAnonymousElement(b,e.stripScripts());d.removeChild(c);if(f){a.each(function(g){d.insertBefore(g,f)})}else{a.each(function(g){d.appendChild(g)})}}else{c.outerHTML=e.stripScripts()}e.evalScripts.bind(e).defer();return c}}Element._returnOffset=function(b,c){var a=[b,c];a.left=b;a.top=c;return a};Element._getContentFromAnonymousElement=function(e,d,f){var g=new Element("div"),c=Element._insertionTranslations.tags[e];var a=false;if(c){a=true}else{if(f){a=true;c=["","",0]}}if(a){g.innerHTML=" "+c[0]+d+c[1];g.removeChild(g.firstChild);for(var b=c[2];b--;){g=g.firstChild}}else{g.innerHTML=d}return $A(g.childNodes)};Element._insertionTranslations={before:function(a,b){a.parentNode.insertBefore(b,a)},top:function(a,b){a.insertBefore(b,a.firstChild)},bottom:function(a,b){a.appendChild(b)},after:function(a,b){a.parentNode.insertBefore(b,a.nextSibling)},tags:{TABLE:["","
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d=c("object");if(Prototype.BrowserFeatures.SpecificElementExtensions){if(d){return function(h){if(h&&typeof h._extendedByPrototype=="undefined"){var g=h.tagName;if(g&&(/^(?:object|applet|embed)$/i.test(g))){b(h,Element.Methods);b(h,Element.Methods.Simulated);b(h,Element.Methods.ByTag[g.toUpperCase()])}}return h}}return Prototype.K}var a={},e=Element.Methods.ByTag;var f=Object.extend(function(i){if(!i||typeof i._extendedByPrototype!="undefined"||i.nodeType!=1||i==window){return i}var g=Object.clone(a),h=i.tagName.toUpperCase();if(e[h]){Object.extend(g,e[h])}b(i,g);i._extendedByPrototype=Prototype.emptyFunction;return i},{refresh:function(){if(!Prototype.BrowserFeatures.ElementExtensions){Object.extend(a,Element.Methods);Object.extend(a,Element.Methods.Simulated)}}});f.refresh();return f})();if(document.documentElement.hasAttribute){Element.hasAttribute=function(a,b){return a.hasAttribute(b)}}else{Element.hasAttribute=Element.Methods.Simulated.hasAttribute}Element.addMethods=function(c){var i=Prototype.BrowserFeatures,d=Element.Methods.ByTag;if(!c){Object.extend(Form,Form.Methods);Object.extend(Form.Element,Form.Element.Methods);Object.extend(Element.Methods.ByTag,{FORM:Object.clone(Form.Methods),INPUT:Object.clone(Form.Element.Methods),SELECT:Object.clone(Form.Element.Methods),TEXTAREA:Object.clone(Form.Element.Methods),BUTTON:Object.clone(Form.Element.Methods)})}if(arguments.length==2){var b=c;c=arguments[1]}if(!b){Object.extend(Element.Methods,c||{})}else{if(Object.isArray(b)){b.each(g)}else{g(b)}}function g(k){k=k.toUpperCase();if(!Element.Methods.ByTag[k]){Element.Methods.ByTag[k]={}}Object.extend(Element.Methods.ByTag[k],c)}function a(m,l,k){k=k||false;for(var o in m){var n=m[o];if(!Object.isFunction(n)){continue}if(!k||!(o in l)){l[o]=n.methodize()}}}function e(n){var k;var m={OPTGROUP:"OptGroup",TEXTAREA:"TextArea",P:"Paragraph",FIELDSET:"FieldSet",UL:"UList",OL:"OList",DL:"DList",DIR:"Directory",H1:"Heading",H2:"Heading",H3:"Heading",H4:"Heading",H5:"Heading",H6:"Heading",Q:"Quote",INS:"Mod",DEL:"Mod",A:"Anchor",IMG:"Image",CAPTION:"TableCaption",COL:"TableCol",COLGROUP:"TableCol",THEAD:"TableSection",TFOOT:"TableSection",TBODY:"TableSection",TR:"TableRow",TH:"TableCell",TD:"TableCell",FRAMESET:"FrameSet",IFRAME:"IFrame"};if(m[n]){k="HTML"+m[n]+"Element"}if(window[k]){return window[k]}k="HTML"+n+"Element";if(window[k]){return window[k]}k="HTML"+n.capitalize()+"Element";if(window[k]){return window[k]}var l=document.createElement(n),o=l.__proto__||l.constructor.prototype;l=null;return o}var h=window.HTMLElement?HTMLElement.prototype:Element.prototype;if(i.ElementExtensions){a(Element.Methods,h);a(Element.Methods.Simulated,h,true)}if(i.SpecificElementExtensions){for(var j in Element.Methods.ByTag){var f=e(j);if(Object.isUndefined(f)){continue}a(d[j],f.prototype)}}Object.extend(Element,Element.Methods);delete Element.ByTag;if(Element.extend.refresh){Element.extend.refresh()}Element.cache={}};document.viewport={getDimensions:function(){return{width:this.getWidth(),height:this.getHeight()}},getScrollOffsets:function(){return Element._returnOffset(window.pageXOffset||document.documentElement.scrollLeft||document.body.scrollLeft,window.pageYOffset||document.documentElement.scrollTop||document.body.scrollTop)}};(function(b){var g=Prototype.Browser,e=document,c,d={};function a(){if(g.WebKit&&!e.evaluate){return document}if(g.Opera&&window.parseFloat(window.opera.version())<9.5){return document.body}return document.documentElement}function f(h){if(!c){c=a()}d[h]="client"+h;b["get"+h]=function(){return c[d[h]]};return b["get"+h]()}b.getWidth=f.curry("Width");b.getHeight=f.curry("Height")})(document.viewport);Element.Storage={UID:1};Element.addMethods({getStorage:function(b){if(!(b=$(b))){return}var a;if(b===window){a=0}else{if(typeof b._prototypeUID==="undefined"){b._prototypeUID=Element.Storage.UID++}a=b._prototypeUID}if(!Element.Storage[a]){Element.Storage[a]=$H()}return Element.Storage[a]},store:function(b,a,c){if(!(b=$(b))){return}if(arguments.length===2){Element.getStorage(b).update(a)}else{Element.getStorage(b).set(a,c)}return b},retrieve:function(c,b,a){if(!(c=$(c))){return}var e=Element.getStorage(c),d=e.get(b);if(Object.isUndefined(d)){e.set(b,a);d=a}return d},clone:function(c,a){if(!(c=$(c))){return}var e=c.cloneNode(a);e._prototypeUID=void 0;if(a){var d=Element.select(e,"*"),b=d.length;while(b--){d[b]._prototypeUID=void 0}}return Element.extend(e)},purge:function(c){if(!(c=$(c))){return}var a=Element._purgeElement;a(c);var d=c.getElementsByTagName("*"),b=d.length;while(b--){a(d[b])}return null}});(function(){function h(v){var u=v.match(/^(\d+)%?$/i);if(!u){return null}return(Number(u[1])/100)}function o(F,G,v){var y=null;if(Object.isElement(F)){y=F;F=y.getStyle(G)}if(F===null){return null}if((/^(?:-)?\d+(\.\d+)?(px)?$/i).test(F)){return window.parseFloat(F)}var A=F.include("%"),w=(v===document.viewport);if(/\d/.test(F)&&y&&y.runtimeStyle&&!(A&&w)){var u=y.style.left,E=y.runtimeStyle.left;y.runtimeStyle.left=y.currentStyle.left;y.style.left=F||0;F=y.style.pixelLeft;y.style.left=u;y.runtimeStyle.left=E;return F}if(y&&A){v=v||y.parentNode;var x=h(F);var B=null;var z=y.getStyle("position");var D=G.include("left")||G.include("right")||G.include("width");var C=G.include("top")||G.include("bottom")||G.include("height");if(v===document.viewport){if(D){B=document.viewport.getWidth()}else{if(C){B=document.viewport.getHeight()}}}else{if(D){B=$(v).measure("width")}else{if(C){B=$(v).measure("height")}}}return(B===null)?0:B*x}return 0}function 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y=this.element;if(j(y)){this._prepared=true;return}var A={position:y.style.position||"",width:y.style.width||"",visibility:y.style.visibility||"",display:y.style.display||""};y.store("prototype_original_styles",A);var B=y.getStyle("position"),u=y.getStyle("width");if(u==="0px"||u===null){y.style.display="block";u=y.getStyle("width")}var v=(B==="fixed")?document.viewport:y.parentNode;y.setStyle({position:"absolute",visibility:"hidden",display:"block"});var w=y.getStyle("width");var x;if(u&&(w===u)){x=o(y,"width",v)}else{if(B==="absolute"||B==="fixed"){x=o(y,"width",v)}else{var C=y.parentNode,z=$(C).getLayout();x=z.get("width")-this.get("margin-left")-this.get("border-left")-this.get("padding-left")-this.get("padding-right")-this.get("border-right")-this.get("margin-right")}}y.setStyle({width:x+"px"});this._prepared=true},_end:function(){var v=this.element;var 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15.1983 -7.7420 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 13.4320 -12.2893 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 10.7020 -10.0181 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 + 10.7020 -9.1931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 10.7020 -10.8431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 9.8770 -10.0181 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 5 1 0 0 0 0 + 2 3 1 1 0 0 0 + 2 7 1 0 0 0 0 + 3 4 1 1 0 0 0 + 3 6 1 0 0 0 0 + 5 4 1 1 0 0 0 + 5 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 14 9 1 0 0 0 0 + 9 17 1 0 0 0 0 + 10 11 2 0 0 0 0 + 10 16 1 0 0 0 0 + 10 18 1 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 16 14 2 0 0 0 0 + 15 16 1 0 0 0 0 + 15 17 2 0 0 0 0 + 4 19 1 0 0 0 0 + 8 20 1 0 0 0 0 + 20 21 2 0 0 0 0 + 20 22 1 0 0 0 0 + 20 23 1 0 0 0 0 +M END +> +23 + +> +25 + +$$$$ +Adenosine diphosphate + SMMXDraw10031318122D + + 27 29 0 0 1 0 0 0 0 0999 V2000 + 11.2820 -9.5684 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 10.6145 -9.8900 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 + 10.8695 -10.5112 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 + 11.6945 -10.5112 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + 11.9494 -9.8900 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 + 10.8695 -11.3362 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 10.6145 -9.0650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.7895 -9.0650 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 11.9494 -9.0650 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 + 13.4608 -7.6139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.1752 -8.0265 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 14.1752 -8.8515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.4608 -9.2640 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 12.7463 -8.8515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.0193 -7.7320 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 12.7463 -8.0265 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.5001 -8.3731 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.4608 -6.7889 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 11.6945 -11.3362 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.9645 -9.0650 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 + 8.9645 -8.2400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.9645 -9.8900 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.1395 -9.0650 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3145 -9.0650 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 + 7.3145 -8.2400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3145 -9.8900 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4895 -9.0650 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 5 1 0 0 0 0 + 2 3 1 1 0 0 0 + 2 7 1 0 0 0 0 + 3 4 1 1 0 0 0 + 3 6 1 0 0 0 0 + 5 4 1 1 0 0 0 + 5 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 14 9 1 0 0 0 0 + 9 17 1 0 0 0 0 + 10 11 2 0 0 0 0 + 10 16 1 0 0 0 0 + 10 18 1 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 16 14 2 0 0 0 0 + 15 16 1 0 0 0 0 + 15 17 2 0 0 0 0 + 4 19 1 0 0 0 0 + 8 20 1 0 0 0 0 + 20 21 2 0 0 0 0 + 20 22 1 0 0 0 0 + 20 23 1 0 0 0 0 + 23 24 1 0 0 0 0 + 24 25 2 0 0 0 0 + 24 26 1 0 0 0 0 + 24 27 1 0 0 0 0 +M END +> +27 + +> +29 + +$$$$ +Adenosine triphosphate + SMMXDraw10031318252D + + 31 33 0 0 1 0 0 0 0 0999 V2000 + 14.6695 -10.5215 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 14.0020 -10.8431 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 + 14.2570 -11.4643 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 + 15.0820 -11.4643 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 + 15.3369 -10.8431 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 + 14.2570 -12.2893 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 14.0020 -10.0181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.1770 -10.0181 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 15.3369 -10.0181 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 + 16.8483 -8.5670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 17.5627 -8.9796 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 17.5627 -9.8046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.8483 -10.2171 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 16.1338 -9.8046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.4068 -8.6851 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 16.1338 -8.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.8876 -9.3262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.8483 -7.7420 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 15.0820 -12.2893 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 12.3520 -10.0181 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 + 12.3520 -9.1931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 12.3520 -10.8431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 11.5270 -10.0181 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 10.7020 -10.0181 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 + 10.7020 -9.1931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 10.7020 -10.8431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 9.8770 -10.0181 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 9.0520 -10.0181 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 + 9.0520 -9.1931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 9.0520 -10.8431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.2270 -10.0181 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 5 1 0 0 0 0 + 2 3 1 1 0 0 0 + 2 7 1 0 0 0 0 + 3 4 1 1 0 0 0 + 3 6 1 0 0 0 0 + 5 4 1 1 0 0 0 + 5 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 14 9 1 0 0 0 0 + 9 17 1 0 0 0 0 + 10 11 2 0 0 0 0 + 10 16 1 0 0 0 0 + 10 18 1 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 16 14 2 0 0 0 0 + 15 16 1 0 0 0 0 + 15 17 2 0 0 0 0 + 4 19 1 0 0 0 0 + 8 20 1 0 0 0 0 + 20 21 2 0 0 0 0 + 20 22 1 0 0 0 0 + 20 23 1 0 0 0 0 + 23 24 1 0 0 0 0 + 24 25 2 0 0 0 0 + 24 26 1 0 0 0 0 + 24 27 1 0 0 0 0 + 27 28 1 0 0 0 0 + 28 29 2 0 0 0 0 + 28 30 1 0 0 0 0 + 28 31 1 0 0 0 0 +M END +> +31 + +> +33 + +$$$$ From 9efd9717017bb936eef6e36e18f2f01d5d18b240 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 6 Jul 2017 16:05:19 -0700 Subject: [PATCH 191/576] Added routes expected by Ketcher API that hit new ACAS Roo structure routes for converting smiles and cleaning molecules. Changed ketcher URI to reference new api routes and take it out of standalone mode. --- .../server/routes/ChemStructureRoutes.coffee | 63 +++++++++++++++++++ .../client/ACASFormChemicalStructure.coffee | 2 +- 2 files changed, 64 insertions(+), 1 deletion(-) diff --git a/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee b/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee index 57aa53247..0e2838e38 100644 --- a/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee +++ b/modules/ChemStructure/src/server/routes/ChemStructureRoutes.coffee @@ -9,6 +9,9 @@ exports.setupAPIRoutes = (app) -> app.post '/api/chemStructure/renderMolStructureBase64', exports.renderMolStructureBase64 app.post '/api/chemStructure/acasStructureMetaSearch', exports.acasStructureMetaSearch app.post '/api/chemStructure/acasStructureSearch', exports.acasStructureSearch + app.get '/api/chemStructure/ketcher/knocknock', exports.ketcherKnocknock + app.get '/api/chemStructure/ketcher/layout', exports.ketcherConvertSmiles + app.post '/api/chemStructure/ketcher/layout', exports.ketcherLayout exports.setupRoutes = (app, loginRoutes) -> app.get '/api/chemStructure/renderStructureByThingCode', loginRoutes.ensureAuthenticated, exports.renderStructureByThingCode @@ -21,6 +24,9 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/chemStructure/renderMolStructureBase64', loginRoutes.ensureAuthenticated, exports.renderMolStructureBase64 app.post '/api/chemStructure/acasStructureMetaSearch', loginRoutes.ensureAuthenticated, exports.acasStructureMetaSearch app.post '/api/chemStructure/acasStructureSearch', loginRoutes.ensureAuthenticated, exports.acasStructureSearch + app.get '/api/chemStructure/ketcher/knocknock', loginRoutes.ensureAuthenticated, exports.ketcherKnocknock + app.get '/api/chemStructure/ketcher/layout', loginRoutes.ensureAuthenticated, exports.ketcherConvertSmiles + app.post '/api/chemStructure/ketcher/layout', loginRoutes.ensureAuthenticated, exports.ketcherLayout _ = require 'underscore' @@ -253,3 +259,60 @@ exports.acasStructureMetaSearch = (req, resp) -> resp.statusCode = 500 resp.end JSON.stringify "ACAS structure search failed" ) + +exports.ketcherKnocknock = (req, resp) -> + resp.end "You are welcome!" + +exports.ketcherConvertSmiles = (req, resp) -> + if global.specRunnerTestmode + resp.end "Ok.\n\n -INDIGO-06301717442D\n\n 4 3 0 0 0 0 0 0 0 0999 V2000\n -1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.7713 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 1 0 0 0 0\nM END\n" + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"structure/convertSmilesToMol" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: req.query.smiles + json: true + , (error, response, json) => + console.log response + console.log json + if !error && response.statusCode == 200 + statusMessage = "Ok.\n" + resp.end statusMessage+json + else + console.log 'got ajax error trying to convert smiles to MOL' + console.log error + console.log json + console.log response + resp.statusCode = 500 + resp.end JSON.stringify "Smiles to MOL conversion failed" + ) + +exports.ketcherLayout = (req, resp) -> + if global.specRunnerTestmode + resp.end "Ok.\n\n -INDIGO-06301717442D\n\n 4 3 0 0 0 0 0 0 0 0999 V2000\n -1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.3856 -0.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.7713 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 1 0 0 0 0\nM END\n" + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"structure/cleanMolStructure" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: req.body.moldata + json: true + , (error, response, json) => + console.log response + console.log json + if !error && response.statusCode == 200 + statusMessage = "Ok.\n" + resp.end statusMessage+json + else + console.log 'got ajax error trying to clean MOL' + console.log error + console.log json + console.log response + resp.statusCode = 500 + resp.end JSON.stringify "Cleaning MOL conversion failed" + ) \ No newline at end of file diff --git a/modules/Components/src/client/ACASFormChemicalStructure.coffee b/modules/Components/src/client/ACASFormChemicalStructure.coffee index 54ca2da13..cfe56527b 100644 --- a/modules/Components/src/client/ACASFormChemicalStructure.coffee +++ b/modules/Components/src/client/ACASFormChemicalStructure.coffee @@ -71,7 +71,7 @@ class window.KetcherChemicalStructureController extends Backbone.View $(@el).empty() $(@el).html @template() - searchFrameURL = "/lib/ketcher-2.0.0-alpha.3/ketcher.html" + searchFrameURL = "/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/chemStructure/ketcher/" @$('.bv_sketcherIFrame').attr 'src', searchFrameURL From a74da4df3e1b65699e0429f4cea1d4fec3cf4171 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 26 Sep 2017 16:21:57 -0700 Subject: [PATCH 192/576] emitting 'end' at the beginning of gulp coffee onError catch --- gulpfile.coffee | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gulpfile.coffee b/gulpfile.coffee index 008eb654e..9cf80819b 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -43,10 +43,10 @@ getRPath = (path) -> return path getLegacyRPath = (path) -> - console.warn "Warning: All R code in modules path 'modules/**/src/server/**/*.{R,r}' should be moved to 'modules/**/src/server/r/*.{R,r}'" + # console.warn "Warning: All R code in modules path 'modules/**/src/server/**/*.{R,r}' should be moved to 'modules/**/src/server/r/*.{R,r}'" module = path.dirname.split('/')[0] additionalPath = path.dirname.replace(module + '/src/server/', '') - console.log "Warning: Please move '#{path.dirname}/#{path.basename}#{path.extname}' to '#{module}/src/server/r/#{additionalPath}/#{path.basename}#{path.extname}'" + # console.log "Warning: Please move '#{path.dirname}/#{path.basename}#{path.extname}' to '#{module}/src/server/r/#{additionalPath}/#{path.basename}#{path.extname}'" if path.basename == 'r' and path.extname == '' path.basename = '' path.dirname = '' @@ -410,19 +410,19 @@ createExecuteTask = (options) => onError = (err) -> + @emit 'end' process.stdout.write '\x07' if os.platform() == 'darwin' - return notify.onError( + notify.onError( title: '<%= error.message %>' # subtitle: 'Failure!' message: 'Error: <%= error.stack %>' sound: false) err else - return notify.onError((options, callback) -> + notify.onError((options, callback) -> console.log "\x1b[34m[#{options.message}]\x1b[0m \x1b[31mError: #{options.stack}\x1b[0m" return ) err - @emit 'end' createTask = (options, type) -> From 48b06d027d445469ea13b1d3715e3a45eef5223c Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 22 Sep 2017 16:50:23 -0700 Subject: [PATCH 193/576] Lot inventory mods in progress --- conf/config.properties.example | 1 + .../src/client/AbstractFormController.coffee | 8 +- .../routes/InventoryServiceRoutes.coffee | 329 +++++++++++++++++- .../routes/ServerUtilityFunctions.coffee | 7 + 4 files changed, 333 insertions(+), 12 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 7918017a8..dc55ab1a2 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -543,3 +543,4 @@ client.roles.crossProjectLoaderRole=ROLE_ACAS-CROSS-PROJECT-LOADER # For whether protocols and experiments should have sequential user defined corpName labels client.entity.saveInitialsCorpName=false +client.compoundInventory.enforceUppercaseBarcodes=false diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index b881f513d..6a77e30ae 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -114,7 +114,7 @@ class window.AbstractFormController extends Backbone.View class window.AbstractThingFormController extends AbstractFormController - setupFormFields: (fieldDefs) -> + setupFormFields: (fieldDefs, useDirectRef) -> unless @formFields? @formFields = {} @@ -125,6 +125,10 @@ class window.AbstractThingFormController extends AbstractFormController if fieldDefs.secondLsThingItxs? then fDefs = fDefs.concat fieldDefs.secondLsThingItxs for field in fDefs + if useDirectRef? and useDirectRef + mdl = @model.get field.key + else + mdl = @model opts = modelKey: field.key inputClass: field.fieldSettings.inputClass @@ -132,7 +136,7 @@ class window.AbstractThingFormController extends AbstractFormController placeholder: field.fieldSettings.placeholder required: field.fieldSettings.required url: field.fieldSettings.url - thingRef: @model + thingRef: mdl insertUnassigned: field.fieldSettings.insertUnassigned modelDefaults: field.modelDefaults allowedFileTypes: field.fieldSettings.allowedFileTypes diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 6bc9aa2b4..e2d075282 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -4,6 +4,8 @@ _ = require 'underscore' preferredEntityCodeService = require '../routes/PreferredEntityCodeService.js' config = require '../conf/compiled/conf.js' RUN_CUSTOM_FLAG = "0" +fs = require('fs') +parse = require('csv-parse') exports.setupAPIRoutes = (app) -> @@ -56,6 +58,7 @@ exports.setupAPIRoutes = (app) -> app.post '/api/getContainerStatesByContainerValue', exports.getContainerStatesByContainerValue app.post '/api/getContainerLogsByContainerCodes', exports.getContainerLogsByContainerCodes app.post '/api/getTubesFromBatchCode', exports.getTubesFromBatchCode + app.post '/api/loadParentVialsFromCSV', exports.loadParentVialsFromCSV exports.setupRoutes = (app, loginRoutes) -> @@ -1228,6 +1231,38 @@ getContainerCodesFromLabels = (req, callback) -> callback json ) +getContainerCodesFromLabelsInternal = (barcodes, containerType, containerKind, callback) -> + if global.specRunnerTestmode + response = + codeName: 'CONT-0000001' + label: 'test label' + callback response + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"containers/getContainerCodesByLabels?" + url = baseurl+"containerType=#{containerType}&containerKind=#{containerKind}" + postBody = barcodes + console.debug postBody + console.debug url + request = require 'request' + request( + method: 'POST' + url: url + body: postBody + json: true + timeout: 86400000 + , (error, response, json) => + console.debug response.statusCode + console.debug json + if !error and !json.error + callback json + else + console.error 'got ajax error trying to lookup lsContainer name' + console.error error + console.error response + callback json + ) + exports.getContainerCodesFromLabels = (req, resp) -> req.setTimeout 86400000 getContainerCodesFromLabels req, (json) -> @@ -2481,16 +2516,16 @@ exports.getTubesFromBatchCodeInternal = (input, callback) => { "lsType": "container" , "lsKind": "tube", - "values":[ - { - "stateType":"metadata", - "stateKind":"information", - "valueType": "codeValue", - "valueKind": "status", - "operator": "!=", - "value":"expired" - } - ], +# "values":[ +# { +# "stateType":"metadata", +# "stateKind":"information", +# "valueType": "codeValue", +# "valueKind": "status", +# "operator": "!=", +# "value":"expired" +# } +# ], "secondInteractions":[ { "interactionType": "has member", @@ -2533,3 +2568,277 @@ exports.getTubesFromBatchCodeInternal = (input, callback) => callback null, 500 #resp.end JSON.stringify "getContainerStatesByContainerValue failed" ) + +PARENT_COMPOUND_LOT_INDEX = 0 +PARENT_DESTINATION_VIAL_INDEX = 1 +PARENT_AMOUNT_INDEX = 2 +PARENT_AMOUNT_UNITS_INDEX = 3 +PARENT_PREPARED_BY_INDEX = 4 +PARENT_PREPARED_DATE_INDEX = 5 +PARENT_PHYSICAL_STATE_INDEX = 6 +PARENT_CONCENTRATION_INDEX = 7 +PARENT_CONC_UNITS_INDEX = 8 +PARENT_SOLVENT_INDEX = 9 + +DAUGHTER_SOURCE_VIAL_INDEX = 0 +DAUGHTER_DESTINATION_VIAL_INDEX = 1 +DAUGHTER_AMOUNT_INDEX = 2 +DAUGHTER_AMOUNT_UNITS_INDEX = 3 +DAUGHTER_PREPARED_BY_INDEX = 4 +DAUGHTER_PREPARED_DATE_INDEX = 5 +DAUGHTER_PHYSICAL_STATE_INDEX = 6 +DAUGHTER_CONCENTRATION_INDEX = 7 +DAUGHTER_CONC_UNITS_INDEX = 8 +DAUGHTER_SOLVENT_INDEX = 9 + +exports.loadParentVialsFromCSV = (req, resp) -> + exports.loadParentVialsFromCSVInternal req.body.fileToParse, req.body.dryRunMode, req.body.user, (response) -> + resp.json response + +exports.loadParentVialsFromCSVInternal = (csvFileName, dryRun, user, callback) -> + if dryRun + exports.validateParentVialsFromCSVInternal csvFileName, (validationResponse) -> + callback validationResponse + else + exports.createParentVialsFromCSVInternal csvFileName, user, (createVialsResponse) -> + callback createVialsResponse + +exports.validateParentVialsFromCSV = (req, resp) -> + exports.validateParentVialsFromCSVInternal req.body.csvFileName, (validationResponse) -> + resp.json validationResponse + +exports.validateParentVialsFromCSVInternal = (csvFileName, callback) -> + getFileExists csvFileName, (exists, path) -> + validationResponse = + results: + dryRun: true + fileToParse: csvFileName + htmlSummary: '' + hasError: true + hasWarning: false + errorMessages: [] + transactionId: null + if exists + validationResponse.results.path = path + createParentVialFileEntryArray csvFileName, (fileEntryArray) -> + console.log fileEntryArray + checkRequiredAttributes fileEntryArray, (requiredAttributeErrors) -> + if requiredAttributeErrors? + validationResponse.errorMessages.push requiredAttributeErrors... + checkDataTypeErrors fileEntryArray, (dataTypeErrors) -> + if dataTypeErrors? + validationResponse.errorMessages.push dataTypeErrors... + checkBatchCodesExist fileEntryArray, (missingBatchCodeErrors) -> + if missingBatchCodeErrors? and missingBatchCodeErrors.length > 1 + error = + level: 'error' + message: "The following batches do not exist: "+ missingBatchCodeErrors.join ', ' + validationResponse.errorMessages.push error + barcodes = _.pluck fileEntryArray, 'destinationVialBarcode' + checkBarcodesExist barcodes, (existingBarcodes, newBarcodes) -> + if existingBarcodes? and existingBarcodes.length > 1 + error = + level: 'error' + message: "The following barcodes already exist: " + existingBarcodes.join ', ' + validationResponse.errorMessages.push error + if validationResponse.errorMessages.length < 1 + validationResponse.hasError = false + validationResponse.results.htmlSummary = prepareValidationHTMLSummary validationResponse.hasError, validationResponse.errorMessages + callback validationResponse + else + error = + level: 'error' + message: "File cannot be found" + validationResponse.errorMessages.push error + callback validationResponse + +getFileExists = (csvFileName, callback) => + exists = false + path = config.all.server.file.server.path + '/' + fileName = csvFileName + fs.stat path+fileName, (err, stats) -> + console.log 'path+fileName', path+fileName + console.log stats + console.log err + if stats?.isFile() + exists = true + callback exists, path+fileName + else + callback exists, path+fileName + +createParentVialFileEntryArray = (csvFileName, callback) => + csvFileEntries = [] + path = config.all.server.file.server.path + '/' + fileName = csvFileName + rowCount = 0 + fs.createReadStream(path + fileName) + .pipe(parse({delimiter: ','})) + .on('data', (csvrow) -> + fileEntry = + batchCode: csvrow[PARENT_COMPOUND_LOT_INDEX].trim() + destinationVialBarcode: csvrow[PARENT_DESTINATION_VIAL_INDEX].trim() + amount: csvrow[PARENT_AMOUNT_INDEX].trim() + amountUnits: csvrow[PARENT_AMOUNT_UNITS_INDEX].trim() + preparedBy: csvrow[PARENT_PREPARED_BY_INDEX].trim() + preparedDate: csvrow[PARENT_PREPARED_DATE_INDEX].trim() + physicalState: csvrow[PARENT_PHYSICAL_STATE_INDEX].trim() + concentration: csvrow[PARENT_CONCENTRATION_INDEX].trim() + concUnits:csvrow[PARENT_CONC_UNITS_INDEX].trim() + solvent: csvrow[PARENT_SOLVENT_INDEX].trim() + rowNumber: rowCount + if rowCount? and rowCount > 0 + csvFileEntries.push(fileEntry) + rowCount++ + ) + .on('end', () -> + return callback csvFileEntries, 200 + ) + +createDaughterVialFileEntryArray = (csvFileName, callback) => + csvFileEntries = [] + path = config.all.server.file.server.path + '/' + fileName = csvFileName + rowCount = 0 + fs.createReadStream(path + fileName) + .pipe(parse({delimiter: ','})) + .on('data', (csvrow) -> + fileEntry = + sourceVialBarcode: csvrow[DAUGHTER_SOURCE_VIAL_INDEX].trim() + destinationVialBarcode: csvrow[DAUGHTER_DESTINATION_VIAL_INDEX].trim() + amount: csvrow[DAUGHTER_AMOUNT_INDEX].trim() + amountUnits: csvrow[DAUGHTER_AMOUNT_UNITS_INDEX].trim() + preparedBy: csvrow[DAUGHTER_PREPARED_BY_INDEX].trim() + preparedDate: csvrow[DAUGHTER_PREPARED_DATE_INDEX].trim() + physicalState: csvrow[DAUGHTER_PHYSICAL_STATE_INDEX].trim() + concentration: csvrow[DAUGHTER_CONCENTRATION_INDEX].trim() + concUnits: csvrow[DAUGHTER_CONC_UNITS_INDEX].trim() + solvent: csvrow[DAUGHTER_SOLVENT_INDEX].trim() + rowNumber: rowCount + if rowCount? and rowCount > 0 + csvFileEntries.push(fileEntry) + rowCount++ + ) + .on('end', () -> + return callback csvFileEntries, 200 + ) + +checkRequiredAttributes = (fileEntryArray, callback) -> + requiredAttributeErrors = [] + _.each fileEntryArray, (entry) -> + missingAttributes = [] + for attr in ['batchCode', 'destinationVialBarcode', 'sourceVialBarcode', 'amount', 'amountUnits', 'preparedBy', 'preparedDate', 'physicalState', 'concentration', 'concUnits', 'solvent'] + if entry[attr]? + if attr in ['concentration', 'concUnits', 'solvent'] + if entry.physicalState == 'solution' + if entry[attr] == "" + missingAttributes.push attr + else + if entry[attr] == "" + missingAttributes.push attr + if missingAttributes.length > 0 + error = + level: 'error' + message: "Row #{entry.rowNumber} is missing the required attributes: " + missingAttributes.join ', ' + requiredAttributeErrors.push error + callback requiredAttributeErrors + +checkDataTypeErrors = (fileEntryArray, callback) -> + dataTypeErrors = [] + _.each fileEntryArray, (entry) -> + if entry.amount? and entry.amount.length > 0 and isNaN(parseFloat(entry.amount)) + error = + level: 'error' + message: "Row #{entry.rowNumber} contains the invalid amount: #{entry.amount}" + dataTypeErrors.push error + if entry.concentration? and entry.concentration.length > 0 and isNaN(parseFloat(entry.concentration)) + error = + level: 'error' + message: "Row #{entry.rowNumber} contains the invalid concentration: #{entry.concentration}" + dataTypeErrors.push error + callback dataTypeErrors + +checkBatchCodesExist = (fileEntryArray, callback) -> + requests = [] + _.each fileEntryArray, (entry) -> + request = + requestName: entry.batchCode + requests.push request + csUtilities.getPreferredBatchIds requests, (batchIdResponse) -> + missingBatchCodes = [] + _.each batchIdResponse, (batchCodeRequest) -> + if batchCodeRequest.preferredName.length < 1 + missingBatchCodes.push batchCodeRequest.requestName + callback missingBatchCodes + +checkBarcodesExist = (barcodes, callback) -> + getContainerCodesFromLabelsInternal barcodes, 'container', 'tube', (containerCodes) -> + existingBarcodes = [] + newBarcodes = [] + _.each containerCodes, (containerCodeEntry) -> + if containerCodeEntry.foundCodeNames? and containerCodeEntry.foundCodeNames.length > 0 + existingBarcodes.push containerCodeEntry.requestLabel + else + newBarcodes.push containerCodeEntry.requestLabel + callback existingBarcodes, newBarcodes + +prepareValidationHTMLSummary = (hasError, errorMessages) -> + + 'html summary goes here' + +exports.createParentVialsFromCSVInternal = (csvFileName, user, callback) -> + getFileExists csvFileName, (exists, path) -> + createResponse = + results: + dryRun: true + fileToParse: csvFileName + htmlSummary: '' + hasError: true + hasWarning: false + errorMessages: [] + transactionId: null + if exists + createResponse.results.path = path + createParentVialFileEntryArray csvFileName, (fileEntryArray) -> + exports.getContainerTubeDefinitionCode (definitionCode) -> + if !definitionCode? + error = + level: 'error' + message: 'Could not find definition container for tube' + createResponse.errorMessages.push error + tubesToCreate = [] + _.each fileEntryArray, (entry) -> + tube = + barcode: entry.destinationVialBarcode + definition: definitionCode + recordedBy: user + createdUser: entry.preparedBy + createdDate: entry.createdDate + physicalState: entry.physicalState + wells: [ + wellName: "A001" + batchCode: entry.batchCode + amount: parseFloat(entry.amount) + amountUnits: entry.amountUnits + physicalState: entry.physicalState + recordedBy: user + recordedDate: (new Date()).getTime() + ] + if entry.physicalState == 'solution' + tube.wells[0].batchConcentration = parseFloat(entry.concentration) + tube.wells[0].batchConcUnits = entry.concUnits + tube.wells[0].solventCode = entry.solvent + tubesToCreate.push tube + console.log JSON.stringify tubesToCreate + exports.createTubesInternal tubesToCreate, 0, (json, statusCode) -> + console.log json + callback json + else + error = + level: 'error' + message: "File cannot be found" + createResponse.errorMessages.push error + callback createResponse + +exports.getContainerTubeDefinitionCode = (callback) -> + exports.containersByTypeKindInternal 'definition container', 'tube', 'codetable', false, false, (definitionContainers) -> + callback definitionContainers[0].code \ No newline at end of file diff --git a/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee b/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee index dbf39acf2..ea627a209 100644 --- a/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee +++ b/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee @@ -2154,7 +2154,14 @@ class ContainerTube extends ContainerPlate stateKind: 'information' type: 'codeValue' kind: 'type' + , + key: 'comments' + stateType: 'metadata' + stateKind: 'information' + type: 'stringValue' + kind: 'comments' ] + class AnalysisGroup extends Backbone.Model defaults: kind: "" From 28a5b8bee4575140d2cf470e70cb2a6677d71c66 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 26 Sep 2017 17:30:16 -0700 Subject: [PATCH 194/576] Wrapped SaltForm structure sketcher getMolecule in useMarvin / useKetcher so it properly uses Ketcher when in that mode. --- modules/CmpdReg/src/client/src/SaltForm.js | 31 +++++++++++++--------- 1 file changed, 19 insertions(+), 12 deletions(-) diff --git a/modules/CmpdReg/src/client/src/SaltForm.js b/modules/CmpdReg/src/client/src/SaltForm.js index c13080c71..b6ec00564 100755 --- a/modules/CmpdReg/src/client/src/SaltForm.js +++ b/modules/CmpdReg/src/client/src/SaltForm.js @@ -161,20 +161,27 @@ $(function() { this.isosaltEquivListController.updateModel(); var mol = ''; - if(this.sketcherLoaded && this.$('.structureWrapper').is(':visible')) { - self = this; - this.marvinSketcherInstance.exportStructure(this.exportFormat).then(function(molecule) { - if ( molecule.indexOf("0 0 0 0 0 0 0 0 0 0999")>-1) - mol = ''; - else - mol = molecule; - self.model.set({molStructure: mol}); + if (this.sketcherLoaded && this.$('.structureWrapper').is(':visible')) { + if (this.useMarvin) { + self = this; + this.marvinSketcherInstance.exportStructure(this.exportFormat).then(function (molecule) { + if (molecule.indexOf("0 0 0 0 0 0 0 0 0 0999") > -1) + mol = ''; + else + mol = molecule; + self.model.set({molStructure: mol}); + callback(); + }, function (error) { + alert("Molecule export failed from search sketcher:" + error); + }); + }else if (this.useKetcher) { + mol = this.ketcher.getMolfile(); + if (mol.indexOf(" 0 0 0 0 0 999") > -1) mol = ''; + this.model.set({molStructure: mol}); callback(); - }, function(error) { - alert("Molecule export failed from search sketcher:"+error); - }); + } } else { - this.model.set({molStructure: mol}); + this.model.set({molStructure: mol}); callback(); } } else { From ccc0f7275b00ef90c900fd76857a9070c559e5a2 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 27 Sep 2017 08:43:45 -0700 Subject: [PATCH 195/576] ading a script to configure backups in a docker setup --- .../src/server/config_backups_docker.sh | 171 ++++++++++++++++++ 1 file changed, 171 insertions(+) create mode 100755 modules/BuildUtilities/src/server/config_backups_docker.sh diff --git a/modules/BuildUtilities/src/server/config_backups_docker.sh b/modules/BuildUtilities/src/server/config_backups_docker.sh new file mode 100755 index 000000000..6b0cf79e8 --- /dev/null +++ b/modules/BuildUtilities/src/server/config_backups_docker.sh @@ -0,0 +1,171 @@ +#!/bin/sh + +usage () +{ + echo 'Usage : Script -d -u ' + echo '' + exit +} + +while [ "$1" != "" ]; do +case $1 in + -d ) shift + BACKUP_DIRECTORY=$1 + ;; + -u ) shift + BACKUP_USER=$1 + ;; + -p ) shift + PROJECT=$1 + ;; + * ) QUERY=$1 + esac + shift +done + +if [ "$BACKUP_DIRECTORY" = "" ] +then + echo "backup_directory cannot be empty" + usage +fi +if [ "$PROJECT" = "" ] +then + echo "project cannot be empty" + usage +fi +if [ "$BACKUP_USER" = "" ] +then + echo "backup_user cannot be empty" + usage +else + userCount=$(grep -c '^'$BACKUP_USER':' /etc/passwd) + if [ $userCount -lt 1 ] + then + echo "backup_user '$BACKUP_USER' does not exist" + usage + fi +fi + +#Get ACAS config variables +source /dev/stdin <<< "$(docker exec colas_acas_1 bash -c 'cat $ACAS_HOME/conf/compiled/conf.properties | awk -f $ACAS_HOME/bin/readproperties.awk')" + +server_database_name=${server_database_name} +server_database_username=${server_database_username} +server_database_password=${server_database_password} +server_database_port=${server_database_port} +server_datafiles_relative_path=${server_datafiles_relative_path} + + +##########Setup folder heirarchy +###if $BACKUP_DIRECTORY does not exist then create it +echo "configuring backup base directories" +if [ -d "$BACKUP_DIRECTORY" ]; then + echo " exists $BACKUP_DIRECTORY" +else + echo " creating $BACKUP_DIRECTORY" + mkdir "$BACKUP_DIRECTORY/$PROJECT" +fi + +###Now setup the base backup location for seurat instance +backupsLocation=$BACKUP_DIRECTORY/$PROJECT +echo " creating $backupsLocation/backups/backup_hourly" +mkdir -p $backupsLocation/backups/backup_hourly +echo " creating $backupsLocation/backups/backup_daily" +mkdir -p $backupsLocation/backups/backup_daily +echo " creating $backupsLocation/backups/backup_weekly" +mkdir -p $backupsLocation/backups/backup_weekly +echo " creating $backupsLocation/backups/scripts" +mkdir -p $backupsLocation/scripts + +#############Begin Creating Scripts +echo "configuring backup scripts" +###backup_hourly +###Create tmp file +echo " creating $backupsLocation/scripts/backup_hourly.sh" +touch $backupsLocation/scripts/backup_hourly.sh +cat /dev/null > $backupsLocation/scripts/backup_hourly.sh +###Setup Script specific variables +backupDirLine="BaseBackupDir=$backupsLocation/backups" +logDateLine="date >> \$BaseBackupDir/backup_hourly/backuplog.txt" +logStartLineDaily="echo \"$PROJECT Hourly Backup\" >> \$BaseBackupDir/backup_hourly/backuplog.txt" +ACASNameDaily="acasArchNameGz=filestore_\`date +%H\`.tar.gz" +DBNameDaily="dbNameGz=dbstore_${server_database_name}_\`date +%H\`.gz" +acasImageLine="ACAS_IMAGE=\$(docker ps --filter \"name=``$PROJECT``_acas_1\" --format \"{{.Image}}\")" +dbImageLine="DB_IMAGE=\$(docker ps --filter \"name=``$PROJECT``_db_1\" --format \"{{.Image}}\")" +acasTarLine="docker run --rm -e acasArchNameGz=\$acasArchNameGz -v \$BaseBackupDir/backup_hourly:/backup -v ``$PROJECT``_filestore:/home/runner/build/privateUploads \$ACAS_IMAGE tar -pPzcf /backup/\$acasArchNameGz $server_datafiles_relative_path >> \$BaseBackupDir/backup_hourly/backuplog.txt 2>&1" +dbDumpLine="docker run --rm --network ``$PROJECT``_default -e dbNameGz=\$dbNameGz -e PGPASSWORD=${server_database_password} -e server_database_host=$server_database_host -e server_database_port=$server_database_port -e server_database_username=server_database_username -e server_database_password=server_database_password -v \$BaseBackupDir/backup_hourly:/backup -v ``$PROJECT``_dbstore:/var/lib/postgresql/data \$DB_IMAGE bash -c \"pg_dump --host=${server_database_host} --port=${server_database_port} --username=${server_database_username} --clean ${server_database_name} | gzip -c > /backup/\$dbNameGz\" >> \$BaseBackupDir/backup_hourly/backuplog.txt 2>&1" + +##Add Lines to Temp File +echo $backupDirLine >> $backupsLocation/scripts/backup_hourly.sh +echo $logStartLineDaily >> $backupsLocation/scripts/backup_hourly.sh +echo $logDateLine >> $backupsLocation/scripts/backup_hourly.sh +echo $ACASNameDaily >> $backupsLocation/scripts/backup_hourly.sh +echo $DBNameDaily >> $backupsLocation/scripts/backup_hourly.sh +echo $acasImageLine >> $backupsLocation/scripts/backup_hourly.sh +echo $dbImageLine >> $backupsLocation/scripts/backup_hourly.sh +echo $acasTarLine >> $backupsLocation/scripts/backup_hourly.sh +echo $dbDumpLine >> $backupsLocation/scripts/backup_hourly.sh + +###backup_daily +###Create File +echo " creating $backupsLocation/scripts/backup_daily.sh" +touch $backupsLocation/scripts/backup_daily.sh +cat /dev/null > $backupsLocation/scripts/backup_daily.sh +###Variables +backupDirLine="BaseBackupDir=$backupsLocation/backups" +logDateLine="date >> \$BaseBackupDir/backup_daily/backuplog.txt" +logStartLineDaily="echo \"$BackupName Daily Backup\" >> \$BaseBackupDir/backup_daily/backuplog.txt" +ACASNameDaily="acasArchNameGz=filestore_\`date +%a\`.tar.gz" +DBNameDaily="dbNameGz=dbstore_${server_database_name}_\`date +%a\`.gz" +cpLine1Daily="cp \$BaseBackupDir/backup_hourly/filestore_23.tar.gz \$BaseBackupDir/backup_daily/\$acasArchNameGz >> \$BaseBackupDir/backup_daily/backuplog.txt 2>&1" +cpLine2Daily="cp \$BaseBackupDir/backup_hourly/dbstore_${server_database_name}_23.gz \$BaseBackupDir/backup_daily/\$dbNameGz >> \$BaseBackupDir/backup_daily/backuplog.txt 2>&1" +##Add to File +echo $backupDirLine >> $backupsLocation/scripts/backup_daily.sh +echo $logStartLineDaily >> $backupsLocation/scripts/backup_daily.sh +echo $logDateLine >> $backupsLocation/scripts/backup_daily.sh +echo $ACASNameDaily >> $backupsLocation/scripts/backup_daily.sh +echo $DBNameDaily >> $backupsLocation/scripts/backup_daily.sh +echo $cpLine1Daily >> $backupsLocation/scripts/backup_daily.sh +echo $cpLine2Daily >> $backupsLocation/scripts/backup_daily.sh + +###backup_weekly +###Create File +echo " creating $backupsLocation/scripts/backup_weekly.sh" +touch $backupsLocation/scripts/backup_weekly.sh +cat /dev/null > $backupsLocation/scripts/backup_weekly.sh +###Variables +backupDirLine="BaseBackupDir=$backupsLocation/backups" +logDateLine="date >> \$BaseBackupDir/backup_weekly/backuplog.txt" +logStartLineWeekly="echo \"$BackupName Weekly Backup\" >> \$BaseBackupDir/backup_weekly/backuplog.txt" +ACASNameWeekly="acasArchNameGz=filestore_\`date +%m_%d_%y\`.tar.gz" +DBNameWeekly="dbNameGz=dbstore_${server_database_name}_\`date +%m_%d_%y\`.gz" +cpLine1Weekly="cp \$BaseBackupDir/backup_daily/filestore_Fri.tar.gz \$BaseBackupDir/backup_weekly/\$acasArchNameGz >> \$BaseBackupDir/backup_weekly/backuplog.txt 2>&1" +cpLine2Weekly="cp \$BaseBackupDir/backup_daily/dbstore_${server_database_name}_Fri.gz \$BaseBackupDir/backup_weekly/\$dbNameGz >> \$BaseBackupDir/backup_weekly/backuplog.txt 2>&1" +##Add to File +echo $backupDirLine >> $backupsLocation/scripts/backup_weekly.sh +echo $logStartLineWeekly >> $backupsLocation/scripts/backup_weekly.sh +echo $logDateLine >> $backupsLocation/scripts/backup_weekly.sh +echo $ACASNameWeekly >> $backupsLocation/scripts/backup_weekly.sh +echo $DBNameWeekly >> $backupsLocation/scripts/backup_weekly.sh +echo $cpLine1Weekly >> $backupsLocation/scripts/backup_weekly.sh +echo $cpLine2Weekly >> $backupsLocation/scripts/backup_weekly.sh + +###Now Setup crontab +su - $BACKUP_USER -c "touch /tmp/crontabFile.txt" +su - $BACKUP_USER -c "crontab -l > /tmp/crontabFile.txt" + +echo "removing any old cron for backup_user $BACKUP_USER, instance ${PROJECT}" +su - $BACKUP_USER -c "sed -i '/#START ${PROJECT} backup scripts section/,/#END ${PROJECT} backup scripts section/d' /tmp/crontabFile.txt" + +echo "installing cron for backup_user $BACKUP_USER" +su - $BACKUP_USER -c "echo \"#START ${PROJECT} backup scripts section\" >> /tmp/crontabFile.txt" +su - $BACKUP_USER -c "echo \"01 23 * * * $backupsLocation/scripts/backup_hourly.sh 2>&1\" >> /tmp/crontabFile.txt" +su - $BACKUP_USER -c "echo \"30 23 * * * $backupsLocation/scripts/backup_daily.sh 2>&1\" >> /tmp/crontabFile.txt" +su - $BACKUP_USER -c "echo \"40 23 * * 5 $backupsLocation/scripts/backup_weekly.sh 2>&1\" >> /tmp/crontabFile.txt" +su - $BACKUP_USER -c "echo \"#END ${PROJECT} backup scripts section\" >> /tmp/crontabFile.txt" +su - $BACKUP_USER -c "crontab /tmp/crontabFile.txt" +su - $BACKUP_USER -c "rm -f /tmp/crontabFile.txt" + +##Set permissions for these new files to the backup user +chown -R $BACKUP_USER $backupsLocation +chmod -R 700 $backupsLocation From 3a2efd91799f7fe8b1a3652c27ecbf9bdf42fbb5 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 27 Sep 2017 09:16:08 -0700 Subject: [PATCH 196/576] adding usage statement --- modules/BuildUtilities/src/server/config_backups_docker.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/BuildUtilities/src/server/config_backups_docker.sh b/modules/BuildUtilities/src/server/config_backups_docker.sh index 6b0cf79e8..5f5e3451c 100755 --- a/modules/BuildUtilities/src/server/config_backups_docker.sh +++ b/modules/BuildUtilities/src/server/config_backups_docker.sh @@ -2,7 +2,7 @@ usage () { - echo 'Usage : Script -d -u ' + echo 'Usage : Script -d -u -p ' echo '' exit } From 49343c2ff30c75bd73c8a26e9d7957bde2425c4e Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Wed, 27 Sep 2017 15:38:00 -0700 Subject: [PATCH 197/576] feature/acas-author-manager: created Author editor module --- conf/config.properties.example | 6 + docker-compose.yml | 6 +- .../routes/ACASLabelSequencesRoutes.coffee | 4 +- .../client/ModuleMenusConfiguration.coffee | 6 + .../ServerAPI/src/client/AuthorEditor.coffee | 556 ++++++++++++++++++ .../ServerAPI/src/client/AuthorEditor.html | 115 ++++ .../src/server/routes/AuthorRoutes.coffee | 30 + 7 files changed, 718 insertions(+), 5 deletions(-) create mode 100644 modules/ServerAPI/src/client/AuthorEditor.coffee create mode 100644 modules/ServerAPI/src/client/AuthorEditor.html diff --git a/conf/config.properties.example b/conf/config.properties.example index 5f81bf189..d8194b707 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -318,7 +318,13 @@ server.service.external.inventory.database.password= ## options for auth. strategy are: properties, database, ldap server.security.authstrategy=database #server.security.properties.path=/opt/seurat/SeuratServer/users.txt +#to make authstrategy config accessible to the client +client.security.authstrategy=${server.security.authstrategy} +#Controls whether Roo syncs the AuthorRole table with authorities granted in LDAP +server.security.syncLdapAuthRoles=false +#to make authstrategy config accessible to the client +client.security.syncLdapAuthRoles=${server.security.syncLdapAuthRoles} ## ACAS Home Page Options # If module is customized and the ACAS header name needs to be replaced, you can set the following options diff --git a/docker-compose.yml b/docker-compose.yml index 4bc3b9fd9..8f2e54c5f 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -60,7 +60,7 @@ services: ports: - "5432:5432" tomcat: - image: mcneilco/tomcat-maven + image: mcneilco/tomcat-maven:openjdk8 restart: always depends_on: - db @@ -81,12 +81,12 @@ services: - ./conf/docker/cmpdreg/environment/cmpdreg.env command: catalina.sh run roo: - image: mcneilco/acas-roo-server-oss:${ACAS_TAG} + image: mcneilco/acas-roo-server-oss:develop volumes: - /usr/local/tomcat/webapps/acas command: /bin/true cmpdreg: - image: mcneilco/acas-cmpdreg-roo-server-oss:${ACAS_TAG} + image: mcneilco/acas-cmpdreg-roo-server-oss:develop volumes: - /usr/local/tomcat/webapps/cmpdreg # Add chemaxon license files here diff --git a/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee b/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee index 5c18d75c3..8cd26903c 100644 --- a/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee +++ b/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee @@ -166,9 +166,9 @@ exports.getLsRoleCodeTables = (req, resp) -> else baseurl = config.all.client.service.persistence.fullpath+"lsRoles?format=codeTable" if req.query.lsType? - baseurl += "&lsType=#{lsType}" + baseurl += "&lsType=#{req.query.lsType}" if req.query.lsKind? - baseurl += "&lsKind=#{lsKind}" + baseurl += "&lsKind=#{req.query.lsKind}" serverUtilityFunctions.getFromACASServer(baseurl, resp) exports.getLabelTypeAndKindCodeTables = (req, resp) -> diff --git a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee index f9f951d4c..75a315261 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee @@ -47,6 +47,12 @@ window.ModuleMenusConfiguration = , isHeader: true menuName: "Admin" + , + isHeader: false + menuName: "Author Editor" + mainControllerClassName: "AuthorEditorController" + autoLaunchName: "author" + requireUserRoles: [] , isHeader: false menuName: "Admin Panel" diff --git a/modules/ServerAPI/src/client/AuthorEditor.coffee b/modules/ServerAPI/src/client/AuthorEditor.coffee new file mode 100644 index 000000000..b1e97426f --- /dev/null +++ b/modules/ServerAPI/src/client/AuthorEditor.coffee @@ -0,0 +1,556 @@ +class window.AuthorRole extends Backbone.Model + +class window.AuthorRoleList extends Backbone.Collection + model: AuthorRole + + validateCollection: => + modelErrors = [] + usedRoles={} + if @.length != 0 + for index in [0..@.length-1] + model = @.at(index) + currentRole = model.get('id') + if currentRole of usedRoles + modelErrors.push + attribute: "authorRole:eq("+index+")" + message: "The same role can not be chosen more than once" + modelErrors.push + attribute: "authorRole:eq("+usedRoles[currentRole]+")" + message: "The same role can not be chosen more than once" + else + usedRoles[currentRole] = index + modelErrors + +class window.Author extends Backbone.Model +# urlRoot: TODO: fill in once have service + + defaults: -> + lsType: "author" + lsKind: "author" + recordedBy: window.AppLaunchParams.loginUser.userName + recordedDate: new Date().getTime() + enabled: false + authorRoles: [] + + validate: (attrs) -> + errors = [] + firstName = attrs.firstName + if !firstName? or firstName is "" + errors.push + attribute: 'firstName' + message: "First name must be set" + lastName = attrs.lastName + if !lastName? or lastName is "" + errors.push + attribute: 'lastName' + message: "Last name must be set" + userName = attrs.userName + if !userName? or userName is "" + errors.push + attribute: 'userName' + message: "Username must be set" + emailAddress = attrs.emailAddress + if !emailAddress? or emailAddress is "" + errors.push + attribute: 'emailAddress' + message: "Email must be set" + activationDate = attrs.activationDate + if _.isNaN(attrs.activationDate) and !activationDate? + errors.push + attribute: 'activationDate' + message: "Date of activation must be a valid date" + + + if errors.length > 0 + return errors + else + return null + + getSystemRoles: => + systemRoles = _.filter @get('authorRoles'), (role) => + if role.roleEntry?.lsType? + role.roleEntry.lsType is "System" + + trimmedSystemRoles = _.pluck systemRoles, 'roleEntry' + return new AuthorRoleList trimmedSystemRoles + + getLdapRoles: => + ldapRoles = _.filter @get('authorRoles'), (role) => + if role.roleEntry?.lsType? + role.roleEntry.lsType is "LDAP" + + trimmedLdapRoles = _.pluck ldapRoles, 'roleEntry' + return new AuthorRoleList trimmedLdapRoles + + getProjectRoles: => + projectRoles = _.filter @get('authorRoles'), (role) => + if role.roleEntry?.lsType? + role.roleEntry.lsType is "Project" + + trimmedProjectRoles = _.pluck projectRoles, 'roleEntry' + + return new AuthorRoleList trimmedProjectRoles + +class window.AuthorRoleController extends AbstractFormController + template: _.template($("#AuthorRoleView").html()) + + events: -> + "change .bv_authorRole": "attributeChanged" + "click .bv_deleteAuthorRole": "clear" + + initialize: -> + @errorOwnerName = 'AuthorRoleController' + @setBindings() + @model.on "destroy", @remove, @ + if @options?.roleType? + @roleType = @options.roleType + else + @roleType = null + if @options?.roleKind? + @roleKind = @options.roleKind + else + @roleKind = null + + render: => + $(@el).empty() + $(@el).html @template() + @setupAuthorRoleSelect() + + @ + + setupAuthorRoleSelect: -> + @getAuthorRoles() + + finishSetupAuthorRoleSelect: => + @authorRoleListController = new PickListSelectController + el: @$('.bv_authorRole') + collection: @authorRoleList + insertFirstOption: new PickList + code: "unassigned" + name: "Select Role" + autoFetch: false + selectedCode: @model.get('id') + + getAuthorRoles: => + authorRoleListUrl = "/api/lsRoles/codeTable" + if @roleType? + authorRoleListUrl += "?lsType=#{@roleType}" + if @roleKind? + authorRoleListUrl += "&lsKind=#{@roleKind}" + else if @roleKind? + authorRoleListUrl += "?lsKind=#{@roleKind}" + + $.ajax + type: 'GET' + json: true + url: authorRoleListUrl + success: (response) => + #change the code to be id + _.each response, (role) => + role.code = role.id + @authorRoleList = new PickListList response + @finishSetupAuthorRoleSelect() + error: (err) => + alert 'could not get the nhp test subjects' + @serviceReturn = null + + + updateModel: => + roleId = @authorRoleListController.getSelectedCode() + @model.set + id: roleId + @trigger 'amDirty' + + clear: => + if @model.id? + @model.unset 'id' + @model.unset 'cid' + @model.destroy() + @trigger 'amDirty' + +class window.AuthorRoleListController extends Backbone.View + template: _.template($("#AuthorRoleListView").html()) + + events: + "click .bv_addAuthorRoleButton": "addNewAuthorRole" + + initialize: -> + unless @collection? + @collection = new Backbone.Collection() + newModel = new @collection.model + @collection.add newModel + if @options?.roleType? + @roleType = @options.roleType + else + @roleType = null + if @options?.roleKind? + @roleKind = @options.roleKind + else + @roleKind = null + if @options?.readOnly? + @readOnly = @options.readOnly + else + @readOnly = false + + + render: => + $(@el).empty() + $(@el).html @template() + + @collection.each (roleInfo) => + @addAuthorRole(roleInfo) + if @collection.length == 0 + @addNewAuthorRole() + @trigger 'renderComplete' + + if @readOnly + @displayInReadOnlyMode() + @ + + addNewAuthorRole: => + newModel = new @collection.model + newModel.set + lsType: @roleType + lsKind: @roleKind + @collection.add newModel + @addAuthorRole(newModel) + @trigger 'amDirty' + + addAuthorRole: (roleInfo) => + plc = new AuthorRoleController + model: roleInfo + roleType: @roleType + roleKind: @roleKind + plc.on 'amDirty', => + @trigger 'amDirty' + @$('.bv_authorRoleInfo').append plc.render().el + + isValid: => + validCheck = true + errors = @collection.validateCollection() + if errors.length > 0 + validCheck = false + @validationError(errors) + validCheck + + validationError: (errors) => + @clearValidationErrorStyles() + _.each errors, (err) => + unless @$('.bv_'+err.attribute).attr('disabled') is 'disabled' + @$('.bv_group_'+err.attribute).attr('data-toggle', 'tooltip') + @$('.bv_group_'+err.attribute).attr('data-placement', 'bottom') + @$('.bv_group_'+err.attribute).attr('data-original-title', err.message) + # @$('.bv_group_'+err.attribute).tooltip(); + @$("[data-toggle=tooltip]").tooltip(); + @$("body").tooltip selector: '.bv_group_'+err.attribute + @$('.bv_group_'+err.attribute).addClass 'input_error error' + @trigger 'notifyError', owner: this.errorOwnerName, errorLevel: 'error', message: err.message + + clearValidationErrorStyles: => + errorElms = @$('.input_error') + _.each errorElms, (ee) => + $(ee).removeAttr('data-toggle') + $(ee).removeAttr('data-placement') + $(ee).removeAttr('title') + $(ee).removeAttr('data-original-title') + $(ee).removeClass 'input_error error' + + displayInReadOnlyMode: => + @$('.bv_deleteAuthorRole').hide() + @$('.bv_addAuthorRoleButton').hide() + @disableAllInputs() + + disableAllInputs: -> + @$('input').not('.dontdisable').attr 'disabled', 'disabled' + @$('button').not('.dontdisable').attr 'disabled', 'disabled' + @$('select').not('.dontdisable').attr 'disabled', 'disabled' + @$("textarea").not('.dontdisable').attr 'disabled', 'disabled' + @$(".bv_activationDateIcon").not('.dontdisable').addClass "uneditable-input" + @$(".bv_activationDateIcon").not('.dontdisable').on "click", -> + return false + @$(".bv_group_tags input").not('.dontdisable').prop "placeholder", "" + @$(".bv_group_tags input").not('.dontdisable').css "background-color", "#eeeeee" + @$(".bv_group_tags input").not('.dontdisable').css "color", "#333333" + @$(".bv_group_tags div.bootstrap-tagsinput").not('.dontdisable').css "background-color", "#eeeeee" + @$("span.tag.label.label-info span").not('.dontdisable').attr "data-role", "" + + +class window.AuthorEditorController extends AbstractFormController + template: _.template($("#AuthorEditorView").html()) + moduleLaunchName: "author" + + events: -> + "keyup .bv_firstName": "attributeChanged" + "keyup .bv_lastName": "attributeChanged" + "keyup .bv_userName": "handleUsernameChanged" + "keyup .bv_emailAddress": "handleEmailChanged" + "change .bv_activationDate": "handleActivationDateChanged" + "click .bv_activationDateIcon": "handleActivationDateIconClicked" + "click .bv_enabled": "attributeChanged" + "click .bv_save": "handleSaveClicked" + "click .bv_newEntity": "handleNewEntityClicked" + "click .bv_cancel": "handleCancelClicked" + "click .bv_cancelClear": "handleCancelClearClicked" + "click .bv_confirmClear": "handleConfirmClearClicked" + + + + initialize: -> + if @model? + @completeInitialization() + else + if window.AppLaunchParams.moduleLaunchParams? + if window.AppLaunchParams.moduleLaunchParams.moduleName == @moduleLaunchName + $.ajax + type: 'GET' + url: "/api/authorByCodename/"+window.AppLaunchParams.moduleLaunchParams.code + dataType: 'json' + error: (err) => + alert 'Could not get author object with this code. Creating a new author' + @completeInitialization() + success: (authorObj) => + #TODO: need to restrict users who have role to view module + @model = new Author authorObj[0] + @completeInitialization() + else + @completeInitialization() + else + @completeInitialization() + + + completeInitialization: => + unless @model? + @model = new Author() + @errorOwnerName = 'AuthorEditorController' + @setBindings() + + if @options.readOnly? + @readOnly = @options.readOnly + else + @readOnly = false + $(@el).empty() + $(@el).html @template() + @$('.bv_save').attr('disabled', 'disabled') + @listenTo @model, 'sync', @modelSyncCallback + @listenTo @model, 'change', @modelChangeCallback + if (window.conf.security?.authstrategy? and window.conf.security.authstrategy is 'database') or (window.conf.security?.authstrategy? and window.conf.security.authstrategy is 'ldap' and window.conf.security?.syncLdapAuthRoles? and window.conf.security.syncLdapAuthRoles is false) + @setupSystemRoleListController() + @$('.bv_systemRoleListWrapper').show() + @$('.bv_ldapRoleListWrapper').hide() + else if (window.conf.security?.authstrategy? and window.conf.security.authstrategy is 'ldap') or (window.conf.security?.authstrategy? and window.conf.security.authstrategy is 'ldap' and window.conf.security?.syncLdapAuthRoles? and window.conf.security.syncLdapAuthRoles is true) + @setupLdapRoleListController() + @$('.bv_systemRoleListWrapper').hide() + @$('.bv_ldapRoleListWrapper').show() + @setupProjectRoleListController() + + @render() + + render: => + unless @model? + @model = new Author() + @$('.bv_firstName').val(@model.get('firstName')) + @$('.bv_lastName').val(@model.get('lastName')) + @$('.bv_userName').val(@model.get('userName')) + @$('.bv_emailAddress').val(@model.get('emailAddress')) + @$('.bv_activationDate').datepicker(); + @$('.bv_activationDate').datepicker( "option", "dateFormat", "yy-mm-dd" ); + if @model.get('activationDate')? + @$('.bv_activationDate').val UtilityFunctions::convertMSToYMDDate(@model.get('activationDate')) + enabled = @$('.bv_enabled').is(":checked") + if enabled + @$('.bv_enabled').attr 'checked', 'checked' + else + @$('.bv_enabled').removeAttr 'checked' + if @model.isNew() + @$('.bv_save').html("Save") + @$('.bv_newEntity').hide() + else + @$('.bv_save').html("Update") + @$('.bv_newEntity').show() + @$('.bv_save').attr('disabled', 'disabled') + @$('.bv_cancel').attr('disabled','disabled') + + if @readOnly is true + @displayInReadOnlyMode() + + @ + + modelSyncCallback: => + @trigger 'amClean' + @$('.bv_saving').hide() + @$('.bv_saveComplete').show() + if (window.conf.security?.authstrategy? and window.conf.security.authstrategy is 'database') or (window.conf.security?.authstrategy? and window.conf.security.authstrategy is 'ldap' and window.conf.security?.syncLdapAuthRoles? and window.conf.security.syncLdapAuthRoles is false) + @setupSystemRoleListController() + @$('.bv_systemRoleListWrapper').show() + @$('.bv_ldapRoleListWrapper').hide() + else if (window.conf.security?.authstrategy? and window.conf.security.authstrategy is 'ldap') or (window.conf.security?.authstrategy? and window.conf.security.authstrategy is 'ldap' and window.conf.security?.syncLdapAuthRoles? and window.conf.security.syncLdapAuthRoles is true) + @setupLdapRoleListController() + @$('.bv_systemRoleListWrapper').hide() + @$('.bv_ldapRoleListWrapper').show() + @setupProjectRoleListController() + @render() + + modelChangeCallback: => + @trigger 'amDirty' + @$('.bv_saveComplete').hide() + @$('.bv_cancel').removeAttr('disabled') + @$('.bv_cancelComplete').hide() + + setupSystemRoleListController: -> + if @systemRoleListController? + @systemRoleListController.undelegateEvents() + + systemRoles = @model.getSystemRoles() + @systemRoleListController= new AuthorRoleListController + el: @$('.bv_systemRoleList') + collection: systemRoles + roleType: "System" + + @finishAuthorRoleListControllerSetup @systemRoleListController + + setupLdapRoleListController: -> + if @ldapRoleListController? + @ldapRoleListController.undelegateEvents() + + ldapRoles = @model.getLdapRoles() + + @ldapRoleListController= new AuthorRoleListController + el: @$('.bv_ldapRoleList') + collection: ldapRoles + roleType: "LDAP" + readOnly: true + + @finishAuthorRoleListControllerSetup @ldapRoleListController + + setupProjectRoleListController: -> + if @projectRoleListController? + @projectRoleListController.undelegateEvents() + + projectRoles = @model.getProjectRoles() + + @projectRoleListController= new AuthorRoleListController + el: @$('.bv_projectRoleList') + collection: projectRoles + roleType: "Project" + readOnly: true + + @finishAuthorRoleListControllerSetup @projectRoleListController + + finishAuthorRoleListControllerSetup: (controller) -> + controller.on 'amClean', => + @trigger 'amClean' + controller.on 'renderComplete', => + @checkDisplayMode() + controller.render() + controller.on 'amDirty', => + @trigger 'amDirty' + @$('.bv_saveComplete').hide() + @$('.bv_saveFailed').hide() + @checkFormValid() + + + updateModel: => + @model.set 'firstName', UtilityFunctions::getTrimmedInput @$('.bv_firstName') + @model.set 'lastName', UtilityFunctions::getTrimmedInput @$('.bv_lastName') + @model.set 'enabled', @$('.bv_enabled').is(":checked") + + handleUsernameChanged: => + @model.set 'userName', UtilityFunctions::getTrimmedInput @$('.bv_userName') + + handleEmailChanged: => + @model.set 'emailAddress', UtilityFunctions::getTrimmedInput @$('.bv_emailAddress') + + handleActivationDateChanged: => + date = UtilityFunctions::getTrimmedInput @$('.bv_activationDate') + if date? and date != "" + date = UtilityFunctions::convertYMDDateToMs(UtilityFunctions::getTrimmedInput @$('.bv_activationDate')) + else + date = null + @model.set 'activationDate', date + + handleActivationDateIconClicked: => + @$( ".bv_activationDate" ).datepicker( "show" ) + + handleSaveClicked: => + @model.set 'authorRoles', [] + @prepareToSaveSystemRoles() + if @model.isNew() + @$('.bv_saveComplete').html "Save Complete" + else + @$('.bv_saveComplete').html "Update Complete" + @$('.bv_save').attr('disabled', 'disabled') + @$('.bv_saving').show() + console.log "handleSaveClicked" + console.log JSON.stringify @model +# @model.save() TODO: uncomment when service works + + prepareToSaveSystemRoles: => + authorRoles = [] + @systemRoleListController.collection.each (role) => + authorRoles.push + roleEntry: role + ar = @model.get 'authorRoles' + ar.push authorRoles... + @model.set 'authorRoles', ar + + handleNewEntityClicked: => + @$('.bv_confirmClearEntity').modal('show') + @$('.bv_confirmClear').removeAttr('disabled') + @$('.bv_cancelClear').removeAttr('disabled') + @$('.bv_closeModalButton').removeAttr('disabled') + + handleCancelClearClicked: => + @$('.bv_confirmClearEntity').modal('hide') + + handleConfirmClearClicked: => + @$('.bv_confirmClearEntity').modal('hide') + @model = null + @completeInitialization() + @trigger 'amClean' + + handleCancelClicked: => + if @model.isNew() + @model = null + @completeInitialization() + else + @$('.bv_canceling').show() + @model.fetch + success: @handleCancelComplete + @trigger 'amClean' + + handleCancelComplete: => + @$('.bv_canceling').hide() + @$('.bv_cancelComplete').show() + + validationError: => + super() + @$('.bv_save').attr('disabled', 'disabled') + + clearValidationErrorStyles: => + super() + @$('.bv_save').removeAttr('disabled') + + checkDisplayMode: => + if @readOnly is true + @displayInReadOnlyMode() + + displayInReadOnlyMode: => + @$(".bv_save").hide() + @$(".bv_cancel").hide() + @$(".bv_newEntity").hide() + @$(".bv_addFileInfo").hide() + @disableAllInputs() + + + checkFormValid: => + if @isValid() + @$('.bv_save').removeAttr('disabled') + else + @$('.bv_save').attr('disabled', 'disabled') + + isValid: => + validCheck = super() + if @systemRoleListController? + if @systemRoleListController.isValid() is false + validCheck = false + validCheck diff --git a/modules/ServerAPI/src/client/AuthorEditor.html b/modules/ServerAPI/src/client/AuthorEditor.html new file mode 100644 index 000000000..4d35612ab --- /dev/null +++ b/modules/ServerAPI/src/client/AuthorEditor.html @@ -0,0 +1,115 @@ + + + + + diff --git a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee index 478411bc5..0c5b47c02 100644 --- a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee @@ -1,10 +1,12 @@ exports.setupAPIRoutes = (app, loginRoutes) -> app.get '/api/authorByUsername/:username', exports.getAuthorByUsername + app.get '/api/authorByCodename/:codename', exports.getAuthorByCodename app.get '/api/authorModulePreferences/:userName/:moduleName', exports.getAuthorModulePreferences app.put '/api/authorModulePreferences/:userName/:moduleName', exports.updateAuthorModulePreferences exports.setupRoutes = (app, loginRoutes) -> app.get '/api/authorByUsername/:username', loginRoutes.ensureAuthenticated, exports.getAuthorByUsername + app.get '/api/authorByCodename/:codename', exports.getAuthorByCodename app.get '/api/authorModulePreferences/:userName/:moduleName', loginRoutes.ensureAuthenticated, exports.getAuthorModulePreferences app.put '/api/authorModulePreferences/:userName/:moduleName', loginRoutes.ensureAuthenticated, exports.updateAuthorModulePreferences @@ -56,6 +58,34 @@ exports.getAuthorByUsernameInternal = (username, callback) -> callback JSON.stringify("getContainersInLocation failed"), 500 ) +exports.getAuthorByCodename = (req, resp) -> + exports.getAuthorByCodenameInternal req.params.codeName, (json, statusCode) -> + resp.statusCode = statusCode + resp.json json + +exports.getAuthorByCodenameInternal = (codename, callback) -> + if global.specRunnerTestmode + authorServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/AuthorServiceTestJSON.js' + resp.json authorServiceTestJSON.getAuthorByUsernameInternalResponse + else + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"authors?find=ByCodeName&codeName="+codename + request = require 'request' + request( + method: 'GET' + url: baseurl + json: true + , (error, response, json) => + if !error && response.statusCode == 200 + callback json, 200 + else + console.error 'got ajax error trying to get author by codename' + console.error error + console.error json + console.error response + callback JSON.stringify("get author by codename failed"), 500 + ) + exports.getAuthorModulePreferences = (req, resp) -> exports.getAuthorModulePreferencesInternal req.params.userName, req.params.moduleName, (json, statusCode) -> resp.statusCode = statusCode From a0a7544cd1b3f45ced883ae0d4e6c8c8994dc2e5 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Wed, 27 Sep 2017 15:47:37 -0700 Subject: [PATCH 198/576] feature/acas-author-manager: hide activation date and enabled fields when authstrategy is 'ldap' --- .../ServerAPI/src/client/AuthorEditor.coffee | 23 +++++++++++-------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/modules/ServerAPI/src/client/AuthorEditor.coffee b/modules/ServerAPI/src/client/AuthorEditor.coffee index b1e97426f..b8dab5624 100644 --- a/modules/ServerAPI/src/client/AuthorEditor.coffee +++ b/modules/ServerAPI/src/client/AuthorEditor.coffee @@ -352,15 +352,20 @@ class window.AuthorEditorController extends AbstractFormController @$('.bv_lastName').val(@model.get('lastName')) @$('.bv_userName').val(@model.get('userName')) @$('.bv_emailAddress').val(@model.get('emailAddress')) - @$('.bv_activationDate').datepicker(); - @$('.bv_activationDate').datepicker( "option", "dateFormat", "yy-mm-dd" ); - if @model.get('activationDate')? - @$('.bv_activationDate').val UtilityFunctions::convertMSToYMDDate(@model.get('activationDate')) - enabled = @$('.bv_enabled').is(":checked") - if enabled - @$('.bv_enabled').attr 'checked', 'checked' - else - @$('.bv_enabled').removeAttr 'checked' + + if window.conf.security?.authstrategy? and window.conf.security.authStrategy is 'database' + @$('.bv_activationDate').datepicker(); + @$('.bv_activationDate').datepicker( "option", "dateFormat", "yy-mm-dd" ); + if @model.get('activationDate')? + @$('.bv_activationDate').val UtilityFunctions::convertMSToYMDDate(@model.get('activationDate')) + enabled = @$('.bv_enabled').is(":checked") + if enabled + @$('.bv_enabled').attr 'checked', 'checked' + else + @$('.bv_enabled').removeAttr 'checked' + else if window.conf.security?.authstrategy? and window.conf.security.authstrategy is 'ldap' + @$('.bv_group_activationDate').hide() + @$('.bv_group_enabled').hide() if @model.isNew() @$('.bv_save').html("Save") @$('.bv_newEntity').hide() From 176a434642e36559a520d8f6ec2eafa92d5136fd Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Thu, 28 Sep 2017 09:58:49 -0700 Subject: [PATCH 199/576] feature/acas-author-manager: added further author and system roles editing restrictions based on authstrategy and whether user is admin --- .../ServerAPI/src/client/AuthorEditor.coffee | 20 ++++++++++++++++--- .../ServerAPI/src/client/AuthorEditor.html | 4 ++-- 2 files changed, 19 insertions(+), 5 deletions(-) diff --git a/modules/ServerAPI/src/client/AuthorEditor.coffee b/modules/ServerAPI/src/client/AuthorEditor.coffee index b8dab5624..fabdc1f69 100644 --- a/modules/ServerAPI/src/client/AuthorEditor.coffee +++ b/modules/ServerAPI/src/client/AuthorEditor.coffee @@ -309,7 +309,6 @@ class window.AuthorEditorController extends AbstractFormController alert 'Could not get author object with this code. Creating a new author' @completeInitialization() success: (authorObj) => - #TODO: need to restrict users who have role to view module @model = new Author authorObj[0] @completeInitialization() else @@ -327,7 +326,16 @@ class window.AuthorEditorController extends AbstractFormController if @options.readOnly? @readOnly = @options.readOnly else - @readOnly = false + if window.conf.security?.authstrategy? and window.conf.security.authstrategy is 'database' + #if authstrategy is database, then only admins can create/edit + acasAdminRole = window.conf.roles.acas.adminRole + if acasAdminRole != "" and !UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, [acasAdminRole]) + @readOnly = true + else + @readOnly = false + else + #else anyone can create/edit + @readOnly = false $(@el).empty() $(@el).html @template() @$('.bv_save').attr('disabled', 'disabled') @@ -363,7 +371,7 @@ class window.AuthorEditorController extends AbstractFormController @$('.bv_enabled').attr 'checked', 'checked' else @$('.bv_enabled').removeAttr 'checked' - else if window.conf.security?.authstrategy? and window.conf.security.authstrategy is 'ldap' + else @$('.bv_group_activationDate').hide() @$('.bv_group_enabled').hide() if @model.isNew() @@ -402,6 +410,11 @@ class window.AuthorEditorController extends AbstractFormController @$('.bv_cancelComplete').hide() setupSystemRoleListController: -> + acasAdminRole = window.conf.roles.acas.adminRole + readOnly = false + if acasAdminRole != "" and !UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, [acasAdminRole]) + readOnly = true + if @systemRoleListController? @systemRoleListController.undelegateEvents() @@ -410,6 +423,7 @@ class window.AuthorEditorController extends AbstractFormController el: @$('.bv_systemRoleList') collection: systemRoles roleType: "System" + readOnly: readOnly @finishAuthorRoleListControllerSetup @systemRoleListController diff --git a/modules/ServerAPI/src/client/AuthorEditor.html b/modules/ServerAPI/src/client/AuthorEditor.html index 4d35612ab..3b65c1169 100644 --- a/modules/ServerAPI/src/client/AuthorEditor.html +++ b/modules/ServerAPI/src/client/AuthorEditor.html @@ -42,13 +42,13 @@

