Merge branch 'release/1.13.5' into feature/archive

# Conflicts:
#	app_api_template.coffee
#	app_template.coffee
#	modules/CmpdReg/src/server/routes/CmpdRegRoutes.coffee
#	modules/CmpdRegBulkLoader/src/server/routes/CmpdRegBulkLoaderRoutes.coffee
#	package.json

.env

@@ -1 +1 @@
-ACAS_TAG=latest
+ACAS_TAG=latest

.gitignore

@@ -24,5 +24,7 @@ Dockerfile*
 docker-compose*.yml
 build
 licenses
+venv
 #this is for the soft link in .dockerfile (git ignore .git by default)
 .git
+chemaxon

Dockerfile

@@ -1,26 +1,33 @@
-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 clean all
+  dnf install -y tar git && \
+  dnf install -y fontconfig urw-fonts && \
+  dnf clean all
 
 # 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
@@ -42,14 +49,14 @@ 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
 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 $ACAS_BASE
 USER    runner
@@ -66,8 +73,17 @@ ENV     PREPARE_MODULE_CONF_JSON=true
 ENV     PREPARE_CONFIG_FILES=true
 ENV     RUN_SYSTEM_TEST=true
 ENV     ACAS_HOME=$BUILD_PATH
+RUN     gulp execute:prepare_config_files
 
-EXPOSE 3000
-EXPOSE 3001
+#Install python dependencies
+USER	root
+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"]

Dockerfile-rservices

@@ -1,4 +1,4 @@
-FROM mcneilco/racas-oss:${ACAS_TAG}
+FROM mcneilco/racas-oss:develop
 
 # RSTUDIO INSTALL
 USER root

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.

app_api_template.coffee

@@ -59,6 +59,9 @@ startApp = ->
 
 	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()
 	)
 
 	csUtilities.logUsage("ACAS API server started", "started", "")

app_template.coffee

@@ -94,7 +94,7 @@ 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'), ->
@@ -150,7 +150,7 @@ 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()

bin/acas.sh

@@ -1,4 +1,13 @@
 #!/bin/bash
+### BEGIN INIT INFO
+# Provides:		acas
+# Required-Start:	$local_fs
+# Required-Stop:	$local_fs
+# Default-Start:	2 3 4 5
+# Default-Stop:		0 1 6
+# Short-Description: start and stop the acas app.js, server.js and apache instance
+# Description: start and stop the acas app.js, server.js and apache instance
+### END INIT INFO
 # chkconfig: 2345 64 02
 # description: start and stop the acas app.js, server.js and apache instance
 # processname: acas
@@ -98,7 +107,7 @@ export LANG
 running() {
     runningCommand="export FOREVER_ROOT=$ACAS_HOME/bin && forever list 2>/dev/null | grep $ACAS_HOME/app.js 2>&1 >/dev/null"
     if [ $(whoami) != "$ACAS_USER" ]; then
-        runningCommand="su - $ACAS_USER $suAdd -c \"($runningCommand)\""
+        runningCommand="su -p - $ACAS_USER $suAdd -c \"($runningCommand)\""
     fi
     eval $runningCommand
     return $?
@@ -107,7 +116,7 @@ running() {
 start_server() {
     startCommand="export FOREVER_ROOT=$ACAS_HOME/bin && forever start --killSignal=SIGTERM --workingDir --append -l $logname -o $logout -e $logerr $ACAS_HOME/app.js 2>&1 >/dev/null"
     if [ $(whoami) != "$ACAS_USER" ]; then
-        startCommand="su - $ACAS_USER $suAdd -c \"(cd `dirname $ACAS_HOME/app.js` && $startCommand)\""
+        startCommand="su -p - $ACAS_USER $suAdd -c \"(cd `dirname $ACAS_HOME/app.js` && $startCommand)\""
     fi
     eval $startCommand
     return $?
@@ -121,7 +130,7 @@ run_server() {
     fi
     echo "runCommand: $runCommand"
     if [ $(whoami) != "$ACAS_USER" ]; then
-        startCommand="su - $ACAS_USER $suAdd -c \"(cd `dirname $ACAS_HOME/app.js` && $startCommand)\""
+        startCommand="su -p - $ACAS_USER $suAdd -c \"(cd `dirname $ACAS_HOME/app.js` && $startCommand)\""
     fi
     eval "($runCommand)" &
     return $?
@@ -130,7 +139,7 @@ run_server() {
 stop_server() {
     stopCommand="export FOREVER_ROOT=$ACAS_HOME/bin && forever stop $ACAS_HOME/app.js 2>&1 >/dev/null"
     if [ $(whoami) != "$ACAS_USER" ]; then
-        stopCommand="su - $ACAS_USER $suAdd -c \"($stopCommand)\""
+        stopCommand="su -p - $ACAS_USER $suAdd -c \"($stopCommand)\""
     fi
     eval $stopCommand
 
