Merge branch 'release/2024.1.x' into ACAS-744

.github/workflows/docker-image.yml

@@ -3,10 +3,10 @@ name: Docker Image CI
 on:
   push:
     branches: ["master", "release/*"]
+    tags:
+      - "*"
   pull_request:
     types: [opened, synchronize]
-  create:
-    tags: "**"
 jobs:
   acas:
     runs-on: ubuntu-latest
@@ -61,13 +61,15 @@ jobs:
           # Check out the branch specified by ACAS_CLIENT_REF
           ref: ${{ env.ACAS_CLIENT_REF }}
       - name: Build (no push)
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           push: false
           load: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
           file: Dockerfile
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
           build-args: |
             BUILDTIME=${{ fromJSON(steps.meta.outputs.json).labels['org.opencontainers.image.created'] }}
             VERSION=${{ env.ACAS_TAG }}
@@ -110,15 +112,18 @@ jobs:
           pip install ./acasclient
       - name: Run tests
         run: python -m unittest discover -s ./acasclient -p "test_*.py" -v
-      - name: Build and push
-        uses: docker/build-push-action@v3
+      - name: Build multi-arch and push
+        # Only push tags and release branches
+        if: ${{ startsWith(github.ref, 'refs/heads/release/') || startsWith(github.ref, 'refs/tags/') }}
+        uses: docker/build-push-action@v5
         with:
-          # Only push tags and release branches
-          push: ${{ startsWith(github.ref, 'refs/heads/release/') || startsWith(github.ref, 'refs/tags/') }}
+          push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
           file: Dockerfile
           platforms: linux/amd64,linux/arm64/v8
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
           build-args: |
             BUILDTIME=${{ fromJSON(steps.meta.outputs.json).labels['org.opencontainers.image.created'] }}
             VERSION=${{ env.ACAS_TAG }}

Dockerfile

@@ -29,7 +29,7 @@ RUN   dnf install -y initscripts python3-psycopg2
 
 # node
 ENV NPM_CONFIG_LOGLEVEL warn
-ENV NODE_VERSION 14.x
+ENV NODE_VERSION 18.x
 RUN curl -fsSL https://rpm.nodesource.com/setup_$NODE_VERSION | bash - && \
   dnf install -y nodejs
 

conf/config.properties.example

@@ -506,6 +506,12 @@ server.sel.protocolStatus=created
 server.sel.assayStage=unassigned
 server.sel.validateDoseResponseCurves=true
 
+# Default protocol/experiment description when loaded through experiment loader
+# server.sel.protocolDescription=${client.protocol.label} created by generic data parser
+# server.sel.experimentDescription=${client.experiment.label} created by generic data parser
+server.sel.protocolDescription=
+server.sel.experimentDescription=
+
 # Cron- change to "false" to not start cron jobs on startup
 server.service.cron.startOnRestart=true
 server.service.cron.enable=true
@@ -631,6 +637,9 @@ server.systemTest.runDestructive=false
 # Behavior without this config set to true is to give all users access to all projects
 server.project.roles.enable=true
 
+# Require project type to be returned by project CustomerSpecificFunctions
+server.project.type.required=false
+
 #Controls whether to try to sync projects list from ACAS to CmpdReg
 server.project.sync.cmpdReg=true
 
@@ -710,7 +719,7 @@ client.cmpdreg.metaLot.requireLotNumber=false
 client.cmpdreg.metaLot.allowManualLotNumber=false
 client.cmpdreg.metaLot.autoPopulateNextLotNumber=true
 client.cmpdreg.metaLot.maxAutoLotNumber=1000
-client.cmpdreg.metaLot.allowDuplicateParentAliases=true
+client.cmpdreg.metaLot.allowDuplicateParentAliases=false
 client.cmpdreg.serverSettings.corpPrefix=CMPD
 client.cmpdreg.serverSettings.corpSeparator=-
 client.cmpdreg.serverSettings.saltSeparator=

docker-compose.yml

@@ -49,7 +49,7 @@ services:
       - logs:/home/runner/logs
     command: ["bin/acas.sh", "run", "rservices"]
   db:
-    image: mcneilco/acas-postgres:release-1.13.7
+    image: mcneilco/acas-postgres:release-2023.3.x
     restart: always
     volumes:
      - dbstore:/var/lib/postgresql/data