        ACAS Author

        -
        +
        -
        +
        From a1eec74e490b5fd9cf611acf68169bdeeca0e782 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 28 Sep 2017 10:24:48 -0700 Subject: [PATCH 200/576] Added standalone services saveWellToWelInteractions and createDaughterVials, and refactored CSV loading and validating routes to use more atomic internal functions. Refactored some of the utility functions to follow the (err, data) node standard for callback functions. --- .../routes/InventoryServiceRoutes.coffee | 384 ++++++++++++------ 1 file changed, 265 insertions(+), 119 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index ddea9e109..cdaeeb16e 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -59,6 +59,8 @@ exports.setupAPIRoutes = (app) -> app.post '/api/getContainerLogsByContainerCodes', exports.getContainerLogsByContainerCodes app.post '/api/loadParentVialsFromCSV', exports.loadParentVialsFromCSV app.post '/api/loadDaughterVialsFromCSV', exports.loadDaughterVialsFromCSV + app.post '/api/saveWellToWellInteractions', exports.saveWellToWellInteractions + app.post '/api/createDaughterVials', exports.createDaughterVials exports.setupRoutes = (app, loginRoutes) -> @@ -110,6 +112,8 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/updateContainerHistoryLogs', loginRoutes.ensureAuthenticated, exports.updateContainerHistoryLogs app.post '/api/loadParentVialsFromCSV', loginRoutes.ensureAuthenticated, exports.loadParentVialsFromCSV app.post '/api/loadDaughterVialsFromCSV', loginRoutes.ensureAuthenticated, exports.loadDaughterVialsFromCSV + app.post '/api/saveWellToWellInteractions', loginRoutes.ensureAuthenticated, exports.saveWellToWellInteractions + app.post '/api/createDaughterVials', loginRoutes.ensureAuthenticated, exports.createDaughterVials exports.getContainersInLocation = (req, resp) -> @@ -2583,7 +2587,9 @@ exports.validateParentVialsFromCSVInternal = (csvFileName, dryRun, callback) -> transactionId: null if exists validationResponse.results.path = path - createParentVialFileEntryArray csvFileName, (fileEntryArray) -> + createParentVialFileEntryArray csvFileName, (err, fileEntryArray) -> + if err? + callback err summaryInfo = prepareSummaryInfo fileEntryArray checkRequiredAttributes fileEntryArray, (requiredAttributeErrors) -> if requiredAttributeErrors? @@ -2629,7 +2635,9 @@ exports.createParentVialsFromCSVInternal = (csvFileName, dryRun, user, callback) commit: false if exists createResponse.results.path = path - createParentVialFileEntryArray csvFileName, (fileEntryArray) -> + createParentVialFileEntryArray csvFileName, (err, fileEntryArray) -> + if err? + callback err summaryInfo = prepareSummaryInfo fileEntryArray getContainerTubeDefinitionCode (definitionCode) -> if !definitionCode? @@ -2684,24 +2692,40 @@ exports.createParentVialsFromCSVInternal = (csvFileName, dryRun, user, callback) callback createResponse exports.loadDaughterVialsFromCSV = (req, resp) -> - exports.loadDaughterVialsFromCSVInternal req.body.fileToParse, req.body.dryRunMode, req.body.user, (response) -> - resp.json response + exports.loadDaughterVialsFromCSVInternal req.body.fileToParse, req.body.dryRunMode, req.body.user, (err, response) -> + if err? + resp.statusCode = 500 + resp.json err + else + resp.json response exports.loadDaughterVialsFromCSVInternal = (csvFileName, dryRun, user, callback) -> if dryRun - exports.validateDaughterVialsFromCSVInternal csvFileName, dryRun, (validationResponse) -> - callback validationResponse + exports.validateDaughterVialsFromCSVInternal csvFileName, dryRun, (err, validationResponse) -> + if err? + callback err + else + callback null, validationResponse else - exports.validateDaughterVialsFromCSVInternal csvFileName, dryRun, (validationResponse) -> - if validationResponse.hasError - callback validationResponse + exports.validateDaughterVialsFromCSVInternal csvFileName, dryRun, (err, validationResponse) -> + if err? + callback err + else if validationResponse.hasError + callback null, validationResponse else - exports.createDaughterVialsFromCSVInternal csvFileName, dryRun, user, (createVialsResponse) -> - callback createVialsResponse + exports.createDaughterVialsFromCSVInternal csvFileName, dryRun, user, (err, createVialsResponse) -> + if err? + callback err + else + callback null, createVialsResponse exports.validateDaughterVialsFromCSV = (req, resp) -> - exports.validateDaughterVialsFromCSVInternal req.body.csvFileName, (validationResponse) -> - resp.json validationResponse + exports.validateDaughterVialsFromCSVInternal req.body.csvFileName, (err, validationResponse) -> + if err? + resp.statusCode = 500 + resp.json err + else + resp.json validationResponse exports.validateDaughterVialsFromCSVInternal = (csvFileName, dryRun, callback) -> getFileExists csvFileName, (exists, path) -> @@ -2716,38 +2740,19 @@ exports.validateDaughterVialsFromCSVInternal = (csvFileName, dryRun, callback) - transactionId: null if exists validationResponse.results.path = path - createDaughterVialFileEntryArray csvFileName, (fileEntryArray) -> + createDaughterVialFileEntryArray csvFileName, (err, fileEntryArray) -> + if err? + callback err summaryInfo = prepareSummaryInfo fileEntryArray - checkRequiredAttributes fileEntryArray, (requiredAttributeErrors) -> - if requiredAttributeErrors? - validationResponse.errorMessages.push requiredAttributeErrors... - checkDataTypeErrors fileEntryArray, (dataTypeErrors) -> - if dataTypeErrors? - validationResponse.errorMessages.push dataTypeErrors... - sourceBarcodes = _.pluck fileEntryArray, 'sourceVialBarcode' - checkBarcodesExist sourceBarcodes, (existingBarcodes, newBarcodes) -> - console.log 'checking source vial barcodes which should exist' - console.log existingBarcodes - console.log newBarcodes - if newBarcodes? and newBarcodes.length > 0 - error = - level: 'error' - message: "The following source barcodes do not exist: " + newBarcodes.join ', ' - validationResponse.errorMessages.push error - destinationBarcodes = _.pluck fileEntryArray, 'destinationVialBarcode' - checkBarcodesExist destinationBarcodes, (existingBarcodes, newBarcodes) -> - if existingBarcodes? and existingBarcodes.length > 0 - error = - level: 'error' - message: "The following destination barcodes already exist: " + existingBarcodes.join ', ' - validationResponse.errorMessages.push error - checkParentWellContent fileEntryArray, (parentWellContentErrors) -> - if parentWellContentErrors? - validationResponse.errorMessages.push parentWellContentErrors... - if validationResponse.errorMessages.length < 1 - validationResponse.hasError = false - validationResponse.results.htmlSummary = prepareValidationHTMLSummary validationResponse.hasError, validationResponse.hasWarning, validationResponse.errorMessages, summaryInfo - callback validationResponse + exports.validateDaughterVialsInternal fileEntryArray, (err, errorsAndWarnings) -> + if err? + callback err + else + validationResponse.errorMessages.push errorsAndWarnings... + if validationResponse.errorMessages.length < 1 + validationResponse.hasError = false + validationResponse.results.htmlSummary = prepareValidationHTMLSummary validationResponse.hasError, validationResponse.hasWarning, validationResponse.errorMessages, summaryInfo + callback null, validationResponse else error = level: 'error' @@ -2767,80 +2772,30 @@ exports.createDaughterVialsFromCSVInternal = (csvFileName, dryRun, user, callbac errorMessages: [] transactionId: null commit: false - if exists - createResponse.results.path = path - createDaughterVialFileEntryArray csvFileName, (fileEntryArray) -> - summaryInfo = prepareSummaryInfo fileEntryArray - getContainerTubeDefinitionCode (definitionCode) -> - if !definitionCode? - error = - level: 'error' - message: 'Could not find definition container for tube' - createResponse.errorMessages.push error - tubesToCreate = [] - _.each fileEntryArray, (entry) -> - tube = - barcode: entry.destinationVialBarcode - definition: definitionCode - recordedBy: user - createdUser: entry.preparedBy - createdDate: entry.createdDate - physicalState: entry.physicalState - wells: [ - wellName: "A001" - batchCode: entry.batchCode - amount: parseFloat(entry.amount) - amountUnits: entry.amountUnits - physicalState: entry.physicalState - recordedBy: user - recordedDate: (new Date()).getTime() - ] - if entry.physicalState == 'solution' - tube.wells[0].batchConcentration = parseFloat(entry.concentration) - tube.wells[0].batchConcUnits = entry.concUnits - tube.wells[0].solventCode = entry.solvent - tubesToCreate.push tube - console.log JSON.stringify tubesToCreate - exports.createTubesInternal tubesToCreate, 0, (json, statusCode) -> - console.log statusCode - console.log json - if statusCode != 200 - createResponse.hasError = true - console.error json - error = - level: 'error' - message: json - createResponse.errorMessages.push error - else - createResponse.hasError = false - createResponse.commit = true - if !createResponse.hasError - #TODO: create interactions or values of daughter to parent relation - parentVialsToDecrement = [] - _.each fileEntryArray, (entry) -> - toDecrement = - barcode: entry.sourceVialBarcode - amountToDecrement: parseFloat(entry.amount) - amountToDecrementUnits: entry.amountUnits - parentVialsToDecrement.push toDecrement - decrementAmountsFromVials parentVialsToDecrement, user, (decrementVialsResponse, decrementVialsStatusCode) -> - if decrementVialsStatusCode != 200 - error = - level: 'error' - message: decrementVialsResponse - createResponse.errorMessages.push error - createResponse.hasError = true - createResponse.results.htmlSummary = prepareCreateDaughterVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo - callback createResponse - else - createResponse.results.htmlSummary = prepareCreateDaughterVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo - callback createResponse - else + if !exists error = level: 'error' message: "File cannot be found" createResponse.errorMessages.push error callback createResponse + else + createResponse.results.path = path + createDaughterVialFileEntryArray csvFileName, (err, fileEntryArray) -> + if err? + callback err + summaryInfo = prepareSummaryInfo fileEntryArray + exports.createDaughterVialsInternal fileEntryArray, user, (err, response) -> + if err? + error = + level: 'error' + message: err + createResponse.errorMessages.push error + else + createResponse.hasError = false + createResponse.commit = true + createResponse.results.htmlSummary = prepareCreateDaughterVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo + callback null, createResponse + getFileExists = (csvFileName, callback) => @@ -2882,7 +2837,7 @@ createParentVialFileEntryArray = (csvFileName, callback) => rowCount++ ) .on('end', () -> - return callback csvFileEntries, 200 + return callback null, csvFileEntries ) createDaughterVialFileEntryArray = (csvFileName, callback) => @@ -2910,7 +2865,7 @@ createDaughterVialFileEntryArray = (csvFileName, callback) => rowCount++ ) .on('end', () -> - return callback csvFileEntries, 200 + return callback null, csvFileEntries ) checkRequiredAttributes = (fileEntryArray, callback) -> @@ -3082,9 +3037,9 @@ decrementAmountsFromVials = (parentVialsToDecrement, user, callback) -> exports.getWellContentByContainerLabelsInternal vialBarcodes, 'container', 'tube', 'barcode', 'barcode', (wellContentList, statusCode) -> wellsToUpdate = [] _.each parentVialsToDecrement, (toDecrement) -> - wellCode = (_.findWhere plateWellCodes, {plateBarcode: toDecrement.barcode}).wellCodeName - oldContainerWellContent = _.findWhere wellContentList, {containerCodeName: wellCode} + oldContainerWellContent = _.findWhere wellContentList, {label: toDecrement.barcode} oldWellContent = oldContainerWellContent.wellContent[0] + wellCode = oldWellContent.containerCodeName newWellContent = containerCodeName: wellCode amount: oldWellContent.amount - toDecrement.amountToDecrement @@ -3096,7 +3051,7 @@ decrementAmountsFromVials = (parentVialsToDecrement, user, callback) -> if updateWellsStatusCode != 204 callback "Error: #{updateWellsResponse}" else - callback updateWellsResponse, 200 + callback null, updateWellsResponse prepareCreateDaughterVialsHTMLSummary = (hasError, hasWarning, errorMessages, summaryInfo) -> errors = _.where errorMessages, {level: 'error'} @@ -3128,4 +3083,195 @@ prepareSummaryInfo = (fileEntryArray) -> batchCodes = _.pluck fileEntryArray, 'batchCode' if batchCodes? summaryInfo.totalBatchCodes = (_.uniq batchCodes).length - summaryInfo \ No newline at end of file + summaryInfo + + +exports.saveWellToWellInteractions = (req, resp) -> + if req.session?.passport?.user?.username? + user = req.session.passport.user.username + else + user = 'anonymous' + exports.saveWellToWellInteractionsInternal req.body, user, (err, data) -> + if err? + resp.statusCode = 500 + resp.json err + else + resp.json data + +exports.saveWellToWellInteractionsInternal = (interactionsToSave, user, callback) -> + barcodes = [] + barcodes.push (_.pluck interactionsToSave, 'firstContainerBarcode')... + barcodes.push (_.pluck interactionsToSave, 'secondContainerBarcode')... + console.log barcodes + exports.getWellCodesByPlateBarcodesInternal barcodes, (plateWellCodes) -> + wellCodes = _.pluck plateWellCodes, 'wellCodeName' + exports.getContainersByCodeNamesInternal wellCodes, (wells, statusCode) -> + if statusCode? && statusCode != 200 + callback wells + else + formattedItxList = [] + _.each interactionsToSave, (itx) -> + requiredParams = ['firstContainerBarcode', 'firstWellLabel', 'secondContainerBarcode', 'secondWellLabel', 'interactionType', 'interactionKind'] + for param in requiredParams + if !itx[param]? + callback "Error: all entries must include #{param}" + firstWellCode = (_.findWhere plateWellCodes, {plateBarcode: itx.firstContainerBarcode, wellLabel: itx.firstWellLabel}).wellCodeName + firstWell = (_.findWhere wells, {containerCodeName: firstWellCode}).container + secondWellCode = (_.findWhere plateWellCodes, {plateBarcode: itx.secondContainerBarcode, wellLabel: itx.secondWellLabel}).wellCodeName + secondWell = (_.findWhere wells, {containerCodeName: secondWellCode}).container + formattedItx = + lsType: itx.interactionType + lsKind: itx.interactionKind + recordedBy: user + recordedDate: new Date().getTime() + firstContainer: firstWell + secondContainer: secondWell + if itx.interactionStates? + _.each itx.interactionStates, (state) -> + state.recordedBy = user + state.recordedDate = new Date().getTime() + _.each state.lsValues, (value) -> + value.recordedBy = user + value.recordedDate = new Date().getTime() + formattedItx.lsStates = itx.interactionStates + formattedItxList.push formattedItx + baseurl = config.all.client.service.persistence.fullpath+"itxcontainercontainers/jsonArray" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: formattedItxList + json: true + timeout: 86400000 + , (error, response, json) => + if !error && response.statusCode == 201 + callback null, json + else + console.error 'error trying to save container container interactions' + console.error error + console.log response.statusCode + console.error json + callback "Error trying to save container container interactions: #{error}" + ) + +exports.validateDaughterVialsInternal = (vialsToValidate, callback) -> + errorMessages = [] + checkRequiredAttributes vialsToValidate, (requiredAttributeErrors) -> + if requiredAttributeErrors? + errorMessages.push requiredAttributeErrors... + checkDataTypeErrors vialsToValidate, (dataTypeErrors) -> + if dataTypeErrors? + errorMessages.push dataTypeErrors... + sourceBarcodes = _.pluck vialsToValidate, 'sourceVialBarcode' + checkBarcodesExist sourceBarcodes, (existingBarcodes, newBarcodes) -> + if newBarcodes? and newBarcodes.length > 0 + error = + level: 'error' + message: "The following source barcodes do not exist: " + newBarcodes.join ', ' + errorMessages.push error + destinationBarcodes = _.pluck vialsToValidate, 'destinationVialBarcode' + checkBarcodesExist destinationBarcodes, (existingBarcodes, newBarcodes) -> + if existingBarcodes? and existingBarcodes.length > 0 + error = + level: 'error' + message: "The following destination barcodes already exist: " + existingBarcodes.join ', ' + errorMessages.push error + checkParentWellContent vialsToValidate, (parentWellContentErrors) -> + if parentWellContentErrors? + errorMessages.push parentWellContentErrors... + callback null, errorMessages + +exports.createDaughterVials = (req, resp) -> + if req.session?.passport?.user?.username? + user = req.session.passport.user.username + else + user = 'anonymous' + exports.validateDaughterVialsInternal req.body, (err, errorsAndWarnings) -> + if err? + resp.statusCode = 500 + resp.json err + else + errors = _.where errorsAndWarnings, {level: 'error'} + warnings = _.where errorsAndWarnings, {level: 'warning'} + if errors? and errors.length > 0 + resp.statusCode = 400 + resp.json errorsAndWarnings + else + exports.createDaughterVialsInternal req.body, user, (err, response) -> + if err? + resp.statusCode = 500 + resp.json err + else + resp.json response + +exports.createDaughterVialsInternal = (vialsToCreate, user, callback) -> + getContainerTubeDefinitionCode (definitionCode) -> + if !definitionCode? + callback 'Could not find definition container for tube' + tubesToCreate = [] + _.each vialsToCreate, (entry) -> + tube = + barcode: entry.destinationVialBarcode + definition: definitionCode + recordedBy: user + createdUser: entry.preparedBy + createdDate: entry.createdDate + physicalState: entry.physicalState + wells: [ + wellName: "A001" + batchCode: entry.batchCode + amount: parseFloat(entry.amount) + amountUnits: entry.amountUnits + physicalState: entry.physicalState + recordedBy: user + recordedDate: (new Date()).getTime() + ] + if entry.physicalState == 'solution' + tube.wells[0].batchConcentration = parseFloat(entry.concentration) + tube.wells[0].batchConcUnits = entry.concUnits + tube.wells[0].solventCode = entry.solvent + tubesToCreate.push tube + console.log JSON.stringify tubesToCreate + exports.createTubesInternal tubesToCreate, 0, (json, statusCode) -> + console.log statusCode + console.log json + if statusCode != 200 + callback json + else + interactionsToCreate = [] + _.each vialsToCreate, (entry) -> + interaction = + interactionType: 'added to' + interactionKind: 'well_well' + firstContainerBarcode: entry.sourceVialBarcode + secondContainerBarcode: entry.destinationVialBarcode + firstWellLabel: 'A001' + secondWellLabel: 'A001' + interactionStates: [ + lsType: 'metadata' + lsKind: 'information' + lsValues: [ + lsType: 'numericValue' + lsKind: 'amount added' + numericValue: parseFloat(entry.amount) + unitKind: entry.amountUnits + ] + ] + interactionsToCreate.push interaction + exports.saveWellToWellInteractionsInternal interactionsToCreate, user, (err, itxResponse) -> + if err? + callback err + else + parentVialsToDecrement = [] + _.each vialsToCreate, (entry) -> + toDecrement = + barcode: entry.sourceVialBarcode + amountToDecrement: parseFloat(entry.amount) + amountToDecrementUnits: entry.amountUnits + parentVialsToDecrement.push toDecrement + decrementAmountsFromVials parentVialsToDecrement, user, (err, decrementVialsResponse) -> + if err? + callback err + else + #TODO see what this service should respond with + callback null, 'successfully created daughter vials' \ No newline at end of file From 327d45f453c8688a491aab7e6d199d7bc797a2e8 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Thu, 28 Sep 2017 11:24:43 -0700 Subject: [PATCH 201/576] more aliquot inventory progress --- .../src/server/routes/ServerUtilityFunctions.coffee | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee b/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee index ea627a209..d16754d1b 100644 --- a/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee +++ b/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee @@ -2160,6 +2160,12 @@ class ContainerTube extends ContainerPlate stateKind: 'information' type: 'stringValue' kind: 'comments' + , + key: 'locationName' + stateType: 'metadata' + stateKind: 'information' + type: 'stringValue' + kind: 'locationName' ] class AnalysisGroup extends Backbone.Model From c21fceedbbe2ff0b2f4fad4296dc5d66b5df6a8b Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Thu, 28 Sep 2017 13:50:56 -0700 Subject: [PATCH 202/576] feature/acas-author-manager: added author editing and deleting roles, fixed bug in testUserHasRole and testUserHasRoleTypeKindName, added Author Browser module, deep link to author module by username rather than codeName (roo route doesn't exist for get by codename), disable username editing, added node proxies for deleting author and searching for author --- conf/config.properties.example | 4 + .../src/client/UtilityFunctions.coffee | 4 +- .../client/ModuleMenusConfiguration.coffee | 3 + .../ServerAPI/src/client/AuthorBrowser.coffee | 234 ++++++++++++++++++ .../ServerAPI/src/client/AuthorBrowser.html | 139 +++++++++++ .../ServerAPI/src/client/AuthorEditor.coffee | 24 +- .../src/server/routes/AuthorRoutes.coffee | 96 ++++--- 7 files changed, 461 insertions(+), 43 deletions(-) create mode 100644 modules/ServerAPI/src/client/AuthorBrowser.coffee create mode 100644 modules/ServerAPI/src/client/AuthorBrowser.html diff --git a/conf/config.properties.example b/conf/config.properties.example index d8194b707..8234bb8d3 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -415,6 +415,10 @@ client.protocol.showAssayTreeRule=false client.protocol.showCurveDisplayParams=true client.experiment.uneditableFileTypes=["source file", "annotation file"] +#Controls privileges for who can create/edit and delete authors +client.author.editingRoles= +client.author.deletingRoles= + # Default status for experiments loaded thorugh experiment loader server.sel.experimentStatus=approved server.sel.protocolStatus=created diff --git a/modules/Components/src/client/UtilityFunctions.coffee b/modules/Components/src/client/UtilityFunctions.coffee index 10731f3a6..aaee23e19 100644 --- a/modules/Components/src/client/UtilityFunctions.coffee +++ b/modules/Components/src/client/UtilityFunctions.coffee @@ -4,7 +4,7 @@ class window.UtilityFunctions testUserHasRole: (user, roleNames) -> - if not user.roles? then return true + if not user.roles? then return false if not roleNames? || roleNames.length == 0 then return true match = false for roleName in roleNames @@ -17,7 +17,7 @@ class window.UtilityFunctions testUserHasRoleTypeKindName: (user, roleInfo) -> #roleInfo = list of objects with role type, kind, and name - if not user.roles? then return true + if not user.roles? then return false if not roleInfo? || roleInfo.length == 0 then return true match = false for role in roleInfo diff --git a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee index 75a315261..cd742d140 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee @@ -44,6 +44,9 @@ window.ModuleMenusConfiguration = , isHeader: false, menuName: "Project Browser" mainControllerClassName: "ProjectBrowserController" + , + isHeader: false, menuName: "Author Browser" + mainControllerClassName: "AuthorBrowserController" , isHeader: true menuName: "Admin" diff --git a/modules/ServerAPI/src/client/AuthorBrowser.coffee b/modules/ServerAPI/src/client/AuthorBrowser.coffee new file mode 100644 index 000000000..e8439b8e9 --- /dev/null +++ b/modules/ServerAPI/src/client/AuthorBrowser.coffee @@ -0,0 +1,234 @@ +class window.AuthorSearch extends Backbone.Model + defaults: + protocolCode: null + authorCode: null + +class window.AuthorSearch extends Backbone.Model + defaults: + protocolCode: null + authorCode: null + +class window.AuthorSimpleSearchController extends AbstractFormController + template: _.template($("#AuthorSimpleSearchView").html()) + genericSearchUrl: "/api/genericSearch/authors" + + events: + 'keyup .bv_authorSearchTerm': 'updateAuthorSearchTerm' + 'click .bv_doSearch': 'handleDoSearchClicked' + + render: => + $(@el).empty() + $(@el).html @template() + + updateAuthorSearchTerm: (e) => + ENTER_KEY = 13 + authorSearchTerm = $.trim(@$(".bv_authorSearchTerm").val()) + if authorSearchTerm isnt "" + @$(".bv_doSearch").attr("disabled", false) + if e.keyCode is ENTER_KEY + $(':focus').blur() + @handleDoSearchClicked() + else + @$(".bv_doSearch").attr("disabled", true) + + handleDoSearchClicked: => + $(".bv_authorTableController").addClass "hide" + $(".bv_errorOccurredPerformingSearch").addClass "hide" + authorSearchTerm = $.trim(@$(".bv_authorSearchTerm").val()) + $(".bv_exptSearchTerm").val "" + if authorSearchTerm isnt "" + $(".bv_noMatchingAuthorsFoundMessage").addClass "hide" + $(".bv_authorBrowserSearchInstructions").addClass "hide" + $(".bv_searchAuthorsStatusIndicator").removeClass "hide" + if !window.conf.browser.enableSearchAll and authorSearchTerm is "*" + $(".bv_moreSpecificAuthorSearchNeeded").removeClass "hide" + else + $(".bv_searchingAuthorsMessage").removeClass "hide" + $(".bv_exptSearchTerm").html authorSearchTerm + $(".bv_moreSpecificAuthorSearchNeeded").addClass "hide" + @doSearch authorSearchTerm + + doSearch: (authorSearchTerm) => + # disable the search text field while performing a search + @$(".bv_authorSearchTerm").attr "disabled", true + @$(".bv_doSearch").attr "disabled", true + @trigger 'find' + unless authorSearchTerm is "" + $.ajax + type: 'POST' + url: @genericSearchUrl + contentType: "application/json" + dataType: "json" + data: + JSON.stringify + queryString: authorSearchTerm + success: (author) => + @trigger "searchReturned", author + error: (result) => + @trigger "searchReturned", null + complete: => + # re-enable the search text field regardless of if any results found + @$(".bv_authorSearchTerm").attr "disabled", false + @$(".bv_doSearch").attr "disabled", false + + + +class window.AuthorRowSummaryController extends Backbone.View + tagName: 'tr' + className: 'dataTableRow' + events: + "click": "handleClick" + + handleClick: => + @trigger "gotClick", @model + $(@el).closest("table").find("tr").removeClass "info" + $(@el).addClass "info" + + initialize: -> + @template = _.template($('#AuthorRowSummaryView').html()) + + render: => + toDisplay = + userName: @model.get('userName') + firstName: @model.get('firstName') + lastName: @model.get('lastName') + emailAddress: @model.get('emailAddress') + $(@el).html(@template(toDisplay)) + + @ + +class window.AuthorSummaryTableController extends Backbone.View + initialize: -> + + selectedRowChanged: (row) => + @trigger "selectedRowUpdated", row + + render: => + @template = _.template($('#AuthorSummaryTableView').html()) + $(@el).html @template + if @collection.models.length is 0 + $(".bv_noMatchingAuthorsFoundMessage").removeClass "hide" + # display message indicating no results were found + else + $(".bv_noMatchingAuthorsFoundMessage").addClass "hide" + @collection.each (auth) => + prsc = new AuthorRowSummaryController + model: auth + prsc.on "gotClick", @selectedRowChanged + @$("tbody").append prsc.render().el + + @$("table").dataTable oLanguage: + sSearch: "Filter results: " #rename summary table's search bar + + @ + + +class window.AuthorBrowserController extends Backbone.View + events: + "click .bv_deleteAuthor": "handleDeleteAuthorClicked" + "click .bv_editAuthor": "handleEditAuthorClicked" + "click .bv_confirmDeleteAuthorButton": "handleConfirmDeleteAuthorClicked" + "click .bv_cancelDelete": "handleCancelDeleteClicked" + + initialize: -> + template = _.template($("#AuthorBrowserView").html()) + $(@el).empty() + $(@el).html template + @searchController = new AuthorSimpleSearchController + model: new AuthorSearch() + el: @$('.bv_authorSearchController') + @searchController.render() + @searchController.on "searchReturned", @setupAuthorSummaryTable + @$('.bv_queryToolDisplayName').html window.conf.service.result.viewer.displayName + + setupAuthorSummaryTable: (authors) => + @destroyAuthorSummaryTable() + + $(".bv_searchingAuthorsMessage").addClass "hide" + if authors is null + @$(".bv_errorOccurredPerformingSearch").removeClass "hide" + + else if authors.length is 0 + @$(".bv_noMatchingAuthorsFoundMessage").removeClass "hide" + @$(".bv_authorTableController").html "" + else + $(".bv_searchAuthorsStatusIndicator").addClass "hide" + @$(".bv_authorTableController").removeClass "hide" + @authorSummaryTable = new AuthorSummaryTableController + collection: new AuthorList authors + + @authorSummaryTable.on "selectedRowUpdated", @selectedAuthorUpdated + $(".bv_authorTableController").html @authorSummaryTable.render().el + + selectedAuthorUpdated: (author) => + @trigger "selectedAuthorUpdated" + @authorController = new AuthorEditorController + model: new Author author.attributes + readOnly: true + + $('.bv_authorController').html @authorController.render().el + $(".bv_authorController").removeClass("hide") + $(".bv_authorControllerContainer").removeClass("hide") + + @$('.bv_editAuthor').show() + if window.conf.author?.editingRoles? + editingRoles = window.conf.author.editingRoles.split(",") + if !UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, editingRoles) + @$('.bv_editAuthor').hide() + + @$('.bv_deleteAuthor').show() + if window.conf.author?.deletingRoles? + deletingRoles= window.conf.author.deletingRoles.split(",") + if !UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, deletingRoles) + @$('.bv_deleteAuthor').hide() + + handleDeleteAuthorClicked: => + @$(".bv_authorUserName").html @authorController.model.get("userName") + @$(".bv_deleteButtons").removeClass "hide" + @$(".bv_okayButton").addClass "hide" + @$(".bv_errorDeletingAuthorMessage").addClass "hide" + @$(".bv_deleteWarningMessage").removeClass "hide" + @$(".bv_deletingStatusIndicator").addClass "hide" + @$(".bv_authorDeletedSuccessfullyMessage").addClass "hide" + $(".bv_confirmDeleteAuthor").removeClass "hide" + $('.bv_confirmDeleteAuthor').modal({ + keyboard: false, + backdrop: true + }) + + handleConfirmDeleteAuthorClicked: => + @$(".bv_deleteWarningMessage").addClass "hide" + @$(".bv_deletingStatusIndicator").removeClass "hide" + @$(".bv_deleteButtons").addClass "hide" + $.ajax( + url: "/api/authors/#{@authorController.model.get("id")}", + type: 'DELETE', + success: (result) => + @$(".bv_okayButton").removeClass "hide" + @$(".bv_deletingStatusIndicator").addClass "hide" + @$(".bv_authorDeletedSuccessfullyMessage").removeClass "hide" + @searchController.handleDoSearchClicked() + error: (result) => + @$(".bv_okayButton").removeClass "hide" + @$(".bv_deletingStatusIndicator").addClass "hide" + @$(".bv_errorDeletingAuthorMessage").removeClass "hide" + ) + + handleCancelDeleteClicked: => + @$(".bv_confirmDeleteAuthor").modal('hide') + + handleEditAuthorClicked: => + window.open("/author/codeName/#{@authorController.model.get("userName")}",'_blank'); + + destroyAuthorSummaryTable: => + if @authorSummaryTable? + @authorSummaryTable.remove() + if @authorController? + @authorController.remove() + $(".bv_authorController").addClass("hide") + $(".bv_authorControllerContainer").addClass("hide") + $(".bv_noMatchingAuthorsFoundMessage").addClass("hide") + + render: => + + @ diff --git a/modules/ServerAPI/src/client/AuthorBrowser.html b/modules/ServerAPI/src/client/AuthorBrowser.html new file mode 100644 index 000000000..b294d090e --- /dev/null +++ b/modules/ServerAPI/src/client/AuthorBrowser.html @@ -0,0 +1,139 @@ + + + + + + + diff --git a/modules/ServerAPI/src/client/AuthorEditor.coffee b/modules/ServerAPI/src/client/AuthorEditor.coffee index fabdc1f69..c67094978 100644 --- a/modules/ServerAPI/src/client/AuthorEditor.coffee +++ b/modules/ServerAPI/src/client/AuthorEditor.coffee @@ -91,6 +91,9 @@ class window.Author extends Backbone.Model return new AuthorRoleList trimmedProjectRoles +class window.AuthorList extends Backbone.Collection + model: Author + class window.AuthorRoleController extends AbstractFormController template: _.template($("#AuthorRoleView").html()) @@ -303,13 +306,13 @@ class window.AuthorEditorController extends AbstractFormController if window.AppLaunchParams.moduleLaunchParams.moduleName == @moduleLaunchName $.ajax type: 'GET' - url: "/api/authorByCodename/"+window.AppLaunchParams.moduleLaunchParams.code + url: "/api/authorByUsername/"+window.AppLaunchParams.moduleLaunchParams.code dataType: 'json' error: (err) => alert 'Could not get author object with this code. Creating a new author' @completeInitialization() success: (authorObj) => - @model = new Author authorObj[0] + @model = new Author authorObj @completeInitialization() else @completeInitialization() @@ -326,16 +329,13 @@ class window.AuthorEditorController extends AbstractFormController if @options.readOnly? @readOnly = @options.readOnly else - if window.conf.security?.authstrategy? and window.conf.security.authstrategy is 'database' - #if authstrategy is database, then only admins can create/edit - acasAdminRole = window.conf.roles.acas.adminRole - if acasAdminRole != "" and !UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, [acasAdminRole]) + #create/edit based on whether user has create/edit role + @readOnly = false + if window.conf.author?.editingRoles? + editingRoles = window.conf.author.editingRoles.split(",") + if !UtilityFunctions::testUserHasRole(window.AppLaunchParams.loginUser, editingRoles) @readOnly = true - else - @readOnly = false - else - #else anyone can create/edit - @readOnly = false + $(@el).empty() $(@el).html @template() @$('.bv_save').attr('disabled', 'disabled') @@ -375,9 +375,11 @@ class window.AuthorEditorController extends AbstractFormController @$('.bv_group_activationDate').hide() @$('.bv_group_enabled').hide() if @model.isNew() + @$('.bv_userName').removeAttr 'disabled' @$('.bv_save').html("Save") @$('.bv_newEntity').hide() else + @$('.bv_userName').attr 'disabled', 'disabled' @$('.bv_save').html("Update") @$('.bv_newEntity').show() @$('.bv_save').attr('disabled', 'disabled') diff --git a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee index 0c5b47c02..416c844b0 100644 --- a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee @@ -1,14 +1,16 @@ exports.setupAPIRoutes = (app, loginRoutes) -> app.get '/api/authorByUsername/:username', exports.getAuthorByUsername - app.get '/api/authorByCodename/:codename', exports.getAuthorByCodename app.get '/api/authorModulePreferences/:userName/:moduleName', exports.getAuthorModulePreferences app.put '/api/authorModulePreferences/:userName/:moduleName', exports.updateAuthorModulePreferences + app.post '/api/genericSearch/authors', exports.genericAuthorSearch + app.delete '/api/authors/:id', exports.deleteAuthor exports.setupRoutes = (app, loginRoutes) -> app.get '/api/authorByUsername/:username', loginRoutes.ensureAuthenticated, exports.getAuthorByUsername - app.get '/api/authorByCodename/:codename', exports.getAuthorByCodename app.get '/api/authorModulePreferences/:userName/:moduleName', loginRoutes.ensureAuthenticated, exports.getAuthorModulePreferences app.put '/api/authorModulePreferences/:userName/:moduleName', loginRoutes.ensureAuthenticated, exports.updateAuthorModulePreferences + app.post '/api/genericSearch/authors', loginRoutes.ensureAuthenticated, exports.genericAuthorSearch + app.delete '/api/authors/:id', loginRoutes.ensureAuthenticated, exports.deleteAuthor serverUtilityFunctions = require './ServerUtilityFunctions.js' _ = require 'underscore' @@ -58,34 +60,6 @@ exports.getAuthorByUsernameInternal = (username, callback) -> callback JSON.stringify("getContainersInLocation failed"), 500 ) -exports.getAuthorByCodename = (req, resp) -> - exports.getAuthorByCodenameInternal req.params.codeName, (json, statusCode) -> - resp.statusCode = statusCode - resp.json json - -exports.getAuthorByCodenameInternal = (codename, callback) -> - if global.specRunnerTestmode - authorServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/AuthorServiceTestJSON.js' - resp.json authorServiceTestJSON.getAuthorByUsernameInternalResponse - else - config = require '../conf/compiled/conf.js' - baseurl = config.all.client.service.persistence.fullpath+"authors?find=ByCodeName&codeName="+codename - request = require 'request' - request( - method: 'GET' - url: baseurl - json: true - , (error, response, json) => - if !error && response.statusCode == 200 - callback json, 200 - else - console.error 'got ajax error trying to get author by codename' - console.error error - console.error json - console.error response - callback JSON.stringify("get author by codename failed"), 500 - ) - exports.getAuthorModulePreferences = (req, resp) -> exports.getAuthorModulePreferencesInternal req.params.userName, req.params.moduleName, (json, statusCode) -> resp.statusCode = statusCode @@ -193,6 +167,68 @@ exports.createNewAuthorInternal = (author, cb) -> cb null, json ) +exports.genericAuthorSearch = (req, resp) -> + if req.query.testMode is true or global.specRunnerTestmode is true + resp.end JSON.stringify "Stubs mode not implemented yet for author search" + else + config = require '../conf/compiled/conf.js' + console.log "search req - generic author" + console.log req + unless req.body.queryDTO? + req.body.queryDTO = {} + # req.body needs queryString and queryDTO + baseurl = config.all.client.service.persistence.fullpath+"authors/genericBrowserSearch" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: req.body + json: true + , (error, response, json) => + if !error && response.statusCode == 200 + #filter out ignored authors + if json.numberOfResults > 0 + nonIgnoredAuthors = _.filter json.results, (auth) => + !auth.ignored + resp.json nonIgnoredAuthors + else + resp.json [] + else + console.log 'got ajax error trying to search for authors' + console.log error + console.log json + console.log response + resp.statusCode = 500 + resp.end json + ) + +exports.deleteAuthor = (req, resp) -> + if global.specRunnerTestmode + res.end JSON.stringify "stubs mode for deleting author not implemented" + else + config = require '../conf/compiled/conf.js' + authorId = req.params.id + baseurl = config.all.client.service.persistence.fullpath+"authors/"+authorId + console.log baseurl + request = require 'request' + + request( + method: 'DELETE' + url: baseurl + json: true + , (error, response, json) => + console.log response.statusCode + if !error && response.statusCode == 200 + console.log "deleted author" + resp.json json + else + console.log 'got ajax error trying to delete author' + console.log error + console.log response + resp.statusCode = 500 + resp.end json + ) + class Author extends Backbone.Model lsProperties: {} From 28ca17e9cc125457b5fef2d5ed2be4a99a250a9a Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 28 Sep 2017 15:22:34 -0700 Subject: [PATCH 203/576] Updated docker-compose.yml and .env to bump up tomcat to openjdk8 and Roo + CmpdReg Roo to "develop", which now requires Java 8. --- .env | 2 +- docker-compose.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.env b/.env index 08100ff60..b6a34d3d5 100644 --- a/.env +++ b/.env @@ -1 +1 @@ -ACAS_TAG=latest \ No newline at end of file +ACAS_TAG=develop diff --git a/docker-compose.yml b/docker-compose.yml index 5243463b5..d8d7b8c6c 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -60,7 +60,7 @@ services: ports: - "5432:5432" tomcat: - image: mcneilco/tomcat-maven:openjdk7 + image: mcneilco/tomcat-maven:openjdk8 restart: always depends_on: - db @@ -86,7 +86,7 @@ services: - /usr/local/tomcat/webapps/acas command: /bin/true cmpdreg: - image: mcneilco/acas-cmpdreg-roo-server-oss:indigo + image: mcneilco/acas-cmpdreg-roo-server-oss:${ACAS_TAG} volumes: - /usr/local/tomcat/webapps/cmpdreg # Add chemaxon license files here From 6a8d3c9f9e7b0bf9d0156853d8d42b4fc3494855 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 29 Sep 2017 09:13:41 -0700 Subject: [PATCH 204/576] Added two new inventory services: getParentVialByDaughterVialBarcode which takes daughterVialBarcode as a query param, and returns a flat object of the barcode/label and codenames for the parent vial, parent well, daughter vial, and daughter well. advancedSearchContainers: POST route that exposes the deep value/label/interaction searching route in Node. --- .../routes/InventoryServiceRoutes.coffee | 80 ++++++++++++++++++- 1 file changed, 79 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 16e257b31..578b96c94 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -6,6 +6,7 @@ config = require '../conf/compiled/conf.js' RUN_CUSTOM_FLAG = "0" fs = require('fs') parse = require('csv-parse') +request = require 'request' exports.setupAPIRoutes = (app) -> @@ -62,6 +63,8 @@ exports.setupAPIRoutes = (app) -> app.post '/api/loadDaughterVialsFromCSV', exports.loadDaughterVialsFromCSV app.post '/api/saveWellToWellInteractions', exports.saveWellToWellInteractions app.post '/api/createDaughterVials', exports.createDaughterVials + app.post '/api/advancedSearchContainers', exports.advancedSearchContainers + app.get '/api/getParentVialByDaughterVialBarcode', exports.getParentVialByDaughterVialBarcode exports.setupRoutes = (app, loginRoutes) -> @@ -116,6 +119,8 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/loadDaughterVialsFromCSV', loginRoutes.ensureAuthenticated, exports.loadDaughterVialsFromCSV app.post '/api/saveWellToWellInteractions', loginRoutes.ensureAuthenticated, exports.saveWellToWellInteractions app.post '/api/createDaughterVials', loginRoutes.ensureAuthenticated, exports.createDaughterVials + app.post '/api/advancedSearchContainers', loginRoutes.ensureAuthenticated, exports.advancedSearchContainers + app.get '/api/getParentVialByDaughterVialBarcode', loginRoutes.ensureAuthenticated, exports.getParentVialByDaughterVialBarcode exports.getContainersInLocation = (req, resp) -> @@ -3343,4 +3348,77 @@ exports.createDaughterVialsInternal = (vialsToCreate, user, callback) -> callback err else #TODO see what this service should respond with - callback null, 'successfully created daughter vials' \ No newline at end of file + callback null, 'successfully created daughter vials' + +exports.advancedSearchContainers = (req, resp) -> + exports.advancedSearchContainersInternal req.body, req.query.format, (err, response) -> + if err? + resp.statusCode = 500 + resp.json err + else + resp.json response + +exports.advancedSearchContainersInternal = (itxSearchBody, format, callback) -> + baseurl = config.all.client.service.persistence.fullpath+"containers/advancedSearchContainers" + if format? + baseurl += "?with=#{format}" + request( + method: 'POST' + url: baseurl + body: itxSearchBody + json: true + timeout: 86400000 + headers: 'content-type': 'application/json' + , (error, response, json) => + if !error && response.statusCode == 200 + console.debug "returned successfully from #{baseurl}" + callback null, json + else + console.error 'got ajax error trying to get getWellCodesByContainerCodes' + console.error error + console.error json + console.error response + callback JSON.stringify "getWellCodesByContainerCodes failed" + ) + +exports.getParentVialByDaughterVialBarcode = (req, resp) -> + exports.getParentVialByDaughterVialBarcodeInternal req.query.daughterVialBarcode, (err, response) -> + if err? + resp.statusCode = 500 + resp.json err + else + resp.json response + +exports.getParentVialByDaughterVialBarcodeInternal = (daughterVialBarcode, callback) -> + exports.getWellCodesByPlateBarcodesInternal [daughterVialBarcode], (plateWellCodes) -> + plateWellCode = plateWellCodes[0] + responseStub = + daughterVialBarcode: plateWellCode.plateBarcode + daughterVialCodeName: plateWellCode.plateCodeName + daughterWellCodeName: plateWellCode.wellCodeName + daughterWellLabel: plateWellCode.wellLabel + itxSearch = + lsType: 'well' + lsKind: 'default' + secondInteractions: [ + interactionType: 'added to' + interactionKind: 'well_well' + thingType: 'well' + thingKind: 'default' + thingCodeName: responseStub.daughterWellCodeName + ] + format = 'nestedstub' + exports.advancedSearchContainersInternal itxSearch, format, (err, advSearchReturn) -> + parentWell = advSearchReturn.results[0] + responseStub.parentWellCodeName = parentWell.codeName + parentWellLabel = _.findWhere parentWell.lsLabels, {lsType: 'name', lsKind: 'well name', ignored: false} + responseStub.parentWellLabel = parentWellLabel.labelText + parentVialItx = _.findWhere parentWell.firstContainers, {lsType: 'has member', lsKind: 'container_well', ignored: false} + if !parentVialItx? + callback 'Parent vial not found' + else + parentVial = parentVialItx.firstContainer + responseStub.parentVialCodeName = parentVial.codeName + parentVialBarcode = _.findWhere parentVial.lsLabels, {lsType: 'barcode', lsKind: 'barcode', ignored: false} + responseStub.parentVialBarcode = parentVialBarcode.labelText + callback null, responseStub \ No newline at end of file From 53098880afdc5554dbb26738f1678c76c19d6622 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Fri, 29 Sep 2017 17:26:36 -0700 Subject: [PATCH 205/576] Added feature to metalot to optionally load lot inventory iframe --- modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css | 9 +++++++-- modules/CmpdReg/src/client/custom/configuration.json | 5 ++++- modules/CmpdReg/src/client/src/MetaLot.js | 5 +++++ .../CmpdReg/src/client/templates/LotForm/MetaLotView.inc | 3 ++- 4 files changed, 18 insertions(+), 4 deletions(-) diff --git a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css index 0715a7810..6b3fb9f98 100755 --- a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css +++ b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css @@ -219,6 +219,12 @@ div { .MetaLotView div.floatingPanel.newIsotopeView div { height: 20px; } + +.MetaLotView .bv_lotInventory iframe { + width: 700px; + height: 1000px; +} + .NewLotSuccessView .labelCorpName { margin-left: 10px; margin-bottom: 40px; @@ -1030,7 +1036,6 @@ input.FormInput.supplier, .FormInput.supplierID, .FormInput.percentEE, .FormInpu width: 160px; } - /*** SYNTH DATE COLUMN ***/ .MetaLotView .LotForm_LotViewSynth { @@ -1113,7 +1118,7 @@ div.MetaLotViewButtons.buttons { .LotForm_LotView a.editAnalyticalFiles { background: no-repeat url('../images/view_edit_files.png'); - position: absolute; + /*position: absolute;*/ left: 556px; bottom: 40px; margin-left: 150px; diff --git a/modules/CmpdReg/src/client/custom/configuration.json b/modules/CmpdReg/src/client/custom/configuration.json index 17ba6861f..fc112affd 100755 --- a/modules/CmpdReg/src/client/custom/configuration.json +++ b/modules/CmpdReg/src/client/custom/configuration.json @@ -41,7 +41,8 @@ "useProjectRolesToRestrictLotDetails": false, "showTareWeight": false, "showTotalAmoundStored": false, - "disableAliasEdit": false + "disableAliasEdit": false, + "showLotInventory": true }, "serverSettings": { "corpPrefix": "CMPD", @@ -109,3 +110,5 @@ ] } } + + diff --git a/modules/CmpdReg/src/client/src/MetaLot.js b/modules/CmpdReg/src/client/src/MetaLot.js index c9b6f2ee8..5f4627f64 100755 --- a/modules/CmpdReg/src/client/src/MetaLot.js +++ b/modules/CmpdReg/src/client/src/MetaLot.js @@ -229,6 +229,11 @@ $(function() { if (!this.allowedToUpdate()) { this.$('.saveButton').hide(); } + console.log("about to load inventory"); + console.log(window.configuration.metaLot.showLotInventory); + if (window.configuration.metaLot.showLotInventory) { + this.$('.bv_lotInventory').append("") + } } diff --git a/modules/CmpdReg/src/client/templates/LotForm/MetaLotView.inc b/modules/CmpdReg/src/client/templates/LotForm/MetaLotView.inc index 8032d3268..5a4a533ee 100755 --- a/modules/CmpdReg/src/client/templates/LotForm/MetaLotView.inc +++ b/modules/CmpdReg/src/client/templates/LotForm/MetaLotView.inc @@ -11,5 +11,6 @@
        - +
        + From 3aea4d405fd01c75f61e46e5afe91e0a02e9c580 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 2 Oct 2017 13:15:10 -0700 Subject: [PATCH 206/576] AuthorRoutes: Added fully featured save and update author routes which check the user has permissions to make the edit they're trying to make, validates duplicate username and email on save and edit, and persists changes in author roles. In database mode, saving a new author also triggers an account activation email to be sent to the entered email address. AuthorEditor: uncommented save method, and provided urlRoot now that save and update services exist. Fixed copy/paste error. Tweaked roles lists so they sort by save order, just so they stay consistent. ModuleMenus: moved author browser down into Admin section and made CmpdReg Admin collapsible. --- .../client/ModuleMenusConfiguration.coffee | 9 +- .../ServerAPI/src/client/AuthorEditor.coffee | 19 +- .../ServerAPI/src/client/AuthorEditor.html | 2 +- .../src/server/routes/AuthorRoutes.coffee | 369 +++++++++++++++++- 4 files changed, 384 insertions(+), 15 deletions(-) diff --git a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee index 93ea24bd1..55a4bc2dc 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee @@ -50,9 +50,6 @@ window.ModuleMenusConfiguration = , isHeader: false, menuName: "Project Browser" mainControllerClassName: "ProjectBrowserController" - , - isHeader: false, menuName: "Author Browser" - mainControllerClassName: "AuthorBrowserController" , isHeader: true menuName: "Admin" @@ -63,6 +60,11 @@ window.ModuleMenusConfiguration = mainControllerClassName: "AuthorEditorController" autoLaunchName: "author" requireUserRoles: [] + , + isHeader: false + menuName: "Author Browser" + mainControllerClassName: "AuthorBrowserController" + requireUserRoles: [] , isHeader: false menuName: "Admin Panel" @@ -88,6 +90,7 @@ window.ModuleMenusConfiguration = isHeader: true menuName: "CmpdReg Admin" requireUserRoles: [] + collapsible: true , isHeader: false menuName: "CmpdReg Vendors" diff --git a/modules/ServerAPI/src/client/AuthorEditor.coffee b/modules/ServerAPI/src/client/AuthorEditor.coffee index c67094978..ea315aa2e 100644 --- a/modules/ServerAPI/src/client/AuthorEditor.coffee +++ b/modules/ServerAPI/src/client/AuthorEditor.coffee @@ -22,7 +22,7 @@ class window.AuthorRoleList extends Backbone.Collection modelErrors class window.Author extends Backbone.Model -# urlRoot: TODO: fill in once have service + urlRoot: '/api/author' defaults: -> lsType: "author" @@ -70,25 +70,24 @@ class window.Author extends Backbone.Model systemRoles = _.filter @get('authorRoles'), (role) => if role.roleEntry?.lsType? role.roleEntry.lsType is "System" - - trimmedSystemRoles = _.pluck systemRoles, 'roleEntry' + sortedSystemRoles = _.sortBy systemRoles, 'id' + trimmedSystemRoles = _.pluck sortedSystemRoles, 'roleEntry' return new AuthorRoleList trimmedSystemRoles getLdapRoles: => ldapRoles = _.filter @get('authorRoles'), (role) => if role.roleEntry?.lsType? role.roleEntry.lsType is "LDAP" - - trimmedLdapRoles = _.pluck ldapRoles, 'roleEntry' + sortedLdapRoles = _.sortBy ldapRoles, 'id' + trimmedLdapRoles = _.pluck sortedLdapRoles, 'roleEntry' return new AuthorRoleList trimmedLdapRoles getProjectRoles: => projectRoles = _.filter @get('authorRoles'), (role) => if role.roleEntry?.lsType? role.roleEntry.lsType is "Project" - - trimmedProjectRoles = _.pluck projectRoles, 'roleEntry' - + sortedProjectRoles = _.sortBy projectRoles, 'id' + trimmedProjectRoles = _.pluck sortedProjectRoles, 'roleEntry' return new AuthorRoleList trimmedProjectRoles class window.AuthorList extends Backbone.Collection @@ -154,7 +153,7 @@ class window.AuthorRoleController extends AbstractFormController @authorRoleList = new PickListList response @finishSetupAuthorRoleSelect() error: (err) => - alert 'could not get the nhp test subjects' + alert 'could not get the list of author roles' @serviceReturn = null @@ -503,7 +502,7 @@ class window.AuthorEditorController extends AbstractFormController @$('.bv_saving').show() console.log "handleSaveClicked" console.log JSON.stringify @model -# @model.save() TODO: uncomment when service works + @model.save() prepareToSaveSystemRoles: => authorRoles = [] diff --git a/modules/ServerAPI/src/client/AuthorEditor.html b/modules/ServerAPI/src/client/AuthorEditor.html index 3b65c1169..c375f2c26 100644 --- a/modules/ServerAPI/src/client/AuthorEditor.html +++ b/modules/ServerAPI/src/client/AuthorEditor.html @@ -111,5 +111,5 @@

        Clear Form

        diff --git a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee index 416c844b0..2604c9743 100644 --- a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee @@ -4,6 +4,8 @@ exports.setupAPIRoutes = (app, loginRoutes) -> app.put '/api/authorModulePreferences/:userName/:moduleName', exports.updateAuthorModulePreferences app.post '/api/genericSearch/authors', exports.genericAuthorSearch app.delete '/api/authors/:id', exports.deleteAuthor + app.post '/api/author', exports.saveAuthor + app.put '/api/author/:id', exports.updateAuthor exports.setupRoutes = (app, loginRoutes) -> app.get '/api/authorByUsername/:username', loginRoutes.ensureAuthenticated, exports.getAuthorByUsername @@ -11,11 +13,15 @@ exports.setupRoutes = (app, loginRoutes) -> app.put '/api/authorModulePreferences/:userName/:moduleName', loginRoutes.ensureAuthenticated, exports.updateAuthorModulePreferences app.post '/api/genericSearch/authors', loginRoutes.ensureAuthenticated, exports.genericAuthorSearch app.delete '/api/authors/:id', loginRoutes.ensureAuthenticated, exports.deleteAuthor + app.post '/api/author', loginRoutes.ensureAuthenticated, exports.saveAuthor + app.put '/api/author/:id', loginRoutes.ensureAuthenticated, exports.updateAuthor serverUtilityFunctions = require './ServerUtilityFunctions.js' _ = require 'underscore' Backbone = require 'backbone' $ = require 'jquery' +request = require 'request' +config = require '../conf/compiled/conf.js' Label = serverUtilityFunctions.Label LabelList = serverUtilityFunctions.LabelList Value = serverUtilityFunctions.Value @@ -160,9 +166,11 @@ exports.createNewAuthorInternal = (author, cb) -> body: author json: true timeout: 6000000 - , (error, response, json) => + , (err, response, json) => if err? cb err, null + else if response.statusCode != 201 + cb json, null else cb null, json ) @@ -505,3 +513,362 @@ class Author extends Backbone.Model exports.Author = Author AppLaunchParams = loginUser:username:"acas" + +exports.saveAuthor = (req, resp) -> + if req.session?.passport?.user? + user = req.session.passport.user + else + user = + username: 'anonymous' + roles: [] + exports.saveAuthorInternal req.body, user, (err, response) -> + if err? + resp.statusCode = 500 + resp.json err + else + resp.json response + +exports.updateAuthor = (req, resp) -> + if req.session?.passport?.user? + user = req.session.passport.user + else + user = + username: 'anonymous' + roles: [] + exports.updateAuthorAndRolesInternal req.body, user, (err, response) -> + if err? + resp.statusCode = 500 + resp.json err + else + resp.json response + +exports.saveAuthorInternal = (author, user, callback) -> + validateAuthorAttributes author, (authorValidationErrors) -> + if authorValidationErrors? + callback authorValidationErrors + else + checkUserCanCreateOrEditAuthor user, (err, userCanCreate) -> + if err? + callback err + else if !userCanCreate + console.error "ALERT: User #{user.username} attempted to create an author without having the proper roles." + callback 'You do not have permissions to create authors! This incident will be reported to your system administrator.' + else + checkUserNameAndEmailAreUnique author, (userNameEmailUniqueError) -> + if userNameEmailUniqueError? + callback userNameEmailUniqueError + else + parseSystemRoles author, (err, author, systemRoles) -> + if err? + callback err + else + author.recordedBy = user.username + createOrSignupAuthorInternal author, (err, savedAuthor) -> + if err? + callback err + else + fetchSystemRoles systemRoles, (err, systemRoles) -> + flatAuthorRoles = [] + _.each systemRoles, (role) -> + flatAuthorRole = + roleType: role.lsType + roleKind: role.lsKind + roleName: role.roleName + userName: author.userName + flatAuthorRoles.push flatAuthorRole + saveAuthorRoles flatAuthorRoles, (err, savedRoles) -> + if err? + callback err + else + exports.getAuthorByUsernameInternal author.userName, (response, statusCode) -> + if statusCode != 200 + callback err + else + callback null, response + +exports.updateAuthorAndRolesInternal = (author, user, callback) -> + validateAuthorAttributes author, (authorValidationErrors) -> + if authorValidationErrors? + callback authorValidationErrors + else + checkUserCanCreateOrEditAuthor user, (err, userCanEdit) -> + if err? + callback err + else if !userCanEdit + console.error "ALERT: User #{user.username} attempted to edit an author without having the proper roles." + callback 'You do not have permissions to edit authors! This incident will be reported to your system administrator.' + else + parseSystemRoles author, (err, author, systemRoles) -> + if err? + callback err + else + exports.getAuthorByUsernameInternal author.userName, (savedAuthor, statusCode) -> + if statusCode != 200 + callback savedAuthor + else + checkIfEmailHasChangedAndIsUnique author, savedAuthor, (err) -> + if err? + callback err + else + parseSystemRoles savedAuthor, (err, savedAuthor, savedSystemRoles) -> + diffSystemRolesWithSaved author.userName, systemRoles, savedSystemRoles, (err, rolesToAdd, rolesToDelete) -> + if rolesToAdd.length > 0 or rolesToDelete.length > 0 + checkUserCanEditSystemRoles user, (err, userCanEditRoles) -> + if err? + callback err + else if !userCanEditRoles + console.error "ALERT: User #{user.username} attempted to edit system roles without having the proper authorities." + callback 'You do not have permissions to edit system roles! This incident will be reported to your system administrator.' + else + exports.updateAuthorInternal author, (updatedAuthor, statusCode) -> + if statusCode != 200 + callback updatedAuthor + else + saveAuthorRoles rolesToAdd, (err, savedRoles) -> + if err? + callback err + else + deleteAuthorRoles rolesToDelete, (err, deletedRoles) -> + if err? + callback err + else + #save successful. Fetch the new author and return. + exports.getAuthorByUsernameInternal author.userName, (response, statusCode) -> + if statusCode != 200 + callback err + else + callback null, response + +validateAuthorAttributes = (author, callback) -> + requiredAttrs = ['firstName', 'lastName', 'userName', 'emailAddress'] + missingAttrs = [] + for attr in requiredAttrs + if !author[attr]? or author[attr].length < 1 + missingAttrs.push attr + if missingAttrs.length > 0 + callback missingAttrs + else + callback null + +parseUserRoles = (user) -> + userRoles = [] + if user.roles? + _.each user.roles, (authorRole) -> + userRoles.push authorRole.roleEntry.roleName + return userRoles + +checkUserCanCreateOrEditAuthor = (user, callback) -> + userRoles = parseUserRoles user + authStrategy = config.all.server.security.authstrategy + adminRole = config.all.client.roles.acas.adminRole + if !config.all.client.author.editingRoles? + editingRoles = [] + else + editingRoles = config.all.client.author.editingRoles.split(",") + if !adminRole? or adminRole.length < 1 + callback null, true + else + if authStrategy == 'database' and (userRoles.indexOf(adminRole) > -1) + callback null, true + else if authStrategy == 'database' + callback null, false + else if editingRoles? and editingRoles.length > 1 + hasEditingRole = ((_.intersection userRoles, editingRoles).length > 0) + callback null, hasEditingRole + else + callback null, true + +checkUserCanEditSystemRoles = (user, callback) -> + userRoles = parseUserRoles user + authStrategy = config.all.server.security.authstrategy + adminRole = config.all.client.roles.acas.adminRole + if !adminRole? or adminRole.length < 1 + callback null, true + else + if (userRoles.indexOf(adminRole) > -1) + callback null, true + else + callback null, false + +checkUserNameAndEmailAreUnique = (author, callback) -> + checkUserNameIsUnique author, (err, userNameUnique) -> + if err? + callback err + else + checkEmailIsUnique author, (err, emailIsUnique) -> + if err? + callback err + else + if !userNameUnique and !emailIsUnique + callback 'That username and email address are both already in use.' + else if !userNameUnique + callback 'That username is already in use.' + else if !emailIsUnique + callback 'That email address is already in use.' + else + callback null + +checkUserNameIsUnique = (author, callback) -> + baseurl = config.all.client.service.persistence.fullpath+"authors?find=ByUserName&userName="+author.userName + request( + method: 'GET' + url: baseurl + json: true + , (error, response, json) => + if !error && response.statusCode == 200 + if json.length < 1 + callback null, true + else + console.debug json + callback null, false + else + console.error 'got error checking if author username exists' + console.error error + console.error json + console.error response + callback JSON.stringify("failed checking author username") + ) + +checkEmailIsUnique = (author, callback) -> + baseurl = config.all.client.service.persistence.fullpath+"authors?find=ByEmailAddress&emailAddress="+author.emailAddress + request( + method: 'GET' + url: baseurl + json: true + , (error, response, json) => + if !error && response.statusCode == 200 + if json.length < 1 + callback null, true + else + console.debug json + callback null, false + else + console.error 'got error checking if author emailAddress exists' + console.error error + console.error json + console.error response + callback JSON.stringify("failed checking author emailAddress") + ) + +checkIfEmailHasChangedAndIsUnique = (author, savedAuthor, callback) -> + if author.emailAddress == savedAuthor.emailAddress + callback null + else + checkEmailIsUnique author (err, isUnique) -> + if err? + callback err + else if isUnique + callback null + else + callback 'That email address is already in use.' + +parseSystemRoles = (author, callback) -> + roleEntries = _.pluck author.authorRoles, 'roleEntry' + systemRoles = _.where roleEntries, {lsType: 'System'} + delete author['authorRoles'] + callback null, author, systemRoles + + +diffSystemRolesWithSaved = (userName, systemRoles, savedSystemRoles, callback) -> + rolesToAdd = _.filter systemRoles, (sysRole) -> + !(_.findWhere savedSystemRoles, (id: sysRole.id))? + rolesToDelete = _.filter savedSystemRoles, (savedSysRole) -> + !(_.findWhere systemRoles, (id: savedSysRole.id))? + fetchSystemRoles rolesToAdd, (err, rolesToAdd) -> + if err? + callback err + else + flatAuthRolesToAdd = [] + _.each rolesToAdd, (role) -> + flatAuthorRole = + roleType: role.lsType + roleKind: role.lsKind + roleName: role.roleName + userName: userName + flatAuthRolesToAdd.push flatAuthorRole + flatAuthRolesToDelete = [] + _.each rolesToDelete, (role) -> + flatAuthorRole = + roleType: role.lsType + roleKind: role.lsKind + roleName: role.roleName + userName: userName + flatAuthRolesToDelete.push flatAuthorRole + callback null, flatAuthRolesToAdd, flatAuthRolesToDelete + +saveAuthorRoles = (rolesToCreate, cb) -> + request( + method: 'POST' + url: config.all.client.service.persistence.fullpath + "authorroles/saveRoles" + body: rolesToCreate + json: true + timeout: 6000000 + , (err, response, json) => + if err? + cb err, null + else + cb null, json + ) + +deleteAuthorRoles = (rolesToDelete, cb) -> + request( + method: 'POST' + url: config.all.client.service.persistence.fullpath + "authorroles/deleteRoles" + body: rolesToDelete + json: true + timeout: 6000000 + , (err, response, json) => + if err? + cb err, null + else + cb null, json + ) + +fetchSystemRoles = (incompleteSystemRoles, callback) -> + request( + method: 'GET' + url: config.all.client.service.persistence.fullpath + 'lsRoles?lsType=System' + json: true + , (error, response, json) => + if !error && response.statusCode == 200 + allSystemRoles = json + ids = {} + _.each incompleteSystemRoles, (partialRole) -> + ids[partialRole.id] = true + filteredSystemRoles = _.filter allSystemRoles, (val) -> + return ids[val.id] + callback null, filteredSystemRoles + else + console.error 'got error trying to get fetch system roles' + console.error error + console.error json + callback 'failed to fetch system roles' + ) + + +createOrSignupAuthorInternal = (author, cb) -> + authStrategy = config.all.server.security.authstrategy + if authStrategy == 'database' + exports.signupNewAuthorInternal author, (err, savedAuthor) -> + cb err, savedAuthor + else + exports.createNewAuthorInternal author, (err, savedAuthor) -> + cb err, savedAuthor + +exports.signupNewAuthorInternal = (author, cb) -> + config = require '../conf/compiled/conf.js' + request = require 'request' + request( + method: 'POST' + url: config.all.client.service.persistence.fullpath + "authors/signupAuthor" + body: author + json: true + timeout: 6000000 + , (err, response, json) => + if err? + cb err, null + else if response.statusCode != 201 + cb json, null + else + cb null, json + ) \ No newline at end of file From 63f2f424ea7c42338af4e10477b216ed9a789644 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 2 Oct 2017 13:21:55 -0700 Subject: [PATCH 207/576] loginRoutes: Fixed change password route to use the username from the authenticated user in the session rather than allowing input from a form, and also cleaned up some English. passwordChange.jade: Removed "email or username" input from change password form. Change Password is behind the login page, so the only password being changed should be the one of the logged in user. CustomerSpecificServerFunctions: Switched changeAuth to use a new Roo API route "authorization/changePassword" instead of the basic Roo change password route that was not working. AuthorRoutes: Added new route to be used in account activation emails, which activates the user, then redirects them to passwordChange, which goes through login first. --- .../src/server/routes/loginRoutes.coffee | 5 ++-- .../ServerAPI/src/client/passwordChange.jade | 4 ---- .../CustomerSpecificServerFunctions.coffee | 24 ++++++++++++------- .../src/server/routes/AuthorRoutes.coffee | 12 ++++++++++ 4 files changed, 30 insertions(+), 15 deletions(-) diff --git a/modules/Login/src/server/routes/loginRoutes.coffee b/modules/Login/src/server/routes/loginRoutes.coffee index 545fca03a..8c5b914eb 100644 --- a/modules/Login/src/server/routes/loginRoutes.coffee +++ b/modules/Login/src/server/routes/loginRoutes.coffee @@ -159,7 +159,7 @@ exports.resetAuthenticationService = (req, resp) -> exports.changeAuthenticationService = (req, resp) -> callback = (results) -> console.log results - if results.indexOf("You password has been successfully been changed")>=0 + if results.indexOf("Your password has successfully been changed")>=0 req.flash 'error','Your new password is set.' resp.redirect '/login' else if results.indexOf("connection_error")>=0 @@ -172,7 +172,8 @@ exports.changeAuthenticationService = (req, resp) -> if global.specRunnerTestmode callback("Success") else - csUtilities.changeAuth req.body.user, req.body.oldPassword, req.body.newPassword, req.body.newPasswordAgain, callback + user = req.session.passport.user.username + csUtilities.changeAuth user, req.body.oldPassword, req.body.newPassword, req.body.newPasswordAgain, callback exports.resetpage = (req, res) -> user = null diff --git a/modules/ServerAPI/src/client/passwordChange.jade b/modules/ServerAPI/src/client/passwordChange.jade index 8042ba935..4b5404a73 100644 --- a/modules/ServerAPI/src/client/passwordChange.jade +++ b/modules/ServerAPI/src/client/passwordChange.jade @@ -10,10 +10,6 @@ block content h3 Change Password div.well form.form-horizontal(action="/passwordChange", method="post") - div.control-group - label.control-label Email or Username: - div.controls - input.span5(type="text", name="username") div.control-group label.control-label Old Password: div.controls diff --git a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee index 07b0c017a..fba0fe0ec 100644 --- a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee +++ b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee @@ -75,22 +75,28 @@ exports.resetAuth = (email, retFun) -> exports.changeAuth = (user, passOld, passNew, passNewAgain, retFun) -> config = require "#{ACAS_HOME}/conf/compiled/conf.js" request = require 'request' + body = + username: user + oldPassword: passOld + newPassword: passNew + newPasswordAgain: passNewAgain request( headers: accept: 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8' method: 'POST' - url: config.all.server.roologin.changeLink - form: - username: user - oldPassword: passOld - newPassword: passNew - newPasswordAgain: passNewAgain - json: false + url: config.all.client.service.persistence.fullpath+"authorization/changePassword" + body: body + json: true , (error, response, json) => + console.log error + console.log response.statusCode + console.log json if !error && response.statusCode == 200 - retFun JSON.stringify json + retFun "Your password has successfully been changed" + else if response.statusCode == 400 + retFun "Invalid password or new password does not match" else - console.log 'got ajax error trying authenticate a user' + console.log 'got ajax error trying change password' console.log error console.log json console.log response diff --git a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee index 2604c9743..7db5ecf10 100644 --- a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee @@ -15,6 +15,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.delete '/api/authors/:id', loginRoutes.ensureAuthenticated, exports.deleteAuthor app.post '/api/author', loginRoutes.ensureAuthenticated, exports.saveAuthor app.put '/api/author/:id', loginRoutes.ensureAuthenticated, exports.updateAuthor + app.get '/activateUser', exports.activateUserAndRedirectToChangePassword serverUtilityFunctions = require './ServerUtilityFunctions.js' _ = require 'underscore' @@ -845,6 +846,17 @@ fetchSystemRoles = (incompleteSystemRoles, callback) -> callback 'failed to fetch system roles' ) +exports.activateUserAndRedirectToChangePassword = (req, resp) -> + request( + method: 'GET' + url: config.all.client.service.persistence.fullpath + "authorization/activateUser?emailAddress=#{req.query.emailAddress}&activate=#{req.query.activate}" + json: true + , (error, response, json) => + if !error && response.statusCode == 200 + resp.redirect '/passwordChange' + else + #redirect to error page + ) createOrSignupAuthorInternal = (author, cb) -> authStrategy = config.all.server.security.authstrategy From bbd4a8c557cf748ce832cfee034b20ed22bf5c4e Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 2 Oct 2017 16:48:31 -0700 Subject: [PATCH 208/576] Refactored reset password to use new Roo API route and fixed retFun for successful response. --- .../server/CustomerSpecificServerFunctions.coffee | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee index fba0fe0ec..8a0380015 100644 --- a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee +++ b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee @@ -57,15 +57,17 @@ exports.resetAuth = (email, retFun) -> headers: accept: 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8' method: 'POST' - url: config.all.server.roologin.resetLink - form: - emailAddress: email - json: false + url: config.all.client.service.persistence.fullpath+"authorization/resetPassword" + body: email + json: true , (error, response, json) => + console.log error + console.log response.statusCode + console.log json if !error && response.statusCode == 200 - retFun JSON.stringify json + retFun "Your new password has been sent to your email address." else - console.log 'got ajax error trying authenticate a user' + console.log 'got ajax error trying reset password' console.log error console.log json console.log response From 4d0cbc92fc289778218319239703790f3cb2cd2a Mon Sep 17 00:00:00 2001 From: John McNeil Date: Mon, 2 Oct 2017 18:21:01 -0700 Subject: [PATCH 209/576] fixes to make inventory work --- .../src/client/css/NewCmpdReg_nocompile.css | 1 + .../routes/InventoryServiceRoutes.coffee | 43 ++++++++++--------- 2 files changed, 24 insertions(+), 20 deletions(-) diff --git a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css index 6b3fb9f98..12e359042 100755 --- a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css +++ b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css @@ -1122,6 +1122,7 @@ div.MetaLotViewButtons.buttons { left: 556px; bottom: 40px; margin-left: 150px; + padding-right: 39px; /* margin-top: 5px; margin-left: 15px; diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 16e257b31..3b8619bb8 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -2548,16 +2548,16 @@ exports.getTubesFromBatchCodeInternal = (input, callback) => { "lsType": "container" , "lsKind": "tube", - "values":[ - { - "stateType":"metadata", - "stateKind":"information", - "valueType": "codeValue", - "valueKind": "status", - "operator": "!=", - "value":"expired" - } - ], +# "values":[ +# { +# "stateType":"metadata", +# "stateKind":"information", +# "valueType": "codeValue", +# "valueKind": "status", +# "operator": "!=", +# "value":"expired" +# } +# ], "secondInteractions":[ { "interactionType": "has member", @@ -2708,7 +2708,7 @@ exports.createParentVialsFromCSVInternal = (csvFileName, dryRun, user, callback) if err? callback err summaryInfo = prepareSummaryInfo fileEntryArray - getContainerTubeDefinitionCode (definitionCode) -> + exports.getContainerTubeDefinitionCode (definitionCode) -> if !definitionCode? error = level: 'error' @@ -2996,7 +2996,7 @@ checkBarcodesExist = (barcodes, callback) -> newBarcodes.push containerCodeEntry.requestLabel callback existingBarcodes, newBarcodes -checkParentWellContent = (fileEntryArray, callback) -> +exports.checkParentWellContent = (fileEntryArray, callback) -> #The purpose of this function is to check that the source vial content is compatible with the daughter content being loaded in, including #physical state must match #amount in parent vial would be negative if the daughter amount is removed @@ -3097,7 +3097,7 @@ prepareCreateParentVialsHTMLSummary = (hasError, hasWarning, errorMessages, summ htmlSummary += warningsBlock htmlSummary -getContainerTubeDefinitionCode = (callback) -> +exports.getContainerTubeDefinitionCode = (callback) -> exports.containersByTypeKindInternal 'definition container', 'tube', 'codetable', false, false, (definitionContainers) -> callback definitionContainers[0].code @@ -3232,11 +3232,11 @@ exports.validateDaughterVialsInternal = (vialsToValidate, callback) -> if dataTypeErrors? errorMessages.push dataTypeErrors... sourceBarcodes = _.pluck vialsToValidate, 'sourceVialBarcode' - checkBarcodesExist sourceBarcodes, (existingBarcodes, newBarcodes) -> - if newBarcodes? and newBarcodes.length > 0 + checkBarcodesExist sourceBarcodes, (existingSourceBarcodes, missingSourceBarcodes) -> + if missingSourceBarcodes? and missingSourceBarcodes.length > 0 error = level: 'error' - message: "The following source barcodes do not exist: " + newBarcodes.join ', ' + message: "The following source barcodes do not exist: " + missingSourceBarcodes.join ', ' errorMessages.push error destinationBarcodes = _.pluck vialsToValidate, 'destinationVialBarcode' checkBarcodesExist destinationBarcodes, (existingBarcodes, newBarcodes) -> @@ -3245,10 +3245,13 @@ exports.validateDaughterVialsInternal = (vialsToValidate, callback) -> level: 'error' message: "The following destination barcodes already exist: " + existingBarcodes.join ', ' errorMessages.push error - checkParentWellContent vialsToValidate, (parentWellContentErrors) -> - if parentWellContentErrors? - errorMessages.push parentWellContentErrors... + if missingSourceBarcodes.length > 0 callback null, errorMessages + else + checkParentWellContent vialsToValidate, (parentWellContentErrors) -> + if parentWellContentErrors? + errorMessages.push parentWellContentErrors... + callback null, errorMessages exports.createDaughterVials = (req, resp) -> if req.session?.passport?.user?.username? @@ -3274,7 +3277,7 @@ exports.createDaughterVials = (req, resp) -> resp.json response exports.createDaughterVialsInternal = (vialsToCreate, user, callback) -> - getContainerTubeDefinitionCode (definitionCode) -> + exports.getContainerTubeDefinitionCode (definitionCode) -> if !definitionCode? callback 'Could not find definition container for tube' tubesToCreate = [] From 681daebee593e89e9a47c1cb64e0a39a0bf71977 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 3 Oct 2017 09:49:40 -0700 Subject: [PATCH 210/576] Tweaked passwordChange page to make the ACAS text appear the same, but be a link so a user has a way to get out of the passwordChange page. --- modules/ServerAPI/src/client/passwordChange.jade | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/client/passwordChange.jade b/modules/ServerAPI/src/client/passwordChange.jade index 4b5404a73..191d27632 100644 --- a/modules/ServerAPI/src/client/passwordChange.jade +++ b/modules/ServerAPI/src/client/passwordChange.jade @@ -3,7 +3,9 @@ block content div.navbar.navbar-inverse.navbar-fixed-top div.navbar-inner div.container-fluid - div.brand ACAS + ul.nav + li + a.bv_headerName(href="/") ACAS div.container.loginContainer div.span8.offset1 From 3ac15763cbbc8051af5a94251450aae0eaf10630 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 3 Oct 2017 14:34:32 -0700 Subject: [PATCH 211/576] Commented out extra logging from createTube service, fixed dryRun and level->errorLevel attributes for bulk vial loaders to communicate properly with BasicFileValidateAndSave. Fixed datatype of amount and concentration to be numeric and to do parsing in the CSV file read. Consolidated summary HTML helper functions. Also removed superfluous README from ServerAPI that is no longer accurate. --- .../README.txt | 6 - .../routes/InventoryServiceRoutes.coffee | 149 ++++++++---------- 2 files changed, 69 insertions(+), 86 deletions(-) delete mode 100644 modules/ServerAPI/src/server/python/createLiveDesignLiveReportForACAS/createLiveDesignLiveReportForACAS/README.txt diff --git a/modules/ServerAPI/src/server/python/createLiveDesignLiveReportForACAS/createLiveDesignLiveReportForACAS/README.txt b/modules/ServerAPI/src/server/python/createLiveDesignLiveReportForACAS/createLiveDesignLiveReportForACAS/README.txt deleted file mode 100644 index 8e73f31d9..000000000 --- a/modules/ServerAPI/src/server/python/createLiveDesignLiveReportForACAS/createLiveDesignLiveReportForACAS/README.txt +++ /dev/null @@ -1,6 +0,0 @@ -#The create_lr_for_acas.py script relies on an up-to-date ldclient library. -#To install, first download the ldclient from the LD server that is paired with this ACAS server using: -#wget https://relevant-ld-server.onschrodinger.com/livedesign/ldclient.tar.gz -#Then unpack the war and make a symlink as follows: -#tar -zxf ldclient.tar.gz -#ln -s ldclient-version-build/ldclient ldclient \ No newline at end of file diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 578b96c94..8fff7c784 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -2263,12 +2263,12 @@ exports.createTubesInternal = (tubes, callCustom, callback) -> json: true timeout: 6000000 , (error, response, json) => - console.log "error" - console.log error - console.log "response" - console.log response - console.log "json" - console.log json +# console.log "error" +# console.log error +# console.log "response" +# console.log response +# console.log "json" +# console.log json if !error && response.statusCode == 200 # If call custom doesn't equal 0 then call custom callCustom = callCustom != "0" @@ -2633,7 +2633,7 @@ exports.loadParentVialsFromCSV = (req, resp) -> resp.json response exports.loadParentVialsFromCSVInternal = (csvFileName, dryRun, user, callback) -> - if dryRun + if dryRun == 'true' exports.validateParentVialsFromCSVInternal csvFileName, dryRun, (validationResponse) -> callback validationResponse else @@ -2674,14 +2674,14 @@ exports.validateParentVialsFromCSVInternal = (csvFileName, dryRun, callback) -> checkBatchCodesExist fileEntryArray, (missingBatchCodeErrors) -> if missingBatchCodeErrors? and missingBatchCodeErrors.length > 0 error = - level: 'error' + errorLevel: 'error' message: "The following batches do not exist: "+ missingBatchCodeErrors.join ', ' validationResponse.errorMessages.push error barcodes = _.pluck fileEntryArray, 'destinationVialBarcode' checkBarcodesExist barcodes, (existingBarcodes, newBarcodes) -> if existingBarcodes? and existingBarcodes.length > 0 error = - level: 'error' + errorLevel: 'error' message: "The following barcodes already exist: " + existingBarcodes.join ', ' validationResponse.errorMessages.push error if validationResponse.errorMessages.length < 1 @@ -2690,7 +2690,7 @@ exports.validateParentVialsFromCSVInternal = (csvFileName, dryRun, callback) -> callback validationResponse else error = - level: 'error' + errorLevel: 'error' message: "File cannot be found" validationResponse.errorMessages.push error callback validationResponse @@ -2716,7 +2716,7 @@ exports.createParentVialsFromCSVInternal = (csvFileName, dryRun, user, callback) getContainerTubeDefinitionCode (definitionCode) -> if !definitionCode? error = - level: 'error' + errorLevel: 'error' message: 'Could not find definition container for tube' createResponse.errorMessages.push error tubesToCreate = [] @@ -2731,14 +2731,14 @@ exports.createParentVialsFromCSVInternal = (csvFileName, dryRun, user, callback) wells: [ wellName: "A001" batchCode: entry.batchCode - amount: parseFloat(entry.amount) + amount: entry.amount amountUnits: entry.amountUnits physicalState: entry.physicalState recordedBy: user recordedDate: (new Date()).getTime() ] if entry.physicalState == 'solution' - tube.wells[0].batchConcentration = parseFloat(entry.concentration) + tube.wells[0].batchConcentration = entry.concentration tube.wells[0].batchConcUnits = entry.concUnits tube.wells[0].solventCode = entry.solvent tubesToCreate.push tube @@ -2750,17 +2750,17 @@ exports.createParentVialsFromCSVInternal = (csvFileName, dryRun, user, callback) createResponse.hasError = true console.error json error = - level: 'error' + errorLevel: 'error' message: json createResponse.errorMessages.push error else createResponse.hasError = false createResponse.commit = true - createResponse.results.htmlSummary = prepareCreateParentVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo + createResponse.results.htmlSummary = prepareCreateVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo callback createResponse else error = - level: 'error' + errorLevel: 'error' message: "File cannot be found" createResponse.errorMessages.push error callback createResponse @@ -2774,7 +2774,7 @@ exports.loadDaughterVialsFromCSV = (req, resp) -> resp.json response exports.loadDaughterVialsFromCSVInternal = (csvFileName, dryRun, user, callback) -> - if dryRun + if dryRun == 'true' exports.validateDaughterVialsFromCSVInternal csvFileName, dryRun, (err, validationResponse) -> if err? callback err @@ -2829,7 +2829,7 @@ exports.validateDaughterVialsFromCSVInternal = (csvFileName, dryRun, callback) - callback null, validationResponse else error = - level: 'error' + errorLevel: 'error' message: "File cannot be found" validationResponse.errorMessages.push error callback validationResponse @@ -2848,7 +2848,7 @@ exports.createDaughterVialsFromCSVInternal = (csvFileName, dryRun, user, callbac commit: false if !exists error = - level: 'error' + errorLevel: 'error' message: "File cannot be found" createResponse.errorMessages.push error callback createResponse @@ -2861,13 +2861,13 @@ exports.createDaughterVialsFromCSVInternal = (csvFileName, dryRun, user, callbac exports.createDaughterVialsInternal fileEntryArray, user, (err, response) -> if err? error = - level: 'error' + errorLevel: 'error' message: err createResponse.errorMessages.push error else createResponse.hasError = false createResponse.commit = true - createResponse.results.htmlSummary = prepareCreateDaughterVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo + createResponse.results.htmlSummary = prepareCreateVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo callback null, createResponse @@ -2897,12 +2897,12 @@ createParentVialFileEntryArray = (csvFileName, callback) => fileEntry = batchCode: csvrow[PARENT_COMPOUND_LOT_INDEX].trim() destinationVialBarcode: csvrow[PARENT_DESTINATION_VIAL_INDEX].trim() - amount: csvrow[PARENT_AMOUNT_INDEX].trim() + amount: parseFloat(csvrow[PARENT_AMOUNT_INDEX].trim()) amountUnits: csvrow[PARENT_AMOUNT_UNITS_INDEX].trim() preparedBy: csvrow[PARENT_PREPARED_BY_INDEX].trim() preparedDate: csvrow[PARENT_PREPARED_DATE_INDEX].trim() physicalState: csvrow[PARENT_PHYSICAL_STATE_INDEX].trim() - concentration: csvrow[PARENT_CONCENTRATION_INDEX].trim() + concentration: parseFloat(csvrow[PARENT_CONCENTRATION_INDEX].trim()) concUnits:csvrow[PARENT_CONC_UNITS_INDEX].trim() solvent: csvrow[PARENT_SOLVENT_INDEX].trim() rowNumber: rowCount @@ -2925,12 +2925,12 @@ createDaughterVialFileEntryArray = (csvFileName, callback) => fileEntry = sourceVialBarcode: csvrow[DAUGHTER_SOURCE_VIAL_INDEX].trim() destinationVialBarcode: csvrow[DAUGHTER_DESTINATION_VIAL_INDEX].trim() - amount: csvrow[DAUGHTER_AMOUNT_INDEX].trim() + amount: parseFloat(csvrow[DAUGHTER_AMOUNT_INDEX].trim()) amountUnits: csvrow[DAUGHTER_AMOUNT_UNITS_INDEX].trim() preparedBy: csvrow[DAUGHTER_PREPARED_BY_INDEX].trim() preparedDate: csvrow[DAUGHTER_PREPARED_DATE_INDEX].trim() physicalState: csvrow[DAUGHTER_PHYSICAL_STATE_INDEX].trim() - concentration: csvrow[DAUGHTER_CONCENTRATION_INDEX].trim() + concentration: parseFloat(csvrow[DAUGHTER_CONCENTRATION_INDEX].trim()) concUnits: csvrow[DAUGHTER_CONC_UNITS_INDEX].trim() solvent: csvrow[DAUGHTER_SOLVENT_INDEX].trim() rowNumber: rowCount @@ -2957,7 +2957,7 @@ checkRequiredAttributes = (fileEntryArray, callback) -> missingAttributes.push attr if missingAttributes.length > 0 error = - level: 'error' + errorLevel: 'error' message: "Row #{entry.rowNumber} is missing the required attributes: " + missingAttributes.join ', ' requiredAttributeErrors.push error callback requiredAttributeErrors @@ -2965,14 +2965,14 @@ checkRequiredAttributes = (fileEntryArray, callback) -> checkDataTypeErrors = (fileEntryArray, callback) -> dataTypeErrors = [] _.each fileEntryArray, (entry) -> - if entry.amount? and entry.amount.length > 0 and isNaN(parseFloat(entry.amount)) + if entry.amount? and entry.amount.length > 0 and isNaN(entry.amount) error = - level: 'error' + errorLevel: 'error' message: "Row #{entry.rowNumber} contains the invalid amount: #{entry.amount}" dataTypeErrors.push error - if entry.concentration? and entry.concentration.length > 0 and isNaN(parseFloat(entry.concentration)) + if entry.concentration? and entry.concentration.length > 0 and isNaN(entry.concentration) error = - level: 'error' + errorLevel: 'error' message: "Row #{entry.rowNumber} contains the invalid concentration: #{entry.concentration}" dataTypeErrors.push error callback dataTypeErrors @@ -3016,27 +3016,27 @@ checkParentWellContent = (fileEntryArray, callback) -> parentWellContent = parentVialAndWellContent.wellContent[0] if parentWellContent.physicalState != fileEntry.physicalState error = - level: 'error' + errorLevel: 'error' message: "Daughter vial #{fileEntry.destinationVialBarcode} must be of the same physical state as parent vial #{fileEntry.sourceVialBarcode}, which is #{parentWellContent.physicalState}." errorMessages.push error - if fileEntry.physicalState == 'solution' and (Math.abs(parseFloat(fileEntry.concentration) - parentWellContent.batchConcentration) > 0.0001 or fileEntry.concUnits != parentWellContent.batchConcUnits) + if fileEntry.physicalState == 'solution' and (Math.abs(fileEntry.concentration - parentWellContent.batchConcentration) > 0.0001 or fileEntry.concUnits != parentWellContent.batchConcUnits) error = - level: 'error' + errorLevel: 'error' message: "Daughter vial #{fileEntry.destinationVialBarcode} must have the same concentration as parent vial #{fileEntry.sourceVialBarcode}, which is #{parentWellContent.batchConcentration} #{parentWellContent.batchConcUnits}." errorMessages.push error if parentWellContent.amountUnits != fileEntry.amountUnits error = - level: 'error' + errorLevel: 'error' message: "Daughter vial #{fileEntry.destinationVialBarcode} must use the same amount units as parent vial #{fileEntry.sourceVialBarcode}, which is in #{parentWellContent.amountUnits}." errorMessages.push error - else if parentWellContent.amount < parseFloat(fileEntry.amount) + else if parentWellContent.amount < fileEntry.amount error = - level: 'warning' + errorLevel: 'warning' message: "Creating daughter vial #{fileEntry.destinationVialBarcode} will remove more than the total amount currently in parent vial #{fileEntry.sourceVialBarcode}, leaving a negative amount in the parent vial." errorMessages.push error else error = - level: 'error' + errorLevel: 'error' message: "Could not find a well for barcode #{fileEntry.sourceVialBarcode}" errorMessages.push error console.log errorMessages @@ -3046,8 +3046,8 @@ checkParentWellContent = (fileEntryArray, callback) -> prepareValidationHTMLSummary = (hasError, hasWarning, errorMessages, summaryInfo) -> - errors = _.where errorMessages, {level: 'error'} - warnings = _.where errorMessages, {level: 'warning'} + errors = _.where errorMessages, {errorLevel: 'error'} + warnings = _.where errorMessages, {errorLevel: 'warning'} errorHeader = "

        Please fix the following errors and use the 'Back' button at the bottom of this screen to upload a new version of the file.

        " if hasWarning successHeader = "

        Please review the warnings and summary before uploading.

        " @@ -3079,11 +3079,17 @@ prepareValidationHTMLSummary = (hasError, hasWarning, errorMessages, summaryInfo htmlSummary += htmlSummaryInfo htmlSummary -prepareCreateParentVialsHTMLSummary = (hasError, hasWarning, errorMessages, summaryInfo) -> - errors = _.where errorMessages, {level: 'error'} - warnings = _.where errorMessages, {level: 'warning'} +prepareCreateVialsHTMLSummary = (hasError, hasWarning, errorMessages, summaryInfo) -> + errors = _.where errorMessages, {errorLevel: 'error'} + warnings = _.where errorMessages, {errorLevel: 'warning'} errorHeader = "

        An error occurred during uploading. If the messages below are unhelpful, you will need to contact your system administrator.

        " - #TODO implement HTML summary for successful upload + htmlSummaryInfo = "

        Summary

        Information:

        \n
          \n " + htmlSummaryInfo += "
        • Total Vials: #{summaryInfo.totalNumberOfVials}
          • " + htmlSummaryInfo += "
        • Solid Vials: #{summaryInfo.numSolidVials}
          • " + htmlSummaryInfo += "
        • Liquid Vials: #{summaryInfo.numLiquidVials}
          • " + if summaryInfo.totalBatchCodes? + htmlSummaryInfo += "
        • Unique Corporate Batch ID's: #{summaryInfo.totalBatchCodes}
          • " + htmlSummaryInfo += "\n
        " successHeader = "

        Upload completed.

        " errorsBlock = "\n

        Errors: #{errors.length}

        \n
          " _.each errors, (error) -> @@ -3100,6 +3106,8 @@ prepareCreateParentVialsHTMLSummary = (hasError, hasWarning, errorMessages, summ htmlSummary += successHeader if hasWarning htmlSummary += warningsBlock + if !hasError + htmlSummary += htmlSummaryInfo htmlSummary getContainerTubeDefinitionCode = (callback) -> @@ -3127,28 +3135,6 @@ decrementAmountsFromVials = (parentVialsToDecrement, user, callback) -> else callback null, updateWellsResponse -prepareCreateDaughterVialsHTMLSummary = (hasError, hasWarning, errorMessages, summaryInfo) -> - errors = _.where errorMessages, {level: 'error'} - warnings = _.where errorMessages, {level: 'warning'} - errorHeader = "

          An error occurred during uploading. If the messages below are unhelpful, you will need to contact your system administrator.

          " - successHeader = "

          Upload completed.

          " - errorsBlock = "\n

          Errors: #{errors.length}

          \n
            " - _.each errors, (error) -> - errorsBlock += "
          • #{error.message}
            • " - errorsBlock += "
          " - warningsBlock = "\n

          Warnings: #{warnings.length}

          \n

          Warnings provide information on issues found in the upload file. You can proceed with warnings; however, it is recommended that, if possible, you make the changes suggested by the warnings and upload a new version of the file by using the 'Back' button at the bottom of this screen.

          \n
            " - _.each warnings, (warning) -> - warningsBlock += "
          • #{warning.message}
            • " - warningsBlock += "
          " - htmlSummary = "" - if hasError - htmlSummary += errorHeader + errorsBlock - else - htmlSummary += successHeader - if hasWarning - htmlSummary += warningsBlock - htmlSummary - prepareSummaryInfo = (fileEntryArray) -> summaryInfo = totalNumberOfVials: fileEntryArray.length @@ -3237,23 +3223,26 @@ exports.validateDaughterVialsInternal = (vialsToValidate, callback) -> if dataTypeErrors? errorMessages.push dataTypeErrors... sourceBarcodes = _.pluck vialsToValidate, 'sourceVialBarcode' - checkBarcodesExist sourceBarcodes, (existingBarcodes, newBarcodes) -> - if newBarcodes? and newBarcodes.length > 0 + checkBarcodesExist sourceBarcodes, (existingSourceBarcodes, missingSourceBarcodes) -> + if missingSourceBarcodes? and missingSourceBarcodes.length > 0 error = - level: 'error' - message: "The following source barcodes do not exist: " + newBarcodes.join ', ' + errorLevel: 'error' + message: "The following source barcodes do not exist: " + missingSourceBarcodes.join ', ' errorMessages.push error destinationBarcodes = _.pluck vialsToValidate, 'destinationVialBarcode' checkBarcodesExist destinationBarcodes, (existingBarcodes, newBarcodes) -> if existingBarcodes? and existingBarcodes.length > 0 error = - level: 'error' + errorLevel: 'error' message: "The following destination barcodes already exist: " + existingBarcodes.join ', ' errorMessages.push error - checkParentWellContent vialsToValidate, (parentWellContentErrors) -> - if parentWellContentErrors? - errorMessages.push parentWellContentErrors... + if missingSourceBarcodes.length > 0 callback null, errorMessages + else + checkParentWellContent vialsToValidate, (parentWellContentErrors) -> + if parentWellContentErrors? + errorMessages.push parentWellContentErrors... + callback null, errorMessages exports.createDaughterVials = (req, resp) -> if req.session?.passport?.user?.username? @@ -3265,8 +3254,8 @@ exports.createDaughterVials = (req, resp) -> resp.statusCode = 500 resp.json err else - errors = _.where errorsAndWarnings, {level: 'error'} - warnings = _.where errorsAndWarnings, {level: 'warning'} + errors = _.where errorsAndWarnings, {errorLevel: 'error'} + warnings = _.where errorsAndWarnings, {errorLevel: 'warning'} if errors? and errors.length > 0 resp.statusCode = 400 resp.json errorsAndWarnings @@ -3294,14 +3283,14 @@ exports.createDaughterVialsInternal = (vialsToCreate, user, callback) -> wells: [ wellName: "A001" batchCode: entry.batchCode - amount: parseFloat(entry.amount) + amount: entry.amount amountUnits: entry.amountUnits physicalState: entry.physicalState recordedBy: user recordedDate: (new Date()).getTime() ] if entry.physicalState == 'solution' - tube.wells[0].batchConcentration = parseFloat(entry.concentration) + tube.wells[0].batchConcentration = entry.concentration tube.wells[0].batchConcUnits = entry.concUnits tube.wells[0].solventCode = entry.solvent tubesToCreate.push tube @@ -3327,7 +3316,7 @@ exports.createDaughterVialsInternal = (vialsToCreate, user, callback) -> lsValues: [ lsType: 'numericValue' lsKind: 'amount added' - numericValue: parseFloat(entry.amount) + numericValue: entry.amount unitKind: entry.amountUnits ] ] @@ -3340,7 +3329,7 @@ exports.createDaughterVialsInternal = (vialsToCreate, user, callback) -> _.each vialsToCreate, (entry) -> toDecrement = barcode: entry.sourceVialBarcode - amountToDecrement: parseFloat(entry.amount) + amountToDecrement: entry.amount amountToDecrementUnits: entry.amountUnits parentVialsToDecrement.push toDecrement decrementAmountsFromVials parentVialsToDecrement, user, (err, decrementVialsResponse) -> @@ -3421,4 +3410,4 @@ exports.getParentVialByDaughterVialBarcodeInternal = (daughterVialBarcode, callb responseStub.parentVialCodeName = parentVial.codeName parentVialBarcode = _.findWhere parentVial.lsLabels, {lsType: 'barcode', lsKind: 'barcode', ignored: false} responseStub.parentVialBarcode = parentVialBarcode.labelText - callback null, responseStub \ No newline at end of file + callback null, responseStub From da82ecc79529600b6ff195ed0207740e71e87d20 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 3 Oct 2017 14:53:39 -0700 Subject: [PATCH 212/576] Added reporting of model save errors, and added guard clause for if systemRoleListController fails to initialize. --- modules/ServerAPI/src/client/AuthorEditor.coffee | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/modules/ServerAPI/src/client/AuthorEditor.coffee b/modules/ServerAPI/src/client/AuthorEditor.coffee index ea315aa2e..926163f66 100644 --- a/modules/ServerAPI/src/client/AuthorEditor.coffee +++ b/modules/ServerAPI/src/client/AuthorEditor.coffee @@ -502,13 +502,19 @@ class window.AuthorEditorController extends AbstractFormController @$('.bv_saving').show() console.log "handleSaveClicked" console.log JSON.stringify @model - @model.save() + @model.save null, + success: (model, response) -> + console.log 'save successful' + , + error: (model, response) -> + alert JSON.parse response.responseText prepareToSaveSystemRoles: => authorRoles = [] - @systemRoleListController.collection.each (role) => - authorRoles.push - roleEntry: role + if @systemRoleListController? + @systemRoleListController.collection.each (role) => + authorRoles.push + roleEntry: role ar = @model.get 'authorRoles' ar.push authorRoles... @model.set 'authorRoles', ar From 1be8d91cc2ac9720cea10f30dbd25a967c1ec86c Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 3 Oct 2017 15:31:38 -0700 Subject: [PATCH 213/576] Added code to decrementAmountsFromVials used in Daughter Vial creation to save changes to the parent change log. --- .../server/routes/InventoryServiceRoutes.coffee | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 8fff7c784..0213cb31b 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -3118,6 +3118,7 @@ decrementAmountsFromVials = (parentVialsToDecrement, user, callback) -> vialBarcodes = _.pluck parentVialsToDecrement, 'barcode' exports.getWellContentByContainerLabelsInternal vialBarcodes, 'container', 'tube', 'barcode', 'barcode', (wellContentList, statusCode) -> wellsToUpdate = [] + changes = [] _.each parentVialsToDecrement, (toDecrement) -> oldContainerWellContent = _.findWhere wellContentList, {label: toDecrement.barcode} oldWellContent = oldContainerWellContent.wellContent[0] @@ -3127,13 +3128,24 @@ decrementAmountsFromVials = (parentVialsToDecrement, user, callback) -> amount: oldWellContent.amount - toDecrement.amountToDecrement recordedBy: user wellsToUpdate.push newWellContent + change = + codeName: oldContainerWellContent.containerCodeName + recordedBy: user + recordedDate: (new Date()).getMilliseconds() + entryType: 'UPDATE' + entry: "Amount #{toDecrement.amountToDecrement} #{toDecrement.amountToDecrementUnits} taken out to create daughter vial #{toDecrement.daughterVialBarcode}" + changes.push change console.log wellsToUpdate exports.updateWellContentInternal wellsToUpdate, true, false, (updateWellsResponse, updateWellsStatusCode) -> console.log updateWellsStatusCode if updateWellsStatusCode != 204 callback "Error: #{updateWellsResponse}" else - callback null, updateWellsResponse + exports.containerLogsInternal changes, 0, (logs, statusCode) -> + if statusCode != 200 + callback logs + else + callback null, updateWellsResponse prepareSummaryInfo = (fileEntryArray) -> summaryInfo = @@ -3331,6 +3343,7 @@ exports.createDaughterVialsInternal = (vialsToCreate, user, callback) -> barcode: entry.sourceVialBarcode amountToDecrement: entry.amount amountToDecrementUnits: entry.amountUnits + daughterVialBarcode: entry.destinationVialBarcode parentVialsToDecrement.push toDecrement decrementAmountsFromVials parentVialsToDecrement, user, (err, decrementVialsResponse) -> if err? From 82dad187c8d899a84cbbb4ae386e677079f13e62 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Wed, 4 Oct 2017 11:15:33 -0700 Subject: [PATCH 214/576] tweaks to support lot inventory --- .../src/server/routes/InventoryServiceRoutes.coffee | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index f7f674e0d..130c9b57d 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -3251,7 +3251,7 @@ exports.validateDaughterVialsInternal = (vialsToValidate, callback) -> if missingSourceBarcodes.length > 0 callback null, errorMessages else - checkParentWellContent vialsToValidate, (parentWellContentErrors) -> + exports.checkParentWellContent vialsToValidate, (parentWellContentErrors) -> if parentWellContentErrors? errorMessages.push parentWellContentErrors... callback null, errorMessages @@ -3411,6 +3411,11 @@ exports.getParentVialByDaughterVialBarcodeInternal = (daughterVialBarcode, callb ] format = 'nestedstub' exports.advancedSearchContainersInternal itxSearch, format, (err, advSearchReturn) -> + if err? + callback err + return + if advSearchReturn.results.length < 1 + callback null, responseStub parentWell = advSearchReturn.results[0] responseStub.parentWellCodeName = parentWell.codeName parentWellLabel = _.findWhere parentWell.lsLabels, {lsType: 'name', lsKind: 'well name', ignored: false} From 9a85dba4597a0519216d6a4c73c06923c6a520b9 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 4 Oct 2017 11:38:04 -0700 Subject: [PATCH 215/576] Fixed mistakes in default configuration.json --- modules/CmpdReg/src/client/custom/configuration.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/CmpdReg/src/client/custom/configuration.json b/modules/CmpdReg/src/client/custom/configuration.json index 5c25477f2..f2b99776a 100755 --- a/modules/CmpdReg/src/client/custom/configuration.json +++ b/modules/CmpdReg/src/client/custom/configuration.json @@ -35,7 +35,7 @@ "useExactMass": true, "useProjectRolesToRestrictLotDetails": false, "showTareWeight": false, - "showTotalAmoundStored": false, + "showTotalAmountStored": false, "disableAliasEdit": false, "showLotInventory": true, "disableEditMyLots": false @@ -63,7 +63,7 @@ "unitTestDB": true, "initalDBLoad": true, "projectRestrictions": false, - "jchemVersion": "16.4.11.0" + "jchemVersion": "16.4.25.0" }, "bulkLoadSettings": { "useProjectRoles":false, From dd53f5eba79e5e062a2099d3007fca7e713f2a30 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Thu, 5 Oct 2017 20:01:22 -0700 Subject: [PATCH 216/576] fixed issues found in testing --- modules/Components/src/client/ACASFormFields.coffee | 5 +++++ modules/Components/src/client/AbstractFormController.coffee | 1 + 2 files changed, 6 insertions(+) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index f2544030f..249cdc8a9 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -102,6 +102,8 @@ class window.ACASFormAbstractFieldController extends Backbone.View @setPlaceholder @options.placeholder if @options.firstSelectText? @firstSelectText = @options.firstSelectText + if @options.tabIndex? + @setTabIndex @options.tabIndex @required = if @options.required? then @options.required else false setFormLabel: (value) -> @@ -134,6 +136,9 @@ class window.ACASFormAbstractFieldController extends Backbone.View enableInput: -> @$('input').removeAttr 'disabled' + setTabIndex: (index) -> + @$('input, select').attr 'tabindex', index + class window.ACASFormLSLabelFieldController extends ACASFormAbstractFieldController ### Launching controller must: diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 9736a722a..d2425404a 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -144,6 +144,7 @@ class window.AbstractThingFormController extends AbstractFormController modelDefaults: field.modelDefaults allowedFileTypes: field.fieldSettings.allowedFileTypes extendedLabel: field.fieldSettings.extendedLabel + tabIndex: field.fieldSettings.tabIndex switch field.fieldSettings.fieldType when 'label' From 42d4ca656af7361902bee378c89ba65ebc997a35 Mon Sep 17 00:00:00 2001 From: Fiona McNeil Date: Fri, 6 Oct 2017 08:56:06 -0700 Subject: [PATCH 217/576] Changed iframe height. --- modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css index 12e359042..c5e25f056 100755 --- a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css +++ b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css @@ -222,7 +222,7 @@ div { .MetaLotView .bv_lotInventory iframe { width: 700px; - height: 1000px; + height: 700px; } .NewLotSuccessView .labelCorpName { From 56aad0b87760e461f81fc582774da713dd7faa96 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 6 Oct 2017 16:59:43 -0700 Subject: [PATCH 218/576] locking down packages with "*" to specific versions --- package.json | 48 ++++++++++++++++++++++++------------------------ 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/package.json b/package.json index 11867916a..d495ebd5f 100644 --- a/package.json +++ b/package.json @@ -17,57 +17,57 @@ "dependencies": { "assert": "~1.1.1", "async": "^0.9.0", - "asyncblock": "*", + "asyncblock": "2.2.11", "backbone": "^1.2.3", "backbone-validation": "^0.11.5", - "bluebird": "*", - "bootstrap": "*", + "bluebird": "3.5.0", + "bootstrap": "3.3.7", "chai": "^3.5.0", "cookie-parser": "^1.4.3", "connect-flash": "~0.1.0", - "cron": "*", + "cron": "1.3.0", "csv-parse": "^1.1.1", "each": ">= 0.0.0", - "exports-loader": "*", + "exports-loader": "0.6.4", "express": "3.0.2", - "extract-text-webpack-plugin": "*", - "file-loader": "*", - "flat": "*", - "forever-monitor": "*", - "glob": "*", + "extract-text-webpack-plugin": "3.0.0", + "file-loader": "0.11.2", + "flat": "4.0.0", + "forever-monitor": "1.7.1", + "glob": "7.1.2", "jade": "0.35.0", "jasmine-core": "^2.4.1", "jasmine-jquery": "^2.1.1", "jquery": "^2.2.0", "jquery-file-upload-middleware": "https://github.com/mcneilco/jquery-file-upload-middleware.git", "json2csv": "^3.9.1", - "jszip": "*", + "jszip": "3.1.4", "less": "^2.6.0", "lodash": "^4.0.0", - "marked": "*", - "mocha": "*", + "marked": "0.3.6", + "mocha": "3.5.3", "mochawesome": "^2.0.2", - "mongojs": "*", - "ncp": "*", - "open-graph": "*", + "mongojs": "2.4.1", + "ncp": "2.0.0", + "open-graph": "0.2.3", "passport": ">= 0.0.0", "passport-local": ">= 0.0.0", - "properties": "*", - "properties-parser": "*", + "properties": "1.2.1", + "properties-parser": "0.3.1", "request": "2.34.0", - "request-promise": "*", + "request-promise": "4.2.1", "shelljs": "0.6.0", "socket.io": "^1.7.3", "passport.socketio": "^3.7.0", "promise": "7.1.1", - "style-loader": "*", + "style-loader": "0.18.2", "temporary": ">= 0.0.0", "underscore": ">= 0.0.0", "underscore-deep-extend": ">= 0.0.0", - "url-loader": "*", - "winston": "*", - "winston-mongodb": "*", - "yamljs": "*", + "url-loader": "0.5.9", + "winston": "0.5.9", + "winston-mongodb": "2.0.10", + "yamljs": "0.3.0", "webshot": "0.18.0", "archiver": "2.0.0" }, From 6913457ab4e7da35c727d26713442e3680c86462 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 6 Oct 2017 17:02:15 -0700 Subject: [PATCH 219/576] fixing winston package --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index d495ebd5f..d4d905fa9 100644 --- a/package.json +++ b/package.json @@ -65,7 +65,7 @@ "underscore": ">= 0.0.0", "underscore-deep-extend": ">= 0.0.0", "url-loader": "0.5.9", - "winston": "0.5.9", + "winston": "2.3.1", "winston-mongodb": "2.0.10", "yamljs": "0.3.0", "webshot": "0.18.0", From b4a344b76f2d9883e62d8ff2f08c9062e96a7d09 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Mon, 9 Oct 2017 15:16:03 -0700 Subject: [PATCH 220/576] minor lot inventory fixes --- modules/CmpdReg/src/client/custom/LotView_Custom.inc | 6 +++++- modules/CmpdReg/src/client/custom/Lot_Custom.js | 7 +++++++ .../src/server/routes/InventoryServiceRoutes.coffee | 2 +- 3 files changed, 13 insertions(+), 2 deletions(-) diff --git a/modules/CmpdReg/src/client/custom/LotView_Custom.inc b/modules/CmpdReg/src/client/custom/LotView_Custom.inc index 13c5154ae..0958d0522 100755 --- a/modules/CmpdReg/src/client/custom/LotView_Custom.inc +++ b/modules/CmpdReg/src/client/custom/LotView_Custom.inc @@ -77,11 +77,15 @@
        -
        +
        +
        + +
        +

