diff --git a/app_api_template.coffee b/app_api_template.coffee
index f770f5630..f188ed1c7 100644
--- a/app_api_template.coffee
+++ b/app_api_template.coffee
@@ -54,8 +54,7 @@ startApp = ->
console.error 'Caught api exception: ' + err.stack
return
- ###TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES###
-
+ #TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES
http.createServer(app).listen(app.get('port'), ->
console.log("ACAS API server listening on port " + app.get('port'))
diff --git a/app_template.coffee b/app_template.coffee
index ae919f224..01b924bc9 100644
--- a/app_template.coffee
+++ b/app_template.coffee
@@ -15,6 +15,7 @@ startApp = ->
logger = require('morgan')
methodOverride = require('method-override')
session = require('express-session')
+ MemoryStore = require('memorystore')(session)
bodyParser = require('body-parser')
# multer = require('multer')
errorHandler = require('errorhandler')
@@ -71,7 +72,7 @@ startApp = ->
# next()
loginRoutes = require './routes/loginRoutes'
-
+ sessionStore = new MemoryStore();
global.app = express()
app.set 'port', config.all.client.port
app.set 'views', __dirname + '/views'
@@ -85,10 +86,12 @@ startApp = ->
app.use 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
-# app.use express.bodyParser()
+ # app.use express.bodyParser()
app.use(bodyParser.json({limit: '100mb'}))
app.use(bodyParser.urlencoded({limit: '100mb', extended: true,parameterLimit: 1000000}))
# app.use(multer())
@@ -102,8 +105,8 @@ startApp = ->
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 server listening on port " + app.get('port'))
)
else
console.log "------ Starting in SSL Mode"
@@ -115,12 +118,23 @@ startApp = ->
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'), ->
- console.log("Express server listening on port " + app.get('port'))
+ console.log("ACAS 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"
- ###TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES###
+ io = require('socket.io')(httpServer)
+ 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/ACASLabelSequences/src/client/ACASLabelSequences.coffee b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee
index cf68cf9ec..d7e07a44a 100644
--- a/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee
+++ b/modules/ACASLabelSequences/src/client/ACASLabelSequences.coffee
@@ -210,7 +210,8 @@ class window.ACASLabelSequenceController extends AbstractFormController
"click .bv_save": "handleSaveClicked"
"click .bv_cancel": "handleCancelClicked"
- initialize: ->
+ initialize: (options) ->
+ @options = options
if @model?
@completeInitialization()
else
diff --git a/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee b/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee
index 9333eab00..fa0c89281 100644
--- a/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee
+++ b/modules/ACASLabelSequences/src/server/routes/ACASLabelSequencesRoutes.coffee
@@ -1,6 +1,5 @@
exports.setupAPIRoutes = (app) ->
app.get '/api/labelSequences', exports.getAllLabelSequences
- app.get '/api/labelSequences/reagents/codename', exports.getReagentByCodename
app.post '/api/labelSequences/jsonArray', exports.saveLabelSequenceArray
exports.setupRoutes = (app, loginRoutes) ->
diff --git a/modules/AdminPanel/src/client/AdminPanel.coffee b/modules/AdminPanel/src/client/AdminPanel.coffee
index 6956305e2..986aeee9e 100644
--- a/modules/AdminPanel/src/client/AdminPanel.coffee
+++ b/modules/AdminPanel/src/client/AdminPanel.coffee
@@ -45,11 +45,11 @@ class window.AdminPanelController extends AbstractFormController
recursivelyIterateAndDisplayValues = (dict) ->
keys = Object.keys dict
_.each(keys, (key) ->
- if isObject dict[key]
- recursivelyIterateAndDisplayValues dict[key]
- else
- unless typeof dict[key] is "object"
- @$('.bv_configProperties').append("" + key + ": " + dict[key] + "
")
+ if isObject dict[key]
+ recursivelyIterateAndDisplayValues dict[key]
+ else
+ unless typeof dict[key] is "object"
+ @$('.bv_configProperties').append("" + key + ": " + dict[key] + "
")
)
#TODO add full paths - Matt
diff --git a/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee b/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee
index 64c3c8af7..82aad2912 100644
--- a/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee
+++ b/modules/BuildUtilities/src/server/PrepareModuleIncludes.coffee
@@ -121,6 +121,6 @@ prepRouteIncludes = (apiMode) ->
routeLines
routeLines = prepRouteIncludes(false)
-insertToLayoutTemplate " /*TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES */", routeLines, "#{ACAS_HOME}/app_template.js", "#{ACAS_HOME}/app.js"
+insertToLayoutTemplate "//TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES", routeLines, "#{ACAS_HOME}/app_template.js", "#{ACAS_HOME}/app.js"
routeLines = prepRouteIncludes(true)
-insertToLayoutTemplate " /*TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES */", routeLines, "#{ACAS_HOME}/app_api_template.js", "#{ACAS_HOME}/app_api.js"
+insertToLayoutTemplate "//TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES", routeLines, "#{ACAS_HOME}/app_api_template.js", "#{ACAS_HOME}/app_api.js"
diff --git a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee
index e00c913b2..5d54308e6 100644
--- a/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee
+++ b/modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee
@@ -1,5 +1,4 @@
exports.setupAPIRoutes = (app) ->
- app.post '/api/cmpdReg', exports.postAssignedProperties
app.get '/cmpdReg/scientists', exports.getScientists
app.get '/cmpdReg/metalots/corpName/[\\S]*', exports.getMetaLot
app.post '/cmpdReg/metalots', exports.metaLots
diff --git a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee
index bcd18b0de..a73e3eeaf 100644
--- a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee
+++ b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdmin.coffee
@@ -18,7 +18,8 @@ class window.AbstractCmpdRegAdminController extends AbstractFormController
"click .bv_cancelClear": "handleCancelClearClicked"
"click .bv_confirmClear": "handleConfirmClearClicked"
- initialize: ->
+ initialize: (options) ->
+ @options = options
console.log "initializing Abstract Controller"
if @model?
