Merge pull request #1694 from data-team-uhn/CARDS-2317-base

CARDS-2317: Split CARDS into multiple projects

compose-cluster/generate_compose_yaml.py

@@ -714,7 +714,7 @@ def newListIfEmpty(yaml_object, *keys):
   newListIfEmpty(yaml_obj, 'services', 'cardsinitial', 'ports').append("127.0.0.1:5005:5005")
 
 if args.cards_project:
-  yaml_obj['services']['cardsinitial']['environment'].append("CARDS_PROJECT={}".format(args.cards_project))
+  yaml_obj['services']['cardsinitial']['environment'].append("PROJECT_NAME={}".format(args.cards_project))
 
 if args.composum:
   yaml_obj['services']['cardsinitial']['environment'].append("DEV=true")

distribution/Dockerfile

@@ -51,7 +51,8 @@ RUN apk upgrade --available
 RUN apk add \
   openjdk11-jre \
   python3 \
-  tzdata
+  tzdata \
+  bash
 
 # Optional: enable remote debugging at port 5005
 ENV DEBUG=
@@ -87,6 +88,12 @@ COPY --from=0 /root/.m2 /root/.m2
 # Copy in the build metadata
 COPY --from=0 /metadata /metadata
 
+# Copy in the generic CARDS logo
+COPY --from=0 /cards/modules/homepage/src/main/media/SLING-INF/content/libs/cards/resources/media/default/logo_light_bg.png /metadata/logo.png
+
+# Create the ~/.cards-generic-m2/repository empty directory
+RUN mkdir -p /root/.cards-generic-m2/repository
+
 # This is the default command executed when starting the container
 COPY docker_entry.sh /docker_entry.sh
 RUN chmod +x /docker_entry.sh

distribution/docker_entry.sh

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 
 # Licensed to the Apache Software Foundation (ASF) under one
 # or more contributor license agreements.  See the NOTICE file
@@ -37,106 +37,63 @@ then
   PERMISSIONS="${PERMISSIONS:-trusted}"
 fi
 
-PROJECT_ARTIFACTID=$1
-PROJECT_VERSION=$2
+CARDS_ARTIFACTID=$1
+CARDS_VERSION=$2
 
-VALID_CARDS_PROJECTS="||cards4kids|cards4lfs|cards4proms|cards4prems|cards4heracles|"
-echo "${VALID_CARDS_PROJECTS}" | grep -q "|${CARDS_PROJECT}|" || { echo "Invalid project specified - defaulting to generic CARDS."; unset CARDS_PROJECT; }
-
-featureFlagString=""
-if [ ! -z $CARDS_PROJECT ]
+if [ -z $PROJECT_VERSION ]
 then
-  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/${CARDS_PROJECT}/${PROJECT_VERSION}/slingosgifeature"
+  PROJECT_VERSION=$CARDS_VERSION
 fi
 
-[[ "${CARDS_PROJECT}" == 'cards4proms' || "${CARDS_PROJECT}" == 'cards4prems' ]] && SMTPS_ENABLED="true"
+VALID_PROJECT_NAMES="||cards4kids|cards4lfs|cards4proms|cards4prems|cards4heracles|"
+[ -e /external_project/project_code.txt ] && VALID_PROJECT_NAMES="${VALID_PROJECT_NAMES}$(cat /external_project/project_code.txt | head -n 1 | tr -d '\n')|"
+echo "${VALID_PROJECT_NAMES}" | grep -q "|${PROJECT_NAME}|" || { echo "Invalid project specified - defaulting to generic CARDS."; unset PROJECT_NAME; }
 
-[[ "${CARDS_PROJECT}" == 'cards4prems' ]] && CSV_EXPORT_ENABLED="true"
-[[ "${CARDS_PROJECT}" == 'cards4proms' || "${CARDS_PROJECT}" == 'cards4prems' ]] && CLARITY_IMPORT_ENABLED="true"
+featureFlagString=""
+if [ ! -z $PROJECT_NAME ] && [ ! -z $PROJECT_VERSION ]
+then
+  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/${PROJECT_NAME}/${PROJECT_VERSION}/slingosgifeature"
+fi
 
 if [ ! -z $DEV ]
 then
-  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards/${PROJECT_VERSION}/slingosgifeature/composum"
+  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards/${CARDS_VERSION}/slingosgifeature/composum"
 fi
 
 if [ ! -z $DEMO ]
 then
-  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-modules-demo-banner/${PROJECT_VERSION}/slingosgifeature,"
-  featureFlagString="${featureFlagString}mvn:io.uhndata.cards/cards-modules-upgrade-marker/${PROJECT_VERSION}/slingosgifeature,"
-  featureFlagString="${featureFlagString}mvn:io.uhndata.cards/cards-dataentry/${PROJECT_VERSION}/slingosgifeature/forms_demo"
+  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-modules-demo-banner/${CARDS_VERSION}/slingosgifeature,"
+  featureFlagString="${featureFlagString}mvn:io.uhndata.cards/cards-modules-upgrade-marker/${CARDS_VERSION}/slingosgifeature,"
+  featureFlagString="${featureFlagString}mvn:io.uhndata.cards/cards-dataentry/${CARDS_VERSION}/slingosgifeature/forms_demo"
 else
   if [ ! -z $DEMO_BANNER ]
   then
-    featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-modules-demo-banner/${PROJECT_VERSION}/slingosgifeature"
+    featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-modules-demo-banner/${CARDS_VERSION}/slingosgifeature"
   fi
 fi
 