modules/BuildUtilities/src/server/routes/RequiredClientScripts_template.js

@@ -49,6 +49,7 @@ exports.applicationScripts = [
 	'/javascripts/src/Components/ACASFormStateTable.js',
 	'/javascripts/src/Components/BasicFileValidateAndSave.js',
 	'/javascripts/src/Components/BasicFileValidateReviewAndSave.js',
+	'/javascripts/src/Components/BasicThingValidateAndSave.js',
 	'/javascripts/src/Components/ACASThingBrowser.js',
 	'/javascripts/src/Components/PickList.js',
 	'/javascripts/src/CodeTablesAdmin/AbstractCodeTable.js',

modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee

@@ -42,8 +42,8 @@ exports.setupRoutes = (app, loginRoutes) ->
 	app.post '/cmpdReg/api/v1/structureServices/hydrogenizer', loginRoutes.ensureAuthenticated, exports.genericStructureService
 	app.post '/cmpdReg/api/v1/structureServices/cipStereoInfo', loginRoutes.ensureAuthenticated, exports.genericStructureService
 	app.post '/cmpdReg/export/searchResults', loginRoutes.ensureAuthenticated, exports.exportSearchResults
-	app.post '/cmpdReg/validateParent', loginRoutes.ensureAuthenticated, loginRoutes.ensureCmpdRegAdmin, exports.validateParent
-	app.post '/cmpdReg/updateParent', loginRoutes.ensureAuthenticated, loginRoutes.ensureCmpdRegAdmin, exports.updateParent
+	app.post '/cmpdReg/validateParent', loginRoutes.ensureAuthenticated, exports.validateParent
+	app.post '/cmpdReg/updateParent', loginRoutes.ensureAuthenticated, exports.updateParent
 	app.post '/cmpdReg/swapParentStructures', loginRoutes.ensureAuthenticated, loginRoutes.ensureCmpdRegAdmin, exports.swapParentStructures
 	app.post '/cmpdReg/api/v1/lotServices/update/lot/metadata', loginRoutes.ensureAuthenticated, exports.updateLotMetadata
 	app.post '/cmpdReg/api/v1/lotServices/update/lot/metadata/jsonArray', loginRoutes.ensureAuthenticated, exports.updateLotsMetadata

modules/GenericDataParser/src/server/generic_data_parser.R

@@ -706,27 +706,58 @@ validateCalculatedResults <- function(calculatedResults, dryRun, curveNames, tes
         # A project can only be used in the experiment if it's an unrestricted project or belongs to the project which this experiment belongs to
         projectsDT <- data.table(projectDF)
 
-        # Loop through by project code and create a projectAllowedForExperiment column
+        # Add project type if its missing
+        if(!"type" %in% colnames(projectsDT)) {
+          projectsDT[ , type := NA]
+        }
+
+        # Get the project type of the experiment project if required by configurations
+        projectType <- NA
+        if(configList$server.project.type.required) {
+          projectType <- projectsDT[code == projectCode]$type
+          if(is.na(projectType)) {
+            stopUser(paste0("Project '",projectCode,"' does not have a type. Please contact your system administrator."))
+          }
+        }
+
+        # Here we are annotating each of the projects with a boolean as to whether it can be used in the experiment if its used by a lot     
         projectsDT[ , projectAllowedForExperiment := {
-          # Check if the project is unrestricted or if it equals the projectCode of the experiment
-          !isRestricted | code == projectCode
+          # projectType and projectCode are referring to the experiment project
+          # type, code, and isRestricted are referring to the batch project
+          if(is.na(projectType)) {
+            # If the project type is na then this is not a system with project type
+            # so we just check if the project is restricted and if the lot project is the same as the experiment project
+            !isRestricted | code == projectCode
+          } else {
+            # If project type is not na then this is a system with project type
+            switch(projectType,
+                    "RESTRICTED" =  !isRestricted | code == projectCode,
+                    "HYPER_RESTRICTED" = code == projectCode,
+                    "UNRESTRICTED" = ifelse(identical(type, "HYPER_RESTRICTED"), FALSE, TRUE),
+                    "GLOBAL" = ifelse(identical(type, "HYPER_RESTRICTED"), FALSE, TRUE),
+                    stopUser(paste0("Project '",projectCode,"' has an invalid type. Please contact your system administrator."))
+            )
+          }
+
         }, by = code]
 