@completeInitialization()
diff --git a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee
index 56b3474ba..0304b5c52 100644
--- a/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee
+++ b/modules/CmpdRegAdmin/src/client/AbstractCmpdRegAdminBrowser.coffee
@@ -19,7 +19,8 @@ class window.CmpdRegAdminSimpleSearchController extends AbstractFormController
Instantiating controller must provide urlRoot and toDisplay in options
###
- initialize: ->
+ initialize: (options) ->
+ @options = options
@searchUrl = ""
@searchUrl = @options.urlRoot + '/search/'
diff --git a/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee b/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee
index 8263a4cae..c83d0afe0 100644
--- a/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee
+++ b/modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee
@@ -1,7 +1,6 @@
path = require 'path'
-exports.setupAPIRoutes = (app) ->
- app.post '/api/cmpdRegBulkLoader', exports.postAssignedProperties
+exports.setupAPIRoutes = (app, loginRoutes) ->
app.post '/api/cmpdRegBulkLoader/registerCmpds', exports.registerCmpds
app.post '/api/cmpdRegBulkLoader/validateCmpds', exports.validateCmpds
app.post '/api/cmpdRegBulkLoader/validationProperties', exports.validationProperties
@@ -17,7 +16,6 @@ exports.setupRoutes = (app, loginRoutes) ->
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
diff --git a/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdmin.coffee b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdmin.coffee
index 517c09d60..0b3e35db4 100644
--- a/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdmin.coffee
+++ b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdmin.coffee
@@ -25,7 +25,8 @@ class window.AbstractCodeTablesAdminController extends AbstractFormController
"click .bv_cancelClear": "handleCancelClearClicked"
"click .bv_confirmClear": "handleConfirmClearClicked"
- initialize: ->
+ initialize: (options) ->
+ @options = options
console.log "initializing Abstract Controller"
if @model?
@completeInitialization()
diff --git a/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminBrowser.coffee b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminBrowser.coffee
index cc5dfa18a..0b356ba60 100644
--- a/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminBrowser.coffee
+++ b/modules/CodeTablesAdmin/src/client/AbstractCodeTablesAdminBrowser.coffee
@@ -21,7 +21,8 @@ class window.CodeTablesAdminSimpleSearchController extends AbstractFormControlle
Instantiating controller must provide urlRoot and toDisplay in options
###
- initialize: ->
+ initialize: (options) ->
+ @options = options
@searchUrl = ""
@searchUrl = @options.urlRoot + '/search/'
@@ -111,7 +112,8 @@ class window.CodeTablesAdminRowSummaryController extends Backbone.View
############################################################################
class window.CodeTablesAdminSummaryTableController extends Backbone.View
- initialize: ->
+ initialize: (options) ->
+ @options = options
if @options.showIgnore?
@showIgnore = @options.showIgnore
else
diff --git a/modules/Components/src/client/ACASFormChemicalStructure.coffee b/modules/Components/src/client/ACASFormChemicalStructure.coffee
index 70f857464..58a15f25e 100644
--- a/modules/Components/src/client/ACASFormChemicalStructure.coffee
+++ b/modules/Components/src/client/ACASFormChemicalStructure.coffee
@@ -68,6 +68,9 @@ class window.ACASFormChemicalStructureController extends Backbone.View
tagName: "DIV"
template: _.template($("#ACASFormChemicalStructureControllerView").html())
+ initialize: (options) ->
+ @options = options
+
render: =>
$(@el).empty()
$(@el).html @template()
diff --git a/modules/Components/src/client/ACASFormFields.coffee b/modules/Components/src/client/ACASFormFields.coffee
index 3606f3a61..bb65cdc5f 100644
--- a/modules/Components/src/client/ACASFormFields.coffee
+++ b/modules/Components/src/client/ACASFormFields.coffee
@@ -28,7 +28,8 @@ class window.ACASFormAbstractFieldController extends Backbone.View
"mouseover .label-tooltip": "handleToolTipMouseover"
"mouseoff .label-tooltip": "handleToolTipMouseoff"
- initialize: ->
+ initialize: (options) ->
+ @options = options
@modelKey = @options.modelKey
@thingRef = @options.thingRef
@errorSet = false
@@ -331,7 +332,7 @@ class window.ACASFormLSCodeValueFieldController extends ACASFormAbstractFieldCon
Do whatever else is required or optional in ACASFormAbstractFieldController
###
events: ->
- _.extend {}, super,
+ _.extend {}, super(),
"change select": "handleInputChanged"
template: _.template($("#ACASFormLSCodeValueFieldView").html())
@@ -437,9 +438,11 @@ class window.ACASFormLSThingInteractionFieldController extends ACASFormAbstractF
Do whatever else is required or optional in ACASFormAbstractFieldController
###
events: ->
- _.extend {}, super,
+ _.extend {}, super(),
"change select": "handleInputChanged"
+ initialize: (options) ->
+ @options = options
template: _.template($("#ACASFormLSThingInteractionFieldView").html())
applyOptions: ->
@@ -642,7 +645,7 @@ class window.ACASFormLSDateValueFieldController extends ACASFormAbstractFieldCon
template: _.template($("#ACASFormLSDateValueFieldView").html())
events: ->
- _.extend {}, super,
+ _.extend {}, super(),