        diff --git a/modules/CmpdReg/src/client/custom/Lot_Custom.js b/modules/CmpdReg/src/client/custom/Lot_Custom.js index 52ff3f248..b9b2ca6d0 100755 --- a/modules/CmpdReg/src/client/custom/Lot_Custom.js +++ b/modules/CmpdReg/src/client/custom/Lot_Custom.js @@ -249,6 +249,11 @@ $(function() { this.$('.synthesisDate').datepicker( "option", "dateFormat", "mm/dd/yy" ); this.$('.editAnalyticalFiles').hide(); this.$('.analyticalFiles').html('Add analytical files by editing lot after it is saved'); + } else { + if (window.configuration.metaLot.showLotInventory) { + this.$('.amountWrapper').hide(); + this.$('.barcodeWrapper').hide(); + } } return this; }, @@ -272,6 +277,7 @@ $(function() { comments: '', color: '', amount: null, + barcode: null, purity: null, physicalState: null, purityOperator: null, @@ -329,6 +335,7 @@ $(function() { amount: (jQuery.trim(this.$('.amount').val())=='') ? null : parseFloat(jQuery.trim(this.$('.amount').val())), + barcode: (jQuery.trim(this.$('.barcode').val())=='') ? null : jQuery.trim(this.$('.barcode').val()), retain: (jQuery.trim(this.$('.retain').val())=='') ? null : parseFloat(jQuery.trim(this.$('.retain').val())), diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 130c9b57d..e69583796 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -3131,7 +3131,7 @@ decrementAmountsFromVials = (parentVialsToDecrement, user, callback) -> change = codeName: oldContainerWellContent.containerCodeName recordedBy: user - recordedDate: (new Date()).getMilliseconds() + recordedDate: new Date().getTime() entryType: 'UPDATE' entry: "Amount #{toDecrement.amountToDecrement} #{toDecrement.amountToDecrementUnits} taken out to create daughter vial #{toDecrement.daughterVialBarcode}" changes.push change From b880be7bbe418e736abdb2dfe0272647b0d2efb6 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 9 Oct 2017 15:22:41 -0700 Subject: [PATCH 221/576] Changed new salt sketcher to not show itself when marvin load is complete in MarvinJS mode. Fixes #258 --- modules/CmpdReg/src/client/src/Salt.js | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/CmpdReg/src/client/src/Salt.js b/modules/CmpdReg/src/client/src/Salt.js index 6bce90060..37d05395a 100755 --- a/modules/CmpdReg/src/client/src/Salt.js +++ b/modules/CmpdReg/src/client/src/Salt.js @@ -177,7 +177,6 @@ $(function() { sketcherInstance.addTemplate(window.marvinStructureTemplates[i]); } } - self.show(); self.sketcherLoaded = true; }, function (error) { alert("Cannot retrieve newSaltMarvinSketch sketcher instance from iframe:" + error); From d378322205c7f3578e9f711a1d1ae11e17455425 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 9 Oct 2017 16:03:36 -0700 Subject: [PATCH 222/576] Changed password change success function to set "returnTo" to /, then redirect to login, so user is sent to ACAS homepage instead of back to changePassword. Fixes #260 --- modules/Login/src/server/routes/loginRoutes.coffee | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/Login/src/server/routes/loginRoutes.coffee b/modules/Login/src/server/routes/loginRoutes.coffee index 8c5b914eb..7c4a87299 100644 --- a/modules/Login/src/server/routes/loginRoutes.coffee +++ b/modules/Login/src/server/routes/loginRoutes.coffee @@ -161,6 +161,7 @@ exports.changeAuthenticationService = (req, resp) -> console.log results if results.indexOf("Your password has successfully been changed")>=0 req.flash 'error','Your new password is set.' + req.session.returnTo = '/' resp.redirect '/login' else if results.indexOf("connection_error")>=0 req.flash 'error','Cannot connect to authentication service. Please contact an administrator.' From 4f79d4b105b747275e422f8328d1b7519fff2547 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 9 Oct 2017 16:28:48 -0700 Subject: [PATCH 223/576] Fixed LabelSequence modelSaveCallback. It no longer clears the LsRoles list, and it disables all inputs and selects and hides the update and cancel buttons. Fixes #262 --- .../ACASLabelSequences/src/client/ACASLabelSequences.coffee | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee index 77d5b0125..3824e1f6b 100644 --- a/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee +++ b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee @@ -307,12 +307,14 @@ class window.ACASLabelSequenceController extends AbstractFormController @$('.bv_saving').hide() modelSaveCallback: (method, model) => - @$('.bv_save').show() + @$('.bv_save').hide() + @$('.bv_cancel').hide() @$('.bv_save').attr('disabled', 'disabled') unless @$('.bv_saveFailed').is(":visible") @$('.bv_saveComplete').show() @$('.bv_saving').hide() - @setupACASLabelSequenceRoleListController() + @$('input').prop 'disabled', true + @$('select').prop 'disabled', true @render() @trigger 'amClean' From dc4bb6681fd27e5e91aba45eb6d1ce4af847d014 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 10 Oct 2017 10:30:30 -0700 Subject: [PATCH 224/576] Added check to checkParentWellContent in daughter vial validation that if a batchCode was passed in, it needs to match the parent vial's batch code. Fixes #265 Refactored createDaughterVialsInternal to get parent well content earlier, fill in the parent vial's batch code if the daughter does not specify a batch code. Fixes #264 Also refactored decrementAmountsFromVials to accept the parentWellContent as a variable so we don't query that same data twice. Fixed another issue with the error/warning reporting regarding hasError / hasWarning. --- .../routes/InventoryServiceRoutes.coffee | 227 ++++++++++-------- 1 file changed, 123 insertions(+), 104 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index e69583796..26af77848 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -2655,7 +2655,7 @@ exports.validateParentVialsFromCSVInternal = (csvFileName, dryRun, callback) -> dryRun: dryRun fileToParse: csvFileName htmlSummary: '' - hasError: true + hasError: false hasWarning: false errorMessages: [] transactionId: null @@ -2684,8 +2684,12 @@ exports.validateParentVialsFromCSVInternal = (csvFileName, dryRun, callback) -> errorLevel: 'error' message: "The following barcodes already exist: " + existingBarcodes.join ', ' validationResponse.errorMessages.push error - if validationResponse.errorMessages.length < 1 - validationResponse.hasError = false + errors = _.where validationResponse.errorMessages, {errorLevel: 'error'} + warnings = _.where validationResponse.errorMessages, {errorLevel: 'warning'} + if errors.length > 0 + validationResponse.hasError = true + if warnings.length > 0 + validationResponse.hasWarning = true validationResponse.results.htmlSummary = prepareValidationHTMLSummary validationResponse.hasError, validationResponse.hasWarning, validationResponse.errorMessages, summaryInfo callback validationResponse else @@ -2808,7 +2812,7 @@ exports.validateDaughterVialsFromCSVInternal = (csvFileName, dryRun, callback) - dryRun: dryRun fileToParse: csvFileName htmlSummary: '' - hasError: true + hasError: false hasWarning: false errorMessages: [] transactionId: null @@ -2823,8 +2827,12 @@ exports.validateDaughterVialsFromCSVInternal = (csvFileName, dryRun, callback) - callback err else validationResponse.errorMessages.push errorsAndWarnings... - if validationResponse.errorMessages.length < 1 - validationResponse.hasError = false + errors = _.where validationResponse.errorMessages, {errorLevel: 'error'} + warnings = _.where validationResponse.errorMessages, {errorLevel: 'warning'} + if errors.length > 0 + validationResponse.hasError = true + if warnings.length > 0 + validationResponse.hasWarning = true validationResponse.results.htmlSummary = prepareValidationHTMLSummary validationResponse.hasError, validationResponse.hasWarning, validationResponse.errorMessages, summaryInfo callback null, validationResponse else @@ -3034,6 +3042,11 @@ exports.checkParentWellContent = (fileEntryArray, callback) -> errorLevel: 'warning' message: "Creating daughter vial #{fileEntry.destinationVialBarcode} will remove more than the total amount currently in parent vial #{fileEntry.sourceVialBarcode}, leaving a negative amount in the parent vial." errorMessages.push error + if fileEntry.batchCode? and fileEntry.batchCode != parentWellContent.batchCode + error = + errorLevel: 'error' + message: "Daughter vial #{fileEntry.destinationVialBarcode} must reference the same lot #{parentWellContent.batchCode} as the parent vial #{fileEntry.destinationVialBarcode}." + errorMessages.push error else error = errorLevel: 'error' @@ -3114,38 +3127,36 @@ exports.getContainerTubeDefinitionCode = (callback) -> exports.containersByTypeKindInternal 'definition container', 'tube', 'codetable', false, false, (definitionContainers) -> callback definitionContainers[0].code -decrementAmountsFromVials = (parentVialsToDecrement, user, callback) -> - vialBarcodes = _.pluck parentVialsToDecrement, 'barcode' - exports.getWellContentByContainerLabelsInternal vialBarcodes, 'container', 'tube', 'barcode', 'barcode', (wellContentList, statusCode) -> - wellsToUpdate = [] - changes = [] - _.each parentVialsToDecrement, (toDecrement) -> - oldContainerWellContent = _.findWhere wellContentList, {label: toDecrement.barcode} - oldWellContent = oldContainerWellContent.wellContent[0] - wellCode = oldWellContent.containerCodeName - newWellContent = - containerCodeName: wellCode - amount: oldWellContent.amount - toDecrement.amountToDecrement - recordedBy: user - wellsToUpdate.push newWellContent - change = - codeName: oldContainerWellContent.containerCodeName - recordedBy: user - recordedDate: new Date().getTime() - entryType: 'UPDATE' - entry: "Amount #{toDecrement.amountToDecrement} #{toDecrement.amountToDecrementUnits} taken out to create daughter vial #{toDecrement.daughterVialBarcode}" - changes.push change - console.log wellsToUpdate - exports.updateWellContentInternal wellsToUpdate, true, false, (updateWellsResponse, updateWellsStatusCode) -> - console.log updateWellsStatusCode - if updateWellsStatusCode != 204 - callback "Error: #{updateWellsResponse}" - else - exports.containerLogsInternal changes, 0, (logs, statusCode) -> - if statusCode != 200 - callback logs - else - callback null, updateWellsResponse +decrementAmountsFromVials = (toDecrementList, parentWellContentList, user, callback) -> + wellsToUpdate = [] + changes = [] + _.each toDecrementList, (toDecrement) -> + oldContainerWellContent = _.findWhere parentWellContentList, {label: toDecrement.barcode} + oldWellContent = oldContainerWellContent.wellContent[0] + wellCode = oldWellContent.containerCodeName + newWellContent = + containerCodeName: wellCode + amount: oldWellContent.amount - toDecrement.amountToDecrement + recordedBy: user + wellsToUpdate.push newWellContent + change = + codeName: oldContainerWellContent.containerCodeName + recordedBy: user + recordedDate: new Date().getTime() + entryType: 'UPDATE' + entry: "Amount #{toDecrement.amountToDecrement} #{toDecrement.amountToDecrementUnits} taken out to create daughter vial #{toDecrement.daughterVialBarcode}" + changes.push change + console.log wellsToUpdate + exports.updateWellContentInternal wellsToUpdate, true, false, (updateWellsResponse, updateWellsStatusCode) -> + console.log updateWellsStatusCode + if updateWellsStatusCode != 204 + callback "Error: #{updateWellsResponse}" + else + exports.containerLogsInternal changes, 0, (logs, statusCode) -> + if statusCode != 200 + callback logs + else + callback null, updateWellsResponse prepareSummaryInfo = (fileEntryArray) -> summaryInfo = @@ -3283,74 +3294,82 @@ exports.createDaughterVialsInternal = (vialsToCreate, user, callback) -> exports.getContainerTubeDefinitionCode (definitionCode) -> if !definitionCode? callback 'Could not find definition container for tube' - tubesToCreate = [] - _.each vialsToCreate, (entry) -> - tube = - barcode: entry.destinationVialBarcode - definition: definitionCode - recordedBy: user - createdUser: entry.preparedBy - createdDate: entry.createdDate - physicalState: entry.physicalState - wells: [ - wellName: "A001" - batchCode: entry.batchCode - amount: entry.amount - amountUnits: entry.amountUnits - physicalState: entry.physicalState + return + parentVialBarcodes = _.pluck vialsToCreate, 'sourceVialBarcode' + exports.getWellContentByContainerLabelsInternal parentVialBarcodes, 'container', 'tube', 'barcode', 'barcode', (parentWellContentList, statusCode) -> + tubesToCreate = [] + _.each vialsToCreate, (entry) -> + parentVialAndWellContent = _.findWhere parentWellContentList, {label: entry.sourceVialBarcode} + parentWellContent = parentVialAndWellContent.wellContent[0] + batchCode = parentWellContent.batchCode + if entry.batchCode? and entry.batchCode.length > 0 + batchCode = entry.batchCode + tube = + barcode: entry.destinationVialBarcode + definition: definitionCode recordedBy: user - recordedDate: (new Date()).getTime() - ] - if entry.physicalState == 'solution' - tube.wells[0].batchConcentration = entry.concentration - tube.wells[0].batchConcUnits = entry.concUnits - tube.wells[0].solventCode = entry.solvent - tubesToCreate.push tube - console.log JSON.stringify tubesToCreate - exports.createTubesInternal tubesToCreate, 0, (json, statusCode) -> - console.log statusCode - console.log json - if statusCode != 200 - callback json - else - interactionsToCreate = [] - _.each vialsToCreate, (entry) -> - interaction = - interactionType: 'added to' - interactionKind: 'well_well' - firstContainerBarcode: entry.sourceVialBarcode - secondContainerBarcode: entry.destinationVialBarcode - firstWellLabel: 'A001' - secondWellLabel: 'A001' - interactionStates: [ - lsType: 'metadata' - lsKind: 'information' - lsValues: [ - lsType: 'numericValue' - lsKind: 'amount added' - numericValue: entry.amount - unitKind: entry.amountUnits + createdUser: entry.preparedBy + createdDate: entry.createdDate + physicalState: entry.physicalState + wells: [ + wellName: "A001" + batchCode: batchCode + amount: entry.amount + amountUnits: entry.amountUnits + physicalState: entry.physicalState + recordedBy: user + recordedDate: (new Date()).getTime() + ] + if entry.physicalState == 'solution' + tube.wells[0].batchConcentration = entry.concentration + tube.wells[0].batchConcUnits = entry.concUnits + tube.wells[0].solventCode = entry.solvent + tubesToCreate.push tube + console.log JSON.stringify tubesToCreate + exports.createTubesInternal tubesToCreate, 0, (json, statusCode) -> + console.log statusCode + console.log json + if statusCode != 200 + callback json + else + interactionsToCreate = [] + _.each vialsToCreate, (entry) -> + interaction = + interactionType: 'added to' + interactionKind: 'well_well' + firstContainerBarcode: entry.sourceVialBarcode + secondContainerBarcode: entry.destinationVialBarcode + firstWellLabel: 'A001' + secondWellLabel: 'A001' + interactionStates: [ + lsType: 'metadata' + lsKind: 'information' + lsValues: [ + lsType: 'numericValue' + lsKind: 'amount added' + numericValue: entry.amount + unitKind: entry.amountUnits + ] ] - ] - interactionsToCreate.push interaction - exports.saveWellToWellInteractionsInternal interactionsToCreate, user, (err, itxResponse) -> - if err? - callback err - else - parentVialsToDecrement = [] - _.each vialsToCreate, (entry) -> - toDecrement = - barcode: entry.sourceVialBarcode - amountToDecrement: entry.amount - amountToDecrementUnits: entry.amountUnits - daughterVialBarcode: entry.destinationVialBarcode - parentVialsToDecrement.push toDecrement - decrementAmountsFromVials parentVialsToDecrement, user, (err, decrementVialsResponse) -> - if err? - callback err - else - #TODO see what this service should respond with - callback null, 'successfully created daughter vials' + interactionsToCreate.push interaction + exports.saveWellToWellInteractionsInternal interactionsToCreate, user, (err, itxResponse) -> + if err? + callback err + else + toDecrementList = [] + _.each vialsToCreate, (entry) -> + toDecrement = + barcode: entry.sourceVialBarcode + amountToDecrement: entry.amount + amountToDecrementUnits: entry.amountUnits + daughterVialBarcode: entry.destinationVialBarcode + toDecrementList.push toDecrement + decrementAmountsFromVials toDecrementList, parentWellContentList, user, (err, decrementVialsResponse) -> + if err? + callback err + else + #TODO see what this service should respond with + callback null, 'successfully created daughter vials' exports.advancedSearchContainers = (req, resp) -> exports.advancedSearchContainersInternal req.body, req.query.format, (err, response) -> From 0a035d00dd285f13130bba2519a0b725c3e78d6e Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 10 Oct 2017 10:42:48 -0700 Subject: [PATCH 225/576] Fixed calculation of unique batch codes to filter out undefined. Fixes #266 --- .../ServerAPI/src/server/routes/InventoryServiceRoutes.coffee | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 26af77848..f98f0c1dd 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -3164,7 +3164,9 @@ prepareSummaryInfo = (fileEntryArray) -> numSolidVials: (_.where fileEntryArray, {physicalState: 'solid'}).length numLiquidVials: (_.where fileEntryArray, {physicalState: 'solution'}).length batchCodes = _.pluck fileEntryArray, 'batchCode' - if batchCodes? + batchCodes = _.filter batchCodes, (entry) -> + entry? + if batchCodes? and batchCodes.length > 0 summaryInfo.totalBatchCodes = (_.uniq batchCodes).length summaryInfo From 01fab093a1f51219c48985192b9d69246c11fbe4 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 10 Oct 2017 14:50:27 -0700 Subject: [PATCH 226/576] Made tweak suggested by developer on Indigo forums to force Ketcher to always set the Chiral flag --- public/lib/ketcher-2.0.0-alpha.3/ketcher.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.js b/public/lib/ketcher-2.0.0-alpha.3/ketcher.js index 2c9589f28..1e5ddd121 100644 --- a/public/lib/ketcher-2.0.0-alpha.3/ketcher.js +++ b/public/lib/ketcher-2.0.0-alpha.3/ketcher.js @@ -922,7 +922,7 @@ require("./struct"),require("./cis_trans"),require("./dfs"),require("./molfile") }).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) },{"./cis_trans":8,"./dfs":9,"./molfile":12,"./sgroup":13,"./smiles":14,"./stereocenters":15,"./struct":16,"./struct_valence":17}],12:[function(require,module,exports){ (function (global){ -var Map=require("../util/map"),Set=require("../util/set"),Vec2=require("../util/vec2"),element=require("./element"),util=require("../util"),chem=global.chem=global.chem||{};chem.Molfile=function(){},chem.Molfile.loadRGroupFragments=!0,chem.Molfile.parseDecimalInt=function(e){var t=parseInt(e,10);return isNaN(t)?0:t},chem.Molfile.partitionLine=function(e,t,r){for(var i=[],a=0,n=0;a0&&(M.ifthen=g),M.resth=1==w,M.range=S,n[d]=M}else if("APO"==c)o.get("attpnt")||o.set("attpnt",new Map),o.get("attpnt").update(l.readKeyValuePairs(p));else if("ALS"==c){o.get("atomList")||o.set("atomList",new Map);var v=l.parsePropertyLineAtomList(l.partitionLine(p,[1,3,3,1,1,1]),l.partitionLineFixed(p.slice(10),4,!1));o.get("atomList").update(v),o.get("label")||o.set("label",new Map);for(var D in v)o.get("label").set(D,"L#")}else if("STY"==c)l.initSGroup(a,p);else if("SST"==c)l.applySGroupProp(a,"subtype",p);else if("SLB"==c)l.applySGroupProp(a,"label",p,!0);else if("SPL"==c)l.applySGroupProp(a,"parent",p,!0,!0);else if("SCN"==c)l.applySGroupProp(a,"connectivity",p);else if("SAL"==c)l.applySGroupArrayProp(a,"atoms",p,-1);else if("SBL"==c)l.applySGroupArrayProp(a,"bonds",p,-1);else if("SPA"==c)l.applySGroupArrayProp(a,"patoms",p,-1);else if("SMT"==c){var b=l.parseDecimalInt(p.slice(0,4))-1;a[b].data.subscript=p.slice(4).strip()}else"SDT"==c?l.applyDataSGroupDesc(a,p):"SDD"==c?l.applyDataSGroupInfoLine(a,p):"SCD"==c?l.applyDataSGroupDataLine(a,p,!1):"SED"==c&&l.applyDataSGroupDataLine(a,p,!0)}++r}return o},chem.Molfile.applyAtomProp=function(e,t,r,i){t.each(function(t,i){e.get(t)[r]=i})},chem.Molfile.parseCTabV2000=function(e,t){var r,i=new chem.Struct,a=chem.Molfile,n=a.parseDecimalInt(t[0]),l=a.parseDecimalInt(t[1]),o=a.parseDecimalInt(t[2]);i.isChiral=0!=a.parseDecimalInt(t[4]);var s=a.parseDecimalInt(t[5]),c=a.parseDecimalInt(t[10]),p=0,h=e.slice(p,p+n);p+=n;var u=e.slice(p,p+l);p+=l;var m=e.slice(p,p+o);p+=o+s;var f=h.map(a.parseAtomLine);for(r=0;r=0){var b=g[D-1];"GEN"===b.type&&(v.atoms=util.array(b.atoms))}}}for(S in g)chem.SGroup.addGroup(i,g[S],M);var N=[];for(S in g)chem.SGroup.filter(i,g[S],M),0!=g[S].atoms.length||g[S].allAtoms||N.push(S);for(r=0;rn+1&&i.push(e.slice(n+1,r)),n=r);return r>n+1&&i.push(e.slice(n+1,r)),n=r,i},chem.Molfile.splitonce=function(e,t){var r=e.indexOf(t);return[e.slice(0,r),e.slice(r+1)]},chem.Molfile.splitSGroupDef=function(e){for(var t=[],r=0,i=!1,a=0;a0&&t.push(e.strip()),t},chem.Molfile.parseBracedNumberList=function(e,t){if(!e)return null;var r=[];e=e.strip(),e=e.substr(1,e.length-2);var i=e.split(" ");t=t||0;for(var a=1;a0&&(d.ifthen=u),d.resth=1==m,d.range=f,i[l]=d,a++}}}for(var g in r)for(var w=0;wr[s];)++s;n[s]=n[s]||{},Set.mergeIn(n[s],t[a])}var c=[],p=[],h=[];for(a=0;a0,e.rxnArrows.count()>1)throw new Error("Reaction may not contain more than one arrow");if(this.molfile="",this.reaction){if(e.rgroups.count()>0)throw new Error("Unable to save the structure - reactions with r-groups are not supported at the moment");var a=chem.MolfileSaver.getComponents(e),n=a.reactants,l=a.products,o=n.concat(l);this.molfile="$RXN\n\n\n\n"+util.paddedInt(n.length,3)+util.paddedInt(l.length,3)+util.paddedInt(0,3)+"\n";for(var s=0;s0){if(!r){var u=new chem.MolfileSaver(!1).getCTab(e.getScaffold(),e.rgroups);return this.molfile="$MDL REV 1\n$MOL\n$HDR\n\n\n\n$END HDR\n",this.molfile+="$CTAB\n"+u+"$END CTAB\n",e.rgroups.each(function(t,r){this.molfile+="$RGP\n",this.writePaddedNumber(t,3),this.molfile+="\n",r.frags.each(function(t,r){var i=new chem.MolfileSaver(!1).getCTab(e.getFragment(r));this.molfile+="$CTAB\n"+i+"$END CTAB\n"},this),this.molfile+="$END RGP\n"},this),this.molfile+="$END MOL\n",this.molfile}e=e.getScaffold()}return this.molecule=e.clone(),this.prepareSGroups(t,i),this.writeHeader(),this.writeCTab2000(),this.molfile},chem.MolfileSaver.prototype.writeHeader=function(){var e=new Date;this.writeCR(),this.writeWhiteSpace(2),this.write("Ketcher"),this.writeWhiteSpace(),this.writeCR((e.getMonth()+1).toPaddedString(2)+e.getDate().toPaddedString(2)+(e.getFullYear()%100).toPaddedString(2)+e.getHours().toPaddedString(2)+e.getMinutes().toPaddedString(2)+"2D 1 1.00000 0.00000 0"),this.writeCR()},chem.MolfileSaver.prototype.write=function(e){this.molfile+=e},chem.MolfileSaver.prototype.writeCR=function(e){0==arguments.length&&(e=""),this.molfile+=e+"\n"},chem.MolfileSaver.prototype.writeWhiteSpace=function(e){0==arguments.length&&(e=1),e.times(function(){this.write(" ")},this)},chem.MolfileSaver.prototype.writePadded=function(e,t){this.write(e),this.writeWhiteSpace(t-e.length)},chem.MolfileSaver.prototype.writePaddedNumber=function(e,t){var r=(e-0).toString();this.writeWhiteSpace(t-r.length),this.write(r)},chem.MolfileSaver.prototype.writePaddedFloat=function(e,t,r){this.write(util.paddedFloat(e,t,r))},chem.MolfileSaver.prototype.writeCTab2000Header=function(){this.writePaddedNumber(this.molecule.atoms.count(),3),this.writePaddedNumber(this.molecule.bonds.count(),3),this.writePaddedNumber(0,3),this.writeWhiteSpace(3),this.writePaddedNumber(this.molecule.isChiral?1:0,3),this.writePaddedNumber(0,3),this.writeWhiteSpace(12),this.writePaddedNumber(999,3),this.writeCR(" V2000")},chem.MolfileSaver.prototype.writeCTab2000=function(e){this.writeCTab2000Header(),this.mapping={};var t=1,r=[],i=[];for(this.molecule.atoms.each(function(e,a){this.writePaddedFloat(a.pp.x,10,4),this.writePaddedFloat(-a.pp.y,10,4),this.writePaddedFloat(0,10,4),this.writeWhiteSpace();var n=a.label;null!=a.atomList?(n="L",r.push(e)):null==element.getElementByLabel(n)&&-1==["A","Q","X","*","R#"].indexOf(n)&&(n="C",i.push(e)),this.writePadded(n,3),this.writePaddedNumber(0,2),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),Object.isUndefined(a.hCount)&&(a.hCount=0),this.writePaddedNumber(a.hCount,3),Object.isUndefined(a.stereoCare)&&(a.stereoCare=0),this.writePaddedNumber(a.stereoCare,3),this.writePaddedNumber(a.explicitValence<0?0:0==a.explicitValence?15:a.explicitValence,3),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),Object.isUndefined(a.aam)&&(a.aam=0),this.writePaddedNumber(a.aam,3),Object.isUndefined(a.invRet)&&(a.invRet=0),this.writePaddedNumber(a.invRet,3),Object.isUndefined(a.exactChangeFlag)&&(a.exactChangeFlag=0),this.writePaddedNumber(a.exactChangeFlag,3),this.writeCR(),this.mapping[e]=t,t++},this),this.bondMapping={},t=1,this.molecule.bonds.each(function(e,r){this.bondMapping[e]=t++,this.writePaddedNumber(this.mapping[r.begin],3),this.writePaddedNumber(this.mapping[r.end],3),this.writePaddedNumber(r.type,3),Object.isUndefined(r.stereo)&&(r.stereo=0),this.writePaddedNumber(r.stereo,3),this.writeWhiteSpace(3),Object.isUndefined(r.topology)&&(r.topology=0),this.writePaddedNumber(r.topology,3),Object.isUndefined(r.reactingCenterStatus)&&(r.reactingCenterStatus=0),this.writePaddedNumber(r.reactingCenterStatus,3),this.writeCR()},this);i.length>0;)this.write("A "),this.writePaddedNumber(i[0]+1,3),this.writeCR(),this.writeCR(this.molecule.atoms.get(i[0]).label),i.splice(0,1);var a=new Array,n=new Array,l=new Array,o=new Array,s=new Array,c=new Array,p=new Array,h=new Array,u=new Array;this.molecule.atoms.each(function(e,t){if(0!=t.charge&&a.push([e,t.charge]),0!=t.isotope&&n.push([e,t.isotope]),0!=t.radical&&l.push([e,t.radical]),null!=t.rglabel&&"R#"==t.label)for(var r=0;r<32;r++)t.rglabel&1<0||t.range.length>0){var r=" 1 "+util.paddedInt(e,3)+" "+util.paddedInt(t.ifthen,3)+" "+util.paddedInt(t.resth?1:0,3)+" "+t.range;s.push(r)}});var m=function(e,t){for(;t.length>0;){for(var r=new Array;t.length>0&&r.length<8;)r.push(t[0]),t.splice(0,1);this.write(e),this.writePaddedNumber(r.length,3),r.each(function(e){this.writeWhiteSpace(),this.writePaddedNumber(this.mapping[e[0]],3),this.writeWhiteSpace(),this.writePaddedNumber(e[1],3)},this),this.writeCR()}};m.call(this,"M CHG",a),m.call(this,"M ISO",n),m.call(this,"M RAD",l),m.call(this,"M RGP",o);for(var f=0;f0)for(f=0;f=0&&(this.write("M SPL"),this.writePaddedNumber(1,3),this.writeWhiteSpace(1),this.writePaddedNumber(N,3),this.writeWhiteSpace(1),this.writePaddedNumber(M[T],3),this.writeCR()),"SRU"==A.type&&A.data.connectivity){var C="";C+=" ",C+=util.stringPadded(N.toString(),3),C+=" ",C+=util.stringPadded(A.data.connectivity,3,!0),this.write("M SCN"),this.writePaddedNumber(1,3),this.write(C.toUpperCase()),this.writeCR()}"SRU"==A.type&&(this.write("M SMT "),this.writePaddedNumber(N,3),this.writeWhiteSpace(),this.write(A.data.subscript||"n"),this.writeCR()),this.writeCR(A.saveToMolfile(this.molecule,M,this.mapping,this.bondMapping))}this.writeCR("M END")},chem.Molfile.parseRxn=function(e){var t=chem.Molfile,r=e[0].strip().split(" ");return r.length>1&&"V3000"==r[1]?t.parseRxn3000(e):t.parseRxn2000(e)},chem.Molfile.parseRxn2000=function(e){var t=chem.Molfile;e=e.slice(4);var r=t.partitionLine(e[0],t.fmtInfo.rxnItemsPartition),i=r[0]-0,a=r[1]-0,n=r[2]-0;e=e.slice(1);for(var l=[];e.length>0&&"$MOL"==e[0].substr(0,4);){e=e.slice(1);for(var o=0;o2?r[2]-0:0,l=function(e){util.assert(e,"CTab format invalid")},o=[],s=[],c=null,p=[],h=0;h0&&(M.ifthen=g),M.resth=1==w,M.range=S,n[d]=M}else if("APO"==c)o.get("attpnt")||o.set("attpnt",new Map),o.get("attpnt").update(l.readKeyValuePairs(p));else if("ALS"==c){o.get("atomList")||o.set("atomList",new Map);var v=l.parsePropertyLineAtomList(l.partitionLine(p,[1,3,3,1,1,1]),l.partitionLineFixed(p.slice(10),4,!1));o.get("atomList").update(v),o.get("label")||o.set("label",new Map);for(var D in v)o.get("label").set(D,"L#")}else if("STY"==c)l.initSGroup(a,p);else if("SST"==c)l.applySGroupProp(a,"subtype",p);else if("SLB"==c)l.applySGroupProp(a,"label",p,!0);else if("SPL"==c)l.applySGroupProp(a,"parent",p,!0,!0);else if("SCN"==c)l.applySGroupProp(a,"connectivity",p);else if("SAL"==c)l.applySGroupArrayProp(a,"atoms",p,-1);else if("SBL"==c)l.applySGroupArrayProp(a,"bonds",p,-1);else if("SPA"==c)l.applySGroupArrayProp(a,"patoms",p,-1);else if("SMT"==c){var b=l.parseDecimalInt(p.slice(0,4))-1;a[b].data.subscript=p.slice(4).strip()}else"SDT"==c?l.applyDataSGroupDesc(a,p):"SDD"==c?l.applyDataSGroupInfoLine(a,p):"SCD"==c?l.applyDataSGroupDataLine(a,p,!1):"SED"==c&&l.applyDataSGroupDataLine(a,p,!0)}++r}return o},chem.Molfile.applyAtomProp=function(e,t,r,i){t.each(function(t,i){e.get(t)[r]=i})},chem.Molfile.parseCTabV2000=function(e,t){var r,i=new chem.Struct,a=chem.Molfile,n=a.parseDecimalInt(t[0]),l=a.parseDecimalInt(t[1]),o=a.parseDecimalInt(t[2]);i.isChiral=0!=a.parseDecimalInt(t[4]);var s=a.parseDecimalInt(t[5]),c=a.parseDecimalInt(t[10]),p=0,h=e.slice(p,p+n);p+=n;var u=e.slice(p,p+l);p+=l;var m=e.slice(p,p+o);p+=o+s;var f=h.map(a.parseAtomLine);for(r=0;r=0){var b=g[D-1];"GEN"===b.type&&(v.atoms=util.array(b.atoms))}}}for(S in g)chem.SGroup.addGroup(i,g[S],M);var N=[];for(S in g)chem.SGroup.filter(i,g[S],M),0!=g[S].atoms.length||g[S].allAtoms||N.push(S);for(r=0;rn+1&&i.push(e.slice(n+1,r)),n=r);return r>n+1&&i.push(e.slice(n+1,r)),n=r,i},chem.Molfile.splitonce=function(e,t){var r=e.indexOf(t);return[e.slice(0,r),e.slice(r+1)]},chem.Molfile.splitSGroupDef=function(e){for(var t=[],r=0,i=!1,a=0;a0&&t.push(e.strip()),t},chem.Molfile.parseBracedNumberList=function(e,t){if(!e)return null;var r=[];e=e.strip(),e=e.substr(1,e.length-2);var i=e.split(" ");t=t||0;for(var a=1;a0&&(d.ifthen=u),d.resth=1==m,d.range=f,i[l]=d,a++}}}for(var g in r)for(var w=0;wr[s];)++s;n[s]=n[s]||{},Set.mergeIn(n[s],t[a])}var c=[],p=[],h=[];for(a=0;a0,e.rxnArrows.count()>1)throw new Error("Reaction may not contain more than one arrow");if(this.molfile="",this.reaction){if(e.rgroups.count()>0)throw new Error("Unable to save the structure - reactions with r-groups are not supported at the moment");var a=chem.MolfileSaver.getComponents(e),n=a.reactants,l=a.products,o=n.concat(l);this.molfile="$RXN\n\n\n\n"+util.paddedInt(n.length,3)+util.paddedInt(l.length,3)+util.paddedInt(0,3)+"\n";for(var s=0;s0){if(!r){var u=new chem.MolfileSaver(!1).getCTab(e.getScaffold(),e.rgroups);return this.molfile="$MDL REV 1\n$MOL\n$HDR\n\n\n\n$END HDR\n",this.molfile+="$CTAB\n"+u+"$END CTAB\n",e.rgroups.each(function(t,r){this.molfile+="$RGP\n",this.writePaddedNumber(t,3),this.molfile+="\n",r.frags.each(function(t,r){var i=new chem.MolfileSaver(!1).getCTab(e.getFragment(r));this.molfile+="$CTAB\n"+i+"$END CTAB\n"},this),this.molfile+="$END RGP\n"},this),this.molfile+="$END MOL\n",this.molfile}e=e.getScaffold()}return this.molecule=e.clone(),this.prepareSGroups(t,i),this.writeHeader(),this.writeCTab2000(),this.molfile},chem.MolfileSaver.prototype.writeHeader=function(){var e=new Date;this.writeCR(),this.writeWhiteSpace(2),this.write("Ketcher"),this.writeWhiteSpace(),this.writeCR((e.getMonth()+1).toPaddedString(2)+e.getDate().toPaddedString(2)+(e.getFullYear()%100).toPaddedString(2)+e.getHours().toPaddedString(2)+e.getMinutes().toPaddedString(2)+"2D 1 1.00000 0.00000 0"),this.writeCR()},chem.MolfileSaver.prototype.write=function(e){this.molfile+=e},chem.MolfileSaver.prototype.writeCR=function(e){0==arguments.length&&(e=""),this.molfile+=e+"\n"},chem.MolfileSaver.prototype.writeWhiteSpace=function(e){0==arguments.length&&(e=1),e.times(function(){this.write(" ")},this)},chem.MolfileSaver.prototype.writePadded=function(e,t){this.write(e),this.writeWhiteSpace(t-e.length)},chem.MolfileSaver.prototype.writePaddedNumber=function(e,t){var r=(e-0).toString();this.writeWhiteSpace(t-r.length),this.write(r)},chem.MolfileSaver.prototype.writePaddedFloat=function(e,t,r){this.write(util.paddedFloat(e,t,r))},chem.MolfileSaver.prototype.writeCTab2000Header=function(){this.writePaddedNumber(this.molecule.atoms.count(),3),this.writePaddedNumber(this.molecule.bonds.count(),3),this.writePaddedNumber(0,3),this.writeWhiteSpace(3),this.writePaddedNumber(1,3),this.writePaddedNumber(0,3),this.writeWhiteSpace(12),this.writePaddedNumber(999,3),this.writeCR(" V2000")},chem.MolfileSaver.prototype.writeCTab2000=function(e){this.writeCTab2000Header(),this.mapping={};var t=1,r=[],i=[];for(this.molecule.atoms.each(function(e,a){this.writePaddedFloat(a.pp.x,10,4),this.writePaddedFloat(-a.pp.y,10,4),this.writePaddedFloat(0,10,4),this.writeWhiteSpace();var n=a.label;null!=a.atomList?(n="L",r.push(e)):null==element.getElementByLabel(n)&&-1==["A","Q","X","*","R#"].indexOf(n)&&(n="C",i.push(e)),this.writePadded(n,3),this.writePaddedNumber(0,2),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),Object.isUndefined(a.hCount)&&(a.hCount=0),this.writePaddedNumber(a.hCount,3),Object.isUndefined(a.stereoCare)&&(a.stereoCare=0),this.writePaddedNumber(a.stereoCare,3),this.writePaddedNumber(a.explicitValence<0?0:0==a.explicitValence?15:a.explicitValence,3),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),this.writePaddedNumber(0,3),Object.isUndefined(a.aam)&&(a.aam=0),this.writePaddedNumber(a.aam,3),Object.isUndefined(a.invRet)&&(a.invRet=0),this.writePaddedNumber(a.invRet,3),Object.isUndefined(a.exactChangeFlag)&&(a.exactChangeFlag=0),this.writePaddedNumber(a.exactChangeFlag,3),this.writeCR(),this.mapping[e]=t,t++},this),this.bondMapping={},t=1,this.molecule.bonds.each(function(e,r){this.bondMapping[e]=t++,this.writePaddedNumber(this.mapping[r.begin],3),this.writePaddedNumber(this.mapping[r.end],3),this.writePaddedNumber(r.type,3),Object.isUndefined(r.stereo)&&(r.stereo=0),this.writePaddedNumber(r.stereo,3),this.writeWhiteSpace(3),Object.isUndefined(r.topology)&&(r.topology=0),this.writePaddedNumber(r.topology,3),Object.isUndefined(r.reactingCenterStatus)&&(r.reactingCenterStatus=0),this.writePaddedNumber(r.reactingCenterStatus,3),this.writeCR()},this);i.length>0;)this.write("A "),this.writePaddedNumber(i[0]+1,3),this.writeCR(),this.writeCR(this.molecule.atoms.get(i[0]).label),i.splice(0,1);var a=new Array,n=new Array,l=new Array,o=new Array,s=new Array,c=new Array,p=new Array,h=new Array,u=new Array;this.molecule.atoms.each(function(e,t){if(0!=t.charge&&a.push([e,t.charge]),0!=t.isotope&&n.push([e,t.isotope]),0!=t.radical&&l.push([e,t.radical]),null!=t.rglabel&&"R#"==t.label)for(var r=0;r<32;r++)t.rglabel&1<0||t.range.length>0){var r=" 1 "+util.paddedInt(e,3)+" "+util.paddedInt(t.ifthen,3)+" "+util.paddedInt(t.resth?1:0,3)+" "+t.range;s.push(r)}});var m=function(e,t){for(;t.length>0;){for(var r=new Array;t.length>0&&r.length<8;)r.push(t[0]),t.splice(0,1);this.write(e),this.writePaddedNumber(r.length,3),r.each(function(e){this.writeWhiteSpace(),this.writePaddedNumber(this.mapping[e[0]],3),this.writeWhiteSpace(),this.writePaddedNumber(e[1],3)},this),this.writeCR()}};m.call(this,"M CHG",a),m.call(this,"M ISO",n),m.call(this,"M RAD",l),m.call(this,"M RGP",o);for(var f=0;f0)for(f=0;f=0&&(this.write("M SPL"),this.writePaddedNumber(1,3),this.writeWhiteSpace(1),this.writePaddedNumber(N,3),this.writeWhiteSpace(1),this.writePaddedNumber(M[T],3),this.writeCR()),"SRU"==A.type&&A.data.connectivity){var C="";C+=" ",C+=util.stringPadded(N.toString(),3),C+=" ",C+=util.stringPadded(A.data.connectivity,3,!0),this.write("M SCN"),this.writePaddedNumber(1,3),this.write(C.toUpperCase()),this.writeCR()}"SRU"==A.type&&(this.write("M SMT "),this.writePaddedNumber(N,3),this.writeWhiteSpace(),this.write(A.data.subscript||"n"),this.writeCR()),this.writeCR(A.saveToMolfile(this.molecule,M,this.mapping,this.bondMapping))}this.writeCR("M END")},chem.Molfile.parseRxn=function(e){var t=chem.Molfile,r=e[0].strip().split(" ");return r.length>1&&"V3000"==r[1]?t.parseRxn3000(e):t.parseRxn2000(e)},chem.Molfile.parseRxn2000=function(e){var t=chem.Molfile;e=e.slice(4);var r=t.partitionLine(e[0],t.fmtInfo.rxnItemsPartition),i=r[0]-0,a=r[1]-0,n=r[2]-0;e=e.slice(1);for(var l=[];e.length>0&&"$MOL"==e[0].substr(0,4);){e=e.slice(1);for(var o=0;o2?r[2]-0:0,l=function(e){util.assert(e,"CTab format invalid")},o=[],s=[],c=null,p=[],h=0;h Date: Wed, 11 Oct 2017 15:39:27 -0700 Subject: [PATCH 227/576] Added line to hide Add Ls Role button after save comes back #270 --- modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee index 3824e1f6b..dfc6c4e0b 100644 --- a/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee +++ b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee @@ -315,6 +315,7 @@ class window.ACASLabelSequenceController extends AbstractFormController @$('.bv_saving').hide() @$('input').prop 'disabled', true @$('select').prop 'disabled', true + @$('.bv_addLabelSequenceRoleButton').hide() @render() @trigger 'amClean' From 6c3aedc5e78bd50f8aaaa01050d7b90afcd0bd2e Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 11 Oct 2017 16:36:11 -0700 Subject: [PATCH 228/576] Completed updateAuthorAndRolesInternal route that was missing an else case for when permissions are all in order for an update but the ls roles have not been changed. Fixes #272 Also fixed an internal function that still said resp.json instead of callback. --- .../src/server/routes/AuthorRoutes.coffee | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee index 7db5ecf10..e69d78ddc 100644 --- a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee @@ -122,7 +122,7 @@ exports.updateAuthorModulePreferencesInternal = (userName, moduleName, settings, exports.updateAuthorInternal = (author, callback) -> if global.specRunnerTestmode authorServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/AuthorServiceTestJSON.js' - resp.json authorServiceTestJSON.updateAuthor + callback authorServiceTestJSON.updateAuthor else config = require '../conf/compiled/conf.js' # if author.has('transactionOptions') @@ -639,6 +639,18 @@ exports.updateAuthorAndRolesInternal = (author, user, callback) -> callback err else callback null, response + else + #roles have not changed, just update the author + exports.updateAuthorInternal author, (updatedAuthor, statusCode) -> + if statusCode != 200 + callback updatedAuthor + else + #save successful. Fetch the new author and return. + exports.getAuthorByUsernameInternal author.userName, (response, statusCode) -> + if statusCode != 200 + callback err + else + callback null, response validateAuthorAttributes = (author, callback) -> requiredAttrs = ['firstName', 'lastName', 'userName', 'emailAddress'] From 690a2a4180b9608524c20268e75b91fbb40226bd Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Thu, 12 Oct 2017 11:45:37 -0700 Subject: [PATCH 229/576] feature/sel-required-attributes: Issue #274 (Specify required SEL attributes in Protocol Editor), fix styling for curve display params --- .../ServerAPI/conf/ProtocolConfJSON.coffee | 3 ++ modules/ServerAPI/src/client/Protocol.coffee | 44 +++++++++++++++++++ modules/ServerAPI/src/client/Protocol.html | 3 +- 3 files changed, 49 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/conf/ProtocolConfJSON.coffee b/modules/ServerAPI/conf/ProtocolConfJSON.coffee index 3f65708ad..97bd4f053 100644 --- a/modules/ServerAPI/conf/ProtocolConfJSON.coffee +++ b/modules/ServerAPI/conf/ProtocolConfJSON.coffee @@ -179,6 +179,9 @@ , typeName: "protocol" kindName: "review status" + , + typeName: "protocol" + kindName: "sel required attribute" , typeName: "assay" kindName: "scientist" diff --git a/modules/ServerAPI/src/client/Protocol.coffee b/modules/ServerAPI/src/client/Protocol.coffee index 5340ba8d2..3b2354491 100644 --- a/modules/ServerAPI/src/client/Protocol.coffee +++ b/modules/ServerAPI/src/client/Protocol.coffee @@ -66,6 +66,16 @@ class window.Protocol extends BaseEntity projectCodeValue + getSelRequiredAttr: (attr) => + selRequiredAttrCodeValue = @.get('lsStates').getOrCreateValueByTypeAndKind "metadata", "protocol metadata", "codeValue", attr + if selRequiredAttrCodeValue.get('codeValue') is undefined or selRequiredAttrCodeValue.get('codeValue') is "" + selRequiredAttrCodeValue.set codeValue: "false" + selRequiredAttrCodeValue.set codeType: "protocol" + selRequiredAttrCodeValue.set codeKind: "sel required attribute" + selRequiredAttrCodeValue.set codeOrigin: "ACAS DDICT" + + selRequiredAttrCodeValue + getCurveDisplayMin: -> minY = @.get('lsStates').getOrCreateValueByTypeAndKind "metadata", "screening assay", "numericValue", "curve display min" if (minY.get('numericValue') is undefined or minY.get('numericValue') is "") and @isNew() @@ -235,6 +245,7 @@ class window.ProtocolBaseController extends BaseEntityController @$('.bv_group_projectCode').hide() else @setupProjectSelect() + @setupSelRequiredAttrs() @render() @listenTo @model, 'sync', @modelSyncCallback @listenTo @model, 'change', @modelChangeCallback @@ -324,6 +335,39 @@ class window.ProtocolBaseController extends BaseEntityController @trigger 'amDirty' #need to put this after the first time @attachFileListController is rendered or else the module will always start off dirty @model.trigger 'change' + setupSelRequiredAttrs: => + #get codetable values for required sel attrs + $.ajax + type: 'GET' + url: "/api/codetables/protocol/sel required attribute" + dataType: 'json' + error: (err) -> + alert 'Could not get list of sel required attributes' + success: (json) => + unless json.length == 0 + for attr in json + @setupSelRequiredAttrCheckboxes attr + + setupSelRequiredAttrCheckboxes: (attr) => + camelCaseAttrCode = attr.code.replace /\s(.)/g, (match, group1) -> group1.toUpperCase() + @$('.bv_selRequiredAttributesSection').append '
        +
        ' + + currentVal = @model.getSelRequiredAttr attr.code + if currentVal.get('codeValue') is "true" + @$(".bv_#{camelCaseAttrCode}").attr 'checked', 'checked' + else + @$(".bv_#{camelCaseAttrCode}").removeAttr 'checked' + @$(".bv_#{camelCaseAttrCode}").on "click", => + @handleSelRequiredAttrChkbxChanged attr.code, camelCaseAttrCode + + handleSelRequiredAttrChkbxChanged: (attrCode, camelCaseAttrCode) => + currentVal = @model.getSelRequiredAttr attrCode + unless currentVal.isNew() + currentVal.set 'ignored', true + currentVal = @model.getSelRequiredAttr attrCode + currentVal.set 'codeValue', JSON.stringify(@$(".bv_#{camelCaseAttrCode}").is(":checked")) + handleDeleteStatusChosen: => @$(".bv_deleteButtons").removeClass "hide" @$(".bv_okayButton").addClass "hide" diff --git a/modules/ServerAPI/src/client/Protocol.html b/modules/ServerAPI/src/client/Protocol.html index 4ccab610d..292ed55ca 100644 --- a/modules/ServerAPI/src/client/Protocol.html +++ b/modules/ServerAPI/src/client/Protocol.html @@ -88,10 +88,11 @@
        +
        - + From fdde72c77d954fd082dcedcd2b2e1fa14c172a8e Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 12 Oct 2017 14:09:16 -0700 Subject: [PATCH 230/576] Added new config: client.compoundInventory.daughterVials.strictMatchPhysicalState=false, which turns unit and physical state mismatches into warnings instead of errors. Changed createDaughterVialsInternal to skip decrementing from the parent vials if any of these properties are mismatched. Refactored decrementAmountsFromVials to pass in additional fields. Fixes #276 --- conf/config.properties.example | 1 + .../routes/InventoryServiceRoutes.coffee | 76 ++++++++++--------- 2 files changed, 41 insertions(+), 36 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 6719e298c..25f064771 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -553,3 +553,4 @@ client.roles.crossProjectLoaderRole=ROLE_ACAS-CROSS-PROJECT-LOADER client.entity.saveInitialsCorpName=false client.compoundInventory.enforceUppercaseBarcodes=false +client.compoundInventory.daughterVials.strictMatchPhysicalState=false diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index f98f0c1dd..0ce42be86 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -3017,6 +3017,10 @@ exports.checkParentWellContent = (fileEntryArray, callback) -> #concentration and concentration units match if solution errorMessages = [] vialBarcodes = _.pluck fileEntryArray, 'sourceVialBarcode' + strictMatch = config.all.client.compoundInventory.daughterVials.strictMatchPhysicalState + flexibleErrorLevel = 'warning' + if strictMatch? and strictMatch + flexibleErrorLevel = 'error' exports.getWellContentByContainerLabelsInternal vialBarcodes, 'container', 'tube', 'barcode', 'barcode', (wellContentList, statusCode) -> _.each fileEntryArray, (fileEntry) -> parentVialAndWellContent = _.findWhere wellContentList, {label: fileEntry.sourceVialBarcode} @@ -3024,17 +3028,17 @@ exports.checkParentWellContent = (fileEntryArray, callback) -> parentWellContent = parentVialAndWellContent.wellContent[0] if parentWellContent.physicalState != fileEntry.physicalState error = - errorLevel: 'error' + errorLevel: flexibleErrorLevel message: "Daughter vial #{fileEntry.destinationVialBarcode} must be of the same physical state as parent vial #{fileEntry.sourceVialBarcode}, which is #{parentWellContent.physicalState}." errorMessages.push error if fileEntry.physicalState == 'solution' and (Math.abs(fileEntry.concentration - parentWellContent.batchConcentration) > 0.0001 or fileEntry.concUnits != parentWellContent.batchConcUnits) error = - errorLevel: 'error' + errorLevel: flexibleErrorLevel message: "Daughter vial #{fileEntry.destinationVialBarcode} must have the same concentration as parent vial #{fileEntry.sourceVialBarcode}, which is #{parentWellContent.batchConcentration} #{parentWellContent.batchConcUnits}." errorMessages.push error if parentWellContent.amountUnits != fileEntry.amountUnits error = - errorLevel: 'error' + errorLevel: flexibleErrorLevel message: "Daughter vial #{fileEntry.destinationVialBarcode} must use the same amount units as parent vial #{fileEntry.sourceVialBarcode}, which is in #{parentWellContent.amountUnits}." errorMessages.push error else if parentWellContent.amount < fileEntry.amount @@ -3131,32 +3135,40 @@ decrementAmountsFromVials = (toDecrementList, parentWellContentList, user, callb wellsToUpdate = [] changes = [] _.each toDecrementList, (toDecrement) -> - oldContainerWellContent = _.findWhere parentWellContentList, {label: toDecrement.barcode} + oldContainerWellContent = _.findWhere parentWellContentList, {label: toDecrement.sourceVialBarcode} oldWellContent = oldContainerWellContent.wellContent[0] - wellCode = oldWellContent.containerCodeName - newWellContent = - containerCodeName: wellCode - amount: oldWellContent.amount - toDecrement.amountToDecrement - recordedBy: user - wellsToUpdate.push newWellContent - change = - codeName: oldContainerWellContent.containerCodeName - recordedBy: user - recordedDate: new Date().getTime() - entryType: 'UPDATE' - entry: "Amount #{toDecrement.amountToDecrement} #{toDecrement.amountToDecrementUnits} taken out to create daughter vial #{toDecrement.daughterVialBarcode}" - changes.push change + #Check that the amount is valid to decrement. + differentState = (oldWellContent.physicalState != toDecrement.physicalState) + concentrationMismatch = (toDecrement.physicalState == 'solution' and (Math.abs(toDecrement.concentration - oldWellContent.batchConcentration) > 0.0001 or toDecrement.concUnits != oldWellContent.batchConcUnits)) + unitMismatch = (oldWellContent.amountUnits != toDecrement.amountUnits) + if !differentState and !concentrationMismatch and !unitMismatch + wellCode = oldWellContent.containerCodeName + newWellContent = + containerCodeName: wellCode + amount: oldWellContent.amount - toDecrement.amount + recordedBy: user + wellsToUpdate.push newWellContent + change = + codeName: oldContainerWellContent.containerCodeName + recordedBy: user + recordedDate: new Date().getTime() + entryType: 'UPDATE' + entry: "Amount #{toDecrement.amount} #{toDecrement.amountUnits} taken out to create daughter vial #{toDecrement.destinationVialBarcode}" + changes.push change console.log wellsToUpdate - exports.updateWellContentInternal wellsToUpdate, true, false, (updateWellsResponse, updateWellsStatusCode) -> - console.log updateWellsStatusCode - if updateWellsStatusCode != 204 - callback "Error: #{updateWellsResponse}" - else - exports.containerLogsInternal changes, 0, (logs, statusCode) -> - if statusCode != 200 - callback logs - else - callback null, updateWellsResponse + if wellsToUpdate.length > 0 + exports.updateWellContentInternal wellsToUpdate, true, false, (updateWellsResponse, updateWellsStatusCode) -> + console.log updateWellsStatusCode + if updateWellsStatusCode != 204 + callback "Error: #{updateWellsResponse}" + else + exports.containerLogsInternal changes, 0, (logs, statusCode) -> + if statusCode != 200 + callback logs + else + callback null, updateWellsResponse + else + callback null prepareSummaryInfo = (fileEntryArray) -> summaryInfo = @@ -3358,15 +3370,7 @@ exports.createDaughterVialsInternal = (vialsToCreate, user, callback) -> if err? callback err else - toDecrementList = [] - _.each vialsToCreate, (entry) -> - toDecrement = - barcode: entry.sourceVialBarcode - amountToDecrement: entry.amount - amountToDecrementUnits: entry.amountUnits - daughterVialBarcode: entry.destinationVialBarcode - toDecrementList.push toDecrement - decrementAmountsFromVials toDecrementList, parentWellContentList, user, (err, decrementVialsResponse) -> + decrementAmountsFromVials vialsToCreate, parentWellContentList, user, (err, decrementVialsResponse) -> if err? callback err else From 7baa6c5491b3cebca5d2f21acdaa169f2a08247a Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Thu, 12 Oct 2017 14:13:16 -0700 Subject: [PATCH 231/576] bugfix/creg-fix-add-alias-clear-type-picklist-bug: Issue #227 (CReg - Click add alias clears selected option in type picklists) - need to update typeKind after type is selected --- modules/CmpdReg/src/client/src/AddAlias.js | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/modules/CmpdReg/src/client/src/AddAlias.js b/modules/CmpdReg/src/client/src/AddAlias.js index 10760c99b..03654315d 100644 --- a/modules/CmpdReg/src/client/src/AddAlias.js +++ b/modules/CmpdReg/src/client/src/AddAlias.js @@ -313,7 +313,10 @@ newAlias = new AliasModel(formValues); return this.trigger("isDirty", newAlias); } else { - return this.model.set(formValues); + this.model.set(formValues); + var typeKind = this.model.get('lsType') + ':' + this.model.get('lsKind'); + this.model.set({'typeKind': typeKind}); + return this; } }; From 27ea3ecfdb317b5d451d9858c5e65b377f89fce8 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 12 Oct 2017 14:17:31 -0700 Subject: [PATCH 232/576] Renamed ketcher folder from ketcher-2.0.0-alpha.3 to ketcher-2.0.0-alpha.3_custom because we have made a custom tweak to ketcher.js to always set the Chiral flag on molecules sent from Ketcher. Fixed all references to the folder name. --- modules/CmpdReg/src/client/src/EditParent.js | 2 +- .../CmpdReg/src/client/src/RegistrationSearch.js | 2 +- modules/CmpdReg/src/client/src/Salt.js | 2 +- modules/CmpdReg/src/client/src/SaltForm.js | 2 +- modules/CmpdReg/src/client/src/SearchForm.js | 2 +- .../src/client/ACASFormChemicalStructure.coffee | 2 +- .../LICENSE | 0 .../demo.html | 0 .../favicon.ico | Bin .../ketcher.css | 0 .../ketcher.eot | Bin .../ketcher.html | 0 .../ketcher.js | 0 .../ketcher.py | 0 .../ketcher.svg | 0 .../ketcher.ttf | Bin .../ketcher.woff | Bin .../logo.jpg | Bin .../prototype-min.js | 0 .../raphael.min.js | 0 .../templates.sdf | 0 21 files changed, 6 insertions(+), 6 deletions(-) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/LICENSE (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/demo.html (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/favicon.ico (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/ketcher.css (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/ketcher.eot (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/ketcher.html (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/ketcher.js (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/ketcher.py (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/ketcher.svg (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/ketcher.ttf (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/ketcher.woff (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/logo.jpg (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/prototype-min.js (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/raphael.min.js (100%) rename public/lib/{ketcher-2.0.0-alpha.3 => ketcher-2.0.0-alpha.3_custom}/templates.sdf (100%) diff --git a/modules/CmpdReg/src/client/src/EditParent.js b/modules/CmpdReg/src/client/src/EditParent.js index e172079f4..ad2b8f3e4 100644 --- a/modules/CmpdReg/src/client/src/EditParent.js +++ b/modules/CmpdReg/src/client/src/EditParent.js @@ -65,7 +65,7 @@ $(function () { }); } else if (this.useKetcher) { - this.$('#editParentMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/cmpdReg/ketcher/"); + this.$('#editParentMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3_custom/ketcher.html?api_path=/api/cmpdReg/ketcher/"); this.$('#editParentMarvinSketch').on('load', function () { self.ketcher = self.$('#editParentMarvinSketch')[0].contentWindow.ketcher; self.ketcher.setMolecule(self.options.parentModel.get('molStructure')); diff --git a/modules/CmpdReg/src/client/src/RegistrationSearch.js b/modules/CmpdReg/src/client/src/RegistrationSearch.js index 7c9b92783..bb4f9b879 100755 --- a/modules/CmpdReg/src/client/src/RegistrationSearch.js +++ b/modules/CmpdReg/src/client/src/RegistrationSearch.js @@ -67,7 +67,7 @@ $(function() { }); } else if (this.useKetcher) { - this.$('#registrationSearchMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/cmpdReg/ketcher/"); + this.$('#registrationSearchMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3_custom/ketcher.html?api_path=/api/cmpdReg/ketcher/"); this.$('#registrationSearchMarvinSketch').on('load', function () { self.ketcher = self.$('#registrationSearchMarvinSketch')[0].contentWindow.ketcher; }); diff --git a/modules/CmpdReg/src/client/src/Salt.js b/modules/CmpdReg/src/client/src/Salt.js index 37d05395a..32e1c6a8f 100755 --- a/modules/CmpdReg/src/client/src/Salt.js +++ b/modules/CmpdReg/src/client/src/Salt.js @@ -183,7 +183,7 @@ $(function() { }); } else if (this.useKetcher) { - this.$('#newSaltMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/cmpdReg/ketcher/"); + this.$('#newSaltMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3_custom/ketcher.html?api_path=/api/cmpdReg/ketcher/"); this.$('#newSaltMarvinSketch').on('load', function () { self.ketcher = self.$('#newSaltMarvinSketch')[0].contentWindow.ketcher; self.sketcherLoaded = true; diff --git a/modules/CmpdReg/src/client/src/SaltForm.js b/modules/CmpdReg/src/client/src/SaltForm.js index b6ec00564..05f30ea6c 100755 --- a/modules/CmpdReg/src/client/src/SaltForm.js +++ b/modules/CmpdReg/src/client/src/SaltForm.js @@ -309,7 +309,7 @@ $(function() { }); } else if (this.useKetcher) { - this.$('#saltFormMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/cmpdReg/ketcher/"); + this.$('#saltFormMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3_custom/ketcher.html?api_path=/api/cmpdReg/ketcher/"); this.$('#saltFormMarvinSketch').on('load', function () { self.ketcher = self.$('#saltFormMarvinSketch')[0].contentWindow.ketcher; if (!self.sketcherLoaded) { diff --git a/modules/CmpdReg/src/client/src/SearchForm.js b/modules/CmpdReg/src/client/src/SearchForm.js index 67049e173..1b666f83f 100755 --- a/modules/CmpdReg/src/client/src/SearchForm.js +++ b/modules/CmpdReg/src/client/src/SearchForm.js @@ -106,7 +106,7 @@ $(function() { }); } else if (this.useKetcher) { - this.$('#searchMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/cmpdReg/ketcher/"); + this.$('#searchMarvinSketch').attr('src',"/lib/ketcher-2.0.0-alpha.3_custom/ketcher.html?api_path=/api/cmpdReg/ketcher/"); this.$('#searchMarvinSketch').on('load', function () { self.ketcher = self.$('#searchMarvinSketch')[0].contentWindow.ketcher; }); diff --git a/modules/Components/src/client/ACASFormChemicalStructure.coffee b/modules/Components/src/client/ACASFormChemicalStructure.coffee index 0cd3cf35f..70f857464 100644 --- a/modules/Components/src/client/ACASFormChemicalStructure.coffee +++ b/modules/Components/src/client/ACASFormChemicalStructure.coffee @@ -110,7 +110,7 @@ class window.KetcherChemicalStructureController extends Backbone.View $(@el).empty() $(@el).html @template() - searchFrameURL = "/lib/ketcher-2.0.0-alpha.3/ketcher.html?api_path=/api/chemStructure/ketcher/" + searchFrameURL = "/lib/ketcher-2.0.0-alpha.3_custom/ketcher.html?api_path=/api/chemStructure/ketcher/" @$('.bv_sketcherIFrame').attr 'src', searchFrameURL diff --git a/public/lib/ketcher-2.0.0-alpha.3/LICENSE b/public/lib/ketcher-2.0.0-alpha.3_custom/LICENSE similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/LICENSE rename to public/lib/ketcher-2.0.0-alpha.3_custom/LICENSE diff --git a/public/lib/ketcher-2.0.0-alpha.3/demo.html b/public/lib/ketcher-2.0.0-alpha.3_custom/demo.html similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/demo.html rename to public/lib/ketcher-2.0.0-alpha.3_custom/demo.html diff --git a/public/lib/ketcher-2.0.0-alpha.3/favicon.ico b/public/lib/ketcher-2.0.0-alpha.3_custom/favicon.ico similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/favicon.ico rename to public/lib/ketcher-2.0.0-alpha.3_custom/favicon.ico diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.css b/public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.css similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/ketcher.css rename to public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.css diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.eot b/public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.eot similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/ketcher.eot rename to public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.eot diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.html b/public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.html similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/ketcher.html rename to public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.html diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.js b/public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.js similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/ketcher.js rename to public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.js diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.py b/public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.py similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/ketcher.py rename to public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.py diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.svg b/public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.svg similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/ketcher.svg rename to public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.svg diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.ttf b/public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.ttf similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/ketcher.ttf rename to public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.ttf diff --git a/public/lib/ketcher-2.0.0-alpha.3/ketcher.woff b/public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.woff similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/ketcher.woff rename to public/lib/ketcher-2.0.0-alpha.3_custom/ketcher.woff diff --git a/public/lib/ketcher-2.0.0-alpha.3/logo.jpg b/public/lib/ketcher-2.0.0-alpha.3_custom/logo.jpg similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/logo.jpg rename to public/lib/ketcher-2.0.0-alpha.3_custom/logo.jpg diff --git a/public/lib/ketcher-2.0.0-alpha.3/prototype-min.js b/public/lib/ketcher-2.0.0-alpha.3_custom/prototype-min.js similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/prototype-min.js rename to public/lib/ketcher-2.0.0-alpha.3_custom/prototype-min.js diff --git a/public/lib/ketcher-2.0.0-alpha.3/raphael.min.js b/public/lib/ketcher-2.0.0-alpha.3_custom/raphael.min.js similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/raphael.min.js rename to public/lib/ketcher-2.0.0-alpha.3_custom/raphael.min.js diff --git a/public/lib/ketcher-2.0.0-alpha.3/templates.sdf b/public/lib/ketcher-2.0.0-alpha.3_custom/templates.sdf similarity index 100% rename from public/lib/ketcher-2.0.0-alpha.3/templates.sdf rename to public/lib/ketcher-2.0.0-alpha.3_custom/templates.sdf From 8d8891b24b335fd4ae46101a4aef2e6e7cd3c940 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Thu, 12 Oct 2017 16:23:47 -0700 Subject: [PATCH 233/576] bugfix/creg-admin-browsers-clear-modal-backdrops: Fixes Issue #279 (Clear modal backdrops after deleting code entry from creg admin browser) --- .../client/AbstractCmpdRegAdminBrowser.coffee | 82 +++++++++---------- 1 file changed, 40 insertions(+), 42 deletions(-) diff --git a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee index 68901f4f7..be4fb31df 100644 --- a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee +++ b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee @@ -43,26 +43,10 @@ class window.CmpdRegAdminSimpleSearchController extends AbstractFormController @$(".bv_doSearch").attr("disabled", false) if e.keyCode is ENTER_KEY $(':focus').blur() - @handleDoSearchClicked() + @trigger 'searchRequested' else @$(".bv_doSearch").attr("disabled", true) - handleDoSearchClicked: => - $(".bv_cmpdRegAdminTableController").addClass "hide" - $(".bv_errorOccurredPerformingSearch").addClass "hide" - cmpdRegAdminSearchTerm = $.trim(@$(".bv_cmpdRegAdminSearchTerm").val()) - if cmpdRegAdminSearchTerm isnt "" - $(".bv_noMatchingCmpdRegAdminsFoundMessage").addClass "hide" - $(".bv_cmpdRegAdminBrowserSearchInstructions").addClass "hide" - $(".bv_searchCmpdRegAdminsStatusIndicator").removeClass "hide" - if !window.conf.browser.enableSearchAll and cmpdRegAdminSearchTerm is "*" - $(".bv_moreSpecificCmpdRegAdminSearchNeeded").removeClass "hide" - else - $(".bv_searchingCmpdRegAdminsMessage").removeClass "hide" - $(".bv_cmpdRegAdminSearchTerm").html cmpdRegAdminSearchTerm - $(".bv_moreSpecificCmpdRegAdminSearchNeeded").addClass "hide" - @doSearch cmpdRegAdminSearchTerm - doSearch: (cmpdRegAdminSearchTerm) => # disable the search text field while performing a search @$(".bv_cmpdRegAdminSearchTerm").attr "disabled", true @@ -122,19 +106,15 @@ class window.CmpdRegAdminSummaryTableController extends Backbone.View render: => @template = _.template($('#CmpdRegAdminSummaryTableView').html()) $(@el).html @template(@options.toDisplay) - if @collection.models.length is 0 - $(".bv_noMatchingCmpdRegAdminsFoundMessage").removeClass "hide" - # display message indicating no results were found - else - $(".bv_noMatchingCmpdRegAdminsFoundMessage").addClass "hide" - @collection.each (admin) => - prsc = new CmpdRegAdminRowSummaryController - model: admin - prsc.on "gotClick", @selectedRowChanged - @$("tbody").append prsc.render().el + #will always be instantiated with at least one model in collection + @collection.each (admin) => + prsc = new CmpdRegAdminRowSummaryController + model: admin + prsc.on "gotClick", @selectedRowChanged + @$("tbody").append prsc.render().el - @$("table").dataTable oLanguage: - sSearch: "Filter results: " #rename summary table's search bar + @$("table").dataTable oLanguage: + sSearch: "Filter results: " #rename summary table's search bar @ @@ -170,6 +150,7 @@ class window.AbstractCmpdRegAdminBrowserController extends Backbone.View urlRoot: "/api/CmpdRegAdmin/#{@entityTypePlural}" toDisplay: @toDisplay @searchController.render() + @searchController.on "searchRequested", @handleSearchRequested @searchController.on "searchReturned", @setupCmpdRegAdminSummaryTable @searchController.on "createNewCmpdRegAdmin", @handleCreateNewCmpdRegAdminClicked #@searchController.on "resetSearch", @destroyCmpdRegAdminSummaryTable @@ -177,7 +158,7 @@ class window.AbstractCmpdRegAdminBrowserController extends Backbone.View setupCmpdRegAdminSummaryTable: (cmpdRegAdmins) => @destroyCmpdRegAdminSummaryTable() - $(".bv_searchingCmpdRegAdminsMessage").addClass "hide" + @$(".bv_searchingCmpdRegAdminsMessage").addClass "hide" if cmpdRegAdmins is null @$(".bv_errorOccurredPerformingSearch").removeClass "hide" @@ -185,14 +166,14 @@ class window.AbstractCmpdRegAdminBrowserController extends Backbone.View @$(".bv_noMatchingCmpdRegAdminsFoundMessage").removeClass "hide" @$(".bv_cmpdRegAdminTableController").html "" else - $(".bv_searchCmpdRegAdminsStatusIndicator").addClass "hide" + @$(".bv_searchCmpdRegAdminsStatusIndicator").addClass "hide" @$(".bv_cmpdRegAdminTableController").removeClass "hide" @cmpdRegAdminSummaryTable = new CmpdRegAdminSummaryTableController collection: new CmpdRegAdminList cmpdRegAdmins toDisplay: @toDisplay @cmpdRegAdminSummaryTable.on "selectedRowUpdated", @selectedCmpdRegAdminUpdated - $(".bv_cmpdRegAdminTableController").html @cmpdRegAdminSummaryTable.render().el + @$(".bv_cmpdRegAdminTableController").html @cmpdRegAdminSummaryTable.render().el selectedCmpdRegAdminUpdated: (cmpdRegAdmin) => @trigger "selectedCmpdRegAdminUpdated" @@ -202,12 +183,28 @@ class window.AbstractCmpdRegAdminBrowserController extends Backbone.View model: new window[@entityClass] cmpdRegAdmin.attributes readOnly: true - $('.bv_cmpdRegAdminController').html @cmpdRegAdminController.render().el - $(".bv_cmpdRegAdminController").removeClass("hide") - $(".bv_cmpdRegAdminControllerContainer").removeClass("hide") + @$('.bv_cmpdRegAdminController').html @cmpdRegAdminController.render().el + @$(".bv_cmpdRegAdminController").removeClass("hide") + @$(".bv_cmpdRegAdminControllerContainer").removeClass("hide") @$('.bv_editCmpdRegAdmin').show() @$('.bv_deleteCmpdRegAdmin').show() + handleSearchRequested: => + @$(".bv_cmpdRegAdminTableController").addClass "hide" + @$(".bv_errorOccurredPerformingSearch").addClass "hide" + cmpdRegAdminSearchTerm = $.trim(@$(".bv_cmpdRegAdminSearchTerm").val()) + if cmpdRegAdminSearchTerm isnt "" + @$(".bv_noMatchingCmpdRegAdminsFoundMessage").addClass "hide" + @$(".bv_cmpdRegAdminBrowserSearchInstructions").addClass "hide" + @$(".bv_searchCmpdRegAdminsStatusIndicator").removeClass "hide" + if !window.conf.browser.enableSearchAll and cmpdRegAdminSearchTerm is "*" + @$(".bv_moreSpecificCmpdRegAdminSearchNeeded").removeClass "hide" + else + @$(".bv_searchingCmpdRegAdminsMessage").removeClass "hide" + @$(".bv_cmpdRegAdminSearchTerm").html cmpdRegAdminSearchTerm + @$(".bv_moreSpecificCmpdRegAdminSearchNeeded").addClass "hide" + @searchController.doSearch cmpdRegAdminSearchTerm + handleDeleteCmpdRegAdminClicked: => @$(".bv_cmpdRegAdminCodeName").html @cmpdRegAdminController.model.get("code") @$(".bv_deleteButtons").removeClass "hide" @@ -216,8 +213,8 @@ class window.AbstractCmpdRegAdminBrowserController extends Backbone.View @$(".bv_deleteWarningMessage").removeClass "hide" @$(".bv_deletingStatusIndicator").addClass "hide" @$(".bv_cmpdRegAdminDeletedSuccessfullyMessage").addClass "hide" - $(".bv_confirmDeleteCmpdRegAdmin").removeClass "hide" - $('.bv_confirmDeleteCmpdRegAdmin').modal({ + @$(".bv_confirmDeleteCmpdRegAdmin").removeClass "hide" + @$('.bv_confirmDeleteCmpdRegAdmin').modal({ keyboard: false, backdrop: true }) @@ -233,7 +230,7 @@ class window.AbstractCmpdRegAdminBrowserController extends Backbone.View @$(".bv_okayButton").removeClass "hide" @$(".bv_deletingStatusIndicator").addClass "hide" @$(".bv_cmpdRegAdminDeletedSuccessfullyMessage").removeClass "hide" - @searchController.handleDoSearchClicked() + @handleSearchRequested() error: (result) => @$(".bv_okayButton").removeClass "hide" @$(".bv_deletingStatusIndicator").addClass "hide" @@ -251,9 +248,10 @@ class window.AbstractCmpdRegAdminBrowserController extends Backbone.View @cmpdRegAdminSummaryTable.remove() if @cmpdRegAdminController? @cmpdRegAdminController.remove() - $(".bv_cmpdRegAdminController").addClass("hide") - $(".bv_cmpdRegAdminControllerContainer").addClass("hide") - $(".bv_noMatchingCmpdRegAdminsFoundMessage").addClass("hide") + + @$(".bv_cmpdRegAdminController").addClass("hide") + @$(".bv_cmpdRegAdminControllerContainer").addClass("hide") + @$(".bv_noMatchingCmpdRegAdminsFoundMessage").addClass("hide") render: => @ @@ -280,5 +278,5 @@ class window.AbstractCmpdRegAdminBrowserController extends Backbone.View handleBackToCmpdRegAdminBrowserClicked: => @$('.bv_cmpdRegAdminBrowserWrapper').show() @$('.bv_cmpdRegAdminControllerWrapper').hide() - @searchController.handleDoSearchClicked() + @handleSearchRequested() @trigger 'amClean' From b7fe95f1b4c70c5be0241728d7a70fc496c6ba16 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 12 Oct 2017 17:28:45 -0700 Subject: [PATCH 234/576] Tweaked Label Sequence save routes to pass back the error response, and changed the GUI to alert the error message on save failed. Fixes #281 --- .../src/client/ACASLabelSequences.coffee | 6 +++++- .../server/routes/ACASLabelSequencesRoutes.coffee | 12 ++++++------ 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee index dfc6c4e0b..cf68cf9ec 100644 --- a/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee +++ b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee @@ -427,6 +427,9 @@ class window.ACASLabelSequenceController extends AbstractFormController @model.trigger 'saveFailed' else @modelSaveCallback + error: (err, response) => + alert response.responseText + @model.trigger 'saveFailed' else @model.save null, @@ -435,7 +438,8 @@ class window.ACASLabelSequenceController extends AbstractFormController @model.trigger 'saveFailed' else @modelSaveCallback - error: (err) => + error: (err, response) => + alert response.responseText @model.trigger 'saveFailed' validationError: => diff --git a/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee b/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee index 8cd26903c..012f26791 100644 --- a/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee +++ b/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee @@ -80,9 +80,9 @@ exports.saveLabelSequence = (req, resp) -> if !error && response.statusCode == 201 resp.json json else - console.error 'got ajax error trying to save label sequence' + console.error 'got error trying to save label sequence' resp.statusCode = 500 - resp.end "saveFailed" + resp.end json ) exports.saveLabelSequenceArray = (req, resp) -> @@ -100,8 +100,8 @@ exports.saveLabelSequenceArray = (req, resp) -> if !error && response.statusCode == 201 resp.json json else - console.error 'got ajax error trying to save label sequence array' - resp.end "saveFailed" + console.error 'got error trying to save label sequence array' + resp.end json ) exports.updateLabelSequence = (req, resp) -> @@ -119,8 +119,8 @@ exports.updateLabelSequence = (req, resp) -> if !error && response.statusCode == 200 resp.json json else - console.error 'got ajax error trying to update label sequence' - resp.end "updateFailed" + console.error 'got error trying to update label sequence' + resp.end json ) exports.updateLabelSequenceArray = (req, resp) -> From 3aac8ca455e7cba9e3d72862fd6b5f84d2ff3817 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Sat, 14 Oct 2017 16:33:21 -0700 Subject: [PATCH 235/576] Fixes #284 adding routes to notify registered forms that a save of a new entity is in progress --- .../AbstractFormControllerRoutes.coffee | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee b/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee index 2c4b5f729..861e6c803 100644 --- a/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee +++ b/modules/Components/src/server/routes/AbstractFormControllerRoutes.coffee @@ -4,6 +4,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.get '/api/formController/clearAllLocks', loginRoutes.ensureAuthenticated, exports.clearAllLocks global.editLockedEntities = {} +global.newFormEntities = {} exports.setupChannels = (io, sessionStore, loginRoutes) -> nsp = io.of('/formController:connected') @@ -20,6 +21,18 @@ exports.setupChannels = (io, sessionStore, loginRoutes) -> for quid in lock.rejectedRequestSocketIDs socket.broadcast.to(quid).emit('editLockAvailable') delete global.editLockedEntities[lockKey] + + for lockKey, lock of global.newFormEntities + if lock.savingLockSocketID==socket.id + console.log "clearing save lock on #{lock}" + lock.savingLockSocketID = null + for quid in lock.savingNotificationRequestSocketIDs + socket.broadcast.to(quid).emit('newEntitySavingComplete') + + index = lock.savingNotificationRequestSocketIDs.indexOf socket.id + if index > -1 + lock.savingNotificationRequestSocketIDs.splice(index, 1) + ) socket.on('editLockEntity', (entityType, codeName) => @@ -69,6 +82,42 @@ exports.setupChannels = (io, sessionStore, loginRoutes) -> now = new Date().getTime() lockedEntity.lastActivityDate = now ) + socket.on('clearEditLock', (entityType, codeName) => + console.log "got clearEditLock #{entityType}, #{codeName}" + lockKey = entityType+"_"+codeName + lockedEntity = global.editLockedEntities[lockKey] + if lockedEntity? and lockedEntity.socketID==socket.id + for quid in lockedEntity.rejectedRequestSocketIDs + socket.broadcast.to(quid).emit('editLockAvailable') + delete global.editLockedEntities[lockKey] + ) + + socket.on('registerForSavingNewLockNotification', (entityType) => + lockKey = entityType+"_savingNewLock" + nfEntity = global.newFormEntities[lockKey] + if nfEntity? + nfEntity.savingNotificationRequestSocketIDs.push socket.id + else + global.newFormEntities[lockKey] = + savingLockSocketID: null + savingNotificationRequestSocketIDs: [socket.id] + ) + socket.on('savingNewLock', (entityType) => + lockKey = entityType+"_savingNewLock" + nfEntity = global.newFormEntities[lockKey] + if nfEntity? + nfEntity.savingLockSocketID = socket.id + for quid in nfEntity.savingNotificationRequestSocketIDs + socket.broadcast.to(quid).emit('newEntitySaveActive') + ) + socket.on('savingNewConplete', (entityType) => + lockKey = entityType+"_savingNewLock" + nfEntity = global.newFormEntities[lockKey] + if nfEntity? and nfEntity.savingLockSocketID==socket.id + nfEntity.savingLockSocketID = null + for quid in nfEntity.savingNotificationRequestSocketIDs + socket.broadcast.to(quid).emit('newEntitySavingComplete') + ) ) exports.clearAllLocks = (req, resp) -> @@ -77,3 +126,4 @@ exports.clearAllLocks = (req, resp) -> global.editLockedEntities = {} console.dir global.editLockedEntities, depth: 3 resp.end() + From 597c3223832fb346a70f73c0ece8653d99059b3a Mon Sep 17 00:00:00 2001 From: John McNeil Date: Mon, 16 Oct 2017 21:29:13 -0700 Subject: [PATCH 236/576] added validation checks on lot_custom to require units for amounts --- modules/CmpdReg/src/client/custom/Lot_Custom.js | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/modules/CmpdReg/src/client/custom/Lot_Custom.js b/modules/CmpdReg/src/client/custom/Lot_Custom.js index b9b2ca6d0..2a74406df 100755 --- a/modules/CmpdReg/src/client/custom/Lot_Custom.js +++ b/modules/CmpdReg/src/client/custom/Lot_Custom.js @@ -111,6 +111,11 @@ $(function() { errors.push({'attribute': 'amount', 'message': "Amount must be a number if provided"}); } } + if (attr.amount!=null && attr.amount!='') { + if(attr.amountUnits==null || attr.amountUnits=='unassigned') { + errors.push({'attribute': 'amountUnits', 'message': "Amount units must be set if amount set"}); + } + } if (attr.retain!=null) { if(isNaN(attr.retain) && attr.retain!='') { errors.push({'attribute': 'retain', 'message': "Retain must be a number if provided"}); @@ -121,6 +126,11 @@ $(function() { errors.push({'attribute': 'solutionAmount', 'message': "Solution Amount must be a number if provided"}); } } + if (attr.solutionAmount!=null && attr.solutionAmount!='') { + if(attr.solutionAmountUnits==null || attr.solutionAmountUnits=='unassigned') { + errors.push({'attribute': 'solutionAmountUnits', 'message': "Solution amount units must be set if amount set"}); + } + } if (attr.tareWeight!=null) { if(isNaN(attr.tareWeight) && attr.tareWeight!='') { errors.push({'attribute': 'tareWeight', 'message': "Tare weight must be a number if provided"}); From 680b3dddf7bd382b91adf92e9339932d2b9b371f Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 17 Oct 2017 08:13:19 -0700 Subject: [PATCH 237/576] Added getAPICmpdReg proxy route, and switched scientists to use API route, which takes a new optional ?withLots boolean parameter. Switched the search form to use that parameter, which limits the list of scientists returned to only those who have registered lots in the system. Fixed some buggy behavior around the search form picklist showing up empty when there are no lots registered. Added an error message for when there are no projects in the system and a user tries to save a lot. Fixes https://github.com/mcneilco/acas-cmpdreg-roo-server/issues/25 added in defaults of several new CmpdReg configs. Removed "Parent LiveDesign Corp Name" from default bulk loader mappings because it is more confusing than useful. --- modules/CmpdReg/src/client/custom/Lot_Custom.js | 6 ++++++ modules/CmpdReg/src/client/custom/configuration.json | 6 ++++-- modules/CmpdReg/src/client/src/PickList.js | 4 ++-- modules/CmpdReg/src/client/src/SearchForm.js | 2 +- modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee | 10 +++++++++- 5 files changed, 22 insertions(+), 6 deletions(-) diff --git a/modules/CmpdReg/src/client/custom/Lot_Custom.js b/modules/CmpdReg/src/client/custom/Lot_Custom.js index b9b2ca6d0..5de973261 100755 --- a/modules/CmpdReg/src/client/custom/Lot_Custom.js +++ b/modules/CmpdReg/src/client/custom/Lot_Custom.js @@ -146,6 +146,9 @@ $(function() { errors.push({'attribute': 'boilingPoint', 'message': "BP must be a number if provided"}); } } + if (attr.project != null && typeof(attr.project) == 'undefined'){ + errors.push({'attribute': 'project', 'message': "Project must be provided"}); + } if (errors.length > 0) {return errors;} } }); @@ -259,6 +262,9 @@ $(function() { }, updateModel: function() { + if (this.projectCodeController.collection.length == 0){ + alert('System Configuration Error: There must be at least one project to proceed') + } this.clearValidationErrors(); if (this.model.isNew() ) { diff --git a/modules/CmpdReg/src/client/custom/configuration.json b/modules/CmpdReg/src/client/custom/configuration.json index f2b99776a..cb3e1638f 100755 --- a/modules/CmpdReg/src/client/custom/configuration.json +++ b/modules/CmpdReg/src/client/custom/configuration.json @@ -62,8 +62,11 @@ "maxSearchResults": 5000, "unitTestDB": true, "initalDBLoad": true, + "compoundInventory": true, + "checkACASDependenciesByBarcode": false, "projectRestrictions": false, - "jchemVersion": "16.4.25.0" + "jchemVersion": "16.4.25.0", + "orderSelectLists": true }, "bulkLoadSettings": { "useProjectRoles":false, @@ -100,7 +103,6 @@ {"name": "Project", "dataType": "string", "required": false}, {"name": "CAS Number", "dataType": "string", "required": false}, {"name": "Parent Corp Name", "dataType": "string", "required": false}, - {"name": "Parent LiveDesign Corp Name", "dataType": "string", "required": false}, {"name": "Parent Common Name", "dataType": "string", "required": false}, {"name": "Parent Stereo Comment", "dataType": "string", "required": false} ] diff --git a/modules/CmpdReg/src/client/src/PickList.js b/modules/CmpdReg/src/client/src/PickList.js index 90066a8d6..fada98e6a 100755 --- a/modules/CmpdReg/src/client/src/PickList.js +++ b/modules/CmpdReg/src/client/src/PickList.js @@ -52,8 +52,8 @@ $(function() { this.collection = new PickListList(); this.collection.setType(this.options.type); this.collection.bind('add', this.addOne); - this.collection.bind('reset', this.handleListReset); - this.collection.fetch(); + //this.collection.bind('reset', this.handleListReset); + this.collection.fetch({success: this.handleListReset}); if (this.options.selectedCode !='') { this.selectedCode = this.options.selectedCode; } else { diff --git a/modules/CmpdReg/src/client/src/SearchForm.js b/modules/CmpdReg/src/client/src/SearchForm.js index 67049e173..3e397deeb 100755 --- a/modules/CmpdReg/src/client/src/SearchForm.js +++ b/modules/CmpdReg/src/client/src/SearchForm.js @@ -86,7 +86,7 @@ $(function() { this.updatePercentSimilarityDisabled(); this.chemistCodeController = - this.setupCodeController('chemist', 'scientists', 'chemist', true); + this.setupCodeController('chemist', 'scientists?withLots=true', 'chemist', true); this.chemistCodeController.collection.bind('reset', this.chemistsLoaded); var self = this; diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index c9a9bcfdf..f5c7bd60f 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -6,7 +6,7 @@ exports.setupAPIRoutes = (app) -> exports.setupRoutes = (app, loginRoutes) -> app.get '/cmpdReg', loginRoutes.ensureAuthenticated, exports.cmpdRegIndex app.get '/marvin4js-license.cxl', loginRoutes.ensureAuthenticated, exports.getMarvinJSLicense - app.get '/cmpdReg/scientists', loginRoutes.ensureAuthenticated, exports.getBasicCmpdReg + app.get '/cmpdReg/scientists', loginRoutes.ensureAuthenticated, exports.getAPICmpdReg app.get '/cmpdReg/parentAliasKinds', loginRoutes.ensureAuthenticated, exports.getBasicCmpdReg app.get '/cmpdReg/units', loginRoutes.ensureAuthenticated, exports.getBasicCmpdReg app.get '/cmpdReg/solutionUnits', loginRoutes.ensureAuthenticated, exports.getBasicCmpdReg @@ -129,6 +129,14 @@ exports.getBasicCmpdReg = (req, resp) -> console.log cmpdRegCall req.pipe(request(cmpdRegCall)).pipe(resp) +exports.getAPICmpdReg = (req, resp) -> + console.log 'in getAPICmpdReg' + console.log req.originalUrl + endOfUrl = (req.originalUrl).replace /\/cmpdreg\//, "" + cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + "/api/v1/" +endOfUrl + console.log cmpdRegCall + req.pipe(request(cmpdRegCall)).pipe(resp) + exports.getAuthorizedCmpdRegProjects = (req, resp) -> exports.getAuthorizedCmpdRegProjectsInternal req, (response) => resp.status "200" From 4da95add85d4a798268fadd8abedb1b3bef941c6 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 12 Oct 2017 14:09:16 -0700 Subject: [PATCH 238/576] Added new config: client.compoundInventory.daughterVials.strictMatchPhysicalState=false, which turns unit and physical state mismatches into warnings instead of errors. Changed createDaughterVialsInternal to skip decrementing from the parent vials if any of these properties are mismatched. Refactored decrementAmountsFromVials to pass in additional fields. Fixes #276 --- conf/config.properties.example | 1 + .../routes/InventoryServiceRoutes.coffee | 76 ++++++++++--------- 2 files changed, 41 insertions(+), 36 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 6719e298c..25f064771 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -553,3 +553,4 @@ client.roles.crossProjectLoaderRole=ROLE_ACAS-CROSS-PROJECT-LOADER client.entity.saveInitialsCorpName=false client.compoundInventory.enforceUppercaseBarcodes=false +client.compoundInventory.daughterVials.strictMatchPhysicalState=false diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index f98f0c1dd..0ce42be86 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -3017,6 +3017,10 @@ exports.checkParentWellContent = (fileEntryArray, callback) -> #concentration and concentration units match if solution errorMessages = [] vialBarcodes = _.pluck fileEntryArray, 'sourceVialBarcode' + strictMatch = config.all.client.compoundInventory.daughterVials.strictMatchPhysicalState + flexibleErrorLevel = 'warning' + if strictMatch? and strictMatch + flexibleErrorLevel = 'error' exports.getWellContentByContainerLabelsInternal vialBarcodes, 'container', 'tube', 'barcode', 'barcode', (wellContentList, statusCode) -> _.each fileEntryArray, (fileEntry) -> parentVialAndWellContent = _.findWhere wellContentList, {label: fileEntry.sourceVialBarcode} @@ -3024,17 +3028,17 @@ exports.checkParentWellContent = (fileEntryArray, callback) -> parentWellContent = parentVialAndWellContent.wellContent[0] if parentWellContent.physicalState != fileEntry.physicalState error = - errorLevel: 'error' + errorLevel: flexibleErrorLevel message: "Daughter vial #{fileEntry.destinationVialBarcode} must be of the same physical state as parent vial #{fileEntry.sourceVialBarcode}, which is #{parentWellContent.physicalState}." errorMessages.push error if fileEntry.physicalState == 'solution' and (Math.abs(fileEntry.concentration - parentWellContent.batchConcentration) > 0.0001 or fileEntry.concUnits != parentWellContent.batchConcUnits) error = - errorLevel: 'error' + errorLevel: flexibleErrorLevel message: "Daughter vial #{fileEntry.destinationVialBarcode} must have the same concentration as parent vial #{fileEntry.sourceVialBarcode}, which is #{parentWellContent.batchConcentration} #{parentWellContent.batchConcUnits}." errorMessages.push error if parentWellContent.amountUnits != fileEntry.amountUnits error = - errorLevel: 'error' + errorLevel: flexibleErrorLevel message: "Daughter vial #{fileEntry.destinationVialBarcode} must use the same amount units as parent vial #{fileEntry.sourceVialBarcode}, which is in #{parentWellContent.amountUnits}." errorMessages.push error else if parentWellContent.amount < fileEntry.amount @@ -3131,32 +3135,40 @@ decrementAmountsFromVials = (toDecrementList, parentWellContentList, user, callb wellsToUpdate = [] changes = [] _.each toDecrementList, (toDecrement) -> - oldContainerWellContent = _.findWhere parentWellContentList, {label: toDecrement.barcode} + oldContainerWellContent = _.findWhere parentWellContentList, {label: toDecrement.sourceVialBarcode} oldWellContent = oldContainerWellContent.wellContent[0] - wellCode = oldWellContent.containerCodeName - newWellContent = - containerCodeName: wellCode - amount: oldWellContent.amount - toDecrement.amountToDecrement - recordedBy: user - wellsToUpdate.push newWellContent - change = - codeName: oldContainerWellContent.containerCodeName - recordedBy: user - recordedDate: new Date().getTime() - entryType: 'UPDATE' - entry: "Amount #{toDecrement.amountToDecrement} #{toDecrement.amountToDecrementUnits} taken out to create daughter vial #{toDecrement.daughterVialBarcode}" - changes.push change + #Check that the amount is valid to decrement. + differentState = (oldWellContent.physicalState != toDecrement.physicalState) + concentrationMismatch = (toDecrement.physicalState == 'solution' and (Math.abs(toDecrement.concentration - oldWellContent.batchConcentration) > 0.0001 or toDecrement.concUnits != oldWellContent.batchConcUnits)) + unitMismatch = (oldWellContent.amountUnits != toDecrement.amountUnits) + if !differentState and !concentrationMismatch and !unitMismatch + wellCode = oldWellContent.containerCodeName + newWellContent = + containerCodeName: wellCode + amount: oldWellContent.amount - toDecrement.amount + recordedBy: user + wellsToUpdate.push newWellContent + change = + codeName: oldContainerWellContent.containerCodeName + recordedBy: user + recordedDate: new Date().getTime() + entryType: 'UPDATE' + entry: "Amount #{toDecrement.amount} #{toDecrement.amountUnits} taken out to create daughter vial #{toDecrement.destinationVialBarcode}" + changes.push change console.log wellsToUpdate - exports.updateWellContentInternal wellsToUpdate, true, false, (updateWellsResponse, updateWellsStatusCode) -> - console.log updateWellsStatusCode - if updateWellsStatusCode != 204 - callback "Error: #{updateWellsResponse}" - else - exports.containerLogsInternal changes, 0, (logs, statusCode) -> - if statusCode != 200 - callback logs - else - callback null, updateWellsResponse + if wellsToUpdate.length > 0 + exports.updateWellContentInternal wellsToUpdate, true, false, (updateWellsResponse, updateWellsStatusCode) -> + console.log updateWellsStatusCode + if updateWellsStatusCode != 204 + callback "Error: #{updateWellsResponse}" + else + exports.containerLogsInternal changes, 0, (logs, statusCode) -> + if statusCode != 200 + callback logs + else + callback null, updateWellsResponse + else + callback null prepareSummaryInfo = (fileEntryArray) -> summaryInfo = @@ -3358,15 +3370,7 @@ exports.createDaughterVialsInternal = (vialsToCreate, user, callback) -> if err? callback err else - toDecrementList = [] - _.each vialsToCreate, (entry) -> - toDecrement = - barcode: entry.sourceVialBarcode - amountToDecrement: entry.amount - amountToDecrementUnits: entry.amountUnits - daughterVialBarcode: entry.destinationVialBarcode - toDecrementList.push toDecrement - decrementAmountsFromVials toDecrementList, parentWellContentList, user, (err, decrementVialsResponse) -> + decrementAmountsFromVials vialsToCreate, parentWellContentList, user, (err, decrementVialsResponse) -> if err? callback err else From 87241a99ef7d233dbad21cae5d452211e7c75dd3 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 17 Oct 2017 08:13:19 -0700 Subject: [PATCH 239/576] Added getAPICmpdReg proxy route, and switched scientists to use API route, which takes a new optional ?withLots boolean parameter. Switched the search form to use that parameter, which limits the list of scientists returned to only those who have registered lots in the system. Fixed some buggy behavior around the search form picklist showing up empty when there are no lots registered. Added an error message for when there are no projects in the system and a user tries to save a lot. Fixes https://github.com/mcneilco/acas-cmpdreg-roo-server/issues/25 added in defaults of several new CmpdReg configs. Removed "Parent LiveDesign Corp Name" from default bulk loader mappings because it is more confusing than useful. --- modules/CmpdReg/src/client/custom/Lot_Custom.js | 6 ++++++ modules/CmpdReg/src/client/custom/configuration.json | 6 ++++-- modules/CmpdReg/src/client/src/PickList.js | 4 ++-- modules/CmpdReg/src/client/src/SearchForm.js | 2 +- modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee | 10 +++++++++- 5 files changed, 22 insertions(+), 6 deletions(-) diff --git a/modules/CmpdReg/src/client/custom/Lot_Custom.js b/modules/CmpdReg/src/client/custom/Lot_Custom.js index b9b2ca6d0..5de973261 100755 --- a/modules/CmpdReg/src/client/custom/Lot_Custom.js +++ b/modules/CmpdReg/src/client/custom/Lot_Custom.js @@ -146,6 +146,9 @@ $(function() { errors.push({'attribute': 'boilingPoint', 'message': "BP must be a number if provided"}); } } + if (attr.project != null && typeof(attr.project) == 'undefined'){ + errors.push({'attribute': 'project', 'message': "Project must be provided"}); + } if (errors.length > 0) {return errors;} } }); @@ -259,6 +262,9 @@ $(function() { }, updateModel: function() { + if (this.projectCodeController.collection.length == 0){ + alert('System Configuration Error: There must be at least one project to proceed') + } this.clearValidationErrors(); if (this.model.isNew() ) { diff --git a/modules/CmpdReg/src/client/custom/configuration.json b/modules/CmpdReg/src/client/custom/configuration.json index f2b99776a..cb3e1638f 100755 --- a/modules/CmpdReg/src/client/custom/configuration.json +++ b/modules/CmpdReg/src/client/custom/configuration.json @@ -62,8 +62,11 @@ "maxSearchResults": 5000, "unitTestDB": true, "initalDBLoad": true, + "compoundInventory": true, + "checkACASDependenciesByBarcode": false, "projectRestrictions": false, - "jchemVersion": "16.4.25.0" + "jchemVersion": "16.4.25.0", + "orderSelectLists": true }, "bulkLoadSettings": { "useProjectRoles":false, @@ -100,7 +103,6 @@ {"name": "Project", "dataType": "string", "required": false}, {"name": "CAS Number", "dataType": "string", "required": false}, {"name": "Parent Corp Name", "dataType": "string", "required": false}, - {"name": "Parent LiveDesign Corp Name", "dataType": "string", "required": false}, {"name": "Parent Common Name", "dataType": "string", "required": false}, {"name": "Parent Stereo Comment", "dataType": "string", "required": false} ] diff --git a/modules/CmpdReg/src/client/src/PickList.js b/modules/CmpdReg/src/client/src/PickList.js index 90066a8d6..fada98e6a 100755 --- a/modules/CmpdReg/src/client/src/PickList.js +++ b/modules/CmpdReg/src/client/src/PickList.js @@ -52,8 +52,8 @@ $(function() { this.collection = new PickListList(); this.collection.setType(this.options.type); this.collection.bind('add', this.addOne); - this.collection.bind('reset', this.handleListReset); - this.collection.fetch(); + //this.collection.bind('reset', this.handleListReset); + this.collection.fetch({success: this.handleListReset}); if (this.options.selectedCode !='') { this.selectedCode = this.options.selectedCode; } else { diff --git a/modules/CmpdReg/src/client/src/SearchForm.js b/modules/CmpdReg/src/client/src/SearchForm.js index 1b666f83f..1b0513d94 100755 --- a/modules/CmpdReg/src/client/src/SearchForm.js +++ b/modules/CmpdReg/src/client/src/SearchForm.js @@ -86,7 +86,7 @@ $(function() { this.updatePercentSimilarityDisabled(); this.chemistCodeController = - this.setupCodeController('chemist', 'scientists', 'chemist', true); + this.setupCodeController('chemist', 'scientists?withLots=true', 'chemist', true); this.chemistCodeController.collection.bind('reset', this.chemistsLoaded); var self = this; diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index c9a9bcfdf..f5c7bd60f 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -6,7 +6,7 @@ exports.setupAPIRoutes = (app) -> exports.setupRoutes = (app, loginRoutes) -> app.get '/cmpdReg', loginRoutes.ensureAuthenticated, exports.cmpdRegIndex app.get '/marvin4js-license.cxl', loginRoutes.ensureAuthenticated, exports.getMarvinJSLicense - app.get '/cmpdReg/scientists', loginRoutes.ensureAuthenticated, exports.getBasicCmpdReg + app.get '/cmpdReg/scientists', loginRoutes.ensureAuthenticated, exports.getAPICmpdReg app.get '/cmpdReg/parentAliasKinds', loginRoutes.ensureAuthenticated, exports.getBasicCmpdReg app.get '/cmpdReg/units', loginRoutes.ensureAuthenticated, exports.getBasicCmpdReg app.get '/cmpdReg/solutionUnits', loginRoutes.ensureAuthenticated, exports.getBasicCmpdReg @@ -129,6 +129,14 @@ exports.getBasicCmpdReg = (req, resp) -> console.log cmpdRegCall req.pipe(request(cmpdRegCall)).pipe(resp) +exports.getAPICmpdReg = (req, resp) -> + console.log 'in getAPICmpdReg' + console.log req.originalUrl + endOfUrl = (req.originalUrl).replace /\/cmpdreg\//, "" + cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + "/api/v1/" +endOfUrl + console.log cmpdRegCall + req.pipe(request(cmpdRegCall)).pipe(resp) + exports.getAuthorizedCmpdRegProjects = (req, resp) -> exports.getAuthorizedCmpdRegProjectsInternal req, (response) => resp.status "200" From 4083bcfc272e35ec35a5ab6e2ef46b03f0211702 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 17 Oct 2017 11:19:57 -0700 Subject: [PATCH 240/576] #286: Uncommenting moveToLocation callCustom code --- .../routes/InventoryServiceRoutes.coffee | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 644e9a0f8..eb814afa4 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -1371,15 +1371,15 @@ exports.moveToLocationInternal = (input, callCustom, updateLocationHistory, call if updateLocationHistory exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> callback json, statusCode - # if callCustom && csUtilities.moveToLocation? - # console.log "running customer specific server function moveToLocation" - # csUtilities.moveToLocation input, (customerResponse, statusCode) -> - # json = _.extend json, customerResponse - # callback json, statusCode - # else - # console.warn "could not find customer specific server function moveToLocation so not running it" - # callback json, response.statusCode - # ) + if callCustom && csUtilities.moveToLocation? + console.log "running customer specific server function moveToLocation" + csUtilities.moveToLocation input, (customerResponse, statusCode) -> + json = _.extend json, customerResponse + callback json, statusCode + else + if callCustom + console.warn "could not find customer specific server function moveToLocation so not running it" + callback json, statusCode ) else callback json, response.statusCode @@ -1392,6 +1392,7 @@ exports.moveToLocationInternal = (input, callCustom, updateLocationHistory, call ) #) + exports.getWellContentByContainerLabel = (req, resp) -> req.setTimeout 86400000 exports.getWellContentByContainerLabelsInternal [req.params.label], req.query.containerType, req.query.containerKind, req.query.labelType, req.query.labelKind, (json, statusCode) -> From 89c57b5ef9a06a92d94ebc0c0d343a454f61db5e Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 17 Oct 2017 14:09:46 -0700 Subject: [PATCH 241/576] #286: Uncommenting was not enough, to provide the right callback heirarchy I created a no op function that returns null if callCustom and csUtilities.moveToLocation are not set. --- .../routes/InventoryServiceRoutes.coffee | 30 +++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index eb814afa4..96b72d5a2 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -1367,22 +1367,14 @@ exports.moveToLocationInternal = (input, callCustom, updateLocationHistory, call #add the call to updateContainerHistoryLogs here... console.debug "response statusCode: #{response.statusCode}" if !error - console.log input[0].containerCodeName - if updateLocationHistory - exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> - callback json, statusCode - if callCustom && csUtilities.moveToLocation? - console.log "running customer specific server function moveToLocation" - csUtilities.moveToLocation input, (customerResponse, statusCode) -> - json = _.extend json, customerResponse - callback json, statusCode - else - if callCustom - console.warn "could not find customer specific server function moveToLocation so not running it" + shouldCallCustom = (callCustom && csUtilities.moveToLocation?) + callFunctionOrReturnNull shouldCallCustom, csUtilities.moveToLocation, input, (customerResponse, statusCode) -> + if updateLocationHistory + exports.updateContainerHistoryLogsInternal(input, (json, statusCode) -> callback json, statusCode - ) - else - callback json, response.statusCode + ) + else + callback json, response.statusCode else console.error 'got ajax error trying to get moveToLocation' console.error error @@ -1392,6 +1384,14 @@ exports.moveToLocationInternal = (input, callCustom, updateLocationHistory, call ) #) +callFunctionOrReturnNull = (callFunctionBoolean, funct, input, callback) -> + if callFunctionBoolean + console.log "running customer specific server function" + funct input, (customerResponse, statusCode) -> + callback customerResponse, statusCode + else + console.log "not running customer specific server function" + callback null exports.getWellContentByContainerLabel = (req, resp) -> req.setTimeout 86400000 From da7ef95b24c99264e09502c0e0560ca899e0c87b Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 17 Oct 2017 17:19:16 -0700 Subject: [PATCH 242/576] Exposed getCodeTableValues as an internal function, then used it in Vial CSV loaders to get the configured list of physical states, validate that the physical states in the CSV are recognized and dealias physical state Names into Codes. Tweaked validation logic to be more permissive. Also reworked validation to report errors when an amount or concentration is supplied but the units are not. Checked that units are uL for liquid and solution, or mg for any other physical state. Also fixed HTML reporting to count up vials by physical state generically based on the configured physical states. Fixes #288 --- .../routes/CodeTableServiceRoutes.coffee | 12 +- .../routes/InventoryServiceRoutes.coffee | 328 ++++++++++-------- 2 files changed, 198 insertions(+), 142 deletions(-) diff --git a/modules/Components/src/server/routes/CodeTableServiceRoutes.coffee b/modules/Components/src/server/routes/CodeTableServiceRoutes.coffee index 422d307f0..7e87f439e 100644 --- a/modules/Components/src/server/routes/CodeTableServiceRoutes.coffee +++ b/modules/Components/src/server/routes/CodeTableServiceRoutes.coffee @@ -37,13 +37,17 @@ exports.getAllCodeTableValues = (req, resp) -> ) exports.getCodeTableValues = (req, resp) -> + exports.getCodeTableValuesInternal req.params.type, req.params.kind, (result) -> + resp.json result + +exports.getCodeTableValuesInternal = (type, kind, cb) -> if global.specRunnerTestmode fullCodeTableJSON = require '../public/javascripts/spec/CodeTableJSON.js' - correctCodeTable = _.findWhere(fullCodeTableJSON.codes, {type:req.params.type, kind:req.params.kind}) - resp.end JSON.stringify correctCodeTable['codes'] + correctCodeTable = _.findWhere(fullCodeTableJSON.codes, {type:type, kind:kind}) + cb correctCodeTable['codes'] else config = require '../conf/compiled/conf.js' - baseurl = "#{config.all.client.service.persistence.fullpath}ddictvalues/all/#{req.params.type}/#{req.params.kind}/codetable" + baseurl = "#{config.all.client.service.persistence.fullpath}ddictvalues/all/#{type}/#{kind}/codetable" request = require 'request' request( method: 'GET' @@ -58,7 +62,7 @@ exports.getCodeTableValues = (req, resp) -> if a.name.toUpperCase() > b.name.toUpperCase() return 1 return 0 - resp.json json + cb json else console.log 'got ajax error trying to get code table entries' console.log error diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 0ce42be86..bfc527b02 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -2,6 +2,7 @@ serverUtilityFunctions = require './ServerUtilityFunctions.js' csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFunctions.js' _ = require 'underscore' preferredEntityCodeService = require '../routes/PreferredEntityCodeService.js' +codeTableRoutes = require './CodeTableServiceRoutes.js' config = require '../conf/compiled/conf.js' RUN_CUSTOM_FLAG = "0" fs = require('fs') @@ -2664,34 +2665,34 @@ exports.validateParentVialsFromCSVInternal = (csvFileName, dryRun, callback) -> createParentVialFileEntryArray csvFileName, (err, fileEntryArray) -> if err? callback err - summaryInfo = prepareSummaryInfo fileEntryArray - checkRequiredAttributes fileEntryArray, (requiredAttributeErrors) -> - if requiredAttributeErrors? - validationResponse.errorMessages.push requiredAttributeErrors... - checkDataTypeErrors fileEntryArray, (dataTypeErrors) -> - if dataTypeErrors? - validationResponse.errorMessages.push dataTypeErrors... - checkBatchCodesExist fileEntryArray, (missingBatchCodeErrors) -> - if missingBatchCodeErrors? and missingBatchCodeErrors.length > 0 - error = - errorLevel: 'error' - message: "The following batches do not exist: "+ missingBatchCodeErrors.join ', ' - validationResponse.errorMessages.push error - barcodes = _.pluck fileEntryArray, 'destinationVialBarcode' - checkBarcodesExist barcodes, (existingBarcodes, newBarcodes) -> - if existingBarcodes? and existingBarcodes.length > 0 + prepareSummaryInfo fileEntryArray, (summaryInfo) -> + checkRequiredAttributes fileEntryArray, (requiredAttributeErrors) -> + if requiredAttributeErrors? + validationResponse.errorMessages.push requiredAttributeErrors... + checkDataTypeErrors fileEntryArray, (dataTypeErrors) -> + if dataTypeErrors? + validationResponse.errorMessages.push dataTypeErrors... + checkBatchCodesExist fileEntryArray, (missingBatchCodeErrors) -> + if missingBatchCodeErrors? and missingBatchCodeErrors.length > 0 error = errorLevel: 'error' - message: "The following barcodes already exist: " + existingBarcodes.join ', ' + message: "The following batches do not exist: "+ missingBatchCodeErrors.join ', ' validationResponse.errorMessages.push error - errors = _.where validationResponse.errorMessages, {errorLevel: 'error'} - warnings = _.where validationResponse.errorMessages, {errorLevel: 'warning'} - if errors.length > 0 - validationResponse.hasError = true - if warnings.length > 0 - validationResponse.hasWarning = true - validationResponse.results.htmlSummary = prepareValidationHTMLSummary validationResponse.hasError, validationResponse.hasWarning, validationResponse.errorMessages, summaryInfo - callback validationResponse + barcodes = _.pluck fileEntryArray, 'destinationVialBarcode' + checkBarcodesExist barcodes, (existingBarcodes, newBarcodes) -> + if existingBarcodes? and existingBarcodes.length > 0 + error = + errorLevel: 'error' + message: "The following barcodes already exist: " + existingBarcodes.join ', ' + validationResponse.errorMessages.push error + errors = _.where validationResponse.errorMessages, {errorLevel: 'error'} + warnings = _.where validationResponse.errorMessages, {errorLevel: 'warning'} + if errors.length > 0 + validationResponse.hasError = true + if warnings.length > 0 + validationResponse.hasWarning = true + validationResponse.results.htmlSummary = prepareValidationHTMLSummary validationResponse.hasError, validationResponse.hasWarning, validationResponse.errorMessages, summaryInfo + callback validationResponse else error = errorLevel: 'error' @@ -2716,52 +2717,53 @@ exports.createParentVialsFromCSVInternal = (csvFileName, dryRun, user, callback) createParentVialFileEntryArray csvFileName, (err, fileEntryArray) -> if err? callback err - summaryInfo = prepareSummaryInfo fileEntryArray - exports.getContainerTubeDefinitionCode (definitionCode) -> - if !definitionCode? - error = - errorLevel: 'error' - message: 'Could not find definition container for tube' - createResponse.errorMessages.push error - tubesToCreate = [] - _.each fileEntryArray, (entry) -> - tube = - barcode: entry.destinationVialBarcode - definition: definitionCode - recordedBy: user - createdUser: entry.preparedBy - createdDate: entry.createdDate - physicalState: entry.physicalState - wells: [ - wellName: "A001" - batchCode: entry.batchCode - amount: entry.amount - amountUnits: entry.amountUnits - physicalState: entry.physicalState - recordedBy: user - recordedDate: (new Date()).getTime() - ] - if entry.physicalState == 'solution' - tube.wells[0].batchConcentration = entry.concentration - tube.wells[0].batchConcUnits = entry.concUnits - tube.wells[0].solventCode = entry.solvent - tubesToCreate.push tube - console.log JSON.stringify tubesToCreate - exports.createTubesInternal tubesToCreate, 0, (json, statusCode) -> - console.log statusCode - console.log json - if statusCode != 200 - createResponse.hasError = true - console.error json - error = - errorLevel: 'error' - message: json - createResponse.errorMessages.push error - else - createResponse.hasError = false - createResponse.commit = true - createResponse.results.htmlSummary = prepareCreateVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo - callback createResponse + dealiasPhysicalStates fileEntryArray, (fileEntryArray) -> + prepareSummaryInfo fileEntryArray, (summaryInfo) -> + exports.getContainerTubeDefinitionCode (definitionCode) -> + if !definitionCode? + error = + errorLevel: 'error' + message: 'Could not find definition container for tube' + createResponse.errorMessages.push error + tubesToCreate = [] + _.each fileEntryArray, (entry) -> + tube = + barcode: entry.destinationVialBarcode + definition: definitionCode + recordedBy: user + createdUser: entry.preparedBy + createdDate: entry.createdDate + physicalState: entry.physicalState + wells: [ + wellName: "A001" + batchCode: entry.batchCode + amount: entry.amount + amountUnits: entry.amountUnits + physicalState: entry.physicalState + recordedBy: user + recordedDate: (new Date()).getTime() + ] + if entry.physicalState == 'solution' + tube.wells[0].batchConcentration = entry.concentration + tube.wells[0].batchConcUnits = entry.concUnits + tube.wells[0].solventCode = entry.solvent + tubesToCreate.push tube + console.log JSON.stringify tubesToCreate + exports.createTubesInternal tubesToCreate, 0, (json, statusCode) -> + console.log statusCode + console.log json + if statusCode != 200 + createResponse.hasError = true + console.error json + error = + errorLevel: 'error' + message: json + createResponse.errorMessages.push error + else + createResponse.hasError = false + createResponse.commit = true + createResponse.results.htmlSummary = prepareCreateVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo + callback createResponse else error = errorLevel: 'error' @@ -2821,20 +2823,20 @@ exports.validateDaughterVialsFromCSVInternal = (csvFileName, dryRun, callback) - createDaughterVialFileEntryArray csvFileName, (err, fileEntryArray) -> if err? callback err - summaryInfo = prepareSummaryInfo fileEntryArray - exports.validateDaughterVialsInternal fileEntryArray, (err, errorsAndWarnings) -> - if err? - callback err - else - validationResponse.errorMessages.push errorsAndWarnings... - errors = _.where validationResponse.errorMessages, {errorLevel: 'error'} - warnings = _.where validationResponse.errorMessages, {errorLevel: 'warning'} - if errors.length > 0 - validationResponse.hasError = true - if warnings.length > 0 - validationResponse.hasWarning = true - validationResponse.results.htmlSummary = prepareValidationHTMLSummary validationResponse.hasError, validationResponse.hasWarning, validationResponse.errorMessages, summaryInfo - callback null, validationResponse + prepareSummaryInfo fileEntryArray, (summaryInfo) -> + exports.validateDaughterVialsInternal fileEntryArray, (err, errorsAndWarnings) -> + if err? + callback err + else + validationResponse.errorMessages.push errorsAndWarnings... + errors = _.where validationResponse.errorMessages, {errorLevel: 'error'} + warnings = _.where validationResponse.errorMessages, {errorLevel: 'warning'} + if errors.length > 0 + validationResponse.hasError = true + if warnings.length > 0 + validationResponse.hasWarning = true + validationResponse.results.htmlSummary = prepareValidationHTMLSummary validationResponse.hasError, validationResponse.hasWarning, validationResponse.errorMessages, summaryInfo + callback null, validationResponse else error = errorLevel: 'error' @@ -2865,18 +2867,19 @@ exports.createDaughterVialsFromCSVInternal = (csvFileName, dryRun, user, callbac createDaughterVialFileEntryArray csvFileName, (err, fileEntryArray) -> if err? callback err - summaryInfo = prepareSummaryInfo fileEntryArray - exports.createDaughterVialsInternal fileEntryArray, user, (err, response) -> - if err? - error = - errorLevel: 'error' - message: err - createResponse.errorMessages.push error - else - createResponse.hasError = false - createResponse.commit = true - createResponse.results.htmlSummary = prepareCreateVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo - callback null, createResponse + dealiasPhysicalStates fileEntryArray, (fileEntryArray) -> + prepareSummaryInfo fileEntryArray, (summaryInfo) -> + exports.createDaughterVialsInternal fileEntryArray, user, (err, response) -> + if err? + error = + errorLevel: 'error' + message: err + createResponse.errorMessages.push error + else + createResponse.hasError = false + createResponse.commit = true + createResponse.results.htmlSummary = prepareCreateVialsHTMLSummary createResponse.hasError, createResponse.hasWarning, createResponse.errorMessages, summaryInfo + callback null, createResponse @@ -2902,6 +2905,7 @@ createParentVialFileEntryArray = (csvFileName, callback) => fs.createReadStream(path + fileName) .pipe(parse({delimiter: ','})) .on('data', (csvrow) -> + rowCount++ fileEntry = batchCode: csvrow[PARENT_COMPOUND_LOT_INDEX].trim() destinationVialBarcode: csvrow[PARENT_DESTINATION_VIAL_INDEX].trim() @@ -2914,9 +2918,8 @@ createParentVialFileEntryArray = (csvFileName, callback) => concUnits:csvrow[PARENT_CONC_UNITS_INDEX].trim() solvent: csvrow[PARENT_SOLVENT_INDEX].trim() rowNumber: rowCount - if rowCount? and rowCount > 0 + if rowCount? and rowCount > 1 csvFileEntries.push(fileEntry) - rowCount++ ) .on('end', () -> return callback null, csvFileEntries @@ -2930,6 +2933,7 @@ createDaughterVialFileEntryArray = (csvFileName, callback) => fs.createReadStream(path + fileName) .pipe(parse({delimiter: ','})) .on('data', (csvrow) -> + rowCount++ fileEntry = sourceVialBarcode: csvrow[DAUGHTER_SOURCE_VIAL_INDEX].trim() destinationVialBarcode: csvrow[DAUGHTER_DESTINATION_VIAL_INDEX].trim() @@ -2942,27 +2946,33 @@ createDaughterVialFileEntryArray = (csvFileName, callback) => concUnits: csvrow[DAUGHTER_CONC_UNITS_INDEX].trim() solvent: csvrow[DAUGHTER_SOLVENT_INDEX].trim() rowNumber: rowCount - if rowCount? and rowCount > 0 + if rowCount? and rowCount > 1 csvFileEntries.push(fileEntry) - rowCount++ ) .on('end', () -> return callback null, csvFileEntries ) +dealiasPhysicalStates = (fileEntryArray, callback) -> + codeTableRoutes.getCodeTableValuesInternal 'container status', 'physical state', (configuredPhysicalStates) -> + cleanedFileEntryArray = _.map fileEntryArray, (entry) -> + foundPhysicalState = _.findWhere configuredPhysicalStates, {code: entry.physicalState} + if !foundPhysicalState? + foundPhysicalState = _.findWhere configuredPhysicalStates, {name: entry.physicalState} + if foundPhysicalState? + entry.physicalState = foundPhysicalState.code + entry + callback cleanedFileEntryArray + checkRequiredAttributes = (fileEntryArray, callback) -> requiredAttributeErrors = [] _.each fileEntryArray, (entry) -> missingAttributes = [] - for attr in ['batchCode', 'destinationVialBarcode', 'sourceVialBarcode', 'amount', 'amountUnits', 'preparedBy', 'preparedDate', 'physicalState', 'concentration', 'concUnits', 'solvent'] + for attr in ['batchCode', 'destinationVialBarcode', 'sourceVialBarcode','preparedBy', 'preparedDate', 'physicalState'] + #not strictly required: 'amount', 'amountUnits', 'concentration', 'concUnits', 'solvent', if entry[attr]? - if attr in ['concentration', 'concUnits', 'solvent'] - if entry.physicalState == 'solution' - if entry[attr] == "" - missingAttributes.push attr - else - if entry[attr] == "" - missingAttributes.push attr + if entry[attr] == "" + missingAttributes.push attr if missingAttributes.length > 0 error = errorLevel: 'error' @@ -2971,19 +2981,50 @@ checkRequiredAttributes = (fileEntryArray, callback) -> callback requiredAttributeErrors checkDataTypeErrors = (fileEntryArray, callback) -> - dataTypeErrors = [] - _.each fileEntryArray, (entry) -> - if entry.amount? and entry.amount.length > 0 and isNaN(entry.amount) - error = - errorLevel: 'error' - message: "Row #{entry.rowNumber} contains the invalid amount: #{entry.amount}" - dataTypeErrors.push error - if entry.concentration? and entry.concentration.length > 0 and isNaN(entry.concentration) - error = - errorLevel: 'error' - message: "Row #{entry.rowNumber} contains the invalid concentration: #{entry.concentration}" - dataTypeErrors.push error - callback dataTypeErrors + codeTableRoutes.getCodeTableValuesInternal 'container status', 'physical state', (configuredPhysicalStates) -> + dataTypeErrors = [] + _.each fileEntryArray, (entry) -> + foundPhysicalState = _.findWhere configuredPhysicalStates, {code: entry.physicalState} + if !foundPhysicalState? + foundPhysicalState = _.findWhere configuredPhysicalStates, {name: entry.physicalState} + if !foundPhysicalState? + configuredPhysicalStateCodes = _.pluck configuredPhysicalStates, 'code' + configuredPhysicalStateCodeString = configuredPhysicalStateCodes.join(', ') + error = + errorLevel: 'error' + message: "Row #{entry.rowNumber} has a physical state that was not recognized: #{entry.physicalState}. The available options are: #{configuredPhysicalStateCodeString}" + dataTypeErrors.push error + else + entry.physicalState = foundPhysicalState.code + if entry.amount? and !isNaN(entry.amount) + if !entry.amountUnits? or entry.amountUnits.length < 1 + error = + errorLevel: 'error' + message: "Row #{entry.rowNumber} has an amount but no units" + dataTypeErrors.push error + if entry.concentration? and !isNaN(entry.concentration) + if entry.concUnits.length < 1 + error = + errorLevel: 'error' + message: "Row #{entry.rowNumber} has a concentration but no units. Concentration units must be mM" + dataTypeErrors.push error + else if entry.concUnits != 'mM' + error = + errorLevel: 'error' + message: "Row #{entry.rowNumber} must use concentration units of mM" + dataTypeErrors.push error + if entry.physicalState == 'liquid' or entry.physicalState == 'solution' + if entry.amountUnits != 'uL' + error = + errorLevel: 'error' + message: "Row #{entry.rowNumber} uses physical state \"#{entry.physicalState}\" and so must use units uL" + dataTypeErrors.push error + else if entry.amountUnits.length > 0 and entry.amountUnits != 'mg' and foundPhysicalState? + error = + errorLevel: 'error' + message: "Row #{entry.rowNumber} uses physical state \"#{entry.physicalState}\" and so must use amount units mg" + dataTypeErrors.push error + callback dataTypeErrors checkBatchCodesExist = (fileEntryArray, callback) -> requests = [] @@ -2994,7 +3035,7 @@ checkBatchCodesExist = (fileEntryArray, callback) -> csUtilities.getPreferredBatchIds requests, (batchIdResponse) -> missingBatchCodes = [] _.each batchIdResponse, (batchCodeRequest) -> - if batchCodeRequest.preferredName.length < 1 + if batchCodeRequest.preferredName? and batchCodeRequest.preferredName.length < 1 missingBatchCodes.push batchCodeRequest.requestName callback missingBatchCodes @@ -3080,8 +3121,12 @@ prepareValidationHTMLSummary = (hasError, hasWarning, errorMessages, summaryInfo warningsBlock += "" htmlSummaryInfo = "

