Merge branch 'release/1.13.4' into bugfix/open-curve-curator-via-corp…

…Name * release/1.13.4: (166 commits) added long timeout to purge cmpds route fixes #673 setting for allowing no structures compounds to be registered as unique parents send author roles instead of username to the updated POST service fixing some error response messages fixing rendering of log dose export image with .png in file name, fix issues with logResponse add api route for saving label sequences adding options to not use colors by default in plots updating color options #fixes 667 adding route for getting curve metadata quickly in bulk by curve id 667 adding route for getting curve metadata quickly in bulk by curve id fixes #663 removing extra console log line fixes #663 url encode file name when calling resp.sendfile from data files route fixes #661 Provide bootstrap main function fixes #658 add bottom margin to multi interaction remove button to match aligned div fixes #654 url encode protocol label in protocol by label adding additional custom metadata values 651 better handling of errors when persistance fails to purge 644 Fix for lower case project names being sorted to the end fixes #603: prevent ls thing from listening to createNewLabel more than once ... # Conflicts: # conf/config.properties.example
mcneilco · Apr 20, 2020 · e1bc3ec · e1bc3ec
2 parents 8b327d6 + 1309e2c
commit e1bc3ec
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diff --git 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/Dockerfile b/Dockerfile
@@ -12,16 +12,22 @@ 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" || \
+    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
@@ -43,7 +49,7 @@ 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
@@ -73,10 +79,9 @@ 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
-EXPOSE 3001
 
 CMD     ["/bin/sh","bin/acas.sh", "run"]
diff --git 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 +157,31 @@ 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.
+
+This will create a user "bob" with password "secret". 
 
 #### Viewing logs
 
+```
 docker-compose logs --tail=20 -f <service>
+```
 
 e.g. for all containers
+
 ```
-docker-compose logs --tail=20 -f 
+docker-compose logs -f 
 ```
 