"change input": "handleInputChanged"
"click .bv_dateIcon": "handleDateIconClicked"
@@ -693,7 +696,7 @@ class window.ACASFormLSFileValueFieldController extends ACASFormAbstractFieldCon
template: _.template($("#ACASFormLSFileValueFieldView").html())
events: ->
- _.extend {}, super,
+ _.extend {}, super(),
"click .bv_deleteSavedFile": "handleDeleteSavedFile"
applyOptions: ->
diff --git a/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee
index bbde5a18d..19d6bb1b9 100644
--- a/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee
+++ b/modules/Components/src/client/ACASFormMultiCodeValueCheckbox.coffee
@@ -8,7 +8,8 @@ class window.ACASFormCodeValueCheckboxController extends ACASFormAbstractFieldCo
events: ->
"change input": "handleInputChanged"
- initialize: ->
+ initialize: (options) ->
+ @options = options
@stateRef = @options.stateRef
@thingRef = @options.thingRef
@keyBase = @options.keyBase
diff --git a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee
index e97be7080..ca37f2c26 100644
--- a/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee
+++ b/modules/Components/src/client/ACASFormStateDisplayUpdate.coffee
@@ -7,6 +7,9 @@
class window.ACASFormStateDisplayUpdateHeaderRowController extends Backbone.View
tagName: 'tr'
+ initialize: (options) ->
+ @options = options
+
render: =>
for val in @options.tableDef.values
displayName = val.fieldSettings.formLabel
@@ -23,6 +26,9 @@ class window.ACASFormStateDisplayUpdateCellController extends Backbone.View
events: ->
"click": "handleCellClicked"
+ initialize: (options) ->
+ @options = options
+
render: =>
$(@el).empty()
if @collection.length == 0
@@ -52,6 +58,9 @@ class window.ACASFormStateDisplayUpdateCellController extends Backbone.View
class window.ACASFormStateDisplayUpdateRowController extends Backbone.View
tagName: 'tr'
+ initialize: (options) ->
+ @options = options
+
render: =>
for valDef in @options.tableDef.values
vals = @collection.where lsKind: valDef.modelDefaults.kind
@@ -69,7 +78,8 @@ class window.ACASFormStateDisplayUpdateController extends Backbone.View
rowNumberKind: 'row number'
template: _.template($("#ACASFormStateDisplayUpdateView").html())
- initialize: ->
+ initialize: (options) ->
+ @options = options
@thingRef = @options.thingRef
@tableDef = @options.tableDef
@tableSetupComplete = false
@@ -218,6 +228,9 @@ class window.ACASFormStateDisplayOldValueController extends Backbone.View
tagName: 'tr'
template: _.template($("#ACASFormStateDisplayOldValueView").html())
+ initialize: (options) ->
+ @options = options
+
render: =>
value = @model.get(@model.get('lsType'))
if @options.valueDef.displayOverride?
@@ -258,7 +271,8 @@ class window.ACASFormStateDisplayValueEditController extends Backbone.View
"click .bv_cancelBtn": "handleCancelClicked"
"click .bv_saveBtn": "handleSaveClicked"
- initialize: ->
+ initialize: (options) ->
+ @options = options
@tableDef = @options.tableDef
for valDef in @tableDef.values
if valDef.modelDefaults.kind == @collection.at(0).get('lsKind')
diff --git a/modules/Components/src/client/ACASFormStateTable.coffee b/modules/Components/src/client/ACASFormStateTable.coffee
index 7f15e9108..61df6849f 100644
--- a/modules/Components/src/client/ACASFormStateTable.coffee
+++ b/modules/Components/src/client/ACASFormStateTable.coffee
@@ -223,7 +223,7 @@ class window.ACASFormStateTableController extends Backbone.View
columns: @colDefs
search: @tableDef.search
currentRowClassName: 'bv_stateDisplayCurrentRow',
- currentColClassName: 'bv_stateDisplayCurrentColumn'
+ currentColClassName: 'bv_stateDisplayCurrentColumn'
cells: (row, col, prop) =>
cellProperties = {}
if @tableReadOnly
diff --git a/modules/Components/src/client/LSErrorNotification.coffee b/modules/Components/src/client/LSErrorNotification.coffee
index de6b77b30..ca8b28aa5 100644
--- a/modules/Components/src/client/LSErrorNotification.coffee
+++ b/modules/Components/src/client/LSErrorNotification.coffee
@@ -15,7 +15,8 @@ class window.LSAbstractNotificationCounterController extends Backbone.View
container: null
notificationsList: null
- initialize: ->
+ initialize: (options) ->
+ @options = options
_.bindAll(@,
'render')
@notificationsList = @.options.notificationsList
@@ -66,7 +67,8 @@ class window.LSErrorController extends Backbone.View
notificationsList: null
badgeEl: null
- initialize: ->
+ initialize: (options) ->
+ @options = options
_.bindAll(@,
'render')
@notificationsList = @.options.notificationsList
@@ -88,7 +90,8 @@ class window.LSWarningController extends Backbone.View
notificationsList: null
badgeEl: null
- initialize: ->
+ initialize: (options) ->
+ @options = options
_.bindAll(@,
'render')
@notificationsList = @.options.notificationsList
@@ -110,7 +113,8 @@ class window.LSInfoController extends Backbone.View
notificationsList: null
badgeEl: null
- initialize: ->
+ initialize: (options) ->
+ @options = options
_.bindAll(@,
'render')
@notificationsList = @.options.notificationsList
@@ -139,7 +143,8 @@ class window.LSNotificationController extends Backbone.View
events:
'click .bv_notificationCountContainer': 'toggleShowNotificationMessages'
- initialize: ->
+ initialize: (options) ->
+ @options = options
_.bindAll(@,
'render',
'addError',