        Summary

        Information:

        \n
          \n " htmlSummaryInfo += "
        • Total Vials: #{summaryInfo.totalNumberOfVials}
          • " - htmlSummaryInfo += "
        • Solid Vials: #{summaryInfo.numSolidVials}
          • " - htmlSummaryInfo += "
        • Liquid Vials: #{summaryInfo.numLiquidVials}
          • " + console.log summaryInfo + stateNames = Object.keys(summaryInfo.totalsByStates) + stateNames.sort() + console.log stateNames + for stateName in stateNames + htmlSummaryInfo += "
        • #{stateName} Vials: #{summaryInfo.totalsByStates[stateName]}
          • " if summaryInfo.totalBatchCodes? htmlSummaryInfo += "
        • Unique Corporate Batch ID's: #{summaryInfo.totalBatchCodes}
          • " htmlSummaryInfo += "\n
        " @@ -3102,8 +3147,11 @@ prepareCreateVialsHTMLSummary = (hasError, hasWarning, errorMessages, summaryInf errorHeader = "

        An error occurred during uploading. If the messages below are unhelpful, you will need to contact your system administrator.

        " htmlSummaryInfo = "

        Summary

        Information:

        \n
          \n " htmlSummaryInfo += "
        • Total Vials: #{summaryInfo.totalNumberOfVials}
          • " - htmlSummaryInfo += "
        • Solid Vials: #{summaryInfo.numSolidVials}
          • " - htmlSummaryInfo += "
        • Liquid Vials: #{summaryInfo.numLiquidVials}
          • " + stateNames = Object.keys(summaryInfo.totalsByStates) + stateNames.sort() + console.log stateNames + for stateName in stateNames + htmlSummaryInfo += "
        • #{stateName} Vials: #{summaryInfo.totalsByStates[stateName]}
          • " if summaryInfo.totalBatchCodes? htmlSummaryInfo += "
        • Unique Corporate Batch ID's: #{summaryInfo.totalBatchCodes}
          • " htmlSummaryInfo += "\n
        " @@ -3170,17 +3218,21 @@ decrementAmountsFromVials = (toDecrementList, parentWellContentList, user, callb else callback null -prepareSummaryInfo = (fileEntryArray) -> - summaryInfo = - totalNumberOfVials: fileEntryArray.length - numSolidVials: (_.where fileEntryArray, {physicalState: 'solid'}).length - numLiquidVials: (_.where fileEntryArray, {physicalState: 'solution'}).length - batchCodes = _.pluck fileEntryArray, 'batchCode' - batchCodes = _.filter batchCodes, (entry) -> - entry? - if batchCodes? and batchCodes.length > 0 - summaryInfo.totalBatchCodes = (_.uniq batchCodes).length - summaryInfo +prepareSummaryInfo = (fileEntryArray, cb) -> + codeTableRoutes.getCodeTableValuesInternal 'container status', 'physical state', (configuredPhysicalStates) -> + summaryInfo = + totalNumberOfVials: fileEntryArray.length + totalsByStates: {} + _.each configuredPhysicalStates, (configuredPhysicalState) -> + count = (_.where fileEntryArray, {physicalState: configuredPhysicalState.code}).length + (_.where fileEntryArray, {physicalState: configuredPhysicalState.name}).length + if count > 0 + summaryInfo.totalsByStates[configuredPhysicalState.name] = count + batchCodes = _.pluck fileEntryArray, 'batchCode' + batchCodes = _.filter batchCodes, (entry) -> + entry? + if batchCodes? and batchCodes.length > 0 + summaryInfo.totalBatchCodes = (_.uniq batchCodes).length + cb summaryInfo exports.saveWellToWellInteractions = (req, resp) -> From 29c894d6c5a2af2f61526c5db68f865638ed777e Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 17 Oct 2017 18:24:07 -0700 Subject: [PATCH 243/576] #290: R service to bulk load locations --- .../src/server/r/bulkLoadLocations.R | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 modules/ServerAPI/src/server/r/bulkLoadLocations.R diff --git a/modules/ServerAPI/src/server/r/bulkLoadLocations.R b/modules/ServerAPI/src/server/r/bulkLoadLocations.R new file mode 100644 index 000000000..3721f02f3 --- /dev/null +++ b/modules/ServerAPI/src/server/r/bulkLoadLocations.R @@ -0,0 +1,35 @@ +# The next line is used by PrepareConfigFiles to include this file as a route in rapache, do not modify unless you intend to modify rapache routes (it can be anywhere in the files though) +# ROUTE: /bulkLoadLocations + +library(data.table) + +bulkLoadLocations <- function(postData, GET) { + createLocation <- function(labelText, labelType, labelKind, recordedBy) { + label <- createContainerLabel(labelText = labelText, lsType = labelType, lsKind = labelKind, recordedBy = recordedBy, preferred = TRUE) + container <- createContainer(lsType = "location", lsKind = "default", recordedBy = recordedBy, containerLabels = list(label)) + return(container) + } + createInteraction <- function(data, ptempid, firstID, recordedBy) { + interaction <- createContainerContainerInteraction(lsType = "moved to", lsKind = "location_location", recordedBy = recordedBy, firstContainer = firstID, secondContainer = data[tempid == ptempid,]$id) + interaction$firstContainer <- data[tempid == firstID,]$savedContainer[[1]] + interaction$secondContainer <- data[tempid == ptempid,]$savedContainer[[1]] + return(interaction) + } + + data <- as.data.table(jsonlite::fromJSON(postData)) + recordedBy <- GET$recordedBy + data[ , container := list(list(createLocation(label, labeltype, labelkind, recordedBy = recordedBy))), by = tempid] + containers <- saveContainers(data$container) + containerDT <- rbindlist(lapply(containers, function(x) {list(id = x$id, label = x$lsLabels[[1]]$labelText, savedContainer = list(x))})) + setkey(data, label) + setkey(containerDT, label) + data <- data[containerDT] + data[ !is.na(parenttempid), interaction := list(list(createInteraction(data, parenttempid, tempid, recordedBy = recordedBy))), by = tempid] + interactions <- saveContainerContainerInteractions(data[!is.na(parenttempid)]$interaction) + cat(jsonlite::toJSON(data, auto_unbox = TRUE)) +} + +postData <- rawToChar(receiveBin()) +out <- bulkLoadLocations(postData, GET) +cat(out) +DONE From b09b39b6915d4d12d9dd2d0cf656f1e48bd914aa Mon Sep 17 00:00:00 2001 From: Fiona McNeil Date: Tue, 17 Oct 2017 22:38:45 -0700 Subject: [PATCH 244/576] Fixed floating panels positioning. --- .../MultipleFilePicker/css/style_nocompile.css | 6 +++--- .../src/client/css/NewCmpdReg_nocompile.css | 17 +++++++++-------- 2 files changed, 12 insertions(+), 11 deletions(-) diff --git a/modules/CmpdReg/src/client/MultipleFilePicker/css/style_nocompile.css b/modules/CmpdReg/src/client/MultipleFilePicker/css/style_nocompile.css index 28ea02148..7ee2f79e7 100644 --- a/modules/CmpdReg/src/client/MultipleFilePicker/css/style_nocompile.css +++ b/modules/CmpdReg/src/client/MultipleFilePicker/css/style_nocompile.css @@ -11,9 +11,9 @@ div#upload-app { /* ORIGINAL WIDTH width: 510px;*/ width: 625px; - position: absolute; - bottom: 5px; important! -left: 20px; + position: fixed; + bottom: 60px; important! + left: 20px; } diff --git a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css index c5e25f056..db64370f3 100755 --- a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css +++ b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css @@ -168,9 +168,9 @@ div { /****** FLOATING PANELS ******/ /****** div#upload-app LOCATED IN MULTIPICKER CSS ******/ .MetaLotView .floatingPanel, .SearchResultsView .floatingPanel { - position: absolute; - left: 20px; - bottom: 140px; + position: fixed; + left: 220px; + bottom: 60px; padding: 5px; border: 12px solid #D5D8DD; background-color: #EEE; @@ -182,8 +182,9 @@ div { box-shadow: 3px 3px 4px #a7a9ad;*/ } .MetaLotView div.floatingPanel.NewLotSuccessView { - position: absolute; - left: 20px; + position: fixed; + bottom: 85px; + left: 220px; padding: 5px; cursor: hand; } @@ -445,9 +446,9 @@ div { /****** ERROR NOTIFICATION ******/ .ErrrorNotificationListView { - position: absolute; - bottom: -120px; - left: 15px; + position: fixed; + bottom: 60px; + left: 140px; z-index: 100; width: 400px; margin-left: 150px; From dcac1120dbd30eda4f042e6411f3cbbcf61f8bce Mon Sep 17 00:00:00 2001 From: Fiona McNeil Date: Wed, 18 Oct 2017 09:12:26 -0700 Subject: [PATCH 245/576] Fixes issues #292 and #293. Also made a couple spacing adjustments to various buttons. --- modules/ServerAPI/src/client/AuthorEditor.coffee | 14 ++++++++------ modules/ServerAPI/src/client/AuthorEditor.html | 12 ++++++------ 2 files changed, 14 insertions(+), 12 deletions(-) diff --git a/modules/ServerAPI/src/client/AuthorEditor.coffee b/modules/ServerAPI/src/client/AuthorEditor.coffee index 926163f66..cfc5486a3 100644 --- a/modules/ServerAPI/src/client/AuthorEditor.coffee +++ b/modules/ServerAPI/src/client/AuthorEditor.coffee @@ -1,5 +1,5 @@ class window.AuthorRole extends Backbone.Model - + class window.AuthorRoleList extends Backbone.Collection model: AuthorRole @@ -65,7 +65,7 @@ class window.Author extends Backbone.Model return errors else return null - + getSystemRoles: => systemRoles = _.filter @get('authorRoles'), (role) => if role.roleEntry?.lsType? @@ -92,7 +92,7 @@ class window.Author extends Backbone.Model class window.AuthorList extends Backbone.Collection model: Author - + class window.AuthorRoleController extends AbstractFormController template: _.template($("#AuthorRoleView").html()) @@ -112,7 +112,7 @@ class window.AuthorRoleController extends AbstractFormController @roleKind = @options.roleKind else @roleKind = null - + render: => $(@el).empty() $(@el).html @template() @@ -280,7 +280,7 @@ class window.AuthorRoleListController extends Backbone.View class window.AuthorEditorController extends AbstractFormController template: _.template($("#AuthorEditorView").html()) moduleLaunchName: "author" - + events: -> "keyup .bv_firstName": "attributeChanged" "keyup .bv_lastName": "attributeChanged" @@ -381,6 +381,7 @@ class window.AuthorEditorController extends AbstractFormController @$('.bv_userName').attr 'disabled', 'disabled' @$('.bv_save').html("Update") @$('.bv_newEntity').show() + @$('.bv_cancel').hide() @$('.bv_save').attr('disabled', 'disabled') @$('.bv_cancel').attr('disabled','disabled') @@ -467,7 +468,7 @@ class window.AuthorEditorController extends AbstractFormController @$('.bv_saveComplete').hide() @$('.bv_saveFailed').hide() @checkFormValid() - + updateModel: => @model.set 'firstName', UtilityFunctions::getTrimmedInput @$('.bv_firstName') @@ -500,6 +501,7 @@ class window.AuthorEditorController extends AbstractFormController @$('.bv_saveComplete').html "Update Complete" @$('.bv_save').attr('disabled', 'disabled') @$('.bv_saving').show() + @$('.bv_cancel').hide() console.log "handleSaveClicked" console.log JSON.stringify @model @model.save null, diff --git a/modules/ServerAPI/src/client/AuthorEditor.html b/modules/ServerAPI/src/client/AuthorEditor.html index c375f2c26..5f43c4441 100644 --- a/modules/ServerAPI/src/client/AuthorEditor.html +++ b/modules/ServerAPI/src/client/AuthorEditor.html @@ -43,19 +43,19 @@