         # Merge batch projects to project restrition information
         batchProjectWithRestrictionInfo <- as.data.table(merge(batchProjects, projectsDT, by.x="Project.Code", by.y="code"))
-        
+
         # Create a data table with one row per batch with a boolean column as to whether it can be used in the experiment
         # if any of the projects the batch belongs to is allowed to be loaded to this experiment, then the batch can be loaded to the experiment
-        canUseBatchDT <- batchProjectWithRestrictionInfo[ , any(projectAllowedForExperiment), by = Requested.Name]
+        canUseBatchDT <- batchProjectWithRestrictionInfo[ , any(projectAllowedForExperiment), by = c("Requested.Name", "type")]
         setnames(canUseBatchDT, "V1", "batchCanBeLoadedToExperimentProject")
 
         # Get a list of batches which are restricted and cannot be used in this experiment's project
-        rCompounds <- canUseBatchDT[batchCanBeLoadedToExperimentProject == FALSE]$Requested.Name
+        rCompounds <- canUseBatchDT[batchCanBeLoadedToExperimentProject == FALSE]
 
-        if (length(rCompounds) > 0) {
+        if (nrow(rCompounds) > 0) {
           addProjectError <- TRUE
-          shouldCheckRole <- configList$server.project.roles.enable & !is.null(configList$client.roles.crossProjectLoaderRole)
-          if(shouldCheckRole) {
+          crossProjectLoaderRolesEnabled <- configList$server.project.roles.enable & !is.null(configList$client.roles.crossProjectLoaderRole)
+          # HYPER_RESTRICTED projects are not allowed to be loaded to other projects by anyone
+          # So only check cross project loader roles if the project is not HYPER_RESTRICTED
+          if(crossProjectLoaderRolesEnabled && !identical(projectType, "HYPER_RESTRICTED")) {
             response <- getURL(URLencode(paste0(racas::applicationSettings$server.nodeapi.path, racas::applicationSettings$client.service.users.path, "/", user)))
             if(response=="") {
               addError(paste0("Username '",user,"' could not be found in the system"))
@@ -740,8 +771,17 @@ validateCalculatedResults <- function(calculatedResults, dryRun, curveNames, tes
             }
           }
           if(addProjectError) {
-            addError(paste0("Compounds '", paste(rCompounds, collapse = "', '"),
+            # Return error message for each type of project
+            # if projectType (experiment project) is restricted then return error message for specific for hyper restrictions
+            rCompounds[ , {
+              if(identical(projectType, "HYPER_RESTRICTED")) {
+                 addError(paste0("Compounds '", paste(.SD$Requested.Name, collapse = "', '"),
+                            "' are in a project that does not match the hyper restricted project entered for this ",racas::applicationSettings$client.experiment.label,"."))
+              } else {
+                 addError(paste0("Compounds '", paste(.SD$Requested.Name, collapse = "', '"),
                             "' are in a restricted project that does not match the one entered for this ",racas::applicationSettings$client.experiment.label,"."))
+              }
+            }, by = type]
           }
         }
       }
@@ -2106,7 +2146,7 @@ createNewProtocol <- function(metaData, lsTransaction, recordedBy, columnOrderSt
 
   # Create the protocol
   protocol <- createProtocol(lsTransaction = lsTransaction,
-                             shortDescription=paste0(racas::applicationSettings$client.protocol.label," created by generic data parser"),  
+                             shortDescription=racas::applicationSettings$server.sel.protocolDescription,  
                              recordedBy=recordedBy, 
                              protocolLabels=protocolLabels,
                              protocolStates=protocolStates)
@@ -2273,7 +2313,7 @@ createNewExperiment <- function(metaData, protocol, lsTransaction, pathToGeneric
                                  shortDescription = if(!is.null(metaData$"Short Description"[1])) {
                                    metaData$"Short Description"[1]
                                      } else {
-                                   paste0(racas::applicationSettings$client.experiment.label," created by generic data parser")
+                                   racas::applicationSettings$server.sel.experimentDescription
                                      },  
                                  recordedBy=recordedBy, 
                                  experimentLabels=experimentLabels,

modules/ServerAPI/src/client/SaltBrowser.coffee

@@ -333,7 +333,15 @@ class SaltBrowserController extends Backbone.View
 					console.log(errorMsg)
 					@$('.bv_createSalt').hide()
 					@$('.bv_errorCreatingSaltMessage').show()
-					@$('.bv_createSaltErrorMessageHolder') errorMsg
+					errorData = JSON.parse(errorMsg.responseText)
+					errorContainer = @$('.bv_createSaltErrorMessageHolder')
+					errorContainer.empty()
+					errorContainer.append("<p>Error(s):</p>")
+					errorList = $('<ul class="error-list"></ul>')
+					for error in errorData
+						errorMessage = error.message
+						errorList.append("<li>#{errorMessage}</li>")
+					errorContainer.append(errorList)
 			)
 