diff --git a/modules/Components/src/client/LSFileChooser.coffee b/modules/Components/src/client/LSFileChooser.coffee
index c289b4946..2504660e5 100644
--- a/modules/Components/src/client/LSFileChooser.coffee
+++ b/modules/Components/src/client/LSFileChooser.coffee
@@ -28,7 +28,8 @@ class window.LSFileChooserController extends Backbone.View
requiresValidation: true
hideDelete: false #for hiding delete button after successful file upload
- initialize: ->
+ initialize: (options) ->
+ @options = options
_.bindAll(@,
'render',
'handleDragOverDocument',
diff --git a/modules/Components/src/client/LSFileInput.coffee b/modules/Components/src/client/LSFileInput.coffee
index cbee38724..ba327376f 100644
--- a/modules/Components/src/client/LSFileInput.coffee
+++ b/modules/Components/src/client/LSFileInput.coffee
@@ -12,7 +12,8 @@ class window.LSFileInputController extends Backbone.View
allowedFileTypes: ['xls', 'rtf', 'pdf', 'txt', 'csv', 'sdf', 'xlsx', 'doc', 'docx', 'png', 'gif', 'jpg']
- initialize: ->
+ initialize: (options) ->
+ @options = options
_.bindAll(@,
'render',
'handleFileChooserUploadComplete',
diff --git a/modules/CurveAnalysis/src/client/CurveCurator.coffee b/modules/CurveAnalysis/src/client/CurveCurator.coffee
index cf74ab694..3a80aab88 100644
--- a/modules/CurveAnalysis/src/client/CurveCurator.coffee
+++ b/modules/CurveAnalysis/src/client/CurveCurator.coffee
@@ -313,9 +313,9 @@ class window.DoseResponsePlotController extends AbstractFormController
selection = brd.elementsByName.selection
selection.update()
selectionCoords = [selection.vertices[0].coords.usrCoords,
- selection.vertices[1].coords.usrCoords,
- selection.vertices[2].coords.usrCoords,
- selection.vertices[3].coords.usrCoords]
+ selection.vertices[1].coords.usrCoords,
+ selection.vertices[2].coords.usrCoords,
+ selection.vertices[3].coords.usrCoords]
#Sort by response desc (south is on the top)
sorted = _.sortBy selection.vertices.slice(0,4), (vertex) -> vertex.coords.usrCoords[2]
#Sort north and south by response (order will then be 0 = west 1 = east)
diff --git a/modules/Logging/src/server/ConsoleLogWinstonOverride.coffee b/modules/Logging/src/server/ConsoleLogWinstonOverride.coffee
index de790695d..db8ee7eac 100644
--- a/modules/Logging/src/server/ConsoleLogWinstonOverride.coffee
+++ b/modules/Logging/src/server/ConsoleLogWinstonOverride.coffee
@@ -1,7 +1,7 @@
ACAS_HOME="../../.."
util = require('util')
winston = require('winston')
-logger = new (winston.Logger)
+logger = winston.createLogger({})
config = require "#{ACAS_HOME}/conf/compiled/conf.js"
shouldWarn = false
@@ -9,7 +9,7 @@ warningMessage = ""
if config.all.server.log?.level?
logLevel = config.all.server.log.level.toLowerCase()
- allowedLevels = Object.keys(winston.levels)
+ allowedLevels = Object.keys(winston.config.syslog)
if logLevel not in allowedLevels
shouldWarn = true
warningMessage = "log level '#{logLevel}' not in #{"'"+allowedLevels.join("','")+"'"}, setting to 'info'"
@@ -23,7 +23,7 @@ else
formatArgs = (args) ->
[ util.format.apply(util.format, Array::slice.call(args)) ]
-logger.add winston.transports.Console,
+logger.add new winston.transports.Console
colorize: true
timestamp: true
level: logLevel
diff --git a/modules/Logging/src/server/routes/Logger.coffee b/modules/Logging/src/server/routes/Logger.coffee
index dbf03c626..f41d3c5df 100644
--- a/modules/Logging/src/server/routes/Logger.coffee
+++ b/modules/Logging/src/server/routes/Logger.coffee
@@ -9,9 +9,9 @@ if config.all.logging.usemongo
db = require("mongojs").connect(config.all.logging.database, ["logs"])
db.createCollection("logs")
winstonLoggingOptions = {db: config.all.logging.database}
- winston.add(winston.transports.MongoDB, winstonLoggingOptions)
+ winston.add(new winston.transports.MongoDB(winstonLoggingOptions))
else
- winston.add(winston.transports.File, { filename: 'acas.log', json: false } )
+ winston.add(new winston.transports.File({ filename: 'acas.log', json: false } ))
exports.writeToLog = (logLevel, application, action, data, user, transactionId) ->
diff --git a/modules/ModuleMenus/spec/ModuleLauncherSpec.coffee b/modules/ModuleMenus/spec/ModuleLauncherSpec.coffee
index b8ef8e32b..01f16e46f 100644
--- a/modules/ModuleMenus/spec/ModuleLauncherSpec.coffee
+++ b/modules/ModuleMenus/spec/ModuleLauncherSpec.coffee
@@ -43,7 +43,7 @@ describe "Module Menu System Testing", ->
expect(@gotTrigger).toBeTruthy()
##########################################
- describe "Module Launcher List Testing", ->
+ describe "Module Launcher List Testing", ->
beforeEach ->
@modLauncherList = new ModuleLauncherList(window.moduleMenusTestJSON.testMenuItems)
diff --git a/modules/ModuleMenus/src/client/ModuleMenus.coffee b/modules/ModuleMenus/src/client/ModuleMenus.coffee
index e0f3d2804..97a9e8965 100644
--- a/modules/ModuleMenus/src/client/ModuleMenus.coffee
+++ b/modules/ModuleMenus/src/client/ModuleMenus.coffee
@@ -8,8 +8,9 @@ class window.ModuleMenusController extends Backbone.View
'change .bv_fastUserSelect': 'handleLoginUserChange'
# 'click .bv_showModuleMenuControl': "handleShowMenus"
- initialize: ->
window.onbeforeunload = @handleBeforeUnload
+ initialize: (options) ->
+ @options = options
$(@el).html @template()
if window.conf.moduleMenus.menuConfigurationSettings?