 e.g. for only tomcat
@@ -176,6 +190,12 @@ e.g. for only tomcat
 docker-compose logs --tail=20 -f tomcat
 ```
 
+Stop the web stack
+
+```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/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'))
+		bootstrap = require "./src/javascripts/ServerAPI/Bootstrap.js"
+		if bootstrap.main?
+			bootstrap.main()
 	)
 
 	###TO_BE_REPLACED_BY_PREPAREMODULEINCLUDES###

diff --git 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/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=${client.use.ssl}
 client.service.rapache.host=rservices
@@ -283,6 +285,8 @@ client.service.result.viewer.liveDesign.database.username=
 client.service.result.viewer.liveDesign.database.password=
 client.service.result.viewer.liveDesign.database.hostname=
 client.service.result.viewer.liveDesign.database.port=
+server.liveDesign.installClientOnStart=false
+client.service.result.viewer.liveDesign.makeReportReadonly=true
 client.service.result.viewer.simpleSAR.baseUrl=
 client.service.result.viewer.seurat.protocolPrefix=http://${client.service.persistence.host}:9080/seurat/runseurat?cmd=newjob&AssayName=
 client.service.result.viewer.seurat.experimentPrefix=&AssayProtocol=
@@ -320,7 +324,7 @@ server.service.external.file.service.url=
 
 # options for preferred batchid type are: NewLineSepBulkPost, SeuratCmpdReg, GeneCodeCheckByR, AcasCmpdReg, LabSynchCmpdReg, SingleBatchNameQueryString, AllPass
 client.service.external.preferred.batchid.type=NewLineSepBulkPost
-server.service.external.preferred.batchid.url=http://tomcat:8080/cmpdreg/api/v1/getPreferredName
+server.service.external.preferred.batchid.url=http://tomcat:8080/acas/api/v1/getPreferredName
 server.service.external.preferred.batchid.separator=-
 server.service.external.project.url=
 server.service.external.report.registration.url=
@@ -369,9 +373,9 @@ 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
@@ -401,7 +405,11 @@ client.curvefit.modelfitparameter.classes=[{"code":"4 parameter D-R", "parameter
                                             {"code":"4 parameter D-R IC50", "parametersController":"DoseResponseAnalysisParametersController", "parametersClass": "DoseResponseIC50AnalysisParameters", "plotCurveClass": "DoseResponsePlotCurveLL4IC50", "RSource":"src/r/CurveAnalysis/ll4IC50.R", "parametersOptions":{"defaultBaseline":0}},\
                                             {"code":"4 parameter D-R IC50/DMax", "parametersController":"DoseResponseAnalysisParametersController", "parametersClass": "DoseResponseIC50AnalysisParameters", "plotCurveClass": "DoseResponsePlotCurveLL4IC50", "RSource":"src/r/CurveAnalysis/ll4IC50DMax.R", "parametersOptions":{"defaultBaseline":0}},\
                                             {"code":"Michaelis-Menten", "parametersController":"DoseResponseKmAnalysisParametersController", "parametersClass": "DoseResponseKmAnalysisParameters", "plotCurveClass": "DoseResponsePlotCurveKm", "RSource":"src/r/CurveAnalysis/mm2.R", "parametersOptions":{"defaultBaseline":0}},\
-                                            {"code":"Substrate Inhibition", "parametersController":"DoseResponseSubstrateInhibitionAnalysisParametersController", "parametersClass": "DoseResponseSubstrateInhibitionAnalysisParameters", "plotCurveClass": "DoseResponsePlotCurveSubstrateInhibition", "RSource":"src/r/CurveAnalysis/substrateInhibition.R", "parametersOptions":{"defaultBaseline":0}}]
+                                            {"code":"Substrate Inhibition", "parametersController":"DoseResponseSubstrateInhibitionAnalysisParametersController", "parametersClass": "DoseResponseSubstrateInhibitionAnalysisParameters", "plotCurveClass": "DoseResponsePlotCurveSubstrateInhibition", "RSource":"src/r/CurveAnalysis/substrateInhibition.R", "parametersOptions":{"defaultBaseline":0}},\
+                                            {"code":"Scatter", "RSource":"src/r/CurveAnalysis/scatter.R", "renderOptions": {"connectPoints": false}},\
+                                            {"code":"Scatter Log-x", "RSource":"src/r/CurveAnalysis/scatter.R", "renderOptions": {"connectPoints": false}},\
+                                            {"code":"Scatter Log-y", "RSource":"src/r/CurveAnalysis/scatter.R", "renderOptions": {"connectPoints": false}},\
+                                            {"code":"Scatter Log-x,y", "RSource":"src/r/CurveAnalysis/scatter.R", "renderOptions": {"connectPoints": false}}]
 
 
 # Lock when approved filter
@@ -529,10 +537,38 @@ client.basePath=/
 server.curveCurator.onRejectMakeReportedValuesNonPublic=false
 server.curveRender.drawPointsForRejectedCurve=true
 
+### Plot colors
+# Colors of curves to be cycled through when coloring curves.  Black is usually the first color as the first color is used for single, non overlayed curves.
+# If supplied, the config server.curveRender.mostRecentCurveColor will override the first color in this list for the most recent
+# Valid colors can be found here:
+#  http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf
+# Some examples of other color schemes:
+# server.curveRender.plotColors=black,red,blue,orange,purple,cyan,darkolivegreen4,firebrick4,aquamarine4,chocolate3,dodgerblue4,coral2,darkorchid3,cadetblue4,darkgoldenrod3,lightcyan4,seagreen4,mediumvioletred
+# server.curveRender.plotColors=black,#a6cee3,#1f78b4,#b2df8a,#33a02c,#fb9a99,#e31a1c,#fdbf6f,#ff7f00,#cab2d6,#6a3d9a,#ffff99,#b15928
+# server.curveRender.plotColors=black
+server.curveRender.plotColors=black,#0C5BB0FF,#EE0011FF,#15983DFF,#EC579AFF,#FA6B09FF,#149BEDFF,#A1C720FF,#FEC10BFF,#16A08CFF,#9A703EFF
+
+### Most recent curve color
+## Color curves by default according to the plot colors.  The list of plot colors is recycled if there are more curves in the plot than colors
+server.curveRender.usePlotColorsByDefault=true
+
+### Most recent curve color
+## If supplied the most recent uploaded curve will get the supplied color
+server.curveRender.mostRecentCurveColor=green
+
+### Curve line width
+# Default: 1
+# If supplied, a with 0.5, the line widths of curves will be 1/2 the thickness of the default of 1.  Converseley, a value of 2 will produce curves with twice the thickeness.
+server.curveRender.curveLwd=1.5
+
+### Plot points on overlay
+# If true, curves that are overlayed will show points for all the curves in the plot.  If false, no points will be shown on overlayed curves.
+# This does not affect single/non overlayed curves
+server.curveRender.plotPointsOnOverlay=false
+
 # Restrict experiment search by project
 server.service.projects.restrictExperiments=false
 
-flyway.location=db/migration/postgres,com.labsynch.labseer.db.migration.postgres
 flyway.schema=acas
 flyway.database.username=${server.database.username}
 flyway.database.password=${server.database.password}
@@ -558,6 +594,10 @@ client.projectEditor.isRestricted.default=false
 
 client.roles.crossProjectLoaderRole=ROLE_ACAS-CROSS-PROJECT-LOADER
 
+# List of project codes to filter out and hide 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
 
@@ -580,5 +620,13 @@ client.compoundInventory.daughterVials.strictMatchPhysicalState=false
 # Whether to save location as a codeValue or as a full location interaction
 client.compoundInventory.saveLocationAsCodeValue=true
 
+# Allows the override of the words "Experiment" and "Protocol" throughout the ACAS UI
+# These configs should NOT be set to the same value as this would break some functionality
+# of data loaders.
+# The values are often pluralized by putting an "s" at the end, so whatever values are used
+# should be able to be pluralized with an "s" appended to them.
+client.protocol.label=Protocol
+client.experiment.label=Experiment
+
 #config for whether SOLR should be updated when things are saved/updated
 client.solr.updateSolrForThings=false
diff --git 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
@@ -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
 
diff --git 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
@@ -56,11 +56,10 @@ 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:
-    image: mcneilco/tomcat-maven:1.0-openjdk8
+    image: mcneilco/tomcat-maven:1.2-openjdk8
     restart: always
     depends_on:
      - db
@@ -69,12 +68,12 @@ services:
      - "8000:8000"
     environment:
      - ACAS_HOME=/home/runner/build
-     - CATALINA_OPTS=-Xms512M -Xmx1024M -XX:MaxPermSize=512m
+     - CATALINA_OPTS=-Xms512M -Xmx1024M -XX:MaxPermSize=512m -Dlisten.address=$${TOMCAT_LISTEN_ADDRESS}
      - JAVA_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8000
+     - TOMCAT_LISTEN_ADDRESS=0.0.0.0
     volumes_from:
      - roo
      - acas
-     - cmpdreg
     env_file:
       - ./conf/docker/acas/environment/acas.env
       - ./conf/docker/roo/environment/roo.env
@@ -85,14 +84,6 @@ services:
     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
-    command: /bin/true
 volumes:
   dbstore:
   filestore:

diff --git a/docker_bob_setup.sh 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
diff --git 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'
@@ -296,7 +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
@@ -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, ->