        ACAS Author

        - +
        - +
        - +
        @@ -63,7 +63,7 @@

        ACAS Author

        -
        +
        @@ -110,6 +110,6 @@

        Clear Form

        From 584b3f15aff4fe4499f5fe457f1ba0f124c943f0 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 18 Oct 2017 12:48:46 -0700 Subject: [PATCH 246/576] Added new config for the root location label, and added new Node route api/getContainerLocationTree, that gets the container location hierarchy in jsTree-compatible format based on the configured root location. Fixes #294 --- conf/config.properties.example | 3 +- .../routes/InventoryServiceRoutes.coffee | 38 +++++++++++++++++++ 2 files changed, 40 insertions(+), 1 deletion(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 25f064771..8c24e649e 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -267,7 +267,7 @@ client.include.project=FALSE # config for whether project attribute is saved as part of an experiment client.save.project=TRUE client.protocol.save.project=true -client.path= +client.path=http://localhost:3000 client.fullpath=http://${client.host}:${client.port} # Query tool settings @@ -340,6 +340,7 @@ server.service.external.inventory.database.username= server.service.external.inventory.database.password= client.compoundInventory.enforceUppercaseBarcodes=false +client.compoundInventory.rootLocationLabel=COMPANY ## options for auth. strategy are: properties, database, ldap server.security.authstrategy=database diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index bfc527b02..569caff8f 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -66,6 +66,7 @@ exports.setupAPIRoutes = (app) -> app.post '/api/createDaughterVials', exports.createDaughterVials app.post '/api/advancedSearchContainers', exports.advancedSearchContainers app.get '/api/getParentVialByDaughterVialBarcode', exports.getParentVialByDaughterVialBarcode + app.get '/api/getContainerLocationTree', exports.getContainerLocationTree exports.setupRoutes = (app, loginRoutes) -> @@ -122,6 +123,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/createDaughterVials', loginRoutes.ensureAuthenticated, exports.createDaughterVials app.post '/api/advancedSearchContainers', loginRoutes.ensureAuthenticated, exports.advancedSearchContainers app.get '/api/getParentVialByDaughterVialBarcode', loginRoutes.ensureAuthenticated, exports.getParentVialByDaughterVialBarcode + app.get '/api/getContainerLocationTree', loginRoutes.ensureAuthenticated, exports.getContainerLocationTree exports.getContainersInLocation = (req, resp) -> @@ -3506,3 +3508,39 @@ exports.getParentVialByDaughterVialBarcodeInternal = (daughterVialBarcode, callb parentVialBarcode = _.findWhere parentVial.lsLabels, {lsType: 'barcode', lsKind: 'barcode', ignored: false} responseStub.parentVialBarcode = parentVialBarcode.labelText callback null, responseStub + +exports.getContainerLocationTree = (req, resp) -> + exports.getContainerLocationTreeInternal (err, response) -> + if err? + resp.statusCode = 500 + resp.json err + else + resp.json response + +exports.getContainerLocationTreeInternal = (callback) -> + rootLabel = config.all.client.compoundInventory.rootLocationLabel + baseurl = config.all.client.service.persistence.fullpath+"containers/getLocationTreeByRootLabel?rootLabel=#{rootLabel}" + request( + method: 'GET' + url: baseurl + json: true + timeout: 86400000 + headers: 'content-type': 'application/json' + , (error, response, json) => + if !error && response.statusCode == 200 + console.debug "returned successfully from #{baseurl}" + formattedTree = [] + _.each json, (rawLocation) -> + location = + id: rawLocation.codeName + parent: rawLocation.parentCodeName + text: rawLocation.labelText + formattedTree.push location + callback null, formattedTree + else + console.error 'got ajax error trying to get getWellCodesByContainerCodes' + console.error error + console.error json + console.error response + callback JSON.stringify "getWellCodesByContainerCodes failed" + ) \ No newline at end of file From 833d35a97331567d2aa1bca77786a29ed1bf4ef8 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 18 Oct 2017 14:23:55 -0700 Subject: [PATCH 247/576] Tweaked getContainerLocationTreeInternal to set the root node's parent to # instead of null so it is compatible with jsTree --- .../src/server/routes/InventoryServiceRoutes.coffee | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 569caff8f..31b8fbdfe 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -3531,9 +3531,12 @@ exports.getContainerLocationTreeInternal = (callback) -> console.debug "returned successfully from #{baseurl}" formattedTree = [] _.each json, (rawLocation) -> + parent = rawLocation.parentCodeName + if !parent? + parent = '#' location = id: rawLocation.codeName - parent: rawLocation.parentCodeName + parent: parent text: rawLocation.labelText formattedTree.push location callback null, formattedTree From 540ecf3304ae939ee9c4dcf2cfd890118b7d7e39 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 18 Oct 2017 14:52:04 -0700 Subject: [PATCH 248/576] Added breadcrumb to the returned JSON --- .../ServerAPI/src/server/routes/InventoryServiceRoutes.coffee | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 31b8fbdfe..8e94333a6 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -3538,6 +3538,7 @@ exports.getContainerLocationTreeInternal = (callback) -> id: rawLocation.codeName parent: parent text: rawLocation.labelText + breadcrumb: rawLocation.labelTextBreadcrumb formattedTree.push location callback null, formattedTree else From 8a5111c90a7273b29f476a476e85b21058c72891 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Wed, 18 Oct 2017 17:10:43 -0700 Subject: [PATCH 249/576] feature/lot-inventory-location-select: added form field for location tree --- .../src/client/ACASFormLocationTree.coffee | 129 ++++++++++++++++++ .../src/client/ACASFormLocationTreeView.html | 32 +++++ .../src/client/AbstractFormController.coffee | 3 + 3 files changed, 164 insertions(+) create mode 100644 modules/Components/src/client/ACASFormLocationTree.coffee create mode 100644 modules/Components/src/client/ACASFormLocationTreeView.html diff --git a/modules/Components/src/client/ACASFormLocationTree.coffee b/modules/Components/src/client/ACASFormLocationTree.coffee new file mode 100644 index 000000000..252ee8fcf --- /dev/null +++ b/modules/Components/src/client/ACASFormLocationTree.coffee @@ -0,0 +1,129 @@ +class window.ACASFormLocationTreeController extends ACASFormAbstractFieldController + ### + Launching controller must: + - Initialize the model with an LSValue + Do whatever else is required or optional in ACASFormAbstractFieldController + ### + events: -> + "click .bv_editIcon": "handleEditIconClicked" + "click .bv_searchClear": "handleSearchClear" + "click .bv_updateLocation": "handleUpdateLocationClicked" + + template: _.template($("#ACASFormLocationTreeView").html()) + + initialize: -> + super() + @tubeCode = @options.tubeCode + if @tubeCode? + $.ajax + type: 'POST' + url: "/api/getBreadCrumbByContainerCode" + data: JSON.stringify [@tubeCode] + contentType: 'application/json' + success: (response) => + if response.length is 1 + @getModel().set + value: response[0].currentLocationCode + ignored: false + breadcrumb: response[0].labelBreadCrumb + else + @getModel().set + value: null + ignored: false + breadcrumb: "" + @renderModelContent() + + error: (err) => + alert 'error getting breadcrumb for container' + + + setEmptyValue: -> + @getModel().set + value: null + ignored: true + breadcrumb: null + + setInputValue: (inputValue) -> + @$('input').val inputValue + + + renderModelContent: => + @$('input').val @getModel().get('breadcrumb') + super() + + handleEditIconClicked: => + @$('.bv_locationTreeModal').modal + backdrop: 'static' + @getContainerLocationTree() + + getContainerLocationTree: => + $.ajax + type: 'GET' + url: "/api/getContainerLocationTree" + dataType: 'json' + error: (err) => + alert 'Could not get container location tree. Please contact administrator' + @$('.bv_locationTreeModal').modal 'hide' + success: (json) => + @setupTree (json) + + setupTree: (locationTreeObj) -> + _.map locationTreeObj, (loc) => + loc.icon = false + + @$('.bv_locationTree').jstree + core: + data: locationTreeObj + search: + fuzzy: false + show_only_matches: true + plugins: ["search"] + + @$('.bv_locationTree').bind "hover_node.jstree", (e, data) -> + $(e.target).attr("title", data.node.original.breadcrumb) + @$('.bv_locationTree').bind "select_node.jstree", (e, data) => + if data.selected.length is 1 + @$('.bv_updateLocation').removeAttr 'disabled' + else + @$('.bv_updateLocation').attr 'disabled', 'disabled' + + to = false + @$(".bv_searchVal").keyup => + clearTimeout to if to + to = setTimeout(-> + v = @$(".bv_searchVal").val() + @$(".bv_locationTree").jstree(true).search v + return + , 250) + return + + selectedLocation = @getModel().get('value') + if selectedLocation? and $.trim(selectedLocation) != "" + @$(".bv_locationTree").jstree('show_node', selectedLocation) + @$(".bv_locationTree").jstree('select_node', selectedLocation) + + handleSearchClear: => + @$('.bv_searchVal').val("") + + + handleUpdateLocationClicked: => + selectedLocation = @$('.bv_locationTree').jstree('get_selected', true) + @$('.bv_locationTreeModal').modal 'hide' + value = selectedLocation[0].original.id + breadcrumb = selectedLocation[0].original.breadcrumb + + @$('input').val breadcrumb + @handleInputChanged(value, breadcrumb) + + handleInputChanged: (value, breadcrumb) => + @clearError() + @userInputEvent = true + if value == "" + @setEmptyValue() + else + @getModel().set + value: value + ignored: false + breadcrumb: breadcrumb + @checkEmptyAndRequired() + @trigger 'formFieldChanged' diff --git a/modules/Components/src/client/ACASFormLocationTreeView.html b/modules/Components/src/client/ACASFormLocationTreeView.html new file mode 100644 index 000000000..da1e2f11f --- /dev/null +++ b/modules/Components/src/client/ACASFormLocationTreeView.html @@ -0,0 +1,32 @@ + \ No newline at end of file diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index d2425404a..a0554c653 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -166,6 +166,9 @@ class window.AbstractThingFormController extends AbstractFormController when 'stringValue' then newField = new ACASFormLSStringValueFieldController opts when 'dateValue' then newField = new ACASFormLSDateValueFieldController opts when 'fileValue' then newField = new ACASFormLSFileValueFieldController opts + when 'locationTree' + opts.tubeCode = @model.get('tubeCode') + newField = new ACASFormLocationTreeController opts @$("."+field.fieldSettings.fieldWrapper).append newField.render().el newField.afterRender() From 23334e7ceed26164c918b0eeeea8dc6a336affb9 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Wed, 18 Oct 2017 17:42:27 -0700 Subject: [PATCH 250/576] Fixed compound reg issues where open lot details and new lot after a new lot is saved fail to open a tab. Also fixed issues where Ketcher inserts a single C in empty mol --- modules/CmpdReg/src/client/src/EditParent.js | 2 +- modules/CmpdReg/src/client/src/NewLotSuccess.js | 8 +++++--- modules/CmpdReg/src/client/src/RegistrationSearch.js | 10 ++++++---- modules/CmpdReg/src/client/src/Salt.js | 2 +- modules/CmpdReg/src/client/src/SaltForm.js | 2 +- modules/CmpdReg/src/client/src/SearchForm.js | 2 +- 6 files changed, 15 insertions(+), 11 deletions(-) diff --git a/modules/CmpdReg/src/client/src/EditParent.js b/modules/CmpdReg/src/client/src/EditParent.js index ad2b8f3e4..b245f08ed 100644 --- a/modules/CmpdReg/src/client/src/EditParent.js +++ b/modules/CmpdReg/src/client/src/EditParent.js @@ -118,7 +118,7 @@ $(function () { } else if (this.useKetcher) { mol = this.ketcher.getMolfile(); - if (mol.indexOf(" 0 0 0 0 0 999") > -1) mol = null; + if (mol.indexOf(" 0 0 0 1 0 999") > -1) mol = null; editParentSearch.set({ molStructure: mol, corpName: jQuery.trim(self.$('.corpName').val()) diff --git a/modules/CmpdReg/src/client/src/NewLotSuccess.js b/modules/CmpdReg/src/client/src/NewLotSuccess.js index 5532ac718..9c49aab16 100755 --- a/modules/CmpdReg/src/client/src/NewLotSuccess.js +++ b/modules/CmpdReg/src/client/src/NewLotSuccess.js @@ -27,20 +27,22 @@ $(function() { }, openLot: function() { - window.open("#lot/"+this.options.corpName); + console.log("about to open new lot window"); + window.open("#lot/"+this.options.corpName, '_blank'); this.closeLot(); // appController.reset(); // if(appController) {appController.router.navigate('lot/'+this.options.corpName,true);} }, newLot: function() { - window.open("#register/"+this.options.corpName); + window.open("#register/"+this.options.corpName, '_blank'); this.closeLot(); - if(appController) {appController.router.navigate('register/'+this.options.corpName,true);} + // if(appController) {appController.router.navigate('register/'+this.options.corpName,true);} }, closeLot: function() { // $(this.el).hide(); + console.log("about to reset the controller"); appController.reset(); } }); diff --git a/modules/CmpdReg/src/client/src/RegistrationSearch.js b/modules/CmpdReg/src/client/src/RegistrationSearch.js index bb4f9b879..8bd6e3b99 100755 --- a/modules/CmpdReg/src/client/src/RegistrationSearch.js +++ b/modules/CmpdReg/src/client/src/RegistrationSearch.js @@ -12,8 +12,8 @@ $(function() { if (errors.length > 0) {return errors;} } }); - - + + window.RegistrationSearchController = Backbone.View.extend({ template: _.template($('#RegistrationSearch_template').html()), @@ -127,12 +127,14 @@ $(function() { }); } else if (this.useKetcher) { mol = this.ketcher.getMolfile(); - if (mol.indexOf(" 0 0 0 0 0 999") > -1) mol = null; + if (mol.indexOf(" 0 0 0 1 0 999") > -1) mol = null; regSearch.set({ molStructure: mol, corpName: jQuery.trim(self.$('.corpName').val()) }); - + console.log(self.$('.corpName').val()); + console.log(mol); + console.log(regSearch); if ( this.isValid() ) { this.trigger('registrationSearchNext', regSearch); this.hide(); diff --git a/modules/CmpdReg/src/client/src/Salt.js b/modules/CmpdReg/src/client/src/Salt.js index 32e1c6a8f..943c17daf 100755 --- a/modules/CmpdReg/src/client/src/Salt.js +++ b/modules/CmpdReg/src/client/src/Salt.js @@ -280,7 +280,7 @@ $(function() { } else if (this.useKetcher) { mol = this.ketcher.getMolfile(); - if (mol.indexOf(" 0 0 0 0 0 999") > -1) mol = ''; + if (mol.indexOf(" 0 0 0 1 0 999") > -1) mol = ''; gotMol(mol); } else { alert("No new salt sketcher configured"); diff --git a/modules/CmpdReg/src/client/src/SaltForm.js b/modules/CmpdReg/src/client/src/SaltForm.js index 05f30ea6c..1d9ebd484 100755 --- a/modules/CmpdReg/src/client/src/SaltForm.js +++ b/modules/CmpdReg/src/client/src/SaltForm.js @@ -176,7 +176,7 @@ $(function() { }); }else if (this.useKetcher) { mol = this.ketcher.getMolfile(); - if (mol.indexOf(" 0 0 0 0 0 999") > -1) mol = ''; + if (mol.indexOf(" 0 0 0 1 0 999") > -1) mol = ''; this.model.set({molStructure: mol}); callback(); } diff --git a/modules/CmpdReg/src/client/src/SearchForm.js b/modules/CmpdReg/src/client/src/SearchForm.js index 1b666f83f..360a6b54d 100755 --- a/modules/CmpdReg/src/client/src/SearchForm.js +++ b/modules/CmpdReg/src/client/src/SearchForm.js @@ -159,7 +159,7 @@ $(function() { }); } else if (this.useKetcher) { mol = this.ketcher.getMolfile(); - if (mol.indexOf(" 0 0 0 0 0 999") > -1) mol = ''; + if (mol.indexOf(" 0 0 0 1 0 999") > -1) mol = ''; var sf = this.makeSearchFormModel(mol); if (this.isValid()) { this.trigger('searchNext', sf); From d8772145b68619a6c181269169ea884b464de43d Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 19 Oct 2017 09:44:42 -0700 Subject: [PATCH 251/576] Added in optional ?withContainers parameter for getContainerLocationTree that will include non-location containers in the tree. Without the paremeter, or with the parameter set to false, it the tree will only have locations, and not any containers in those locations. --- .../src/server/routes/InventoryServiceRoutes.coffee | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 8e94333a6..7e009f623 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -3510,16 +3510,18 @@ exports.getParentVialByDaughterVialBarcodeInternal = (daughterVialBarcode, callb callback null, responseStub exports.getContainerLocationTree = (req, resp) -> - exports.getContainerLocationTreeInternal (err, response) -> + exports.getContainerLocationTreeInternal req.query.withContainers, (err, response) -> if err? resp.statusCode = 500 resp.json err else resp.json response -exports.getContainerLocationTreeInternal = (callback) -> +exports.getContainerLocationTreeInternal = (withContainers, callback) -> rootLabel = config.all.client.compoundInventory.rootLocationLabel baseurl = config.all.client.service.persistence.fullpath+"containers/getLocationTreeByRootLabel?rootLabel=#{rootLabel}" + if withContainers? + baseurl+= "&withContainers=#{withContainers}" request( method: 'GET' url: baseurl From 7adf730e4147395dfb7144936ea882f0651c9b9a Mon Sep 17 00:00:00 2001 From: Samantha Munoz Date: Thu, 19 Oct 2017 15:19:05 -0400 Subject: [PATCH 252/576] Issue 66 --- .../routes/InventoryServiceRoutes.coffee | 37 ++++++++++++++++++- 1 file changed, 35 insertions(+), 2 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 7e009f623..0eabf4406 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -67,6 +67,7 @@ exports.setupAPIRoutes = (app) -> app.post '/api/advancedSearchContainers', exports.advancedSearchContainers app.get '/api/getParentVialByDaughterVialBarcode', exports.getParentVialByDaughterVialBarcode app.get '/api/getContainerLocationTree', exports.getContainerLocationTree + app.post '/api/checkBatchDependencies', exports.checkBatchDependencies exports.setupRoutes = (app, loginRoutes) -> @@ -124,7 +125,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/advancedSearchContainers', loginRoutes.ensureAuthenticated, exports.advancedSearchContainers app.get '/api/getParentVialByDaughterVialBarcode', loginRoutes.ensureAuthenticated, exports.getParentVialByDaughterVialBarcode app.get '/api/getContainerLocationTree', loginRoutes.ensureAuthenticated, exports.getContainerLocationTree - + app.post '/api/checkBatchDependencies', loginRoutes.ensureAuthenticated, exports.checkBatchDependencies exports.getContainersInLocation = (req, resp) -> req.setTimeout 86400000 @@ -3549,4 +3550,36 @@ exports.getContainerLocationTreeInternal = (withContainers, callback) -> console.error json console.error response callback JSON.stringify "getWellCodesByContainerCodes failed" - ) \ No newline at end of file + ) + +exports.checkBatchDependencies = (req, resp) => + + exports.checkBatchDependenciesInternal(req.body, (json, statusCode) => + resp.statusCode = statusCode + resp.json json + ) + +exports.checkBatchDependenciesInternal = (input, callback) => + batchCodes = input + + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"compounds/checkBatchDependencies" + console.log 'baseurl', baseurl + request = require 'request' + request( + method: 'POST' + url: baseurl + body: batchCodes + json: true + timeout: 86400000 + , (error, response, json) => + if !error && response.statusCode == 200 + callback json, response.statusCode + else + console.error 'got ajax error trying to checkBatchDependencies' + console.error error + console.error json + console.error response + callback null, 500 + #resp.end JSON.stringify "getContainerStatesByContainerValue failed" + ) From bfe4fc688e7f269f80c3f308ff9a0b102f399e64 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Thu, 19 Oct 2017 13:28:19 -0700 Subject: [PATCH 253/576] fixed numericValueFormField so that it works with additional controls appended into its div --- modules/Components/src/client/ACASFormFields.coffee | 6 ++++-- modules/Components/src/client/ACASFormFieldsView.html | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 249cdc8a9..1aac21699 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -187,6 +187,8 @@ class window.ACASFormLSNumericValueFieldController extends ACASFormAbstractField - Initialize the model with an LSValue Do whatever else is required or optional in ACASFormAbstractFieldController ### + events: -> + "keyup .bv_number": "handleInputChanged" template: _.template($("#ACASFormLSNumericValueFieldView").html()) @@ -213,11 +215,11 @@ class window.ACASFormLSNumericValueFieldController extends ACASFormAbstractField ignored: true setInputValue: (inputValue) -> - @$('input').val inputValue + @$('.bv_number').val inputValue renderModelContent: => - @$('input').val @getModel().get('value') + @$('.bv_number').val @getModel().get('value') if @getModel().has 'unitKind' @$('.bv_units').html @getModel().get('unitKind') super() diff --git a/modules/Components/src/client/ACASFormFieldsView.html b/modules/Components/src/client/ACASFormFieldsView.html index 5bc7befc5..cc68f457c 100644 --- a/modules/Components/src/client/ACASFormFieldsView.html +++ b/modules/Components/src/client/ACASFormFieldsView.html @@ -9,7 +9,7 @@ \ No newline at end of file + 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zSIEW1owE>PTfv$asi9$Qlh{gehD~hZO!iUJ9Cp}YhaGm})1CC|!XhkpXh zedp>E_FZ990yL&xL((^u8(X0>l~_}8H`xl4p|M#hlZi9gM@@6sVTT?5E^v0(VTT=d y*kOkqcKAzR!TT^>bJ$^r9d_7ZhaGl!YySY9OUqfHs?!_*0000Sd From 1ea5313fb3dd8d606a5b59b956a98c2af4128d13 Mon Sep 17 00:00:00 2001 From: Fiona McNeil Date: Mon, 23 Oct 2017 16:34:52 -0700 Subject: [PATCH 264/576] Fixes #318. Moved the floating panels in compound reg over some more and got rid of a white background that was obscuring other features. --- modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css index db64370f3..44d331769 100755 --- a/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css +++ b/modules/CmpdReg/src/client/css/NewCmpdReg_nocompile.css @@ -448,11 +448,10 @@ div { .ErrrorNotificationListView { position: fixed; bottom: 60px; - left: 140px; + left: 100px; z-index: 100; width: 400px; margin-left: 150px; - background-color: white; } .ErrrorNotificationListView .showHideButton { margin-left: 7px; From 2dd900457cab27728a0a857cedd585da50175ccb Mon Sep 17 00:00:00 2001 From: John McNeil Date: Mon, 23 Oct 2017 19:29:06 -0700 Subject: [PATCH 265/576] initial progress on sel preprocessor example --- .../client/ACASBarcodeSELPreprocessor.coffee | 12 ++ .../ACASBarcodeSELPreprocessorRoutes.coffee | 116 ++++++++++++++++++ 2 files changed, 128 insertions(+) create mode 100644 modules/ACASBarcodeSELPreprocessor/src/client/ACASBarcodeSELPreprocessor.coffee create mode 100644 modules/ACASBarcodeSELPreprocessor/src/server/routes/ACASBarcodeSELPreprocessorRoutes.coffee diff --git a/modules/ACASBarcodeSELPreprocessor/src/client/ACASBarcodeSELPreprocessor.coffee b/modules/ACASBarcodeSELPreprocessor/src/client/ACASBarcodeSELPreprocessor.coffee new file mode 100644 index 000000000..1f793baee --- /dev/null +++ b/modules/ACASBarcodeSELPreprocessor/src/client/ACASBarcodeSELPreprocessor.coffee @@ -0,0 +1,12 @@ +class window.ACASBarcodeSELPreprocessor extends BasicFileValidateAndSaveController + + initialize: -> + @fileProcessorURL = "/aCASBarcodeSELPreprocessor/parseSEL" + @errorOwnerName = 'ACASBarcodeSELPreprocessor' + @loadReportFile = true + @loadImagesFile = true + @allowedFileTypes = ['csv', 'CSV'] + super() + @$('.bv_moduleTitle').html('Convert Barcodes to Lot/Batch Names and Load Experiment') + + diff --git a/modules/ACASBarcodeSELPreprocessor/src/server/routes/ACASBarcodeSELPreprocessorRoutes.coffee b/modules/ACASBarcodeSELPreprocessor/src/server/routes/ACASBarcodeSELPreprocessorRoutes.coffee new file mode 100644 index 000000000..8d2c4dcd5 --- /dev/null +++ b/modules/ACASBarcodeSELPreprocessor/src/server/routes/ACASBarcodeSELPreprocessorRoutes.coffee @@ -0,0 +1,116 @@ +exports.setupAPIRoutes = (app, loginRoutes) -> + app.post '/aCASBarcodeSELPreprocessor/parseSEL', exports.parseSEL + +exports.setupRoutes = (app, loginRoutes) -> + app.post '/aCASBarcodeSELPreprocessor/parseSEL', loginRoutes.ensureAuthenticated, exports.parseSEL + + +exports.parseSEL = (req, resp) -> + req.connection.setTimeout 6000000 + serverUtilityFunctions = require './ServerUtilityFunctions.js' + fs = require 'fs' + path = require('path') + inventoryServices = require "./InventoryServiceRoutes.js" + serverUtilityFunctions = require './ServerUtilityFunctions.js' + config = require '../conf/compiled/conf.js' + ACAS_HOME = '.' + + selData = req.body + + replyData = + transactionId: null + results: + path: req.body.path + fileToParse: selData.fileToParse + reportFile: selData.reportFile + htmlSummary: "" + dryRunMode: true + hasError: false + hasWarning: false + errorMessages: [] + + addError = (msg) -> + replyData.hasError = true + replyData.errorMessages.push + errorLevel: "error", message: msg + + infilePath = path.join ACAS_HOME, config.all.server.datafiles.relative_path, selData.fileToParse + fs.readFile infilePath, 'utf8', (err, selFile) -> + if err? + addError "Error reading file "+err + resp.json replyData + return + + inLines = selFile.split '\r' + outLines = [] + barcodesToSub = [] + linesToSub = [] + rawLines = [] + foundBarcodeHeader = false + foundRawResultsHeader = false + for line in inLines + console.log line + cells = line.split ',' + if foundBarcodeHeader && !foundRawResultsHeader + if cells[0].trim() != "" + barcodesToSub.push cells[0].trim() + linesToSub.push = cells + else + outLines.push cells.join ',' + else if foundRawResultsHeader + rawLines.push = line + else if !foundBarcodeHeader + outLines.push line + else + if cells[0].trim() == "Barcode" + foundBarcodeHeader = true + cells[0] == "Corporate Batch ID" + outLines.push cells.join ',' + else if cells[0].trim() == "Raw Results" + foundRawResultsHeader = true + rawLines.push line + + if !foundBarcodeHeader + addError "Expected to find left-hand cell containing the word \"Barcode\"" + resp.json replyData + return + + console.log barcodesToSub + inventoryServices.getWellContentByContainerLabelsInternal barcodesToSub, 'container', 'tube', 'barcode', 'barcode', (wells, wellStatusCode) -> + if wellStatusCode != 200 + addError "There was a problem looking up the barcodes" + resp.json replyData + return + + batches = {} + for well in wells + wellInfo = wells[0]?.wellContent[0] + if wellInfo?.batchCode? and wellInfo.batchCode != "" + batches[wellInfo.barcode] = wellInfo.batchCode + else + addError "Could not find lot/bath name for barcode #{wellInfo.barcode}" + if replyData.hasError + resp.json replyData + return + + console.log batches + for line in linesToSub + line[0] = batches[line[0]] + outLines.push line.join ',' + + outLines.push rawLines + console.log "number of lines: "+outLines.length + + outFile = outLines.join '\r\n' + outFileName = selData.fileToParse.slice(0, -4) + "_converted.csv" + outFilePath = path.join ACAS_HOME, config.all.server.datafiles.relative_path, outFileName + fs.writeFile outFilePath, outFile, 'utf8', (err) -> + if err? + addError "Error writing intermediate file "+err + resp.json replyData + return + + selData.fileToParse = outFileName + console.log selData + serverUtilityFunctions.runRFunctionOutsideRequest selData.user, selData, "src/r/GenericDataParser/generic_data_parser.R", "parseGenericData", (rReturn) -> + resp.end rReturn From 5d06701a846704cb0c48fd77b39d67126113a884 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Mon, 23 Oct 2017 20:34:04 -0700 Subject: [PATCH 266/576] Fixes #321 getParentVialByDaughterVialBarcodeInternal throws error if no parent found. This was not breaking anything, just putting errors on the log --- .../ServerAPI/src/server/routes/InventoryServiceRoutes.coffee | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 63685ff77..e2a67e50f 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -3500,6 +3500,7 @@ exports.getParentVialByDaughterVialBarcodeInternal = (daughterVialBarcode, callb return if advSearchReturn.results.length < 1 callback null, responseStub + return parentWell = advSearchReturn.results[0] responseStub.parentWellCodeName = parentWell.codeName parentWellLabel = _.findWhere parentWell.lsLabels, {lsType: 'name', lsKind: 'well name', ignored: false} From 7fa37f337c2008b31b180a8116d667a53c0ff27c Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 24 Oct 2017 20:56:13 -0700 Subject: [PATCH 267/576] #328: add 'Aliquot' to configured entity types and preferred entity services --- conf/ConfiguredEntityTypes.coffee | 9 +++ .../routes/PreferredEntityCodeService.coffee | 68 +++++++++++++++---- 2 files changed, 62 insertions(+), 15 deletions(-) diff --git a/conf/ConfiguredEntityTypes.coffee b/conf/ConfiguredEntityTypes.coffee index f79625447..8b49f5bef 100644 --- a/conf/ConfiguredEntityTypes.coffee +++ b/conf/ConfiguredEntityTypes.coffee @@ -74,3 +74,12 @@ exports.entityTypes = sourceExternal: false parent: false model: require("../routes/ServerUtilityFunctions.js").DefinitionContainerTube + + 'Aliquot': + type: 'container' + kind: 'tube' + codeOrigin: 'ACAS LsContainer' + displayName: 'Aliquot' + sourceExternal: false + parent: false + diff --git a/modules/ServerAPI/src/server/routes/PreferredEntityCodeService.coffee b/modules/ServerAPI/src/server/routes/PreferredEntityCodeService.coffee index de5e97782..96b526e25 100644 --- a/modules/ServerAPI/src/server/routes/PreferredEntityCodeService.coffee +++ b/modules/ServerAPI/src/server/routes/PreferredEntityCodeService.coffee @@ -48,10 +48,11 @@ exports.getSpecificEntityTypeRoute = (req, resp) -> resp.json json exports.getSpecificEntityType = (displayName, callback) -> - if configuredEntityTypes.entityTypes[displayName]? - callback configuredEntityTypes.entityTypes[displayName] + entityType = _.findWhere configuredEntityTypes.entityTypes, {displayName:displayName} + if callback? + callback entityType else - callback {} + return entityType exports.getSpecificEntityTypeByTypeKindAndCodeOrigin = (type, kind, codeOrigin) -> entityType = _.findWhere configuredEntityTypes.entityTypes, {type: type, kind: kind, codeOrigin: codeOrigin} @@ -108,7 +109,7 @@ exports.referenceCodes = (requestData, csv, callback) -> return else # internal source - entityType = configuredEntityTypes.entityTypes[requestData.displayName] + entityType = exports.getSpecificEntityType requestData.displayName if entityType.codeOrigin is "ACAS LsThing" preferredThingService = require "./ThingServiceRoutes.js" reqHashes = @@ -130,19 +131,56 @@ exports.referenceCodes = (requestData, csv, callback) -> else if entityType.codeOrigin is "ACAS LsContainer" console.log "entityType.codeOrigin is ACAS LsContainer" console.log reqList - console.log reqList + # reqList = [reqList[0].requestName] preferredContainerService = require "./InventoryServiceRoutes.js" - reqHashes = - containerType: entityType.type - containerKind: entityType.kind - requests: reqList - preferredContainerService.getContainerCodesFromNamesOrCodes reqHashes, (codeResponse) -> - console.log "codeResponse" - console.log codeResponse - callback - displayName: requestData.displayName - results: formatJSONReferenceCode(codeResponse.results, "referenceName") + if requestData.displayName == "Aliquot" + reqHashes = + containerType: entityType.type + containerKind: entityType.kind + requests: reqList + labels = _.pluck reqList, 'requestName' + preferredContainerService.getWellContentByContainerLabelsInternal labels, null, null, null, null, (response, statusCode) -> + out = [] + for res in response + if res.containerCodeName? && res.wellContent? && res.wellContent.length == 1 && res.wellContent[0].physicalState == "solution" + codeName = res.containerCodeName + else + codeName = "" + out.push + requestName: res.label + referenceName: codeName + if csv + out = for res in out + res.requestName + "," + res.referenceName + outStr = "Requested Name,Reference Code\n"+out.join('\n') + callback + displayName: requestData.displayName + resultCSV: outStr + else + callback + displayName: requestData.displayName + results: out + else + reqHashes = + containerType: entityType.type + containerKind: entityType.kind + requests: reqList + preferredContainerService.getContainerCodesFromNamesOrCodes reqHashes, (codeResponse) -> + console.log "codeResponse" + console.log codeResponse + console.log "sould be :#{csv}" + if csv + out = for res in codeResponse.results + res.requestName + "," + res.referenceName + outStr = "Requested Name,Reference Code\n"+out.join('\n') + callback + displayName: requestData.displayName + resultCSV: outStr + else + callback + displayName: requestData.displayName + results: formatJSONReferenceCode(codeResponse.results, "referenceName") return #this is the fall-through for internal. External fall-through is in csUtilities.getExternalReferenceCodes message = "problem with internal preferred Code request: code type and kind are unknown to system" From 334d5bc6785e7d6bcdbf8babc03f7b63f6d8c3c9 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 24 Oct 2017 20:57:45 -0700 Subject: [PATCH 268/576] #329: SEL should check protocol for required entity type --- .../src/server/generic_data_parser.R | 48 ++++++++++++------- 1 file changed, 32 insertions(+), 16 deletions(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 1d921f0a3..e6452fede 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -470,7 +470,6 @@ validateCalculatedResults <- function(calculatedResults, dryRun, curveNames, tes # a "data.frame" of the validated calculated results require(data.table) - entityTypeAndKindList <- fromJSON(getURLcheckStatus(paste0(racas::applicationSettings$server.nodeapi.path, "/api/entitymeta/configuredEntityTypes/"), requireJSON = TRUE)) @@ -1178,7 +1177,7 @@ organizeCalculatedResults <- function(calculatedResults, inputFormat, formatPara if (lockCorpBatchId) { if(calculatedResultsValueKindRow[1] != mainCode && !precise) { stopUser(paste0("Could not find '", mainCode, "' column. The ", mainCode, - " column should be the first column of the Calculated Results")) + " column should be the first column of the Calculated Results")) } } else { if (!(mainCode %in% unlist(calculatedResultsValueKindRow)) && !precise) { @@ -2815,18 +2814,40 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, # Grab the Calculated Results Section calculatedResults <- getSection(genericDataFileDataFrame, lookFor = formatParameters$lookFor, transpose = FALSE) + # Get the protocol and experiment + newProtocol <- FALSE + if (!useExisting) { + protocol <- getProtocolByNameAndFormat(protocolName = validatedMetaData$'Protocol Name'[1], configList, inputFormat) + newProtocol <- is.na(protocol[[1]]) + if (!newProtocol) { + metaData$'Protocol Name'[1] <- getPreferredProtocolName(protocol, validatedMetaData$'Protocol Name'[1]) + } + } + # Organize the Calculated Results if (inputFormat %in% c("Gene ID Data", "Generic", "Dose Response")) { mainCode <- calculatedResults[2, 1] #Getting this from its standard position } else { mainCode <- "Corporate Batch ID" } + + if(!newProtocol) { + requiredMainCode <- getProtocolRequiredEntityCode(protocol) + if(length(requiredMainCode) > 0) { + requiredMainCode <- requiredMainCode[[1]] + if(mainCode != requiredMainCode) { + warnUser(paste0("'",metaData$'Protocol Name'[1],"' requires an entity type of '",requiredMainCode,"'. Please update your file with this entity type instead of the entity type '",mainCode,"'")) + } + mainCode <- requiredMainCode + calculatedResults[2, 1] <- mainCode + } + } + calculateGroupingID <- if (rawOnlyFormat) {calculateTreatmemtGroupID} else {NA} organizedResultsList <- organizeCalculatedResults( calculatedResults, inputFormat, formatParameters, mainCode, lockCorpBatchId = formatParameters$lockCorpBatchId, rawOnlyFormat = rawOnlyFormat, errorEnv = errorEnv, precise = precise, calculateGroupingID = calculateGroupingID) - calculatedResults <- organizedResultsList[[1]] selColumnOrderInfo <- organizedResultsList[[2]] @@ -2878,21 +2899,11 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, customExperimentMetaDataValues <- NULL } - - # Get the protocol and experiment and, when not on a dry run, create them if they do not exist - newProtocol <- FALSE - if (!useExisting) { - protocol <- getProtocolByNameAndFormat(protocolName = validatedMetaData$'Protocol Name'[1], configList, inputFormat) - newProtocol <- is.na(protocol[[1]]) - if (!newProtocol) { - metaData$'Protocol Name'[1] <- getPreferredProtocolName(protocol, validatedMetaData$'Protocol Name'[1]) - } - } - + # when not on a dry run, create protocol and experiment if they do not exist if (!dryRun && newProtocol && errorFree) { protocol <- createNewProtocol(metaData = validatedMetaData, lsTransaction, recordedBy) } - + useExistingExperiment <- inputFormat %in% c("Use Existing Experiment", "Precise For Existing Experiment") if (useExistingExperiment) { experiment <- getExperimentByCodeName(validatedMetaData$'Experiment Code Name'[1]) @@ -3046,7 +3057,12 @@ getPreviousExperimentCodes <- function(experiment) { previousExperimentCodes <- lapply(previousCodeValues, getElement, "codeValue") return(previousExperimentCodes) } - +getProtocolRequiredEntityCode <- function(protocol) { + metadataState <- getStatesByTypeAndKind(protocol, "metadata_protocol metadata")[[1]] + requiredEntities <- getValuesByTypeAndKind(metadataState, "codeValue_required entity type") + requiredEntityCodes <- lapply(requiredEntities, getElement, "codeValue") + return(requiredEntityCodes) +} translateClassToValueType <- function(x, reverse = F) { # translates Excel style Number formats to ACAS valueTypes (or reverse) valueTypeVector <- c("numericValue", "stringValue", "fileValue", "inlineFileValue", "urlValue", "dateValue", "clobValue", "blobValue", "codeValue") From a9ee604b6b257a8fd611a4a0d318202940d40029 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 25 Oct 2017 11:08:07 -0700 Subject: [PATCH 269/576] #328: Add better seperations between the entity type code identifier and the display name. Fix Aliquot to use the new entityType.code field to distinguish different LsContainers --- conf/ConfiguredEntityTypes.coffee | 44 ++++++++--------- .../routes/PreferredEntityCodeService.coffee | 49 ++++++++++--------- 2 files changed, 47 insertions(+), 46 deletions(-) diff --git a/conf/ConfiguredEntityTypes.coffee b/conf/ConfiguredEntityTypes.coffee index 8b49f5bef..2883a203f 100644 --- a/conf/ConfiguredEntityTypes.coffee +++ b/conf/ConfiguredEntityTypes.coffee @@ -1,45 +1,45 @@ -exports.entityTypes = - 'Corporate Parent ID': +exports.entityTypes = [ + code: 'Corporate Parent ID' type: 'compound' kind: 'parent name' codeOrigin: 'ACAS CmpdReg' displayName: 'Corporate Parent ID' sourceExternal: true parent: true - - 'Corporate Batch ID': + , + code: 'Corporate Batch ID' type: 'compound' kind: 'batch name' codeOrigin: 'ACAS CmpdReg' displayName: 'Corporate Batch ID' sourceExternal: true parent: false - - 'Protein Parent': + , + code: 'Protein Parent' type: 'parent' kind: 'protein' codeOrigin: 'ACAS LsThing' displayName: 'Protein Parent' sourceExternal: false parent: true - - 'Protein Batch': + , + code: 'Protein Batch' type: 'batch' kind: 'protein' codeOrigin: 'ACAS LsThing' displayName: 'Protein Batch' sourceExternal: false parent: false - - 'Gene ID': + , + code: 'Gene ID' type: 'gene' kind: 'entrez gene' codeOrigin: 'ACAS LsThing' displayName: 'Gene ID' sourceExternal: false parent: false - - 'Container Plate': + , + code: 'Container Plate' type: 'container' kind: 'plate' codeOrigin: 'ACAS LsContainer' @@ -47,8 +47,8 @@ exports.entityTypes = sourceExternal: false parent: false model: require("../routes/ServerUtilityFunctions.js").ContainerPlate - - 'Container Tube': + , + code: 'Container Tube' type: 'container' kind: 'tube' codeOrigin: 'ACAS LsContainer' @@ -56,8 +56,8 @@ exports.entityTypes = sourceExternal: false parent: false model: require("../routes/ServerUtilityFunctions.js").ContainerTube - - 'Definition Container Plate': + , + code: 'Definition Container Plate' type: 'definition container' kind: 'plate' codeOrigin: 'ACAS LsContainer' @@ -65,8 +65,8 @@ exports.entityTypes = sourceExternal: false parent: false model: require("../routes/ServerUtilityFunctions.js").DefinitionContainerPlate - - 'Definition Container Tube': + , + code: 'Definition Container Tube' type: 'definition container' kind: 'tube' codeOrigin: 'ACAS LsContainer' @@ -74,12 +74,12 @@ exports.entityTypes = sourceExternal: false parent: false model: require("../routes/ServerUtilityFunctions.js").DefinitionContainerTube - - 'Aliquot': + , + code: 'Aliquot' type: 'container' kind: 'tube' codeOrigin: 'ACAS LsContainer' - displayName: 'Aliquot' + displayName: 'Solution Aliquot' sourceExternal: false parent: false - +] diff --git a/modules/ServerAPI/src/server/routes/PreferredEntityCodeService.coffee b/modules/ServerAPI/src/server/routes/PreferredEntityCodeService.coffee index 96b526e25..94fe08c4d 100644 --- a/modules/ServerAPI/src/server/routes/PreferredEntityCodeService.coffee +++ b/modules/ServerAPI/src/server/routes/PreferredEntityCodeService.coffee @@ -31,11 +31,11 @@ exports.getConfiguredEntityTypesRoute = (req, resp) -> resp.json json exports.getConfiguredEntityTypes = (asCodes, callback) -> - console.log "asCodes: "+asCodes + console.debug "asCodes: "+asCodes if asCodes - codes = for own name, et of configuredEntityTypes.entityTypes - code: name - name: name + codes = for type in configuredEntityTypes.entityTypes + code: type.code + name: type.displayName ignored: false callback codes else @@ -49,6 +49,7 @@ exports.getSpecificEntityTypeRoute = (req, resp) -> exports.getSpecificEntityType = (displayName, callback) -> entityType = _.findWhere configuredEntityTypes.entityTypes, {displayName:displayName} + entityType ?= {} if callback? callback entityType else @@ -80,14 +81,22 @@ exports.referenceCodesRoute = (req, resp) -> resp.json json exports.referenceCodes = (requestData, csv, callback) -> - console.log "stubs mode is: "+global.specRunnerTestmode #Note specRunnerTestMode is handled within functions called from here - console.log("csv is " + csv) + console.debug "stubs mode is: "+global.specRunnerTestmode #Note specRunnerTestMode is handled within functions called from here + console.debug("csv is " + csv) # convert displayName to type and kind - exports.getSpecificEntityType requestData.displayName, (json) -> - requestData.type = json.type - requestData.kind = json.kind - requestData.sourceExternal = json.sourceExternal + entityType = exports.getSpecificEntityType requestData.displayName + if _.isEmpty entityType + #this is the fall-through for internal. External fall-through is in csUtilities.getExternalReferenceCodes + message = "problem with internal preferred Code request: code type and kind are unknown to system" + callback message + console.error message + return + else + console.debug 'not empty' + requestData.type = entityType.type + requestData.kind = entityType.kind + requestData.sourceExternal = entityType.sourceExternal if csv reqList = formatCSVRequestAsReqArray(requestData.entityIdStringLines) @@ -95,7 +104,7 @@ exports.referenceCodes = (requestData, csv, callback) -> reqList = requestData.requests if requestData.sourceExternal - console.log("looking up external entity") + console.debug("looking up external entity") csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFunctions.js' csUtilities.getExternalReferenceCodes requestData.displayName, reqList, (prefResp) -> if csv @@ -109,7 +118,6 @@ exports.referenceCodes = (requestData, csv, callback) -> return else # internal source - entityType = exports.getSpecificEntityType requestData.displayName if entityType.codeOrigin is "ACAS LsThing" preferredThingService = require "./ThingServiceRoutes.js" reqHashes = @@ -129,12 +137,11 @@ exports.referenceCodes = (requestData, csv, callback) -> displayName: requestData.displayName results: formatJSONReferenceCode(codeResponse.results, "referenceName") else if entityType.codeOrigin is "ACAS LsContainer" - console.log "entityType.codeOrigin is ACAS LsContainer" - console.log reqList - -# reqList = [reqList[0].requestName] + console.debug "entityType.codeOrigin is ACAS LsContainer" + console.debug reqList preferredContainerService = require "./InventoryServiceRoutes.js" - if requestData.displayName == "Aliquot" +# reqList = [reqList[0].requestName] + if entityType.code == "Aliquot" reqHashes = containerType: entityType.type containerKind: entityType.kind @@ -167,9 +174,6 @@ exports.referenceCodes = (requestData, csv, callback) -> containerKind: entityType.kind requests: reqList preferredContainerService.getContainerCodesFromNamesOrCodes reqHashes, (codeResponse) -> - console.log "codeResponse" - console.log codeResponse - console.log "sould be :#{csv}" if csv out = for res in codeResponse.results res.requestName + "," + res.referenceName @@ -182,10 +186,7 @@ exports.referenceCodes = (requestData, csv, callback) -> displayName: requestData.displayName results: formatJSONReferenceCode(codeResponse.results, "referenceName") return - #this is the fall-through for internal. External fall-through is in csUtilities.getExternalReferenceCodes - message = "problem with internal preferred Code request: code type and kind are unknown to system" - callback message - console.error message + #################################################################### # BEST LABELS From 627bb11f5b7d2b4d35ec93ae5358fd17adb33e2a Mon Sep 17 00:00:00 2001 From: John McNeil Date: Wed, 25 Oct 2017 13:39:26 -0700 Subject: [PATCH 270/576] Barcode SEL preprocessor is feature complete --- .../ACASBarcodeSELPreprocessorRoutes.coffee | 43 ++++++++++--------- 1 file changed, 23 insertions(+), 20 deletions(-) diff --git a/modules/ACASBarcodeSELPreprocessor/src/server/routes/ACASBarcodeSELPreprocessorRoutes.coffee b/modules/ACASBarcodeSELPreprocessor/src/server/routes/ACASBarcodeSELPreprocessorRoutes.coffee index 8d2c4dcd5..fac6545d0 100644 --- a/modules/ACASBarcodeSELPreprocessor/src/server/routes/ACASBarcodeSELPreprocessorRoutes.coffee +++ b/modules/ACASBarcodeSELPreprocessor/src/server/routes/ACASBarcodeSELPreprocessorRoutes.coffee @@ -33,6 +33,9 @@ exports.parseSEL = (req, resp) -> replyData.hasError = true replyData.errorMessages.push errorLevel: "error", message: msg + if replyData.results.htmlSummary == "" + replyData.results.htmlSummary = "Proproccesor Errors:
        " + replyData.results.htmlSummary += "#{msg}
        " infilePath = path.join ACAS_HOME, config.all.server.datafiles.relative_path, selData.fileToParse fs.readFile infilePath, 'utf8', (err, selFile) -> @@ -41,6 +44,7 @@ exports.parseSEL = (req, resp) -> resp.json replyData return + selFile = selFile.replace '\n', '' inLines = selFile.split '\r' outLines = [] barcodesToSub = [] @@ -51,24 +55,23 @@ exports.parseSEL = (req, resp) -> for line in inLines console.log line cells = line.split ',' - if foundBarcodeHeader && !foundRawResultsHeader - if cells[0].trim() != "" - barcodesToSub.push cells[0].trim() - linesToSub.push = cells - else - outLines.push cells.join ',' - else if foundRawResultsHeader - rawLines.push = line - else if !foundBarcodeHeader - outLines.push line - else + if !foundBarcodeHeader && !foundRawResultsHeader if cells[0].trim() == "Barcode" foundBarcodeHeader = true - cells[0] == "Corporate Batch ID" + cells[0] = "Corporate Batch ID" outLines.push cells.join ',' - else if cells[0].trim() == "Raw Results" + else + outLines.push line + else if !foundRawResultsHeader + if cells[0].trim() == "Raw Results" foundRawResultsHeader = true rawLines.push line + else + if cells[0].trim() != "" + barcodesToSub.push cells[0].trim() + linesToSub.push cells + else + rawLines.push line if !foundBarcodeHeader addError "Expected to find left-hand cell containing the word \"Barcode\"" @@ -84,11 +87,13 @@ exports.parseSEL = (req, resp) -> batches = {} for well in wells - wellInfo = wells[0]?.wellContent[0] + wellInfo = well.wellContent[0] + console.log wellInfo if wellInfo?.batchCode? and wellInfo.batchCode != "" - batches[wellInfo.barcode] = wellInfo.batchCode + console.log "batchCode "+wellInfo.batchCode + batches[well.label] = wellInfo.batchCode else - addError "Could not find lot/bath name for barcode #{wellInfo.barcode}" + addError "Could not find lot/batch name for barcode #{well.label}" if replyData.hasError resp.json replyData return @@ -96,12 +101,10 @@ exports.parseSEL = (req, resp) -> console.log batches for line in linesToSub line[0] = batches[line[0]] + console.log line outLines.push line.join ',' - outLines.push rawLines - console.log "number of lines: "+outLines.length - - outFile = outLines.join '\r\n' + outFile = outLines.join '\n' outFileName = selData.fileToParse.slice(0, -4) + "_converted.csv" outFilePath = path.join ACAS_HOME, config.all.server.datafiles.relative_path, outFileName fs.writeFile outFilePath, outFile, 'utf8', (err) -> From ae2532f3b74aba787742c48b720ab494644ee909 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Wed, 25 Oct 2017 14:33:42 -0700 Subject: [PATCH 271/576] Fixes #333 cleaned up log statements --- .../server/routes/ACASBarcodeSELPreprocessorRoutes.coffee | 7 ------- 1 file changed, 7 deletions(-) diff --git a/modules/ACASBarcodeSELPreprocessor/src/server/routes/ACASBarcodeSELPreprocessorRoutes.coffee b/modules/ACASBarcodeSELPreprocessor/src/server/routes/ACASBarcodeSELPreprocessorRoutes.coffee index fac6545d0..f174de04f 100644 --- a/modules/ACASBarcodeSELPreprocessor/src/server/routes/ACASBarcodeSELPreprocessorRoutes.coffee +++ b/modules/ACASBarcodeSELPreprocessor/src/server/routes/ACASBarcodeSELPreprocessorRoutes.coffee @@ -53,7 +53,6 @@ exports.parseSEL = (req, resp) -> foundBarcodeHeader = false foundRawResultsHeader = false for line in inLines - console.log line cells = line.split ',' if !foundBarcodeHeader && !foundRawResultsHeader if cells[0].trim() == "Barcode" @@ -78,7 +77,6 @@ exports.parseSEL = (req, resp) -> resp.json replyData return - console.log barcodesToSub inventoryServices.getWellContentByContainerLabelsInternal barcodesToSub, 'container', 'tube', 'barcode', 'barcode', (wells, wellStatusCode) -> if wellStatusCode != 200 addError "There was a problem looking up the barcodes" @@ -88,9 +86,7 @@ exports.parseSEL = (req, resp) -> batches = {} for well in wells wellInfo = well.wellContent[0] - console.log wellInfo if wellInfo?.batchCode? and wellInfo.batchCode != "" - console.log "batchCode "+wellInfo.batchCode batches[well.label] = wellInfo.batchCode else addError "Could not find lot/batch name for barcode #{well.label}" @@ -98,10 +94,8 @@ exports.parseSEL = (req, resp) -> resp.json replyData return - console.log batches for line in linesToSub line[0] = batches[line[0]] - console.log line outLines.push line.join ',' outFile = outLines.join '\n' @@ -114,6 +108,5 @@ exports.parseSEL = (req, resp) -> return selData.fileToParse = outFileName - console.log selData serverUtilityFunctions.runRFunctionOutsideRequest selData.user, selData, "src/r/GenericDataParser/generic_data_parser.R", "parseGenericData", (rReturn) -> resp.end rReturn From 7262c946cb5ca0e0ea365ba145b2011fde74aee5 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 25 Oct 2017 16:38:49 -0700 Subject: [PATCH 272/576] Fixed iframe url to be docroot relative instead of absolute path to localhost:3000. Fixes #336 --- modules/CmpdReg/src/client/src/MetaLot.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/CmpdReg/src/client/src/MetaLot.js b/modules/CmpdReg/src/client/src/MetaLot.js index 434ebc523..43dd72a21 100755 --- a/modules/CmpdReg/src/client/src/MetaLot.js +++ b/modules/CmpdReg/src/client/src/MetaLot.js @@ -232,7 +232,7 @@ $(function() { console.log("about to load inventory"); console.log(window.configuration.metaLot.showLotInventory); if (window.configuration.metaLot.showLotInventory) { - this.$('.bv_lotInventory').append("") + this.$('.bv_lotInventory').append("") } } From 2cfc2cd5d8057d49475af6963db99409b972d9f0 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 25 Oct 2017 16:40:33 -0700 Subject: [PATCH 273/576] Switched empty mols to set mol = null instead of to empty string in RegistrationSearch. Only switched it here because SearchForm is already working as expected. Fixes #335 --- modules/CmpdReg/src/client/src/RegistrationSearch.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/CmpdReg/src/client/src/RegistrationSearch.js b/modules/CmpdReg/src/client/src/RegistrationSearch.js index 8bd6e3b99..39bde9fef 100755 --- a/modules/CmpdReg/src/client/src/RegistrationSearch.js +++ b/modules/CmpdReg/src/client/src/RegistrationSearch.js @@ -108,9 +108,9 @@ $(function() { if (this.useMarvin) { this.marvinSketcherInstance.exportStructure(this.exportFormat).then(function (molecule) { if (molecule.indexOf("0 0 0 0 0 0 0 0 0 0999") > -1) - mol = ''; + mol = null; else if (molecule.indexOf("M V30 COUNTS 0 0 0 0 0") > -1) - mol = ''; + mol = null; else mol = molecule; regSearch.set({ From e9b4f572accca11bfb066a6401cc9548abc4fc99 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 25 Oct 2017 16:50:13 -0700 Subject: [PATCH 274/576] Fixed three instances of sketcher not checking for mol V3000 empty mol. Fixes #11 --- modules/CmpdReg/src/client/src/EditParent.js | 2 ++ modules/CmpdReg/src/client/src/Salt.js | 2 ++ modules/CmpdReg/src/client/src/SaltForm.js | 2 ++ 3 files changed, 6 insertions(+) diff --git a/modules/CmpdReg/src/client/src/EditParent.js b/modules/CmpdReg/src/client/src/EditParent.js index b245f08ed..218998dab 100644 --- a/modules/CmpdReg/src/client/src/EditParent.js +++ b/modules/CmpdReg/src/client/src/EditParent.js @@ -101,6 +101,8 @@ $(function () { this.marvinSketcherInstance.exportStructure(this.exportFormat).then(function (molecule) { if (molecule.indexOf("0 0 0 0 0 0 0 0 0 0999") > -1) mol = null; + else if (molecule.indexOf("M V30 COUNTS 0 0 0 0 0") > -1) + mol = null; else mol = molecule; editParentSearch.set({ diff --git a/modules/CmpdReg/src/client/src/Salt.js b/modules/CmpdReg/src/client/src/Salt.js index 943c17daf..40a8b7a74 100755 --- a/modules/CmpdReg/src/client/src/Salt.js +++ b/modules/CmpdReg/src/client/src/Salt.js @@ -230,6 +230,8 @@ $(function() { if (molecule.indexOf("0 0 0 0 0 0 0 0 0 0999") > -1) mol = ''; + else if (molecule.indexOf("M V30 COUNTS 0 0 0 0 0") > -1) + mol = ''; else mol = molecule; self.exportStructComplete = true; // for spec support diff --git a/modules/CmpdReg/src/client/src/SaltForm.js b/modules/CmpdReg/src/client/src/SaltForm.js index 1d9ebd484..77c5a6042 100755 --- a/modules/CmpdReg/src/client/src/SaltForm.js +++ b/modules/CmpdReg/src/client/src/SaltForm.js @@ -167,6 +167,8 @@ $(function() { this.marvinSketcherInstance.exportStructure(this.exportFormat).then(function (molecule) { if (molecule.indexOf("0 0 0 0 0 0 0 0 0 0999") > -1) mol = ''; + else if (molecule.indexOf("M V30 COUNTS 0 0 0 0 0") > -1) + mol = ''; else mol = molecule; self.model.set({molStructure: mol}); From 70fba5f8274a9b2d953b4aa4f12450ea8004e311 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 26 Oct 2017 13:06:54 -0700 Subject: [PATCH 275/576] Fixed typo in one case of author services. Fixes #341 --- modules/ServerAPI/src/server/routes/AuthorRoutes.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee index e69d78ddc..3ef80654c 100644 --- a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee @@ -767,7 +767,7 @@ checkIfEmailHasChangedAndIsUnique = (author, savedAuthor, callback) -> if author.emailAddress == savedAuthor.emailAddress callback null else - checkEmailIsUnique author (err, isUnique) -> + checkEmailIsUnique author, (err, isUnique) -> if err? callback err else if isUnique From c6a68a5b66c7c8fa66813aa4aadb18918929aea8 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Thu, 26 Oct 2017 16:11:11 -0700 Subject: [PATCH 276/576] feature/protocol-editor-add-required-entity-type-select: Add configs for showing and requiring value for Required Entity Type select list in protocol editor, fixes issue #344 --- conf/config.properties.example | 5 +++ .../ServerAPI/conf/ProtocolConfJSON.coffee | 3 ++ modules/ServerAPI/src/client/Protocol.coffee | 44 +++++++++++++++++++ modules/ServerAPI/src/client/Protocol.html | 7 +++ 4 files changed, 59 insertions(+) diff --git a/conf/config.properties.example b/conf/config.properties.example index 8db34cb77..c01efb9bb 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -556,5 +556,10 @@ client.roles.crossProjectLoaderRole=ROLE_ACAS-CROSS-PROJECT-LOADER # For whether protocols and experiments should have sequential user defined corpName labels client.entity.saveInitialsCorpName=false +# Whether to show the Required Entity Type GUI picklist +client.protocol.requiredEntityType.save=false +# Whether the required entity type is a required field +client.protocol.requiredEntityType.allowEmpty=true + client.compoundInventory.enforceUppercaseBarcodes=false client.compoundInventory.daughterVials.strictMatchPhysicalState=false diff --git a/modules/ServerAPI/conf/ProtocolConfJSON.coffee b/modules/ServerAPI/conf/ProtocolConfJSON.coffee index 97bd4f053..d5a5764e1 100644 --- a/modules/ServerAPI/conf/ProtocolConfJSON.coffee +++ b/modules/ServerAPI/conf/ProtocolConfJSON.coffee @@ -139,6 +139,9 @@ , typeName: "codeValue" kindName: "model fit transformation units" + , + typeName: "codeValue" + kindName: "required entity type" ] labeltypes: diff --git a/modules/ServerAPI/src/client/Protocol.coffee b/modules/ServerAPI/src/client/Protocol.coffee index 3b2354491..1d21913b9 100644 --- a/modules/ServerAPI/src/client/Protocol.coffee +++ b/modules/ServerAPI/src/client/Protocol.coffee @@ -49,6 +49,16 @@ class window.Protocol extends BaseEntity assayStage + getRequiredEntityType: -> + requiredEntityType = @.get('lsStates').getOrCreateValueByTypeAndKind "metadata", "protocol metadata", "codeValue", "required entity type" + if requiredEntityType.get('codeValue') is undefined or requiredEntityType.get('codeValue') is "" or requiredEntityType.get('codeValue') is null + requiredEntityType.set codeValue: "unassigned" + requiredEntityType.set codeType: "entity type" + requiredEntityType.set codeKind: "required entity type" + requiredEntityType.set codeOrigin: "ACAS Configured Entity" + + requiredEntityType + getAssayPrinciple: -> assayPrinciple = @.get('lsStates').getOrCreateValueByTypeAndKind "metadata", "protocol metadata", "clobValue", "assay principle" if assayPrinciple.get('clobValue') is undefined @@ -113,6 +123,13 @@ class window.Protocol extends BaseEntity errors.push attribute: 'assayTreeRule' message: "Assay tree rule should not end with '/'" + if window.conf.protocol?.requiredEntityType?.save? and window.conf.protocol.requiredEntityType.save + if window.conf.protocol?.requiredEntityType?.allowEmpty? and window.conf.protocol.requiredEntityType.allowEmpty is false + ret = @getRequiredEntityType().get('codeValue') + if ret is "unassigned" or ret is undefined or ret is "" or ret is null + errors.push + attribute: 'requiredEntityType' + message: "Required entity type must be set" if window.conf.protocol?.showCurveDisplayParams? showCurveDisplayParams = window.conf.protocol.showCurveDisplayParams else @@ -161,6 +178,7 @@ class window.ProtocolBaseController extends BaseEntityController "keyup .bv_protocolName": "handleNameChanged" "keyup .bv_assayTreeRule": "handleAssayTreeRuleChanged" "change .bv_assayStage": "handleAssayStageChanged" + "change .bv_requiredEntityType": "handleRequiredEntityTypeChanged" "change .bv_projectCode": "handleProjectCodeChanged" "keyup .bv_assayPrinciple": "handleAssayPrincipleChanged" "change .bv_creationDate": "handleCreationDateChanged" @@ -272,6 +290,13 @@ class window.ProtocolBaseController extends BaseEntityController @$('.bv_minY').val(@model.getCurveDisplayMin().get('numericValue')) else @$('.bv_group_curveDisplayWrapper').hide() + showRequiredEntityType = false + if window.conf.protocol?.requiredEntityType?.save? + showRequiredEntityType = window.conf.protocol.requiredEntityType.save + if showRequiredEntityType + @setupRequiredEntityType() + else + @$('.bv_group_requiredEntityType').hide() super() @ @@ -304,6 +329,21 @@ class window.ProtocolBaseController extends BaseEntityController name: "Select Assay Stage" selectedCode: @model.getAssayStage().get('codeValue') + setupRequiredEntityType: -> + if window.conf.protocol?.requiredEntityType?.allowEmpty? and window.conf.protocol.requiredEntityType.allowEmpty is false + @$('.bv_requiredEntityTypeLabel').html '*Required Entity Type' + else + @$('.bv_requiredEntityTypeLabel').html 'Required Entity Type' + @requiredEntityTypeList = new PickListList() + @requiredEntityTypeList.url = "/api/entitymeta/configuredEntityTypes/displayName?asCodes=true" + @requiredEntityTypeListController = new PickListSelectController + el: @$('.bv_requiredEntityType') + collection: @requiredEntityTypeList + insertFirstOption: new PickList + code: "unassigned" + name: "Select Entity Type" + selectedCode: @model.getRequiredEntityType().get('codeValue') + setupProjectSelect: -> @projectList = new PickListList() @projectList.url = "/api/projects" @@ -419,6 +459,10 @@ class window.ProtocolBaseController extends BaseEntityController value = @assayStageListController.getSelectedCode() @handleValueChanged "AssayStage", value + handleRequiredEntityTypeChanged: => + value = @requiredEntityTypeListController.getSelectedCode() + @handleValueChanged "RequiredEntityType", value + handleProjectCodeChanged: => value = @projectListController.getSelectedCode() @handleValueChanged "ProjectCode", value diff --git a/modules/ServerAPI/src/client/Protocol.html b/modules/ServerAPI/src/client/Protocol.html index 292ed55ca..6c0589db1 100644 --- a/modules/ServerAPI/src/client/Protocol.html +++ b/modules/ServerAPI/src/client/Protocol.html @@ -84,6 +84,13 @@
        +
        + +
        + +
        +
        +
        From 53d7da2a77308c684466c5577797eb08cf99d8b9 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 26 Oct 2017 16:21:09 -0700 Subject: [PATCH 277/576] #329: Guard against NA, "", and "unassigned" --- modules/GenericDataParser/src/server/generic_data_parser.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index e6452fede..4dae3efe8 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -2833,7 +2833,7 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, if(!newProtocol) { requiredMainCode <- getProtocolRequiredEntityCode(protocol) - if(length(requiredMainCode) > 0) { + if(length(requiredMainCode) > 0 && !is.na(requiredMainCode) && requiredMainCode != "" && requiredMainCode != "unassigned") { requiredMainCode <- requiredMainCode[[1]] if(mainCode != requiredMainCode) { warnUser(paste0("'",metaData$'Protocol Name'[1],"' requires an entity type of '",requiredMainCode,"'. Please update your file with this entity type instead of the entity type '",mainCode,"'")) From 2a1700d3d831d206eae315657a950b54a3dea3f4 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 26 Oct 2017 16:38:34 -0700 Subject: [PATCH 278/576] #328: changing the code of 'Aliquot' to the more descriptive 'Solution Container Tube' --- conf/ConfiguredEntityTypes.coffee | 2 +- .../src/server/routes/PreferredEntityCodeService.coffee | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/ConfiguredEntityTypes.coffee b/conf/ConfiguredEntityTypes.coffee index 2883a203f..645de3a40 100644 --- a/conf/ConfiguredEntityTypes.coffee +++ b/conf/ConfiguredEntityTypes.coffee @@ -75,7 +75,7 @@ exports.entityTypes = [ parent: false model: require("../routes/ServerUtilityFunctions.js").DefinitionContainerTube , - code: 'Aliquot' + code: 'Solution Container Tube' type: 'container' kind: 'tube' codeOrigin: 'ACAS LsContainer' diff --git a/modules/ServerAPI/src/server/routes/PreferredEntityCodeService.coffee b/modules/ServerAPI/src/server/routes/PreferredEntityCodeService.coffee index 94fe08c4d..8132b1260 100644 --- a/modules/ServerAPI/src/server/routes/PreferredEntityCodeService.coffee +++ b/modules/ServerAPI/src/server/routes/PreferredEntityCodeService.coffee @@ -141,7 +141,7 @@ exports.referenceCodes = (requestData, csv, callback) -> console.debug reqList preferredContainerService = require "./InventoryServiceRoutes.js" # reqList = [reqList[0].requestName] - if entityType.code == "Aliquot" + if entityType.code == "Solution Container Tube" reqHashes = containerType: entityType.type containerKind: entityType.kind From 8b6e31aa7bb6e528eb7fdc4d944848191e4d622f Mon Sep 17 00:00:00 2001 From: John McNeil Date: Sat, 28 Oct 2017 17:55:22 -0700 Subject: [PATCH 279/576] Fixes #351 numeric form field rounding interfered with input --- .../src/client/ACASFormFields.coffee | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 05268ea7f..a8c06ef9c 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -193,6 +193,10 @@ class window.ACASFormLSNumericValueFieldController extends ACASFormAbstractField template: _.template($("#ACASFormLSNumericValueFieldView").html()) + initialize: -> + super() + @userInputEvent = false + applyOptions: -> super() if @options.toFixed? @@ -214,6 +218,7 @@ class window.ACASFormLSNumericValueFieldController extends ACASFormAbstractField value: numVal ignored: false super() + @userInputEvent = false setEmptyValue: -> @getModel().set @@ -224,13 +229,14 @@ class window.ACASFormLSNumericValueFieldController extends ACASFormAbstractField @$('.bv_number').val inputValue renderModelContent: => - if @toFixed? and @getModel().get('value')? - if !isNaN @getModel().get('value') - @$('.bv_number').val @getModel().get('value').toFixed(@toFixed) + unless @userInputEvent + if @toFixed? and @getModel().get('value')? + if !isNaN @getModel().get('value') + @$('.bv_number').val @getModel().get('value').toFixed(@toFixed) + else + @$('.bv_number').val "" else - @$('.bv_number').val "" - else - @$('.bv_number').val @getModel().get('value') + @$('.bv_number').val @getModel().get('value') if @getModel().has 'unitKind' @$('.bv_units').html @getModel().get('unitKind') From 1e120d5a2b776b5640d4cfe45fcf06e356a59bd1 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Sun, 29 Oct 2017 08:30:59 -0700 Subject: [PATCH 280/576] Fixes #353 added JQuery show/hide to location tree form field in addition to modal show/hide to fix issue where tree interferes with lot form editing even when hidden --- modules/Components/src/client/ACASFormLocationTree.coffee | 3 +++ 1 file changed, 3 insertions(+) diff --git a/modules/Components/src/client/ACASFormLocationTree.coffee b/modules/Components/src/client/ACASFormLocationTree.coffee index c9be5cb32..5892c1269 100644 --- a/modules/Components/src/client/ACASFormLocationTree.coffee +++ b/modules/Components/src/client/ACASFormLocationTree.coffee @@ -52,6 +52,7 @@ class window.ACASFormLocationTreeController extends ACASFormAbstractFieldControl super() handleEditIconClicked: => + @$('.bv_locationTreeModal').show() @$('.bv_locationTreeModal').modal backdrop: 'static' @getContainerLocationTree() @@ -64,6 +65,7 @@ class window.ACASFormLocationTreeController extends ACASFormAbstractFieldControl error: (err) => alert 'Could not get container location tree. Please contact administrator' @$('.bv_locationTreeModal').modal 'hide' + @$('.bv_locationTreeModal').hide() success: (json) => @setupTree (json) @@ -109,6 +111,7 @@ class window.ACASFormLocationTreeController extends ACASFormAbstractFieldControl handleUpdateLocationClicked: => selectedLocation = @$('.bv_locationTree').jstree('get_selected', true) @$('.bv_locationTreeModal').modal 'hide' + @$('.bv_locationTreeModal').hide() value = selectedLocation[0].original.id breadcrumb = selectedLocation[0].original.breadcrumb From bd46dc564de3bdede6160b6acfe27c71bafb63ab Mon Sep 17 00:00:00 2001 From: John McNeil Date: Mon, 30 Oct 2017 13:40:32 -0700 Subject: [PATCH 281/576] Fixes #355 where location tree filter input has error styling when form field shows error --- .../src/client/ACASFormLocationTree.coffee | 8 ++++++++ .../src/client/ACASFormLocationTreeView.html | 15 ++++++++------- 2 files changed, 16 insertions(+), 7 deletions(-) diff --git a/modules/Components/src/client/ACASFormLocationTree.coffee b/modules/Components/src/client/ACASFormLocationTree.coffee index 5892c1269..8f03adaf9 100644 --- a/modules/Components/src/client/ACASFormLocationTree.coffee +++ b/modules/Components/src/client/ACASFormLocationTree.coffee @@ -9,6 +9,8 @@ class window.ACASFormLocationTreeController extends ACASFormAbstractFieldControl "click .bv_searchClear": "handleSearchClear" "click .bv_updateLocation": "handleUpdateLocationClicked" + className: "" + template: _.template($("#ACASFormLocationTreeView").html()) initialize: -> @@ -37,6 +39,12 @@ class window.ACASFormLocationTreeController extends ACASFormAbstractFieldControl error: (err) => alert 'error getting breadcrumb for container' + render: => + super() + + @$('.bv_controlGroup').addClass "bv_group_"+@modelKey + @ + setEmptyValue: -> @getModel().set value: null diff --git a/modules/Components/src/client/ACASFormLocationTreeView.html b/modules/Components/src/client/ACASFormLocationTreeView.html index 0bdc50d13..bc5ebba29 100644 --- a/modules/Components/src/client/ACASFormLocationTreeView.html +++ b/modules/Components/src/client/ACASFormLocationTreeView.html @@ -1,13 +1,14 @@ diff --git a/modules/CurveAnalysis/src/client/DoseResponseFit.coffee b/modules/CurveAnalysis/src/client/DoseResponseFit.coffee index fb93ff47c..b39da5031 100644 --- a/modules/CurveAnalysis/src/client/DoseResponseFit.coffee +++ b/modules/CurveAnalysis/src/client/DoseResponseFit.coffee @@ -50,6 +50,7 @@ class window.DoseResponseFitController extends Backbone.View drapType = window[parametersClass] controllerClass = curveFitClasses.get 'parametersController' drapcType = window[controllerClass] + parametersOptions = curveFitClasses.get 'parametersOptions' else drapType = 'unassigned' @@ -59,9 +60,9 @@ class window.DoseResponseFitController extends Backbone.View else @$('.bv_fitModelButton').show() if @options? && @options.initialAnalysisParameters? - drap = new drapType @options.initialAnalysisParameters + drap = new drapType @options.initialAnalysisParameters, parametersOptions else - drap = new drapType() + drap = new drapType null, parametersOptions @parameterController = new drapcType el: @$('.bv_analysisParameterForm') model: drap From 10e6b5840897eb482de8b1b8912efcc91fae5b28 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 30 Nov 2017 12:40:09 -0800 Subject: [PATCH 327/576] #423: Protocols created via SEL should have scientist set Currently protocols created through SEL do not have a scientist value. It should be set to be the same as the scientist for the experiment created through SEL --- .../src/server/generic_data_parser.R | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 94f449701..4da50f2b6 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -1716,6 +1716,17 @@ createNewProtocol <- function(metaData, lsTransaction, recordedBy) { if (is.null(protocolStatus) || protocolStatus == "") { protocolStatus <- "created" } + + protocolValues[[length(protocolValues)+1]] <- createStateValue( + recordedBy = recordedBy, + lsType = "codeValue", + lsKind = "scientist", + codeValue = metaData$Scientist, + codeType = "assay", + codeKind = "scientist", + codeOrigin = racas::applicationSettings$client.scientistCodeOrigin, + lsTransaction= lsTransaction) + protocolValues[[length(protocolValues)+1]] <- createStateValue( recordedBy = recordedBy, lsType = "codeValue", From 73fbb70b5ac7809529f58367be545e319f5027b9 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 4 Dec 2017 16:00:24 -0800 Subject: [PATCH 328/576] Added new config client.moduleMenus.logoTextLink to make homepage ACAS button URL configurable. Resolves #419 --- conf/config.properties.example | 1 + modules/ModuleMenus/src/client/ModuleMenus.coffee | 2 ++ 2 files changed, 3 insertions(+) diff --git a/conf/config.properties.example b/conf/config.properties.example index 545c93967..a21c6879b 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -185,6 +185,7 @@ client.service.external.lotDetails.url=/cmpdreg/#lot/ # If module is customized and the ACAS header name needs to be replaced, you can set the following options client.moduleMenus.logoText=ACAS client.moduleMenus.logoImageFilePath= +client.moduleMenus.logoTextLink=/ client.moduleMenus.homePageMessage=Welcome to ACAS client.moduleMenus.copyrightMessage=© John McNeil & Company 2012-2017 # client.moduleMenus.menuConfigurationSettings=ModuleMenusConfiguration diff --git a/modules/ModuleMenus/src/client/ModuleMenus.coffee b/modules/ModuleMenus/src/client/ModuleMenus.coffee index 946e6ca6b..e0f3d2804 100644 --- a/modules/ModuleMenus/src/client/ModuleMenus.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenus.coffee @@ -48,6 +48,8 @@ class window.ModuleMenusController extends Backbone.View if window.conf.moduleMenus.logoImageFilePath? logoInfo = ''+logoInfo @$('.bv_headerName').html logoInfo + if window.conf.moduleMenus.logoTextLink? + @$('.bv_headerName').attr('href', window.conf.moduleMenus.logoTextLink) if window.conf.moduleMenus.homePageMessage? @$('.bv_homePageMessage').html(window.conf.moduleMenus.homePageMessage) if window.conf.moduleMenus.copyrightMessage? From c6b64896e08ee1e29a060ed9038e6cb7b24e304b Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Fri, 8 Dec 2017 13:42:39 -0800 Subject: [PATCH 329/576] Rc/1.12.0: fixed bug in rendering unregistered entities for printing --- modules/ServerAPI/src/server/routes/index.coffee | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/index.coffee b/modules/ServerAPI/src/server/routes/index.coffee index b5afd7c0f..398c3c049 100644 --- a/modules/ServerAPI/src/server/routes/index.coffee +++ b/modules/ServerAPI/src/server/routes/index.coffee @@ -53,14 +53,16 @@ exports.toPrint = (req, res, moduleLaunchParams) -> console.log "toPrint" console.log req.query.moduleName console.log req.query.controller - #TODO: on redirect, pass in moduleName and code. Hardcoded right now. + unregistered = req.query.unregistered + if typeof unregistered is "string" + unregistered = (unregistered.toLowerCase() is "true") moduleLaunchParams = moduleName: req.query.moduleName code: req.params.code copy: false createFromOtherEntity: false print: true - unregistered: req.query.unregistered + unregistered: unregistered console.log "moduleLaunchParams" console.log moduleLaunchParams From e2877a720765f93e185aa86543461bd5d72ab515 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 12 Dec 2017 11:01:04 -0800 Subject: [PATCH 330/576] fixes #430: Curve curator doesn't fire a refit a when Smart mode is deselected --- modules/CurveAnalysis/src/client/DoseResponseAnalysis.coffee | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/CurveAnalysis/src/client/DoseResponseAnalysis.coffee b/modules/CurveAnalysis/src/client/DoseResponseAnalysis.coffee index 91ec19be8..f76bb53e0 100755 --- a/modules/CurveAnalysis/src/client/DoseResponseAnalysis.coffee +++ b/modules/CurveAnalysis/src/client/DoseResponseAnalysis.coffee @@ -101,7 +101,7 @@ class window.DoseResponseAnalysisParameters extends Backbone.Model errors.push attribute: 'theoreticalMax' message: "Theoretical max value must be set to a number" - if (_.isNaN(attrs.baseline.get('value')) or attrs.baseline.get('value') == null) + if (attrs.smartMode && (_.isNaN(attrs.baseline.get('value')) or attrs.baseline.get('value') == null)) errors.push attribute: 'baseline' message: "Baseline value must be set to a number" @@ -185,7 +185,6 @@ class window.DoseResponseAnalysisParametersController extends AbstractFormContro @$('.bv_theoreticalMax').attr 'disabled', 'disabled' @$('.bv_theoreticalMax').val "" @$('.bv_baseline').attr 'disabled', 'disabled' - @$('.bv_baseline').val "" @attributeChanged() From b3d3d69547a79a4fa5969f229699c4776f9cbed3 Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Thu, 14 Dec 2017 16:09:12 -0800 Subject: [PATCH 331/576] Rc/1.12.0: added config for which protocol clobValues from protocol metadata state are copied over to experiments --- conf/config.properties.example | 3 ++ .../ServerAPI/src/client/Experiment.coffee | 29 +++++++++++++++++-- 2 files changed, 29 insertions(+), 3 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 7995342f3..5f45a2a1b 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -534,3 +534,6 @@ client.roles.crossProjectLoaderRole=ROLE_ACAS-CROSS-PROJECT-LOADER # For whether protocols and experiments should have sequential user defined corpName labels client.entity.saveInitialsCorpName=false + +# For which protocol clobValues from protocol metadata state are copied over to experiments +client.experiment.copiedProtocolMetadataAttrs= \ No newline at end of file diff --git a/modules/ServerAPI/src/client/Experiment.coffee b/modules/ServerAPI/src/client/Experiment.coffee index 678442dc4..83a6822ef 100644 --- a/modules/ServerAPI/src/client/Experiment.coffee +++ b/modules/ServerAPI/src/client/Experiment.coffee @@ -45,15 +45,22 @@ class window.Experiment extends BaseEntity resp copyProtocolAttributes: (protocol) => -#only need to copy protocol's experiment metadata attributes + #copy protocol's experiment metadata attributes + #copy protocol values from protocol metadata state as defined in config + if window.conf.experiment?.copiedProtocolMetadataAttrs? + protocolMetaAttrsToCopy = window.conf.experiment.copiedProtocolMetadataAttrs + protocolMetaAttrsToCopy = protocolMetaAttrsToCopy.split "," + else + protocolMetaAttrsToCopy = [] + pstates = protocol.get('lsStates') pExptMeta = pstates.getStatesByTypeAndKind "metadata", "experiment metadata" + eExptMeta = @.get('lsStates').getStatesByTypeAndKind "metadata", "experiment metadata" if pExptMeta.length > 0 - eExptMeta = @.get('lsStates').getStatesByTypeAndKind "metadata", "experiment metadata" if eExptMeta.length > 0 dapVal = eExptMeta[0].getValuesByTypeAndKind "clobValue", "data analysis parameters" if dapVal.length > 0 -#mark existing data analysis parameters, model fit parameters, and model fit type as ignored + #mark existing data analysis parameters, model fit parameters, and model fit type as ignored if dapVal[0].isNew() eExptMeta[0].get('lsValues').remove dapVal[0] else @@ -109,6 +116,22 @@ class window.Experiment extends BaseEntity mftu.unset 'lsTransaction' eExptMeta[0].get('lsValues').add mftu + pMetaState = pstates.getStatesByTypeAndKind "metadata", "protocol metadata" + if pMetaState.length > 0 + _.each protocolMetaAttrsToCopy, (pma) => + unless eExptMeta.length > 0 + eExptMeta = [@.get('lsStates').getOrCreateStateByTypeAndKind("metadata", "experiment metadata")] + pmaVal = eExptMeta[0].getValuesByTypeAndKind "clobValue", pma + if pmaVal.length > 0 + if pmaVal[0].isNew() + eExptMeta[0].get('lsValues').remove pmaVal[0] + else + pmaVal[0].set ignored: true + newVal = new Value(_.clone(pstates.getOrCreateValueByTypeAndKind "metadata", "protocol metadata", "clobValue", pma).attributes) + newVal.unset 'id' + newVal.unset 'lsTransaction' + eExptMeta[0].get('lsValues').add newVal + # commented because experiment base does not have these values # @getDryRunStatus().set ignored: true # @getDryRunStatus().set codeValue: 'not started' From 5b3c635b9dbfd2856042aaceb210ff8705cadcf0 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 14 Dec 2017 17:39:12 -0800 Subject: [PATCH 332/576] Set sensible defaults for new configs in config.properties.example, removed duplicate config, and reorganized related new configs to be together. Set sensible defaults for configuration.json and synced changes from client configuration.json and server. --- conf/config.properties.example | 19 +- .../src/client/custom/configuration.json | 207 ++++++++++-------- 2 files changed, 123 insertions(+), 103 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index a21c6879b..648d741a1 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -339,11 +339,6 @@ server.service.external.inventory.database.name= server.service.external.inventory.database.username= server.service.external.inventory.database.password= -client.compoundInventory.enforceUppercaseBarcodes=false -client.compoundInventory.rootLocationLabel=COMPANY -client.compoundInventory.trashLocationLabel=trash -client.compoundInventory.benchesLocationLabel=Benches - ## options for auth. strategy are: properties, database, ldap server.security.authstrategy=database #server.security.properties.path=/opt/seurat/SeuratServer/users.txt @@ -352,7 +347,7 @@ client.security.authstrategy=${server.security.authstrategy} #Controls whether Roo syncs the AuthorRole table with authorities granted in LDAP server.security.syncLdapAuthRoles=false -#to make authstrategy config accessible to the client +#to make syncLdapAuthRoles config accessible to the client client.security.syncLdapAuthRoles=${server.security.syncLdapAuthRoles} client.scientistCodeOrigin=ACAS authors client.molecularTargetCodeOrigin=ACAS DDICT @@ -448,8 +443,8 @@ client.protocol.showCurveDisplayParams=true client.experiment.uneditableFileTypes=["source file", "annotation file"] #Controls privileges for who can create/edit and delete authors -client.author.editingRoles= -client.author.deletingRoles= +client.author.editingRoles=ROLE_ACAS-ADMINS +client.author.deletingRoles=ROLE_ACAS-ADMINS # Default status for experiments loaded thorugh experiment loader server.sel.experimentStatus=approved @@ -571,8 +566,14 @@ client.protocol.requiredEntityType.save=false # Whether the required entity type is a required field client.protocol.requiredEntityType.allowEmpty=true +#Compound Inventory configs client.compoundInventory.enforceUppercaseBarcodes=false +#Default location tree labels +client.compoundInventory.rootLocationLabel=COMPANY +client.compoundInventory.trashLocationLabel=trash +client.compoundInventory.benchesLocationLabel=Benches +#Disallow loading daughter vials with different physical state than the parent vial client.compoundInventory.daughterVials.strictMatchPhysicalState=false # Whether to save location as a codeValue or as a full location interaction -client.compoundInventory.saveLocationAsCodeValue=false +client.compoundInventory.saveLocationAsCodeValue=true diff --git a/modules/CmpdReg/src/client/custom/configuration.json b/modules/CmpdReg/src/client/custom/configuration.json index cb3e1638f..8fa528ae4 100755 --- a/modules/CmpdReg/src/client/custom/configuration.json +++ b/modules/CmpdReg/src/client/custom/configuration.json @@ -1,15 +1,16 @@ { - "serverConnection": { - "connectToServer": true, - "baseServerURL": "/cmpdreg/", - "logoutURL": "/logout", - "acasURL": "http://localhost:8080/acas/api/v1/" - }, - "clientUILabels": { - "corpNameLabel": "CMPD Number", - "applicationNameForTitleBar": "ACAS Compound Registration", - "commonNameLabel": "Original ID:" - }, + "serverConnection": { + "connectToServer": true, + "baseServerURL": "/cmpdreg/", + "logoutURL": "/logout", + "acasURL": "http://localhost:8080/acas/api/v1/", + "acasAppURL": "http://localhost:3001/api/" + }, + "clientUILabels": { + "corpNameLabel": "CMPD Number", + "applicationNameForTitleBar": "ACAS Compound Registration", + "commonNameLabel": "Original ID:" + }, "ketcher": true, "regSearchResults": { "hideVirtualOption": false @@ -17,96 +18,114 @@ "searchForm": { "defaultMaxResults": 100 }, - "metaLot": { - "saltBeforeLot": false, - "lotCalledBatch": false, - "showBuid": false, - "includeAbbrevInIsoSaltOption": true, - "saltListNoneOption": "A: none", - "isotopeListNoneOption": "A: none", - "sortSaltsByAbbrev": true, - "sortIsotopesByAbbrev": true, - "showSelectCategoryOption": true, - "showSelectCompoundTypeOption": true, - "showSelectParentAnnotationOption": true, - "showSelectCompoundTypeList": false, - "showSelectParentAnnotationList": false, - "fileSaveDirNamedForBatchName": true, - "useExactMass": true, + "metaLot": { + "saltBeforeLot": false, + "lotCalledBatch": false, + "showBuid": false, + "includeAbbrevInIsoSaltOption": true, + "saltListNoneOption": "A: none", + "isotopeListNoneOption": "A: none", + "sortSaltsByAbbrev": true, + "sortIsotopesByAbbrev": true, + "showSelectCategoryOption": true, + "showSelectCompoundTypeOption": true, + "showSelectParentAnnotationOption": true, + "showSelectCompoundTypeList": false, + "showSelectParentAnnotationList": false, + "fileSaveDirNamedForBatchName": true, + "useExactMass": true, "useProjectRolesToRestrictLotDetails": false, "showTareWeight": false, "showTotalAmountStored": false, "disableAliasEdit": false, - "showLotInventory": true, + "showLotInventory": false, "disableEditMyLots": false - }, - "serverSettings": { + }, + "serverSettings": { "corpPrefix": "CMPD", - "corpSeparator": "-", - "saltSeparator": "", - "batchSeparator": "-", - "numberCorpDigits": 7, - "formatBatchDigits": 2, - "startingCorpNumber": 0, - "fancyCorpNumberFormat": false, - "corpParentFormat": "standard", - "corpBatchFormat": "corp_batch_saltcode", - "appendSaltCodeToLotName": true, - "noSaltCode": "A", - "usePredefinedList": false, - "newUserIsChemist": false, - "uniqueNotebook": false, - "notebookSavePath": "/opt/cmpdreg/noteBookFiles/noteBook/", - "exactMatchDef": "DUPLICATE_TAUTOMER", - "maxSearchTime": 180000, - "maxSearchResults": 5000, - "unitTestDB": true, - "initalDBLoad": true, - "compoundInventory": true, - "checkACASDependenciesByBarcode": false, - "projectRestrictions": false, - "jchemVersion": "16.4.25.0", + "corpSeparator": "-", + "saltSeparator": "", + "batchSeparator": "-", + "numberCorpDigits": 7, + "formatBatchDigits": 3, + "startingCorpNumber": 0, + "fancyCorpNumberFormat": false, + "corpParentFormat": "standard", + "corpBatchFormat": "corp_batch_saltcode", + "appendSaltCodeToLotName": true, + "noSaltCode": "", + "usePredefinedList": false, + "newUserIsChemist": false, + "uniqueNotebook": false, + "notebookSavePath": "/opt/cmpdreg/noteBookFiles/noteBook/", + "exactMatchDef": "DUPLICATE_TAUTOMER", + "maxSearchTime": 180000, + "maxSearchResults": 5000, + "unitTestDB": false, + "initalDBLoad": false, + "projectRestrictions": false, + "compoundInventory": false, + "disableTubeCreationIfNoBarcode": false, + "checkACASDependenciesByContainerCode": false, + "jchemVersion": "16.4.25.0", + "databaseType": "postgres", + "standardizeStructure": false, + "useExternalStandardizerConfig": false, + "standardizerConfigFilePath": "/opt/acas/conf/standardizerConfig.xml", "orderSelectLists": true - }, - "bulkLoadSettings": { - "useProjectRoles":false, - "dbProperties": [ - {"name": "Lot Synthesis Date", "dataType": "date", "required": false}, - {"name": "Lot Notebook Page", "dataType": "string", "required": false}, - {"name": "Lot Chemist", "dataType": "string", "required": true}, - {"name": "Lot Purity Measured By", "dataType": "string", "required": false}, - {"name": "Parent Stereo Category", "dataType": "string", "required": true}, - {"name": "Lot Corp Name", "dataType": "string", "required": false}, - {"name": "Lot Number", "dataType": "numeric", "required": false}, - {"name": "Lot Barcode", "dataType": "string", "required": false}, - {"name": "Lot Color", "dataType": "string", "required": false}, - {"name": "Lot Salt Abbrev", "dataType": "string", "required": false}, - {"name": "Lot Salt Equivalents", "dataType": "string", "required": false}, - {"name": "Lot Amount", "dataType": "numeric", "required": false}, - {"name": "Lot Amount Units", "dataType": "string", "required": false}, - {"name": "Lot Solution Amount", "dataType": "numeric", "required": false}, - {"name": "Lot Solution Amount Units", "dataType": "string", "required": false}, - {"name": "Lot Supplier", "dataType": "string", "required": false}, - {"name": "Lot Supplier ID", "dataType": "string", "required": false}, - {"name": "Lot Purity", "dataType": "numeric", "required": false}, - {"name": "Lot Purity Operator", "dataType": "string", "required": false}, - {"name": "Lot Percent ee", "dataType": "numeric", "required": false}, - {"name": "Lot Comments", "dataType": "string", "required": false}, - {"name": "Lot Is Virtual", "dataType": "boolean", "required": false}, - {"name": "Lot Physical State", "dataType": "string", "required": false}, - {"name": "Lot Vendor", "dataType": "string", "required": false}, - {"name": "Lot Retain", "dataType": "numeric", "required": false}, - {"name": "Lot Retain Units", "dataType": "string", "required": false}, - {"name": "Lot Melting Point", "dataType": "numeric", "required": false}, - {"name": "Lot Boiling Point", "dataType": "numeric", "required": false}, - {"name": "Lot Supplier Lot", "dataType": "string", "required": false}, - {"name": "Project", "dataType": "string", "required": false}, - {"name": "CAS Number", "dataType": "string", "required": false}, - {"name": "Parent Corp Name", "dataType": "string", "required": false}, - {"name": "Parent Common Name", "dataType": "string", "required": false}, - {"name": "Parent Stereo Comment", "dataType": "string", "required": false} + }, + "bulkLoadSettings": { + "useProjectRoles": false, + "dbProperties": [ + {"name": "CAS Number", "dataType": "string", "required": false}, + {"name": "Lot Absorbance", "dataType": "numeric", "required": false}, + {"name": "Lot Alias", "dateType": "string", "required": false}, + {"name": "Lot Amount Units", "dataType": "string", "required": false}, + {"name": "Lot Amount", "dataType": "numeric", "required": false}, + {"name": "Lot Barcode", "dataType": "string", "required": false}, + {"name": "Lot Boiling Point", "dataType": "numeric", "required": false}, + {"name": "Lot Chemist", "dataType": "string", "required": true}, + {"name": "Lot Color", "dataType": "string", "required": false}, + {"name": "Lot Comments", "dataType": "string", "required": false}, + {"name": "Lot Corp Name", "dataType": "string", "required": false}, + {"name": "Lot Is Virtual", "dataType": "boolean", "required": false}, + {"name": "Lot Lambda", "dataType": "numeric", "required": false}, + {"name": "Lot Melting Point", "dataType": "numeric", "required": false}, + {"name": "Lot Notebook Page", "dataType": "string", "required": false}, + {"name": "Lot Number", "dataType": "numeric", "required": false}, + {"name": "Lot Observed Mass #1", "dataType": "numeric", "required": false}, + {"name": "Lot Observed Mass #2", "dataType": "numeric", "required": false}, + {"name": "Lot Percent ee", "dataType": "numeric", "required": false}, + {"name": "Lot Physical State", "dataType": "string", "required": false}, + {"name": "Lot Purity Measured By", "dataType": "string", "required": false}, + {"name": "Lot Purity Operator", "dataType": "string", "required": false}, + {"name": "Lot Purity", "dataType": "numeric", "required": false}, + {"name": "Lot Retain Location", "dataType": "string", "required": false}, + {"name": "Lot Retain Units", "dataType": "string", "required": false}, + {"name": "Lot Retain", "dataType": "numeric", "required": false}, + {"name": "Lot Salt Abbrev", "dataType": "string", "required": false}, + {"name": "Lot Salt Equivalents", "dataType": "string", "required": false}, + {"name": "Lot Solution Amount Units", "dataType": "string", "required": false}, + {"name": "Lot Solution Amount", "dataType": "numeric", "required": false}, + {"name": "Lot Stock Location", "dataType": "string", "required": false}, + {"name": "Lot Stock Solvent", "dataType": "string", "required": false}, + {"name": "Lot Storage Location", "dataType": "string", "required": false}, + {"name": "Lot Supplier ID", "dataType": "string", "required": false}, + {"name": "Lot Supplier Lot", "dataType": "string", "required": false}, + {"name": "Lot Supplier", "dataType": "string", "required": false}, + {"name": "Lot Synthesis Date", "dataType": "date", "required": false}, + {"name": "Lot Tare Weight Units", "dataType": "string", "required": false}, + {"name": "Lot Tare Weight", "dataType": "numeric", "required": false}, + {"name": "Lot Total Amount Stored Units", "dataType": "string", "required": false}, + {"name": "Lot Total Amount Stored", "dataType": "numeric", "required": false}, + {"name": "Lot Vendor", "dataType": "string", "required": false}, + {"name": "Parent Alias", "dateType": "string", "required": false}, + {"name": "Parent Common Name", "dataType": "string", "required": false}, + {"name": "Parent Corp Name", "dataType": "string", "required": false}, + {"name": "Parent LiveDesign Corp Name", "dataType": "string", "required": false}, + {"name": "Parent Stereo Category", "dataType": "string", "required": true}, + {"name": "Parent Stereo Comment", "dataType": "string", "required": false}, + {"name": "Project", "dataType": "string", "required": false} ] } } - - From 8e60b0366f9507c52adf298c286add59d44f5180 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 15 Dec 2017 08:42:12 -0800 Subject: [PATCH 333/576] Cleaned up default ModuleMenusConfiguration by: Removing module stubs Chem Struct, Admin Panel, and Logging Making all headers consistently non-collapsible Moving Project Editor and Project Browser down into Admin section --- .../client/ModuleMenusConfiguration.coffee | 42 +++++++------------ 1 file changed, 14 insertions(+), 28 deletions(-) diff --git a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee index fa030dd68..6443792dc 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee @@ -3,12 +3,8 @@ window.ModuleMenusConfiguration = isHeader: true menuName: "Load Data" requireUserRoles: [window.conf.roles.acas.userRole] -# collapsible: true + collapsible: false , -# isHeader: false -# menuName: "Chem Struct" -# mainControllerClassName: "ACASFormChemicalStructureExampleController" -# , isHeader: false menuName: "Experiment Loader" mainControllerClassName: "GenericDataParserController" @@ -31,12 +27,6 @@ window.ModuleMenusConfiguration = mainControllerClassName: window.conf.experiment.mainControllerClassName autoLaunchName:"experiment_base" requireUserRoles: [window.conf.roles.acas.userRole] - , - isHeader: false - menuName: "Project Editor" - mainControllerClassName: "ProjectController" - autoLaunchName:"project" - requireUserRoles: [window.conf.roles.acas.adminRole] , isHeader: false, menuName: "Example Thing" mainControllerClassName: "ExampleThingController" @@ -45,7 +35,7 @@ window.ModuleMenusConfiguration = , isHeader: true menuName: "Search and Edit" - collapsible: true + collapsible: false requireUserRoles: [window.conf.roles.acas.userRole] , isHeader: false, menuName: "Protocol Browser" @@ -55,15 +45,21 @@ window.ModuleMenusConfiguration = isHeader: false, menuName: "Experiment Browser" mainControllerClassName: "ExperimentBrowserController" requireUserRoles: [window.conf.roles.acas.userRole] - , - isHeader: false, menuName: "Project Browser" - mainControllerClassName: "ProjectBrowserController" - requireUserRoles: [window.conf.roles.acas.userRole] , isHeader: true menuName: "Admin" - collapsible: true + collapsible: false requireUserRoles: [window.conf.roles.acas.adminRole] + , + isHeader: false + menuName: "Project Editor" + mainControllerClassName: "ProjectController" + autoLaunchName:"project" + requireUserRoles: [window.conf.roles.acas.adminRole] + , + isHeader: false, menuName: "Project Browser" + mainControllerClassName: "ProjectBrowserController" + requireUserRoles: [window.conf.roles.acas.userRole] , isHeader: false menuName: "Author Editor" @@ -75,16 +71,6 @@ window.ModuleMenusConfiguration = menuName: "Author Browser" mainControllerClassName: "AuthorBrowserController" requireUserRoles: [window.conf.roles.acas.adminRole] - , - isHeader: false - menuName: "Admin Panel" - mainControllerClassName: "AdminPanelController" - autoLaunchName: "admin_panel" - requireUserRoles: [window.conf.roles.acas.adminRole] - , - isHeader: false, menuName: "Logging" - mainControllerClassName: "LoggingController" - requireUserRoles: [window.conf.roles.acas.adminRole] , isHeader: false menuName: "System Test" @@ -101,7 +87,7 @@ window.ModuleMenusConfiguration = isHeader: true menuName: "CmpdReg Admin" requireUserRoles: [window.conf.roles.cmpdreg.adminRole] - collapsible: true + collapsible: false , isHeader: false menuName: "CmpdReg Vendors" From b06fb865422985e7c54f19bb31963d9f4bc4fddd Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 15 Dec 2017 09:46:27 -0800 Subject: [PATCH 334/576] Fixed copyright year on CmpdReg --- modules/CmpdReg/src/client/templates/AppControllerView.inc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/CmpdReg/src/client/templates/AppControllerView.inc b/modules/CmpdReg/src/client/templates/AppControllerView.inc index 38f3a99e1..62d1a34b3 100755 --- a/modules/CmpdReg/src/client/templates/AppControllerView.inc +++ b/modules/CmpdReg/src/client/templates/AppControllerView.inc @@ -31,7 +31,7 @@
        - + From aa57152cec68ecfc3f2d0d9c89331b87984158f8 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 15 Dec 2017 11:30:03 -0800 Subject: [PATCH 335/576] Fixed configuration.json so it does not append salt code to lot corp name --- modules/CmpdReg/src/client/custom/configuration.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/CmpdReg/src/client/custom/configuration.json b/modules/CmpdReg/src/client/custom/configuration.json index 8fa528ae4..2a9bff507 100755 --- a/modules/CmpdReg/src/client/custom/configuration.json +++ b/modules/CmpdReg/src/client/custom/configuration.json @@ -52,7 +52,7 @@ "fancyCorpNumberFormat": false, "corpParentFormat": "standard", "corpBatchFormat": "corp_batch_saltcode", - "appendSaltCodeToLotName": true, + "appendSaltCodeToLotName": false, "noSaltCode": "", "usePredefinedList": false, "newUserIsChemist": false, From 5ce70a4332025546293373791d9b594093561a8f Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 15 Dec 2017 12:07:30 -0800 Subject: [PATCH 336/576] Added in four missing Parent properties to DB Properties list so the default list is a complete set of available DB properties. NOTE: Not all of these are exposed to all users in the UI --- modules/CmpdReg/src/client/custom/configuration.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/modules/CmpdReg/src/client/custom/configuration.json b/modules/CmpdReg/src/client/custom/configuration.json index 2a9bff507..b9a575f73 100755 --- a/modules/CmpdReg/src/client/custom/configuration.json +++ b/modules/CmpdReg/src/client/custom/configuration.json @@ -120,8 +120,12 @@ {"name": "Lot Total Amount Stored", "dataType": "numeric", "required": false}, {"name": "Lot Vendor", "dataType": "string", "required": false}, {"name": "Parent Alias", "dateType": "string", "required": false}, + {"name": "Parent Annotation", "dateType": "string", "required": false}, + {"name": "Parent Comment", "dataType": "string", "required": false}, {"name": "Parent Common Name", "dataType": "string", "required": false}, + {"name": "Parent Compound Type", "dateType": "string", "required": false}, {"name": "Parent Corp Name", "dataType": "string", "required": false}, + {"name": "Parent Is Mixture", "dataType": "boolean", "required": false}, {"name": "Parent LiveDesign Corp Name", "dataType": "string", "required": false}, {"name": "Parent Stereo Category", "dataType": "string", "required": true}, {"name": "Parent Stereo Comment", "dataType": "string", "required": false}, From 2eedee23d1ecbdd620ec1c50b277891cf6fecd86 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 15 Dec 2017 13:40:46 -0800 Subject: [PATCH 337/576] Removed Example Thing from default ModuleMenus --- .../ModuleMenus/src/client/ModuleMenusConfiguration.coffee | 5 ----- 1 file changed, 5 deletions(-) diff --git a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee index 6443792dc..ab025af82 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee @@ -27,11 +27,6 @@ window.ModuleMenusConfiguration = mainControllerClassName: window.conf.experiment.mainControllerClassName autoLaunchName:"experiment_base" requireUserRoles: [window.conf.roles.acas.userRole] - , - isHeader: false, menuName: "Example Thing" - mainControllerClassName: "ExampleThingController" - autoLaunchName:"example_thing" - requireUserRoles: [window.conf.roles.acas.userRole] , isHeader: true menuName: "Search and Edit" From 5b8f6b2b179810ab5db39f5fbceccd55108d6609 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 15 Dec 2017 14:19:54 -0800 Subject: [PATCH 338/576] Bumped CmpdReg copyright notice to 2018 --- modules/CmpdReg/src/client/templates/AppControllerView.inc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/CmpdReg/src/client/templates/AppControllerView.inc b/modules/CmpdReg/src/client/templates/AppControllerView.inc index 62d1a34b3..fb66bab28 100755 --- a/modules/CmpdReg/src/client/templates/AppControllerView.inc +++ b/modules/CmpdReg/src/client/templates/AppControllerView.inc @@ -31,7 +31,7 @@
        - + From aa4f1b55c7298bd16175e673d0a9745393f274e0 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 15 Dec 2017 14:31:24 -0800 Subject: [PATCH 339/576] setting ACAS_TAG, db tag and tomcat tag for release --- .env | 2 +- docker-compose.yml | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.env b/.env index b6a34d3d5..d1785277b 100644 --- a/.env +++ b/.env @@ -1 +1 @@ -ACAS_TAG=develop +ACAS_TAG=latest diff --git a/docker-compose.yml b/docker-compose.yml index ff54e7f45..9413322c5 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -47,7 +47,7 @@ services: - logs:/home/runner/logs command: ["bin/acas.sh", "run", "rservices"] db: - image: mcneilco/acas-postgres:bingo + image: mcneilco/acas-postgres:1.0-bingo restart: always volumes: - dbstore:/var/lib/postgresql/data @@ -60,7 +60,7 @@ services: ports: - "5432:5432" tomcat: - image: mcneilco/tomcat-maven:openjdk8 + image: mcneilco/tomcat-maven:1.0-openjdk8 restart: always depends_on: - db @@ -81,12 +81,12 @@ services: - ./conf/docker/cmpdreg/environment/cmpdreg.env command: catalina.sh run roo: - image: mcneilco/acas-roo-server-oss:RC-1.13.0 + image: mcneilco/acas-roo-server-oss:${ACAS_TAG} volumes: - /usr/local/tomcat/webapps/acas command: /bin/true cmpdreg: - image: mcneilco/acas-cmpdreg-roo-server-oss:RC-1.13.0 + image: mcneilco/acas-cmpdreg-roo-server-oss:${ACAS_TAG} volumes: - /usr/local/tomcat/webapps/cmpdreg # Add chemaxon license files here From 771ef146ffaf98c7a9f1039b6246d0f8e11db4da Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 4 Jan 2018 13:28:35 -0800 Subject: [PATCH 340/576] #435: Remove SEL R warnings that occur when configured entity types are a ragged array --- modules/GenericDataParser/src/server/generic_data_parser.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 2e2ac355f..373a9d9b6 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -641,7 +641,7 @@ getEntityCodeFromEntityDisplayNameOrCode <- function(mainCodeOrDisplayName) { "/api/entitymeta/configuredEntityTypes/"), requireJSON = TRUE)) # Expected column names: 'type', 'kind', 'codeOrigin', 'displayName', 'sourceExternal' - entityTypeAndKindTable <- as.data.table(do.call(rbind, entityTypeAndKindList)) + entityTypeAndKindTable <- rbindlist(entityTypeAndKindList, fill = TRUE) entityTypeAndKindTable[, displayName := unlist(displayName)] if (length(entityTypeAndKindTable[displayName == mainCodeOrDisplayName, code])) { mainCode <- entityTypeAndKindTable[displayName == mainCodeOrDisplayName, code][[1]] @@ -659,7 +659,7 @@ getDisplayNameFromEntityCode <- function(mainCode) { "/api/entitymeta/configuredEntityTypes/"), requireJSON = TRUE)) # Expected column names: 'type', 'kind', 'codeOrigin', 'displayName', 'sourceExternal' - entityTypeAndKindTable <- as.data.table(do.call(rbind, entityTypeAndKindList)) + entityTypeAndKindTable <- rbindlist(entityTypeAndKindList, fill = TRUE) entityTypeAndKindTable[, displayName := unlist(displayName)] if (length(entityTypeAndKindTable[code == mainCode, displayName])) { displayName <- entityTypeAndKindTable[code == mainCode, displayName][[1]] From 43bec12d97297648684f30f05bf240646496c5b0 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 5 Jan 2018 15:36:24 -0800 Subject: [PATCH 341/576] #437 Correct display name for SEL report file --- modules/GenericDataParser/src/server/generic_data_parser.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 2e2ac355f..bbf9e6eaa 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -2988,7 +2988,7 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL, # Upload the data if this is not a dry run if(!dryRun & errorFree) { - reportFileSummary <- paste0(validatedMetaData$'Protocol Name', " - ", validatedMetaData$'Experiment Name') + reportFileSummary <- basename(reportFilePath) if(rawOnlyFormat) { uploadRawDataOnly(metaData = validatedMetaData, lsTransaction, subjectData = calculatedResults, experiment, fileStartLocation = pathToGenericDataFormatExcelFile, configList, From 20f5412c9375373de8dfcba4393abda7e07a95d5 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Sun, 14 Jan 2018 13:19:24 -0800 Subject: [PATCH 342/576] exposed function getContainerCodesFromLabelsInternal on exports --- .../src/server/routes/InventoryServiceRoutes.coffee | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 6f02c1200..23d676089 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -1293,7 +1293,7 @@ getContainerCodesFromLabels = (req, callback) -> callback json ) -getContainerCodesFromLabelsInternal = (barcodes, containerType, containerKind, callback) -> +exports.getContainerCodesFromLabelsInternal = (barcodes, containerType, containerKind, callback) -> if global.specRunnerTestmode response = codeName: 'CONT-0000001' @@ -1362,7 +1362,7 @@ exports.updateWellContentInternal = (wellContent, copyPreviousValues, callCustom inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' resp.json inventoryServiceTestJSON.getContainerCodesByLabelsResponse else - console.debug 'incoming updateWellContentInternal request: ', JSON.stringify(wellContent.wells) + console.debug 'incoming updateWellContentInternal request: ', JSON.stringify(wellContent) config = require '../conf/compiled/conf.js' baseurl = config.all.client.service.persistence.fullpath+"containers/updateWellContent?copyPreviousValues="+copyPreviousValues console.debug 'base url: ', baseurl @@ -3152,7 +3152,7 @@ checkLocationsExist = (fileEntryArray, callback) -> callback missingLocations checkBarcodesExist = (barcodes, callback) -> - getContainerCodesFromLabelsInternal barcodes, 'container', 'tube', (containerCodes) -> + exports.getContainerCodesFromLabelsInternal barcodes, 'container', 'tube', (containerCodes) -> existingBarcodes = [] newBarcodes = [] _.each containerCodes, (containerCodeEntry) -> From a35b2a052fa3695363fb7c40dace33317e974aa7 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Sun, 14 Jan 2018 13:24:06 -0800 Subject: [PATCH 343/576] Revert "exposed function getContainerCodesFromLabelsInternal on exports" This reverts commit 20f5412c9375373de8dfcba4393abda7e07a95d5. --- .../src/server/routes/InventoryServiceRoutes.coffee | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 23d676089..6f02c1200 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -1293,7 +1293,7 @@ getContainerCodesFromLabels = (req, callback) -> callback json ) -exports.getContainerCodesFromLabelsInternal = (barcodes, containerType, containerKind, callback) -> +getContainerCodesFromLabelsInternal = (barcodes, containerType, containerKind, callback) -> if global.specRunnerTestmode response = codeName: 'CONT-0000001' @@ -1362,7 +1362,7 @@ exports.updateWellContentInternal = (wellContent, copyPreviousValues, callCustom inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' resp.json inventoryServiceTestJSON.getContainerCodesByLabelsResponse else - console.debug 'incoming updateWellContentInternal request: ', JSON.stringify(wellContent) + console.debug 'incoming updateWellContentInternal request: ', JSON.stringify(wellContent.wells) config = require '../conf/compiled/conf.js' baseurl = config.all.client.service.persistence.fullpath+"containers/updateWellContent?copyPreviousValues="+copyPreviousValues console.debug 'base url: ', baseurl @@ -3152,7 +3152,7 @@ checkLocationsExist = (fileEntryArray, callback) -> callback missingLocations checkBarcodesExist = (barcodes, callback) -> - exports.getContainerCodesFromLabelsInternal barcodes, 'container', 'tube', (containerCodes) -> + getContainerCodesFromLabelsInternal barcodes, 'container', 'tube', (containerCodes) -> existingBarcodes = [] newBarcodes = [] _.each containerCodes, (containerCodeEntry) -> From 6e3f6080154a483cc558258f58fc43165d8ac1a8 Mon Sep 17 00:00:00 2001 From: John McNeil Date: Sun, 14 Jan 2018 13:27:12 -0800 Subject: [PATCH 344/576] Fixes #439 getContainerCodesFromLabelsInternal is not available outside InventoryServiceRoutes.coffee --- .../src/server/routes/InventoryServiceRoutes.coffee | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee index 6f02c1200..23d676089 100644 --- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee @@ -1293,7 +1293,7 @@ getContainerCodesFromLabels = (req, callback) -> callback json ) -getContainerCodesFromLabelsInternal = (barcodes, containerType, containerKind, callback) -> +exports.getContainerCodesFromLabelsInternal = (barcodes, containerType, containerKind, callback) -> if global.specRunnerTestmode response = codeName: 'CONT-0000001' @@ -1362,7 +1362,7 @@ exports.updateWellContentInternal = (wellContent, copyPreviousValues, callCustom inventoryServiceTestJSON = require '../public/javascripts/spec/ServerAPI/testFixtures/InventoryServiceTestJSON.js' resp.json inventoryServiceTestJSON.getContainerCodesByLabelsResponse else - console.debug 'incoming updateWellContentInternal request: ', JSON.stringify(wellContent.wells) + console.debug 'incoming updateWellContentInternal request: ', JSON.stringify(wellContent) config = require '../conf/compiled/conf.js' baseurl = config.all.client.service.persistence.fullpath+"containers/updateWellContent?copyPreviousValues="+copyPreviousValues console.debug 'base url: ', baseurl @@ -3152,7 +3152,7 @@ checkLocationsExist = (fileEntryArray, callback) -> callback missingLocations checkBarcodesExist = (barcodes, callback) -> - getContainerCodesFromLabelsInternal barcodes, 'container', 'tube', (containerCodes) -> + exports.getContainerCodesFromLabelsInternal barcodes, 'container', 'tube', (containerCodes) -> existingBarcodes = [] newBarcodes = [] _.each containerCodes, (containerCodeEntry) -> From 54e85216f819a53d37ff0e5d5b07028261ee4d45 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 16 Jan 2018 11:34:53 -0800 Subject: [PATCH 345/576] fixes #442: Logger should write to stderr when in docker --- conf/config.properties.example | 2 ++ 1 file changed, 2 insertions(+) diff --git a/conf/config.properties.example b/conf/config.properties.example index 648d741a1..f7b45c0a9 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -149,6 +149,8 @@ server.ssl.cert.passphrase=selfCertForACASServer client.service.rapache.port=1080 server.rapache.listen=* +server.rapache.forceAllToStdErrOnly=true + #todo not in codebase 6/2015 client.service.rapache.use.ssl=${client.use.ssl} client.service.rapache.host=rservices From 3df98d8529cdaf1b2a64ba5481de2d18c046c42a Mon Sep 17 00:00:00 2001 From: Eva Gao Date: Tue, 16 Jan 2018 13:08:58 -0800 Subject: [PATCH 346/576] feature/add-ignore-option-for-cmpdreg-scientist: added ignore option for all of the cmpdreg admin modules. Fixes Issue #441 --- .../CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee | 9 +++++++++ .../src/client/AbstractCmpdRegAdminBrowser.coffee | 2 ++ .../src/client/AbstractCmpdRegAdminBrowserView.html | 2 ++ .../src/client/AbstractCmpdRegAdminView.html | 6 ++++++ modules/CmpdRegAdmin/src/client/CmpdRegScientist.coffee | 1 + 5 files changed, 20 insertions(+) diff --git a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee index 9736c1570..397db4541 100644 --- a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee +++ b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee @@ -10,6 +10,7 @@ class window.AbstractCmpdRegAdminController extends AbstractFormController events: -> "keyup .bv_cmpdRegAdminCode": "handleCmpdRegAdminCodeNameChanged" "keyup .bv_cmpdRegAdminName": "handleCmpdRegAdminNameChanged" + "click .bv_cmpdRegAdminIgnore": "handleCmpdRegAdminIgnoreChanged" "click .bv_save": "handleSaveClicked" "click .bv_backToCmpdRegAdminBrowserBtn": "handleBackToCmpdRegAdminBrowserClicked" # "click .bv_newEntity": "handleNewEntityClicked" @@ -69,6 +70,11 @@ class window.AbstractCmpdRegAdminController extends AbstractFormController code = @model.get('code') @$('.bv_cmpdRegAdminCode').val(code) @$('.bv_cmpdRegAdminCode').html(code) + if @model.get('ignore') is true + @$('.bv_cmpdRegAdminIgnore').attr 'checked', 'checked' + else + @$('.bv_cmpdRegAdminIgnore').removeAttr 'checked' + if @model.isNew() @$('.bv_save').html("Save") # @$('.bv_newEntity').hide() @@ -153,6 +159,9 @@ class window.AbstractCmpdRegAdminController extends AbstractFormController handleCmpdRegAdminNameChanged: => @model.set("name", UtilityFunctions::getTrimmedInput @$('.bv_cmpdRegAdminName')) + handleCmpdRegAdminIgnoreChanged: => + @model.set("ignore", @$('.bv_cmpdRegAdminIgnore').is(":checked")) + handleSaveClicked: => @callNameValidationService() diff --git a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee index be4fb31df..a6cadc4f9 100644 --- a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee +++ b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee @@ -92,6 +92,8 @@ class window.CmpdRegAdminRowSummaryController extends Backbone.View toDisplay = code: @model.get('code') name: @model.get('name') + ignored: if @model.get('ignore')? then @model.get('ignore') else false + $(@el).html(@template(toDisplay)) @ diff --git a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowserView.html b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowserView.html index fe3d6ddd0..d526cc797 100644 --- a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowserView.html +++ b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowserView.html @@ -36,6 +36,7 @@ + diff --git a/modules/LotPropertyBulkLoader/src/client/LotPropertyBulkLoader.coffee b/modules/LotPropertyBulkLoader/src/client/LotPropertyBulkLoader.coffee new file mode 100644 index 000000000..e59bf7bce --- /dev/null +++ b/modules/LotPropertyBulkLoader/src/client/LotPropertyBulkLoader.coffee @@ -0,0 +1,93 @@ +class window.LotPropertyBulkLoader extends Backbone.Model + defaults: + overwriteExisting: false + + validate: (attrs) => + errors = [] + return null + + +class window.LotPropertyBulkLoaderController extends AbstractParserFormController + template: _.template($("#LotPropertyBulkLoaderView").html()) + + events: + "change .bv_overwriteExisting": "handleOverwriteExistingCheckboxChanged" + + initialize: -> + @errorOwnerName = 'LotPropertyBulkLoaderController' + $(@el).html @template @model.attributes + @setBindings() + @setupProjectSelect() + @setupProtocolSelect("Lot Property Bulk Loader") + + render: => + super() + @ + + updateModel: -> + @trigger 'amDirty' + + handleOverwriteExistingCheckboxChanged: () => + overwriteExisting = @$('.bv_overwriteExisting').is(":checked") + @model.set overwriteExisting: overwriteExisting + @attributeChanged() + + +class window.LotPropertyBulkLoaderParserController extends BasicFileValidateAndSaveController + template: _.template($("#BasicFileValidateAndSaveViewLotPropertyBulkLoader").html()) + + initialize: -> + @fileProcessorURL = "/api/LotPropertyBulkLoader/fileProcessor" + @errorOwnerName = 'LotPropertyBulkLoaderController' + @allowedFileTypes = ['xls','xlsx', 'csv'] + @loadReportFile = false + super() + @$('.bv_moduleTitle').html('Lot Property Bulk Loader') + + @lpblc = new LotPropertyBulkLoaderController + model: new LotPropertyBulkLoader() + el: @$('.bv_additionalValuesForm') + @lpblc.on 'valid', @handleLPBLFormValid + @lpblc.on 'invalid', @handleLPBLFormInvalid + @lpblc.on 'notifyError', @notificationController.addNotification + @lpblc.on 'clearErrors', @notificationController.clearAllNotificiations + @lpblc.on 'amDirty', => + @trigger 'amDirty' + @lpblc.render() + + handleLPBLFormValid: => + if @parseFileUploaded + @handleFormValid() + + handleLPBLFormInvalid: => + @handleFormInvalid() + + handleFormValid: -> + if @lpblc.isValid() + super() + + handleValidationReturnSuccess: (json) => + @additionalData = + inputParameters: @lpblc.model.toJSON() + super(json) + @lpblc.disableAllInputs() + + showFileSelectPhase: -> + super() + if @lpblc? + @lpblc.enableAllInputs() + + validateParseFile: => + @lpblc.updateModel() + unless !@lpblc.isValid() + @additionalData = + inputParameters: @lpblc.model.toJSON() + super() + + validateParseFile: => + @lpblc.updateModel() + unless !@lpblc.isValid() + @additionalData = + inputParameters: @lpblc.model.toJSON() + super() + diff --git a/modules/LotPropertyBulkLoader/src/client/LotPropertyBulkLoaderView.html b/modules/LotPropertyBulkLoader/src/client/LotPropertyBulkLoaderView.html new file mode 100644 index 000000000..974b482a3 --- /dev/null +++ b/modules/LotPropertyBulkLoader/src/client/LotPropertyBulkLoaderView.html @@ -0,0 +1,11 @@ + \ No newline at end of file diff --git a/modules/LotPropertyBulkLoader/src/server/r/LotPropertyBulkLoader.R b/modules/LotPropertyBulkLoader/src/server/r/LotPropertyBulkLoader.R new file mode 100644 index 000000000..1cedc9858 --- /dev/null +++ b/modules/LotPropertyBulkLoader/src/server/r/LotPropertyBulkLoader.R @@ -0,0 +1,250 @@ +# Brian Bolt +# 2018 +# brian.bolt@boltengineered.com +library(RCurl) +library(data.table) +library(xtable) + + +validateNumeric <- function(inputValue) { + value <- suppressWarnings(as.numeric(gsub(",", "", as.character(inputValue)))) + isNumeric <- !is.na(value) + return(list(value, isNumeric)) +} +areNumbersEqual <- function(val1, val2) { + if(is.na(val1) & is.na(val2)) { + return(TRUE) + } + if((is.na(val1) & !is.na(val2)) || (!is.na(val1) & is.na(val1))) { + return(FALSE) + } + identical(val1, val2) +} + +validateFileInput <- function(fileData, headerMap, errorEnv) { + expectedHeaders <- "Lot Corporate Name" + + fileHeaders <- as.character(fileData[1,]) + missingNames <- expectedHeaders[!expectedHeaders %in% fileHeaders] + if(length(missingNames) > 0) { + stopUser(paste0("Missing columns in file: ",paste0("'",paste(missingNames, collapse = "','"), "'"))) + } + optionalHeaders <- fileHeaders[ !fileHeaders %in% expectedHeaders] + if(length(optionalHeaders) == 0) { + stopUser(paste0("You must provide atleast one property to load: ",paste0("'",paste(headerMap$fileHeader, collapse = "','"), "'"))) + } + unusedColumns <- optionalHeaders[!optionalHeaders %in% headerMap$fileHeader] + if(length(unusedColumns) > 0) { + racasMessenger$addWarning(paste0("The following columns are unused: ",paste0("'",paste(unusedColumns, collapse = "','"), "'"))) + } + usedHeaders <- optionalHeaders[ !optionalHeaders %in% unusedColumns] + if(length(usedHeaders) == 0) { + stopUser(paste0("You must provide atleast one property to load: ",paste0("'",paste(headerMap$fileHeader, collapse = "','"), "'"))) + } + validatedFileData <- fileData[2:nrow(fileData),fileHeaders %in% c(expectedHeaders, usedHeaders)] + names(validatedFileData) <- c(expectedHeaders, usedHeaders) + + mainCode <- "Corporate Batch ID" + newBatchIds <- as.data.table(getPreferredId2(validatedFileData$`Lot Corporate Name`, displayName = mainCode)) + newBatchIds[ , c("error", "warning", "Issues") := { + issues <- NA_character_ + error <- FALSE + warning <- FALSE + if (is.null(Reference.Code) || is.na(Reference.Code) || Reference.Code == "") { + error <- TRUE + issues <- paste0(mainCode, " '", Requested.Name, + "' has not been registered in the system. Contact your system administrator for help.") + } else if (as.character(Requested.Name) != as.character(Reference.Code)) { + warning <- TRUE + issues <- paste0("A ", mainCode, " that you entered, '", Requested.Name, + "', was replaced by preferred ", mainCode, " '", Reference.Code, + "'. If this is not what you intended, replace the ", mainCode, " with the correct ID.") + + } + list(error, warning, issues) + }, by = "Requested.Name"] + + validatedFileDataDT <- as.data.table(validatedFileData) + newBatchIds <- as.data.table(newBatchIds) + setkey(newBatchIds, 'Requested.Name' ) + setkey(validatedFileDataDT, 'Lot Corporate Name' ) + validatedFileDataDT[newBatchIds, c('Lot Corporate Name','error','warning','Issues') := list(Reference.Code, error, warning, Issues)] + return(validatedFileDataDT) +} +requestHandler <- function(request) { + racasMessenger <- messenger() + racasMessenger$reset() + racasMessenger$logger <- logger(logName = "com.mcneilco.acas.LotPropertyBulkLoader", reset=TRUE) + + fileData <- readExcelOrCsv(getUploadedFilePath(request$fileToParse)) + errorEnv <- globalenv() + + headerMap <- data.frame(fileHeader = c("Purity","Observed Mass #1","Observed Mass #2"), + ## These settings should come from the bulk load configuration but remove "Lot" from the name as this is already the context + mappedProperty = c("purity", "observedMassOne", "observedMassTwo"), + type = c("numeric", "numeric", "numeric") + , stringsAsFactors = FALSE) + + validatedData <- validateFileInput(fileData, headerMap, errorEnv) + + metaLotBaseURL <- paste0(applicationSettings$client.service.cmpdReg.persistence.basepath,"/metalots") + metaLotCorpNameURL <- paste0(metaLotBaseURL,"/corpName") + getPropertyNames <- names(validatedData)[ !names(validatedData) %in% c('Lot Corporate Name', 'error','warning', 'Issues')] + getProperties <- headerMap[match(getPropertyNames, headerMap$fileHeader),] + overwriteExisting <- as.logical(request$inputParameters$overwriteExisting) + validatedData[ error == FALSE, c(paste0(c("Current ", "New "), rep(getProperties$fileHeader, each = 2)),"error","warning","Issues") := { + metaLotBaseURL <- paste0(applicationSettings$client.service.cmpdReg.persistence.basepath,"/metalots") + metaLotCorpNameURL <- paste0(metaLotBaseURL,"/corpName") + metaLot <- fromJSON(getURL(paste0(metaLotCorpNameURL, "/",`Lot Corporate Name`)), ) + properties <- metaLot$lot[getProperties$mappedProperty] + values <- list() + issues <- Issues + for(i in 1:nrow(getProperties)) { + type <- getProperties$type[[i]] + if(is.null(properties[[i]])) { + currentProperty <- switch(type, + numeric = NA_real_, + character = NA_character_ + ) + } else { + currentProperty <- properties[[i]] + } + + inputProperty <- get(getProperties$fileHeader[[i]]) + validatedInputProperty <- switch(type, + numeric = validateNumeric(inputProperty), + character = validateCharacter(inputProperty)) + + if(!is.na(inputProperty) && validatedInputProperty[[2]] == FALSE) { + error <- TRUE + issues <- c(issues,"Input value not numeric") + } else { + numbersEqual <- areNumbersEqual(currentProperty, validatedInputProperty[[1]]) + if(!numbersEqual & !is.na(currentProperty)) { + if(overwriteExisting) { + warning <- TRUE + } else { + error <- TRUE + } + issues <- c(issues, paste0(getProperties$fileHeader[[i]]," overwrite")) + } + } + if(!error) { + print(error) + if(is.na(validatedInputProperty[[1]])) { + metaLot$lot[getProperties$mappedProperty[[i]]] <- NULL + } else { + metaLot$lot[getProperties$mappedProperty[[i]]] <- validatedInputProperty[[1]] + } + } + values <- c(values,list(currentProperty, validatedInputProperty[[1]])) + } + issues <- stats::na.omit(issues) + if(length(issues) > 0) { + issues <- paste0(issues, collapse = ", ") + } else { + issues <- NA_character_ + } + if(!as.logical(request$dryRunMode)) { + if(!error) { + metaLotJson <- toJSON(metaLot) + postJSONURL(metaLotBaseURL, metaLotJson) + } + } + c(values, list(error, warning, unique(issues))) + }, by = 'Lot Corporate Name', with = FALSE] + + validatedData[ , getProperties$fileHeader := NULL, with = FALSE] + + hasError <- FALSE + if(any(validatedData$error) | length(racasMessenger$errors) > 0) { + hasError <- TRUE + } + hasWarning <- FALSE + if(any(validatedData$warning) | length(racasMessenger$warnings) > 0) { + hasWarning <- TRUE + } + errorList <- lapply(racasMessenger$errors, function(x) {x$message}) + warningList <- lapply(racasMessenger$warnings, function(x) {x$message}) + errorMessages <- list() + errorMessages <- c(errorMessages, lapply(errorList, function(x) {list(errorLevel="error", message=x)})) + errorMessages <- c(errorMessages, lapply(warningList, function(x) {list(errorLevel="warning", message=x)})) + transactionId = NULL + fileName <- request[[1]] + dryRun <- request[[2]] + addToRow <- NULL + + if(!as.logical(request$dryRun)) { + validatedData[ , names(validatedData)[grepl("Current", names(validatedData))] := NULL, with = FALSE] + validatedData[ , "Issues" := NULL, with = FALSE] + } else { + errorRows <- which(validatedData$error)-1 + warningRows <- which(validatedData$warning & !validatedData$error)-1 + addToRows <- c(errorRows, warningRows) + if(length(errorRows) > 0) { + errorList <- c(errorList, list("See table for additional errors")) + } + if(length(warningRows) > 0) { + warningList <- c(warningList, list("See table for additional warnings")) + } + if(length(addToRows) > 0) { + command <- c(rep("error", times = length(errorRows)), rep("warning", times = length(warningRows))) + addToRow <- list(pos = as.list(addToRows), command = command) + } + } + + table <- print.xtable( + xtable(validatedData[ , c("error", "warning") := NULL]), "html",hline.after=c(-1,0, 1:nrow(validatedData)), + include.rownames=FALSE, caption.placement='top', + html.table.attributes='align="left"', print.rules = FALSE, size = "small", + add.to.row = addToRow + ) + + table <- paste('',table) + table <- gsub("",'