diff --git a/modules/ServerAPI/spec/testFixtures/EntityPropertyDescriptorsServiceTestJSON.coffee b/modules/ServerAPI/spec/testFixtures/EntityPropertyDescriptorsServiceTestJSON.coffee
index 0532eb245..69a94a237 100644
--- a/modules/ServerAPI/spec/testFixtures/EntityPropertyDescriptorsServiceTestJSON.coffee
+++ b/modules/ServerAPI/spec/testFixtures/EntityPropertyDescriptorsServiceTestJSON.coffee
@@ -12,204 +12,204 @@
}
},
{
- 'valueDescriptor': {
- 'name': 'FORMULA',
- 'prettyName': 'Molecular Formula',
- 'description': 'Property for Molecular Formula Calculation',
- 'valueType': { 'name': 'STRING' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'MONOISOTOPIC_MASS',
- 'prettyName': 'Monoisotopic Mass',
- 'description': 'Property for Monoisotopic Mass Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'ELEMENTAL_COMPOSITION',
- 'prettyName': 'Elemental Composition',
- 'description': 'Property for Elemental Composition Calculation',
- 'valueType': { 'name': 'STRING' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'CLOGP',
- 'prettyName': 'ClogP',
- 'description': 'Property for ClogP Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'LOGD_7_4',
- 'prettyName': 'logD (7.4)',
- 'description': 'Property for logD (7.4) Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'TPSA_7_4',
- 'prettyName': 'TPSA (7.4)',
- 'description': 'Property for TPSA (7.4) Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'CHARGE_7_4',
- 'prettyName': 'Charge (7.4)',
- 'description': 'Property for Charge (7.4) Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'PKA_ACID_1',
- 'prettyName': 'Strongest Acidic pKa',
- 'description': 'Property for Strongest Acidic pKa Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'PKA_ACID_2',
- 'prettyName': 'Second Strongest Acidic pKa',
- 'description': 'Property for Second Strongest Acidic pKa Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'PKA_BASE_1',
- 'prettyName': 'Strongest Basic pKa',
- 'description': 'Property for Strongest Basic pKa Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'PKA_BASE_2',
- 'prettyName': 'Second Strongest Basic pKa',
- 'description': 'Property for Second Strongest Basic pKa Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'HBA_ATOM_COUNT_PARENT',
- 'prettyName': 'HBA atoms (parent)',
- 'description': 'Property for HBA atoms (parent) Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'HBA_ATOM_COUNT_7_4',
- 'prettyName': 'HBA atoms (7.4)',
- 'description': 'Property for HBA atoms (7.4) Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'HBD_COUNT_PARENT',
- 'prettyName': 'HBDs (parent)',
- 'description': 'Property for HBDs (parent) Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'HBD_COUNT_7_4',
- 'prettyName': 'HBDs (7.4)',
- 'description': 'Property for HBDs (7.4) Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'ROTATABLE_BOND_COUNT',
- 'prettyName': 'Rotatable Bonds',
- 'description': 'Property for Rotatable Bonds Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'N_COUNT',
- 'prettyName': 'N count',
- 'description': 'Property for N count Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'O_COUNT',
- 'prettyName': 'O count',
- 'description': 'Property for O count Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'N_O_COUNT',
- 'prettyName': 'N+O count',
- 'description': 'Property for N+O count Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'HEAVY_ATOM_COUNT',
- 'prettyName': 'Heavy Atom count',
- 'description': 'Property for Heavy Atom count Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'SMILES',
- 'prettyName': 'SMILES',
- 'description': 'Property for SMILES Calculation',
- 'valueType': { 'name': 'SMILES' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'IUPAC',
- 'prettyName': 'IUPAC Name',
- 'description': 'Property for IUPAC Name Calculation',
- 'valueType': { 'name': 'STRING' },
- 'multivalued': false,
- }
- }
- ]
+ 'valueDescriptor': {
+ 'name': 'FORMULA',
+ 'prettyName': 'Molecular Formula',
+ 'description': 'Property for Molecular Formula Calculation',
+ 'valueType': { 'name': 'STRING' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'MONOISOTOPIC_MASS',
+ 'prettyName': 'Monoisotopic Mass',
+ 'description': 'Property for Monoisotopic Mass Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'ELEMENTAL_COMPOSITION',
+ 'prettyName': 'Elemental Composition',
+ 'description': 'Property for Elemental Composition Calculation',
+ 'valueType': { 'name': 'STRING' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'CLOGP',
+ 'prettyName': 'ClogP',
+ 'description': 'Property for ClogP Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'LOGD_7_4',
+ 'prettyName': 'logD (7.4)',
+ 'description': 'Property for logD (7.4) Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'TPSA_7_4',
+ 'prettyName': 'TPSA (7.4)',
+ 'description': 'Property for TPSA (7.4) Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'CHARGE_7_4',
+ 'prettyName': 'Charge (7.4)',
+ 'description': 'Property for Charge (7.4) Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'PKA_ACID_1',
+ 'prettyName': 'Strongest Acidic pKa',
+ 'description': 'Property for Strongest Acidic pKa Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'PKA_ACID_2',
+ 'prettyName': 'Second Strongest Acidic pKa',
+ 'description': 'Property for Second Strongest Acidic pKa Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'PKA_BASE_1',
+ 'prettyName': 'Strongest Basic pKa',
+ 'description': 'Property for Strongest Basic pKa Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'PKA_BASE_2',
+ 'prettyName': 'Second Strongest Basic pKa',
+ 'description': 'Property for Second Strongest Basic pKa Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'HBA_ATOM_COUNT_PARENT',
+ 'prettyName': 'HBA atoms (parent)',
