[RFC72] Spring Boot Upgrade

.circleci/config.yml

@@ -6,7 +6,7 @@ version: 2
 jobs:
     build_backend:
         docker:
-            - image: maven:3-openjdk-11
+            - image: maven:3-eclipse-temurin-21
         working_directory: /tmp/repos/cbioportal
         steps:
             - checkout
@@ -18,10 +18,10 @@ jobs:
                     - v1-mvn-dependencies-{{ checksum "poms_combined" }}
                     - v1-mvn-dependencies-
             - run:
-                name: Build and unzip war
+                name: Build and unzip jar
                 command: |
-                    mvn -DskipTests clean install && \
-                    unzip portal/target/cbioportal*.war -d portal/target/war-exploded
+                    cp src/main/resources/application.properties.EXAMPLE src/main/resources/application.properties && \
+                    mvn -DskipTests clean package
             - save_cache:
                 paths:
                   - ~/.m2
@@ -39,12 +39,12 @@ jobs:
             - run:
                 name: Pull frontend code
                 command: |
-                    export FRONTEND_VERSION=$(grep 'frontend\.version' pom.xml | sed 's/<frontend\.version>//g' | sed 's|</frontend\.version>||' | tr -d '[:blank:]') && \
+                    export FRONTEND_VERSION=$(grep '<frontend\.version>' pom.xml | sed 's/<frontend\.version>//g' | sed 's|</frontend\.version>||' | tr -d '[:blank:]') && \
                     export FRONTEND_ORG=$(grep 'frontend\.groupId' pom.xml | sed 's/<frontend\.groupId>//g' | sed 's|</frontend\.groupId>||' | tr -d '[:blank:]' | cut -d. -f3) && \
                     git clone https://github.com/$FRONTEND_ORG/cbioportal-frontend.git && \
                     cd cbioportal-frontend && \
                     git fetch --tags && \
-                    git checkout ${FRONTEND_VERSION}
+                    git checkout demo-rfc72
             - persist_to_workspace:
                 root: /tmp/repos
                 paths:
@@ -145,11 +145,6 @@ jobs:
                 command: |
                     $TEST_HOME/docker_compose/setup.sh
                 no_output_timeout: 25m
-            - run:
-                name: Generate checksum of data that populates the test database
-                command: |
-                    bash -x $TEST_HOME/runtime-config/db_content_fingerprint.sh | tee /tmp/db_data_md5key
-                no_output_timeout: 25m
             - run:
                 name: Create MySQL data directory
                 command: |
@@ -219,7 +214,7 @@ jobs:
             - store_artifacts:
                     path: /tmp/repos/cbioportal-frontend/end-to-end-test/local/junit/errors/
                     destination: /errors
-                
+
         environment:
             PORTAL_SOURCE_DIR: /tmp/repos/cbioportal-frontend/
             TEST_HOME: /tmp/repos/cbioportal-frontend/end-to-end-test/local

.github/workflows/core-test.yml

@@ -17,10 +17,11 @@ jobs:
         uses: actions/checkout@v2
         with:
           path: ./cbioportal
-      - name: 'Set up JDK 11'
-        uses: actions/setup-java@v1
+      - name: 'Set up JDK 21'
+        uses: oracle-actions/setup-java@v1
         with:
-          java-version: 11
+          website: oracle.com
+          release: 21
       - name: 'Cache Maven packages'
         uses: actions/cache@v1
         with:
@@ -40,6 +41,10 @@ jobs:
         run: |
           mkdir -p ~/.m2 && \
           cp .github/settings.xml ~/.m2
+      - name: 'Create application.properties'
+        working-directory: ./cbioportal
+        run: |
+          cp src/main/resources/application.properties.EXAMPLE src/main/resources/application.properties
       - name: 'Build cBioPortal once without tests'
         working-directory: ./cbioportal
         run: |

.github/workflows/dockerimage.yml

@@ -18,7 +18,9 @@ jobs:
     steps:
       - name: Checkout git repo
         uses: actions/checkout@v3
-
+      - name: 'Create application.properties'
+        run: |
+          cp src/main/resources/application.properties.EXAMPLE src/main/resources/application.properties
       - name: Extract metadata
         id: meta
         uses: docker/metadata-action@v4
@@ -30,19 +32,19 @@ jobs:
             type=ref,event=branch
             type=semver,pattern={{version}}
 