        ', table) + table <- gsub("warning ", '', table) + table <- gsub("error ", '', table) + + htmlSummary <- createHtmlSummary(hasError, errorList, hasWarning, warningList, + summaryInfo=NULL, as.logical(request$dryRun)) + + htmlSummary <- paste0(htmlSummary,"
        ",table) + + racasMessenger + response <- list( + commit= FALSE, + transactionId= transactionId, + results= list( + path= getwd(), + fileToParse= fileName, + dryRun= dryRun, + htmlSummary= htmlSummary + ), + hasError= hasError, + hasWarning = hasWarning, + errorMessages= errorMessages + ) + return( response) + +} \ No newline at end of file diff --git a/modules/LotPropertyBulkLoader/src/server/r/LotPropertyBulkLoader.Rmd b/modules/LotPropertyBulkLoader/src/server/r/LotPropertyBulkLoader.Rmd new file mode 100644 index 000000000..a5ef4d1d4 --- /dev/null +++ b/modules/LotPropertyBulkLoader/src/server/r/LotPropertyBulkLoader.Rmd @@ -0,0 +1,22 @@ +--- +title: "Lot Property Bulk Loader" +author: "`r request$user`" +date: '`r format(Sys.time(), "%Y/%m/%d")`' +output: + html_document: + self_contained: no +--- + + + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = FALSE) +``` + +```{r} +validatedData +``` \ No newline at end of file diff --git a/modules/LotPropertyBulkLoader/src/server/routes/LotPropertyBulkLoader.coffee b/modules/LotPropertyBulkLoader/src/server/routes/LotPropertyBulkLoader.coffee new file mode 100644 index 000000000..90112d0bd --- /dev/null +++ b/modules/LotPropertyBulkLoader/src/server/routes/LotPropertyBulkLoader.coffee @@ -0,0 +1,30 @@ +### To install this Module + +Add this line to modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee + isHeader: false + menuName: "Substance Loader" + mainControllerClassName: "SubstanceLoaderController" +### + +exports.setupAPIRoutes = (app, loginRoutes) -> + app.post '/api/lotPropertyBulkLoader/fileProcessor', exports.lotPropertyBulkLoader + +exports.setupRoutes = (app, loginRoutes) -> + app.post '/api/lotPropertyBulkLoader/fileProcessor', loginRoutes.ensureAuthenticated, exports.lotPropertyBulkLoader + +config = require '../conf/compiled/conf.js' +serverUtilityFunctions = require "./ServerUtilityFunctions" + +exports.lotPropertyBulkLoader = (request, response) -> + request.connection.setTimeout 86400000 + serverUtilityFunctions = require './ServerUtilityFunctions.js' + + response.writeHead(200, {'Content-Type': 'application/json'}); + serverUtilityFunctions.runRFunction( + request, + "src/r/LotPropertyBulkLoader/LotPropertyBulkLoader.R", + "requestHandler", + (rReturn) -> + response.end rReturn + ) + From 3380cca386c007d89526728194c55a7de3ed89b8 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 7 Dec 2018 16:34:32 -0800 Subject: [PATCH 409/576] modify creg to get scientists from customer specific functions, use strings for chemist, registered_by and modified_by --- conf/config.properties.example | 4 +-- docker-compose.yml | 18 +++++----- .../CmpdReg/src/client/custom/Lot_Custom.js | 2 +- modules/CmpdReg/src/client/src/MetaLot.js | 4 +-- modules/CmpdReg/src/client/src/Parent.js | 2 +- .../src/server/routes/CmpdRegRoutes.coffee | 33 +++++++------------ .../src/server/routes/loginRoutes.coffee | 12 ++++++- .../CustomerSpecificServerFunctions.coffee | 9 +++-- 8 files changed, 42 insertions(+), 42 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 9f1a8e332..ecd989330 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -371,9 +371,9 @@ client.browser.enableSearchAll=true ## Cmpd Reg Bulk Loader Options client.service.cmpdReg.persistence.host=tomcat -client.service.cmpdReg.persistence.path=cmpdreg/api/v1 +client.service.cmpdReg.persistence.path=acas/api/v1 client.service.cmpdReg.persistence.fullpath=http://${client.service.cmpdReg.persistence.host}:${client.service.persistence.port}/${client.service.cmpdReg.persistence.path}/ -client.service.cmpdReg.persistence.basepath=http://${client.service.cmpdReg.persistence.host}:${client.service.persistence.port}/cmpdreg +client.service.cmpdReg.persistence.basepath=http://${client.service.cmpdReg.persistence.host}:${client.service.persistence.port}/acas # If project select is shown separately in the Configuration part of the GUI client.cmpdReg.showProjectSelect=true diff --git a/docker-compose.yml b/docker-compose.yml index b0b214547..091a94cb5 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -75,24 +75,24 @@ services: volumes_from: - roo - acas - - cmpdreg + # - cmpdreg env_file: - ./conf/docker/acas/environment/acas.env - ./conf/docker/roo/environment/roo.env - ./conf/docker/cmpdreg/environment/cmpdreg.env command: catalina.sh run roo: - image: mcneilco/acas-roo-server-oss:${ACAS_TAG} + image: test volumes: - /usr/local/tomcat/webapps/acas command: /bin/true - cmpdreg: - image: mcneilco/acas-cmpdreg-roo-server-oss:${ACAS_TAG} - volumes: - - /usr/local/tomcat/webapps/cmpdreg - # Add chemaxon license files here - # - ./chemaxon/licenses/marvin4js-license.cxl:/usr/local/tomcat/webapps/ROOT/marvin4js-license.cxl - # - ./chemaxon/licenses/license.cxl:/root/.chemaxon/license.cxl + # cmpdreg: + # image: test + # volumes: + # - /usr/local/tomcat/webapps/cmpdreg + # # Add chemaxon license files here + # # - ./chemaxon/licenses/marvin4js-license.cxl:/usr/local/tomcat/webapps/ROOT/marvin4js-license.cxl + # # - ./chemaxon/licenses/license.cxl:/root/.chemaxon/license.cxl command: /bin/true volumes: dbstore: diff --git a/modules/CmpdReg/src/client/custom/Lot_Custom.js b/modules/CmpdReg/src/client/custom/Lot_Custom.js index 716d197ae..7484bdf0e 100755 --- a/modules/CmpdReg/src/client/custom/Lot_Custom.js +++ b/modules/CmpdReg/src/client/custom/Lot_Custom.js @@ -435,7 +435,7 @@ $(function() { this.model.set({ notebookPage: jQuery.trim(this.$('.notebookPage').val()), synthesisDate: jQuery.trim(this.$('.synthesisDate').val()), - chemist: this.chemistCodeController.getSelectedModel(), + chemist: this.chemistCodeController.getSelectedModel().get("code"), lotNumber: (jQuery.trim(this.$('.lotNumber').val())=='') ? null : parseInt(jQuery.trim(this.$('.lotNumber').val())) diff --git a/modules/CmpdReg/src/client/src/MetaLot.js b/modules/CmpdReg/src/client/src/MetaLot.js index 9db8b498d..27861aae1 100755 --- a/modules/CmpdReg/src/client/src/MetaLot.js +++ b/modules/CmpdReg/src/client/src/MetaLot.js @@ -380,7 +380,7 @@ $(function() { this.lotController.updateModel(); if (this.lotController.model.isNew() && this.user != null) { this.lotController.model.set({ - 'registeredBy': this.user + 'registeredBy': this.user.get("code") }); } this.parentController.updateModel(); @@ -422,7 +422,7 @@ $(function() { if (this.user.get('isAdmin')) { return true; - }else if (!window.configuration.metaLot.disableEditMyLots && (this.user.get('code') == chemist.get('code') || (registeredBy != null && this.user.get('code') == registeredBy.code))) { + }else if (!window.configuration.metaLot.disableEditMyLots && (this.user.get('code') == chemist || (registeredBy != null && this.user.get('code') == registeredBy))) { return true; } else { return false; diff --git a/modules/CmpdReg/src/client/src/Parent.js b/modules/CmpdReg/src/client/src/Parent.js index d0933d724..a738b4108 100755 --- a/modules/CmpdReg/src/client/src/Parent.js +++ b/modules/CmpdReg/src/client/src/Parent.js @@ -32,7 +32,7 @@ $(function() { exactMass: js.exactMass, molFormula: js.molFormula, comment: js.comment, - chemist: new PickList(js.chemist), + chemist: js.chemist, parentAliases: new AliasCollection(js.parentAliases), registrationDate: js.registrationDate, cdId: js.cdId, diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index 75e63fd7a..0114eddf2 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -1,12 +1,13 @@ exports.setupAPIRoutes = (app) -> app.post '/api/cmpdReg', exports.postAssignedProperties - app.get '/cmpdReg/scientists', exports.getBasicCmpdReg + app.get '/cmpdReg/scientists', exports.getScientists app.get '/cmpdReg/metalots/corpName/[\\S]*', exports.getMetaLot + app.post '/cmpdReg/metalots', exports.metaLots exports.setupRoutes = (app, loginRoutes) -> app.get '/cmpdReg', loginRoutes.ensureAuthenticated, exports.cmpdRegIndex app.get '/marvin4js-license.cxl', loginRoutes.ensureAuthenticated, exports.getMarvinJSLicense - app.get '/cmpdReg/scientists', loginRoutes.ensureAuthenticated, exports.getAPICmpdReg + app.get '/cmpdReg/scientists', loginRoutes.ensureAuthenticated, exports.getScientists app.get '/cmpdReg/parentAliasKinds', loginRoutes.ensureAuthenticated, exports.getBasicCmpdReg app.get '/cmpdReg/units', loginRoutes.ensureAuthenticated, exports.getBasicCmpdReg app.get '/cmpdReg/solutionUnits', loginRoutes.ensureAuthenticated, exports.getBasicCmpdReg @@ -102,7 +103,7 @@ exports.cmpdRegIndex = (req, res) -> cmpdRegConfig: cmpdRegConfig syncCmpdRegUser = (req, cmpdRegUser) -> - exports.getScientists req, (scientistResponse) -> + exports.getScientistsInternal (scientistResponse) -> foundScientists = JSON.parse scientistResponse if (_.findWhere foundScientists, {code: cmpdRegUser.code})? #update scientist @@ -224,24 +225,14 @@ exports.updateProjects = (jsonBody, callback) -> callback JSON.stringify {error: "something went wrong :("} ) -exports.getScientists = (req, callback) -> - console.log 'in getScientists' - cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + "/scientists" - request( - method: 'GET' - url: cmpdRegCall - json: true - , (error, response, json)=> - if !error - console.log JSON.stringify json - callback JSON.stringify json - else - console.log 'got ajax error trying to get CmpdReg scientists' - console.log error - console.log json - console.log response - callback JSON.stringify {error: "something went wrong :("} - ) +exports.getScientists = (req, resp) => + exports.getScientistsInternal (authors) -> + resp.json authors + +exports.getScientistsInternal = (callback) -> + loginRoutes = require './loginRoutes.js' + loginRoutes.getAuthorsInternal {}, (statusCode, authors) => + callback authors exports.saveScientists = (jsonBody, callback) -> console.log 'in saveScientists' diff --git a/modules/Login/src/server/routes/loginRoutes.coffee b/modules/Login/src/server/routes/loginRoutes.coffee index 7c4a87299..6c7541bda 100644 --- a/modules/Login/src/server/routes/loginRoutes.coffee +++ b/modules/Login/src/server/routes/loginRoutes.coffee @@ -222,4 +222,14 @@ exports.getAuthors = (req, resp) -> baseEntityServiceTestJSON = require '../src/javascripts/spec/testFixtures/BaseEntityServiceTestJSON.js' resp.end JSON.stringify baseEntityServiceTestJSON.authorsList else - csUtilities.getAuthors req, resp + if csUtilities.getAuthors? + csUtilities.getAuthors req, resp + else + opts = req.query + exports.getAuthorsInternal opts, (statusCode, response) => + resp.json response + +exports.getAuthorsInternal = (opts, callback) -> + csUtilities.getAllAuthors(opts, (statusCode, response) -> + callback statusCode, response + ) \ No newline at end of file diff --git a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee index 11d82342d..893feecd1 100644 --- a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee +++ b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee @@ -240,16 +240,15 @@ exports.validateCloneAndGetTarget = (req, resp) -> psProtocolServiceTestJSON = require "#{ACAS_HOME}/public/javascripts/spec/PrimaryScreen/testFixtures/PrimaryScreenProtocolServiceTestJSON.js" resp.json psProtocolServiceTestJSON.successfulCloneValidation -exports.getAuthors = (req, resp) -> #req passed in as input to be able to filter users by roles +exports.getAllAuthors = (opts, callback) -> config = require "#{ACAS_HOME}/conf/compiled/conf.js" serverUtilityFunctions = require "#{ACAS_HOME}/routes/ServerUtilityFunctions.js" baseurl = config.all.client.service.persistence.fullpath+"authors/codeTable" - - if req.query.roleType? and req.query.roleKind? and req.query.roleName? + if opts.roleType? and opts.roleKind? and opts.roleName? baseurl = config.all.client.service.persistence.fullpath+"authors/findByRoleTypeKindAndName" baseurl += "?roleType=#{req.query.roleType}&roleKind=#{req.query.roleKind}&roleName=#{req.query.roleName}&format=codeTable" - - serverUtilityFunctions.getFromACASServer(baseurl, resp) + serverUtilityFunctions.getFromACASServerInternal baseurl, (statusCode, json) -> + callback statusCode, json exports.getAllAuthorObjectsInternal = (callback) -> config = require "#{ACAS_HOME}/conf/compiled/conf.js" From 9ad3986cff452ae6f64f20bab6de2b19d1408264 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 20 Dec 2018 09:31:50 -0800 Subject: [PATCH 410/576] fixes #209: Adding multiple gpg key-servers for reliability of builds (#541) --- Dockerfile | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 8b3958f67..5fa365a71 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,16 +12,19 @@ RUN \ # node RUN set -ex \ && for key in \ - 9554F04D7259F04124DE6B476D5A82AC7E37093B \ 94AE36675C464D64BAFA68DD7434390BDBE9B9C5 \ - 0034A06D9D9B0064CE8ADF6BF1747F4AD2306D93 \ FD3A5288F042B6850C66B31F09FE44734EB7990E \ 71DCFD284A79C3B38668286BC97EC7A07EDE3FC1 \ DD8F2338BAE7501E3DD5AC78C273792F7D83545D \ - B9AE9905FFD7803F25714661B63B535A4C206CA9 \ C4F0DFFF4E8C1A8236409D08E73BC641CC11F4C8 \ + B9AE9905FFD7803F25714661B63B535A4C206CA9 \ + 56730D5401028683275BD23C23EFEFE93C4CFFFE \ + 77984A986EBC2AA786BC0F66B01FBB92821C587A \ + 8FCCA13FEF1D0C2E91008E09770F7A9A5AE15600 \ ; do \ - gpg --keyserver ha.pool.sks-keyservers.net --recv-keys "$key"; \ + gpg --keyserver ha.pool.sks-keyservers.net --recv-keys "$key" || \ + gpg --keyserver pgp.mit.edu --recv-keys "$key" || \ + gpg --keyserver keyserver.pgp.com --recv-keys "$key"; \ done ENV NPM_CONFIG_LOGLEVEL warn From 28ff907568473aca66e4a9d7c8210b7d6c028984 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 20 Dec 2018 09:50:13 -0800 Subject: [PATCH 411/576] fixes 542: install gulp 4 from tagged npm version, fix issue with watch for npm install (#543) --- Dockerfile | 2 +- gulpfile.coffee | 5 ++++- package.json | 2 +- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 5fa365a71..07645b23d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -46,7 +46,7 @@ ENV ACAS_BASE /home/runner/acas ENV ACAS_CUSTOM /home/runner/acas_custom ENV ACAS_SHARED /home/runner/acas_shared ENV APACHE Redhat -RUN npm install -g gulpjs/gulp.git#4.0 forever nodemon mocha coffee-script +RUN npm install -g gulp@4.0.0 forever nodemon mocha coffeescript COPY package.json $ACAS_BASE/package.json RUN chown -R runner:runner $ACAS_BASE USER runner diff --git a/gulpfile.coffee b/gulpfile.coffee index 53246ca97..85c7cbc79 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -218,6 +218,9 @@ taskConfigs = command: 'npm' args: [ 'install' ] options: _.extend _.clone(globalExecuteOptions), cwd: build + src: [ + build + '/package.json' + ] , taskName: "prepare_config_files" command: 'node' @@ -397,7 +400,7 @@ createExecuteTask = (options) => return command.on 'exit', (code) -> cb code - unless watch == false + unless watch == false || !options.src? watchTaskName = "watch:#{taskName}" watchOptions = watch?.options ? {} gulp.task watchTaskName, -> diff --git a/package.json b/package.json index ca031238e..80d6d619c 100644 --- a/package.json +++ b/package.json @@ -75,7 +75,7 @@ "devDependencies": { "coffee-script": "^1.12.4", "del": "^2.2.2", - "gulp": "github:gulpjs/gulp#4.0", + "gulp": "^4.0.0", "gulp-coffee": "^2.3.3", "gulp-coffeeify": "^0.1.8", "gulp-copy": "^1.0.0", From 1f8f14e6f4c481c4e49fa9feee28c00044028936 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 20 Dec 2018 09:50:23 -0800 Subject: [PATCH 412/576] fixes #544: A bug caused by (a6f202f) was comparing the code name with id, this reverts that bug (#545) --- modules/GenericDataParser/src/server/generic_data_parser.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 2a625a20d..7c368cfa6 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -1782,7 +1782,7 @@ getExperimentByNameCheck <- function(experimentName, protocol, configList, dupli protocolOfExperiment <- getProtocolByCodeName(experimentList[[1]]$protocol$codeName) - if (is.na(protocol) || protocolOfExperiment$id != protocol$codeName) { + if (is.na(protocol) || protocolOfExperiment$id != protocol$id) { if (duplicateNamesAllowed) { experiment <- NA } else { From 9213ec938f9672ce9472adecc0f328b268667601 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 20 Dec 2018 12:26:09 -0800 Subject: [PATCH 413/576] fixes #546 #547: allow case mismatch in image file names and SEL matching, instead of error warn user if an image is uploaded without a cooresponding SEL line --- .../src/server/generic_data_parser.R | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 7c368cfa6..11d27f840 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -980,20 +980,22 @@ validateUploadedImages <- function(imageLocation, listedImageFiles, experimentFo uploadedImageFiles <- list.files(imageLocation) # Make sure all elements are part of both vectors. - # We allow the same file to be listed multiple times -- setdiff disregards duplicates (and you can't + # We allow the same file to be listed multiple times -- %in% disregards duplicates (and you can't # put the same file into a directory twice, so we don't have a problem there) - notUploaded <- setdiff(listedImageFiles, uploadedImageFiles) - notListed <- setdiff(uploadedImageFiles, listedImageFiles) + listedImageFilesLower <- tolower(listedImageFiles) + uploadedImageFilesLower <- tolower(uploadedImageFiles) + notUploaded <- listedImageFiles[!listedImageFilesLower %in% uploadedImageFilesLower] + notListed <- uploadedImageFiles[!uploadedImageFilesLower %in% listedImageFilesLower] if (length(notListed) > 0) { unlink(experimentFolderLocation, recursive = TRUE) - stopUser(paste0("The following files were uploaded in a zip file, but were not listed in the spreadsheet: ", - paste(notListed, collapse = ", "), ". If in doubt, please check your capitalization.")) + warnUser(paste0("The following files were uploaded in a zip file, but were not listed in the spreadsheet: ", + paste(notListed, collapse = ", "))) } if (length(notUploaded) > 0) { unlink(experimentFolderLocation, recursive = TRUE) stopUser(paste0("The following files were listed in the spreadsheet, but were not uploaded in a zip file: ", - paste(notUploaded, collapse = ", "), ". If in doubt, please check your capitalization.")) + paste(notUploaded, collapse = ", "))) } return(TRUE) From 60062c88f4e212d7395882a8106bb9bc99b5ea39 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 26 Dec 2018 11:57:15 -0800 Subject: [PATCH 414/576] setting flyway path for oss --- conf/docker/acas/environment/acas.env | 2 +- conf/docker/roo/environment/roo.env | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/conf/docker/acas/environment/acas.env b/conf/docker/acas/environment/acas.env index 70f8f5848..22fbc845e 100644 --- a/conf/docker/acas/environment/acas.env +++ b/conf/docker/acas/environment/acas.env @@ -5,4 +5,4 @@ ACAS_DB_NAME=acas ACAS_SCHEMA=acas ACAS_USERNAME=acas ACAS_PASSWORD=acas -ACAS_FLYWAY_LOCATION=com.labsynch.labseer.db.migration.postgres,db/migration/postgres +ACAS_FLYWAY_LOCATION=com.labsynch.labseer.db.migration.postgres,db/migration/postgres,db/migration/indigo/postgres diff --git a/conf/docker/roo/environment/roo.env b/conf/docker/roo/environment/roo.env index e4d4a5d15..f81c10cbc 100644 --- a/conf/docker/roo/environment/roo.env +++ b/conf/docker/roo/environment/roo.env @@ -3,5 +3,4 @@ DATABASE_DRIVER=org.postgresql.Driver DATABASE_URL=jdbc:postgresql://db:5432/${ACAS_DB_NAME} VALIDATION_QUERY=select version() CATALINA_OPTS="-Xms512M -Xmx1536M -XX:MaxPermSize=512m" -ACAS_FLYWAY_LOCATION=com.labsynch.labseer.db.migration.postgres,db/migration/postgres From ed4f427129a5860a3098323e5b1c68d5243116bc Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 26 Dec 2018 12:47:58 -0800 Subject: [PATCH 415/576] setting flyway location in acas configs --- conf/config.properties.example | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index ecd989330..1621bc157 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -538,7 +538,7 @@ server.curveRender.drawPointsForRejectedCurve=true # Restrict experiment search by project server.service.projects.restrictExperiments=false -flyway.location=db/migration/postgres,com.labsynch.labseer.db.migration.postgres +flyway.location=db/migration/postgres,com.labsynch.labseer.db.migration.postgres,db/migration/indigo/postgres flyway.schema=acas flyway.database.username=${server.database.username} flyway.database.password=${server.database.password} From fb94206f7db1a44c21847707b3a5e7ce5dbb709e Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 26 Dec 2018 14:54:36 -0800 Subject: [PATCH 416/576] send project code only when registering a lot --- modules/CmpdReg/src/client/custom/Lot_Custom.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/CmpdReg/src/client/custom/Lot_Custom.js b/modules/CmpdReg/src/client/custom/Lot_Custom.js index 7484bdf0e..7c4419108 100755 --- a/modules/CmpdReg/src/client/custom/Lot_Custom.js +++ b/modules/CmpdReg/src/client/custom/Lot_Custom.js @@ -458,7 +458,7 @@ $(function() { purityOperator: null, amountUnits: null, purityMeasuredBy: null, - project: this.projectCodeController.getSelectedModel(), + project: this.projectCodeController.getSelectedModel().get("code"), supplierLot: '', meltingPoint: null, boilingPoint: null, @@ -536,7 +536,7 @@ $(function() { tareWeightUnits: tareWeightUnits, totalAmountStoredUnits: totalAmountStoredUnits, purityMeasuredBy: purityMeasuredBy, - project: this.projectCodeController.getSelectedModel(), + project: this.projectCodeController.getSelectedModel().get("code"), vendor: vendor, supplierLot: jQuery.trim(this.$('.supplierLot').val()), meltingPoint: From 0fa620206b3cad8a86dd500b3e60ef297de7b37a Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 26 Dec 2018 16:45:52 -0800 Subject: [PATCH 417/576] fixing issue due to an easter egg built into search --- modules/CmpdReg/src/client/src/SearchForm.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/CmpdReg/src/client/src/SearchForm.js b/modules/CmpdReg/src/client/src/SearchForm.js index cf1ca9801..c68d15e02 100755 --- a/modules/CmpdReg/src/client/src/SearchForm.js +++ b/modules/CmpdReg/src/client/src/SearchForm.js @@ -7,7 +7,7 @@ $(function() { _.each(attributes, function(att, key) { if( (att != '' && att!=null) && key!='aliasContSelect' && key!='searchType' && key!='percentSimilarity' && key!='maxResults' && key!='loggedInUser' ) { if( key=='chemist') { - if( att.get('code')!='anyone') { + if( att!='anyone') { allEmpty = false; } } else { @@ -187,7 +187,7 @@ $(function() { percentSimilarity: (jQuery.trim(this.$('.percentSimilarity').val())=='') ? null : parseFloat(jQuery.trim(this.$('.percentSimilarity').val())), - chemist: this.chemistCodeController.getSelectedModel(), + chemist: this.chemistCodeController.getSelectedModel().get("code"), maxResults: (jQuery.trim(this.$('.maxResults').val())=='') ? null : parseFloat(jQuery.trim(this.$('.maxResults').val())), From d61e351b093ae3917958f858631f98d8a32639d4 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 28 Dec 2018 15:43:16 -0800 Subject: [PATCH 418/576] call validation service to validate the submitted chemists --- .../routes/CmpdRegBulkLoaderRoutes.coffee | 86 ++++++++++++++----- 1 file changed, 63 insertions(+), 23 deletions(-) diff --git a/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee b/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee index 9eafb358e..d76c48f8b 100644 --- a/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee +++ b/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee @@ -3,6 +3,7 @@ path = require 'path' exports.setupAPIRoutes = (app) -> app.post '/api/cmpdRegBulkLoader', exports.postAssignedProperties app.post '/api/cmpdRegBulkLoader/registerCmpds', exports.registerCmpds + app.post '/api/cmpdRegBulkLoader/validationProperties', exports.validationProperties app.get '/api/cmpdRegBulkLoader/getFilesToPurge', exports.getFilesToPurge app.post '/api/cmpdRegBulkLoader/purgeFile', exports.purgeFile @@ -126,12 +127,41 @@ exports.saveTemplate = (req, resp) -> resp.end JSON.stringify "Error" ) +exports.validationProperties = (req, resp) -> + req.connection.setTimeout 6000000 + exports.validationPropertiesInternal req.body, (json) => + resp.json json + +exports.validationPropertiesInternal = (reqObject, callback) -> + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.cmpdReg.persistence.fullpath+"bulkload/validationProperties" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: reqObject + json: true + , (error, response, json) => + console.log json + if !error && response.statusCode == 200 + callback json + else + console.error 'got ajax error trying to validate sdf properties' + console.error error + console.error json + console.error response + callback {error: json} + ) + +exports.getScientistsInternal = (callback) -> + loginRoutes = require './loginRoutes.js' + loginRoutes.getAuthorsInternal {}, (statusCode, authors) => + callback authors + exports.registerCmpds = (req, resp) -> req.connection.setTimeout 6000000 createSummaryZip = (fileName, json) -> #remove .sdf from fileName - console.log "fileName" - console.log fileName fileName = fileName.substring(0, fileName.length-4) zipFileName = fileName+".zip" fs = require 'fs' @@ -166,28 +196,38 @@ exports.registerCmpds = (req, resp) -> else fileName = req.body.fileName delete req.body.fileName - config = require '../conf/compiled/conf.js' - baseurl = config.all.client.service.cmpdReg.persistence.fullpath+"bulkload/registerSdf" - request = require 'request' - request( - method: 'POST' - url: baseurl - body: req.body - json: true - , (error, response, json) => - console.log json - if !error && response.statusCode == 200 && json.reportFiles? - createSummaryZip fileName, json - else - console.log 'got ajax error trying to register compounds' - console.log error - console.log json - console.log response - if json.summary? - resp.json [json] + exports.getScientistsInternal (authors) => + _ = require 'underscore' + + authorCodes = _.pluck authors, "code" + + exports.validationPropertiesInternal req.body, (sdfProperties) => + missingAuthorCodes = _.difference sdfProperties.chemists, authorCodes + if missingAuthorCodes.length > 0 + resp.json [{summary: "Some chemists have not been registered please make sure they are registered and try again: #{JSON.stringify(missingAuthorCodes)}"}] + return else - resp.end JSON.stringify "Error" - ) + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.cmpdReg.persistence.fullpath+"bulkload/registerSdf" + request = require 'request' + request( + method: 'POST' + url: baseurl + body: req.body + json: true + , (error, response, json) => + if !error && response.statusCode == 200 && json.reportFiles? + createSummaryZip fileName, json + else + console.log 'got ajax error trying to register compounds' + console.log error + console.log json + console.log response + if json.summary? + resp.json [json] + else + resp.end JSON.stringify "Error" + ) moveSdfFile = (req, resp, callback) -> fileName = req.body.fileName From 81fd608b68b6a0437da1493e8b0b647a9ea90186 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 2 Jan 2019 18:19:35 -0800 Subject: [PATCH 419/576] add route/function to get users allowed projects using customer specific server functions, pass the list of allowed projects to search routes for experiments and protocols --- .../src/server/routes/AuthorRoutes.coffee | 37 +++++++++++++++++++ .../routes/ExperimentServiceRoutes.coffee | 14 ++++--- .../routes/ProtocolServiceRoutes.coffee | 16 +++++--- 3 files changed, 56 insertions(+), 11 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee index 3ef80654c..65f8bdcdf 100644 --- a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee @@ -16,6 +16,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/author', loginRoutes.ensureAuthenticated, exports.saveAuthor app.put '/api/author/:id', loginRoutes.ensureAuthenticated, exports.updateAuthor app.get '/activateUser', exports.activateUserAndRedirectToChangePassword + app.get '/api/allowedProjects', loginRoutes.ensureAuthenticated, exports.allowedProjects serverUtilityFunctions = require './ServerUtilityFunctions.js' _ = require 'underscore' @@ -39,6 +40,42 @@ FirstLsThingItxList = serverUtilityFunctions.FirstLsThingItxList SecondLsThingItxList = serverUtilityFunctions.SecondLsThingItxList +exports.allowedProjects = (req, resp) -> + exports.allowedProjectsInternal req.user, (statusCode, json) -> + resp.statusCode = statusCode + resp.json json + +exports.allowedProjectsInternal = (user, callback) -> + csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFunctions.js' + csUtilities.getProjectStubsInternal (statusCode, allProjects) -> + config = require '../conf/compiled/conf.js' + _ = require 'underscore' + if (config.all.server.project.roles.enable) + filteredProjects = [] + isAdmin = false; + roles = user.roles + allowedProjectCodes = [] + user.roles.forEach (role) -> + if role.roleEntry.lsType != null && role.roleEntry.lsType == "Project" + allowedProjectCodes.push role.lsKind + else if role.roleEntry.roleName == config.all.client.roles.acas.adminRole + isAdmin = true + if isAdmin + filteredProjects = allProjects + else + allProjects.forEach (project) -> + isRestricted = project.isRestricted + if isRestricted + if _.contains(allowedProjectCodes, project.code) + filteredProjects.push(project) + else + filteredProjects.push(project) + projects = filteredProjects + else + projects = allProjects + callback 200, projects + + exports.getAuthorByUsername = (req, resp) -> exports.getAuthorByUsernameInternal req.params.username, (json, statusCode) -> resp.statusCode = statusCode diff --git a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee index 0ebc3af33..d3d1a1470 100644 --- a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee @@ -490,11 +490,15 @@ exports.genericExperimentSearch = (req, res) -> username = req.query.username else username = "none" - baseurl = config.all.client.service.persistence.fullpath+"experiments/search?q="+req.params.searchTerm+"&userName="+username - console.log "baseurl" - console.log baseurl - serverUtilityFunctions = require './ServerUtilityFunctions.js' - serverUtilityFunctions.getFromACASServer(baseurl, res) + authorRoutes = require './AuthorRoutes.js' + authorRoutes.allowedProjectsInternal req.user, (statusCode, allowedUserProjects) -> + _ = require "underscore" + allowedProjectCodes = _.pluck(allowedUserProjects, "code") + baseurl = config.all.client.service.persistence.fullpath+"experiments/search?q="+req.params.searchTerm+"&projects=#{allowedProjectCodes.join(',')}" + console.log "baseurl" + console.log baseurl + serverUtilityFunctions = require './ServerUtilityFunctions.js' + serverUtilityFunctions.getFromACASServer(baseurl, res) exports.editExperimentLookupAndRedirect = (req, res) -> if global.specRunnerTestmode diff --git a/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee index fd0ee05e5..ca0927c54 100644 --- a/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee @@ -490,12 +490,16 @@ exports.genericProtocolSearch = (req, res) -> else res.end JSON.stringify [protocolServiceTestJSON.fullSavedProtocol, protocolServiceTestJSON.fullDeletedProtocol] else - config = require '../conf/compiled/conf.js' - baseurl = config.all.client.service.persistence.fullpath+"protocols/search?q="+req.params.searchTerm+"&userName="+req.user.username - console.log "baseurl" - console.log baseurl - serverUtilityFunctions = require './ServerUtilityFunctions.js' - serverUtilityFunctions.getFromACASServer(baseurl, res) + authorRoutes = require './AuthorRoutes.js' + authorRoutes.allowedProjectsInternal req.user, (statusCode, allowedUserProjects) -> + _ = require "underscore" + allowedProjectCodes = _.pluck(allowedUserProjects, "code") + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"protocols/search?q="+req.params.searchTerm+"&projects=#{allowedProjectCodes.join(',')}" + console.log "baseurl" + console.log baseurl + serverUtilityFunctions = require './ServerUtilityFunctions.js' + serverUtilityFunctions.getFromACASServer(baseurl, res) exports.deleteProtocol = (req, res) -> if global.specRunnerTestmode From c262339c134753627a615f3c53f909e78a45aafb Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 3 Jan 2019 10:48:51 -0800 Subject: [PATCH 420/576] use author routes to get authorized projects --- modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index 0114eddf2..cf35d4030 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -140,9 +140,10 @@ exports.getAPICmpdReg = (req, resp) -> req.pipe(request(cmpdRegCall)).pipe(resp) exports.getAuthorizedCmpdRegProjects = (req, resp) -> - exports.getAuthorizedCmpdRegProjectsInternal req, (response) => + authorRoutes = require './AuthorRoutes.js' + authorRoutes.allowedProjectsInternal req.user, (statusCode, allowedUserProjects) -> resp.status "200" - resp.end JSON.stringify response + resp.end JSON.stringify allowedUserProjects exports.getAuthorizedCmpdRegProjectsInternal = (req, callback) -> exports.getACASProjects req, (statusCode, acasProjectsResponse)-> From 84a750947990ccd52be2f40a7de79be5e7e2572b Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Sun, 6 Jan 2019 14:48:38 -0800 Subject: [PATCH 421/576] adding call to Boostrap.js to allow for custom setup scripts --- app_api_template.coffee | 1 + modules/ServerAPI/src/server/Bootstrap.coffee | 14 ++++++++++++++ 2 files changed, 15 insertions(+) create mode 100644 modules/ServerAPI/src/server/Bootstrap.coffee diff --git a/app_api_template.coffee b/app_api_template.coffee index 31d143ccd..406a132c4 100644 --- a/app_api_template.coffee +++ b/app_api_template.coffee @@ -49,6 +49,7 @@ startApp = -> httpServer = http.createServer(app).listen(app.get('port'), -> console.log("ACAS API server listening on port " + app.get('port')) + require "./src/javascripts/ServerAPI/Bootstrap.js" ) ###TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES### diff --git a/modules/ServerAPI/src/server/Bootstrap.coffee b/modules/ServerAPI/src/server/Bootstrap.coffee new file mode 100644 index 000000000..aa7ab17aa --- /dev/null +++ b/modules/ServerAPI/src/server/Bootstrap.coffee @@ -0,0 +1,14 @@ +# Do not add content to this file, this is strictly for client usage to allow a script to be executed on start + +# Example install of LD client python library on start +console.log "No custom Bootstrap script provided" +# ACAS_HOME="../../.." +# config = require "#{ACAS_HOME}/conf/compiled/conf.js" +# exec = require('child_process').exec +# command = "pip2.7 install --user #{config.all.client.service.result.viewer.liveDesign.baseUrl}/ldclient.tar.gz" +# console.log "About to call python using command: "+command +# child = exec command, (error, stdout, stderr) -> +# console.log stdout +# if error? +# console.warn "Error installing ld client. This can happen if Live Design was down during ACAS start or otherwise ACAS could not communicate with Live Design. This is just a warning as LD client might already be installed and be the correction version." +# console.error stderr From 1bc9ab9a546ed0521e8130413b057c57b21305de Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Sun, 6 Jan 2019 14:50:31 -0800 Subject: [PATCH 422/576] remove unneccessary routes from cmpd reg, reconfiguring internal functions to call author services allowed projects function --- .../src/server/routes/CmpdRegRoutes.coffee | 43 +------------------ .../server/routes/ProjectServiceRoutes.coffee | 13 ++---- .../src/server/routes/AuthorRoutes.coffee | 1 + 3 files changed, 6 insertions(+), 51 deletions(-) diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index cf35d4030..102c3a4ac 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -145,46 +145,6 @@ exports.getAuthorizedCmpdRegProjects = (req, resp) -> resp.status "200" resp.end JSON.stringify allowedUserProjects -exports.getAuthorizedCmpdRegProjectsInternal = (req, callback) -> - exports.getACASProjects req, (statusCode, acasProjectsResponse)-> - acasProjects = acasProjectsResponse - exports.getProjects req, (cmpdRegProjectsResponse)-> - cmpdRegProjects = JSON.parse cmpdRegProjectsResponse - allowedProjectCodes = _.pluck acasProjects, 'code' - allowedProjects = _.filter cmpdRegProjects, (cmpdRegProject) -> - return (cmpdRegProject.code in allowedProjectCodes) - callback allowedProjects - - -exports.getACASProjects = (req, callback) -> - csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFunctions.js' - if !req.user? - req.user = {} - req.user.username = req.params.username - if global.specRunnerTestmode - resp.end JSON.stringify "testMode not implemented" - else - csUtilities.getProjectsInternal req, callback - -exports.getProjects = (req, callback) -> - console.log 'in getProjects' - cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + "/projects" - request( - method: 'GET' - url: cmpdRegCall - json: true - , (error, response, json)=> - if !error - console.log JSON.stringify json - callback JSON.stringify json - else - console.log 'got ajax error trying to get CmpdReg projects' - console.log error - console.log json - console.log response - callback JSON.stringify {error: "something went wrong :("} - ) - exports.saveProjects = (jsonBody, callback) -> console.log 'in saveProjects' @@ -325,7 +285,7 @@ exports.getMetaLot = (req, resp) -> if json?.lot?.project?.code? projectCode = json.lot.project.code if cmpdRegConfig.metaLot.useProjectRolesToRestrictLotDetails - exports.getACASProjects req, (statusCode, acasProjectsForUsers) => + authorRoutes.allowedProjectsInternal req.user, (statusCode, acasProjectsForUsers) => if statusCode != 200 resp.statusCode = statusCode resp.end JSON.stringify acasProjectsForUsers @@ -343,7 +303,6 @@ exports.getMetaLot = (req, resp) -> resp.end JSON.stringify "Could not find lot" else resp.json json - else console.log 'got ajax error trying to get CmpdReg MetaLot' console.log error diff --git a/modules/Components/src/server/routes/ProjectServiceRoutes.coffee b/modules/Components/src/server/routes/ProjectServiceRoutes.coffee index f8234ef92..5c3935107 100644 --- a/modules/Components/src/server/routes/ProjectServiceRoutes.coffee +++ b/modules/Components/src/server/routes/ProjectServiceRoutes.coffee @@ -8,15 +8,10 @@ exports.setupRoutes = (app, loginRoutes) -> app.get '/api/projects/getAllProjects/stubs', loginRoutes.ensureAuthenticated, exports.getProjectStubs exports.getProjects = (req, resp) -> - csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFunctions.js' - if !req.user? - req.user = {} - req.user.username = req.params.username - if global.specRunnerTestmode - projectServiceTestJSON = require '../public/javascripts/spec/testFixtures/projectServiceTestJSON.js' - resp.end JSON.stringify projectServiceTestJSON.projects - else - csUtilities.getProjects req, resp + authorRoutes = require './AuthorRoutes.js' + authorRoutes.allowedProjectsInternal req.user, (statusCode, allowedUserProjects) -> + resp.status "200" + resp.end JSON.stringify allowedUserProjects exports.getProjectStubs = (req, resp) -> csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFunctions.js' diff --git a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee index 65f8bdcdf..f79f2c826 100644 --- a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee @@ -73,6 +73,7 @@ exports.allowedProjectsInternal = (user, callback) -> projects = filteredProjects else projects = allProjects + console.error "Authorized projects: #{JSON.stringify(projects)}" callback 200, projects From 667d7cb1bfbfdb331f2e9c32fd10cf1e804c03a7 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 11 Jan 2019 07:57:45 -0800 Subject: [PATCH 423/576] adding ld client install as part of default bootstrap if setting is set to true --- conf/config.properties.example | 1 + modules/ServerAPI/src/server/Bootstrap.coffee | 18 ++++++++++++++---- 2 files changed, 15 insertions(+), 4 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 1621bc157..8693e7d64 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -285,6 +285,7 @@ client.service.result.viewer.liveDesign.database.username= client.service.result.viewer.liveDesign.database.password= client.service.result.viewer.liveDesign.database.hostname= client.service.result.viewer.liveDesign.database.port= +server.liveDesign.installClientOnStart=false client.service.result.viewer.simpleSAR.baseUrl= client.service.result.viewer.seurat.protocolPrefix=http://${client.service.persistence.host}:9080/seurat/runseurat?cmd=newjob&AssayName= client.service.result.viewer.seurat.experimentPrefix=&AssayProtocol= diff --git a/modules/ServerAPI/src/server/Bootstrap.coffee b/modules/ServerAPI/src/server/Bootstrap.coffee index aa7ab17aa..67e135b8b 100644 --- a/modules/ServerAPI/src/server/Bootstrap.coffee +++ b/modules/ServerAPI/src/server/Bootstrap.coffee @@ -1,11 +1,21 @@ # Do not add content to this file, this is strictly for client usage to allow a script to be executed on start # Example install of LD client python library on start -console.log "No custom Bootstrap script provided" -# ACAS_HOME="../../.." -# config = require "#{ACAS_HOME}/conf/compiled/conf.js" +ACAS_HOME="../../.." +config = require "#{ACAS_HOME}/conf/compiled/conf.js" +if config.all.server.liveDesign.installClientOnStart? && config.all.server.liveDesign.installClientOnStart + exec = require('child_process').exec + command = "pip2.7 install --upgrade --force-reinstall --user #{config.all.client.service.result.viewer.liveDesign.baseUrl}/ldclient.tar.gz" + console.log "About to call python using command: "+command + child = exec command, (error, stdout, stderr) -> + console.log stdout + if error? + console.warn "Error installing ld client. This can happen if Live Design was down during ACAS start or otherwise ACAS could not communicate with Live Design. This is just a warning as LD client might already be installed and be the correction version." + console.error stderr + +# Example install of LD client python library from local location on start # exec = require('child_process').exec -# command = "pip2.7 install --user #{config.all.client.service.result.viewer.liveDesign.baseUrl}/ldclient.tar.gz" +# command = "pip2.7 install --upgrade --force-reinstall --user /tmp/ld_client" # console.log "About to call python using command: "+command # child = exec command, (error, stdout, stderr) -> # console.log stdout From 840c019e2c5cdb6f0bfe738370feed9dc2c43eca Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 11 Jan 2019 07:58:30 -0800 Subject: [PATCH 424/576] removing unnecessary logging --- modules/ServerAPI/src/server/routes/AuthorRoutes.coffee | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee index f79f2c826..65f8bdcdf 100644 --- a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee @@ -73,7 +73,6 @@ exports.allowedProjectsInternal = (user, callback) -> projects = filteredProjects else projects = allProjects - console.error "Authorized projects: #{JSON.stringify(projects)}" callback 200, projects From ab0888b202ab271f1cbfb499c37854b1be5b390b Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 11 Jan 2019 07:59:14 -0800 Subject: [PATCH 425/576] ignore venv and remove commented out code --- .gitignore | 1 + app_template.coffee | 12 ------------ gulpfile.coffee | 2 +- 3 files changed, 2 insertions(+), 13 deletions(-) diff --git a/.gitignore b/.gitignore index fbc19bffb..a18177bca 100644 --- a/.gitignore +++ b/.gitignore @@ -24,6 +24,7 @@ Dockerfile* docker-compose*.yml build licenses +venv #this is for the soft link in .dockerfile (git ignore .git by default) .git chemaxon diff --git a/app_template.coffee b/app_template.coffee index 182b4d9d2..6f64ba8eb 100644 --- a/app_template.coffee +++ b/app_template.coffee @@ -48,18 +48,6 @@ startApp = -> else passport.use new LocalStrategy csUtilities.loginStrategy -# passport.isAdmin = (req, resp, next) -> -# if req.isAuthenticated() and csUtilities.isUserAdmin(req.user) -# next() -# else -# next new handler.NotAuthorizedError "Sorry, you don't have the right!" -# passport.isAuthenticated = (req, resp, next) -> -# console.log "running passort.isAuthenticated" -# unless req.isAuthenticated() -# next new handler.NotAuthorizedError "Sorry, you don't have the right!" -# else -# next() - loginRoutes = require './routes/loginRoutes' MemoryStore = express.session.MemoryStore; sessionStore = new MemoryStore(); diff --git a/gulpfile.coffee b/gulpfile.coffee index 85c7cbc79..63586d4d6 100644 --- a/gulpfile.coffee +++ b/gulpfile.coffee @@ -299,7 +299,7 @@ taskConfigs = renameFunction: getRPath , taskName: "python" - src: getGlob('modules/**/src/server/python/**') + src: getGlob('modules/**/src/server/python/**', '!modules/**/src/server/python/**/venv/**') dest: build + '/src/python' options: _.extend _.clone(globalCopyOptions), {} renameFunction: getPythonPath From 095f8c64eba7b1344415e34d3fb89f1cd99d5ff3 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 11 Jan 2019 08:00:54 -0800 Subject: [PATCH 426/576] add a translation layer between ld client and acas customer specific server functions --- .../src/server/python/acas_ldclient/README.md | 4 + .../python/acas_ldclient/acasldclient.py | 189 ++++++++++++++++++ 2 files changed, 193 insertions(+) create mode 100644 modules/ServerAPI/src/server/python/acas_ldclient/README.md create mode 100644 modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py diff --git a/modules/ServerAPI/src/server/python/acas_ldclient/README.md b/modules/ServerAPI/src/server/python/acas_ldclient/README.md new file mode 100644 index 000000000..35a1ae724 --- /dev/null +++ b/modules/ServerAPI/src/server/python/acas_ldclient/README.md @@ -0,0 +1,4 @@ +SERVER_FQDN= +PYTHON=/usr/local/bin/python +virtualenv -p $PYTHON venv && source venv/bin/activate +pip install https://$SERVER_FQDN/livedesign/ldclient.tar.gz \ No newline at end of file diff --git a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py new file mode 100644 index 000000000..22643512c --- /dev/null +++ b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py @@ -0,0 +1,189 @@ +""" +Interface for fetching data for ACAS API +""" +from ldclient.client import LDClient +import argparse +import json +import os, sys + +def get_parser(): + """ + @return: + A command-line parser with switches and defaults defined. + @rtype: + argparse.ArgumentParser + + """ + # Get an argsparse parser, and populate it + script_usage = "python {} [-t] (optional: none curerntly) [Test(s) to run]".format(os.path.basename(sys.argv[0])) + script_desc = "Run lambda_function tests" + parser = argparse.ArgumentParser( + usage=script_usage, + description=script_desc + ) + parser.add_argument( + '--ldserver', + '-l', + help='Live Design Server', + dest='ld_server', + required=True + ) + parser.add_argument( + '--user', + '-u', + help='LD client user', + dest='username', + required=True + ) + parser.add_argument( + '--password', + '-p', + help='LD client password', + dest='password', + required=True + ) + parser.add_argument( + '--method', + '-m', + help='Method to call', + dest='method', + required=True + ) + parser.add_argument( + '--args', + '-a', + nargs='*', + help='arguments to the method', + dest='args', + required=False + ) + return parser + +def list_groups(client, test): + print test + return client.list_groups() + +def auth_check(client, username, password): + auth_return = client.auth_check(username = username, password = password) + return auth_return + +def ld_group_to_acas_role(group): + # u'LDAP_Auto_ROLE_SEURAT-USERS' + # u'Project_ProjectX_Administrator' + split = group["name"].split('_') + ls_type = split[0] + ls_kind = split[1] + role_name = "_".join(split[2:len(split)]) + acas_role = { + "id": group["id"], + "roleEntry": { + 'id': group["id"], + 'lsType': ls_type, + 'lsKind': ls_kind, + 'lsTypeAndKind': ls_type + "_" + ls_kind, + 'roleDescription': "Original group fetched from Live Design: "+ group["name"], + 'roleName': role_name, + 'version': 0 + } + } + return acas_role + +def ld_user_to_acas_user_code_table(ld_user): + acas_user = { + "code":ld_user["username"], + "id":ld_user["id"], + "ignored":False, + "name":ld_user["username"] + } + return acas_user + +def get_users(client, ls_type = None, ls_kind = None, role_name = None): + ld_users = client.list_users() + if ls_type == None and ls_kind == None and role_name == None: + acas_users = map(ld_user_to_acas_user_code_table, ld_users) + else: + groups = client.list_groups() + roles = map(ld_group_to_acas_role, groups) + role = [r for r in roles if r["roleEntry"]["lsType"] == ls_type and r["roleEntry"]["lsKind"] == ls_kind and r["roleEntry"]["roleName"] == role_name] + if len(role) == 0: + return [] + users = [] + memberships = client.list_memberships() + userDict = {} + for u in ld_users: + userDict[u["id"]] = u + for m in memberships: + if m["group_id"] == role[0]["id"]: + users.append(userDict[m["user_id"]]) + acas_users = map(ld_user_to_acas_user_code_table, users) + return acas_users + +def ld_user_to_acas_user(ld_user, roles): + acas_user = { + 'id': ld_user["id"], + 'username': ld_user["username"], + 'email': ld_user["username"], + 'firstName': ld_user["username"], + 'lastName': ld_user["username"], + 'roles': roles + } + return acas_user + +def get_users_roles(client, users): + usersDict = {} + for u in users: + usersDict[u["id"]] = u + groups = client.list_groups() + roles = map(ld_group_to_acas_role, groups) + roleDict = {} + for r in roles: + roleDict[r["id"]] = r + memberships = client.list_memberships() + for m in memberships: + usersDict[m["user_id"]].append(roleDict[m["group_id"]]) + users = [] + for user in usersDict.iteritems(): + users.append(user) + return users + +def get_user(client, username): + user = client.get_user(username) + permissions = client.list_permissions() + memberships = client.list_memberships() + groups = client.list_groups() + user_memberships = [m for m in memberships if m['user_id'] == user['id']] + user_groups = [next(g for g in groups if g["id"]==m["group_id"]) for m in user_memberships] + roles = map(ld_group_to_acas_role, user_groups) + acas_user = ld_user_to_acas_user(user, roles) + # user = {"id":1,"username":"bob","email":"bob@mcneilco.com","firstName":"Ham","lastName":"Cheese","roles":[{"id":2,"roleEntry":{"id":1,"lsKind":"ACAS","lsType":"System","lsTypeAndKind":"System_ACAS","roleDescription":"ROLE_ACAS-USERS autocreated by ACAS","roleName":"ROLE_ACAS-USERS","version":0},"version":0},{"id":1,"roleEntry":{"id":2,"lsKind":"ACAS","lsType":"System","lsTypeAndKind":"System_ACAS","roleDescription":"ROLE_ACAS-ADMINS autocreated by ACAS","roleName":"ROLE_ACAS-ADMINS","version":0},"version":0},{"id":4,"roleEntry":{"id":4,"lsKind":"CmpdReg","lsType":"System","lsTypeAndKind":"System_CmpdReg","roleDescription":"ROLE_CMPDREG-ADMINS autocreated by ACAS","roleName":"ROLE_CMPDREG-ADMINS","version":0},"version":0},{"id":3,"roleEntry":{"id":5,"lsKind":"ACAS","lsType":"System","lsTypeAndKind":"System_ACAS","roleDescription":"ROLE_ACAS-CROSS-PROJECT-LOADER autocreated by ACAS","roleName":"ROLE_ACAS-CROSS-PROJECT-LOADER","version":0},"version":0},{"id":5,"roleEntry":{"id":3,"lsKind":"CmpdReg","lsType":"System","lsTypeAndKind":"System_CmpdReg","roleDescription":"ROLE_CMPDREG-USERS autocreated by ACAS","roleName":"ROLE_CMPDREG-USERS","version":0},"version":0},{"id":6,"roleEntry":{"id":6,"lsKind":"PROJ-00000001","lsType":"Project","lsTypeAndKind":"Project_PROJ-00000001","roleDescription":"User autocreated by ACAS","roleName":"User","version":0},"version":0}]} + + return acas_user + +def get_projects(client): + ld_projects = client.projects() + projects = map(ld_project_to_acas, ld_projects) + return projects + +def ld_project_to_acas(ld_project): + acas_project = { + 'id': ld_project.id, + 'code': ld_project.alternate_id, + 'alias': ld_project.name, + 'active': True if ld_project.active == "Y" else False, + 'isRestricted': ld_project.restricted, + 'name': ld_project.name + } + return acas_project + +def main(): + parser = get_parser() + args = parser.parse_args() + endpoint = "{0}/api".format(args.ld_server) + client = LDClient(host=endpoint, username=args.username, password=args.password) + method = eval(args.method) + + result = method(client, *args.args) + print json.dumps(result) + +if __name__ == "__main__": + main() From afbb9e5c61a34685a0b03ff69604054e8fa2cea3 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 11 Jan 2019 08:10:55 -0800 Subject: [PATCH 427/576] adding more key servers --- Dockerfile | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 07645b23d..07061e2cd 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,7 +24,10 @@ RUN set -ex \ ; do \ gpg --keyserver ha.pool.sks-keyservers.net --recv-keys "$key" || \ gpg --keyserver pgp.mit.edu --recv-keys "$key" || \ - gpg --keyserver keyserver.pgp.com --recv-keys "$key"; \ + gpg --keyserver keyserver.pgp.com --recv-keys "$key"; || \ + gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys "$key"; || \ + gpg --keyserver hkp://p80.pool.sks-keyservers.net:80 "$key"; || \ + gpg --keyserver pgp.mit.edu "$key"; \ done ENV NPM_CONFIG_LOGLEVEL warn From 8d22d44de8c11dc330a89b62ffeacdaa27fb5fa8 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 11 Jan 2019 08:18:22 -0800 Subject: [PATCH 428/576] fixing syntax --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 07061e2cd..4401e511a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,9 +24,9 @@ RUN set -ex \ ; do \ gpg --keyserver ha.pool.sks-keyservers.net --recv-keys "$key" || \ gpg --keyserver pgp.mit.edu --recv-keys "$key" || \ - gpg --keyserver keyserver.pgp.com --recv-keys "$key"; || \ - gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys "$key"; || \ - gpg --keyserver hkp://p80.pool.sks-keyservers.net:80 "$key"; || \ + gpg --keyserver keyserver.pgp.com --recv-keys "$key" || \ + gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys "$key" || \ + gpg --keyserver hkp://p80.pool.sks-keyservers.net:80 "$key" || \ gpg --keyserver pgp.mit.edu "$key"; \ done From ab7176777d4b8aba73b5d3739246c8edad926066 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 11 Jan 2019 12:54:13 -0800 Subject: [PATCH 429/576] removing flywaylocation from configs --- conf/config.properties.example | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 8693e7d64..e5e5ffb6b 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -539,7 +539,6 @@ server.curveRender.drawPointsForRejectedCurve=true # Restrict experiment search by project server.service.projects.restrictExperiments=false -flyway.location=db/migration/postgres,com.labsynch.labseer.db.migration.postgres,db/migration/indigo/postgres flyway.schema=acas flyway.database.username=${server.database.username} flyway.database.password=${server.database.password} From 4376ca250b6c478003702970ce9bae236cb502b1 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 16 Jan 2019 07:48:15 -0800 Subject: [PATCH 430/576] jchem license route --- modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index 102c3a4ac..7b07b9632 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -335,7 +335,7 @@ exports.regSearch = (req, resp) -> ) exports.getMarvinJSLicense = (req, resp) -> - cmpdRegCall = (config.all.client.service.cmpdReg.persistence.basepath).replace '\/cmpdreg', "/" + cmpdRegCall = (config.all.client.service.cmpdReg.persistence.basepath).replace '\/acas', "/" licensePath = cmpdRegCall + 'marvin4js-license.cxl' console.log licensePath req.pipe(request(licensePath)).pipe(resp) From 7e15ea99d7abfe78536c68910ceaece2fe468fb9 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 17 Jan 2019 08:48:40 -0800 Subject: [PATCH 431/576] the file value should match the file name not the text given by the user which may be upper or lower case versions of the file name --- modules/GenericDataParser/src/server/generic_data_parser.R | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 11d27f840..f81489b23 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -997,8 +997,8 @@ validateUploadedImages <- function(imageLocation, listedImageFiles, experimentFo stopUser(paste0("The following files were listed in the spreadsheet, but were not uploaded in a zip file: ", paste(notUploaded, collapse = ", "))) } - - return(TRUE) + matchedUploadedFileNames <- uploadedImageFiles[match(listedImageFilesLower,uploadedImageFilesLower)] + return(matchedUploadedFileNames) } getExcelColumnFromNumber <- function(number) { @@ -1654,7 +1654,8 @@ addImageFiles <- function(imagesFile, calculatedResults, experiment, dryRun, rec if (!is.null(imagesFile)) { imageLocation <- unzipUploadedImages(imagesFile = racas::getUploadedFilePath(imagesFile), experimentFolderLocation = experimentFolderLocation) listedImageFiles <- calculatedResults[!is.na(calculatedResults$inlineFileValue),]$inlineFileValue - isValid <- validateUploadedImages(imageLocation = imageLocation, listedImageFiles = listedImageFiles, experimentFolderLocation = experimentFolderLocation) + matchedUploadedFileNames <- validateUploadedImages(imageLocation = imageLocation, listedImageFiles = listedImageFiles, experimentFolderLocation = experimentFolderLocation) + calculatedResults[!is.na(calculatedResults$inlineFileValue),]$inlineFileValue <- matchedUploadedFileNames calculatedResults <- addComment(calculatedResults = calculatedResults) if (racas::applicationSettings$server.service.external.file.type == "custom") { fileValueVector <- ifelse(is.na(calculatedResults$inlineFileValue), From 3cfa30b0a972cae1606f7c00e28891e37b35679e Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 17 Jan 2019 15:44:15 -0800 Subject: [PATCH 432/576] remove cmpdreg roo container --- docker-compose.yml | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 091a94cb5..48b0440f0 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -75,25 +75,16 @@ services: volumes_from: - roo - acas - # - cmpdreg env_file: - ./conf/docker/acas/environment/acas.env - ./conf/docker/roo/environment/roo.env - ./conf/docker/cmpdreg/environment/cmpdreg.env command: catalina.sh run roo: - image: test + image: mcneilco/acas-roo-server-oss:${ACAS_TAG} volumes: - /usr/local/tomcat/webapps/acas command: /bin/true - # cmpdreg: - # image: test - # volumes: - # - /usr/local/tomcat/webapps/cmpdreg - # # Add chemaxon license files here - # # - ./chemaxon/licenses/marvin4js-license.cxl:/usr/local/tomcat/webapps/ROOT/marvin4js-license.cxl - # # - ./chemaxon/licenses/license.cxl:/root/.chemaxon/license.cxl - command: /bin/true volumes: dbstore: filestore: From 6f7c059bb2b0da240385f5cfff93d226b62fef74 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 29 Jan 2019 10:55:49 -0800 Subject: [PATCH 433/576] pass allowed projects to creg search, push postgres default container to one that does not include seurat/compound schema creation --- docker-compose.yml | 3 +- .../src/server/routes/CmpdRegRoutes.coffee | 44 +++++++++++-------- 2 files changed, 26 insertions(+), 21 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 48b0440f0..151a67aba 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -47,7 +47,7 @@ services: - logs:/home/runner/logs command: ["bin/acas.sh", "run", "rservices"] db: - image: mcneilco/acas-postgres:1.0-bingo + image: mcneilco/acas-postgres:1.1-bingo restart: always volumes: - dbstore:/var/lib/postgresql/data @@ -56,7 +56,6 @@ services: - ./conf/docker/db/environment/db.env - ./conf/docker/acas/environment/acas.env - ./conf/docker/cmpdreg/environment/cmpdreg.env - - ./conf/docker/seurat/environment/seurat.env ports: - "5432:5432" tomcat: diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index 7b07b9632..c3a7fdd44 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -236,25 +236,31 @@ exports.updateScientists = (jsonBody, callback) -> ) exports.searchCmpds = (req, resp) -> - cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + '/search/cmpds' - request( - method: 'POST' - url: cmpdRegCall - body: JSON.stringify req.body - json: true - timeout: 6000000 - , (error, response, json) => - if !error - console.log JSON.stringify json - resp.setHeader('Content-Type', 'application/json') - resp.end JSON.stringify json - else - console.log 'got ajax error trying to search for compounds' - console.log error - console.log json - console.log response - resp.end JSON.stringify {error: "something went wrong :("} - ) + authorRoutes = require './AuthorRoutes.js' + authorRoutes.allowedProjectsInternal req.user, (statusCode, allowedUserProjects) -> + _ = require "underscore" + allowedProjectCodes = _.pluck(allowedUserProjects, "code") + req.body.projects = allowedProjectCodes + console.log req.body + cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + '/search/cmpds' + request( + method: 'POST' + url: cmpdRegCall + body: JSON.stringify req.body + json: true + timeout: 6000000 + , (error, response, json) => + if !error + console.log JSON.stringify json + resp.setHeader('Content-Type', 'application/json') + resp.end JSON.stringify json + else + console.log 'got ajax error trying to search for compounds' + console.log error + console.log json + console.log response + resp.end JSON.stringify {error: "something went wrong :("} + ) exports.getStructureImage = (req, resp) -> imagePath = (req.originalUrl).replace /\/cmpdreg\/structureimage/, "" From e8f119a6eda067247ddc13bcbee8755923402d74 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 30 Jan 2019 09:52:20 -0800 Subject: [PATCH 434/576] set modified by to chemist code, pass modified by to lot and parent update services if null in the request --- modules/CmpdReg/src/client/custom/Lot_Custom.js | 1 + .../src/server/routes/CmpdRegRoutes.coffee | 17 +++++++++++++---- 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/modules/CmpdReg/src/client/custom/Lot_Custom.js b/modules/CmpdReg/src/client/custom/Lot_Custom.js index 7c4419108..2626ba371 100755 --- a/modules/CmpdReg/src/client/custom/Lot_Custom.js +++ b/modules/CmpdReg/src/client/custom/Lot_Custom.js @@ -536,6 +536,7 @@ $(function() { tareWeightUnits: tareWeightUnits, totalAmountStoredUnits: totalAmountStoredUnits, purityMeasuredBy: purityMeasuredBy, + chemist: this.chemistCodeController.getSelectedModel().get("code"), project: this.projectCodeController.getSelectedModel().get("code"), vendor: vendor, supplierLot: jQuery.trim(this.$('.supplierLot').val()), diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index c3a7fdd44..47a015ca4 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -358,6 +358,8 @@ exports.fileSave = (req, resp) -> req.pipe(request[req.method.toLowerCase()](cmpdRegCall)).pipe(resp) exports.metaLots = (req, resp) -> + if req.user? && !req.body.modifiedBy? + req.body.lot.modifiedBy = req.user.username cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + '/metalots' request( method: 'POST' @@ -547,7 +549,8 @@ exports.validateParent = (req, resp) -> exports.updateParent = (req, resp) -> console.log "exports.updateParent" - + if req.user? && !req.body.modifiedBy? + req.body.modifiedBy = req.user.username cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/parents/updateParent' request( method: 'POST' @@ -575,7 +578,8 @@ exports.updateLotMetadata = (req, resp) -> console.log 'in update lot metaData' cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/parentLot/updateLot/metadata' console.log cmpdRegCall - + if req.user? && !req.body.modifiedBy? + req.body.modifiedBy = req.user.username request( method: 'POST' url: cmpdRegCall @@ -599,7 +603,11 @@ exports.updateLotsMetadata = (req, resp) -> console.log 'in update lot array metaData' cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/parentLot/updateLot/metadata/jsonArray' console.log cmpdRegCall - + if req.user? + req.body.map((lot) -> + if !lot.modifiedBy? + lot.modifiedBy = req.user.username + ) request( method: 'POST' url: cmpdRegCall @@ -623,7 +631,8 @@ exports.updateParentMetadata = (req, resp) -> console.log 'in update parent metaData' cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/parents/updateParent/metadata' console.log cmpdRegCall - + if req.user? && !req.body.modifiedBy? + req.body.modifiedBy = req.user.username request( method: 'POST' url: cmpdRegCall From 5f4bb2e6d70b87f54d2720fa8ddfc235aa2b9293 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 4 Feb 2019 14:50:39 -0800 Subject: [PATCH 435/576] fixes #556: Replace new line characters in entity reference codes and warn the user of the changed data --- .../src/server/generic_data_parser.R | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index 7c368cfa6..ce00610f0 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -495,6 +495,19 @@ validateCalculatedResults <- function(calculatedResults, dryRun, curveNames, tes # Get the current batch Ids batchesToCheck <- calculatedResults$originalMainID != replaceFakeCorpBatchId + + # The preferred id function strips new line characters from entity reference codes because it + # posts the list as a new line seperated string. The best way to deal with this is to clean up + # the codes beforehand and warn the user of the changed data. + newLineCharacterRegex <- "\n|\r" + batchIdsWithNewLine <- grepl(newLineCharacterRegex,calculatedResults$batchCode) + if(any(batchIdsWithNewLine)) { + calculatedResults$batchCode[batchIdsWithNewLine] <- gsub(newLineCharacterRegex, "", calculatedResults$batchCode[batchIdsWithNewLine]) + warnUser(paste0("The loader found and removed new line characters from ", mainCode, " rows: '", + paste(unique(calculatedResults$batchCode[batchIdsWithNewLine]),collapse="' ,'"), + "'.")) + } + batchIds <- unique(calculatedResults$batchCode[batchesToCheck]) if (inputFormat == "Gene ID Data") { From f29799ba4451d0a03e1f1c8c940203e8714c12fb Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 7 Feb 2019 15:22:13 -0800 Subject: [PATCH 436/576] fix issue with filling in saved chemist, project from saved lot json --- modules/CmpdReg/src/client/custom/Lot_Custom.js | 12 ++++++------ modules/CmpdReg/src/client/src/Lot.js | 10 +++++++++- modules/CmpdReg/src/client/src/MetaLot.js | 7 +++---- modules/CmpdReg/src/client/src/SaltForm.js | 1 + 4 files changed, 19 insertions(+), 11 deletions(-) diff --git a/modules/CmpdReg/src/client/custom/Lot_Custom.js b/modules/CmpdReg/src/client/custom/Lot_Custom.js index 2626ba371..e323e2587 100755 --- a/modules/CmpdReg/src/client/custom/Lot_Custom.js +++ b/modules/CmpdReg/src/client/custom/Lot_Custom.js @@ -56,8 +56,8 @@ $(function() { totalAmountStoredUnits: new PickList(js.totalAmountStoredUnits), purityMeasuredBy: new PickList(js.purityMeasuredBy), purityOperator: new PickList(js.purityOperator), - chemist: new PickList(js.chemist), - project: new PickList(js.project), + chemist: new PickList({selectedCode: js.chemist}), + project: new PickList({selectedCode: js.project}), vendor: new PickList(js.vendor) }) // replace composite object pointers with real objects @@ -435,7 +435,7 @@ $(function() { this.model.set({ notebookPage: jQuery.trim(this.$('.notebookPage').val()), synthesisDate: jQuery.trim(this.$('.synthesisDate').val()), - chemist: this.chemistCodeController.getSelectedModel().get("code"), + chemist: this.chemistCodeController.getSelectedModel(), lotNumber: (jQuery.trim(this.$('.lotNumber').val())=='') ? null : parseInt(jQuery.trim(this.$('.lotNumber').val())) @@ -458,7 +458,7 @@ $(function() { purityOperator: null, amountUnits: null, purityMeasuredBy: null, - project: this.projectCodeController.getSelectedModel().get("code"), + project: this.projectCodeController.getSelectedModel(), supplierLot: '', meltingPoint: null, boilingPoint: null, @@ -536,8 +536,8 @@ $(function() { tareWeightUnits: tareWeightUnits, totalAmountStoredUnits: totalAmountStoredUnits, purityMeasuredBy: purityMeasuredBy, - chemist: this.chemistCodeController.getSelectedModel().get("code"), - project: this.projectCodeController.getSelectedModel().get("code"), + chemist: this.chemistCodeController.getSelectedModel(), + project: this.projectCodeController.getSelectedModel(), vendor: vendor, supplierLot: jQuery.trim(this.$('.supplierLot').val()), meltingPoint: diff --git a/modules/CmpdReg/src/client/src/Lot.js b/modules/CmpdReg/src/client/src/Lot.js index 23a5cd377..609ed617f 100755 --- a/modules/CmpdReg/src/client/src/Lot.js +++ b/modules/CmpdReg/src/client/src/Lot.js @@ -5,6 +5,8 @@ $(function() { getModelForSave: function() { var mts = new Backbone.Model(this.attributes); mts.set({fileList: this.get('fileList').getUploadedFiles()}); + mts.set({chemist: this.get('chemist').get('code')}); + mts.set({project: this.get('project').get('code')}); mts.unset('json'); return mts; @@ -58,7 +60,13 @@ $(function() { setupCodeController: function(elClass, type, attribute) { var tcode = ''; if(this.model.get(attribute)) { - tcode = this.model.get(attribute).get('code'); + if(this.model.get(attribute).get("code")) { + tcode = this.model.get(attribute).get('code'); + } else { + if(this.model.get(attribute).get("selectedCode")) { + tcode = this.model.get(attribute).get("selectedCode"); + } + } } return new PickListSelectController({ el: this.$('.'+elClass), diff --git a/modules/CmpdReg/src/client/src/MetaLot.js b/modules/CmpdReg/src/client/src/MetaLot.js index 27861aae1..2ae999091 100755 --- a/modules/CmpdReg/src/client/src/MetaLot.js +++ b/modules/CmpdReg/src/client/src/MetaLot.js @@ -258,7 +258,7 @@ $(function() { this.saltFormController.updateModel(function () { if (mlself.saltFormController.model.isNew()) { mlself.saltFormController.model.set({ - 'chemist': mlself.lotController.model.get('chemist') + 'chemist': mlself.lotController.model.get('chemist').get("code") }); } @@ -288,7 +288,6 @@ $(function() { message: 'Saving ' + (lisb ? 'batch' : 'lot') + '...' }); mlself.delegateEvents({}); // stop listening to buttons - $.ajax({ type: "POST", url: url, @@ -386,7 +385,7 @@ $(function() { this.parentController.updateModel(); if (this.parentController.model.isNew()) { this.parentController.model.set({ - 'chemist': this.lotController.model.get('chemist') + 'chemist': this.lotController.model.get('chemist').get("code") }); } }, @@ -415,7 +414,7 @@ $(function() { }, allowedToUpdate: function () { - var chemist = this.model.get('lot').get('chemist'); + var chemist = this.model.get('lot').get('chemist').get('selectedCode'); var registeredBy = this.model.get('lot').get('registeredBy'); if (this.user == null || chemist == null || this.model.get('lot').isNew()) return true; // test mode or new diff --git a/modules/CmpdReg/src/client/src/SaltForm.js b/modules/CmpdReg/src/client/src/SaltForm.js index 77c5a6042..5c623528f 100755 --- a/modules/CmpdReg/src/client/src/SaltForm.js +++ b/modules/CmpdReg/src/client/src/SaltForm.js @@ -33,6 +33,7 @@ $(function() { id: js.id, corpName: js.corpName, casNumber: js.casNumber, + chemist: js.chemist, isosalts: isel, molStructure: js.molStructure }); From 738fc64143cf480b600d19deb0f72c81cdc38605 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 7 Feb 2019 15:51:43 -0800 Subject: [PATCH 437/576] remove call to auth check --- .../python/acas_ldclient/acasldclient.py | 20 +++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py index 22643512c..18f0d2924 100644 --- a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py +++ b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py @@ -63,8 +63,13 @@ def list_groups(client, test): print test return client.list_groups() -def auth_check(client, username, password): - auth_return = client.auth_check(username = username, password = password) +def auth_check(endpoint, username, password): + auth_return = {'authorized': True, 'error': None} + try: + sessionClient = LDClient(host=endpoint, username=username, password=password) + except Exception as e: + auth_return['authorized'] = False + auth_return['error'] = e.message return auth_return def ld_group_to_acas_role(group): @@ -75,7 +80,7 @@ def ld_group_to_acas_role(group): ls_kind = split[1] role_name = "_".join(split[2:len(split)]) acas_role = { - "id": group["id"], + "id": group["id"], "roleEntry": { 'id': group["id"], 'lsType': ls_type, @@ -179,10 +184,13 @@ def main(): parser = get_parser() args = parser.parse_args() endpoint = "{0}/api".format(args.ld_server) - client = LDClient(host=endpoint, username=args.username, password=args.password) - method = eval(args.method) + if args.method != "auth_check": + client = LDClient(host=endpoint, username=args.username, password=args.password) + method = eval(args.method) + result = method(client, *args.args) + else: + result = auth_check(endpoint, *args.args) - result = method(client, *args.args) print json.dumps(result) if __name__ == "__main__": From 3d7c8abe78a92a5b701a111266fc99a31030a11b Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 8 Feb 2019 09:42:03 -0800 Subject: [PATCH 438/576] fix error reporting string when service returns fail --- modules/GenericDataParser/src/server/generic_data_parser.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index c26bb0e5d..3be7ddb8e 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -1760,7 +1760,7 @@ getExperimentByNameCheck <- function(experimentName, protocol, configList, dupli tryCatch({ experimentList <- getExperimentsByName(experimentName) }, error = function(e) { - stopUser("There was an error checking if the ",racas::applicationSettings$client.experiment.label," already exists. Please contact your system administrator.") + stopUser(paste0("There was an error checking if the ",racas::applicationSettings$client.experiment.label," already exists. Please contact your system administrator.")) }) # Warn the user if the experiment already exists (the else block) @@ -1785,7 +1785,7 @@ getExperimentByNameCheck <- function(experimentName, protocol, configList, dupli } } }, error = function(e) { - stopUser("There was an error checking if the experiment is in the correct ",racas::applicationSettings$client.protocol.label,". Please contact your system administrator.") + stopUser(paste0("There was an error checking if the experiment is in the correct ",racas::applicationSettings$client.protocol.label,". Please contact your system administrator.")) }) # Finish if the previous experiment was part of a deleted protocol, we can just delete and reload if (experimentList[[1]]$protocol$ignored) { @@ -2133,7 +2133,7 @@ validateProject <- function(projectName, configList, username, protocolName = NU tryCatch({ protocolList <- getProtocolsByName(protocolName) }, error = function(e) { - stopUser("There was an error in accessing the ",racas::applicationSettings$client.protocol.label,". Please contact your system administrator.") + stopUser(paste0("There was an error in accessing the ",racas::applicationSettings$client.protocol.label,". Please contact your system administrator.")) }) if (length(protocolList) !=0) { protocol <- getProtocolByCodeName(protocolList[[1]]$codeName) From 0cf3844248630fb6f18dd4fdd0838f6b3f7b1966 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 11 Feb 2019 12:19:00 -0800 Subject: [PATCH 439/576] fixes #558: Additional codes in scientist picklists --- modules/CmpdReg/conf/CmpdRegConfJSON.coffee | 9 +++++++++ .../src/server/routes/CmpdRegRoutes.coffee | 2 +- .../routes/CmpdRegBulkLoaderRoutes.coffee | 2 +- .../src/server/generic_data_parser.R | 17 +++++++++-------- modules/ServerAPI/conf/ProtocolConfJSON.coffee | 8 ++++---- modules/ServerAPI/src/client/BaseEntity.coffee | 2 +- .../CustomerSpecificServerFunctions.coffee | 10 +++++++++- 7 files changed, 34 insertions(+), 16 deletions(-) diff --git a/modules/CmpdReg/conf/CmpdRegConfJSON.coffee b/modules/CmpdReg/conf/CmpdRegConfJSON.coffee index e71bb94f4..313db5931 100644 --- a/modules/CmpdReg/conf/CmpdRegConfJSON.coffee +++ b/modules/CmpdReg/conf/CmpdRegConfJSON.coffee @@ -21,5 +21,14 @@ typeName: "id" kindName: "corpName" ] + ddicttypes: + [ + typeName: "compound" + ] + ddictkinds: + [ + typeName: "compound" + kindName: "scientist" + ] ) (if (typeof process is "undefined" or not process.versions) then window.cmpdRegConfJSON = window.cmpdRegConfJSON or {} else exports) diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index 47a015ca4..7280ffb75 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -192,7 +192,7 @@ exports.getScientists = (req, resp) => exports.getScientistsInternal = (callback) -> loginRoutes = require './loginRoutes.js' - loginRoutes.getAuthorsInternal {}, (statusCode, authors) => + loginRoutes.getAuthorsInternal {additionalCodeType: 'compound', additionalCodeKind: 'scientist'}, (statusCode, authors) => callback authors exports.saveScientists = (jsonBody, callback) -> diff --git a/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee b/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee index d76c48f8b..541445c78 100644 --- a/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee +++ b/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee @@ -155,7 +155,7 @@ exports.validationPropertiesInternal = (reqObject, callback) -> exports.getScientistsInternal = (callback) -> loginRoutes = require './loginRoutes.js' - loginRoutes.getAuthorsInternal {}, (statusCode, authors) => + loginRoutes.getAuthorsInternal {additionalCodeType: 'compound', additionalCodeKind: 'scientist'}, (statusCode, authors) => callback authors exports.registerCmpds = (req, resp) -> diff --git a/modules/GenericDataParser/src/server/generic_data_parser.R b/modules/GenericDataParser/src/server/generic_data_parser.R index c072cc01b..e57c9e41b 100644 --- a/modules/GenericDataParser/src/server/generic_data_parser.R +++ b/modules/GenericDataParser/src/server/generic_data_parser.R @@ -2224,7 +2224,7 @@ validateScientist <- function(scientistName, configList, testMode = FALSE) { if (!testMode) { response <- tryCatch({ - getURL(URLencode(paste0(racas::applicationSettings$server.nodeapi.path, racas::applicationSettings$client.service.users.path, "/", scientistName))) + getURL(URLencode(paste0(racas::applicationSettings$server.nodeapi.path, "/api/authors?additionalCodeType=assay&additionalCodeKind=scientist"))) }, error = function(e) { addError( paste("There was an error in validating the scientist's name:", scientistName)) return("") @@ -2238,14 +2238,15 @@ validateScientist <- function(scientistName, configList, testMode = FALSE) { response <- toJSON(list(username = scientistName)) } } - - if (response == "") { - addError( paste0("The Scientist you supplied, '", scientistName, "', is not a valid name. Please enter the scientist's login name.")) - return("") - } - + username <- tryCatch({ - fromJSON(response)$username + response <- jsonlite::fromJSON(response) + if (nrow(response) == 0 || nrow(response[response$code == scientistName, ]) == 0) { + addError( paste0("The Scientist you supplied, '", scientistName, "', is not a valid name. Please enter the scientist's name.")) + return("") + } else { + return(scientistName) + } }, error = function(e) { addError( paste("There was an error in validating the scientist's name:", scientistName)) return("") diff --git a/modules/ServerAPI/conf/ProtocolConfJSON.coffee b/modules/ServerAPI/conf/ProtocolConfJSON.coffee index d5a5764e1..2dc0c277b 100644 --- a/modules/ServerAPI/conf/ProtocolConfJSON.coffee +++ b/modules/ServerAPI/conf/ProtocolConfJSON.coffee @@ -470,11 +470,11 @@ name: "None" ignored: false , - codeType: "model fit" - codeKind: "transformation units" + codeType: "compound" + codeKind: "scientist" codeOrigin: "ACAS DDICT" - code: "%" - name: "%" + code: "Pharmaron" + name: "Pharmaron" ignored: false ] diff --git a/modules/ServerAPI/src/client/BaseEntity.coffee b/modules/ServerAPI/src/client/BaseEntity.coffee index 7f983e3c7..980bdf02a 100644 --- a/modules/ServerAPI/src/client/BaseEntity.coffee +++ b/modules/ServerAPI/src/client/BaseEntity.coffee @@ -441,7 +441,7 @@ class window.BaseEntityController extends AbstractThingFormController #TODO: che setupScientistSelect: -> @scientistList = new PickListList() - @scientistList.url = "/api/authors" + @scientistList.url = "/api/authors?additionalCodeType=assay&additionalCodeKind=scientist" @scientistListController = new PickListSelectController el: @$('.bv_scientist') collection: @scientistList diff --git a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee index 893feecd1..6f0f54362 100644 --- a/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee +++ b/modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee @@ -248,7 +248,15 @@ exports.getAllAuthors = (opts, callback) -> baseurl = config.all.client.service.persistence.fullpath+"authors/findByRoleTypeKindAndName" baseurl += "?roleType=#{req.query.roleType}&roleKind=#{req.query.roleKind}&roleName=#{req.query.roleName}&format=codeTable" serverUtilityFunctions.getFromACASServerInternal baseurl, (statusCode, json) -> - callback statusCode, json + # If additional codeType and codeKind parameters are supplied then append the code values for the additional authors + # This is was added for the purpose of allowing additional non-authors to show up in picklists throughout ACAS and Creg + if opts.additionalCodeType? and opts.additionalCodeKind? + codeTableServiceRoutes = require "#{ACAS_HOME}/routes/CodeTableServiceRoutes.js" + codeTableServiceRoutes.getCodeTableValuesInternal opts.additionalCodeType, opts.additionalCodeKind, (codes) -> + Array::push.apply json, codes + callback statusCode, json + else + callback statusCode, json exports.getAllAuthorObjectsInternal = (callback) -> config = require "#{ACAS_HOME}/conf/compiled/conf.js" From 0c944ab1cba70489ff55ce61b84873c344dddc4e Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 11 Feb 2019 12:55:43 -0800 Subject: [PATCH 440/576] removing mistaken file checkin changes --- modules/ServerAPI/conf/ProtocolConfJSON.coffee | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/ServerAPI/conf/ProtocolConfJSON.coffee b/modules/ServerAPI/conf/ProtocolConfJSON.coffee index 2dc0c277b..d5a5764e1 100644 --- a/modules/ServerAPI/conf/ProtocolConfJSON.coffee +++ b/modules/ServerAPI/conf/ProtocolConfJSON.coffee @@ -470,11 +470,11 @@ name: "None" ignored: false , - codeType: "compound" - codeKind: "scientist" + codeType: "model fit" + codeKind: "transformation units" codeOrigin: "ACAS DDICT" - code: "Pharmaron" - name: "Pharmaron" + code: "%" + name: "%" ignored: false ] From 5674eabb55bff9947a223ef258d21e75fe73a44f Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 27 Feb 2019 16:46:06 -0800 Subject: [PATCH 441/576] fixes #562: dont sync to compound project any longer --- .../server/routes/SyncProjectsUsers.coffee | 71 +++---------------- 1 file changed, 9 insertions(+), 62 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/SyncProjectsUsers.coffee b/modules/ServerAPI/src/server/routes/SyncProjectsUsers.coffee index b197bab4e..5ffe3157b 100644 --- a/modules/ServerAPI/src/server/routes/SyncProjectsUsers.coffee +++ b/modules/ServerAPI/src/server/routes/SyncProjectsUsers.coffee @@ -14,16 +14,15 @@ exports.syncLiveDesignProjectsUsers = (req, resp) -> exports.syncLiveDesignProjects caughtErrors, pythonErrors, configJSON, projectsJSON, (caughtErrors, pythonErrors) -> console.debug caughtErrors console.debug pythonErrors - exports.syncCmpdRegProjects req, acasGroupsAndProjects, caughtErrors, (syncCmpdRegProjectsCallback, caughtErrors) -> - exports.syncLiveDesignRoles caughtErrors, pythonErrors, configJSON, groupsJSON, (caughtErrors, pythonErrors) -> - if !caughtErrors - resp.statusCode = 200 - console.log "Successfully synced projects and permissions with LiveDesign and Compound Reg" - resp.end "Successfully synced projects and permissions with LiveDesign and Compound Reg" - else - resp.statusCode = 500 - console.log "An error has occurred trying to sync projects and permissions with LiveDesign and Compound Reg. Please contact an administrator." - resp.end "An error has occurred trying to sync projects and permissions with LiveDesign and Compound Reg. Please contact an administrator." + exports.syncLiveDesignRoles caughtErrors, pythonErrors, configJSON, groupsJSON, (caughtErrors, pythonErrors) -> + if !caughtErrors + resp.statusCode = 200 + console.log "Successfully synced projects and permissions with LiveDesign" + resp.end "Successfully synced projects and permissions with LiveDesign" + else + resp.statusCode = 500 + console.log "An error has occurred trying to sync projects and permissions with LiveDesign. Please contact an administrator." + resp.end "An error has occurred trying to sync projects and permissions with LiveDesign. Please contact an administrator." exports.getGroupsJSON = (callback) -> request = require 'request' @@ -114,58 +113,6 @@ exports.syncLiveDesignProjects = (caughtErrors, pythonErrors, configJSON, projec console.warn "some live design configs are null, skipping sync of live design projects" callback caughtErrors, pythonErrors -exports.syncCmpdRegProjects = (req, acasGroupsAndProjects, caughtErrors, callback) -> - config = require '../conf/compiled/conf.js' - if config.all.server.project?.sync?.cmpdReg? && config.all.server.project.sync.cmpdReg - cmpdRegRoutes = require '../routes/CmpdRegRoutes.js' - _ = require "underscore" - #Get or create projects in CmpdReg - projectCodes = _.pluck acasGroupsAndProjects.projects, 'code' - console.debug 'project codes are:' + JSON.stringify projectCodes - cmpdRegRoutes.getProjects req, (projectResponse) -> - if (projectResponse.indexOf '') > -1 - console.error "Caught error getting CmpdReg projects" - console.error projectResponse - caughtErrors = true - callback 'ERROR', caughtErrors - foundProjects = JSON.parse projectResponse - foundProjectCodes = _.pluck foundProjects, 'code' - console.debug 'found projects are: '+foundProjectCodes - newProjectCodes = _.difference projectCodes, foundProjectCodes - newProjects = _.filter acasGroupsAndProjects.projects, (project) -> - return project.code in newProjectCodes - projectsToUpdate = _.filter acasGroupsAndProjects.projects, (project) -> - found = (_.findWhere foundProjects, {code: project.code})? - unchanged = (_.findWhere foundProjects, {code: project.code, name: project.name})? - return (found and !unchanged) - if (newProjects? and newProjects.length > 0) or (projectsToUpdate? and projectsToUpdate.length > 0) - if (newProjects? and newProjects.length > 0) - console.debug 'saving new projects with JSON: '+ JSON.stringify newProjects - cmpdRegRoutes.saveProjects newProjects, (saveProjectsResponse) -> - if (saveProjectsResponse.indexOf '') > -1 - console.error "Caught error saving CmpdReg projects" - console.error projectResponse - caughtErrors = true - callback 'ERROR', caughtErrors - else - for projectToUpdate in projectsToUpdate - oldProject = _.findWhere foundProjects, {code: projectToUpdate.code} - projectToUpdate.id = oldProject.id - projectToUpdate.version = oldProject.version - console.debug 'updating projects with JSON: '+ JSON.stringify projectsToUpdate - cmpdRegRoutes.updateProjects projectsToUpdate, (updateProjectsResponse) -> - if (updateProjectsResponse.indexOf '') > -1 - console.error "Caught error updating CmpdReg projects" - console.error updateProjectsResponse - caughtErrors = true - callback 'ERROR', caughtErrors - else - console.debug 'CmpdReg projects are up-to-date' - callback 'CmpdReg projects are up-to-date', caughtErrors - else - console.warn "config server.project.sync.cmpdReg is not set to true, skipping sync of CmpdReg projects" - callback 'Skipped sync of CmpdReg projects', caughtErrors - exports.validateLiveDesignConfigs = (configJSON) -> _ = require "underscore" countNull = _.map configJSON, (configs) -> From 810228379923145edd155a190e0dd61cf9d1d25c Mon Sep 17 00:00:00 2001 From: keng Date: Thu, 16 May 2019 15:50:27 -0700 Subject: [PATCH 442/576] Updated README, added shell script for creating initial user for local development environment --- README.md | 26 ++++++++++++++++++++++---- docker_bob_setup.sh | 7 +++++++ 2 files changed, 29 insertions(+), 4 deletions(-) create mode 100755 docker_bob_setup.sh diff --git a/README.md b/README.md index 5b94fb228..9fca2fcf7 100644 --- a/README.md +++ b/README.md @@ -102,7 +102,7 @@ cd acas-cmpdreg-roo-server * Login and/or Sign-Up * Click Download > JChem Suite > JChem * Scroll down to Archives and select 16.4.25.0, click Get Archive -* Download jchem-merged-lib-16.4.25.0.zip +* Download [jchem-merged-lib-16.4.25.0.zip](https://chemaxon.com/download?dl=%2Fdata%2Fdownload%2Fjchem%2F16.4.25.0%2Fjchem-merged-lib-16.4.25.0.zip) * Unzip it and rename jchem.jar to jchem-16.4.25.0.jar ##### Add chemaxon jar file to a lib folder in the checkout @@ -157,17 +157,29 @@ docker-compose up -d ``` #### Login + +Visit `http://localhost:3000` in your browser to login. You will need to create a user in order to access the web app: + +```bash +curl localhost:3001/api/systemTest/getOrCreateACASBob +curl localhost:3001/api/systemTest/getOrCreateGlobalProject +curl localhost:3001/api/systemTest/getOrCreateGlobalProjectRole +curl localhost:3001/api/systemTest/giveBobRoles +curl localhost:3001/api/systemTest/getOrCreateCmpdRegBob +curl localhost:3001/api/systemTest/syncRoles ``` -http://localhost:3000 -``` +Optionally you could run the shell script `docker_bob_setup.sh` in this repository instead of manually `curl`ing each endpoint. #### Viewing logs +``` docker-compose logs --tail=20 -f +``` e.g. for all containers + ``` -docker-compose logs --tail=20 -f +docker-compose logs -f ``` e.g. for only tomcat @@ -176,6 +188,12 @@ e.g. for only tomcat docker-compose logs --tail=20 -f tomcat ``` +Once you want to bring everything down: + +```bash +docker-compose down +``` + #### Troubleshooting * There is a known timing issue where tomcat may try to connect to the database before the database is accepting connections. If this happens, try restarting tomcat. diff --git a/docker_bob_setup.sh b/docker_bob_setup.sh new file mode 100755 index 000000000..a9bd2bff0 --- /dev/null +++ b/docker_bob_setup.sh @@ -0,0 +1,7 @@ +curl localhost:3001/api/systemTest/getOrCreateACASBob +curl localhost:3001/api/systemTest/getOrCreateGlobalProject +curl localhost:3001/api/systemTest/getOrCreateGlobalProjectRole +curl localhost:3001/api/systemTest/giveBobRoles +curl localhost:3001/api/systemTest/getOrCreateCmpdRegBob +curl localhost:3001/api/systemTest/syncRoles +#curl localhost:3001/api/systemTest/getOrCreateCmpds \ No newline at end of file From 3fd6c4cd4070239c45ab4deb975e03b4655f56e2 Mon Sep 17 00:00:00 2001 From: keng Date: Thu, 16 May 2019 16:00:31 -0700 Subject: [PATCH 443/576] Edit to readme --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 9fca2fcf7..f368305fa 100644 --- a/README.md +++ b/README.md @@ -170,6 +170,8 @@ curl localhost:3001/api/systemTest/syncRoles ``` Optionally you could run the shell script `docker_bob_setup.sh` in this repository instead of manually `curl`ing each endpoint. +This will create a user "bob" with password "secret". + #### Viewing logs ``` @@ -188,7 +190,7 @@ e.g. for only tomcat docker-compose logs --tail=20 -f tomcat ``` -Once you want to bring everything down: +Stop the web stack ```bash docker-compose down From fe4fc8ff73be6fda2ffbc9c7886420381da0ecac Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Sun, 23 Jun 2019 12:39:20 -0700 Subject: [PATCH 444/576] call api endpoint instead of client method so we can include_permissions=false url attrute --- .../ServerAPI/src/server/python/acas_ldclient/acasldclient.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py index 18f0d2924..466c76a77 100644 --- a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py +++ b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py @@ -103,7 +103,8 @@ def ld_user_to_acas_user_code_table(ld_user): return acas_user def get_users(client, ls_type = None, ls_kind = None, role_name = None): - ld_users = client.list_users() + # ld_users = client.list_users() + ld_users = client.client.get("/users?include_permissions=false", '') if ls_type == None and ls_kind == None and role_name == None: acas_users = map(ld_user_to_acas_user_code_table, ld_users) else: From 89e08fe514ef81d0d5683cea84c9352e3a44a800 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Sun, 23 Jun 2019 13:32:34 -0700 Subject: [PATCH 445/576] switching to using psycopg2-binary as psycopg2 seems to require postgres-devel also be installed now --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 4401e511a..2a03bb2a3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -79,7 +79,7 @@ USER root RUN curl -SLO dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm && rpm -ivh epel-release-6-8.noarch.rpm && rm epel-release-6-8.noarch.rpm RUN yum install -y centos-release-SCL RUN yum install -y python-pip python-psycopg2 python27 -RUN source /opt/rh/python27/enable && pip install argparse requests psycopg2 +RUN source /opt/rh/python27/enable && pip install argparse requests psycopg2-binary USER runner EXPOSE 3000 From 8c90fbac74601b206bdd95a4271adbbc548d51ce Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 26 Jun 2019 14:27:31 -0700 Subject: [PATCH 446/576] Fixes #567: allowed project codes was getting set to null in author routes so the user was not getting access to a project they should have --- modules/ServerAPI/src/server/routes/AuthorRoutes.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee index 65f8bdcdf..6354264a9 100644 --- a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee @@ -57,7 +57,7 @@ exports.allowedProjectsInternal = (user, callback) -> allowedProjectCodes = [] user.roles.forEach (role) -> if role.roleEntry.lsType != null && role.roleEntry.lsType == "Project" - allowedProjectCodes.push role.lsKind + allowedProjectCodes.push role.roleEntry.lsKind else if role.roleEntry.roleName == config.all.client.roles.acas.adminRole isAdmin = true if isAdmin From 7813239b7bbc7885024cda48740caccf5783853f Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 1 Jul 2019 19:29:56 -0700 Subject: [PATCH 447/576] #568: Remove CmpdReg scientists module, add Additional Compound Scientists and Additional Assay Scientists code table editors --- .../src/client/CmpdRegScientist.coffee | 67 ---- .../src/client/CmpdRegScientist.html | 8 - .../src/client/AbstractCodeTablesAdmin.coffee | 252 ++++++++++++++ .../AbstractCodeTablesAdminBrowser.coffee | 308 ++++++++++++++++++ .../AbstractCodeTablesAdminBrowserView.html | 146 +++++++++ .../client/AbstractCodeTablesAdminView.html | 125 +++++++ .../client/CodeTablesAssayScientist.coffee | 69 ++++ .../src/client/CodeTablesAssayScientist.html | 8 + .../client/CodeTablesCompoundScientist.coffee | 69 ++++ .../client/CodeTablesCompoundScientist.html | 8 + .../routes/CodeTablesAdminRoutes.coffee | 176 ++++++++++ .../routes/CodeTableServiceRoutes.coffee | 54 ++- .../client/ModuleMenusConfiguration.coffee | 12 +- 13 files changed, 1213 insertions(+), 89 deletions(-) delete mode 100644 modules/CmpdRegAdmin/src/client/CmpdRegScientist.coffee delete mode 100644 modules/CmpdRegAdmin/src/client/CmpdRegScientist.html create mode 100644 modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdmin.coffee create mode 100644 modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminBrowser.coffee create mode 100644 modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminBrowserView.html create mode 100644 modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminView.html create mode 100644 modules/CodeTablesAdmin/src/client/CodeTablesAssayScientist.coffee create mode 100644 modules/CodeTablesAdmin/src/client/CodeTablesAssayScientist.html create mode 100644 modules/CodeTablesAdmin/src/client/CodeTablesCompoundScientist.coffee create mode 100644 modules/CodeTablesAdmin/src/client/CodeTablesCompoundScientist.html create mode 100644 modules/CodeTablesAdmin/src/server/routes/CodeTablesAdminRoutes.coffee diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegScientist.coffee b/modules/CmpdRegAdmin/src/client/CmpdRegScientist.coffee deleted file mode 100644 index d05527a11..000000000 --- a/modules/CmpdRegAdmin/src/client/CmpdRegScientist.coffee +++ /dev/null @@ -1,67 +0,0 @@ -############################################################################ -# models -############################################################################ -class window.Scientist extends Backbone.Model - urlRoot: "/api/cmpdRegAdmin/scientists" - defaults: - name: null - code: null - id: null - ignored: false - - validate: (attrs) -> - errors = [] - if attrs.code? and @isNew() - validChars = attrs.code.match(/[a-zA-Z0-9 _\-+]/g) - unless validChars.length is attrs.code.length - errors.push - attribute: 'scientistCode' - message: "Scientist code can not contain special characters" - if !attrs.name? or attrs.name is "" - errors.push - attribute: 'scientistName' - message: "Scientist name must be set and unique" - if errors.length > 0 - return errors - else - return null - -############################################################################ -class window.Scientists extends Backbone.Collection - model: Scientist -############################################################################ - -############################################################################ -# controllers -############################################################################ - -class window.ScientistController extends AbstractCmpdRegAdminController - wrapperTemplate: _.template($("#ScientistView").html()) - moduleLaunchName: "scientist" - entityType: "scientist" - entityTypePlural: "scientists" - entityTypeUpper: "Scientist" - entityTypeUpperPlural: "Scientists" - modelClass: "Scientist" - showIgnore: true - - completeInitialization: => - @errorOwnerName = 'ScientistController' - $(@el).empty() - $(@el).html @wrapperTemplate() -# @$('.bv_scientistControllerDiv').html - console.log @$('.bv_scientistControllerDiv') - console.log "completing initialization of ScientistController" - @$('.bv_scientistControllerDiv').html super() - - -class window.ScientistBrowserController extends AbstractCmpdRegAdminBrowserController - wrapperTemplate: _.template($("#ScientistBrowserView").html()) - entityType: "scientist" - entityTypePlural: "scientists" - entityTypeUpper: "Scientist" - entityTypeUpperPlural: "Scientists" - entityClass: "Scientist" - entityControllerClass: "ScientistController" - moduleLaunchName: "scientist_browser" - showIgnore: true diff --git a/modules/CmpdRegAdmin/src/client/CmpdRegScientist.html b/modules/CmpdRegAdmin/src/client/CmpdRegScientist.html deleted file mode 100644 index af4f979a0..000000000 --- a/modules/CmpdRegAdmin/src/client/CmpdRegScientist.html +++ /dev/null @@ -1,8 +0,0 @@ - - - diff --git a/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdmin.coffee b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdmin.coffee new file mode 100644 index 000000000..517c09d60 --- /dev/null +++ b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdmin.coffee @@ -0,0 +1,252 @@ +class window.AbstractCodeTablesAdminController extends AbstractFormController + ### + Instances of this controller must supply "moduleLaunchName", "codeType", and "modelClass" + e.g. other required fields + codeType: "assay" + codeKind: "scientist" + displayName: "assay scientist" + pluralDisplayName: "assay scientists" + upperDisplayName: "Assay Scientist" + upperPluralDisplayName: "Assay Scientists" + entityClass: "AssayScientist" + entityControllerClass: "AssayScientistController" + moduleLaunchName: "assay_scientist_browser" + ### + template: _.template($("#AbstractCodeTablesAdminView").html()) + + events: -> + "keyup .bv_codeTablesAdminCode": "handleCodeTablesAdminCodeNameChanged" + "keyup .bv_codeTablesAdminName": "handleCodeTablesAdminNameChanged" + "click .bv_codeTablesAdminIgnore": "handleCodeTablesAdminIgnoreChanged" + "click .bv_save": "handleSaveClicked" + "click .bv_backToCodeTablesAdminBrowserBtn": "handleBackToCodeTablesAdminBrowserClicked" +# "click .bv_newEntity": "handleNewEntityClicked" + "click .bv_cancel": "handleCancelClicked" + "click .bv_cancelClear": "handleCancelClearClicked" + "click .bv_confirmClear": "handleConfirmClearClicked" + + initialize: -> + console.log "initializing Abstract Controller" + if @model? + @completeInitialization() + else + if window.AppLaunchParams.moduleLaunchParams? + if window.AppLaunchParams.moduleLaunchParams.moduleName == @moduleLaunchName + $.ajax + type: 'GET' + url: @model.urlRoot + '/codeName/'+window.AppLaunchParams.moduleLaunchParams.code + dataType: 'json' + error: (err) => + alert "Error getting #{@codeType} for code in this URL. Creating a new project" + @completeInitialization() + success: (json) => + if json.id? + @model = new window[@modelClass] json + else + alert "Could not get #{@codeType} for code in this URL. Creating a new project" + @completeInitialization() + else + @completeInitialization() + else + @completeInitialization() + + + completeInitialization: => + unless @model? + @model=new window[@modelClass]() + @setBindings() + if @options.readOnly? + @readOnly = @options.readOnly + else + @readOnly = false + unless @showIgnore? + @showIgnore = false + @listenTo @model, 'saveFailed', @handleSaveFailed + @listenTo @model, 'sync', @modelSaveCallback + @listenTo @model, 'change', @modelChangeCallback + $(@el).empty() + toDisplay = + displayName: @displayName + pluralDisplayName: @pluralDisplayName + upperDisplayName: @upperDisplayName + upperPluralDisplayName: @upperPluralDisplayName + $(@el).html(@template(toDisplay)) + if @showIgnore + @$(".bv_group_codeTablesAdminIgnore").show() + else + @$(".bv_group_codeTablesAdminIgnore").hide() + @render() + + render: => + unless @model? + @model = new window[@modelClass]() + code = @model.get('code') + @$('.bv_codeTablesAdminCode').val(code) + @$('.bv_codeTablesAdminCode').html(code) + if @showIgnore + if @model.get('ignored') is true + @$('.bv_codeTablesAdminIgnore').attr 'checked', 'checked' + else + @$('.bv_codeTablesAdminIgnore').removeAttr 'checked' + + if @model.isNew() + @$('.bv_save').html("Save") +# @$('.bv_newEntity').hide() + else + @$('.bv_save').html("Update") + # @$('.bv_newEntity').show() + @$('.bv_codeTablesAdminName').val @model.get('name') + + if @readOnly is true + @displayInReadOnlyMode() + @$('.bv_backToCodeTablesAdminBrowserBtn').hide() + @$('.bv_save').attr('disabled','disabled') + @$('.bv_cancel').attr('disabled','disabled') + + @ + + handleSaveFailed: => + @$('.bv_saveFailed').show() + @$('.bv_saveComplete').hide() + @$('.bv_saving').hide() + + modelSaveCallback: (method, model) => + @$('.bv_save').show() + @$('.bv_save').attr('disabled', 'disabled') + unless @$('.bv_saveFailed').is(":visible") + @$('.bv_saveComplete').show() + @$('.bv_saving').hide() + @$('.bv_cancel').removeAttr 'disabled' + @render() + @trigger 'amClean' + + modelChangeCallback: (method, model) => + @trigger 'amDirty' + @checkFormValid() + @$('.bv_saveComplete').hide() + @$('.bv_saveFailed').hide() + @$('.bv_cancel').removeAttr('disabled') + @$('.bv_cancelComplete').hide() + + handleCodeTablesAdminCodeNameChanged: => + code = UtilityFunctions::getTrimmedInput @$('.bv_codeTablesAdminCode') + + if code is "" + @model.set 'code', null + else + @model.set 'code', code + @model.trigger 'change' + + handleBackToCodeTablesAdminBrowserClicked: => + @trigger 'backToBrowser' + + +# handleNewEntityClicked: => +# @$('.bv_confirmClearEntity').modal('show') +# @$('.bv_confirmClear').removeAttr('disabled') +# @$('.bv_cancelClear').removeAttr('disabled') +# @$('.bv_closeModalButton').removeAttr('disabled') + + handleCancelClearClicked: => + @$('.bv_confirmClearEntity').modal('hide') + + handleConfirmClearClicked: => + @$('.bv_confirmClearEntity').modal('hide') + @model = null + @completeInitialization() + @trigger 'amClean' + + handleCancelClicked: => + if @model.isNew() + @model = null + @completeInitialization() + else + @$('.bv_canceling').show() + @model.fetch + success: @handleCancelComplete + @trigger 'amClean' + + handleCancelComplete: => + @$('.bv_canceling').hide() + @$('.bv_cancelComplete').show() + + handleCodeTablesAdminNameChanged: => + @model.set("name", UtilityFunctions::getTrimmedInput @$('.bv_codeTablesAdminName')) + + handleCodeTablesAdminIgnoreChanged: => + @model.set("ignored", @$('.bv_codeTablesAdminIgnore').is(":checked")) + + handleSaveClicked: => + @callNameValidationService() + + @$('.bv_saving').show() + @$('.bv_saveFailed').hide() + @$('.bv_saveComplete').hide() + + + callNameValidationService: => + @$('.bv_saving').show() + @$('.bv_save').attr('disabled', 'disabled') + validateURL = @model.urlRoot + '/validateBeforeSave' + dataToPost = + data: JSON.stringify(@model) + $.ajax + type: 'POST' + url: validateURL + data: dataToPost + dataType: 'json' + success: (response) => + @handleValidateReturn(response) + error: (err) => + @handleValidateError(JSON.parse err.responseText) + + handleValidateError: (err) => + if err?