+ 'description': 'Property for HBA atoms (parent) Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'HBA_ATOM_COUNT_7_4',
+ 'prettyName': 'HBA atoms (7.4)',
+ 'description': 'Property for HBA atoms (7.4) Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'HBD_COUNT_PARENT',
+ 'prettyName': 'HBDs (parent)',
+ 'description': 'Property for HBDs (parent) Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'HBD_COUNT_7_4',
+ 'prettyName': 'HBDs (7.4)',
+ 'description': 'Property for HBDs (7.4) Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'ROTATABLE_BOND_COUNT',
+ 'prettyName': 'Rotatable Bonds',
+ 'description': 'Property for Rotatable Bonds Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'N_COUNT',
+ 'prettyName': 'N count',
+ 'description': 'Property for N count Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'O_COUNT',
+ 'prettyName': 'O count',
+ 'description': 'Property for O count Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'N_O_COUNT',
+ 'prettyName': 'N+O count',
+ 'description': 'Property for N+O count Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'HEAVY_ATOM_COUNT',
+ 'prettyName': 'Heavy Atom count',
+ 'description': 'Property for Heavy Atom count Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'SMILES',
+ 'prettyName': 'SMILES',
+ 'description': 'Property for SMILES Calculation',
+ 'valueType': { 'name': 'SMILES' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'IUPAC',
+ 'prettyName': 'IUPAC Name',
+ 'description': 'Property for IUPAC Name Calculation',
+ 'valueType': { 'name': 'STRING' },
+ 'multivalued': false,
+ }
+ }
+ ]
batch: [
{
'valueDescriptor': {
diff --git a/modules/ServerAPI/spec/testFixtures/ParentPropertyDescriptorServiceTestJSON.coffee b/modules/ServerAPI/spec/testFixtures/ParentPropertyDescriptorServiceTestJSON.coffee
index 98ef11296..9c2f37ea2 100644
--- a/modules/ServerAPI/spec/testFixtures/ParentPropertyDescriptorServiceTestJSON.coffee
+++ b/modules/ServerAPI/spec/testFixtures/ParentPropertyDescriptorServiceTestJSON.coffee
@@ -1,212 +1,212 @@
((exports) ->
exports.parentPropertyDescriptors = [
- {
- 'valueDescriptor': {
- 'name': 'MOLWEIGHT',
- 'prettyName': 'Molecular Weight',
- 'description': 'Property for Molecular Weight Calculation',
- 'valueType':
- 'name': 'DOUBLE' ,
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'FORMULA',
- 'prettyName': 'Molecular Formula',
- 'description': 'Property for Molecular Formula Calculation',
- 'valueType': { 'name': 'STRING' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'MONOISOTOPIC_MASS',
- 'prettyName': 'Monoisotopic Mass',
- 'description': 'Property for Monoisotopic Mass Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'ELEMENTAL_COMPOSITION',
- 'prettyName': 'Elemental Composition',
- 'description': 'Property for Elemental Composition Calculation',
- 'valueType': { 'name': 'STRING' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'CLOGP',
- 'prettyName': 'ClogP',
- 'description': 'Property for ClogP Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'LOGD_7_4',
- 'prettyName': 'logD (7.4)',
- 'description': 'Property for logD (7.4) Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'TPSA_7_4',
- 'prettyName': 'TPSA (7.4)',
- 'description': 'Property for TPSA (7.4) Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'CHARGE_7_4',
- 'prettyName': 'Charge (7.4)',
- 'description': 'Property for Charge (7.4) Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'PKA_ACID_1',
- 'prettyName': 'Strongest Acidic pKa',
- 'description': 'Property for Strongest Acidic pKa Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'PKA_ACID_2',
- 'prettyName': 'Second Strongest Acidic pKa',
- 'description': 'Property for Second Strongest Acidic pKa Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'PKA_BASE_1',
- 'prettyName': 'Strongest Basic pKa',
- 'description': 'Property for Strongest Basic pKa Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'PKA_BASE_2',
- 'prettyName': 'Second Strongest Basic pKa',
- 'description': 'Property for Second Strongest Basic pKa Calculation',
- 'valueType': { 'name': 'DOUBLE' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'HBA_ATOM_COUNT_PARENT',
- 'prettyName': 'HBA atoms (parent)',
- 'description': 'Property for HBA atoms (parent) Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'HBA_ATOM_COUNT_7_4',
- 'prettyName': 'HBA atoms (7.4)',
- 'description': 'Property for HBA atoms (7.4) Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'HBD_COUNT_PARENT',
- 'prettyName': 'HBDs (parent)',
- 'description': 'Property for HBDs (parent) Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'HBD_COUNT_7_4',
- 'prettyName': 'HBDs (7.4)',
- 'description': 'Property for HBDs (7.4) Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'ROTATABLE_BOND_COUNT',
- 'prettyName': 'Rotatable Bonds',
- 'description': 'Property for Rotatable Bonds Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'N_COUNT',
- 'prettyName': 'N count',
- 'description': 'Property for N count Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'O_COUNT',
- 'prettyName': 'O count',
- 'description': 'Property for O count Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'N_O_COUNT',
- 'prettyName': 'N+O count',
- 'description': 'Property for N+O count Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'HEAVY_ATOM_COUNT',
- 'prettyName': 'Heavy Atom count',
- 'description': 'Property for Heavy Atom count Calculation',
- 'valueType': { 'name': 'INT' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'SMILES',
- 'prettyName': 'SMILES',
- 'description': 'Property for SMILES Calculation',
- 'valueType': { 'name': 'SMILES' },
- 'multivalued': false,
- }
- },
- {
- 'valueDescriptor': {
- 'name': 'IUPAC',
- 'prettyName': 'IUPAC Name',
- 'description': 'Property for IUPAC Name Calculation',
- 'valueType': { 'name': 'STRING' },
