[RFC72] Update frontend for backend Spring Boot

end-to-end-test/local/docker_compose/build.sh

@@ -11,7 +11,6 @@ cd $E2E_WORKSPACE
 git clone --depth 1 --branch $BACKEND_BRANCH --single-branch https://github.com/$BACKEND_PROJECT_USERNAME/cbioportal.git
 cd cbioportal
 mvn -DskipTests clean install
-unzip portal/target/cbioportal*.war -d portal/target/war-exploded
 
 cd $PWD
 

end-to-end-test/local/docker_compose/cbioportal.yml

@@ -3,7 +3,7 @@ version: '3'
 services:
   cbioportal:
     volumes:
-    - $TEST_HOME/runtime-config/portal.properties:/cbioportal/portal.properties:ro
+    - $TEST_HOME/runtime-config/portal.properties:/cbioportal-webapp/portal.properties:ro
     - $E2E_WORKSPACE/portalInfo:/portalInfo
 
 volumes:

end-to-end-test/local/docker_compose/keycloak.yml

@@ -2,11 +2,11 @@ version: '3'
 
 services:
   cbioportal:
+    image: cbioportal/cbioportal:demo-rfc72
     volumes:
-      - $TEST_HOME/docker_compose/keycloak/samlKeystore.jks:/cbioportal-webapp/WEB-INF/classes/samlKeystore.jks:ro
-      - $E2E_WORKSPACE/keycloak/idp-metadata.xml:/cbioportal-webapp/WEB-INF/classes/client-tailored-saml-idp-metadata.xml:ro
-    command: /bin/sh -c "java -Xms2g -Xmx4g -Dauthenticate=saml -Dsession.service.url=http://cbioportal-session:5000/api/sessions/my_portal/ -jar webapp-runner.jar -AmaxHttpHeaderSize=16384 -AconnectionTimeout=20000 --enable-compression /cbioportal-webapp"
-
+      - $TEST_HOME/docker_compose/keycloak/samlKeystore.jks:/cbioportal-webapp/samlKeystore.jks:ro
+      - $E2E_WORKSPACE/keycloak/idp-metadata.xml:/cbioportal-webapp/client-tailored-saml-idp-metadata.xml:ro
+    command: /bin/sh -c "rm -rf /cbioportal-webapp/lib/servlet-api-2.5.jar && java -Xms2g -Xmx4g -Ddat.method=none -Dmultithread.core_pool_size=1 -Dauthenticate=saml -Dspring.security.saml2.relyingparty.registration.cbio-idp.identityprovider.metadata-uri=classpath://saml2-idp-metadata.xml -Dsession.service.url=http://cbioportal-session:5000/api/sessions/my_portal/ -cp '/cbioportal-webapp:/cbioportal-webapp/lib/*' org.cbioportal.PortalApplication"
   keycloak:
     networks:
     - cbio-net

end-to-end-test/local/docker_compose/setup.sh

@@ -11,6 +11,9 @@ mkdir -p $E2E_WORKSPACE/keycloak
 cd $E2E_WORKSPACE
 git clone https://github.com/cBioPortal/cbioportal-docker-compose.git
 cd cbioportal-docker-compose
+#TODO: temporarily use docker compose for demo-rfc72
+# https://github.com/cBioPortal/cbioportal-docker-compose/pull/23
+git checkout demo-rfc72
 
 # update keycloak config with permissions for test studies
 config_json="$(cat $TEST_HOME/docker_compose/keycloak/keycloak-config.json)"

end-to-end-test/local/runtime-config/portal.properties

@@ -2,6 +2,12 @@
 app.name=cbioportal
 
 # database
+spring.datasource.url=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false&allowPublicKeyRetrieval=true
+spring.datasource.username=cbio_user
+spring.datasource.password=somepassword
+spring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver
+spring.jpa.database-platform=org.hibernate.dialect.MySQL5InnoDBDialect
+spring.datasource.driver-class-name=com.mysql.jdbc.Driver
 db.user=cbio_user
 db.password=somepassword
 db.driver=com.mysql.jdbc.Driver

env/custom.sh

@@ -1,2 +1,3 @@
 #export CBIOPORTAL_URL="http://localhost:8081"
 #export GENOME_NEXUS_URL="https://www.genomenexus.org"
+BACKEND=cbioportal:demo-rfc72