[0]?.level? and err[0].level is "ERROR" + alert "The requested code has already been used" + @$('.bv_saving').hide() + @$('.bv_saveFailed').show() + + handleValidateReturn: (validateResp) => + if validateResp?[0]?.errorLevel? + alert "The requested #{@codeType} #{@codeKind} code has already been registered. Please choose a new #{@codeType} #{@codeKind} code." + @$('.bv_saving').hide() + @$('.bv_saveFailed').show() + else + @saveCodeTablesAdmin() + + saveCodeTablesAdmin: => + if @model.isNew() + @$('.bv_saveComplete').html('Save Complete') + else + @$('.bv_saveComplete').html('Update Complete') + @$('.bv_save').attr('disabled', 'disabled') + + @model.save null, + success: (model, response) => + if response is "update #{@codeType} failed" + @model.trigger 'saveFailed' + + validationError: => + super() + @$('.bv_save').attr('disabled', 'disabled') + + clearValidationErrorStyles: => + super() + @$('.bv_save').removeAttr('disabled') + + checkDisplayMode: => + if @readOnly is true + @displayInReadOnlyMode() + + displayInReadOnlyMode: => + @$(".bv_save").hide() + @$(".bv_cancel").hide() + # @$(".bv_newEntity").hide() + @$('button').attr 'disabled', 'disabled' + @disableAllInputs() + + checkFormValid: => + if @isValid() + @$('.bv_save').removeAttr('disabled') + else + @$('.bv_save').attr('disabled', 'disabled') \ No newline at end of file diff --git a/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminBrowser.coffee b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminBrowser.coffee new file mode 100644 index 000000000..cc5dfa18a --- /dev/null +++ b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminBrowser.coffee @@ -0,0 +1,308 @@ +############################################################################ +# models +############################################################################ +class window.CodeTablesAdminSearch extends Backbone.Model + defaults: + codeType: null + codeKind: null + name: null + code: null + id: null + +############################################################################ +class window.CodeTablesAdminList extends Backbone.Collection + model: CodeTablesAdminSearch + +############################################################################ +# controllers +############################################################################ +class window.CodeTablesAdminSimpleSearchController extends AbstractFormController + ### + Instantiating controller must provide urlRoot and toDisplay in options + ### + + initialize: -> + @searchUrl = "" + @searchUrl = @options.urlRoot + '/search/' + + events: + 'keyup .bv_codeTablesAdminSearchTerm': 'updateCodeTablesAdminSearchTerm' + 'click .bv_doSearch': 'handleDoSearchClicked' + "click .bv_createNewCodeTablesAdminBtn": "handleCreateNewCodeTablesAdminClicked" + + render: => + console.log "rendering SimpleSearchController" + template = _.template($("#CodeTablesAdminSimpleSearchView").html()) + $(@el).empty() + console.log @options.toDisplay + $(@el).html(template(@options.toDisplay)) + @ + + updateCodeTablesAdminSearchTerm: (e) => + ENTER_KEY = 13 + codeTablesAdminSearchTerm = $.trim(@$(".bv_codeTablesAdminSearchTerm").val()) + if codeTablesAdminSearchTerm isnt "" + @$(".bv_doSearch").attr("disabled", false) + if e.keyCode is ENTER_KEY + $(':focus').blur() + @trigger 'searchRequested' + else + @$(".bv_doSearch").attr("disabled", true) + + doSearch: (codeTablesAdminSearchTerm) => +# disable the search text field while performing a search + @$(".bv_codeTablesAdminSearchTerm").attr "disabled", true + @$(".bv_doSearch").attr "disabled", true + @trigger 'find' + unless codeTablesAdminSearchTerm is "" + $.ajax + type: 'GET' + url: @searchUrl + codeTablesAdminSearchTerm + dataType: "json" + data: + testMode: false + +#fullObject: true + success: (codeTablesAdmin) => + @trigger "searchReturned", codeTablesAdmin + error: (result) => + @trigger "searchReturned", null + complete: => +# re-enable the search text field regardless of if any results found + @$(".bv_codeTablesAdminSearchTerm").attr "disabled", false + @$(".bv_doSearch").attr "disabled", false + + handleCreateNewCodeTablesAdminClicked: => + @trigger 'createNewCodeTablesAdmin' + +############################################################################ +class window.CodeTablesAdminRowSummaryController extends Backbone.View + tagName: 'tr' + className: 'dataTableRow' + events: + "click": "handleClick" + + handleClick: => + @trigger "gotClick", @model + $(@el).closest("table").find("tr").removeClass "info" + $(@el).addClass "info" + + initialize: -> + @template = _.template($('#CodeTablesAdminRowSummaryView').html()) + if @options.showIgnore? + @showIgnore = @options.showIgnore + else + @showIgnore = false + + render: => + toDisplay = + code: @model.get('code') + name: @model.get('name') + + $(@el).html(@template(toDisplay)) + if @showIgnore + ignored = if @model.get('ignored')? then @model.get('ignored') else false + + @$(".bv_codeTablesAdminIgnore").show() + @$(".bv_codeTablesAdminIgnore").html ignored.toString() + else + @$(".bv_codeTablesAdminIgnore").hide() + @ + +############################################################################ +class window.CodeTablesAdminSummaryTableController extends Backbone.View + initialize: -> + if @options.showIgnore? + @showIgnore = @options.showIgnore + else + @showIgnore = false + + selectedRowChanged: (row) => + @trigger "selectedRowUpdated", row + + render: => + @template = _.template($('#CodeTablesAdminSummaryTableView').html()) + $(@el).html @template(@options.toDisplay) + #will always be instantiated with at least one model in collection + @collection.each (admin) => + prsc = new CodeTablesAdminRowSummaryController + model: admin + showIgnore: @showIgnore + prsc.on "gotClick", @selectedRowChanged + @$("tbody").append prsc.render().el + + @$("table").dataTable oLanguage: + sSearch: "Filter results: " #rename summary table's search bar + + if @showIgnore + @$(".bv_ignoredHeader").show() + else + @$(".bv_ignoredHeader").hide() + + @ + +############################################################################ +class window.AbstractCodeTablesAdminBrowserController extends Backbone.View + ### + Instantiating controller must provide: + codeType + entityClass + entityControllerClass + moduleLaunchName + ### + includeDuplicateAndEdit: false + events: + "click .bv_deleteCodeTablesAdmin": "handleDeleteCodeTablesAdminClicked" + "click .bv_editCodeTablesAdmin": "handleEditCodeTablesAdminClicked" + "click .bv_confirmDeleteCodeTablesAdminButton": "handleConfirmDeleteCodeTablesAdminClicked" + "click .bv_cancelDelete": "handleCancelDeleteClicked" + + + initialize: -> + template = _.template( $("#AbstractCodeTablesAdminBrowserView").html()); + $(@el).empty() + @toDisplay = + displayName: @displayName + pluralDisplayName: @pluralDisplayName + upperDisplayName: @upperDisplayName + upperPluralDisplayName: @upperPluralDisplayName + $(@el).html(template(@toDisplay)) + unless @showIgnore? + @showIgnore = false + @searchController = new CodeTablesAdminSimpleSearchController + model: new CodeTablesAdminSearch() + el: @$('.bv_codeTablesAdminSearchController') + urlRoot: "/api/codeTablesAdmin/#{@codeType}/#{@codeKind}" + toDisplay: @toDisplay + @searchController.render() + @searchController.on "searchRequested", @handleSearchRequested + @searchController.on "searchReturned", @setupCodeTablesAdminSummaryTable + @searchController.on "createNewCodeTablesAdmin", @handleCreateNewCodeTablesAdminClicked + #@searchController.on "resetSearch", @destroyCodeTablesAdminSummaryTable + + setupCodeTablesAdminSummaryTable: (codeTablesAdmins) => + @destroyCodeTablesAdminSummaryTable() + + @$(".bv_searchingCodeTablesAdminsMessage").addClass "hide" + if codeTablesAdmins is null + @$(".bv_errorOccurredPerformingSearch").removeClass "hide" + + else if codeTablesAdmins.length is 0 + @$(".bv_noMatchingCodeTablesAdminsFoundMessage").removeClass "hide" + @$(".bv_codeTablesAdminTableController").html "" + else + @$(".bv_searchCodeTablesAdminsStatusIndicator").addClass "hide" + @$(".bv_codeTablesAdminTableController").removeClass "hide" + @codeTablesAdminSummaryTable = new CodeTablesAdminSummaryTableController + collection: new CodeTablesAdminList codeTablesAdmins + toDisplay: @toDisplay + showIgnore: @showIgnore + + @codeTablesAdminSummaryTable.on "selectedRowUpdated", @selectedCodeTablesAdminUpdated + @$(".bv_codeTablesAdminTableController").html @codeTablesAdminSummaryTable.render().el + + selectedCodeTablesAdminUpdated: (codeTablesAdmin) => + @trigger "selectedCodeTablesAdminUpdated" + if @codeTablesAdminController? + @codeTablesAdminController.undelegateEvents() + @codeTablesAdminController = new window[@entityControllerClass] + model: new window[@entityClass] codeTablesAdmin.attributes + readOnly: true + + @$('.bv_codeTablesAdminController').html @codeTablesAdminController.render().el + @$(".bv_codeTablesAdminController").removeClass("hide") + @$(".bv_codeTablesAdminControllerContainer").removeClass("hide") + @$('.bv_editCodeTablesAdmin').show() + @$('.bv_deleteCodeTablesAdmin').show() + + handleSearchRequested: => + @$(".bv_codeTablesAdminTableController").addClass "hide" + @$(".bv_errorOccurredPerformingSearch").addClass "hide" + codeTablesAdminSearchTerm = $.trim(@$(".bv_codeTablesAdminSearchTerm").val()) + if codeTablesAdminSearchTerm isnt "" + @$(".bv_noMatchingCodeTablesAdminsFoundMessage").addClass "hide" + @$(".bv_codeTablesAdminBrowserSearchInstructions").addClass "hide" + @$(".bv_searchCodeTablesAdminsStatusIndicator").removeClass "hide" + if !window.conf.browser.enableSearchAll and codeTablesAdminSearchTerm is "*" + @$(".bv_moreSpecificCodeTablesAdminSearchNeeded").removeClass "hide" + else + @$(".bv_searchingCodeTablesAdminsMessage").removeClass "hide" + @$(".bv_codeTablesAdminSearchTerm").html codeTablesAdminSearchTerm + @$(".bv_moreSpecificCodeTablesAdminSearchNeeded").addClass "hide" + @searchController.doSearch codeTablesAdminSearchTerm + + handleDeleteCodeTablesAdminClicked: => + @$(".bv_codeTablesAdminCodeName").html @codeTablesAdminController.model.get("code") + @$(".bv_deleteButtons").removeClass "hide" + @$(".bv_okayButton").addClass "hide" + @$(".bv_errorDeletingCodeTablesAdminMessage").addClass "hide" + @$(".bv_deleteWarningMessage").removeClass "hide" + @$(".bv_deletingStatusIndicator").addClass "hide" + @$(".bv_codeTablesAdminDeletedSuccessfullyMessage").addClass "hide" + @$(".bv_confirmDeleteCodeTablesAdmin").removeClass "hide" + @$('.bv_confirmDeleteCodeTablesAdmin').modal({ + keyboard: false, + backdrop: true + }) + + handleConfirmDeleteCodeTablesAdminClicked: => + @$(".bv_deleteWarningMessage").addClass "hide" + @$(".bv_deletingStatusIndicator").removeClass "hide" + @$(".bv_deleteButtons").addClass "hide" + $.ajax( + url: "/api/codeTablesAdmin/#{@codeTablesAdminController.model.get("id")}", + type: 'DELETE', + success: (result) => + @$(".bv_okayButton").removeClass "hide" + @$(".bv_deletingStatusIndicator").addClass "hide" + @$(".bv_codeTablesAdminDeletedSuccessfullyMessage").removeClass "hide" + @handleSearchRequested() + error: (result) => + @$(".bv_okayButton").removeClass "hide" + @$(".bv_deletingStatusIndicator").addClass "hide" + @$(".bv_errorDeletingCodeTablesAdminMessage").removeClass "hide" + ) + + handleCancelDeleteClicked: => + @$(".bv_confirmDeleteCodeTablesAdmin").modal('hide') + + handleEditCodeTablesAdminClicked: => + @createCodeTablesAdminController @codeTablesAdminController.model + + destroyCodeTablesAdminSummaryTable: => + if @codeTablesAdminSummaryTable? + @codeTablesAdminSummaryTable.remove() + if @codeTablesAdminController? + @codeTablesAdminController.remove() + + @$(".bv_codeTablesAdminController").addClass("hide") + @$(".bv_codeTablesAdminControllerContainer").addClass("hide") + @$(".bv_noMatchingCodeTablesAdminsFoundMessage").addClass("hide") + + render: => + @ + + handleCreateNewCodeTablesAdminClicked: => + @createCodeTablesAdminController new window[@entityClass]() + + createCodeTablesAdminController: (mdl) => + @$('.bv_codeTablesAdminBrowserWrapper').hide() + @$('.bv_codeTablesAdminControllerWrapper').show() + if @codeTablesAdminController? + @codeTablesAdminController.undelegateEvents() + @$(".bv_codeTablesAdminControllerWrapper").html "" + @codeTablesAdminController = new window[@entityControllerClass] + model: mdl + @codeTablesAdminController.on 'backToBrowser', @handleBackToCodeTablesAdminBrowserClicked + @codeTablesAdminController.on 'amDirty', => + @trigger 'amDirty' + @codeTablesAdminController.on 'amClean', => + @trigger 'amClean' + @$(".bv_codeTablesAdminControllerWrapper").append @codeTablesAdminController.render().el + @codeTablesAdminController.$('.bv_backToCodeTablesAdminBrowserBtn').show() + + handleBackToCodeTablesAdminBrowserClicked: => + @$('.bv_codeTablesAdminBrowserWrapper').show() + @$('.bv_codeTablesAdminControllerWrapper').hide() + @handleSearchRequested() + @trigger 'amClean' diff --git a/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminBrowserView.html b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminBrowserView.html new file mode 100644 index 000000000..8d7d339c7 --- /dev/null +++ b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminBrowserView.html @@ -0,0 +1,146 @@ + + + + + + + diff --git a/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminView.html b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminView.html new file mode 100644 index 000000000..ee252bc18 --- /dev/null +++ b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminView.html @@ -0,0 +1,125 @@ + + diff --git a/modules/CodeTablesAdmin/src/client/CodeTablesAssayScientist.coffee b/modules/CodeTablesAdmin/src/client/CodeTablesAssayScientist.coffee new file mode 100644 index 000000000..a0f74dc25 --- /dev/null +++ b/modules/CodeTablesAdmin/src/client/CodeTablesAssayScientist.coffee @@ -0,0 +1,69 @@ +############################################################################ +# models +############################################################################ +class window.AssayScientist extends Backbone.Model + urlRoot: "/api/codeTablesAdmin/assay/scientist" + defaults: + name: null + code: null + id: null + ignored: false + + validate: (attrs) -> + errors = [] + if attrs.code? and @isNew() + validChars = attrs.code.match(/[a-zA-Z0-9 _\-+]/g) + unless validChars.length is attrs.code.length + errors.push + attribute: 'scientistCode' + message: "Assay Scientist code can not contain special characters" + if !attrs.code? or attrs.code is "" + errors.push + attribute: 'scientistCode' + message: "Assay Scientist code must be set and unique" + if !attrs.name? or attrs.name is "" + errors.push + attribute: 'scientistName' + message: "Assay Scientist name must be set and unique" + if errors.length > 0 + return errors + else + return null + +############################################################################ +# controllers +############################################################################ + +class window.AssayScientistController extends AbstractCodeTablesAdminController + wrapperTemplate: _.template($("#AssayScientistView").html()) + moduleLaunchName: "scientist" + codeType: "assay" + codeKind: "scientist" + displayName: "assay scientist" + pluralDisplayName: "assay scientists" + upperDisplayName: "Assay Scientist" + upperPluralDisplayName: "Scientists" + modelClass: "AssayScientist" + showIgnore: true + + completeInitialization: => + @errorOwnerName = 'AssayScientistController' + $(@el).empty() + $(@el).html @wrapperTemplate() + console.log @$('.bv_assayAssayScientistControllerDiv') + console.log "completing initialization of AssayScientistController" + @$('.bv_assayAssayScientistControllerDiv').html super() + + +class window.AssayScientistBrowserController extends AbstractCodeTablesAdminBrowserController + wrapperTemplate: _.template($("#AssayScientistBrowserView").html()) + codeType: "assay" + codeKind: "scientist" + displayName: "assay scientist" + pluralDisplayName: "assay scientists" + upperDisplayName: "Assay Scientist" + upperPluralDisplayName: "Assay Scientists" + entityClass: "AssayScientist" + entityControllerClass: "AssayScientistController" + moduleLaunchName: "assay_scientist_browser" + showIgnore: true diff --git a/modules/CodeTablesAdmin/src/client/CodeTablesAssayScientist.html b/modules/CodeTablesAdmin/src/client/CodeTablesAssayScientist.html new file mode 100644 index 000000000..a1198b5d8 --- /dev/null +++ b/modules/CodeTablesAdmin/src/client/CodeTablesAssayScientist.html @@ -0,0 +1,8 @@ + + + diff --git a/modules/CodeTablesAdmin/src/client/CodeTablesCompoundScientist.coffee b/modules/CodeTablesAdmin/src/client/CodeTablesCompoundScientist.coffee new file mode 100644 index 000000000..49cc6a0cd --- /dev/null +++ b/modules/CodeTablesAdmin/src/client/CodeTablesCompoundScientist.coffee @@ -0,0 +1,69 @@ +############################################################################ +# models +############################################################################ +class window.CompoundScientist extends Backbone.Model + urlRoot: "/api/codeTablesAdmin/compound/scientist" + defaults: + name: null + code: null + id: null + ignored: false + + validate: (attrs) -> + errors = [] + if attrs.code? and @isNew() + validChars = attrs.code.match(/[a-zA-Z0-9 _\-+]/g) + unless validChars.length is attrs.code.length + errors.push + attribute: 'scientistCode' + message: "Compound Scientist code can not contain special characters" + if !attrs.code? or attrs.code is "" + errors.push + attribute: 'scientistCode' + message: "Compound Scientist code must be set and unique" + if !attrs.name? or attrs.name is "" + errors.push + attribute: 'scientistName' + message: "Compound Scientist name must be set and unique" + if errors.length > 0 + return errors + else + return null + +############################################################################ +# controllers +############################################################################ + +class window.CompoundScientistController extends AbstractCodeTablesAdminController + wrapperTemplate: _.template($("#CompoundScientistView").html()) + moduleLaunchName: "scientist" + codeType: "compound" + codeKind: "scientist" + displayName: "compound scientist" + pluralDisplayName: "compound scientists" + upperDisplayName: "Compound Scientist" + upperPluralDisplayName: "Scientists" + modelClass: "CompoundScientist" + showIgnore: true + + completeInitialization: => + @errorOwnerName = 'CompoundScientistController' + $(@el).empty() + $(@el).html @wrapperTemplate() + console.log @$('.bv_compoundCompoundScientistControllerDiv') + console.log "completing initialization of CompoundScientistController" + @$('.bv_compoundCompoundScientistControllerDiv').html super() + + +class window.CompoundScientistBrowserController extends AbstractCodeTablesAdminBrowserController + wrapperTemplate: _.template($("#CompoundScientistBrowserView").html()) + codeType: "compound" + codeKind: "scientist" + displayName: "compound scientist" + pluralDisplayName: "compound scientists" + upperDisplayName: "Compound Scientist" + upperPluralDisplayName: "Compound Scientists" + entityClass: "CompoundScientist" + entityControllerClass: "CompoundScientistController" + moduleLaunchName: "compound_scientist_browser" + showIgnore: true diff --git a/modules/CodeTablesAdmin/src/client/CodeTablesCompoundScientist.html b/modules/CodeTablesAdmin/src/client/CodeTablesCompoundScientist.html new file mode 100644 index 000000000..e8a18af2a --- /dev/null +++ b/modules/CodeTablesAdmin/src/client/CodeTablesCompoundScientist.html @@ -0,0 +1,8 @@ + + + diff --git a/modules/CodeTablesAdmin/src/server/routes/CodeTablesAdminRoutes.coffee b/modules/CodeTablesAdmin/src/server/routes/CodeTablesAdminRoutes.coffee new file mode 100644 index 000000000..970fda4f8 --- /dev/null +++ b/modules/CodeTablesAdmin/src/server/routes/CodeTablesAdminRoutes.coffee @@ -0,0 +1,176 @@ +exports.setupAPIRoutes = (app, loginRoutes) -> + app.get '/api/codeTablesAdmin/:entityType', exports.getCodeTablesEntities + app.get '/api/codeTablesAdmin/:entityType/d/:code', exports.validateCodeTablesEntity + app.get '/api/codeTablesAdmin/:entityType/codeName/:code', exports.getCodeTablesEntityByCode + app.post '/api/codeTablesAdmin/:codeType/:codeKind/validateBeforeSave', exports.validateCodeTablesEntityBeforeSave + app.post '/api/codeTablesAdmin/:entityType', exports.saveCodeTablesEntity + app.put '/api/codeTablesAdmin/:codeType/:codeKind/:id', exports.updateCodeTablesEntity + app.delete '/api/codeTablesAdmin/:codeType/:codeKind/:id', exports.deleteCodeTablesEntity + +exports.setupRoutes = (app, loginRoutes) -> + app.get '/api/codeTablesAdmin/:codeType/:codeKind/search/:searchTerm', loginRoutes.ensureAuthenticated, exports.searchCodeTablesEntities + app.post '/api/codeTablesAdmin/:codeType/:codeKind/validateBeforeSave', loginRoutes.ensureAuthenticated, exports.validateCodeTablesEntityBeforeSave + app.post '/api/codeTablesAdmin/:codeType/:codeKind', loginRoutes.ensureAuthenticated, exports.saveCodeTablesEntity + app.put '/api/codeTablesAdmin/:codeType/:codeKind/:id', loginRoutes.ensureAuthenticated, exports.updateCodeTablesEntity + app.delete '/api/codeTablesAdmin/:id', loginRoutes.ensureAuthenticated, exports.deleteCodeTablesEntity + +exports.validateCodeTablesEntity = (req, resp) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + entityType = req.params.entityType + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + "#{entityType}/validate?code=" + req.params.code + request( + method: 'GET' + url: cmpdRegCall + json: false + timeout: 6000000 + , (error, response, validEntity) => + if !error and !validEntity.startsWith('<') + resp.statusCode = response.statusCode + resp.setHeader('Content-Type', 'application/json') + resp.end validEntity + console.log "done validating the #{entityType} testString" + else + console.log 'got ajax error trying to do validate #{entityType}' + resp.statusCode = 500 + resp.end JSON.stringify {error: "something went wrong validating the #{entityType}"} + ) + +exports.validateCodeTablesEntityBeforeSave = (req, resp) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + codeTableServiceRoutes = require "./CodeTableServiceRoutes.js" + searchTerm = req.params.searchTerm + codeTableServiceRoutes.getCodeTableValuesInternal req.params.codeType, req.params.codeKind, (results) -> + for r in results + data = JSON.parse(req.body.data) + if (!data.id? || data.id!=r.id) && r.code == data.code + resp.end JSON.stringify([{"errorLevel": "ERROR", "message": "Code value already exists for #{req.params.codeType} #{req.params.codeKind}"}]) + return + resp.end req.body.data + +exports.getCodeTablesEntityById = (req, resp) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + entityType = req.params.entityType + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + "#{entityType}/" + req.params.id + request( + method: 'GET' + url: cmpdRegCall + json: true + timeout: 6000000 + , (error, response, json) => + if !error && response.statusCode == 200 + console.log JSON.stringify json + resp.statusCode = response.statusCode + resp.setHeader('Content-Type', 'application/json') + resp.json json + else + resp.statusCode = 404 + console.error "got ajax error trying to do find #{entityType}" + console.log json + resp.end JSON.stringify {error: "something went wrong :("} + ) + +exports.getCodeTablesEntityByCode = (req, resp) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + entityType = req.params.entityType + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + "#{entityType}/findByCodeEquals?code=" + req.params.code + request( + method: 'GET' + url: cmpdRegCall + json: true + timeout: 6000000 + , (error, response, json) => + if !error && response.statusCode == 200 + console.log JSON.stringify json + resp.statusCode = response.statusCode + resp.setHeader('Content-Type', 'application/json') + resp.json json + else + resp.statusCode = 404 + console.log "got ajax error trying to do find #{entityType}" + console.log json + resp.end JSON.stringify {error: "something went wrong :("} + ) + +exports.searchCodeTablesEntities = (req, resp) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + codeTableServiceRoutes = require "./CodeTableServiceRoutes.js" + searchTerm = req.params.searchTerm.toLowerCase().trim() + codeTableServiceRoutes.getCodeTableValuesInternal req.params.codeType, req.params.codeKind, (results) -> + searchResults = [] + if searchTerm == "*" || searchTerm == "" + searchResults = results + else + for r in results + if r.code.toLowerCase().indexOf(searchTerm) >= 0 || r.comments.toLowerCase().indexOf(searchTerm) >= 0 || r.description.toLowerCase().indexOf(searchTerm) >= 0 || r.name.toLowerCase().indexOf(searchTerm) >= 0 + searchResults.push(r) + resp.json searchResults + +exports.getCodeTablesEntities = (req, resp) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + entityType = req.params.entityType + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + "#{entityType}" + request( + method: 'GET' + url: cmpdRegCall + json: true + timeout: 6000000 + , (error, response, json) => + if !error + console.log JSON.stringify json + resp.statusCode = response.statusCode + resp.setHeader('Content-Type', 'application/json') + resp.json json + else + console.log "got ajax error trying to do get #{entityType}" + console.log json + resp.statusCode = 404 + resp.end JSON.stringify {error: "something went wrong :("} + ) + +exports.saveCodeTablesEntity = (req, resp) -> + codeTableServiceRoutes = require "./CodeTableServiceRoutes.js" + codeEntry = { + comments: "registered with code tables admin module", + description: "registered with code tables admin module", + displayOrder: null, + ignored: req.body.ignored, + name: req.body.name, + codeOrigin: "ACAS" + codeKind: req.params.codeKind, + codeType: req.params.codeType, + code: req.body.code + } + codeTableServiceRoutes.postCodeTableInternal codeEntry, (statusCode, response) -> + resp.end response + +exports.updateCodeTablesEntity = (req, resp) -> + codeTableServiceRoutes = require "./CodeTableServiceRoutes.js" + codeEntry = { + comments: "registered with code tables admin module", + description: "registered with code tables admin module", + displayOrder: null, + ignored: req.body.ignored, + name: req.body.name, + codeOrigin: "ACAS" + codeKind: req.params.codeKind, + codeType: req.params.codeType, + code: req.body.code + id: req.body.id + } + codeTableServiceRoutes.putCodeTableInternal codeEntry, (statusCode, response) -> + resp.end response + + +exports.deleteCodeTablesEntity = (req, resp) -> + codeTableServiceRoutes = require "./CodeTableServiceRoutes.js" + + codeTableServiceRoutes.deleteCodeTableInternal {id: req.params.id}, (statusCode, response) -> + console.log(statusCode) + console.log(response) + resp.json response diff --git a/modules/Components/src/server/routes/CodeTableServiceRoutes.coffee b/modules/Components/src/server/routes/CodeTableServiceRoutes.coffee index 7e87f439e..1e30160b9 100644 --- a/modules/Components/src/server/routes/CodeTableServiceRoutes.coffee +++ b/modules/Components/src/server/routes/CodeTableServiceRoutes.coffee @@ -72,9 +72,13 @@ exports.getCodeTableValuesInternal = (type, kind, cb) -> exports.postCodeTable = (req, resp) -> + exports.postCodeTableInternal req.body.codeEntry, (statusCode, response) => + resp.end JSON.stringify response + +exports.postCodeTableInternal = (codeTableEntry, callback) -> if global.specRunnerTestmode codeTablePostTestJSON = require '../public/javascripts/spec/Components/testFixtures/codeTablePostTestJSON.js' - resp.end JSON.stringify codeTablePostTestJSON.codeEntry + callback 201, JSON.stringify codeTablePostTestJSON.codeEntry else console.log "attempting to post new code table value" config = require '../conf/compiled/conf.js' @@ -83,48 +87,76 @@ exports.postCodeTable = (req, resp) -> request( method: 'POST' url: baseurl - body: req.body.codeEntry + body: codeTableEntry json: true , (error, response, json) => if !error && response.statusCode == 201 - resp.end JSON.stringify json + callback 201, JSON.stringify json else console.log 'got ajax error trying to save new code table' console.log error console.log json - console.log response + callback response.statusCode, response.json ) - exports.putCodeTable = (req, resp) -> - #console.log JSON.stringify req.body + exports.putCodeTableInternal req.body.codeEntry, (statusCode, response) => + resp.end JSON.stringify response + +exports.putCodeTableInternal = (codeTableEntry, callback) -> if global.specRunnerTestmode codeTablePostTestJSON = require '../public/javascripts/spec/Components/testFixtures/codeTablePutTestJSON.js' resp.end JSON.stringify codeTablePostTestJSON.codeEntry else config = require '../conf/compiled/conf.js' - putId = req.body.id + putId = codeTableEntry.id baseurl = "#{config.all.client.service.persistence.fullpath}ddictvalues/codetable/#{putId}" request = require 'request' request( method: 'PUT' url: baseurl - body: req.body + body: codeTableEntry json: true , (error, response, json) => console.log response.statusCode if !error && response.statusCode == 200 - resp.end JSON.stringify json + callback 200, JSON.stringify json else console.log 'got ajax error trying to update code table' console.log error console.log response + callback response.statusCode, response.json ) +exports.deleteCodeTable = (req, resp) -> + exports.deleteCodeTableInternal req.body.codeEntry, (statusCode, response) => + resp.end JSON.stringify response - - +exports.deleteCodeTableInternal = (codeTableEntry, callback) -> + config = require '../conf/compiled/conf.js' + console.log "#{config.all.client.service.persistence.fullpath}ddictvalues/#{codeTableEntry.id}" + if global.specRunnerTestmode + codeTablePostTestJSON = require '../public/javascripts/spec/Components/testFixtures/codeTablePostTestJSON.js' + callback 201, JSON.stringify codeTablePostTestJSON.codeEntry + else + console.log "attempting to delete code table value" + config = require '../conf/compiled/conf.js' + baseurl = "#{config.all.client.service.persistence.fullpath}ddictvalues/#{codeTableEntry.id}" + request = require 'request' + request( + method: 'DELETE' + url: baseurl + json: true + , (error, response, json) => + if !error && response.statusCode == 200 + callback 200, JSON.stringify json + else + console.log 'got ajax error trying to delete code table' + console.log error + console.log json + callback response.statusCode, response.json + ) diff --git a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee index a040b8d7c..d39a5b4ed 100644 --- a/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee +++ b/modules/ModuleMenus/src/client/ModuleMenusConfiguration.coffee @@ -78,6 +78,12 @@ window.ModuleMenusConfiguration = mainControllerClassName: "ACASLabelSequenceController" autoLaunchName: "acasLabelSequence" requireUserRoles: [window.conf.roles.acas.adminRole] + , + isHeader: false + menuName: "Additional Assay Scientists" + mainControllerClassName: "AssayScientistBrowserController" + autoLaunchName: "assay_scientist_browser" + requireUserRoles: [window.conf.roles.acas.adminRole] , isHeader: true menuName: "CmpdReg Admin" @@ -97,8 +103,8 @@ window.ModuleMenusConfiguration = requireUserRoles: [window.conf.roles.cmpdreg.adminRole] , isHeader: false - menuName: "CmpdReg Scientists" - mainControllerClassName: "ScientistBrowserController" - autoLaunchName: "scientist_browser" + menuName: "Additional CmpdReg Scientists" + mainControllerClassName: "CompoundScientistBrowserController" + autoLaunchName: "compound_scientist_browser" requireUserRoles: [window.conf.roles.cmpdreg.adminRole] ] From 6338412f00b201f8e94f1934c61d153565d5e2a7 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 1 Jul 2019 19:35:13 -0700 Subject: [PATCH 448/576] update acasclient to simplify user acls --- .../python/acas_ldclient/acasldclient.py | 61 ++++++++++++++----- 1 file changed, 46 insertions(+), 15 deletions(-) diff --git a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py index 466c76a77..280eb3f64 100644 --- a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py +++ b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py @@ -109,19 +109,28 @@ def get_users(client, ls_type = None, ls_kind = None, role_name = None): acas_users = map(ld_user_to_acas_user_code_table, ld_users) else: groups = client.list_groups() - roles = map(ld_group_to_acas_role, groups) - role = [r for r in roles if r["roleEntry"]["lsType"] == ls_type and r["roleEntry"]["lsKind"] == ls_kind and r["roleEntry"]["roleName"] == role_name] - if len(role) == 0: - return [] - users = [] + permissions = client.list_permissions() memberships = client.list_memberships() - userDict = {} - for u in ld_users: - userDict[u["id"]] = u - for m in memberships: - if m["group_id"] == role[0]["id"]: - users.append(userDict[m["user_id"]]) - acas_users = map(ld_user_to_acas_user_code_table, users) + projects = client.projects() + user_projects = {} + for p in permissions: + for g in groups: + if p["group_id"] == g["id"]: + for proj in projects: + if p["project_id"] == proj.id: + if proj.name in user_projects: + user_projects[proj.name]["granting_groups"].append(g["name"]) + else: + user_projects[proj.name] = {"id":proj.id, "granting_groups": [g["name"]], "ld_users": []} + for m in memberships: + if m["group_id"] == g["id"]: + for u in ld_users: + if u["id"] == m["user_id"]: + user_projects[proj.name]["ld_users"].append(u) + if ls_kind in user_projects: + acas_users = map(ld_user_to_acas_user_code_table, user_projects[ls_kind]["ld_users"]) + else: + acas_users = [] return acas_users def ld_user_to_acas_user(ld_user, roles): @@ -156,13 +165,35 @@ def get_user(client, username): user = client.get_user(username) permissions = client.list_permissions() memberships = client.list_memberships() + projects = client.projects() groups = client.list_groups() user_memberships = [m for m in memberships if m['user_id'] == user['id']] user_groups = [next(g for g in groups if g["id"]==m["group_id"]) for m in user_memberships] - roles = map(ld_group_to_acas_role, user_groups) + user_projects = {} + for p in permissions: + for g in user_groups: + if p["group_id"] == g["id"]: + for proj in projects: + if p["project_id"] == proj.id: + if proj.name in user_projects: + user_projects[proj.name]["granting_groups"].append(g["name"]) + else: + user_projects[proj.name] = {"id":proj.id, "granting_groups": [g["name"]]} + roles = [] + for proj, data in user_projects.iteritems(): + roles.append({ + "id": data["id"], + "roleEntry": { + 'id': data["id"], + 'lsType': 'Project', + 'lsKind': proj, + 'lsTypeAndKind': "Project_" + proj, + 'roleDescription': "Permission to Project granted by Live Design group(s): "+', '.join("'{0}'".format(g) for g in data["granting_groups"]), + 'roleName': "User", + 'version': 0 + } + }) acas_user = ld_user_to_acas_user(user, roles) - # user = {"id":1,"username":"bob","email":"bob@mcneilco.com","firstName":"Ham","lastName":"Cheese","roles":[{"id":2,"roleEntry":{"id":1,"lsKind":"ACAS","lsType":"System","lsTypeAndKind":"System_ACAS","roleDescription":"ROLE_ACAS-USERS autocreated by ACAS","roleName":"ROLE_ACAS-USERS","version":0},"version":0},{"id":1,"roleEntry":{"id":2,"lsKind":"ACAS","lsType":"System","lsTypeAndKind":"System_ACAS","roleDescription":"ROLE_ACAS-ADMINS autocreated by ACAS","roleName":"ROLE_ACAS-ADMINS","version":0},"version":0},{"id":4,"roleEntry":{"id":4,"lsKind":"CmpdReg","lsType":"System","lsTypeAndKind":"System_CmpdReg","roleDescription":"ROLE_CMPDREG-ADMINS autocreated by ACAS","roleName":"ROLE_CMPDREG-ADMINS","version":0},"version":0},{"id":3,"roleEntry":{"id":5,"lsKind":"ACAS","lsType":"System","lsTypeAndKind":"System_ACAS","roleDescription":"ROLE_ACAS-CROSS-PROJECT-LOADER autocreated by ACAS","roleName":"ROLE_ACAS-CROSS-PROJECT-LOADER","version":0},"version":0},{"id":5,"roleEntry":{"id":3,"lsKind":"CmpdReg","lsType":"System","lsTypeAndKind":"System_CmpdReg","roleDescription":"ROLE_CMPDREG-USERS autocreated by ACAS","roleName":"ROLE_CMPDREG-USERS","version":0},"version":0},{"id":6,"roleEntry":{"id":6,"lsKind":"PROJ-00000001","lsType":"Project","lsTypeAndKind":"Project_PROJ-00000001","roleDescription":"User autocreated by ACAS","roleName":"User","version":0},"version":0}]} - return acas_user def get_projects(client): From 34ef3a8fffa106adca19b61468dbdbf8582046d9 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 2 Jul 2019 10:12:43 -0700 Subject: [PATCH 449/576] roo sparesely fills null values on object so need to test for their existance during search --- .../src/server/routes/CodeTablesAdminRoutes.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/CodeTablesAdmin/src/server/routes/CodeTablesAdminRoutes.coffee b/modules/CodeTablesAdmin/src/server/routes/CodeTablesAdminRoutes.coffee index 970fda4f8..764ad85a7 100644 --- a/modules/CodeTablesAdmin/src/server/routes/CodeTablesAdminRoutes.coffee +++ b/modules/CodeTablesAdmin/src/server/routes/CodeTablesAdminRoutes.coffee @@ -106,7 +106,7 @@ exports.searchCodeTablesEntities = (req, resp) -> searchResults = results else for r in results - if r.code.toLowerCase().indexOf(searchTerm) >= 0 || r.comments.toLowerCase().indexOf(searchTerm) >= 0 || r.description.toLowerCase().indexOf(searchTerm) >= 0 || r.name.toLowerCase().indexOf(searchTerm) >= 0 + if (r.code? && r.code.toLowerCase().indexOf(searchTerm) >= 0) || (r.comments? && r.comments.toLowerCase().indexOf(searchTerm) >= 0) || (r.description? && r.description.toLowerCase().indexOf(searchTerm) >= 0) || (r.name? && r.name.toLowerCase().indexOf(searchTerm) >= 0) searchResults.push(r) resp.json searchResults From ddd7d9b97e639fbe64ab0cc58411969818b4d18f Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 2 Jul 2019 11:08:49 -0700 Subject: [PATCH 450/576] add askterisk for required field in code table admin module --- .../CodeTablesAdmin/src/client/AbstractCodeTablesAdminView.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminView.html b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminView.html index ee252bc18..c0b4ba05e 100644 --- a/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminView.html +++ b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminView.html @@ -1,7 +1,7 @@ + + diff --git a/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee b/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee index d4ebda39b..23d28aca3 100644 --- a/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee +++ b/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee @@ -3,6 +3,7 @@ path = require 'path' exports.setupAPIRoutes = (app) -> app.post '/api/cmpdRegBulkLoader', exports.postAssignedProperties app.post '/api/cmpdRegBulkLoader/registerCmpds', exports.registerCmpds + app.post '/api/cmpdRegBulkLoader/validateCmpds', exports.validateCmpds app.post '/api/cmpdRegBulkLoader/validationProperties', exports.validationProperties app.get '/api/cmpdRegBulkLoader/getFilesToPurge', exports.getFilesToPurge app.post '/api/cmpdRegBulkLoader/purgeFile', exports.purgeFile @@ -15,6 +16,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/cmpdRegBulkLoader/readSDF', loginRoutes.ensureAuthenticated, exports.cmpdRegBulkLoaderReadSdf app.post '/api/cmpdRegBulkLoader/saveTemplate', loginRoutes.ensureAuthenticated, exports.saveTemplate app.post '/api/cmpdRegBulkLoader/registerCmpds', loginRoutes.ensureAuthenticated, exports.registerCmpds + app.post '/api/cmpdRegBulkLoader/validateCmpds', loginRoutes.ensureAuthenticated, exports.validateCmpds app.post '/api/cmpdRegBulkLoader', loginRoutes.ensureAuthenticated, exports.postAssignedProperties app.post '/api/cmpdRegBulkLoader/checkFileDependencies', loginRoutes.ensureAuthenticated, exports.checkFileDependencies app.post '/api/cmpdRegBulkLoader/purgeFile', loginRoutes.ensureAuthenticated, exports.purgeFile @@ -162,6 +164,10 @@ exports.getScientistsInternal = (callback) -> loginRoutes.getAuthorsInternal {additionalCodeType: 'compound', additionalCodeKind: 'scientist', roleName: roleName}, (statusCode, authors) => callback authors +exports.validateCmpds = (req, resp) -> + req.body.validate = true + exports.registerCmpds(req, resp) + exports.registerCmpds = (req, resp) -> req.connection.setTimeout 6000000 createSummaryZip = (fileName, json) -> @@ -267,7 +273,17 @@ exports.registerCmpds = (req, resp) -> console.log "Can't find or create bulkload folder: " + bulkLoadFolder callback "error", resp else - fs.rename oldPath, newPath, (err) -> + if req.body.validate + # new node has fs.copyFile but we don't currently:( + fsFuct = (oldPath, newPath, callback) -> + stream = fs.createReadStream(oldPath).pipe fs.createWriteStream(newPath) + stream.on 'error', (err) -> + callback err + stream.on 'close', -> + callback null + else + fsFuct = fs.rename + fsFuct oldPath, newPath, (err) -> if err? console.log err callback "error", resp From 9f00755bab0e96a84619e321f2a1e367c69abe15 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 8 Oct 2019 09:57:17 -0700 Subject: [PATCH 465/576] fixes #594 Add route for experiment metada by date start/date end or hours back --- .../src/server/r/GetExperimentalMetadata.R | 59 +++++++++++++++++++ .../routes/ExperimentServiceRoutes.coffee | 9 +++ 2 files changed, 68 insertions(+) create mode 100644 modules/ServerAPI/src/server/r/GetExperimentalMetadata.R diff --git a/modules/ServerAPI/src/server/r/GetExperimentalMetadata.R b/modules/ServerAPI/src/server/r/GetExperimentalMetadata.R new file mode 100644 index 000000000..002ef7ec6 --- /dev/null +++ b/modules/ServerAPI/src/server/r/GetExperimentalMetadata.R @@ -0,0 +1,59 @@ +# The next line is used by PrepareConfigFiles to include this file as a route in rapache, do not modify unless you intend to modify rapache routes (it can be anywhere in the files though) +# ROUTE: /getExperimentalMetadata + +library(racas) + +# Sample usage: +# curl "http://localhost:1080/r-services-api/getExperimentalMetadata?startTime=2019-09-05%2020:00:00&endTime=2019-09-05%2021:00:00" +# curl "http://localhost:1080/r-services-api/getExperimentalMetadata?hoursBack=24" + +findExperiments <- function(GET) { + + startTime = NA + endTime = NA + hoursBack = NA + + if (("hoursBack" %in% names(GET)) && (!is.na(GET$hoursBack))) { + hoursBack = as.integer(URLdecode(GET$hoursBack)) + } else { + if (!is.na(GET$startTime)) { + startTime = URLdecode(GET$startTime) + } + if (("endTime" %in% names(GET)) && (!is.na(GET$endTime))) { + endTime = URLdecode(GET$endTime) + } + } + + queryString = paste0("select e.id, e.code_name as current_experiment, el.label_text as experiment_name, e.recorded_date, ev_prev.code_value as previous_experiment, ev_proj.code_value ", + " from experiment e ", + " join experiment_label el on e.id = el.experiment_id and el.ls_type = 'name' and el.ls_kind = 'experiment name' and el.ignored = '0' and el.deleted = '0' ", + " left join experiment_state es on es.experiment_id = e.id and es.ls_type = 'metadata' and es.ls_kind = 'experiment metadata' and es.ignored = '0' and es.deleted = '0' ", + " left join experiment_value ev_prev on ev_prev.experiment_state_id = es.id and ev_prev.ls_type = 'codeValue' and ev_prev.ls_kind = 'previous experiment code' and ev_prev.ignored = '0' and ev_prev.deleted = '0' ", + " left join experiment_value ev_proj on ev_proj.experiment_state_id = es.id and ev_proj.ls_type = 'codeValue' and ev_proj.ls_kind = 'project' and ev_proj.ignored = '0' and ev_proj.deleted = '0' " + ) + + if(!is.na(hoursBack)) { + currentTime <- Sys.time() + hoursBackTime <- currentTime - (hoursBack * 60 * 60) + attributes(hoursBackTime)$tzone <- "UTC" + queryString = paste0(queryString, " where e.recorded_date > '",hoursBackTime,"' "); + } else { + if (!is.na(startTime) && !is.na(endTime)) { + queryString = paste0(queryString, " where e.recorded_date between '",startTime,"' and '",endTime,"'"); + } else if (!is.na(startTime)) { + queryString = paste0(queryString, " where e.recorded_date > '",startTime,"' "); + } else if (!is.na(endTime)) { + queryString = paste0(queryString, " where e.recorded_date < '",endTime,"' "); + } + } + + results <- query(queryString) + names(results) <- tolower(names(results)) + return (jsonlite::toJSON(results)) +} + +resultList <- findExperiments(GET); + +cat(resultList); + +DONE \ No newline at end of file diff --git a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee index 0ebc3af33..d1a44bd56 100644 --- a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee @@ -24,6 +24,7 @@ exports.setupAPIRoutes = (app) -> app.post '/api/experiments/getExperimentCodeByLabel/:exptType/:exptKind', exports.getExperimentCodeByLabel app.post '/api/bulkPostExperiments', exports.bulkPostExperiments app.put '/api/bulkPutExperiments', exports.bulkPutExperiments + app.get '/api/getExperimentalMetadata', exports.getExperimentalMetadata exports.setupRoutes = (app, loginRoutes) -> app.get '/api/experiments/codename/:code', loginRoutes.ensureAuthenticated, exports.experimentByCodename @@ -52,6 +53,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/experiments/getExperimentCodeByLabel/:exptType/:exptKind', loginRoutes.ensureAuthenticated, exports.getExperimentCodeByLabel app.post '/api/bulkPostExperiments', loginRoutes.ensureAuthenticated, exports.bulkPostExperiments app.put '/api/bulkPostExperiments', loginRoutes.ensureAuthenticated, exports.bulkPutExperiments + app.get '/api/getExperimentalMetadata', loginRoutes.ensureAuthenticated, exports.getExperimentalMetadata serverUtilityFunctions = require './ServerUtilityFunctions.js' csUtilities = require '../src/javascripts/ServerAPI/CustomerSpecificServerFunctions.js' @@ -1035,3 +1037,10 @@ exports.getExperimentCodeByLabel = (req, resp) -> resp.statusCode = 500 resp.json json.errorMessages ) + +exports.getExperimentalMetadata = (req, resp) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + redirectQuery = req._parsedUrl.query + rapacheCall = config.all.client.service.rapache.fullpath + '/getExperimentalMetadata?' + redirectQuery + req.pipe(request(rapacheCall)).pipe(resp) From 2f6739ca47fbcc8f4ee64b288006478cb89e4718 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 9 Oct 2019 13:15:56 -0700 Subject: [PATCH 466/576] #596 Add ignored field to project service --- .../ServerAPI/src/server/python/acas_ldclient/acasldclient.py | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py index 6adb46330..6c3752f0b 100644 --- a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py +++ b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py @@ -218,6 +218,7 @@ def ld_project_to_acas(ld_project): 'code': ld_project.name, 'alias': ld_project.name, 'active': True if ld_project.active == "Y" else False, + 'ignored': False if ld_project.active == "Y" else True, 'isRestricted': ld_project.restricted, 'name': ld_project.name } From a4d8974e11750ce10e6a50b8786307baba03753d Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 14 Oct 2019 16:08:11 -0700 Subject: [PATCH 467/576] Expose LsThing advanced search route --- .../server/routes/ThingServiceRoutes.coffee | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee index 753b48db1..71b9527e6 100644 --- a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee @@ -11,6 +11,7 @@ exports.setupAPIRoutes = (app, loginRoutes) -> app.post '/api/validateName', exports.validateName app.get '/api/getAssembliesFromComponent/:lsType/:lsKind/:componentCode', exports.getAssemblies app.get '/api/genericSearch/things/:searchTerm', exports.genericThingSearch + app.post '/api/advancedSearch/things/:lsType/:lsKind', exports.advancedThingSearch app.get '/api/getThingThingItxsByFirstThing/:firstThingId', exports.getThingThingItxsByFirstThing app.get '/api/getThingThingItxsBySecondThing/:secondThingId', exports.getThingThingItxsBySecondThing app.get '/api/getThingThingItxsByFirstThing/:lsType/:lsKind/:firstThingId', exports.getThingThingItxsByFirstThingAndItxTypeKind @@ -38,6 +39,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/validateName', loginRoutes.ensureAuthenticated, exports.validateName app.get '/api/getAssembliesFromComponent/:lsType/:lsKind/:componentCode', loginRoutes.ensureAuthenticated, exports.getAssemblies app.get '/api/genericSearch/things/:searchTerm', loginRoutes.ensureAuthenticated, exports.genericThingSearch + app.post '/api/advancedSearch/things/:lsType/:lsKind', loginRoutes.ensureAuthenticated, exports.advancedThingSearch app.get '/api/getThingThingItxsByFirstThing/:firstThingId', loginRoutes.ensureAuthenticated, exports.getThingThingItxsByFirstThing app.get '/api/getThingThingItxsBySecondThing/:secondThingId', loginRoutes.ensureAuthenticated, exports.getThingThingItxsBySecondThing app.get '/api/getThingThingItxsByFirstThing/:lsType/:lsKind/:firstThingId', loginRoutes.ensureAuthenticated, exports.getThingThingItxsByFirstThingAndItxTypeKind @@ -607,6 +609,47 @@ exports.genericThingSearch = (req, resp) -> serverUtilityFunctions = require './ServerUtilityFunctions.js' serverUtilityFunctions.getFromACASServer(baseurl, resp) +exports.advancedThingSearch = (req, resp) -> + console.log "advanced thing search" + console.log req.query.testMode + console.log global.specRunnerTestmode + if req.query.testMode is true or global.specRunnerTestmode is true + resp.end JSON.stringify "Stubs mode not implemented yet" + else + console.log "search req body" + console.log req.body + exports.advancedThingSearchInternal req.body, req.query.format, (results) => + if typeof response is "string" and results.indexOf("error") > -1 + resp.statusCode = 500 + resp.end results + else + resp.json results + +exports.advancedThingSearchInternal = (input, format, callback) -> + config = require '../conf/compiled/conf.js' + baseurl = config.all.client.service.persistence.fullpath+"lsthings/genericBrowserSearch" + if format? + baseurl += "?with=#{format}" + console.log "advanced thing search baseurl" + console.log baseurl + requestOptions = + method: 'POST' + url: baseurl + body: input + json: true + request requestOptions, (error, response, object) -> + if !error + if response.statusCode == 500 + callback object, response + else + callback object, null + else + console.log 'got ajax error trying to run advancedThingSearch' + console.log error + console.log json + console.log response + callback object, error + exports.getProjectCodesFromNamesOrCodes = (codeRequest, callback) -> #TODO: real implementation console.log "got to getProjectCodesFromNamesOrCodes" From 8db1b4d68d6ccecd6515e5c2781dfe67dd5c746d Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 16 Oct 2019 12:33:35 -0700 Subject: [PATCH 468/576] adding protocol name field, check for no results, ignore deleted experiments, set is_reload field, order by most recent experiment first --- .../src/server/r/GetExperimentalMetadata.R | 20 +++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/modules/ServerAPI/src/server/r/GetExperimentalMetadata.R b/modules/ServerAPI/src/server/r/GetExperimentalMetadata.R index 002ef7ec6..907542a26 100644 --- a/modules/ServerAPI/src/server/r/GetExperimentalMetadata.R +++ b/modules/ServerAPI/src/server/r/GetExperimentalMetadata.R @@ -2,7 +2,7 @@ # ROUTE: /getExperimentalMetadata library(racas) - +library(data.table) # Sample usage: # curl "http://localhost:1080/r-services-api/getExperimentalMetadata?startTime=2019-09-05%2020:00:00&endTime=2019-09-05%2021:00:00" # curl "http://localhost:1080/r-services-api/getExperimentalMetadata?hoursBack=24" @@ -24,8 +24,10 @@ findExperiments <- function(GET) { } } - queryString = paste0("select e.id, e.code_name as current_experiment, el.label_text as experiment_name, e.recorded_date, ev_prev.code_value as previous_experiment, ev_proj.code_value ", - " from experiment e ", + queryString = paste0("select e.id, e.code_name as current_experiment, el.label_text as experiment_name, e.recorded_date, ev_prev.code_value as previous_experiment, ev_proj.code_value project, pl.label_text as protocol_name ", + " from protocol p ", + " join protocol_label pl on p.deleted = '0' and p.ignored = '0' and p.id = pl.protocol_id and pl.ls_type = 'name' and pl.ls_kind = 'protocol name' and pl.ignored = '0' and pl.deleted = '0' ", + " join experiment e on p.id = e.protocol_id and e.deleted = '0' and e.ignored = '0' ", " join experiment_label el on e.id = el.experiment_id and el.ls_type = 'name' and el.ls_kind = 'experiment name' and el.ignored = '0' and el.deleted = '0' ", " left join experiment_state es on es.experiment_id = e.id and es.ls_type = 'metadata' and es.ls_kind = 'experiment metadata' and es.ignored = '0' and es.deleted = '0' ", " left join experiment_value ev_prev on ev_prev.experiment_state_id = es.id and ev_prev.ls_type = 'codeValue' and ev_prev.ls_kind = 'previous experiment code' and ev_prev.ignored = '0' and ev_prev.deleted = '0' ", @@ -47,9 +49,15 @@ findExperiments <- function(GET) { } } - results <- query(queryString) - names(results) <- tolower(names(results)) - return (jsonlite::toJSON(results)) + results <- as.data.table(query(queryString)) + if(nrow(results) > 0) { + setnames(results, tolower(names(results))) + results[ , is_reload := any(!is.na(previous_experiment)), by = id] + results[ , previous_experiment := NULL] + results <- unique(results) + setorder(results, -recorded_date) + } + return (jsonlite::toJSON(results, auto_unbox = TRUE)) } resultList <- findExperiments(GET); From 5c3cfe31ff25d3f5cb5e1b5191aad5366c205b34 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 16 Oct 2019 12:34:28 -0700 Subject: [PATCH 469/576] add mail service --- modules/ServerAPI/src/server/r/sendMail.R | 17 +++++++++++++++++ .../src/server/routes/EmailRoutes.coffee | 12 ++++++++++++ 2 files changed, 29 insertions(+) create mode 100644 modules/ServerAPI/src/server/r/sendMail.R create mode 100644 modules/ServerAPI/src/server/routes/EmailRoutes.coffee diff --git a/modules/ServerAPI/src/server/r/sendMail.R b/modules/ServerAPI/src/server/r/sendMail.R new file mode 100644 index 000000000..cf5161d64 --- /dev/null +++ b/modules/ServerAPI/src/server/r/sendMail.R @@ -0,0 +1,17 @@ +# The next line is used by PrepareConfigFiles to include this file as a route in rapache, do not modify unless you intend to modify rapache routes (it can be anywhere in the files though) +# ROUTE: /sendMail + +library(racas) +library(mailR) + +sendMail <- function(request) { + request <- jsonlite::fromJSON(request) + request$send <- TRUE + request$debug <- TRUE + do.call(mailR::send.mail, request) + return(TRUE) +} + +postData <- rawToChar(receiveBin(-1)) +cat(jsonlite::toJSON(sendMail(postData), auto_unbox = TRUE)) +DONE \ No newline at end of file diff --git a/modules/ServerAPI/src/server/routes/EmailRoutes.coffee b/modules/ServerAPI/src/server/routes/EmailRoutes.coffee new file mode 100644 index 000000000..551d7f3c7 --- /dev/null +++ b/modules/ServerAPI/src/server/routes/EmailRoutes.coffee @@ -0,0 +1,12 @@ +exports.setupAPIRoutes = (app) -> + app.post '/api/sendMail', exports.sendMail + +exports.setupRoutes = (app, loginRoutes) -> + app.post '/api/sendMail', loginRoutes.ensureAuthenticated, exports.sendMail + +exports.sendMail = (req, resp) -> + request = require 'request' + config = require '../conf/compiled/conf.js' + redirectQuery = req._parsedUrl.query + rapacheCall = config.all.client.service.rapache.fullpath + '/sendMail?' + redirectQuery + req.pipe(request(rapacheCall)).pipe(resp) From 886e29620973d756d2a0823ee3779d386eb121f5 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 16 Oct 2019 16:08:19 -0700 Subject: [PATCH 470/576] re-arranging files --- modules/ServerAPI/src/server/{r => }/GetExperimentalMetadata.R | 0 modules/ServerAPI/src/server/{r => }/sendMail.R | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename modules/ServerAPI/src/server/{r => }/GetExperimentalMetadata.R (100%) rename modules/ServerAPI/src/server/{r => }/sendMail.R (100%) diff --git a/modules/ServerAPI/src/server/r/GetExperimentalMetadata.R b/modules/ServerAPI/src/server/GetExperimentalMetadata.R similarity index 100% rename from modules/ServerAPI/src/server/r/GetExperimentalMetadata.R rename to modules/ServerAPI/src/server/GetExperimentalMetadata.R diff --git a/modules/ServerAPI/src/server/r/sendMail.R b/modules/ServerAPI/src/server/sendMail.R similarity index 100% rename from modules/ServerAPI/src/server/r/sendMail.R rename to modules/ServerAPI/src/server/sendMail.R From 491e5756fe5f11d9d45ccb80d7c83494771ee1f2 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 17 Oct 2019 19:55:06 -0700 Subject: [PATCH 471/576] Switch Itx formfield to use regular pickBestLabel --- modules/Components/src/client/ACASFormFields.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index c968b14cb..61d096f3f 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -401,7 +401,7 @@ class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractF if @extendedLabel? and @extendedLabel labelText = labels.getExtendedNameText() else - labelText = labels.pickBestNonEmptyLabel().get('labelText') + labelText = labels.pickBestLabel().get('labelText') @thingSelectController.setSelectedCode code: @getModel().getItxThing().codeName label: labelText From 1263604e0a04330377031b9bcd4c4c69ad11eee6 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 22 Oct 2019 17:12:33 -0700 Subject: [PATCH 472/576] Add Multi Interaction form field widget --- .../client/ACASFormMultiInteraction.coffee | 97 +++++++++++++++++++ .../src/client/ACASFormMultiInteraction.css | 15 +++ .../client/ACASFormMultiInteractionView.html | 17 ++++ .../src/client/AbstractFormController.coffee | 13 ++- modules/ServerAPI/src/client/Thing.coffee | 59 ++++++++--- 5 files changed, 188 insertions(+), 13 deletions(-) create mode 100644 modules/Components/src/client/ACASFormMultiInteraction.coffee create mode 100644 modules/Components/src/client/ACASFormMultiInteraction.css create mode 100644 modules/Components/src/client/ACASFormMultiInteractionView.html diff --git a/modules/Components/src/client/ACASFormMultiInteraction.coffee b/modules/Components/src/client/ACASFormMultiInteraction.coffee new file mode 100644 index 000000000..c28f75521 --- /dev/null +++ b/modules/Components/src/client/ACASFormMultiInteraction.coffee @@ -0,0 +1,97 @@ +class window.ACASFormMultiInteractionController extends Backbone.View + ### + Launched by ACASFormMultiInteractionListController to control one element/row in the list + ### + + template: _.template($("#ACASFormMultiInteractionView").html()) + + events: -> + "click .bv_removeInteractionButton": "handleRemoveInteractionButtonClicked" + + initialize: -> + options = + modelKey: @options.interactionKey + thingType: @options.thingType + thingKind: @options.thingKind + labelType: @options.labelType + queryUrl: @options.queryUrl + placeholder: @options.placeholder + extendedLabel: @options.extendedLabel + inputClass: @options.inputClass + formLabel: @options.formLabel + required: @options.required + thingRef: @options.thingRef + insertUnassigned: @options.insertUnassigned + @interactionController = new ACASFormLSThingInteractionFieldController options + + render: -> + $(@el).empty() + $(@el).html @template() + @$('.bv_multiInteraction').html @interactionController.render().el + @interactionController.renderModelContent() + @ + + handleRemoveInteractionButtonClicked: -> + @interactionController.setEmptyValue() + $(@el).hide() + + +class window.ACASFormMultiInteractionListController extends ACASFormAbstractFieldController + ### + Launching controller must instantiate with the full field conf including modelDefaults, not just the fieldDefinition. + Controls a flexible-length list of LsThingInteraction input fields within ACASFormLSThingInteractionFieldControllers with an add button. + ### + template: _.template($("#ACASFormMultiInteractionListView").html()) + + events: -> + "click .bv_addInteractionButton": "handleAddInteractionButtonClicked" + + initialize: -> + super() + @opts = @options + if @opts.firstItx + @itxClass = FirstThingItx + @thingItxRef = 'firstLsThings' + else + @itxClass = SecondThingItx + @thingItxRef = 'secondLsThings' + + render: => + $(@el).empty() + $(@el).html @template() + @ + + renderModelContent: -> + @render() + multiInteractions = @thingRef.get(@thingItxRef).getItxByTypeAndKind(@opts.modelDefaults.itxType, @opts.modelDefaults.itxKind) + _.each multiInteractions, (interaction) => + @addOneInteraction(interaction) + + handleAddInteractionButtonClicked: => + @addNewInteraction() + + addNewInteraction: (skipAmDirtyTrigger) => + keyBase = @modelKey + newModel = new @itxClass + lsType: @opts.modelDefaults.itxType + lsKind: @opts.modelDefaults.itxKind + currentMultiInteractions = @thingRef.get(@thingItxRef).filter (interaction) -> + interaction.has('key') and (interaction.get('key').indexOf(keyBase) > -1) + newKey = keyBase + currentMultiInteractions.length + newModel.set key: newKey + @thingRef.set newKey, newModel + @thingRef.get(@thingItxRef).add newModel + @addOneInteraction(newModel) + unless skipAmDirtyTrigger is true + newModel.trigger 'amDirty' + + addOneInteraction: (interaction) -> + interactionOpts = @opts + interactionOpts.interactionKey = interaction.get('key') + multiInteractionController = new ACASFormMultiInteractionController interactionOpts + @$('.bv_multiInteractions').append multiInteractionController.render().el + multiInteractionController.on 'updateState', => + @trigger 'updateState' + + + diff --git a/modules/Components/src/client/ACASFormMultiInteraction.css b/modules/Components/src/client/ACASFormMultiInteraction.css new file mode 100644 index 000000000..b629ec8d7 --- /dev/null +++ b/modules/Components/src/client/ACASFormMultiInteraction.css @@ -0,0 +1,15 @@ +.multiInteractionListWell { + margin-bottom: 0; +} + +.bv_removeInteractionButton { + margin-left: 5px; + padding-right: 8px; + padding-left: 8px; +} + +.bv_addInteractionButton { + padding-right: 8px; + padding-left: 8px; + margin-left: 388px; +} \ No newline at end of file diff --git a/modules/Components/src/client/ACASFormMultiInteractionView.html b/modules/Components/src/client/ACASFormMultiInteractionView.html new file mode 100644 index 000000000..9f8e0cfb3 --- /dev/null +++ b/modules/Components/src/client/ACASFormMultiInteractionView.html @@ -0,0 +1,17 @@ + + + \ No newline at end of file diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 3b4034b12..758a5e605 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -124,7 +124,12 @@ class window.AbstractThingFormController extends AbstractFormController fDefs = [] if fieldDefs.labels? then fDefs = fDefs.concat fieldDefs.labels if fieldDefs.values? then fDefs = fDefs.concat fieldDefs.values - if fieldDefs.firstLsThingItxs? then fDefs = fDefs.concat fieldDefs.firstLsThingItxs + if fieldDefs.firstLsThingItxs? + # Tag any firstItx fieldDefinitions with "firstItx" so the controllers know which direction of interaction to create + firstDefs = _.map(fieldDefs.firstLsThingItxs, (fdef) => + fdef.fieldSettings.firstItx = true + return fdef) + fDefs = fDefs.concat firstDefs if fieldDefs.secondLsThingItxs? then fDefs = fDefs.concat fieldDefs.secondLsThingItxs for field in fDefs @@ -166,7 +171,11 @@ class window.AbstractThingFormController extends AbstractFormController opts.thingKind = field.fieldSettings.thingKind opts.queryUrl = field.fieldSettings.queryUrl opts.labelType = field.fieldSettings.labelType - newField = new ACASFormLSThingInteractionFieldController opts + opts.firstItx = field.fieldSettings.firstItx + if field.multiple? and field.multiple + newField = new ACASFormMultiInteractionListController opts + else + newField = new ACASFormLSThingInteractionFieldController opts when 'stringValue' then newField = new ACASFormLSStringValueFieldController opts when 'dateValue' then newField = new ACASFormLSDateValueFieldController opts when 'fileValue' then newField = new ACASFormLSFileValueFieldController opts diff --git a/modules/ServerAPI/src/client/Thing.coffee b/modules/ServerAPI/src/client/Thing.coffee index be6d204f8..a3052815d 100644 --- a/modules/ServerAPI/src/client/Thing.coffee +++ b/modules/ServerAPI/src/client/Thing.coffee @@ -92,21 +92,20 @@ class window.Thing extends Backbone.Model if attsToSave.secondLsThings.length == 0 delete attsToSave.secondLsThings - if @lsProperties.defaultLabels? + if @lsProperties.defaultLabels? and @lsProperties.defaultLabels.length > 0 for dLabel in @lsProperties.defaultLabels delete attsToSave[dLabel.key] - if @lsProperties.defaultFirstLsThingItx? + if @lsProperties.defaultFirstLsThingItx? and @lsProperties.defaultFirstLsThingItx.length > 0 for itx in @lsProperties.defaultFirstLsThingItx delete attsToSave[itx.key] - if @lsProperties.defaultSecondLsThingItx? + if @lsProperties.defaultSecondLsThingItx? and @lsProperties.defaultSecondLsThingItx.length > 0 console.log "deleting empty 2nd ls thing itxs" - for itx in @lsProperties.defaultSecondLsThingItx delete attsToSave[itx.key] - if @lsProperties.defaultValues? + if @lsProperties.defaultValues? and @lsProperties.defaultValues.length > 0 for dValue in @lsProperties.defaultValues if attsToSave[dValue.key]? val = attsToSave[dValue.key].get('value') @@ -277,18 +276,56 @@ class window.Thing extends Backbone.Model # add key as attribute of model if @lsProperties.defaultFirstLsThingItx? for itx in @lsProperties.defaultFirstLsThingItx - #TODO fix - broken when have more than one itx that has same type/kind - thingItx = @get('firstLsThings').getOrCreateItxByTypeAndKind itx.itxType, itx.itxKind - @set itx.key, thingItx + if itx.multiple? and itx.multiple + thingItxs = @get('firstLsThings').getItxByTypeAndKind itx.itxType, itx.itxKind + if thingItxs.length > 0 + counter = 0 + _.each thingItxs, (thingItx) => + if !thingItx.has('key') + thingItxKey = itx.key + counter + counter++ + @set thingItxKey, thingItx + thingItx.set key: thingItxKey + #@listenTo thingItx, 'createNewLabel', @createNewLabel + else + thingItx = @get('firstLsThings').getOrCreateItxByTypeAndKind itx.itxType, itx.itxKind + newKey = itx.key + 0 + @set newKey, thingItx + thingItx.set key: newKey + else + thingItx = @get('firstLsThings').getOrCreateItxByTypeAndKind itx.itxType, itx.itxKind + #@listenTo newLabel, 'createNewLabel', @createNewLabel + @set itx.key, thingItx + # if newLabel.get('preferred') is undefined + thingItx.set key: itx.key createDefaultSecondLsThingItx: => # loop over defaultSecondLsThingItx # add key as attribute of model if @lsProperties.defaultSecondLsThingItx? for itx in @lsProperties.defaultSecondLsThingItx - #TODO fix - broken when have more than one itx that has same type/kind - thingItx = @get('secondLsThings').getOrCreateItxByTypeAndKind itx.itxType, itx.itxKind - @set itx.key, thingItx + if itx.multiple? and itx.multiple + thingItxs = @get('secondLsThings').getItxByTypeAndKind itx.itxType, itx.itxKind + if thingItxs.length > 0 + counter = 0 + _.each thingItxs, (thingItx) => + if !thingItx.has('key') + thingItxKey = itx.key + counter + counter++ + @set thingItxKey, thingItx + thingItx.set key: thingItxKey + #@listenTo thingItx, 'createNewLabel', @createNewLabel + else + thingItx = @get('secondLsThings').getOrCreateItxByTypeAndKind itx.itxType, itx.itxKind + newKey = itx.key + 0 + @set newKey, thingItx + thingItx.set key: newKey + else + thingItx = @get('secondLsThings').getOrCreateItxByTypeAndKind itx.itxType, itx.itxKind + #@listenTo newLabel, 'createNewLabel', @createNewLabel + @set itx.key, thingItx + # if newLabel.get('preferred') is undefined + thingItx.set key: itx.key getAnalyticalFiles: (fileTypes) => #TODO: rename from analytical files to attachFiles or something more generic #get list of possible kinds of analytical files From 195325b1f2f40c09b2f20606a4e816bfe2320b0d Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 22 Oct 2019 17:13:06 -0700 Subject: [PATCH 473/576] Allow disabled grey out for ACASFormLSHTMLClobValueFieldController --- modules/Components/src/client/ACASFormFields.coffee | 4 +++- modules/Components/src/client/ACASFormFields.css | 4 ++++ 2 files changed, 7 insertions(+), 1 deletion(-) create mode 100644 modules/Components/src/client/ACASFormFields.css diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 61d096f3f..346d1e980 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -489,13 +489,15 @@ class window.ACASFormLSHTMLClobValueFieldController extends ACASFormAbstractFiel if @contentToLoad? @editor.setContent @contentToLoad if @disableEditor? - @editor.getBody().setAttribute('contenteditable', @disableEditor) + @editor.getBody().setAttribute('contenteditable', !@disableEditor) + @editor.getBody().setAttribute('disabled', @disableEditor) editor.on 'change', (e) => @textChanged editor.getContent() disableInput: -> if @editor? @editor.getBody().setAttribute('contenteditable', false) + @editor.getBody().setAttribute('disabled', true) else @disableEditor = true diff --git a/modules/Components/src/client/ACASFormFields.css b/modules/Components/src/client/ACASFormFields.css new file mode 100644 index 000000000..e7ec46ce6 --- /dev/null +++ b/modules/Components/src/client/ACASFormFields.css @@ -0,0 +1,4 @@ +.mce-content-body[disabled] { + cursor: not-allowed; + background-color: #eeeeee; +} \ No newline at end of file From 70202713828ed55ccd1d1c779269ed179368e2fb Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 22 Oct 2019 17:13:56 -0700 Subject: [PATCH 474/576] Controversial: Sidestep load order issue with handsontable. Not an actual fix though. --- .../src/client/ACASFormStateTable.coffee | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 176aaeee2..4280da918 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -406,10 +406,11 @@ class window.ACASFormStateTableController extends Backbone.View return newValue disableInput: -> - @hot.updateSettings - readOnly: true - contextMenu: false - comments: false + if @hot? + @hot.updateSettings + readOnly: true + contextMenu: false + comments: false #Other options I decided not to use # disableVisualSelection: true # manualColumnResize: false @@ -420,10 +421,11 @@ class window.ACASFormStateTableController extends Backbone.View contextMenu = @tableDef.contextMenu else contextMenu = true - @hot.updateSettings - readOnly: false - contextMenu: contextMenu - comments: true + if @hot? + @hot.updateSettings + readOnly: false + contextMenu: contextMenu + comments: true #Other options I decided not to use # disableVisualSelection: false # manualColumnResize: true From 29b19abaaa2a4bd2bc068ac82dfd9fe67174b1ce Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 29 Oct 2019 14:18:40 +0000 Subject: [PATCH 475/576] Bump csv-parse from 1.3.3 to 4.6.5 Bumps [csv-parse](https://github.com/wdavidw/node-csv-parse) from 1.3.3 to 4.6.5. - [Release notes](https://github.com/wdavidw/node-csv-parse/releases) - [Changelog](https://github.com/adaltas/node-csv-parse/blob/master/CHANGELOG.md) - [Commits](https://github.com/wdavidw/node-csv-parse/compare/v1.3.3...v4.6.5) Signed-off-by: dependabot[bot] --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 80d6d619c..3ef94cd28 100644 --- a/package.json +++ b/package.json @@ -27,7 +27,7 @@ "cookie-parser": "^1.4.3", "connect-flash": "~0.1.0", "cron": "1.3.0", - "csv-parse": "^1.1.1", + "csv-parse": "^4.6.5", "each": "0.6.1", "exports-loader": "0.6.4", "express": "3.0.2", From 63bdb9328574dbf8fc9b67949097b9dc2e76c3cc Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 30 Oct 2019 14:27:53 -0700 Subject: [PATCH 476/576] fixes #600 plot log y scale and log plot window --- modules/CurveAnalysis/src/server/renderCurve.R | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/modules/CurveAnalysis/src/server/renderCurve.R b/modules/CurveAnalysis/src/server/renderCurve.R index b9a0a8224..c825732b3 100644 --- a/modules/CurveAnalysis/src/server/renderCurve.R +++ b/modules/CurveAnalysis/src/server/renderCurve.R @@ -33,15 +33,19 @@ renderCurve <- function(getParams) { data$parameters$fitted_slope <- -data$parameters$fitted_hillslope[fittedHillSlopes] } + logDose <- TRUE + if(fitData[1]$renderingHint %in% c("Michaelis-Menten", "Substrate Inhibition", "Scatter", "Scatter Log-y")) logDose <- FALSE + logResponse <- FALSE + if(fitData[1]$renderingHint %in% c("Scatter Log-y","Scatter Log-x,y")) logResponse <- TRUE #Get Protocol Curve Display Min and Max for first curve in list if(any(is.na(parsedParams$yMin),is.na(parsedParams$yMax))) { protocol_display_values <- racas::get_protocol_curve_display_min_and_max_by_curve_id(parsedParams$curveIds[[1]]) plotWindowPoints <- rbindlist(fitData[ , points])[!userFlagStatus == "knocked out" & !preprocessFlagStatus == "knocked out" & !algorithmFlagStatus == "knocked out",] if(nrow(plotWindowPoints) == 0) { - plotWindow <- racas::get_plot_window(fitData[1]$points[[1]]) + plotWindow <- racas::get_plot_window(fitData[1]$points[[1]], logDose = logDose, logResponse = logResponse) } else { - plotWindow <- racas::get_plot_window(plotWindowPoints) + plotWindow <- racas::get_plot_window(plotWindowPoints, logDose = logDose, logResponse = logResponse) } recommendedDisplayWindow <- list(ymax = max(protocol_display_values$ymax,plotWindow[2], na.rm = TRUE), ymin = min(protocol_display_values$ymin,plotWindow[4], na.rm = TRUE)) if(is.na(parsedParams$yMin)) parsedParams$yMin <- recommendedDisplayWindow$ymin @@ -56,10 +60,7 @@ renderCurve <- function(getParams) { if(!"connectPoints" %in% names(renderingOptions) || is.na(renderingOptions$connectPoints)) { renderingOptions$connectPoints <- FALSE } - logDose <- TRUE - if(fitData[1]$renderingHint %in% c("Michaelis-Menten", "Substrate Inhibition", "Scatter", "Scatter Log-y")) logDose <- FALSE - logResponse <- FALSE - if(fitData[1]$renderingHint %in% c("Scatter Log-y","Scatter Log-x,y")) logResponse <- FALSE + setContentType("image/png") setHeader("Content-Disposition", paste0("filename=\"",getParams$curveIds,"\"")) t <- tempfile() From 5d73835109c45f2fc931c73ce9a5e45908bf8795 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 1 Nov 2019 17:14:07 -0700 Subject: [PATCH 477/576] fixes #601 encode projects when searching --- .../ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee | 2 +- .../ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee index d3d1a1470..8f43c6d0a 100644 --- a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee @@ -494,7 +494,7 @@ exports.genericExperimentSearch = (req, res) -> authorRoutes.allowedProjectsInternal req.user, (statusCode, allowedUserProjects) -> _ = require "underscore" allowedProjectCodes = _.pluck(allowedUserProjects, "code") - baseurl = config.all.client.service.persistence.fullpath+"experiments/search?q="+req.params.searchTerm+"&projects=#{allowedProjectCodes.join(',')}" + baseurl = config.all.client.service.persistence.fullpath+"experiments/search?q="+req.params.searchTerm+"&projects=#{encodeURIComponent(allowedProjectCodes.join(','))}" console.log "baseurl" console.log baseurl serverUtilityFunctions = require './ServerUtilityFunctions.js' diff --git a/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee index ca0927c54..6fb0d4ac3 100644 --- a/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ProtocolServiceRoutes.coffee @@ -495,7 +495,7 @@ exports.genericProtocolSearch = (req, res) -> _ = require "underscore" allowedProjectCodes = _.pluck(allowedUserProjects, "code") config = require '../conf/compiled/conf.js' - baseurl = config.all.client.service.persistence.fullpath+"protocols/search?q="+req.params.searchTerm+"&projects=#{allowedProjectCodes.join(',')}" + baseurl = config.all.client.service.persistence.fullpath+"protocols/search?q="+req.params.searchTerm+"&projects=#{encodeURIComponent(allowedProjectCodes.join(','))}" console.log "baseurl" console.log baseurl serverUtilityFunctions = require './ServerUtilityFunctions.js' From 763ceff4194393c7220194dd68fe56e53d6bca51 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 11 Nov 2019 14:33:09 -0800 Subject: [PATCH 478/576] Bugfix: CodeValue StateTable values were not getting codeType/codeKind set properly --- modules/Components/src/client/ACASFormStateTable.coffee | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 4280da918..177d2a764 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -219,6 +219,10 @@ class window.ACASFormStateTableController extends Backbone.View newValue.set unitType: valueDef.modelDefaults.unitType if valueDef.modelDefaults.unitKind? newValue.set unitKind: valueDef.modelDefaults.unitKind + if valueDef.modelDefaults.codeType? + newValue.set codeType: valueDef.modelDefaults.codeType + if valueDef.modelDefaults.codeKind? + newValue.set codeKind: valueDef.modelDefaults.codeKind return newState getCurrentStates: -> From 88107d1db13f7a70583204f27d9ba0972ba2f037 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 12 Nov 2019 12:56:51 -0800 Subject: [PATCH 479/576] Fix StateTable bug with empty/null dateValues --- modules/Components/src/client/ACASFormStateTable.coffee | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 177d2a764..da1c5589d 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -243,6 +243,8 @@ class window.ACASFormStateTableController extends Backbone.View else if valDef.modelDefaults.type == 'dateValue' if value.get('dateValue')? displayVal = new Date(value.get('dateValue')).toISOString().split('T')[0] + else: + displayVal = null else displayVal = value.get valDef.modelDefaults.type From 16fb91f735de990592ded0650c587daa769e9825 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 12 Nov 2019 15:43:52 -0800 Subject: [PATCH 480/576] Syntax error in last change --- modules/Components/src/client/ACASFormStateTable.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index da1c5589d..fbc127463 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -243,7 +243,7 @@ class window.ACASFormStateTableController extends Backbone.View else if valDef.modelDefaults.type == 'dateValue' if value.get('dateValue')? displayVal = new Date(value.get('dateValue')).toISOString().split('T')[0] - else: + else displayVal = null else displayVal = value.get valDef.modelDefaults.type From 845568d23cec5190281ed68dd34f55892ed3a277 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 14 Nov 2019 14:12:21 -0800 Subject: [PATCH 481/576] bugfix: StateTable now persists values of type urlValue --- modules/Components/src/client/ACASFormStateTable.coffee | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index fbc127463..6a94e7c68 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -324,6 +324,8 @@ class window.ACASFormStateTableController extends Backbone.View value.set stringValue: if cellContent? then cellContent else "" when 'clobValue' value.set clobValue: if cellContent? then cellContent else "" + when 'urlValue' + value.set urlValue: if cellContent? then cellContent else "" when 'numericValue' numVal = parseFloat(cellContent) if isNaN(numVal) or isNaN(Number(numVal)) From 26e02b1bed2e644ecfd62066041b32be7bb2e39a Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 15 Nov 2019 09:36:19 -0800 Subject: [PATCH 482/576] Revert "Bump csv-parse from 1.3.3 to 4.6.5" --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 3ef94cd28..80d6d619c 100644 --- a/package.json +++ b/package.json @@ -27,7 +27,7 @@ "cookie-parser": "^1.4.3", "connect-flash": "~0.1.0", "cron": "1.3.0", - "csv-parse": "^4.6.5", + "csv-parse": "^1.1.1", "each": "0.6.1", "exports-loader": "0.6.4", "express": "3.0.2", From bd4b67706b20a6d0a0d46fc7230aba053c9e31af Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Wed, 20 Nov 2019 15:39:19 -0800 Subject: [PATCH 483/576] Make it so both table and edit value view show human-readable values for codeValues and dateValues --- .../client/ACASFormStateDisplayUpdate.coffee | 56 ++++++++++++++++--- .../src/client/UtilityFunctions.coffee | 9 +++ 2 files changed, 58 insertions(+), 7 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee index 59699ca6e..9c08adaa8 100644 --- a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee +++ b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee @@ -34,6 +34,8 @@ class window.ACASFormStateDisplayUpdateCellController extends Backbone.View content = @options.cellDef.displayOverride content if val.get('lsType') == 'dateValue' content = UtilityFunctions::convertMSToYMDDate val.get('dateValue') + else if val.get('lsType') == 'codeValue' + content = UtilityFunctions::getNameForCode val, content, @options.pickLists $(@el).html content $(@el).addClass if @collection.length > 1 then "valueWasEdited" else "" @@ -56,6 +58,7 @@ class window.ACASFormStateDisplayUpdateRowController extends Backbone.View cellController = new ACASFormStateDisplayUpdateCellController collection: new ValueList vals cellDef: valDef + pickLists: @options.pickLists $(@el).append cellController.render().el cellController.on 'cellClicked', (values) => @trigger 'cellClicked', values @@ -76,10 +79,44 @@ class window.ACASFormStateDisplayUpdateController extends Backbone.View $(@el).empty() $(@el).html @template() @applyOptions() - @tableSetupComplete = true - - @ - + @fetchPickLists => + @tableSetupComplete = true + @ + + fetchPickLists: (callback) => + @pickLists = {} + listCount = 0 + + for val in @tableDef.values + if val.modelDefaults.type == 'codeValue' and val.fieldSettings.fieldType == 'codeValue' + listCount++ + + doneYet = => + listCount-- + if listCount == 0 + callback() + + if listCount == 0 + callback() + + for val in @tableDef.values + if val.modelDefaults.type == 'codeValue' and val.fieldSettings.fieldType == "codeValue" + if val.fieldSettings.optionURL? + url = val.fieldSettings.optionURL + else + url = "/api/codetables/#{val.modelDefaults.codeType}/#{val.modelDefaults.codeKind}" + kind = val.modelDefaults.kind + + $.ajax + type: 'GET' + url: url + json: true + self: @ + kind: kind + success: (response) -> + this.self.pickLists[this.kind] = new PickListList response + doneYet() + renderModelContent: => if @tableSetupComplete @completeRenderModelContent() @@ -98,6 +135,7 @@ class window.ACASFormStateDisplayUpdateController extends Backbone.View rowController = new ACASFormStateDisplayUpdateRowController collection: state.get 'lsValues' tableDef: @options.tableDef + pickLists: @pickLists @$("tbody").append rowController.render().el rowController.on 'cellClicked', (values) => @@ -108,6 +146,7 @@ class window.ACASFormStateDisplayUpdateController extends Backbone.View el: @$('.bv_valueEditor') tableDef: @tableDef stateID: state.id + pickLists: @pickLists @currentCellEditor.render() @currentCellEditor.on 'saveNewValue', @handleCellUpdate @@ -185,7 +224,11 @@ class window.ACASFormStateDisplayOldValueController extends Backbone.View value = @options.valueDef.displayOverride value if @options.previousLsTransaction prevLsTransaction = @options.previousLsTransaction - + if @model.get('lsType') == 'dateValue' + value = UtilityFunctions::convertMSToYMDDate value + else if @model.get('lsType') == 'codeValue' + value = content = UtilityFunctions::getNameForCode @model, value, @options.pickLists + attrs = value: value attrs.valueClass = if @model.get 'ignored' then "valueWasEdited" else "" @@ -249,6 +292,7 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View valueDef: @valueDef initialVal: initialVal previousLsTransaction: previousLsTransaction + pickLists: @options.pickLists @$("tbody").append oldRow.render().el index++ @@ -325,5 +369,3 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View #TODO value editor: # - maybe show transaction creator as modified by and date? # - add new value where none existed? -# show human readable codevalue instead of code - diff --git a/modules/Components/src/client/UtilityFunctions.coffee b/modules/Components/src/client/UtilityFunctions.coffee index 2c70edd46..e95b365ee 100644 --- a/modules/Components/src/client/UtilityFunctions.coffee +++ b/modules/Components/src/client/UtilityFunctions.coffee @@ -77,3 +77,12 @@ class window.UtilityFunctions return 0 else return Math.round((num+0.000001)*1000)/1000 + + getNameForCode: (value, codeToLookup, pickLists) -> + if pickLists[value.get('lsKind')]? + code = pickLists[value.get('lsKind')].findWhere({code: codeToLookup}) + name = if code? then code.get 'name' else "not found" + return name + else + console.log "can't find entry in pickLists hash for: "+value.get('lsKind') + console.dir pickLists From cf6c966582bfa480900f4435fa67e688662097db Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Sat, 23 Nov 2019 18:00:50 -0800 Subject: [PATCH 484/576] fixes #606 Dont install LD client on calls to create an LR if server.liveDesign.installClientOnStart is true --- .../server/routes/CreateLiveDesignLiveReportForACAS.coffee | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/modules/ServerAPI/src/server/routes/CreateLiveDesignLiveReportForACAS.coffee b/modules/ServerAPI/src/server/routes/CreateLiveDesignLiveReportForACAS.coffee index 33d855c59..f014409c1 100644 --- a/modules/ServerAPI/src/server/routes/CreateLiveDesignLiveReportForACAS.coffee +++ b/modules/ServerAPI/src/server/routes/CreateLiveDesignLiveReportForACAS.coffee @@ -50,8 +50,9 @@ exports.getUrlForNewLiveDesignLiveReportForExperimentInternal = (exptCode, usern exptInfo.username = username console.log @responseJSON #install fresh ldclient - exports.installLiveDesignPythonClientInternal (statusCode, output) -> - console.log 'Updated LDClient' + if !config.all.server.liveDesign.installClientOnStart? || !config.all.server.liveDesign.installClientOnStart + exports.installLiveDesignPythonClientInternal (statusCode, output) -> + console.log 'Updated LDClient' command = "python ./src/python/ServerAPI/createLiveDesignLiveReportForACAS/create_lr_for_acas.py -e " command += "'"+config.all.client.service.result.viewer.liveDesign.baseUrl+"' -u '"+config.all.client.service.result.viewer.liveDesign.username+"' -p '"+config.all.client.service.result.viewer.liveDesign.password+"' -d '"+config.all.client.service.result.viewer.liveDesign.database+"' -r '"+config.all.client.service.result.viewer.liveDesign.makeReportReadonly+"' -i '" # data = {"compounds":["V035000","CMPD-0000002"],"assays":[{"protocolName":"Target Y binding","resultType":"curve id"}]} From f4f1c6f0f891c7dc96a83a0b3bff0d4e0963af28 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Sat, 23 Nov 2019 18:21:12 -0800 Subject: [PATCH 485/576] #608 Restrict the global project instead of hiding it when HIDE_GLOBAL_PROJECT is true --- .../src/server/python/acas_ldclient/acasldclient.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py index 6c3752f0b..f119ae201 100644 --- a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py +++ b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py @@ -201,13 +201,18 @@ def get_projects(client): configs = client.config() # If HIDE_GLOBAL_PROJECT ld config is set to 'true' - # then we need to remove "Global" from the list of projects + # then we set Global to a restricted project. + # Hide Global project in LD is restricted to Admins so we will restrict the Global project in ACAS + # This allows us to give admins and users with ACLs to the Global project rather than just removing it from ACAS hide_global_project_config = next((config for config in configs if config['key'] == "HIDE_GLOBAL_PROJECT"), None) if hide_global_project_config != None: hide_global_project = hide_global_project_config['value'] if hide_global_project == 'true': - ld_projects = [ p for p in ld_projects if p.name != "Global"] - + def set_global_restricted(project): + if project.name == "Global": + project.restricted = True + return project + ld_projects = map(set_global_restricted, ld_projects) projects = map(ld_project_to_acas, ld_projects) return projects From 3c1c091a278520e97e707ef97b6b9723c1e5597c Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 25 Nov 2019 16:22:52 -0800 Subject: [PATCH 486/576] return "not found" if code cannot be looked up --- modules/Components/src/client/UtilityFunctions.coffee | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/Components/src/client/UtilityFunctions.coffee b/modules/Components/src/client/UtilityFunctions.coffee index e95b365ee..4c5c505f2 100644 --- a/modules/Components/src/client/UtilityFunctions.coffee +++ b/modules/Components/src/client/UtilityFunctions.coffee @@ -86,3 +86,4 @@ class window.UtilityFunctions else console.log "can't find entry in pickLists hash for: "+value.get('lsKind') console.dir pickLists + return "not found" From f5b62ef29f1ce0d4a223e5f4858644ae933324dd Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 25 Nov 2019 17:50:08 -0800 Subject: [PATCH 487/576] fixes #610 - Insert selected item into picklist if missing from picklist --- modules/CmpdReg/src/client/src/PickList.js | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) diff --git a/modules/CmpdReg/src/client/src/PickList.js b/modules/CmpdReg/src/client/src/PickList.js index fada98e6a..2b3fd345e 100755 --- a/modules/CmpdReg/src/client/src/PickList.js +++ b/modules/CmpdReg/src/client/src/PickList.js @@ -79,6 +79,12 @@ $(function() { } else { this.showIgnored = false; } + + if (this.options.insertSelectedCode !=null) { + this.insertSelectedCode = this.options.insertSelectedCode; + } else { + this.insertSelectedCode = true; + } }, handleListReset: function() { @@ -90,8 +96,20 @@ $(function() { } if (this.insertFirstOption) { this.collection.add(this.insertFirstOption, {at: 0, silent: true}); - } - this.render(); + } + + //If insert selected code is set to true (it is by default) then + // check if the selectedCode is null or undefined and also if it is in the list + // if it is not in the list then we artificially insert the selected code as to not change + // the value stored in the db. + if (this.insertSelectedCode && this.selectedCode != null && typeof(this.selectedCode) != "undefined" && (typeof(this.collection.getModelWithCode(this.selectedCode)) == "undefined")) { + newOption = new PickList({ + code: this.selectedCode, + name: this.selectedCode + }); + this.collection.add(newOption, {at: 0, silent: true}); + } + this.render(); }, render: function() { From 8b6e60d9e8a6d4ba854323da3a07fd96bf6bf843 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 9 Dec 2019 10:43:02 -0800 Subject: [PATCH 488/576] fixes #613 add configuration for a list of project codes to filter from ACAS --- conf/config.properties.example | 4 ++++ .../python/acas_ldclient/acasldclient.py | 18 +----------------- .../src/server/routes/AuthorRoutes.coffee | 8 ++++++++ 3 files changed, 13 insertions(+), 17 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 0665c3127..7a2dd56ef 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -565,6 +565,10 @@ client.projectEditor.isRestricted.default=false client.roles.crossProjectLoaderRole=ROLE_ACAS-CROSS-PROJECT-LOADER +# List of project codes to filter from ACAS +# e.g. server.projects.filterList = ["SomeProject"] +server.projects.filterList = [] + # For whether protocols and experiments should have sequential user defined corpName labels client.entity.saveInitialsCorpName=false diff --git a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py index f119ae201..0d29ba009 100644 --- a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py +++ b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py @@ -197,24 +197,8 @@ def get_user(client, username): return acas_user def get_projects(client): - ld_projects = client.projects() - configs = client.config() - - # If HIDE_GLOBAL_PROJECT ld config is set to 'true' - # then we set Global to a restricted project. - # Hide Global project in LD is restricted to Admins so we will restrict the Global project in ACAS - # This allows us to give admins and users with ACLs to the Global project rather than just removing it from ACAS - hide_global_project_config = next((config for config in configs if config['key'] == "HIDE_GLOBAL_PROJECT"), None) - if hide_global_project_config != None: - hide_global_project = hide_global_project_config['value'] - if hide_global_project == 'true': - def set_global_restricted(project): - if project.name == "Global": - project.restricted = True - return project - ld_projects = map(set_global_restricted, ld_projects) + ld_projects = client.projects() projects = map(ld_project_to_acas, ld_projects) - return projects def ld_project_to_acas(ld_project): diff --git a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee index 6354264a9..732e56bec 100644 --- a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee @@ -50,6 +50,14 @@ exports.allowedProjectsInternal = (user, callback) -> csUtilities.getProjectStubsInternal (statusCode, allProjects) -> config = require '../conf/compiled/conf.js' _ = require 'underscore' + + # Filter out any projects that exist in the config for filtering projects + projectFilterList = JSON.parse config.all.server.projects.filterList + allProjects = _.filter allProjects, (project, index) -> + console.log project + console.log projectFilterList[0] + ! _.contains projectFilterList, project.code + if (config.all.server.project.roles.enable) filteredProjects = [] isAdmin = false; From 789d1b000ae15f8ccae690eb3776fb267bb92ffd Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Mon, 9 Dec 2019 13:58:48 -0800 Subject: [PATCH 489/576] Add optional inline display of codeTable descriptions --- modules/Components/src/client/ACASFormFields.coffee | 12 ++++++++++++ modules/Components/src/client/ACASFormFields.css | 5 +++++ .../Components/src/client/ACASFormFieldsView.html | 1 + .../src/client/AbstractFormController.coffee | 1 + 4 files changed, 19 insertions(+) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 346d1e980..9f5874cf3 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -282,6 +282,11 @@ class window.ACASFormLSCodeValueFieldController extends ACASFormAbstractFieldCon @getModel().set value: value ignored: false + if @options.showDescription? and @options.showDescription + @clearDescription() + desc = @pickListController.getSelectedModel().get('description') + if desc? + @setDescription(desc) super() setEmptyValue: -> @@ -342,6 +347,13 @@ class window.ACASFormLSCodeValueFieldController extends ACASFormAbstractFieldCon enableInput: -> @$('select').removeAttr 'disabled' + + setDescription: (message) -> + @$('.desc-inline').removeClass 'hide' + @$('.desc-inline').html message + + clearDescription: -> + @$('.desc-inline').addClass 'hide' class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractFieldController ### diff --git a/modules/Components/src/client/ACASFormFields.css b/modules/Components/src/client/ACASFormFields.css index e7ec46ce6..cddce8a91 100644 --- a/modules/Components/src/client/ACASFormFields.css +++ b/modules/Components/src/client/ACASFormFields.css @@ -1,4 +1,9 @@ .mce-content-body[disabled] { cursor: not-allowed; background-color: #eeeeee; +} + +.desc-inline { + font-style: italic; + color: #aaa; } \ No newline at end of file diff --git a/modules/Components/src/client/ACASFormFieldsView.html b/modules/Components/src/client/ACASFormFieldsView.html index cc68f457c..582842d97 100644 --- a/modules/Components/src/client/ACASFormFieldsView.html +++ b/modules/Components/src/client/ACASFormFieldsView.html @@ -20,6 +20,7 @@
        +
        diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 758a5e605..ba4284f86 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -154,6 +154,7 @@ class window.AbstractThingFormController extends AbstractFormController tabIndex: field.fieldSettings.tabIndex toFixed: field.fieldSettings.toFixed pickList: field.fieldSettings.pickList + showDescription: field.fieldSettings.showDescription switch field.fieldSettings.fieldType when 'label' From 05be79142128903d1590898e3fed80f1e04a8df7 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 12 Dec 2019 14:00:06 -0800 Subject: [PATCH 490/576] Add formfield label tooltip option. needs styling help --- modules/Components/src/client/ACASFormFields.coffee | 9 +++++++++ modules/Components/src/client/ACASFormFieldsView.html | 8 ++++++++ .../Components/src/client/AbstractFormController.coffee | 1 + 3 files changed, 18 insertions(+) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 9f5874cf3..cddfacfff 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -97,6 +97,9 @@ class window.ACASFormAbstractFieldController extends Backbone.View @addFormLabelClass @options.formLabelClass if @options.formLabelOrientation? @setupFormLabelOrientation @options.formLabelOrientation + if @options.formLabelTooltip? + @setFormLabelTooltip @options.formLabelTooltip + @showFormLabelTooltip() if @options.inputClass? @addInputClass @options.inputClass if @options.controlGroupClass? @@ -119,6 +122,12 @@ class window.ACASFormAbstractFieldController extends Backbone.View if value is "top" @$('label').removeClass 'control-label' # else set label to left, this is already the default + + setFormLabelTooltip: (value) -> + @$('.label-tooltip').attr 'title', value + + showFormLabelTooltip: -> + @$('.label-tooltip').removeClass 'hide' addInputClass: (value) -> @$('input').addClass value diff --git a/modules/Components/src/client/ACASFormFieldsView.html b/modules/Components/src/client/ACASFormFieldsView.html index 582842d97..446e344c2 100644 --- a/modules/Components/src/client/ACASFormFieldsView.html +++ b/modules/Components/src/client/ACASFormFieldsView.html @@ -1,5 +1,6 @@ + \ No newline at end of file diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 758a5e605..97da2d577 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -179,6 +179,7 @@ class window.AbstractThingFormController extends AbstractFormController when 'stringValue' then newField = new ACASFormLSStringValueFieldController opts when 'dateValue' then newField = new ACASFormLSDateValueFieldController opts when 'fileValue' then newField = new ACASFormLSFileValueFieldController opts + when 'booleanValue' then newField = new ACASFormLSBooleanFieldController opts when 'locationTree' opts.tubeCode = @model.get('tubeCode') newField = new ACASFormLocationTreeController opts diff --git a/modules/ServerAPI/conf/ExampleThingConfJSON.coffee b/modules/ServerAPI/conf/ExampleThingConfJSON.coffee index ba62d9484..97830848a 100644 --- a/modules/ServerAPI/conf/ExampleThingConfJSON.coffee +++ b/modules/ServerAPI/conf/ExampleThingConfJSON.coffee @@ -89,6 +89,8 @@ ddicttypes: [ typeName: "metadata" + , + typeName: "boolean" ] ddictkinds: @@ -98,6 +100,9 @@ , typeName: "metadata" kindName: "color" + , + typeName: "boolean" + kindName: "boolean" ] codetables: @@ -129,6 +134,20 @@ code: "purple" name: "Purple" ignored: false + , + codeType: "boolean" + codeKind: "boolean" + codeOrigin: "ACAS DDict" + code: "true" + name: "true" + ignored: false + , + codeType: "boolean" + codeKind: "boolean" + codeOrigin: "ACAS DDict" + code: "false" + name: "false" + ignored: false ] labelsequences: From 93a17d0676d030141a9696175f2ab26a7a74ce73 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 13 Dec 2019 08:35:09 -0800 Subject: [PATCH 492/576] Adding state table form controller for state fields that should be shown in a form --- .../src/client/ACASFormStateTable.coffee | 182 +++++++++++++++++- .../src/client/ACASFormStateTableView.html | 5 +- .../src/client/AbstractFormController.coffee | 6 + modules/Components/src/client/style.css | 7 + 4 files changed, 193 insertions(+), 7 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 6a94e7c68..905f29783 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -19,8 +19,10 @@ class window.ACASFormStateTableController extends Backbone.View initialize: -> @thingRef = @options.thingRef @tableDef = @options.tableDef + @formWrapper = @options.formWrapper @tableSetupComplete = false @callWhenSetupComplete = null + @stateTableFormControllersCollection = [] getCollection: -> #TODO get states by type and kind @@ -49,6 +51,10 @@ class window.ACASFormStateTableController extends Backbone.View @setTableLabel @tableDef.tableLabel if @tableDef?.tableLabelClass? @addFormLabelClass @options.tableDef.tableLabelClass + anyValuesHaveFieldWrapper = _.some @tableDef.values, (v) -> + _.has v.fieldSettings, 'fieldWrapper' + if @formWrapper? and anyValuesHaveFieldWrapper + @hasFormWrapper = true @tableReadOnly = if @tableDef.tableReadOnly? then @tableDef.tableReadOnly else false @@ -63,6 +69,9 @@ class window.ACASFormStateTableController extends Backbone.View removeTableLabelClass: (value) -> @$('.bv_tableLabel').removeClass value + addFormWrapper: (formEl) -> + @$('.bv_formWrapper').html formEl + defineColumnsAndSetupHOT: -> @fetchPickLists => @defineColumns() @@ -111,19 +120,23 @@ class window.ACASFormStateTableController extends Backbone.View @colHeaders = [] unless @colDefs? @colDefs = [] + unless @formValueDefs? + @formValueDefs = [] unless @unitKeyValueMap? #keeps track of which values unit keys are for @unitKeyValueMap = {} for val in @tableDef.values + isTableValue = !val.fieldSettings.fieldWrapper? displayName = val.fieldSettings.formLabel if @showUnits if val.modelDefaults.unitKind? displayName += "
        (#{val.modelDefaults.unitKind})" - @colHeaders.push - displayName: displayName - keyName: val.modelDefaults.kind - width: if val.fieldSettings.width? then val.fieldSettings.width else 75 + if isTableValue + @colHeaders.push + displayName: displayName + keyName: val.modelDefaults.kind + width: if val.fieldSettings.width? then val.fieldSettings.width else 75 colOpts = data: val.modelDefaults.kind colOpts.readOnly = if val.fieldSettings.readOnly? then val.fieldSettings.readOnly else false @@ -146,7 +159,10 @@ class window.ACASFormStateTableController extends Backbone.View if val.validator? colOpts.validator = val.validator - @colDefs.push colOpts + if isTableValue + @colDefs.push colOpts + else + @formValueDefs.push val if val.fieldSettings.unitColumnKey? @colHeaders.push @@ -176,6 +192,7 @@ class window.ACASFormStateTableController extends Backbone.View afterChange: @handleCellChanged afterValidate: @handleAfterValidate afterCreateRow: @handleRowCreated + afterSelection: @handleSelection minSpareRows: 1, allowInsertRow: true contextMenu: contextMenu @@ -189,11 +206,17 @@ class window.ACASFormStateTableController extends Backbone.View afterRemoveRow: @handleRowRemoved columns: @colDefs search: @tableDef.search + currentRowClassName: 'bv_stateDisplayCurrentRow', + currentColClassName: 'bv_stateDisplayCurrentColumn' cells: (row, col, prop) => cellProperties = {} if @tableReadOnly cellProperties.readOnly = true return cellProperties; + + # Select the first row on start + @hot.selectCell(0,0,0,0) + @hot.addHook 'afterChange', @validateRequiredAndUniqueness readOnlyRenderer: (instance, td, row, col, prop, value, cellProperties) => @@ -223,11 +246,29 @@ class window.ACASFormStateTableController extends Backbone.View newValue.set codeType: valueDef.modelDefaults.codeType if valueDef.modelDefaults.codeKind? newValue.set codeKind: valueDef.modelDefaults.codeKind + + if @hasFormWrapper + @setupFormForNewState newState + @hot.selectCell(row,0,row,0) return newState getCurrentStates: -> @thingRef.get('lsStates').getStatesByTypeAndKind @tableDef.stateType, @tableDef.stateKind + setupFormForNewState: (state) -> + fDiv = @formWrapper.clone() + @$('.bv_formWrapper').append fDiv + formController = new ACASFormStateTableFormController + el: fDiv + thingRef: @thingRef + valueDefs: @formValueDefs + stateType: @tableDef.stateType + stateKind: @tableDef.stateKind + rowNumber: @getRowNumberForState(state) + rowNumberKind: @rowNumberKind + @stateTableFormControllersCollection.push formController + formController.hide() + renderState: (state) -> rowNum = @getRowNumberForState(state) if rowNum? #should always be true @@ -263,6 +304,7 @@ class window.ACASFormStateTableController extends Backbone.View @hot.setDataAtRowProp cols, "autofill" + getRowNumberForState: (state) -> rowValues = state.getValuesByTypeAndKind 'numericValue', @rowNumberKind if rowValues.length == 1 @@ -369,6 +411,28 @@ class window.ACASFormStateTableController extends Backbone.View else state.set ignored: true @trigger 'removedRow', state + + # This happens before the table is rendered and the row really removed + if @hasFormWrapper + # First destroy the form controller we are removing + controllerToRemove = @stateTableFormControllersCollection[rowNum] + controllerToRemove.remove() + controllerToRemove.unbind() + + # Remove the controller from the list + @stateTableFormControllersCollection.splice rowNum, 1 + + # After controller removal we want to select the row that took its place if it exists + # which should be the conroller below it if it exists + if @stateTableFormControllersCollection[rowNum]? + @hot.selectCell(rowNum,0,rowNum,0) + # If it doesn't exist then the row below it doesn't have a controller yet + # This means that we just deleted the last row in the table with a controller + # so we select the row above it if it exists + else if rowNum-1 > -1 + @hot.selectCell(rowNum-1,0,rowNum-1,0) + + nextRow = index+amount nRows = @hot.countRows() + amount #to get number of rows before removing if nextRow < nRows-1 @@ -378,6 +442,17 @@ class window.ACASFormStateTableController extends Backbone.View if rowValues.length == 1 rowValues[0].set numericValue: rowNum - amount + handleSelection: (row, column, row2, column2, preventScrolling, selectionLayerLevel) => + if @hasFormWrapper? + $(@el).find(".bv_moreDetails").show() + for cont, index in @stateTableFormControllersCollection + if index == row + $(@el).find(".bv_moreDetails").hide() + cont.show() + else + cont.hide() + + setCodeForName: (value, nameToLookup) -> if @pickLists[value.get('lsKind')]? code = @pickLists[value.get('lsKind')].findWhere({name: nameToLookup}) @@ -497,4 +572,101 @@ class window.ACASFormStateTableController extends Backbone.View @hot.render() +class window.ACASFormStateTableFormController extends Backbone.View + + initialize: -> + @hide() + @valueDefs = @options.valueDefs + @stateType = @options.stateType + @stateKind = @options.stateKind + @thingRef = @options.thingRef + @rowNumber = @options.rowNumber + @rowNumberKind = @options.rowNumberKind + @setupForm() + @show() + + render: => + @setupForm() + + show: -> + $(@el).show() + + hide: -> + $(@el).hide() + + setupForm: -> + state = @getStateForRow() + + for field in @valueDefs + value = state.getOrCreateValueByTypeAndKind field.modelDefaults.type, field.modelDefaults.kind + keyBase = field.key + newKey = keyBase + value.cid + value.set key: newKey + @thingRef.set newKey, value + + opts = + modelKey: newKey + inputClass: field.fieldSettings.inputClass + formLabel: field.fieldSettings.formLabel + formLabelOrientation: field.fieldSettings.formLabelOrientation + placeholder: field.fieldSettings.placeholder + required: field.fieldSettings.required + url: field.fieldSettings.url + thingRef: @thingRef + insertUnassigned: field.fieldSettings.insertUnassigned + firstSelectText: field.fieldSettings.firstSelectText + modelDefaults: field.modelDefaults + allowedFileTypes: field.fieldSettings.allowedFileTypes + extendedLabel: field.fieldSettings.extendedLabel + tabIndex: field.fieldSettings.tabIndex + toFixed: field.fieldSettings.toFixed + pickList: field.fieldSettings.pickList + rowNumber: @rowNumber + rowNumberKind: @rowNumberKind + stateType: @stateType + stateKind: @stateKind + + #Should refactor this into a function for other places to use when selcting a controller + switch field.fieldSettings.fieldType + when 'label' + if field.multiple? and field.multiple + newField = new ACASFormMultiLabelListController opts + else + newField = new ACASFormLSLabelFieldController opts + when 'numericValue' then newField = new ACASFormLSNumericValueFieldController opts + when 'codeValue' then newField = new ACASFormLSCodeValueFieldController opts + when 'htmlClobValue' + opts.rows = field.fieldSettings?.rows + newField = new ACASFormLSHTMLClobValueFieldController opts + when 'thingInteractionSelect' + opts.thingType = field.fieldSettings.thingType + opts.thingKind = field.fieldSettings.thingKind + opts.queryUrl = field.fieldSettings.queryUrl + opts.labelType = field.fieldSettings.labelType + newField = new ACASFormLSThingInteractionFieldController opts + when 'stringValue' then newField = new ACASFormLSStringValueFieldController opts + when 'dateValue' then newField = new ACASFormLSDateValueFieldController opts + when 'fileValue' then newField = new ACASFormLSFileValueFieldController opts + when 'locationTree' + opts.tubeCode = @model.get('tubeCode') + newField = new ACASFormLocationTreeController opts + + valueDiv = $(@el).find("."+field.fieldSettings.fieldWrapper) + valueDiv[0].append newField.render().el + + getStateForRow: () -> + currentStates = @getCurrentStates() + for state in currentStates + if @getRowNumberForState(state) == @rowNumber + return state + + getCurrentStates: -> + @thingRef.get('lsStates').getStatesByTypeAndKind @stateType, @stateKind + + getRowNumberForState: (state) -> + rowValues = state.getValuesByTypeAndKind 'numericValue', @rowNumberKind + if rowValues.length == 1 + return rowValues[0].get('numericValue') + else + return null diff --git a/modules/Components/src/client/ACASFormStateTableView.html b/modules/Components/src/client/ACASFormStateTableView.html index c19458a33..02121c348 100644 --- a/modules/Components/src/client/ACASFormStateTableView.html +++ b/modules/Components/src/client/ACASFormStateTableView.html @@ -1,6 +1,7 @@ diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 758a5e605..04e5197a9 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -204,9 +204,15 @@ class window.AbstractThingFormController extends AbstractFormController @formTables = {} for tDef in tableDefs tdiv = $("