- 'multivalued': false,
- }
- }
- ]
+ {
+ 'valueDescriptor': {
+ 'name': 'MOLWEIGHT',
+ 'prettyName': 'Molecular Weight',
+ 'description': 'Property for Molecular Weight Calculation',
+ 'valueType':
+ 'name': 'DOUBLE' ,
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'FORMULA',
+ 'prettyName': 'Molecular Formula',
+ 'description': 'Property for Molecular Formula Calculation',
+ 'valueType': { 'name': 'STRING' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'MONOISOTOPIC_MASS',
+ 'prettyName': 'Monoisotopic Mass',
+ 'description': 'Property for Monoisotopic Mass Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'ELEMENTAL_COMPOSITION',
+ 'prettyName': 'Elemental Composition',
+ 'description': 'Property for Elemental Composition Calculation',
+ 'valueType': { 'name': 'STRING' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'CLOGP',
+ 'prettyName': 'ClogP',
+ 'description': 'Property for ClogP Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'LOGD_7_4',
+ 'prettyName': 'logD (7.4)',
+ 'description': 'Property for logD (7.4) Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'TPSA_7_4',
+ 'prettyName': 'TPSA (7.4)',
+ 'description': 'Property for TPSA (7.4) Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'CHARGE_7_4',
+ 'prettyName': 'Charge (7.4)',
+ 'description': 'Property for Charge (7.4) Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'PKA_ACID_1',
+ 'prettyName': 'Strongest Acidic pKa',
+ 'description': 'Property for Strongest Acidic pKa Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'PKA_ACID_2',
+ 'prettyName': 'Second Strongest Acidic pKa',
+ 'description': 'Property for Second Strongest Acidic pKa Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'PKA_BASE_1',
+ 'prettyName': 'Strongest Basic pKa',
+ 'description': 'Property for Strongest Basic pKa Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'PKA_BASE_2',
+ 'prettyName': 'Second Strongest Basic pKa',
+ 'description': 'Property for Second Strongest Basic pKa Calculation',
+ 'valueType': { 'name': 'DOUBLE' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'HBA_ATOM_COUNT_PARENT',
+ 'prettyName': 'HBA atoms (parent)',
+ 'description': 'Property for HBA atoms (parent) Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'HBA_ATOM_COUNT_7_4',
+ 'prettyName': 'HBA atoms (7.4)',
+ 'description': 'Property for HBA atoms (7.4) Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'HBD_COUNT_PARENT',
+ 'prettyName': 'HBDs (parent)',
+ 'description': 'Property for HBDs (parent) Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'HBD_COUNT_7_4',
+ 'prettyName': 'HBDs (7.4)',
+ 'description': 'Property for HBDs (7.4) Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'ROTATABLE_BOND_COUNT',
+ 'prettyName': 'Rotatable Bonds',
+ 'description': 'Property for Rotatable Bonds Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'N_COUNT',
+ 'prettyName': 'N count',
+ 'description': 'Property for N count Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'O_COUNT',
+ 'prettyName': 'O count',
+ 'description': 'Property for O count Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'N_O_COUNT',
+ 'prettyName': 'N+O count',
+ 'description': 'Property for N+O count Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'HEAVY_ATOM_COUNT',
+ 'prettyName': 'Heavy Atom count',
+ 'description': 'Property for Heavy Atom count Calculation',
+ 'valueType': { 'name': 'INT' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'SMILES',
+ 'prettyName': 'SMILES',
+ 'description': 'Property for SMILES Calculation',
+ 'valueType': { 'name': 'SMILES' },
+ 'multivalued': false,
+ }
+ },
+ {
+ 'valueDescriptor': {
+ 'name': 'IUPAC',
+ 'prettyName': 'IUPAC Name',
+ 'description': 'Property for IUPAC Name Calculation',
+ 'valueType': { 'name': 'STRING' },
+ 'multivalued': false,
+ }
+ }
+ ]
) (if (typeof process is "undefined" or not process.versions) then window.parentPropertyDescriptorsTestJSON = window.parentPropertyDescriptorsTestJSON or {} else exports)
diff --git a/modules/ServerAPI/src/server/routes/CreateLiveDesignLiveReportForACAS.coffee b/modules/ServerAPI/src/server/routes/CreateLiveDesignLiveReportForACAS.coffee
index f014409c1..1f922e75d 100644
--- a/modules/ServerAPI/src/server/routes/CreateLiveDesignLiveReportForACAS.coffee
+++ b/modules/ServerAPI/src/server/routes/CreateLiveDesignLiveReportForACAS.coffee
@@ -26,13 +26,13 @@ exports.redirectToNewLiveDesignLiveReportForExperiment = (req, resp) ->
exptCode = req.params.experimentCode
username = req.session.passport.user.username
exports.getUrlForNewLiveDesignLiveReportForExperimentInternal exptCode, username, (url) ->
- resp.redirect url
+ resp.redirect url
exports.getUrlForNewLiveDesignLiveReportForExperiment = (req, resp) ->
exptCode = req.params.experimentCode
username = req.session.passport.user.username
exports.getUrlForNewLiveDesignLiveReportForExperimentInternal exptCode, (url) ->
- resp.json {url: url}
+ resp.json {url: url}
exports.getUrlForNewLiveDesignLiveReportForExperimentInternal = (exptCode, username, callback) ->
exec = require('child_process').exec
diff --git a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee
index 8fad63944..b083aec7f 100644
--- a/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee
+++ b/modules/ServerAPI/src/server/routes/ExperimentServiceRoutes.coffee
@@ -560,10 +560,7 @@ exports.resultViewerURLFromExperimentCodeName = (codeName, callback) ->
# Error callback should be json
_ = require '../public/lib/underscore.js'
config = require '../conf/compiled/conf.js'
- if config.all.client.service.result && config.all.client.service.result.viewer and
- config.all.client.service.result.viewer.experimentPrefix? and
- config.all.client.service.result.viewer.protocolPrefix? and
- config.all.client.service.result.viewer.experimentNameColumn?