 if [ ! -z $ENABLE_TEST_FEATURES ]
 then
-  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-modules-test-forms/${PROJECT_VERSION}/slingosgifeature"
+  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-modules-test-forms/${CARDS_VERSION}/slingosgifeature"
 fi
 
 if [ ! -z $SAML_CLOUD_IAM_DEMO ]
 then
   if [[ ${BEHIND_SSL_PROXY} == 'true' ]]
   then
-    featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-cloud-iam-demo-saml-support-ssl/${PROJECT_VERSION}/slingosgifeature"
+    featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-cloud-iam-demo-saml-support-ssl/${CARDS_VERSION}/slingosgifeature"
   else
-    featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-cloud-iam-demo-saml-support/${PROJECT_VERSION}/slingosgifeature"
+    featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-cloud-iam-demo-saml-support/${CARDS_VERSION}/slingosgifeature"
   fi
 fi
 
 if [ ! -z $ADDITIONAL_SLING_FEATURES ]
 then
-  featureFlagString="$featureFlagString -f $ADDITIONAL_SLING_FEATURES"
+  featureFlagString="$featureFlagString -f ${ADDITIONAL_SLING_FEATURES@P}"
 fi
 
-#Parse the (legacy) ADDITIONAL_RUN_MODES environment variable and determine the features that need to be enabled
-legacyRunModes=$(echo $ADDITIONAL_RUN_MODES | tr "," "\n")
-for legacyRunMode in $legacyRunModes
-do
-  #Perform the translation
-  if [[ ${legacyRunMode} == 'oak_tar' ]]
-  then
-    STORAGE=tar
-  elif [[ ${legacyRunMode} == 'oak_mongo' ]]
-  then
-    STORAGE=mongo
-  elif [[ ${legacyRunMode} == 'dev' ]]
-  then
-    featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards/${PROJECT_VERSION}/slingosgifeature/composum"
-  elif [[ ${legacyRunMode} == 'kids' ]]
-  then
-    featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards4kids/${PROJECT_VERSION}/slingosgifeature"
-  elif [[ ${legacyRunMode} == 'lfs' ]]
-  then
-    featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards4lfs/${PROJECT_VERSION}/slingosgifeature"
-  elif [[ ${legacyRunMode} == 'proms' ]]
-  then
-    featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards4proms/${PROJECT_VERSION}/slingosgifeature"
-    SMTPS_ENABLED="true"
-  elif [[ ${legacyRunMode} == 'test' ]]
-  then
-    featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-modules-test-forms/${PROJECT_VERSION}/slingosgifeature"
-  elif [[ ${legacyRunMode} == 'demo' ]]
-  then
-    featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-modules-demo-banner/${PROJECT_VERSION}/slingosgifeature,"
-    featureFlagString="${featureFlagString}mvn:io.uhndata.cards/cards-modules-upgrade-marker/${PROJECT_VERSION}/slingosgifeature,"
-    featureFlagString="${featureFlagString}mvn:io.uhndata.cards/cards-dataentry/${PROJECT_VERSION}/slingosgifeature/forms_demo"
-  elif [[ ${legacyRunMode} == 'permissions_open' ]]
-  then
-    PERMISSIONS="open"
-  elif [[ ${legacyRunMode} == 'permissions_trusted' ]]
-  then
-    PERMISSIONS="trusted"
-  elif [[ ${legacyRunMode} == 'permissions_ownership' ]]
-  then
-    PERMISSIONS="ownership"
-  fi
-done
-
 # Read /sling-features.json and enable the features required for this project
-PROJECT_REQUIRED_FEATURES=$(CARDS_VERSION=${PROJECT_VERSION} PROJECT_NAME=${CARDS_PROJECT} PROJECT_VERSION=${PROJECT_VERSION} PERMISSIONS=${PERMISSIONS} python3 /get_project_dependency_features.py /sling-features.json)
+PROJECT_REQUIRED_FEATURES=$(CARDS_VERSION=${CARDS_VERSION} PROJECT_NAME=${PROJECT_NAME} PROJECT_VERSION=${PROJECT_VERSION} PERMISSIONS=${PERMISSIONS} python3 /get_project_dependency_features.py /sling-features.json)
 if [ ! -z $PROJECT_REQUIRED_FEATURES ]
 then
   featureFlagString="$featureFlagString -f $PROJECT_REQUIRED_FEATURES"
@@ -150,7 +107,9 @@ echo "DEBUG = $DEBUG"
 echo "PERMISSIONS = $PERMISSIONS"
 echo "ADDITIONAL_RUN_MODES = $ADDITIONAL_RUN_MODES"
 echo "ADDITIONAL_SLING_FEATURES = $ADDITIONAL_SLING_FEATURES"
-echo "PROJECT_ARTIFACTID = $PROJECT_ARTIFACTID"
+echo "CARDS_ARTIFACTID = $CARDS_ARTIFACTID"
+echo "CARDS_VERSION = $CARDS_VERSION"
+echo "PROJECT_NAME = $PROJECT_NAME"
 echo "PROJECT_VERSION = $PROJECT_VERSION"
 