-      # The following two actions are required to build multi-platform images
-      # buildx is an extension of docker build, QUEM is used to convert the binary to varies architecture
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-
       - name: Login to DockerHub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
+      # The following two actions are required to build multi-platform images
+      # buildx is an extension of docker build, QUEM is used to convert the binary to varies architecture
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
       - name: Publish Docker Image on Tag
         uses: docker/build-push-action@v3
         with:
@@ -60,7 +62,9 @@ jobs:
       steps:
         - name: Checkout git repo
           uses: actions/checkout@v3
-
+        - name: 'Create application.properties'
+          run: |
+            cp src/main/resources/application.properties.EXAMPLE src/main/resources/application.properties
         - name: Extract metadata
           id: meta
           uses: docker/metadata-action@v4
@@ -75,19 +79,19 @@ jobs:
               type=ref,event=branch
               type=semver,pattern={{version}}
 
-        # The following two actions are required to build multi-platform images
-        # buildx is an extension of docker build, QUEM is used to convert the binary to varies architecture
-        - name: Set up QEMU
-          uses: docker/setup-qemu-action@v2
-        - name: Set up Docker Buildx
-          uses: docker/setup-buildx-action@v2
-
         - name: Login to DockerHub
-          uses: docker/login-action@v2
+          uses: docker/login-action@v3
           with:
             username: ${{ secrets.DOCKER_USERNAME }}
             password: ${{ secrets.DOCKER_PASSWORD }}
 
+        # The following two actions are required to build multi-platform images
+        # buildx is an extension of docker build, QUEM is used to convert the binary to varies architecture
+        - name: Set up QEMU
+          uses: docker/setup-qemu-action@v3
+        - name: Set up Docker Buildx
+          uses: docker/setup-buildx-action@v3
+
         - name: Publish Docker Image on Tag
           uses: docker/build-push-action@v3
           with:

.github/workflows/integration-test.yml

@@ -19,16 +19,21 @@ jobs:
           sudo apt-get install python3-setuptools && \
           pip3 install -U wheel && \
           pip3 install -r ./requirements.txt
-      - name: 'Set up JDK 11'
-        uses: actions/setup-java@v1
+      - name: 'Set up JDK 21'
+        uses: oracle-actions/setup-java@v1
         with:
-          java-version: 11
+          website: oracle.com
+          release: 21
       - name: 'Cache Maven packages'
         uses: actions/cache@v1
         with:
           path: ~/.m2
           key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
           restore-keys: ${{ runner.os }}-m2
+      - name: 'Copy application.properties'
+        working-directory: ./cbioportal
+        run: |
+          cp src/main/resources/application.properties.EXAMPLE src/main/resources/application.properties
       - name: 'Build cbioportal'
         working-directory: ./cbioportal
         run: |
@@ -37,21 +42,30 @@ jobs:
         uses: actions/checkout@master
         with:
           repository: cbioportal/cbioportal-docker-compose
+          ref: demo-rfc72
           path: ./cbioportal-docker-compose
       - name: 'Initialize cbioportal-docker-compose'
         working-directory: ./cbioportal-docker-compose
         run: |
           cd ./data && ./init.sh && rm -rf ./studies/* && cd ../config && \
-          cat $PORTAL_SOURCE_DIR/portal/target/classes/portal.properties | \
-              sed 's|db.host=.*||' | \
-              sed 's|db.portal_db_name=.*||' | \
-              sed 's|db.use_ssl=.*||' | \
-              sed 's|db.connection_string=.*|db.connection_string=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false\&allowPublicKeyRetrieval=true|' \
-              > portal.properties && more portal.properties
+          cat $PORTAL_SOURCE_DIR/src/main/resources/application.properties | \
+              sed 's|spring.datasource.url=.*|spring.datasource.url=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false|' | \
+              sed 's|spring.datasource.username=.*|spring.datasource.username=cbio_user|' | \
+              sed 's|spring.datasource.password=.*|spring.datasource.password=somepassword|' \
+              > application.properties && \
+          echo "db.user=cbio_user" >> application.properties && \
+          echo "db.password=somepassword" >> application.properties && \
+          echo "db.connection_string=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false" >> application.properties && \
+          echo "db.driver=com.mysql.jdbc.Driver" >> application.properties
+      - name: 'Copy cgds.sql file into Docker Compose'
+        run: cp ./cbioportal/src/main/resources/db-scripts/cgds.sql ./cbioportal-docker-compose/data/.
+      - name: 'Dump Properties'
+        working-directory: ./cbioportal-docker-compose
+        run: cat config/application.properties
       - name: 'Start cbioportal-docker-compose'
         working-directory: ./cbioportal-docker-compose
         run: |
-          docker-compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml up -d
+          export DOCKER_IMAGE_CBIOPORTAL=cbioportal/cbioportal:demo-rfc72-squash && docker-compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml up -d
       - name: 'Wait for cbioportal to initialize ...'
         id: startup
         uses: nev7n/wait_for_response@v1
@@ -60,17 +74,20 @@ jobs:
           responseCode: 200
           timeout: 900000
           interval: 30000
+      - name: Log cBioPortal Service
+        if: ${{ failure() && steps.startup.conclusion == 'failure' }}
+        working-directory: ./cbioportal-docker-compose
+        run: docker-compose logs cbioportal
       - name: 'TEST - Validate and load study_es_0'
         if: steps.startup.conclusion == 'success'
         working-directory: ./cbioportal-docker-compose
         run: |
           $PORTAL_SOURCE_DIR/test/integration/test_load_study.sh
       - name: 'TEST - Add OncoKB annotations to study'
         if: steps.startup.conclusion == 'success'
-        working-directory: ./cbioportal
+        working-directory: ./cbioportal-docker-compose
         run: |
-          export PYTHONPATH=$PORTAL_SOURCE_DIR/core/src/main/scripts && \
-          $PORTAL_SOURCE_DIR/test/integration/integration_test_oncokb_import.sh
+          $PORTAL_SOURCE_DIR/test/integration/test_integration_test_oncokb_import.sh
       - name: 'TEST - Update OncoKB annotations'
         if: steps.startup.conclusion == 'success'
         working-directory: ./cbioportal-docker-compose