+ if config.all.client.service.result && config.all.client.service.result.viewer and config.all.client.service.result.viewer.experimentPrefix? and config.all.client.service.result.viewer.protocolPrefix? and config.all.client.service.result.viewer.experimentNameColumn?
serverUtilityFunctions = require './ServerUtilityFunctions.js'
baseurl = config.all.client.service.persistence.fullpath+"experiments/codename/"+codeName
request = require 'request'
@@ -601,9 +598,9 @@ exports.resultViewerURLFromExperimentCodeName = (codeName, callback) ->
preferredProtocolLabelText = preferredProtocolLabel[0].labelText
callback null,
resultViewerURL: config.all.client.service.result.viewer.protocolPrefix +
- encodeURIComponent(preferredProtocolLabelText) +
- config.all.client.service.result.viewer.experimentPrefix +
- encodeURIComponent(experimentName)
+ encodeURIComponent(preferredProtocolLabelText) +
+ config.all.client.service.result.viewer.experimentPrefix +
+ encodeURIComponent(experimentName)
else
console.log error
console.log response
diff --git a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee
index f4f2333b8..627711b59 100644
--- a/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee
+++ b/modules/ServerAPI/src/server/routes/InventoryServiceRoutes.coffee
@@ -55,7 +55,6 @@ 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
app.post '/api/getContainerInfoFromBatchCode', exports.getContainerInfoFromBatchCode
app.post '/api/getContainerStatesByContainerValue', exports.getContainerStatesByContainerValue
app.post '/api/getContainerLogsByContainerCodes', exports.getContainerLogsByContainerCodes
@@ -119,7 +118,6 @@ 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
app.post '/api/getTubesFromBatchCode', loginRoutes.ensureAuthenticated, exports.getTubesFromBatchCode
app.post '/api/loadParentVialsFromCSV', loginRoutes.ensureAuthenticated, exports.loadParentVialsFromCSV
app.post '/api/loadDaughterVialsFromCSV', loginRoutes.ensureAuthenticated, exports.loadDaughterVialsFromCSV
@@ -163,7 +161,7 @@ exports.getContainersInLocation = (req, resp) ->
console.error json
console.error response
resp.end JSON.stringify "getContainersInLocation failed"
- )
+ )
exports.getContainersInLocationWithTypeAndKind = (req, resp) ->
req.setTimeout 86400000
@@ -428,7 +426,7 @@ exports.getWellCodesByPlateBarcodes = (req, resp) ->
console.error json
console.error response
resp.end JSON.stringify "getWellCodesByPlateBarcodes failed"
- )
+ )
exports.getWellCodesByPlateBarcodesInternal = (plateBarcodes, callback) ->
if global.specRunnerTestmode
@@ -489,7 +487,7 @@ exports.getWellContentInternal = (wellCodeNames, callback) ->
console.error json
console.error response
callback JSON.stringify "getWellContent failed"
- )
+ )
exports.getContainerAndDefinitionContainerByContainerLabel = (req, resp) ->
req.setTimeout 86400000
@@ -1977,9 +1975,8 @@ exports.getContainerLogsByContainerCodesInternal = (containerCodes, callback) =>
response = []
for getContainer in containersByCodeNamesResponse
lsLabels = getContainer.container.lsLabels
- preferredLabelObject = _.filter(lsLabels, (label) ->
- label.preferred == true
- )
+ preferredLabelObject = _.filter lsLabels, (label) ->
+ label.preferred == true
codeName = getContainer.container.codeName
responseObject =
label: preferredLabelObject[0].labelText
@@ -2576,37 +2573,27 @@ exports.getTubesFromBatchCodeInternal = (input, callback) =>
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
- }
- ]
- }
- ]
- }
+ "lsType": "container" ,
+ "lsKind": "tube",
+ "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"
diff --git a/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee b/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee
index 9c44ac7d6..0a088b2b6 100644
--- a/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee
+++ b/modules/ServerAPI/src/server/routes/ServerUtilityFunctions.coffee
@@ -1460,9 +1460,9 @@ class Container extends Backbone.Model
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'))
+ !((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')
@@ -1481,9 +1481,9 @@ class Container extends Backbone.Model
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'))
+ !((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')
diff --git a/package.json b/package.json
index f8c7c4238..e4c1fea09 100644
--- a/package.json
+++ b/package.json
@@ -32,6 +32,7 @@
"errorhandler": "^1.5.1",
"express": "^4.17.1",
"express-session": "^1.17.1",
+ "memorystore": "1.6.4",
"extract-text-webpack-plugin": "3.0.0",
"file-loader": "6.2.0",
"flat": "5.0.2",
@@ -41,14 +42,13 @@
"jasmine-core": "^3.6.0",
"jasmine-jquery": "^2.1.1",
"jquery": "^3.5.1",
- "jquery-file-upload-middleware": "git+https://github.com/mcneilco/jquery-file-upload-middleware.git",
+ "jquery-file-upload-middleware": "0.1.8",
"json2csv": "^5.0.5",
"jszip": "3.5.0",
"less": "^3.12.2",
"lodash": "^4.17.20",
"marked": "1.2.5",
"method-override": "^3.0.0",
- "mkdirp": "1.0.4",
"mocha": "8.2.1",
"mochawesome": "^6.2.1",
"mongojs": "3.1.0",