 #Are we using an external MongoDB service for data storage?
@@ -178,31 +137,31 @@ fi
 #Should the SMTPS OSGi bundle be enabled?
 if [[ "$SMTPS_ENABLED" == "true" ]]
 then
-  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-email-notifications/${PROJECT_VERSION}/slingosgifeature"
+  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-email-notifications/${CARDS_VERSION}/slingosgifeature"
 fi
 
 #Should the SAML OSGi bundle be enabled?
 if [[ "$SAML_AUTH_ENABLED" == "true" ]]
 then
-  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-saml-support/${PROJECT_VERSION}/slingosgifeature/base -C io.dropwizard.metrics:metrics-core:ALL -f mvn:io.uhndata.cards/cards-fetch-requires-saml-login/${PROJECT_VERSION}/slingosgifeature"
+  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-saml-support/${CARDS_VERSION}/slingosgifeature/base -C io.dropwizard.metrics:metrics-core:ALL -f mvn:io.uhndata.cards/cards-fetch-requires-saml-login/${CARDS_VERSION}/slingosgifeature"
 fi
 
 #Should the scheduled-csv-export module be loaded?
 if [[ "$CSV_EXPORT_ENABLED" == "true" ]]
 then
-  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-scheduled-csv-export/${PROJECT_VERSION}/slingosgifeature"
+  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-scheduled-csv-export/${CARDS_VERSION}/slingosgifeature"
 fi
 
 #Should the clarity-integration module be loaded?
 if [[ "$CLARITY_IMPORT_ENABLED" == "true" ]]
 then
-  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-clarity-integration/${PROJECT_VERSION}/slingosgifeature"
+  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-clarity-integration/${CARDS_VERSION}/slingosgifeature"
 fi
 
 #Should the cards-slack-notifications module be loaded?
 if [[ "$SLACK_NOTIFICATIONS_ENABLED" == "true" ]]
 then
-  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-slack-notifications/${PROJECT_VERSION}/slingosgifeature"
+  featureFlagString="$featureFlagString -f mvn:io.uhndata.cards/cards-slack-notifications/${CARDS_VERSION}/slingosgifeature"
 fi
 
 if [[ "$SMTPS_LOCALHOST_PROXY" == "true" ]]
@@ -228,4 +187,4 @@ done
 #Execute the volume_mounted_init.sh script if it is present
 [ -e /volume_mounted_init.sh ] && /volume_mounted_init.sh
 
-java -Djdk.xml.entityExpansionLimit=0 ${CARDS_JAVA_MEMORY_LIMIT_MB:+ -Xmx${CARDS_JAVA_MEMORY_LIMIT_MB}m} ${DEBUG:+ -Xdebug -Xnoagent -Djava.compiler=NONE -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=*:5005} -jar org.apache.sling.feature.launcher.jar -p .cards-data -u "file://$(realpath ${HOME}/.m2/repository),https://nexus.phenotips.org/nexus/content/groups/public,https://repo.maven.apache.org/maven2,https://repository.apache.org/content/groups/snapshots" -f ./${PROJECT_ARTIFACTID}-${PROJECT_VERSION}-core_${STORAGE}_far.far${EXT_MONGO_VARIABLES}${SMTPS_VARIABLES}${featureFlagString}
+java -Djdk.xml.entityExpansionLimit=0 ${CARDS_JAVA_MEMORY_LIMIT_MB:+ -Xmx${CARDS_JAVA_MEMORY_LIMIT_MB}m} ${DEBUG:+ -Xdebug -Xnoagent -Djava.compiler=NONE -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=*:5005} -jar org.apache.sling.feature.launcher.jar -p .cards-data -u "file://$(realpath ${HOME}/.m2/repository),file://$(realpath ${HOME}/.cards-generic-m2/repository),https://nexus.phenotips.org/nexus/content/groups/public,https://repo.maven.apache.org/maven2,https://repository.apache.org/content/groups/snapshots" -f ./${CARDS_ARTIFACTID}-${CARDS_VERSION}-core_${STORAGE}_far.far${EXT_MONGO_VARIABLES}${SMTPS_VARIABLES}${featureFlagString}

start_cards.sh

@@ -353,7 +353,8 @@ do
     ARGS[$ARGS_LENGTH]=mvn:io.uhndata.cards/cards-slack-notifications/${CARDS_VERSION}/slingosgifeature
     ARGS_LENGTH=${ARGS_LENGTH}+1
   else
-    ARGS[$i]=${ARGS[$i]/VERSION/${CARDS_VERSION}}
+    ARGS[$i]=${ARGS[$i]@P}
+    ARGS[$i]=${ARGS[$i]//VERSION/${CARDS_VERSION}}
   fi
 done