 	handleBackConfirmCreateClicked: => 
@@ -392,7 +400,15 @@ class SaltBrowserController extends Backbone.View
 					console.log(errorMsg)
 					@$('.bv_confirmCreateSalt').hide()
 					@$('.bv_errorCreatingSaltMessage').show()
-					@$('.bv_createSaltErrorMessageHolder') errorMsg
+					errorData = JSON.parse(errorMsg.responseText)
+					errorContainer = @$('.bv_createSaltErrorMessageHolder')
+					errorContainer.empty()
+					errorContainer.append("<p>Error(s):</p>")
+					errorList = $('<ul class="error-list"></ul>')
+					for error in errorData
+						errorMessage = error.message
+						errorList.append("<li>#{errorMessage}</li>")
+					errorContainer.append(errorList)
 					@$('.bv_createNotifications').hide()
 			)
 

modules/ServerAPI/src/server/CustomerSpecificServerFunctions.coffee

@@ -368,6 +368,14 @@ exports.getProjectStubsInternal = (callback) ->
 		#remove groups attribute
 		_.each acasGroupsAndProjects.projects, (project) ->
 			delete project.groups
+			# ACAS-754: Adding project type to project object
+			# This is for testing experiment loader with different project types explained in ACAS-754
+			# if project.name == "Global"
+			# 	project.type = "GLOBAL"
+			# else if project.isRestricted
+			# 	project.type = "HYPER_RESTRICTED"
+			# else
+			# 	project.type = "UNRESTRICTED"
 		callback response.statusCode, acasGroupsAndProjects.projects
 
 exports.makeServiceRequestHeaders = (user) ->

modules/ServerAPI/src/server/python/acas_ldclient/acasldclient.py

@@ -6,6 +6,13 @@
 from ldclient.api.requester import SUPPORTED_SERVER_VERSION
 from ldclient.base import version_str_as_tuple
 
+# Prior to Live Design 2024-1, ProjectType was not available in the API
+# so we only import it and use it if it is available in order to maintain backwards compatibility
+try:
+    from ldclient.enums import ProjectType
+except ImportError:
+    ProjectType = None
+
 import argparse
 import json
 import os, sys
@@ -268,15 +275,28 @@ def get_projects(client):
     return projects
 
 def ld_project_to_acas(ld_project):
+
+    # Prior to Live Design 2024-1, the project type was not available in the API
+    # so we only set it if it is available in order to maintain backwards compatibility
+    if ProjectType is not None:
+        project_acls = {
+            'isRestricted': ld_project.project_type not in (ProjectType.GLOBAL, ProjectType.UNRESTRICTED),
+            'type': ld_project.project_type
+        }
+    else:
+        project_acls = {
+            'isRestricted': ld_project.restricted
+        }
+
     acas_project = {
         'id': ld_project.id,
         '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
     }
+    acas_project.update(project_acls)
     return acas_project
 
 def main():

package.json

@@ -32,8 +32,6 @@
     "errorhandler": "^1.5.1",
     "express": "^4.17.1",
     "express-session": "^1.17.1",
-    "extract-text-webpack-plugin": "3.0.0",
-    "file-loader": "6.2.0",
     "flat": "5.0.2",
     "forever-monitor": "3.0.3",
     "glob": "7.1.6",
@@ -43,18 +41,18 @@
     "jasmine-jquery": "^2.1.1",
     "jquery": "^3.5.1",
     "json2csv": "^5.0.5",
-    "jszip": "3.5.0",
+    "jszip": "3.10.1",
     "less": "^3.12.2",
     "lodash": "^4.17.20",
-    "marked": "1.2.5",
+    "marked": "4.0.10",
     "memorystore": "1.6.4",
     "method-override": "^3.0.0",
     "mocha": "8.2.1",
     "mochawesome": "^6.2.1",
     "mongojs": "3.1.0",
     "morgan": "^1.10.0",
     "multer": "^1.4.2",
-    "node-fetch": "3.2.6",
+    "node-fetch": "3.2.10",
     "ncp": "2.0.0",
     "passport": "0.6.0",
     "passport-local": "1.0.0",
@@ -71,7 +69,7 @@
     "socket.io": "2.4.1",
     "style-loader": "2.0.0",
     "temporary": "1.1.0",
-    "underscore": "1.12.0",
+    "underscore": "1.12.1",
     "underscore-deep-extend": "1.1.5",
     "url-loader": "4.1.1",
     "winston": "3.3.3",