.github/workflows/sonarcloud.yml

@@ -13,10 +13,10 @@ jobs:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
-      - name: Set up JDK 11
+      - name: Set up JDK 21
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 21
       - name: Cache SonarCloud packages
         uses: actions/cache@v1
         with:
@@ -29,6 +29,9 @@ jobs:
           path: ~/.m2
           key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
           restore-keys: ${{ runner.os }}-m2
+      - name: 'Create application.properties'
+        run: |
+          cp src/main/resources/application.properties.EXAMPLE src/main/resources/application.properties
       - name: Build and analyze
         env:
           SONAR_TOKEN:  de1b5cc660cd210dde840f492c371da6cc801763

.github/workflows/validate-data.yml

@@ -9,13 +9,18 @@ jobs:
         uses: actions/checkout@v2
         with:
           path: ./cbioportal
+      - name: 'Checkout core module'
+        uses: actions/checkout@v4
+        with:
+          path: ./cbioportal/core
+          repository: cBioPortal/cbioportal-core
       - name: 'Validate tests'
         working-directory: ./cbioportal
         run: |
           docker run -v ${PWD}:/cbioportal python:3.6 /bin/sh -c '
             cd /cbioportal &&
             pip install -r requirements.txt &&
-            export PYTHONPATH=/cbioportal/core/src/main/scripts &&
+            export PYTHONPATH=/cbioportal/core/src/main/resources/scripts &&
             cd /cbioportal/core/src/test/scripts/ &&
             python unit_tests_validate_data.py &&
             python system_tests_validate_data.py &&

.gitignore

@@ -1,3 +1,21 @@
+liftover/target/*
+target/
+portal/target/*
+core/target/*
+annotator/target/*
+importer/target/*
+business/target/*
+model/target/*
+scripts/target
+persistence/persistence-api/target/*
+persistence/persistence-mybatis/target/*
+persistence/persistence-mybatis-test/target/*
+service/target/*
+mutation-assessor/target/*
+cbioportal-client/target/*
+mondrian-cy3-app/target/*
+utils/target/*
+web/target/*
 nb-configuration.xml
 nbactions-private.xml
 oncotator/src/main/resources/db.properties
@@ -55,6 +73,7 @@ portal/src/main/webapp/WEB-INF/logback.xml
 !src/main/resource/*.EXAMPLE
 firehose-importer/reference_data/gene_info
 portal.properties
+application.properties
 importer.properties
 log4j.properties
 build.properties
@@ -64,21 +83,6 @@ syntax: glob
 *.swp
 importer/*.log
 firehose-importer/*.txt
-portal/target/*
-liftover/target/*
-core/target/*
-annotator/target/*
-importer/target/*
-business/target/*
-model/target/*
-persistence/persistence-api/target/*
-persistence/persistence-mybatis/target/*
-persistence/persistence-mybatis-test/target/*
-service/target/*
-web/target/*
-mutation-assessor/target/*
-cbioportal-client/target/*
-mondrian-cy3-app/target/*
 nbactions.xml
 */*.iml
 *.iml
@@ -93,18 +97,16 @@ dependency-reduced-pom.xml
 /core/nbactions-private.xml
 .profile.d/
 Procfile
-scripts/target
 node_modules/
-target/
-portal/META-INF/*
-portal/reactapp/*
 package.json
 .vscode/
 *.tramp_history
 pom.version.*
 pom.xml.*
-db-scripts/src/main/resources/cgds-test.sql
 pom.xml.*
 Dockerfile.local
 .factorypath
-.retype
+.retype
+security.properties
+*.crt
+*.key