        ") + @$("."+tDef.tableWrapper).append tdiv + + formWrapper = null + if tDef.formWrapper? + formWrapper = @$("."+tDef.formWrapper) fTable = new ACASFormStateTableController el: tdiv + formWrapper: formWrapper tableDef: tDef thingRef: @model fTable.render() diff --git a/modules/Components/src/client/style.css b/modules/Components/src/client/style.css index 878aa87c8..c3b845277 100644 --- a/modules/Components/src/client/style.css +++ b/modules/Components/src/client/style.css @@ -47,4 +47,11 @@ .bv_stateDisplayUpdateTable .valueEditable { cursor: pointer; +} + +.bv_stateDisplayCurrentRow { + background-color: rgb(182, 182, 211) !important; +} +.bv_stateDisplayCurrentColumn { + background-color: rgb(182, 182, 211) !important; } \ No newline at end of file From a6280b77729f1918317c023b363aee2cb28b76e0 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Sat, 14 Dec 2019 07:03:45 -0800 Subject: [PATCH 493/576] better configuration description and removing console.log statements --- conf/config.properties.example | 2 +- modules/ServerAPI/src/server/routes/AuthorRoutes.coffee | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/conf/config.properties.example b/conf/config.properties.example index 7a2dd56ef..d8686e3e0 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -565,7 +565,7 @@ client.projectEditor.isRestricted.default=false client.roles.crossProjectLoaderRole=ROLE_ACAS-CROSS-PROJECT-LOADER -# List of project codes to filter from ACAS +# List of project codes to filter out and hide from ACAS # e.g. server.projects.filterList = ["SomeProject"] server.projects.filterList = [] diff --git a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee index 732e56bec..dfac5160c 100644 --- a/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/AuthorRoutes.coffee @@ -54,8 +54,6 @@ exports.allowedProjectsInternal = (user, callback) -> # Filter out any projects that exist in the config for filtering projects projectFilterList = JSON.parse config.all.server.projects.filterList allProjects = _.filter allProjects, (project, index) -> - console.log project - console.log projectFilterList[0] ! _.contains projectFilterList, project.code if (config.all.server.project.roles.enable) From e024121ab6bd6cf79f44caad99b9006495d7b592 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Sun, 15 Dec 2019 14:33:09 -0800 Subject: [PATCH 494/576] Initial MultiCodeValueCheckbox implementation --- .../ACASFormMultiCodeValueCheckbox.coffee | 153 ++++++++++++++++++ .../ACASFormMultiCodeValueCheckbox.html | 11 ++ .../src/client/ACASFormStateTable.coffee | 6 +- .../src/client/AbstractFormController.coffee | 6 +- 4 files changed, 174 insertions(+), 2 deletions(-) create mode 100644 modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee create mode 100644 modules/Components/src/client/ACASFormMultiCodeValueCheckbox.html diff --git a/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee new file mode 100644 index 000000000..e4e90df28 --- /dev/null +++ b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee @@ -0,0 +1,153 @@ +class window.ACASFormCodeValueCheckboxController extends ACASFormAbstractFieldController + ### + Launched by ACASFormMultiCodeValueCheckboxController to control one checkbox in the list + ### + + template: _.template($("#ACASFormCodeValueCheckbox").html()) + + events: -> + "change input": "handleInputChanged" + + initialize: -> + @stateRef = @options.stateRef + @thingRef = @options.thingRef + @keyBase = @options.keyBase + @code = @options.codeTable.get 'code' + @codeType = @options.codeTable.get 'codeType' + @codeKind = @options.codeTable.get 'codeKind' + @stateType = @options.stateType + @stateKind = @options.stateKind + @valueType = @options.valueType + @valueKind = @options.valueKind + @rowNumber = @options.rowNumber + @rowNumberKind = @options.rowNumberKind + @ + + render: -> + super() + @ + + handleInputChanged: -> + @clearError() + @userInputEvent = true + isChecked = @$('input').is(":checked") + if isChecked + value = @getState().createValueByTypeAndKind @valueType, @valueKind + value.set + codeValue: @code + codeType: @codeType + codeKind: @codeKind + codeOrigin: @codeOrigin + ignored: false + newKey = @keyBase + value.cid + value.set key: newKey + @thingRef.set newKey, value + @getState().get('lsValues').add value + else + # Find existing value with codeValue matching this controller's code, and mark as ignored. + value = @getState().get('lsValues').findWhere({lsType: @valueType, lsKind: @valueKind, codeValue: @code}) + value.set + ignored: true + super() + + renderModelContent: => + # Check for value matching this controller's code, and mark as checked if found + if @getState().get('lsValues').findWhere({lsType: @valueType, lsKind: @valueKind, codeValue: @code})? + @$('input').attr 'checked', 'checked' + else + @$('input').removeAttr 'checked' + super() + + getState: () -> + if @rowNumber? and @rowNumberKind? + # If rowNumber is specified, assume operating within a stateTable / stateTableForm and pick the right state + return @getStateForRow() + else + # Otherwise assume operating with only one state of given type/kind on the Thing + return @thingRef.get('lsStates').getOrCreateStateByTypeAndKind @stateType, @stateKind + + getStateForRow: () -> + currentStates = @getCurrentStates() + for state in currentStates + if @getRowNumberForState(state) == @rowNumber + return state + #if we get to here without returning, we need a new state + newState = @thingRef.get('lsStates').createStateByTypeAndKind @stateType, @stateKind + return newState + + getCurrentStates: -> + @thingRef.get('lsStates').getStatesByTypeAndKind @stateType, @stateKind + + getRowNumberForState: (state) -> + rowValues = state.getValuesByTypeAndKind 'numericValue', @rowNumberKind + if rowValues.length == 1 + return rowValues[0].get('numericValue') + else + return null + + +class window.ACASFormMultiCodeValueCheckboxController extends ACASFormAbstractFieldController + ### + Launching controller must instantiate with the full field conf including modelDefaults, not just the fieldDefinition. + Specifying rowNumber and rowNumberKind are optional, and will make this controller act on a specific state. + Controls a list of + ### + template: _.template($("#ACASFormMultiCodeValueCheckbox").html()) + + initialize: -> + @opts = @options + @thingRef = @opts.thingRef + mdl = @opts.modelDefaults + if @opts.stateType? + @stateType = @opts.stateType + else + @stateType = mdl.stateType + if @opts.stateKind? + @stateKind = @opts.stateKind + else + @stateKind = mdl.stateKind + @keyBase = @opts.modelKey + @codeTableCollection = new PickListList() + if @url? + @codeTableCollection.url = @url + else + @codeTableCollection.url = "/api/codetables/#{mdl.codeType}/#{mdl.codeKind}" + @checkboxControllerList = [] + super() + @ + + + + render: -> + $(@el).empty() + $(@el).html @template() + @codeTableCollection.fetch + success: @finishRender + @ + + renderModelContent: -> + @checkboxControllerList.forEach (controller) -> + controller.renderModelContent() + + finishRender: (collection) => + # setup single controllers for each fetched codeTable + collection.each (codeTable) => + @addOneCodeValueSelect codeTable + + addOneCodeValueSelect: (codeTable) -> + # setup single controllers for each fetched codeTable, call renderModelContent on each + opts = + codeTable: codeTable + stateType: @stateType + stateKind: @stateKind + valueType: @opts.modelDefaults.type + valueKind: @opts.modelDefaults.kind + formLabel: codeTable.get 'name' + keyBase: @keyBase + rowNumber: @opts.rowNumber + rowNumberKind: @opts.rowNumberKind + thingRef: @thingRef + checkboxController = new ACASFormCodeValueCheckboxController opts + @checkboxControllerList.push checkboxController + @$('.bv_multiCodeValueCheckboxWrapper').append checkboxController.render().el + diff --git a/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.html b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.html new file mode 100644 index 000000000..e64dfb12f --- /dev/null +++ b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.html @@ -0,0 +1,11 @@ + + + \ No newline at end of file diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 905f29783..f4df6e01e 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -635,7 +635,11 @@ class window.ACASFormStateTableFormController extends Backbone.View else newField = new ACASFormLSLabelFieldController opts when 'numericValue' then newField = new ACASFormLSNumericValueFieldController opts - when 'codeValue' then newField = new ACASFormLSCodeValueFieldController opts + when 'codeValue' + if field.multiple? and field.multiple + newField = new ACASFormMultiCodeValueCheckboxController opts + else + newField = new ACASFormLSCodeValueFieldController opts when 'htmlClobValue' opts.rows = field.fieldSettings?.rows newField = new ACASFormLSHTMLClobValueFieldController opts diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 57dd4b03f..0b3766acc 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -164,7 +164,11 @@ class window.AbstractThingFormController extends AbstractFormController else newField = new ACASFormLSLabelFieldController opts when 'numericValue' then newField = new ACASFormLSNumericValueFieldController opts - when 'codeValue' then newField = new ACASFormLSCodeValueFieldController opts + when 'codeValue' + if field.multiple? and field.multiple + newField = new ACASFormMultiCodeValueCheckboxController opts + else + newField = new ACASFormLSCodeValueFieldController opts when 'htmlClobValue' opts.rows = field.fieldSettings?.rows newField = new ACASFormLSHTMLClobValueFieldController opts From f6bc4c4b82002450b59606e269e22242999ffedb Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Sun, 15 Dec 2019 16:57:16 -0800 Subject: [PATCH 495/576] show description on initial load --- .../Components/src/client/ACASFormFields.coffee | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 5e9b55862..2d9c0ee43 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -291,11 +291,7 @@ class window.ACASFormLSCodeValueFieldController extends ACASFormAbstractFieldCon @getModel().set value: value ignored: false - if @options.showDescription? and @options.showDescription - @clearDescription() - desc = @pickListController.getSelectedModel().get('description') - if desc? - @setDescription(desc) + @showDescription() super() setEmptyValue: -> @@ -305,6 +301,7 @@ class window.ACASFormLSCodeValueFieldController extends ACASFormAbstractFieldCon renderModelContent: => @pickListController.setSelectedCode @getModel().get('value') + @showDescription() super() setupSelect: -> @@ -357,6 +354,14 @@ class window.ACASFormLSCodeValueFieldController extends ACASFormAbstractFieldCon enableInput: -> @$('select').removeAttr 'disabled' + showDescription: -> + if @options.showDescription? and @options.showDescription + @clearDescription() + if @pickListController.getSelectedModel()? + desc = @pickListController.getSelectedModel().get('description') + if desc? + @setDescription(desc) + setDescription: (message) -> @$('.desc-inline').removeClass 'hide' @$('.desc-inline').html message From 25ea9609d28115a0206b9cfd6a9c148e5ca03b54 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Sun, 15 Dec 2019 16:58:09 -0800 Subject: [PATCH 496/576] renderModelContent for formFields within stateTableForm --- .../src/client/ACASFormStateTable.coffee | 21 ++++++++++++++++--- 1 file changed, 18 insertions(+), 3 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 905f29783..b693bd8dc 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -258,15 +258,16 @@ class window.ACASFormStateTableController extends Backbone.View setupFormForNewState: (state) -> fDiv = @formWrapper.clone() @$('.bv_formWrapper').append fDiv + rowNumber = @getRowNumberForState(state) formController = new ACASFormStateTableFormController el: fDiv thingRef: @thingRef valueDefs: @formValueDefs stateType: @tableDef.stateType stateKind: @tableDef.stateKind - rowNumber: @getRowNumberForState(state) + rowNumber: rowNumber rowNumberKind: @rowNumberKind - @stateTableFormControllersCollection.push formController + @stateTableFormControllersCollection[rowNumber] = formController formController.hide() renderState: (state) -> @@ -303,6 +304,7 @@ class window.ACASFormStateTableController extends Backbone.View cols.push unitCellInfo @hot.setDataAtRowProp cols, "autofill" + @setupFormForNewState state getRowNumberForState: (state) -> @@ -583,6 +585,7 @@ class window.ACASFormStateTableFormController extends Backbone.View @thingRef = @options.thingRef @rowNumber = @options.rowNumber @rowNumberKind = @options.rowNumberKind + @formFields = {} @setupForm() @show() @@ -590,6 +593,8 @@ class window.ACASFormStateTableFormController extends Backbone.View @setupForm() show: -> + for modelKey, formField of @formFields + formField.renderModelContent() $(@el).show() hide: -> @@ -600,6 +605,13 @@ class window.ACASFormStateTableFormController extends Backbone.View for field in @valueDefs value = state.getOrCreateValueByTypeAndKind field.modelDefaults.type, field.modelDefaults.kind + if field.modelDefaults.codeType? + value.set 'codeType', field.modelDefaults.codeType + if field.modelDefaults.codeKind? + value.set 'codeKind', field.modelDefaults.codeKind + if field.modelDefaults.codeOrigin? + value.set 'codeOrigin', field.modelDefaults.codeOrigin + value.set 'value', value.get(value.get('lsType')) keyBase = field.key newKey = keyBase + value.cid value.set key: newKey @@ -610,6 +622,7 @@ class window.ACASFormStateTableFormController extends Backbone.View inputClass: field.fieldSettings.inputClass formLabel: field.fieldSettings.formLabel formLabelOrientation: field.fieldSettings.formLabelOrientation + formLabelTooltip: field.fieldSettings.formLabelTooltip placeholder: field.fieldSettings.placeholder required: field.fieldSettings.required url: field.fieldSettings.url @@ -622,6 +635,7 @@ class window.ACASFormStateTableFormController extends Backbone.View tabIndex: field.fieldSettings.tabIndex toFixed: field.fieldSettings.toFixed pickList: field.fieldSettings.pickList + showDescription: field.fieldSettings.showDescription rowNumber: @rowNumber rowNumberKind: @rowNumberKind stateType: @stateType @@ -653,7 +667,8 @@ class window.ACASFormStateTableFormController extends Backbone.View newField = new ACASFormLocationTreeController opts valueDiv = $(@el).find("."+field.fieldSettings.fieldWrapper) - valueDiv[0].append newField.render().el + valueDiv.append newField.render().el + @formFields[newKey] = newField getStateForRow: () -> currentStates = @getCurrentStates() From c905a4dbe08aa687bb62b504df38105dcc194bb0 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Sun, 15 Dec 2019 19:26:14 -0800 Subject: [PATCH 497/576] bugfix: properly wrap setupFormForNewState --- modules/Components/src/client/ACASFormStateTable.coffee | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index ccd567b51..eae2b9876 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -304,7 +304,8 @@ class window.ACASFormStateTableController extends Backbone.View cols.push unitCellInfo @hot.setDataAtRowProp cols, "autofill" - @setupFormForNewState state + if @hasFormWrapper + @setupFormForNewState state getRowNumberForState: (state) -> From cbd96614eb5b827bfe1cb1f32faf254493303267 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 17 Dec 2019 13:14:26 -0800 Subject: [PATCH 498/576] Fix styling of checkboxes --- .../src/client/ACASFormMultiCodeValueCheckbox.coffee | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee index e4e90df28..5982b6ee0 100644 --- a/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee +++ b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee @@ -149,5 +149,7 @@ class window.ACASFormMultiCodeValueCheckboxController extends ACASFormAbstractFi thingRef: @thingRef checkboxController = new ACASFormCodeValueCheckboxController opts @checkboxControllerList.push checkboxController - @$('.bv_multiCodeValueCheckboxWrapper').append checkboxController.render().el + checkBoxEl = checkboxController.render().el + checkBoxEl.style.float = "left" + @$('.bv_multiCodeValueCheckboxWrapper').append checkBoxEl From 3e48c6719d12130c1124cf433b269491cb299b55 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 20 Dec 2019 22:44:49 -0800 Subject: [PATCH 499/576] 619 add row to ACASFormStateTable programatically and hide and show table controller --- .../src/client/ACASFormStateTable.coffee | 57 ++++++++++++++++++- 1 file changed, 56 insertions(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index eae2b9876..e8d1729a8 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -215,16 +215,62 @@ class window.ACASFormStateTableController extends Backbone.View return cellProperties; # Select the first row on start - @hot.selectCell(0,0,0,0) + if @$('.bv_tableWrapper').is ":visible" + @hot.selectCell(0,0,0,0) @hot.addHook 'afterChange', @validateRequiredAndUniqueness + addRow: (values, callback) -> + # when we update the handsontable cell data directly we don't know when the "afterChange" function + # will complete, so we lock the table, count the number of triggers to the number of completions of the + # afterChange function, when it equals the number of changes we expect, we reset the table back to its + # original settings, and trigger the callback function + @hotPseudoTransaction(callback, values.length) + lastRow = @getLastRow() + for value, index in values + @hot.setDataAtCell(lastRow, index, value) + + hotPseudoTransaction: (callback, changeCount) -> + # Get the settings related th elo + originalSettings = @getCurrentLockSettings() + @lockTable() + @changeCount = 0 + @.on "cellChangeComplete", => + @changeCount = @changeCount + 1 + if @changeCount == changeCount + @hot.updateSettings(originalSettings) + callback changeCount + + getCurrentLockSettings: -> + settings = @hot.getSettings() + currentLockSettings = + readOnly: settings.readOnly, # make table cells read-only + contextMenu: settings.contextMenu, # disable context menu to change things + disableVisualSelection: settings.disableVisualSelection, # prevent user from visually selecting + manualColumnResize: settings.manualColumnResize, # prevent dragging to resize columns + manualRowResize: settings.manualRowResize, # prevent dragging to resize rows + comments: settings.comments #3 prevent editing of comments + + lockTable: -> + @hot.updateSettings({ + readOnly: true, # make table cells read-only + contextMenu: false, # disable context menu to change things + disableVisualSelection: true, # prevent user from visually selecting + manualColumnResize: false, # prevent dragging to resize columns + manualRowResize: false, # prevent dragging to resize rows + comments: false #3 prevent editing of comments + }) + readOnlyRenderer: (instance, td, row, col, prop, value, cellProperties) => Handsontable.renderers.TextRenderer.apply(this, arguments) td.style.background = '#EEE' td.style.color = 'black'; cellProperties.readOnly = true; + getLastRow: -> + lastRow = @getCurrentStates().length + return lastRow + getStateForRow: (row, forceNew) -> currentStates = @getCurrentStates() for state in currentStates @@ -252,6 +298,13 @@ class window.ACASFormStateTableController extends Backbone.View @hot.selectCell(row,0,row,0) return newState + show: => + $(@el).show() + @hot.render() + + hide: -> + $(@el).hide() + getCurrentStates: -> @thingRef.get('lsStates').getStatesByTypeAndKind @tableDef.stateType, @tableDef.stateKind @@ -392,6 +445,8 @@ class window.ACASFormStateTableController extends Backbone.View @setCodeForName(value, cellContent) rowNumValue = state.getOrCreateValueByTypeAndKind 'numericValue', @rowNumberKind rowNumValue.set numericValue: changeRow + @trigger 'cellChangeComplete', state + handleRowCreated: (index, amount) => #TODO: if update handsontable version, can add source input to only do something when row created via context menu From c2dc9e417ae90f8f57bfd8bd940ae42d9e16b92e Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 20 Dec 2019 22:46:49 -0800 Subject: [PATCH 500/576] 619 add row to state form controller programatically by supplying values and also hide/show functionality --- .../src/client/ACASFormStateTable.coffee | 57 ++++++++++++++++++- 1 file changed, 56 insertions(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index eae2b9876..e8d1729a8 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -215,16 +215,62 @@ class window.ACASFormStateTableController extends Backbone.View return cellProperties; # Select the first row on start - @hot.selectCell(0,0,0,0) + if @$('.bv_tableWrapper').is ":visible" + @hot.selectCell(0,0,0,0) @hot.addHook 'afterChange', @validateRequiredAndUniqueness + addRow: (values, callback) -> + # when we update the handsontable cell data directly we don't know when the "afterChange" function + # will complete, so we lock the table, count the number of triggers to the number of completions of the + # afterChange function, when it equals the number of changes we expect, we reset the table back to its + # original settings, and trigger the callback function + @hotPseudoTransaction(callback, values.length) + lastRow = @getLastRow() + for value, index in values + @hot.setDataAtCell(lastRow, index, value) + + hotPseudoTransaction: (callback, changeCount) -> + # Get the settings related th elo + originalSettings = @getCurrentLockSettings() + @lockTable() + @changeCount = 0 + @.on "cellChangeComplete", => + @changeCount = @changeCount + 1 + if @changeCount == changeCount + @hot.updateSettings(originalSettings) + callback changeCount + + getCurrentLockSettings: -> + settings = @hot.getSettings() + currentLockSettings = + readOnly: settings.readOnly, # make table cells read-only + contextMenu: settings.contextMenu, # disable context menu to change things + disableVisualSelection: settings.disableVisualSelection, # prevent user from visually selecting + manualColumnResize: settings.manualColumnResize, # prevent dragging to resize columns + manualRowResize: settings.manualRowResize, # prevent dragging to resize rows + comments: settings.comments #3 prevent editing of comments + + lockTable: -> + @hot.updateSettings({ + readOnly: true, # make table cells read-only + contextMenu: false, # disable context menu to change things + disableVisualSelection: true, # prevent user from visually selecting + manualColumnResize: false, # prevent dragging to resize columns + manualRowResize: false, # prevent dragging to resize rows + comments: false #3 prevent editing of comments + }) + readOnlyRenderer: (instance, td, row, col, prop, value, cellProperties) => Handsontable.renderers.TextRenderer.apply(this, arguments) td.style.background = '#EEE' td.style.color = 'black'; cellProperties.readOnly = true; + getLastRow: -> + lastRow = @getCurrentStates().length + return lastRow + getStateForRow: (row, forceNew) -> currentStates = @getCurrentStates() for state in currentStates @@ -252,6 +298,13 @@ class window.ACASFormStateTableController extends Backbone.View @hot.selectCell(row,0,row,0) return newState + show: => + $(@el).show() + @hot.render() + + hide: -> + $(@el).hide() + getCurrentStates: -> @thingRef.get('lsStates').getStatesByTypeAndKind @tableDef.stateType, @tableDef.stateKind @@ -392,6 +445,8 @@ class window.ACASFormStateTableController extends Backbone.View @setCodeForName(value, cellContent) rowNumValue = state.getOrCreateValueByTypeAndKind 'numericValue', @rowNumberKind rowNumValue.set numericValue: changeRow + @trigger 'cellChangeComplete', state + handleRowCreated: (index, amount) => #TODO: if update handsontable version, can add source input to only do something when row created via context menu From eef820e96510afed95313295a29d546f439edaeb Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Thu, 2 Jan 2020 09:57:46 -0800 Subject: [PATCH 501/576] fix typo in comment --- modules/Components/src/client/ACASFormStateTable.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index e8d1729a8..838715072 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -231,7 +231,7 @@ class window.ACASFormStateTableController extends Backbone.View @hot.setDataAtCell(lastRow, index, value) hotPseudoTransaction: (callback, changeCount) -> - # Get the settings related th elo + # Get the current settings related the lock originalSettings = @getCurrentLockSettings() @lockTable() @changeCount = 0 From 2d12e50d93c60ddaec0a11c735069edbf34bac47 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 2 Jan 2020 16:40:53 -0800 Subject: [PATCH 502/576] #619 if re-rendering after a save, we need to destroy the existing state form controller and re-create it with the new state --- modules/Components/src/client/ACASFormStateTable.coffee | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 838715072..9006f46ee 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -309,6 +309,10 @@ class window.ACASFormStateTableController extends Backbone.View @thingRef.get('lsStates').getStatesByTypeAndKind @tableDef.stateType, @tableDef.stateKind setupFormForNewState: (state) -> + if @stateTableFormControllersCollection[rowNumber]? + @stateTableFormControllersCollection[rowNumber].remove() + @stateTableFormControllersCollection[rowNumber].unbind() + fDiv = @formWrapper.clone() @$('.bv_formWrapper').append fDiv rowNumber = @getRowNumberForState(state) From f1651ec648ebf67eff6a09e05fe96ebc9fc7fe08 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 3 Jan 2020 11:06:43 -0800 Subject: [PATCH 503/576] #619 remove listener before starting transaction otherwise the count will be off during subsequent additions and the call back will return to early --- modules/Components/src/client/ACASFormStateTable.coffee | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 9006f46ee..a01295aea 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -235,6 +235,7 @@ class window.ACASFormStateTableController extends Backbone.View originalSettings = @getCurrentLockSettings() @lockTable() @changeCount = 0 + @.off "cellChangeComplete" @.on "cellChangeComplete", => @changeCount = @changeCount + 1 if @changeCount == changeCount From 905cc98963dbd5b262d6feb0e41256d928aca11e Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 3 Jan 2020 13:08:03 -0800 Subject: [PATCH 504/576] Fix rendering and updates to only act on non-ignored values --- .../src/client/ACASFormMultiCodeValueCheckbox.coffee | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee index 5982b6ee0..86d54a4d3 100644 --- a/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee +++ b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee @@ -32,7 +32,7 @@ class window.ACASFormCodeValueCheckboxController extends ACASFormAbstractFieldCo @userInputEvent = true isChecked = @$('input').is(":checked") if isChecked - value = @getState().createValueByTypeAndKind @valueType, @valueKind + value = @getState().getOrCreateValueByTypeAndKind @valueType, @valueKind value.set codeValue: @code codeType: @codeType @@ -45,14 +45,14 @@ class window.ACASFormCodeValueCheckboxController extends ACASFormAbstractFieldCo @getState().get('lsValues').add value else # Find existing value with codeValue matching this controller's code, and mark as ignored. - value = @getState().get('lsValues').findWhere({lsType: @valueType, lsKind: @valueKind, codeValue: @code}) + value = @getState().get('lsValues').findWhere({lsType: @valueType, lsKind: @valueKind, codeValue: @code, ignored: false}) value.set ignored: true super() renderModelContent: => # Check for value matching this controller's code, and mark as checked if found - if @getState().get('lsValues').findWhere({lsType: @valueType, lsKind: @valueKind, codeValue: @code})? + if @getState().get('lsValues').findWhere({lsType: @valueType, lsKind: @valueKind, codeValue: @code, ignored: false})? @$('input').attr 'checked', 'checked' else @$('input').removeAttr 'checked' From a5cf0bcb695ceabc16797fe0bf055f199415947c Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Fri, 3 Jan 2020 15:53:11 -0800 Subject: [PATCH 505/576] Add a proper listener to createNewValue in the right state when StateTableForm values get updated --- .../src/client/ACASFormStateTable.coffee | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 1b2b15374..6c85021ed 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -676,6 +676,14 @@ class window.ACASFormStateTableFormController extends Backbone.View newKey = keyBase + value.cid value.set key: newKey @thingRef.set newKey, value + # Deep copy the field modelDefaults and change the key to the newKey + newField = $.extend( true, {}, field) + newField.modelDefaults.key = newKey + # Save the modelDefaults to the Thing's defaultValues with the new key + # This allows @createNewValue to find the correct modelDefaults when creating a new value should this value be edited + @thingRef.lsProperties.defaultValues.push newField.modelDefaults + # Add a new listener to value changes to create a new value in the proper state + @listenTo value, 'createNewValue', @createNewValue opts = modelKey: newKey @@ -749,3 +757,22 @@ class window.ACASFormStateTableFormController extends Backbone.View return rowValues[0].get('numericValue') else return null + + createNewValue: (vKind, newVal, key) => + state = @getStateForRow() + # Get the modelDefaults for this key that was populated above during setupForm + valInfo = _.where(@thingRef.lsProperties.defaultValues, {key: key})[0] + @thingRef.unset(key) + newValue = state.createValueByTypeAndKind valInfo['type'], valInfo['kind'] + newValue.set valInfo['type'], newVal + newValue.set + unitKind: valInfo['unitKind'] + unitType: valInfo['unitType'] + codeKind: valInfo['codeKind'] + codeType: valInfo['codeType'] + codeOrigin: valInfo['codeOrigin'] + value: newVal + # Replace the Thing's reference to the old ignored value with a reference to the newValue + @thingRef.set key, newValue + # Add a listener in case this new value is changed again + @listenTo newValue, 'createNewValue', @createNewValue From e2c11650f3731da744cb99d5376748147fa03c1e Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 6 Jan 2020 09:19:25 -0800 Subject: [PATCH 506/576] fixes #630 Placeholder text in form table cells, default value in thing definition --- .../src/client/ACASFormStateTable.coffee | 15 ++++++++----- modules/ServerAPI/src/client/Label.coffee | 22 ++++++++++++++----- 2 files changed, 26 insertions(+), 11 deletions(-) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index 1b2b15374..e17f121ec 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -141,6 +141,11 @@ class window.ACASFormStateTableController extends Backbone.View colOpts = data: val.modelDefaults.kind colOpts.readOnly = if val.fieldSettings.readOnly? then val.fieldSettings.readOnly else false colOpts.wordWrap = true + + # put a value or placeholder in place + if val.fieldSettings.placeholder? + colOpts.placeholder = if _.isFunction(val.fieldSettings.placeholder) then val.fieldSettings.placeholder() else val.fieldSettings.placeholder + if val.modelDefaults.type == 'numericValue' colOpts.type = 'numeric' if val.fieldSettings.fieldFormat? @@ -283,7 +288,7 @@ class window.ACASFormStateTableController extends Backbone.View rowValue = newState.createValueByTypeAndKind 'numericValue', @rowNumberKind rowValue.set numericValue: row for valueDef in @tableDef.values - newValue = newState.createValueByTypeAndKind valueDef.modelDefaults.type, valueDef.modelDefaults.kind + newValue = newState.createValueByTypeAndKind valueDef.modelDefaults.type, valueDef.modelDefaults.kind, valueDef.modelDefaults.value if valueDef.modelDefaults.unitType? newValue.set unitType: valueDef.modelDefaults.unitType if valueDef.modelDefaults.unitKind? @@ -333,7 +338,7 @@ class window.ACASFormStateTableController extends Backbone.View cols = [] for valDef in @tableDef.values cellInfo = [] - value = state.getOrCreateValueByTypeAndKind valDef.modelDefaults.type, valDef.modelDefaults.kind + value = state.getOrCreateValueByTypeAndKind valDef.modelDefaults.type, valDef.modelDefaults.kind, valDef.modelDefaults.value if valDef.modelDefaults.type == 'codeValue' if valDef.fieldSettings.fieldType == 'stringValue' displayVal = value.get 'codeValue' @@ -408,7 +413,7 @@ class window.ACASFormStateTableController extends Backbone.View valueDefs = _.filter @tableDef.values, (def) -> def.modelDefaults.kind == attr valueDef = valueDefs[0] - value = state.getOrCreateValueByTypeAndKind valueDef.modelDefaults.type, valueDef.modelDefaults.kind + value = state.getOrCreateValueByTypeAndKind valueDef.modelDefaults.type, valueDef.modelDefaults.kind, valueDef.modelDefaults.value unless value.isNew() oldValueAttr = value.get(valueDef.modelDefaults.type) value = @cloneValueAndIgnoreOld state, value @@ -664,7 +669,7 @@ class window.ACASFormStateTableFormController extends Backbone.View state = @getStateForRow() for field in @valueDefs - value = state.getOrCreateValueByTypeAndKind field.modelDefaults.type, field.modelDefaults.kind + value = state.getOrCreateValueByTypeAndKind field.modelDefaults.type, field.modelDefaults.kind, field.modelDefaults.value if field.modelDefaults.codeType? value.set 'codeType', field.modelDefaults.codeType if field.modelDefaults.codeKind? @@ -683,7 +688,7 @@ class window.ACASFormStateTableFormController extends Backbone.View formLabel: field.fieldSettings.formLabel formLabelOrientation: field.fieldSettings.formLabelOrientation formLabelTooltip: field.fieldSettings.formLabelTooltip - placeholder: field.fieldSettings.placeholder + placeholder: if _.isFunction(field.fieldSettings.placeholder) then field.fieldSettings.placeholder() else field.fieldSettings.placeholder required: field.fieldSettings.required url: field.fieldSettings.url thingRef: @thingRef diff --git a/modules/ServerAPI/src/client/Label.coffee b/modules/ServerAPI/src/client/Label.coffee index 2f50c94a8..2009f3d4b 100644 --- a/modules/ServerAPI/src/client/Label.coffee +++ b/modules/ServerAPI/src/client/Label.coffee @@ -245,17 +245,22 @@ class window.State extends Backbone.Model getFirstValueOfKind: (kind) -> @get('lsValues').findWhere lsKind: kind - getOrCreateValueByTypeAndKind: (vType, vKind) -> + getOrCreateValueByTypeAndKind: (vType, vKind, vValue) -> descVals = @getValuesByTypeAndKind vType, vKind descVal = descVals[0] #TODO should do something smart if there are more than one unless descVal? - descVal = @createValueByTypeAndKind(vType, vKind) + descVal = @createValueByTypeAndKind(vType, vKind, vValue) return descVal - createValueByTypeAndKind: (vType, vKind) -> + createValueByTypeAndKind: (vType, vKind, vValue) -> descVal = new Value lsType: vType lsKind: vKind + if vValue? + if !_.isFunction(vValue) + descVal.set 'value', vValue + else + descVal.set 'value', vValue() @get('lsValues').add descVal descVal.on 'change', => @trigger('change') @@ -285,12 +290,12 @@ class window.StateList extends Backbone.Collection mState = @createStateByTypeAndKind sType, sKind return mState - getOrCreateValueByTypeAndKind: (sType, sKind, vType, vKind) -> + getOrCreateValueByTypeAndKind: (sType, sKind, vType, vKind, vValue) -> metaState = @getOrCreateStateByTypeAndKind sType, sKind descVals = metaState.getValuesByTypeAndKind vType, vKind descVal = descVals[0] #TODO should do something smart if there are more than one unless descVal? - descVal = @createValueByTypeAndKind(sType, sKind, vType, vKind) + descVal = @createValueByTypeAndKind(sType, sKind, vType, vKind, vValue) return descVal createStateByTypeAndKind: (sType, sKind) -> @@ -303,10 +308,15 @@ class window.StateList extends Backbone.Collection return mState - createValueByTypeAndKind: (sType, sKind, vType, vKind) -> + createValueByTypeAndKind: (sType, sKind, vType, vKind, vValue) -> descVal = new Value lsType: vType lsKind: vKind + if vValue? + if !_.isFunction(vValue) + descVal.set 'value', vValue + else + descVal.set 'value', vValue() metaState = @getOrCreateStateByTypeAndKind sType, sKind metaState.get('lsValues').add descVal descVal.on 'change', => From 9588a87827c7ffa65042f45f73c2c77e01f934dc Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 6 Jan 2020 17:20:48 -0800 Subject: [PATCH 507/576] fixes #619 if the table is rerendered then we should destroy all of its current form controllers --- modules/Components/src/client/ACASFormStateTable.coffee | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index a01295aea..3ade24b22 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -43,6 +43,12 @@ class window.ACASFormStateTableController extends Backbone.View @callWhenSetupComplete = @completeRenderModelContent completeRenderModelContent: -> + # Destroy all current form controllers as they will be recreated when rendering the state + if @stateTableFormControllersCollection? + @stateTableFormControllersCollection.forEach (controller) -> + controller.remove() + controller.unbind() + for state in @getCurrentStates() @renderState state From ce9ecfdffd9e8ef006e3ed70f4001a94e58404b4 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 7 Jan 2020 07:12:48 -0800 Subject: [PATCH 508/576] #634 set cells to readonly when disabling all inputs --- modules/Components/src/client/ACASFormStateTable.coffee | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index d3d478d22..ce5da242e 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -568,6 +568,10 @@ class window.ACASFormStateTableController extends Backbone.View readOnly: true contextMenu: false comments: false + cells: (row, col, prop) => + cellProperties = {readOnly: true} + return cellProperties; + #Other options I decided not to use # disableVisualSelection: true # manualColumnResize: false @@ -583,6 +587,10 @@ class window.ACASFormStateTableController extends Backbone.View readOnly: false contextMenu: contextMenu comments: true + cells: (row, col, prop) => + cellProperties = {} + return cellProperties; + #Other options I decided not to use # disableVisualSelection: false # manualColumnResize: true From 14b6acd9f77bb404d0e299ba115e1b18424191b5 Mon Sep 17 00:00:00 2001 From: Brian Frost Date: Tue, 7 Jan 2020 14:49:43 -0800 Subject: [PATCH 509/576] fix new checkbox value creation to find the correct value and also tolerate multiple toggle events and only create one value --- .../ACASFormMultiCodeValueCheckbox.coffee | 30 ++++++++++++------- 1 file changed, 19 insertions(+), 11 deletions(-) diff --git a/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee index 86d54a4d3..d9113247e 100644 --- a/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee +++ b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee @@ -32,17 +32,25 @@ class window.ACASFormCodeValueCheckboxController extends ACASFormAbstractFieldCo @userInputEvent = true isChecked = @$('input').is(":checked") if isChecked - value = @getState().getOrCreateValueByTypeAndKind @valueType, @valueKind - value.set - codeValue: @code - codeType: @codeType - codeKind: @codeKind - codeOrigin: @codeOrigin - ignored: false - newKey = @keyBase + value.cid - value.set key: newKey - @thingRef.set newKey, value - @getState().get('lsValues').add value + # Checkbox was just checked. Check for a new / unsaved ignored value with matching type/kind/code + value = @getState().get('lsValues').findWhere({lsType: @valueType, lsKind: @valueKind, codeValue: @code, ignored: true, id: undefined}) + if value? + # This means the box was toggled on and off multiple times, so we just flip the value to non-ignored + value.set + ignored: false + else + # Create a new value + value = @getState().createValueByTypeAndKind @valueType, @valueKind + value.set + codeValue: @code + codeType: @codeType + codeKind: @codeKind + codeOrigin: @codeOrigin + ignored: false + newKey = @keyBase + value.cid + value.set key: newKey + @thingRef.set newKey, value + @getState().get('lsValues').add value else # Find existing value with codeValue matching this controller's code, and mark as ignored. value = @getState().get('lsValues').findWhere({lsType: @valueType, lsKind: @valueKind, codeValue: @code, ignored: false}) From 12cead63a84831ac0d80684229b00570e155b8b3 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 7 Jan 2020 15:08:16 -0800 Subject: [PATCH 510/576] styling improvments for acas form multi code value checkboxes --- .../src/client/ACASFormFields.coffee | 5 ++++- .../client/ACASFormMultiCodeValueCheckbox.html | 18 +++++++++++++----- 2 files changed, 17 insertions(+), 6 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 2d9c0ee43..37e5a0226 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -113,7 +113,10 @@ class window.ACASFormAbstractFieldController extends Backbone.View @required = if @options.required? then @options.required else false setFormLabel: (value) -> - @$('label').html value + if @$('label .label-text').length + @$('label .label-text').html value + else + @$('label').html value addFormLabelClass: (value) -> @$('label').addClass value diff --git a/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.html b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.html index e64dfb12f..f34ea9412 100644 --- a/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.html +++ b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.html @@ -1,9 +1,17 @@ + + \ No newline at end of file diff --git a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee index 9c08adaa8..e97be7080 100644 --- a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee +++ b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee @@ -357,6 +357,7 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View when 'numericValue' then @newField = new ACASFormLSNumericValueFieldController opts when 'codeValue' then @newField = new ACASFormLSCodeValueFieldController opts when 'stringValue' then @newField = new ACASFormLSStringValueFieldController opts + when 'urlValue' then @newField = new ACASFormLSURLValueFieldController opts when 'dateValue' then @newField = new ACASFormLSDateValueFieldController opts @$('.bv_valueField').append @newField.render().el diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee index ce5da242e..882d40f2e 100644 --- a/modules/Components/src/client/ACASFormStateTable.coffee +++ b/modules/Components/src/client/ACASFormStateTable.coffee @@ -752,6 +752,7 @@ class window.ACASFormStateTableFormController extends Backbone.View opts.labelType = field.fieldSettings.labelType newField = new ACASFormLSThingInteractionFieldController opts when 'stringValue' then newField = new ACASFormLSStringValueFieldController opts + when 'urlValue' then newField = new ACASFormLSURLValueFieldController opts when 'dateValue' then newField = new ACASFormLSDateValueFieldController opts when 'fileValue' then newField = new ACASFormLSFileValueFieldController opts when 'locationTree' diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 0b3766acc..31109f869 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -183,6 +183,7 @@ class window.AbstractThingFormController extends AbstractFormController else newField = new ACASFormLSThingInteractionFieldController opts when 'stringValue' then newField = new ACASFormLSStringValueFieldController opts + when 'urlValue' then newField = new ACASFormLSURLValueFieldController opts when 'dateValue' then newField = new ACASFormLSDateValueFieldController opts when 'fileValue' then newField = new ACASFormLSFileValueFieldController opts when 'booleanValue' then newField = new ACASFormLSBooleanFieldController opts From 941c3e0a31d903bb41022d8eb0a3eed245537de5 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 27 Apr 2020 17:02:44 -0700 Subject: [PATCH 549/576] fixes #685 option to display files inline for image files --- modules/Components/src/client/ACASFormFields.coffee | 11 +++++++++-- .../src/client/AbstractFormController.coffee | 1 + 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index e7f448584..6d815d7b6 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -697,7 +697,11 @@ class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldCon @allowedFileTypes = @options.allowedFileTypes else @allowedFileTypes = ['csv','xlsx','xls','png','jpeg'] - + if @options.displayInline? + @displayInline = @options.displayInline + else + @displayInline = false + render: -> super() @setupFileController() @@ -722,7 +726,10 @@ class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldCon displayText = @getModel().get('comments') if !displayText? displayText = fileValue - @$('.bv_file').html ''+displayText+'' + if @displayInline + @$('.bv_file').html ''+ displayText+'' + else + @$('.bv_file').html ''+displayText+'' @$('.bv_deleteSavedFile').show() createNewFileChooser: -> diff --git a/modules/Components/src/client/AbstractFormController.coffee b/modules/Components/src/client/AbstractFormController.coffee index 0b3766acc..a57a7d465 100644 --- a/modules/Components/src/client/AbstractFormController.coffee +++ b/modules/Components/src/client/AbstractFormController.coffee @@ -151,6 +151,7 @@ class window.AbstractThingFormController extends AbstractFormController firstSelectText: field.fieldSettings.firstSelectText modelDefaults: field.modelDefaults allowedFileTypes: field.fieldSettings.allowedFileTypes + displayInline: field.fieldSettings.displayInline extendedLabel: field.fieldSettings.extendedLabel tabIndex: field.fieldSettings.tabIndex toFixed: field.fieldSettings.toFixed From 62a1aed830d901bb82ebf2bc65e1f635c52f7042 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 27 Apr 2020 17:04:15 -0700 Subject: [PATCH 550/576] fixes #684 adding ACASFormLSURLValueFieldController --- .../src/client/ACASFormFields.coffee | 45 ++++++++++++++++++- 1 file changed, 44 insertions(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index e7f448584..234e4323a 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -795,4 +795,47 @@ class window.ACASFormLSBooleanFieldController extends ACASFormAbstractFieldContr @$('input').removeAttr 'checked' else @$('input').attr 'checked', 'checked' - super() \ No newline at end of file + super() + + + +class window.ACASFormLSURLValueFieldController extends ACASFormAbstractFieldController + ### + Launching controller must: + - Initialize the model with an LSValue + Do whatever else is required or optional in ACASFormAbstractFieldController + ### + + template: _.template($("#ACASFormLSURLValueFieldView").html()) + + events: -> + "click .bv_linkBtn": "handleLinkBtnClicked" + + handleInputChanged: => + @clearError() + @userInputEvent = true + value = UtilityFunctions::getTrimmedInput(@$('input')) + if value == "" + @setEmptyValue() + else + @getModel().set + value: value + ignored: false + super() + + setEmptyValue: -> + @getModel().set + value: null + ignored: true + + setInputValue: (inputValue) -> + @$('input').val inputValue + + handleLinkBtnClicked: => + url = UtilityFunctions::getTrimmedInput(@$('input')) + window.open(url); + + + renderModelContent: => + @$('input').val @getModel().get('value') + super() From dd258cd117ffb0d90ff7d5bf9fb122ff9b105063 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 27 Apr 2020 17:07:15 -0700 Subject: [PATCH 551/576] fixes #686 fix for ls kinds with multiple spaces breaking the html clob viewer (replaces all spaces not just the first one) --- modules/Components/src/client/ACASFormFields.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index e7f448584..e03a13207 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -565,7 +565,7 @@ class window.ACASFormLSHTMLClobValueFieldController extends ACASFormAbstractFiel setupTinyMCE: -> mdl = @getModel() - cname = mdl.get('lsKind').replace(" ","")+"_"+mdl.cid + cname = mdl.get('lsKind').split(' ').join('')+"_"+mdl.cid selector = "."+cname @$('.bv_wysiwygEditor').addClass cname @wysiwygEditor = tinymce.init From 84dc52b0e80e62ff16cfc17a186717ca234fd632 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 27 Apr 2020 17:10:22 -0700 Subject: [PATCH 552/576] fixes #690 disable file value method for acas forms --- modules/Components/src/client/ACASFormFields.coffee | 3 +++ 1 file changed, 3 insertions(+) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index e7f448584..5fb64823f 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -750,6 +750,9 @@ class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldCon value: nameOnServer ignored: false + disableInput: -> + @$('.bv_deleteSavedFile').hide() + handleFileRemoved: => @setEmptyValue() @checkEmptyAndRequired() From dd3b67887518e27ffa2b44dfdd09bd8791406c1c Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 29 Apr 2020 16:34:09 -0700 Subject: [PATCH 553/576] curve curator fixes --- modules/CurveAnalysis/src/server/CurveDetail.R | 2 +- .../CurveAnalysis/src/server/routes/CurveCuratorRoutes.coffee | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/CurveAnalysis/src/server/CurveDetail.R b/modules/CurveAnalysis/src/server/CurveDetail.R index e3156fafb..3d5946daf 100644 --- a/modules/CurveAnalysis/src/server/CurveDetail.R +++ b/modules/CurveAnalysis/src/server/CurveDetail.R @@ -20,7 +20,7 @@ handle_response <- function(http_response_code, response) { get_curve_detail <- function() { postData <- rawToChar(receiveBin()) - if(is.null(postData)) { + if(is.null(postData) || postData == "") { myMessenger$logger$debug(paste0('getting curve detail with get json: ', GET)) myMessenger$capture_output("detail <- racas::api_doseResponse_get_curve_detail(GET)", userError = paste0("There was an error retrieving detail for '", GET, "'")) if(myMessenger$hasErrors()) { diff --git a/modules/CurveAnalysis/src/server/routes/CurveCuratorRoutes.coffee b/modules/CurveAnalysis/src/server/routes/CurveCuratorRoutes.coffee index 44a4e94ba..ec4a96f34 100644 --- a/modules/CurveAnalysis/src/server/routes/CurveCuratorRoutes.coffee +++ b/modules/CurveAnalysis/src/server/routes/CurveCuratorRoutes.coffee @@ -7,6 +7,7 @@ exports.setupAPIRoutes = (app, loginRoutes) -> exports.setupRoutes = (app, loginRoutes) -> app.get '/api/curves/stubs/:exptCode', loginRoutes.ensureAuthenticated, exports.getCurveStubs + app.get '/api/curve/detail/:id', loginRoutes.ensureAuthenticated, exports.getCurveDetail app.post '/api/curves/detail', loginRoutes.ensureAuthenticated, exports.getCurveDetailCurveIds app.put '/api/curve/detail/:id', loginRoutes.ensureAuthenticated, exports.updateCurveDetail app.post '/api/curve/stub/:id', loginRoutes.ensureAuthenticated, exports.updateCurveStub From 68bb1c3ccbd508040461dd02ea62db1e6ceacb5e Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Sat, 2 May 2020 19:29:41 -0700 Subject: [PATCH 554/576] longer timeout on dose response fits --- .../src/server/routes/DoseResponseFitRoutes.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/CurveAnalysis/src/server/routes/DoseResponseFitRoutes.coffee b/modules/CurveAnalysis/src/server/routes/DoseResponseFitRoutes.coffee index 49286ec7e..96d499377 100644 --- a/modules/CurveAnalysis/src/server/routes/DoseResponseFitRoutes.coffee +++ b/modules/CurveAnalysis/src/server/routes/DoseResponseFitRoutes.coffee @@ -3,7 +3,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/doseResponseCurveFit', loginRoutes.ensureAuthenticated, exports.fitDoseResponse exports.fitDoseResponse = (request, response) -> - request.connection.setTimeout 600000 + request.connection.setTimeout 86400000 serverUtilityFunctions = require './ServerUtilityFunctions.js' response.writeHead(200, {'Content-Type': 'application/json'}); From 6015de685c31ad77d6b240d979833afed05047ce Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 6 May 2020 13:06:32 -0700 Subject: [PATCH 555/576] Fix for authorized label sequences --- .../src/server/routes/ACASLabelSequencesRoutes.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee b/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee index 1701aeed2..9333eab00 100644 --- a/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee +++ b/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee @@ -50,7 +50,7 @@ exports.getAuthorizedLabelSequencesInternal = (req, callback) -> callback labelSequenceTestJSON.labelSequenceArray else roles = req.session.passport.user.roles - baseurl = config.all.client.service.persistence.fullpath+"labelsequences/getAuthorizedLabelSequences" + baseurl = config.all.client.service.persistence.fullpath+"labelsequences/getAuthorizedLabelSequences?" if req.query?.thingTypeAndKind? baseurl += "&thingTypeAndKind=#{req.query.thingTypeAndKind}" if req.query?.labelTypeAndKind? From 411279f3692af5b5787a29f511bb4cf6bf9f7624 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 12 May 2020 13:20:03 -0700 Subject: [PATCH 556/576] fixes #694 add route to fetch all authorized lots --- .../src/server/routes/CmpdRegRoutes.coffee | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee index 7cdb8d3ee..e00c913b2 100644 --- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee +++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee @@ -3,6 +3,7 @@ exports.setupAPIRoutes = (app) -> app.get '/cmpdReg/scientists', exports.getScientists app.get '/cmpdReg/metalots/corpName/[\\S]*', exports.getMetaLot app.post '/cmpdReg/metalots', exports.metaLots + app.get '/cmpdReg/parentLot/getAllAuthorizedLots', exports.getAllAuthorizedLots exports.setupRoutes = (app, loginRoutes) -> app.get '/cmpdReg', loginRoutes.ensureAuthenticated, exports.cmpdRegIndex @@ -50,6 +51,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/cmpdReg/ketcher/calculate_cip', loginRoutes.ensureAuthenticated, exports.ketcherCalculateCip app.get '/cmpdReg/labelPrefixes', loginRoutes.ensureAuthenticated, exports.getAuthorizedPrefixes app.get '/cmpdReg/parentLot/getLotsByParent', loginRoutes.ensureAuthenticated, exports.getAPICmpdReg + app.get '/cmpdReg/parentLot/getAllAuthorizedLots', loginRoutes.ensureAuthenticated, exports.getAllAuthorizedLots _ = require 'underscore' request = require 'request' @@ -266,6 +268,37 @@ exports.searchCmpds = (req, resp) -> resp.end JSON.stringify {error: "something went wrong :("} ) + +exports.getAllAuthorizedLots = (req, resp) -> + req.setTimeout 86400000 + authorRoutes = require './AuthorRoutes.js' + authorRoutes.allowedProjectsInternal req.user, (statusCode, allowedUserProjects) -> + _ = require "underscore" + allowedProjectCodes = _.pluck(allowedUserProjects, "code") + requestJSON = allowedProjectCodes + console.log requestJSON + cmpdRegCall = config.all.client.service.cmpdReg.persistence.fullpath + '/parentLot/getLotsByProjectsList' + request( + method: 'POST' + url: cmpdRegCall + body: requestJSON + json: true + timeout: 6000000 + , (error, response, json) => + if !error && response.statusCode == 200 + resp.setHeader('Content-Type', 'application/json') + resp.end JSON.stringify json + else + console.log resp.stat + console.log 'got ajax error trying to get all lots' + console.log error + console.log json + console.log response + resp.statusCode = 500 + console.log response.statusCode + resp.end JSON.stringify {error: "something went wrong :("} + ) + exports.getStructureImage = (req, resp) -> imagePath = (req.originalUrl).replace /\/cmpdreg\/structureimage/, "" cmpdRegCall = config.all.client.service.cmpdReg.persistence.basepath + '/structureimage' + imagePath From 02466274bf26d28bad904335ec01a79a70dd45e4 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 13 May 2020 15:25:39 -0700 Subject: [PATCH 557/576] make sure validation summary page is hiddent when showing purge files --- modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee index 4823ddd3a..eb924c3ed 100644 --- a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee +++ b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee @@ -1118,6 +1118,7 @@ class window.CmpdRegBulkLoaderAppController extends Backbone.View unless @$('.bv_purgeFiles').is(':visible') @$('.bv_bulkReg').hide() @$('.bv_bulkRegSummary').hide() + @$('.bv_bulkValSummary').hide() @$('.bv_purgeFiles').show() @setupPurgeFilesController() @$('.bv_adminDropdown').dropdown('toggle') From 9e343e18c30a666a28d33484c21f575b0d4ad5aa Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 13 May 2020 16:11:49 -0700 Subject: [PATCH 558/576] Fixing issue with saving templates and unable to register compounds --- modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee index eb924c3ed..16400082f 100644 --- a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee +++ b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee @@ -689,7 +689,7 @@ class window.AssignSdfPropertiesController extends Backbone.View data: dataToPost success: (response) => if response.id? - @validateCompounds() + @registerCompounds() else @handleSaveTemplateError() error: (err) => From 293b5b75b4628a26d770d9bc9714b26ff19e4836 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 22 May 2020 13:01:20 -0700 Subject: [PATCH 559/576] fixes #696 optional with parameter to fetch additonal thing depth or formats from generic search route --- modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee index d420439e8..24398e5fe 100644 --- a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee @@ -664,6 +664,8 @@ exports.genericThingSearch = (req, resp) -> typeFilter = "lsType=" + req.query.lsType if req.query.lsKind? kindFilter = "lsKind=" + req.query.lsKind + if req.query.with? + format = "with=#{req.query.with}" searchTerm = "q=" + req.params.searchTerm searchParams = "" @@ -671,6 +673,8 @@ exports.genericThingSearch = (req, resp) -> searchParams += typeFilter + "&" if kindFilter? searchParams += kindFilter + "&" + if format? + searchParams += format + "&" searchParams += searchTerm baseurl = config.all.client.service.persistence.fullpath+"lsthings/search?"+searchParams From 8e488bad801f8a42262698302062d4903b2c6f24 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 27 May 2020 08:53:51 -0700 Subject: [PATCH 560/576] Fixing issue with project mapping. It should only allow you to work in 1 mode (project mapped in - project dropdown off, OR project not mapped in - project dropdown on) --- .../src/client/CmpdRegBulkLoader.coffee | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee index 16400082f..b52ea69f4 100644 --- a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee +++ b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee @@ -704,18 +704,17 @@ class window.AssignSdfPropertiesController extends Backbone.View @$('.bv_errorMessage').html "An error occurred while trying to save the template. The compounds have not been registered yet.
        Please try again or contact an administrator." addProjectToMappingsPayLoad: -> - if @project != false - @assignedPropertiesList.remove(@assignedPropertiesListController.collection.findWhere({dbProperty: "Project"})) - if @project? - dbProjectProperty = new AssignedProperty - dbProperty: "Project" - required: true - sdfProperty: null - defaultVal: @project - @assignedPropertiesListController.collection.add dbProjectProperty + @assignedPropertiesList.remove(@assignedPropertiesListController.collection.findWhere({dbProperty: "Project"})) + dbProjectProperty = new AssignedProperty + dbProperty: "Project" + required: true + sdfProperty: null + defaultVal: @project + @assignedPropertiesListController.collection.add dbProjectProperty registerCompounds: -> - @addProjectToMappingsPayLoad() + if window.conf.cmpdReg.showProjectSelect + @addProjectToMappingsPayLoad() dataToPost = fileName: @fileName mappings: JSON.parse(JSON.stringify(@assignedPropertiesListController.collection.models)) @@ -741,7 +740,8 @@ class window.AssignSdfPropertiesController extends Backbone.View dataType: 'json' validateCompounds: -> - @addProjectToMappingsPayLoad() + if window.conf.cmpdReg.showProjectSelect + @addProjectToMappingsPayLoad() dataToPost = fileName: @fileName mappings: JSON.parse(JSON.stringify(@assignedPropertiesListController.collection.models)) From 824a583e139ad2deb8591aabb1889aa27e116d0b Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 4 Jun 2020 10:33:54 -0700 Subject: [PATCH 561/576] sort before applying colors --- modules/CurveAnalysis/src/server/renderCurve.R | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/modules/CurveAnalysis/src/server/renderCurve.R b/modules/CurveAnalysis/src/server/renderCurve.R index 0c85af3b3..ffb0ad0bf 100644 --- a/modules/CurveAnalysis/src/server/renderCurve.R +++ b/modules/CurveAnalysis/src/server/renderCurve.R @@ -23,16 +23,14 @@ renderCurve <- function(getParams) { # "#149BEDFF", "#A1C720FF", "#FEC10BFF", "#16A08CFF", "#9A703EFF") plotColors <- trimws(strsplit(racas::applicationSettings$server.curveRender.plotColors,",")[[1]]) if(!is.na(parsedParams$colorBy)) { - if(parsedParams$colorBy == "protocol") { - colorCategories <- suppressWarnings(unique(fitData[ , c("protocol_label"), with = FALSE])[, color:=plotColors][ , name:=protocol_label]) - fitData <- merge(fitData, colorCategories, by = "protocol_label") - } else if(parsedParams$colorBy == "experiment") { - colorCategories <- suppressWarnings(unique(fitData[ , c("experiment_label"), with = FALSE])[, color:=plotColors][ , name:=experiment_label]) - fitData <- merge(fitData, colorCategories, by = "experiment_label") - } else if(parsedParams$colorBy == "batch") { - colorCategories <- suppressWarnings(unique(fitData[ , c("batch_code"), with = FALSE])[, color:= plotColors][ , name:=batch_code]) - fitData <- merge(fitData, colorCategories, by = "batch_code") - } + key <- switch(parsedParams$colorBy, + "protocol" = "protocol_label", + "experiment" = "experiment_label", + "batch" = "batch_code" + ) + uniqueKeys <- setkeyv(unique(fitData[ , key, with = FALSE]), key) + colorCategories <- suppressWarnings(uniqueKeys[, color:=plotColors][ , name:=get(key)]) + fitData <- merge(fitData, colorCategories, by = key) } fitData <- fitData[exists("category") && (!is.null(category) & category %in% c("inactive","potent")), c("fittedMax", "fittedMin") := { From 108b29afca46697381452359043e25fc491d283b Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 9 Jun 2020 14:55:50 -0700 Subject: [PATCH 562/576] fixing width issue with select2 --- modules/Components/src/client/PickList.coffee | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/Components/src/client/PickList.coffee b/modules/Components/src/client/PickList.coffee index d42394447..c69de068f 100644 --- a/modules/Components/src/client/PickList.coffee +++ b/modules/Components/src/client/PickList.coffee @@ -618,7 +618,6 @@ class window.ThingLabelComboBoxController extends PickListSelect2Controller placeholder: @placeholder openOnEnter: false allowClear: true - width: "100%" ajax: url: (params) => if !params.term? From ea7512f5d01a587006f749e5b1b8a3d03718a9f6 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 9 Jun 2020 15:26:22 -0700 Subject: [PATCH 563/576] fixes #698 date icon clickable in readonly mode, add disableInput method which is called on readonly fields --- modules/Components/src/client/ACASFormFields.coffee | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 6ddfdc5ba..8bc705776 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -677,6 +677,8 @@ class window.ACASFormLSDateValueFieldController extends ACASFormAbstractFieldCon handleDateIconClicked: => @$('input').datepicker( "show" ) + disableInput: => + $(@el).off('click', '.bv_dateIcon'); class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldController ### From 9d5bed793b1d2033247b264ad82be3d5fc1f7607 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 10 Jun 2020 08:06:19 -0700 Subject: [PATCH 564/576] fixes #700 properly remove the disable attribute when enabling the html clob fields in acas forms --- modules/Components/src/client/ACASFormFields.coffee | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 6ddfdc5ba..3c2e966fa 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -578,7 +578,10 @@ class window.ACASFormLSHTMLClobValueFieldController extends ACASFormAbstractFiel @editor.setContent @contentToLoad if @disableEditor? @editor.getBody().setAttribute('contenteditable', !@disableEditor) - @editor.getBody().setAttribute('disabled', @disableEditor) + if @disableEditor + @editor.getBody().setAttribute('disabled', true) + else + @editor.getBody().removeAttribute('disabled') editor.on 'change', (e) => @textChanged editor.getContent() From 560ad56d8cb58d5f4c6fbf87a6af4f5f997f1daf Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 19 Jun 2020 14:48:31 -0700 Subject: [PATCH 565/576] fixes #708 put things in bulk and update their file values --- .../server/routes/ThingServiceRoutes.coffee | 67 ++++++++++++++++++- 1 file changed, 66 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee index 24398e5fe..98427177b 100644 --- a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee @@ -25,6 +25,7 @@ exports.setupAPIRoutes = (app, loginRoutes) -> app.post '/api/bulkPostThings', exports.bulkPostThings app.put '/api/bulkPutThings', exports.bulkPutThings app.post '/api/bulkPostThingsSaveFile', exports.bulkPostThingsSaveFile + app.put '/api/bulkPutThingsSaveFile', exports.bulkPutThingsSaveFile exports.setupRoutes = (app, loginRoutes) -> @@ -55,6 +56,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.post '/api/bulkPostThings', loginRoutes.ensureAuthenticated, exports.bulkPostThings app.put '/api/bulkPutThings', loginRoutes.ensureAuthenticated, exports.bulkPutThings app.post '/api/bulkPostThingsSaveFile', loginRoutes.ensureAuthenticated, exports.bulkPostThingsSaveFile + app.put '/api/bulkPutThingsSaveFile', loginRoutes.ensureAuthenticated, exports.bulkPutThingsSaveFile request = require 'request' config = require '../conf/compiled/conf.js' @@ -433,6 +435,69 @@ exports.postThingParent = (req, resp) -> exports.postThingBatch = (req, resp) -> postThing true, req, resp +exports.bulkPutThingsSaveFile = (req, resp) -> + + # First save all the ls things that come in + exports.bulkPutThingsInternal req.body, (response) => + + # Local function checkFilesAndUpdate + checkFilesAndUpdate = (thing, callback) -> + + # Check if there are any files to save + fileVals = serverUtilityFunctions.getFileValuesFromEntity thing, false + filesToSave = fileVals.length + console.log("got #{filesToSave} file values to check for updates") + + # Function called after final file is saved + completeThingUpdate = (thingToUpdate)-> + updateThing thingToUpdate, false, (updatedThing) -> + callback updatedThing, 200 + + # Function to call after a file is saved + fileSaveCompleted = (passed) -> + if !passed + callback "file move failed", 500 + # Decrement one from the filesToSave and if this is the final file that was saved call + # completeThingUpdate + if --filesToSave == 0 then completeThingUpdate(thing) + + # If there are any files to save, call the customer specific server function which should handle + # saving the file to the correct location and update the thing file value with the correct path + if filesToSave > 0 + prefix = serverUtilityFunctions.getPrefixFromEntityCode thing.codeName + for fv in fileVals + + # Only update new files + if !fv.id? + console.log("file value was updated #{JSON.stringify(fv)}") + # Send just the file value "fv" to the relocateEntityFile function + # relocate entity file is responsible for moving the file and updating the + # file value of thing in memory and later completeThingUpdate will handle persisting + # the change to the db. + csUtilities.relocateEntityFile fv, prefix, thing.codeName, fileSaveCompleted + else + fileSaveCompleted(true) + else + callback thing, 200 + + # If we failed to bulk save the things then just respond + if response.indexOf("saveFailed") > -1 + resp.json response + else + # Loop through the saved ls things and call the checkFilesAndUpdate function + # which should handle doing the correct thing with the files. + lengthThingsToCheck = response.length + i = 0 + resps = [] + for t in response + console.log("running check on files for thing #{JSON.stringify(t)}") + checkFilesAndUpdate t, (response, statusCode) -> + console.log("got response from check files #{statusCode} #{JSON.stringify(response)}") + resps.push response + i++ + if i == lengthThingsToCheck + resp.json resps + exports.putThingInternal = (thing, lsType, lsKind, testMode, callback) -> thingToSave = thing fileVals = serverUtilityFunctions.getFileValuesFromEntity thingToSave, true @@ -921,7 +986,7 @@ exports.bulkPutThingsInternal = (thingArray, callback) -> body: thingArray json: true , (error, response, json) => - console.log "bulkPutThingsInternal" + console.log "bulkPutThingsInternal complete" console.log response.statusCode if !error && response.statusCode == 200 callback json From ce3e7cb58bacf12125bc2d5a7b0a53d7aedcbb38 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 19 Jun 2020 14:54:23 -0700 Subject: [PATCH 566/576] fixes #706 default ls thing bollean form value should be unchecked if not true --- modules/Components/src/client/ACASFormFields.coffee | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee index 6ddfdc5ba..0b5a1fa00 100644 --- a/modules/Components/src/client/ACASFormFields.coffee +++ b/modules/Components/src/client/ACASFormFields.coffee @@ -801,10 +801,11 @@ class window.ACASFormLSBooleanFieldController extends ACASFormAbstractFieldContr ignored: true renderModelContent: => - if @getModel().get('value') is "false" - @$('input').removeAttr 'checked' - else + # If value is anything other than true (i.e. null), then default to unchecked + if @getModel().get('value') is "true" @$('input').attr 'checked', 'checked' + else + @$('input').removeAttr 'checked' super() From 4ee73d9abfe181440ee9578bb7a2ebd1f2e5b69d Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 19 Jun 2020 14:59:18 -0700 Subject: [PATCH 567/576] fixes #708 add POST request option for rendering curves --- modules/CurveAnalysis/src/server/renderCurve.R | 18 ++++++++++++++---- .../server/routes/CurveCuratorRoutes.coffee | 9 ++++++++- 2 files changed, 22 insertions(+), 5 deletions(-) diff --git a/modules/CurveAnalysis/src/server/renderCurve.R b/modules/CurveAnalysis/src/server/renderCurve.R index ffb0ad0bf..d854a58cd 100644 --- a/modules/CurveAnalysis/src/server/renderCurve.R +++ b/modules/CurveAnalysis/src/server/renderCurve.R @@ -3,7 +3,9 @@ # MEMORY_LIMIT_EXEMPT library(data.table) -renderCurve <- function(getParams) { + +renderCurve <- function(getParams, postData) { + # Redirect to Curator if applicable redirectInfo <- racas::api_get_curve_curator_url(getParams$curveIds, getParams$inTable, globalConnect = TRUE) if(redirectInfo$shouldRedirect == TRUE) { @@ -11,8 +13,15 @@ renderCurve <- function(getParams) { return(HTTP_MOVED_TEMPORARILY) DONE } + + postParams <- NA + saveSession('/tmp/ham') + if(!is.null(postData) && !is.na(postData) && postData != "") { + postParams <- jsonlite::fromJSON(postData) + } # Parse GET Parameters - parsedParams <- racas::parse_params_curve_render_dr(getParams) + parsedParams <- racas::parse_params_curve_render_dr(getParams, postParams) + # GET FIT DATA #fitData <- racas::get_fit_data_curve_id(parsedParams$curveIds) @@ -88,7 +97,7 @@ renderCurve <- function(getParams) { } setContentType("image/png") - setHeader("Content-Disposition", paste0("filename=\"",getParams$curveIds,".png\"")) + setHeader("Content-Disposition", paste0("filename=\"",strtrim(getParams$curveIds,200),".png\"")) t <- tempfile() racas::plotCurve(curveData = data$points, drawIntercept = renderingOptions$drawIntercept, params = data$parameters, fitFunction = renderingOptions$fct, paramNames = renderingOptions$paramNames, drawCurve = TRUE, logDose = logDose, logResponse = logResponse, outFile = t, ymin=parsedParams$yMin, ymax=parsedParams$yMax, xmin=parsedParams$xMin, xmax=parsedParams$xMax, height=parsedParams$height, width=parsedParams$width, showGrid = parsedParams$showGrid, showAxes = parsedParams$showAxes, labelAxes = parsedParams$labelAxes, showLegend=parsedParams$legend, mostRecentCurveColor = parsedParams$mostRecentCurveColor, axes = parsedParams$axes, plotColors = parsedParams$plotColors, curveLwd=parsedParams$curveLwd, plotPoints=parsedParams$plotPoints, connectPoints = renderingOptions$connectPoints, xlabel = parsedParams$xLab, ylabel = parsedParams$yLab) @@ -97,7 +106,8 @@ renderCurve <- function(getParams) { DONE } -renderCurve(getParams = GET) +postData <- rawToChar(receiveBin(-1)) +renderCurve(getParams = GET, postData) diff --git a/modules/CurveAnalysis/src/server/routes/CurveCuratorRoutes.coffee b/modules/CurveAnalysis/src/server/routes/CurveCuratorRoutes.coffee index ec4a96f34..0f292b3ad 100644 --- a/modules/CurveAnalysis/src/server/routes/CurveCuratorRoutes.coffee +++ b/modules/CurveAnalysis/src/server/routes/CurveCuratorRoutes.coffee @@ -4,6 +4,7 @@ exports.setupAPIRoutes = (app, loginRoutes) -> app.post '/api/curves/detail', exports.getCurveDetailCurveIds app.get '/api/curve/detail/:id', exports.getCurveDetail app.get '/api/curve/render/*', exports.renderCurve + app.post '/api/curve/render/*', exports.renderCurve exports.setupRoutes = (app, loginRoutes) -> app.get '/api/curves/stubs/:exptCode', loginRoutes.ensureAuthenticated, exports.getCurveStubs @@ -12,6 +13,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.put '/api/curve/detail/:id', loginRoutes.ensureAuthenticated, exports.updateCurveDetail app.post '/api/curve/stub/:id', loginRoutes.ensureAuthenticated, exports.updateCurveStub app.get '/api/curve/render/*', loginRoutes.ensureAuthenticated, exports.renderCurve + app.post '/api/curve/render/*', loginRoutes.ensureAuthenticated, exports.renderCurve app.get '/curveCurator/*', loginRoutes.ensureAuthenticated, exports.curveCuratorIndex exports.getCurveStubs = (req, resp) -> @@ -216,4 +218,9 @@ exports.renderCurve = (req, resp) -> config = require '../conf/compiled/conf.js' redirectQuery = req._parsedUrl.query rapacheCall = config.all.client.service.rapache.fullpath + '/curve/render/dr/?' + redirectQuery - req.pipe(request(rapacheCall)).pipe(resp) + if req.method == 'GET' + req.pipe(request(rapacheCall)).pipe resp + else + req.pipe(request[req.method.toLowerCase()]( + url: rapacheCall + json: req.body)).pipe resp From 23fbf3dc4f67b6f17076ca2a80fec38d4c00c586 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 19 Jun 2020 16:15:16 -0700 Subject: [PATCH 568/576] 708 remove debug line --- modules/CurveAnalysis/src/server/renderCurve.R | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/CurveAnalysis/src/server/renderCurve.R b/modules/CurveAnalysis/src/server/renderCurve.R index d854a58cd..b1c2a734e 100644 --- a/modules/CurveAnalysis/src/server/renderCurve.R +++ b/modules/CurveAnalysis/src/server/renderCurve.R @@ -15,7 +15,6 @@ renderCurve <- function(getParams, postData) { } postParams <- NA - saveSession('/tmp/ham') if(!is.null(postData) && !is.na(postData) && postData != "") { postParams <- jsonlite::fromJSON(postData) } From df36cf5193a52d1327e4dda0eb06badc6dac27d5 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Mon, 22 Jun 2020 13:50:03 -0700 Subject: [PATCH 569/576] add delete thing route --- .../server/routes/ThingServiceRoutes.coffee | 28 ++++++++++++++++++- 1 file changed, 27 insertions(+), 1 deletion(-) diff --git a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee index 98427177b..b00f31adb 100644 --- a/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee +++ b/modules/ServerAPI/src/server/routes/ThingServiceRoutes.coffee @@ -26,6 +26,7 @@ exports.setupAPIRoutes = (app, loginRoutes) -> app.put '/api/bulkPutThings', exports.bulkPutThings app.post '/api/bulkPostThingsSaveFile', exports.bulkPostThingsSaveFile app.put '/api/bulkPutThingsSaveFile', exports.bulkPutThingsSaveFile + app.delete '/api/things/:lsType/:lsKind/:idOrCodeName', exports.deleteThing exports.setupRoutes = (app, loginRoutes) -> @@ -57,6 +58,7 @@ exports.setupRoutes = (app, loginRoutes) -> app.put '/api/bulkPutThings', loginRoutes.ensureAuthenticated, exports.bulkPutThings app.post '/api/bulkPostThingsSaveFile', loginRoutes.ensureAuthenticated, exports.bulkPostThingsSaveFile app.put '/api/bulkPutThingsSaveFile', loginRoutes.ensureAuthenticated, exports.bulkPutThingsSaveFile + app.delete '/api/things/:lsType/:lsKind/:idOrCodeName', loginRoutes.ensureAuthenticated, exports.deleteThing request = require 'request' config = require '../conf/compiled/conf.js' @@ -994,4 +996,28 @@ exports.bulkPutThingsInternal = (thingArray, callback) -> console.log "got error bulk updating things" console.log error callback JSON.stringify "bulk update things saveFailed: " + JSON.stringify error - ) \ No newline at end of file + ) + +exports.deleteThing = (req, resp) -> + exports.deleteThingInternal req.params.lsType, req.params.lsKind, req.params.idOrCodeName, (status, response) => + resp.statusCode = status + resp.json response + +exports.deleteThingInternal = (lsType, lsKind, idOrCodeName, callback) -> + console.log "deleteThing #{idOrCodeName}" + baseurl = config.all.client.service.persistence.fullpath+"lsthings/#{lsType}/#{lsKind}/#{idOrCodeName}" + console.log baseurl + request( + method: 'DELETE' + url: baseurl + json: true + , (error, response, json) => + console.log "deleteThingInternal complete" + console.log response.statusCode + if !error && response.statusCode == 200 + callback 200, json + else + console.log "got error deleting thing" + console.log error + callback 500, JSON.stringify "delete thing: " + JSON.stringify error + ) From 845e15f8a9cfae97da6be5a58551ff12ea55180d Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 25 Jun 2020 08:14:19 -0700 Subject: [PATCH 570/576] Adding default from email address for email service --- conf/config.properties.example | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/config.properties.example b/conf/config.properties.example index 84191757c..c9ddfb53b 100644 --- a/conf/config.properties.example +++ b/conf/config.properties.example @@ -531,6 +531,7 @@ server.support.smtp.password=null server.support.smtp.auth=false server.support.smtp.tls=false server.support.smtp.ssl=false +server.support.smtp.from= client.basePath=/ From 9d49e17e86dfcb1f141523af7afe0e9da86176b9 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Wed, 8 Jul 2020 16:27:33 -0400 Subject: [PATCH 571/576] fixes #713 ignore db properties when they are marked with ignored: true --- .../src/client/custom/configuration.json | 108 +++++++++--------- .../src/client/CmpdRegBulkLoader.coffee | 26 +++-- 2 files changed, 69 insertions(+), 65 deletions(-) diff --git a/modules/CmpdReg/src/client/custom/configuration.json b/modules/CmpdReg/src/client/custom/configuration.json index 012bfeb9d..9dd58893c 100755 --- a/modules/CmpdReg/src/client/custom/configuration.json +++ b/modules/CmpdReg/src/client/custom/configuration.json @@ -82,60 +82,60 @@ "bulkLoadSettings": { "useProjectRoles": false, "dbProperties": [ - {"name": "CAS Number", "dataType": "string", "required": false}, - {"name": "Lot Absorbance", "dataType": "numeric", "required": false}, - {"name": "Lot Alias", "dateType": "string", "required": false}, - {"name": "Lot Amount Units", "dataType": "string", "required": false}, - {"name": "Lot Amount", "dataType": "numeric", "required": false}, - {"name": "Lot Barcode", "dataType": "string", "required": false}, - {"name": "Lot Boiling Point", "dataType": "numeric", "required": false}, - {"name": "Lot Chemist", "dataType": "string", "required": true}, - {"name": "Lot Color", "dataType": "string", "required": false}, - {"name": "Lot Comments", "dataType": "string", "required": false}, - {"name": "Lot Corp Name", "dataType": "string", "required": false}, - {"name": "Lot Is Virtual", "dataType": "boolean", "required": false}, - {"name": "Lot Lambda", "dataType": "numeric", "required": false}, - {"name": "Lot Melting Point", "dataType": "numeric", "required": false}, - {"name": "Lot Notebook Page", "dataType": "string", "required": false}, - {"name": "Lot Number", "dataType": "numeric", "required": false}, - {"name": "Lot Observed Mass #1", "dataType": "numeric", "required": false}, - {"name": "Lot Observed Mass #2", "dataType": "numeric", "required": false}, - {"name": "Lot Percent ee", "dataType": "numeric", "required": false}, - {"name": "Lot Physical State", "dataType": "string", "required": false}, - {"name": "Lot Purity Measured By", "dataType": "string", "required": false}, - {"name": "Lot Purity Operator", "dataType": "string", "required": false}, - {"name": "Lot Purity", "dataType": "numeric", "required": false}, - {"name": "Lot Retain Location", "dataType": "string", "required": false}, - {"name": "Lot Retain Units", "dataType": "string", "required": false}, - {"name": "Lot Retain", "dataType": "numeric", "required": false}, - {"name": "Lot Salt Abbrev", "dataType": "string", "required": false}, - {"name": "Lot Salt Equivalents", "dataType": "string", "required": false}, - {"name": "Lot Solution Amount Units", "dataType": "string", "required": false}, - {"name": "Lot Solution Amount", "dataType": "numeric", "required": false}, - {"name": "Lot Stock Location", "dataType": "string", "required": false}, - {"name": "Lot Stock Solvent", "dataType": "string", "required": false}, - {"name": "Lot Storage Location", "dataType": "string", "required": false}, - {"name": "Lot Supplier ID", "dataType": "string", "required": false}, - {"name": "Lot Supplier Lot", "dataType": "string", "required": false}, - {"name": "Lot Supplier", "dataType": "string", "required": false}, - {"name": "Lot Synthesis Date", "dataType": "date", "required": false}, - {"name": "Lot Tare Weight Units", "dataType": "string", "required": false}, - {"name": "Lot Tare Weight", "dataType": "numeric", "required": false}, - {"name": "Lot Total Amount Stored Units", "dataType": "string", "required": false}, - {"name": "Lot Total Amount Stored", "dataType": "numeric", "required": false}, - {"name": "Lot Vendor", "dataType": "string", "required": false}, - {"name": "Lot Vendor ID", "dataType": "string", "required": false}, - {"name": "Parent Alias", "dateType": "string", "required": false}, - {"name": "Parent Annotation", "dateType": "string", "required": false}, - {"name": "Parent Comment", "dataType": "string", "required": false}, - {"name": "Parent Common Name", "dataType": "string", "required": false}, - {"name": "Parent Compound Type", "dateType": "string", "required": false}, - {"name": "Parent Corp Name", "dataType": "string", "required": false}, - {"name": "Parent Is Mixture", "dataType": "boolean", "required": false}, - {"name": "Parent LiveDesign Corp Name", "dataType": "string", "required": false}, - {"name": "Parent Stereo Category", "dataType": "string", "required": true}, - {"name": "Parent Stereo Comment", "dataType": "string", "required": false}, - {"name": "Project", "dataType": "string", "required": false} + {"name": "CAS Number", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Absorbance", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Alias", "dateType": "string", "required": false, "ignored": false}, + {"name": "Lot Amount Units", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Amount", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Barcode", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Boiling Point", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Chemist", "dataType": "string", "required": true, "ignored": false}, + {"name": "Lot Color", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Comments", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Corp Name", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Is Virtual", "dataType": "boolean", "required": false, "ignored": false}, + {"name": "Lot Lambda", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Melting Point", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Notebook Page", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Number", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Observed Mass #1", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Observed Mass #2", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Percent ee", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Physical State", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Purity Measured By", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Purity Operator", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Purity", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Retain Location", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Retain Units", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Retain", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Salt Abbrev", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Salt Equivalents", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Solution Amount Units", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Solution Amount", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Stock Location", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Stock Solvent", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Storage Location", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Supplier ID", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Supplier Lot", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Supplier", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Synthesis Date", "dataType": "date", "required": false, "ignored": false}, + {"name": "Lot Tare Weight Units", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Tare Weight", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Total Amount Stored Units", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Total Amount Stored", "dataType": "numeric", "required": false, "ignored": false}, + {"name": "Lot Vendor", "dataType": "string", "required": false, "ignored": false}, + {"name": "Lot Vendor ID", "dataType": "string", "required": false, "ignored": false}, + {"name": "Parent Alias", "dateType": "string", "required": false, "ignored": false}, + {"name": "Parent Annotation", "dateType": "string", "required": false, "ignored": false}, + {"name": "Parent Comment", "dataType": "string", "required": false, "ignored": false}, + {"name": "Parent Common Name", "dataType": "string", "required": false, "ignored": false}, + {"name": "Parent Compound Type", "dateType": "string", "required": false, "ignored": false}, + {"name": "Parent Corp Name", "dataType": "string", "required": false, "ignored": false}, + {"name": "Parent Is Mixture", "dataType": "boolean", "required": false, "ignored": false}, + {"name": "Parent LiveDesign Corp Name", "dataType": "string", "required": false, "ignored": false}, + {"name": "Parent Stereo Category", "dataType": "string", "required": true, "ignored": false}, + {"name": "Parent Stereo Comment", "dataType": "string", "required": false, "ignored": false}, + {"name": "Project", "dataType": "string", "required": false, "ignored": false} ] } } diff --git a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee index afb2d3f9c..2d6afa6b6 100644 --- a/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee +++ b/modules/CmpdRegBulkLoader/src/client/CmpdRegBulkLoader.coffee @@ -18,6 +18,7 @@ class window.AssignedProperty extends Backbone.Model dbProperty: "none" defaultVal: "" required: false + ignored: false # validate: (attrs) => # errors = [] @@ -275,17 +276,18 @@ class window.AssignedPropertyController extends AbstractFormController formatDbSelectOptions: -> formattedOptions = new PickListList() @dbPropertiesList.each (dbProp) -> - code = dbProp.get('name') - if dbProp.get('required') - name = code+"*" - else - name = code - if code.toLowerCase().indexOf("date") > -1 - name += " (YYYY-MM-DD or MM-DD-YYYY)" - newOption = new PickList - code: code - name: name - formattedOptions.add newOption + if !dbProp.get("ignored")? || dbProp.get("ignored") != true + code = dbProp.get('name') + if dbProp.get('required') + name = code+"*" + else + name = code + if code.toLowerCase().indexOf("date") > -1 + name += " (YYYY-MM-DD or MM-DD-YYYY)" + newOption = new PickList + code: code + name: name + formattedOptions.add newOption formattedOptions handleDbPropertyChanged: -> @@ -473,6 +475,7 @@ class window.AssignSdfPropertiesController extends Backbone.View dbProperty: "none" required: false sdfProperty: sdfProperty + ignored: false @assignedPropertiesList.add newAssignedProp handleFileChanged: (newFileName) -> @@ -703,6 +706,7 @@ class window.AssignSdfPropertiesController extends Backbone.View required: true sdfProperty: null defaultVal: @project + ignored: false @assignedPropertiesListController.collection.add dbProjectProperty registerCompounds: -> From 4bdffa5728a4bcc628265f45f2aec36fcd165b2f Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Tue, 14 Jul 2020 12:34:21 -0700 Subject: [PATCH 572/576] fixes #715 add utility function to set width of text fields to the value length --- modules/Components/src/client/UtilityFunctions.coffee | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/modules/Components/src/client/UtilityFunctions.coffee b/modules/Components/src/client/UtilityFunctions.coffee index 4c5c505f2..d84e27a2f 100644 --- a/modules/Components/src/client/UtilityFunctions.coffee +++ b/modules/Components/src/client/UtilityFunctions.coffee @@ -52,6 +52,14 @@ class window.UtilityFunctions text = $(textarea).val().replace(/\r?\n/g,'
        ') $(textarea).after '
        '+text+'
        ' $(textarea).hide() + + setInputsWidthToValue: (controller) => + # increase size of text boxes to fit data + for node in controller.$('input[type="text"]') + minWidth = parseInt(getComputedStyle(node).minWidth) or node.clientWidth + node.style.overflowX = 'auto' + node.style.width = minWidth + 'px' + node.style.width = node.scrollWidth + 'px' showInactiveTabsInfoToPrint: (controller) => for tab in controller.$('.tab-pane') From aa247383eedc31f2c7eab26484edec99fb4cf65c Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 17 Jul 2020 07:22:23 -0700 Subject: [PATCH 573/576] fixes #717 upgrade to python3 --- Dockerfile | 4 +- modules/ServerAPI/src/server/Bootstrap.coffee | 2 +- .../src/server/RunPythonFunctionTestStub.py | 2 +- .../python/acas_ldclient/acasldclient.py | 20 +++--- .../src/server/python/compare_single_csv.py | 6 +- .../create_lr_for_acas.py | 70 +++++++++---------- .../src/server/python/export_live_report.py | 2 +- .../syncProjectsUsers/ld_entitlements.py | 26 +++---- .../python/syncProjectsUsers/sync_projects.py | 18 ++--- 9 files changed, 75 insertions(+), 75 deletions(-) diff --git a/Dockerfile b/Dockerfile index 2a03bb2a3..6b25a836b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -78,8 +78,8 @@ ENV ACAS_HOME=$BUILD_PATH USER root RUN curl -SLO dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm && rpm -ivh epel-release-6-8.noarch.rpm && rm epel-release-6-8.noarch.rpm RUN yum install -y centos-release-SCL -RUN yum install -y python-pip python-psycopg2 python27 -RUN source /opt/rh/python27/enable && pip install argparse requests psycopg2-binary +RUN yum install -y rh-python36-python-pip python-psycopg2 rh-python36 +RUN source /opt/rh/rh-python36/enable && pip install argparse requests psycopg2-binary USER runner EXPOSE 3000 diff --git a/modules/ServerAPI/src/server/Bootstrap.coffee b/modules/ServerAPI/src/server/Bootstrap.coffee index b20fd5a11..fcc242324 100644 --- a/modules/ServerAPI/src/server/Bootstrap.coffee +++ b/modules/ServerAPI/src/server/Bootstrap.coffee @@ -6,7 +6,7 @@ exports.main = (callback) -> config = require "#{ACAS_HOME}/conf/compiled/conf.js" if config.all.server.liveDesign.installClientOnStart? && config.all.server.liveDesign.installClientOnStart exec = require('child_process').exec - command = "pip2.7 install --upgrade --force-reinstall --user #{config.all.client.service.result.viewer.liveDesign.baseUrl}/ldclient.tar.gz" + command = "pip3.6 install --upgrade --force-reinstall --user #{config.all.client.service.result.viewer.liveDesign.baseUrl}/ldclient.tar.gz" console.log "About to call python using command: "+command child = exec command, (error, stdout, stderr) -> console.log stdout diff --git a/modules/ServerAPI/src/server/RunPythonFunctionTestStub.py b/modules/ServerAPI/src/server/RunPythonFunctionTestStub.py index 4e51d8961..a3a7bad55 100644 --- a/modules/ServerAPI/src/server/RunPythonFunctionTestStub.py +++ b/modules/ServerAPI/src/server/RunPythonFunctionTestStub.py @@ -18,7 +18,7 @@ def main(): request=args['input'] response = {"results":request, "hasError":False,"hasWarning":False,"errorMessages":[]} - print json.dumps(response) + print(json.dumps(response)) if __name__ == '__main__': main() diff --git a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py index d38c163b4..fb5c87b16 100644 --- a/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py +++ b/modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py @@ -6,6 +6,7 @@ import json import os, sys import locale +from functools import cmp_to_key def get_parser(): """ @@ -61,7 +62,7 @@ def get_parser(): return parser def list_groups(client, test): - print test + print(test) return client.list_groups() def auth_check(endpoint, username, password): @@ -107,7 +108,7 @@ def get_users(client, ls_type = None, ls_kind = None, role_name = None): # ld_users = client.list_users() ld_users = client.client.get("/users?include_permissions=false", '') if ls_type == None and ls_kind == None and role_name == None: - acas_users = map(ld_user_to_acas_user_code_table, ld_users) + acas_users = list(map(ld_user_to_acas_user_code_table, ld_users)) else: groups = client.list_groups() permissions = client.list_permissions() @@ -129,7 +130,7 @@ def get_users(client, ls_type = None, ls_kind = None, role_name = None): if u["id"] == m["user_id"]: user_projects[proj.name]["ld_users"].append(u) if ls_kind in user_projects: - acas_users = map(ld_user_to_acas_user_code_table, user_projects[ls_kind]["ld_users"]) + acas_users = list(map(ld_user_to_acas_user_code_table, user_projects[ls_kind]["ld_users"])) else: acas_users = [] return acas_users @@ -150,7 +151,7 @@ def get_users_roles(client, users): for u in users: usersDict[u["id"]] = u groups = client.list_groups() - roles = map(ld_group_to_acas_role, groups) + roles = list(map(ld_group_to_acas_role, groups)) roleDict = {} for r in roles: roleDict[r["id"]] = r @@ -158,7 +159,7 @@ def get_users_roles(client, users): for m in memberships: usersDict[m["user_id"]].append(roleDict[m["group_id"]]) users = [] - for user in usersDict.iteritems(): + for user in usersDict.items(): users.append(user) return users @@ -181,7 +182,7 @@ def get_user(client, username): else: user_projects[proj.name] = {"id":proj.id, "granting_groups": [g["name"]]} roles = [] - for proj, data in user_projects.iteritems(): + for proj, data in user_projects.items(): roles.append({ "id": data["id"], "roleEntry": { @@ -200,12 +201,11 @@ def get_user(client, username): def get_projects(client): ld_projects = client.projects() - projects = map(ld_project_to_acas, ld_projects) + projects = list(map(ld_project_to_acas, ld_projects)) # Sort by name locale.setlocale(locale.LC_ALL, '') - projects = sorted(projects, key=lambda k: k['name'], cmp=locale.strcoll) - + projects = sorted(projects, key=lambda x: locale.strxfrm(x['name'])) return projects def ld_project_to_acas(ld_project): @@ -231,7 +231,7 @@ def main(): else: result = auth_check(endpoint, *args.args) - print json.dumps(result) + print(json.dumps(result)) if __name__ == "__main__": main() diff --git a/modules/ServerAPI/src/server/python/compare_single_csv.py b/modules/ServerAPI/src/server/python/compare_single_csv.py index 9f89b23a6..452ccf210 100644 --- a/modules/ServerAPI/src/server/python/compare_single_csv.py +++ b/modules/ServerAPI/src/server/python/compare_single_csv.py @@ -32,8 +32,8 @@ def clean_diff(diffObject): from_list = from_value.split('\n') to_list = to_value.split('\n') - from_list = map(lambda x: clean_units(x), from_list) - to_list = map(lambda x: clean_units(x), to_list) + from_list = [clean_units(x) for x in from_list] + to_list = [clean_units(x) for x in to_list] if compare(from_list, to_list): changed['fields'][fieldkey] = {} if 'onschrodinger.com' in from_value and 'onschrodinger.com' in to_value: @@ -81,7 +81,7 @@ def main(): if lr_key not in diffResult: diffResult[lr_key]={} if 'removed' not in diffResult[lr_key]: diffResult[lr_key]['removed']={} diffResult[lr_key]['removed'][row_key] = row - print(json.dumps(diffResult, sort_keys=True, indent=4)) + print((json.dumps(diffResult, sort_keys=True, indent=4))) if __name__ == '__main__': main() diff --git a/modules/ServerAPI/src/server/python/createLiveDesignLiveReportForACAS/create_lr_for_acas.py b/modules/ServerAPI/src/server/python/createLiveDesignLiveReportForACAS/create_lr_for_acas.py index d4f61a431..dfd524a5e 100755 --- a/modules/ServerAPI/src/server/python/createLiveDesignLiveReportForACAS/create_lr_for_acas.py +++ b/modules/ServerAPI/src/server/python/createLiveDesignLiveReportForACAS/create_lr_for_acas.py @@ -16,7 +16,7 @@ import http.client as http_client except ImportError: # Python 2 - import httplib as http_client + import http.client as http_client http_client.HTTPConnection.debuglevel = 0 import ldclient @@ -34,7 +34,7 @@ requests.packages.urllib3.disable_warnings(SNIMissingWarning) except ImportError: #ignore error, allow warnings - print 'ignoring ImportError' + print('ignoring ImportError') def str2bool(v): if isinstance(v, bool): @@ -52,8 +52,8 @@ def make_acas_live_report(api, compound_ids, assays_to_add, experiment_code, log for folder in api.list_folders([projectId]): if int(folder.project_id) == int(projectId): folder_names[folder.name] = folder.id - if 'Autogenerated ACAS Reports' not in folder_names.keys(): - print 'Autogenerated ACAS Reports folder does not exist in this project. Creating it' + if 'Autogenerated ACAS Reports' not in list(folder_names.keys()): + print('Autogenerated ACAS Reports folder does not exist in this project. Creating it') folder = api.create_folder('Autogenerated ACAS Reports', projectId) folder_id = folder.id else: @@ -75,7 +75,7 @@ def make_acas_live_report(api, compound_ids, assays_to_add, experiment_code, log lr_id = int(lr.id) - print "Live Report ID is:" + str(lr_id) + print("Live Report ID is:" + str(lr_id)) #get the list of assay addable columns if ldClientVersion >= 7.6: assay_column_ids = [] @@ -97,7 +97,7 @@ def make_acas_live_report(api, compound_ids, assays_to_add, experiment_code, log assay_hash[assay.name][assay_type.name] = assay_type.addable_column_id assay_column_ids = [] for assay_to_add in assays_to_add: - assay_column_ids.append(assay_hash[assay_to_add['protocolName']][assay_to_add['resultType']]) + assay_column_ids.append(assay_hash[assay_to_add['protocolName']][assay_to_add['resultType']]) #assay_column_id1 = assay_hash["Peroxisome proliferator-activated receptor delta"]["EC50"] #assay_column_id2 = assay_hash["DRC TEST ASSAY"]["IC50%"] @@ -117,13 +117,13 @@ def make_acas_live_report(api, compound_ids, assays_to_add, experiment_code, log #compound search by id search_results = [] - if isinstance(compound_ids, (str,unicode)): - search_results.extend(api.compound_search_by_id(compound_ids, database_names=[database], project_id = projectId)) + if isinstance(compound_ids, str): + search_results.extend(api.compound_search_by_id(compound_ids, database_names=[database], project_id = projectId)) else: - search_string = "" - for compound_id in compound_ids: - search_string += compound_id +"\n" - search_results.extend(api.compound_search_by_id(search_string, database_names=[database], project_id = projectId)) + search_string = "" + for compound_id in compound_ids: + search_string += compound_id +"\n" + search_results.extend(api.compound_search_by_id(search_string, database_names=[database], project_id = projectId)) # Now add the rows for the compound ids for which we want data #compound_ids = ["V51411","V51412","V51413","V51414"] api.add_rows(lr_id, search_results) @@ -131,20 +131,20 @@ def make_acas_live_report(api, compound_ids, assays_to_add, experiment_code, log return lr_id def findassay(assay_tree, assay_name): - if 'name' in assay_tree and assay_tree['name'] == assay_name: return assay_tree - elif 'name' in assay_tree and assay_name in assay_tree['name'] and 'column_folder_node_type' in assay_tree and assay_tree['column_folder_node_type']=='ROLLUP': return assay_tree - for sub_tree in assay_tree['children']: - item = findassay(sub_tree, assay_name) - if item is not None: - return item - + if 'name' in assay_tree and assay_tree['name'] == assay_name: return assay_tree + elif 'name' in assay_tree and assay_name in assay_tree['name'] and 'column_folder_node_type' in assay_tree and assay_tree['column_folder_node_type']=='ROLLUP': return assay_tree + for sub_tree in assay_tree['children']: + item = findassay(sub_tree, assay_name) + if item is not None: + return item + def extract_endpoints(assay, endpoints): - #print json.dumps(assay) - if 'addable_column_ids' in assay and len(assay['addable_column_ids']) > 0: - endpoints.extend(assay['addable_column_ids']) - for sub_assay in assay['children']: - extract_endpoints(sub_assay, endpoints) - return endpoints + #print json.dumps(assay) + if 'addable_column_ids' in assay and len(assay['addable_column_ids']) > 0: + endpoints.extend(assay['addable_column_ids']) + for sub_assay in assay['children']: + extract_endpoints(sub_assay, endpoints) + return endpoints def main(): #if len(sys.argv) is not 4: @@ -172,13 +172,13 @@ def main(): assays_to_add=args['input']['assays'] experiment_code=args['input']['experimentCode'] try: - project=args['input']['project'] + project=args['input']['project'] except: - project="Global" + project="Global" try: - logged_in_user=args['input']['username'] + logged_in_user=args['input']['username'] except: - logged_in_user=username + logged_in_user=username apiSuffix = "/api" apiEndpoint = endpoint + apiSuffix; api = Api(apiEndpoint, username, password) @@ -190,20 +190,20 @@ def main(): ld_client_version=float(ldclient.api.requester.SUPPORTED_SERVER_VERSION) except: ld_client_version=float(7.3) - print "LDClient version is:"+str(ld_client_version) + print("LDClient version is:"+str(ld_client_version)) try: # projectId = api.get_project_id_by_name(project) - matching_projects = filter(lambda p: p.name == project, api.projects()) + matching_projects = [p for p in api.projects() if p.name == project] projectId = int(matching_projects[0].id.encode('ascii')) - print "Project " + project + " found with id: " + str(projectId) + print("Project " + project + " found with id: " + str(projectId)) except: - projectId = 0 + projectId = 0 if type(projectId) is not int: - projectId = 0 + projectId = 0 lr_id = make_acas_live_report(api, compound_ids, assays_to_add, experiment_code, logged_in_user, database, projectId, ld_client_version, args["readonly"]) liveReportSuffix = "/#/projects/"+str(projectId)+"/livereports/"; - print endpoint + liveReportSuffix + str(lr_id) + print(endpoint + liveReportSuffix + str(lr_id)) #return endpoint + liveReportSuffix + str(lr_id) if __name__ == '__main__': diff --git a/modules/ServerAPI/src/server/python/export_live_report.py b/modules/ServerAPI/src/server/python/export_live_report.py index 2fe1e5645..14fdbd534 100644 --- a/modules/ServerAPI/src/server/python/export_live_report.py +++ b/modules/ServerAPI/src/server/python/export_live_report.py @@ -33,7 +33,7 @@ def main(): # except: # projectId = 0 csv_dump = api.export_live_report(live_report_id, 'csv') - print csv_dump + print(csv_dump) if __name__ == '__main__': main() \ No newline at end of file diff --git a/modules/ServerAPI/src/server/python/syncProjectsUsers/ld_entitlements.py b/modules/ServerAPI/src/server/python/syncProjectsUsers/ld_entitlements.py index b6e2366fe..38d01c519 100755 --- a/modules/ServerAPI/src/server/python/syncProjectsUsers/ld_entitlements.py +++ b/modules/ServerAPI/src/server/python/syncProjectsUsers/ld_entitlements.py @@ -92,7 +92,7 @@ def reverse_mapping(m): """ Reverse a mapping (ignoring duplicate keys) """ - return dict((v, k) for k, v in m.iteritems()) + return dict((v, k) for k, v in m.items()) def retrieve_raw_model(config, session): @@ -108,7 +108,7 @@ def retrieve_raw_model(config, session): } ret = {} - for endpoint, dest in get_targets.iteritems(): + for endpoint, dest in get_targets.items(): url = config['ld_url'] + API + endpoint response = session.get(url) response.raise_for_status() @@ -167,7 +167,7 @@ def resolve_project_selector(model, model_projects_by_name, import_project): if predicate: ret = [] # pattern has a beginning or end wildcard - for pid, name in model['projects'].iteritems(): + for pid, name in model['projects'].items(): if predicate(name, pattern): ret.append(pid) if len(ret) > 0: @@ -183,7 +183,7 @@ def compute_changes(model, import_data): # Have to treat this specially since multiple projects might have same name projects_by_name = {} - for id, name in model['projects'].iteritems(): + for id, name in model['projects'].items(): projects_by_name[name] = projects_by_name.get(name, []) projects_by_name[name].append(id) @@ -199,7 +199,7 @@ def compute_changes(model, import_data): permissions_to_create_by_name = set() # set of (pid, group name) tuples permissions_to_remove = set() # set of (pid, gid) tuples - for group, members in import_data['groups'].iteritems(): + for group, members in import_data['groups'].items(): # Check if the group already exists in the model. if group not in groups_by_name: assert group not in groups_to_create @@ -305,7 +305,7 @@ def apply_changes(config, session, model, changes): projects_by_name = reverse_mapping(model['projects']) url = config['ld_url'] + API + 'groups' - for group, members in changes['create_groups'].iteritems(): + for group, members in changes['create_groups'].items(): data = { 'name': group } response = session.post(url, data=json.dumps(data)) response.raise_for_status() @@ -380,27 +380,27 @@ def main(argv): raw_model = retrieve_raw_model(config, session) model = crunch_model(raw_model) - print 'Current user model:' + print('Current user model:') pprint.pprint(model) - print + print() changes = compute_changes(model, import_data) - print 'Changes to make:' + print('Changes to make:') pprint.pprint(changes) if opts.dry_run: - print '\nExiting, as this is a dry run.' + print('\nExiting, as this is a dry run.') return 0 # Check to see if the current run is a no-op. has_changes = False - for obj in changes.values(): + for obj in list(changes.values()): if len(obj) > 0: has_changes = True break if not has_changes: - print '\nExiting, as no changes need to be made.' + print('\nExiting, as no changes need to be made.') return 0 # Back the current model, import data and proposed changes (for forensics) @@ -429,7 +429,7 @@ def serialize_sets(obj): json.dump(import_data, fp) apply_changes(config, session, model, changes) - print '\nAll changes applied successfully' + print('\nAll changes applied successfully') return 0 diff --git a/modules/ServerAPI/src/server/python/syncProjectsUsers/sync_projects.py b/modules/ServerAPI/src/server/python/syncProjectsUsers/sync_projects.py index 652ef4dec..1e162a000 100644 --- a/modules/ServerAPI/src/server/python/syncProjectsUsers/sync_projects.py +++ b/modules/ServerAPI/src/server/python/syncProjectsUsers/sync_projects.py @@ -2,7 +2,7 @@ import pprint import psycopg2 import threading -import ConfigParser +import configparser class SyncProjectsController: def __init__(self, config_json, projects_json): @@ -22,7 +22,7 @@ def __init__(self, config_json, projects_json): self.projects = json.loads(projects_json) def check_projects_exist(self): - print "Checking for projects:" + print("Checking for projects:") check_project_exists_sql = "SELECT * FROM syn_project WHERE alternate_id = %s;" self.new_projects=[] self.projects_to_update=[] @@ -34,18 +34,18 @@ def check_projects_exist(self): project_check_results=cur.fetchall() self.lock.release() if len(project_check_results)>0: - print "Project "+project['name']+" exists." + print("Project "+project['name']+" exists.") found_project = project_check_results[0] if project['active'] != found_project[1] or project['is_restricted'] != found_project[6] or project['name'] != found_project[4]: self.projects_to_update.append(project) else: - print "Project "+project['name']+" does not exist." + print("Project "+project['name']+" does not exist.") self.new_projects.append(project) return def add_new_projects(self): if len(self.new_projects) > 0: - print "Adding projects:" + print("Adding projects:") add_project_sql = "INSERT INTO syn_project (project_id, active, alternate_id, is_restricted, project_desc, project_name) VALUES(nextval('syn_project_project_id_seq'), %s, %s, %s, %s, %s) returning *;" for project in self.new_projects: self.lock.acquire() @@ -56,12 +56,12 @@ def add_new_projects(self): self.livedesign_db_conn.commit() self.lock.release() cur.close() - print add_project_results + print(add_project_results) return def update_projects(self): if len(self.projects_to_update) > 0: - print "Updating projects:" + print("Updating projects:") update_project_sql = "UPDATE syn_project SET active = %s , is_restricted = %s, project_name = %s where alternate_id = %s returning *;" for project in self.projects_to_update: self.lock.acquire() @@ -72,7 +72,7 @@ def update_projects(self): self.livedesign_db_conn.commit() self.lock.release() cur.close() - print update_project_results + print(update_project_results) return if __name__ == '__main__': @@ -81,7 +81,7 @@ def update_projects(self): sync_projects_controller.check_projects_exist() sync_projects_controller.add_new_projects() sync_projects_controller.update_projects() - print "successfully updated projects" + print("successfully updated projects") #reset_projects_sequence_sql = "psql -h 127.0.0.1 -p 3247 -U postgres -d synaptic -c \"select setval('syn_project_id_seq', (select max(project_id)+1 from syn_project));\"" #psql -h 127.0.0.1 -p 3247 -U postgres -d synaptic -c "INSERT INTO syn_project (active, alternate_id, is_restricted, project_desc, project_name) VALUES ('Y', 'Project Alias', 0, 'Description (optional)','Project name') returning *" From da74811c2c9f9b3cf5a6e634240767403b6f6990 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 17 Jul 2020 08:14:06 -0700 Subject: [PATCH 574/576] fixes #713 lock down mkdirp to older version. Newer version broke jquery middleware. --- package.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/package.json b/package.json index 80d6d619c..1af94f56b 100644 --- a/package.json +++ b/package.json @@ -70,7 +70,8 @@ "webshot": "0.18.0", "winston": "2.3.1", "winston-mongodb": "2.0.10", - "yamljs": "0.3.0" + "yamljs": "0.3.0", + "mkdirp": "0.5.1" }, "devDependencies": { "coffee-script": "^1.12.4", From 2eaa7c2ce6dd9baf98a6fad2e708d9b0d0995d18 Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Fri, 17 Jul 2020 11:53:56 -0700 Subject: [PATCH 575/576] fixes #717 missed checkin of setenv.sh file --- bin/setenv.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/setenv.sh b/bin/setenv.sh index ee229d54b..231deb25b 100644 --- a/bin/setenv.sh +++ b/bin/setenv.sh @@ -1,3 +1,3 @@ # Example: #export LD_LIBRARY_PATH=/usr/lib/oracle/11.2/client64/lib:$LD_LIBRARY_PATH -if [ -e "/opt/rh/python27/enable" ]; then source /opt/rh/python27/enable; fi; \ No newline at end of file +if [ -e "/opt/rh/rh-python36/enable" ]; then source /opt/rh/rh-python36/enable; fi; \ No newline at end of file From 6662c7810aec75507f489377046da84af693ce4d Mon Sep 17 00:00:00 2001 From: Brian Bolt Date: Thu, 3 Dec 2020 12:34:20 -0800 Subject: [PATCH 576/576] update to centos8 in base image --- Dockerfile | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/Dockerfile b/Dockerfile index 6b25a836b..7cd1892da 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,13 +1,13 @@ -FROM centos:centos6 +FROM centos:centos8 # Update RUN \ - yum update -y && \ - yum upgrade -y && \ + dnf update -y && \ + dnf upgrade -y && \ # tar for pulling down node # git required for some npm packages - yum install -y tar git && \ - yum install -y fontconfig urw-fonts && \ - yum clean all + dnf install -y tar git && \ + dnf install -y fontconfig urw-fonts && \ + dnf clean all # node RUN set -ex \ @@ -56,7 +56,7 @@ USER runner WORKDIR $ACAS_BASE # This installs the modules but not acas, doing this makes subsequent builds much faster so that the container isn't invalidated on a small code change RUN npm install --ignore-scripts --loglevel warn -COPY . $ACAS_BASE +COPY --chown=runner:runner . $ACAS_BASE USER root RUN chown -R runner:runner $ACAS_BASE USER runner @@ -73,15 +73,17 @@ ENV PREPARE_MODULE_CONF_JSON=true ENV PREPARE_CONFIG_FILES=true ENV RUN_SYSTEM_TEST=true ENV ACAS_HOME=$BUILD_PATH +RUN gulp execute:prepare_config_files #Install python dependencies USER root -RUN curl -SLO dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm && rpm -ivh epel-release-6-8.noarch.rpm && rm epel-release-6-8.noarch.rpm -RUN yum install -y centos-release-SCL -RUN yum install -y rh-python36-python-pip python-psycopg2 rh-python36 -RUN source /opt/rh/rh-python36/enable && pip install argparse requests psycopg2-binary +RUN dnf install -y python36 python3-pip +RUN alternatives --set python /usr/bin/python3 +RUN alternatives --install /usr/bin/pip pip /usr/bin/pip3 1 +RUN pip install argparse requests psycopg2-binary +RUN dnf install -y initscripts + USER runner EXPOSE 3000 - CMD ["/bin/sh","bin/acas.sh", "run"]