@@ -147,7 +156,7 @@ start_apache() {
     remove_apache_pid
     startCommand=" $apacheCMD -f $ACAS_HOME/conf/compiled/apache.conf -k start 2>&1 >/dev/null"
     if [ $(whoami) != "$RAPACHE_START_ACAS_USER" ]; then
-        startCommand="su - $RAPACHE_START_ACAS_USER $suAdd -c \"($startCommand)\""
+        startCommand="su -p - $RAPACHE_START_ACAS_USER $suAdd -c \"($startCommand)\""
     fi
     eval $startCommand
     return $?
@@ -158,7 +167,7 @@ run_apache() {
     sed -i 's/^ErrorLog.*/ErrorLog "|cat"/' /tmp/apache.conf
     startCommand=" $apacheCMD -f /tmp/apache.conf -k start -DFOREGROUND"
     if [ $(whoami) != "$RAPACHE_START_ACAS_USER" ]; then
-        startCommand="su - $RAPACHE_START_ACAS_USER $suAdd -c \"($startCommand)\""
+        startCommand="su -p - $RAPACHE_START_ACAS_USER $suAdd -c \"($startCommand)\""
     fi
     eval "($startCommand) $1"
     return $?
@@ -167,7 +176,7 @@ run_apache() {
 stop_apache() {
     stopCommand="$apacheCMD -f $ACAS_HOME/conf/compiled/apache.conf -k stop 2>&1 >/dev/null"
     if [ $(whoami) != "$RAPACHE_START_ACAS_USER" ]; then
-        stopCommand="su - $RAPACHE_START_ACAS_USER $suAdd -c \"($stopCommand)\""
+        stopCommand="su -p - $RAPACHE_START_ACAS_USER $suAdd -c \"($stopCommand)\""
     fi
     eval $stopCommand
     return $?
@@ -176,7 +185,7 @@ stop_apache() {
 apache_reload() {
     reloadCommand="$apacheCMD -f $ACAS_HOME/conf/compiled/apache.conf -k graceful 2>&1 >/dev/null"
     if [ $(whoami) != "$RAPACHE_START_ACAS_USER" ]; then
-        reloadCommand="su - $RAPACHE_START_ACAS_USER $suAdd -c \"($reloadCommand)\""
+        reloadCommand="su -p - $RAPACHE_START_ACAS_USER $suAdd -c \"($reloadCommand)\""
     fi
     eval $reloadCommand
     return $?

bin/setenv.sh

@@ -1,2 +1,3 @@
 # Example:
-#export LD_LIBRARY_PATH=/usr/lib/oracle/11.2/client64/lib:$LD_LIBRARY_PATH
+#export LD_LIBRARY_PATH=/usr/lib/oracle/11.2/client64/lib:$LD_LIBRARY_PATH
+if [ -e  "/opt/rh/rh-python36/enable" ]; then source /opt/rh/rh-python36/enable; fi;

conf/ConfiguredEntityTypes.coffee

@@ -1,76 +1,105 @@
-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':
+    isTestedEntity: false
+  ,
+    code: 'Corporate Batch ID'
     type: 'compound'
     kind: 'batch name'
     codeOrigin: 'ACAS CmpdReg'
     displayName: 'Corporate Batch ID'
     sourceExternal: true
     parent: false
-
-  'Protein Parent':
+    isTestedEntity: true
+  ,
+    code: 'Protein Parent'
     type: 'parent'
     kind: 'protein'
     codeOrigin: 'ACAS LsThing'
     displayName: 'Protein Parent'
     sourceExternal: false
     parent: true
-
-  'Protein Batch':
+    isTestedEntity: false
+  ,
+    code: 'Protein Batch'
     type: 'batch'
     kind: 'protein'
     codeOrigin: 'ACAS LsThing'
     displayName: 'Protein Batch'
     sourceExternal: false
     parent: false
-
-  'Gene ID':
+    isTestedEntity: false
+  ,
+    code: 'Gene ID'
     type: 'gene'
     kind: 'entrez gene'
     codeOrigin: 'ACAS LsThing'
     displayName: 'Gene ID'
     sourceExternal: false
     parent: false
-
-  'Container Plate':
+    isTestedEntity: false
+  ,
+    code: 'Container Plate'
     type: 'container'
     kind: 'plate'
     codeOrigin: 'ACAS LsContainer'
     displayName: 'Plate'
     sourceExternal: false
     parent: false
     model: require("../routes/ServerUtilityFunctions.js").ContainerPlate
-
-  'Container Tube':
+    isTestedEntity: false
+  ,
+    code: 'Container Tube'
     type: 'container'
     kind: 'tube'
     codeOrigin: 'ACAS LsContainer'
     displayName: 'Tube'
     sourceExternal: false
     parent: false
     model: require("../routes/ServerUtilityFunctions.js").ContainerTube
-
-  'Definition Container Plate':
+    isTestedEntity: false
+  ,
+    code: 'Definition Container Plate'
     type: 'definition container'
     kind: 'plate'
     codeOrigin: 'ACAS LsContainer'
     displayName: 'Definition Plate'
     sourceExternal: false
     parent: false
     model: require("../routes/ServerUtilityFunctions.js").DefinitionContainerPlate
-
-  'Definition Container Tube':
+    isTestedEntity: false
+  ,
+    code: 'Definition Container Tube'
     type: 'definition container'
     kind: 'tube'
     codeOrigin: 'ACAS LsContainer'
     displayName: 'Definition Tube'
     sourceExternal: false
     parent: false
     model: require("../routes/ServerUtilityFunctions.js").DefinitionContainerTube
+    isTestedEntity: false
+  ,
+    code: 'Solution Container Tube'
+    type: 'container'
+    kind: 'tube'
+    codeOrigin: 'ACAS LsContainer'
+    displayName: 'Solution Aliquot'
+    sourceExternal: false
+    parent: false
+    isTestedEntity: false
+  ,
+    code: 'Location Container'
+    type: 'location'
+    kind: 'default'
+    codeOrigin: 'ACAS LsContainer'
+    displayName: 'Location'
+    sourceExternal: false
+    parent: false
+    model: require("../routes/ServerUtilityFunctions.js").LocationContainer
+    isTestedEntity: false
+]