Resolve conflicts

opencb · Feb 20, 2023 · e85e3ba · e85e3ba
2 parents 6a6bba9 + 586073b
commit e85e3ba
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diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml
@@ -10,114 +10,33 @@ on:
 jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
-    with:
-      maven_opts: -Dcheckstyle.skip -DCELLBASE.WAR.NAME=cellbase
 
   test:
-    name: CellBase Test
-    runs-on: ubuntu-20.04
+    uses: opencb/cellbase/.github/workflows/test-analysis.yml@develop
     needs: build
-    strategy:
-      matrix:
-        mongodb: ["4.2"]
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: '10'
-      - name: Set up JDK 8
-        uses: actions/setup-java@v3
-        with:
-          distribution: 'temurin'
-          java-version: '8'
-          cache: 'maven'
-      - name: Start MongoDB v${{ matrix.mongodb }}
-        uses: supercharge/[email protected]
-        with:
-          mongodb-version: ${{ matrix.mongodb }}
-          mongodb-replica-set: rs-test
-      - name: Build with Maven
-        run: mvn -T 2 clean install -DskipTests -Dcheckstyle.skip
-
-  sonar:
-    uses: opencb/java-common-libs/.github/workflows/sonar-analysis-workflow.yml@develop
-    needs: test
-    with:
-      sonarProjectKey: opencb_cellbase
-    secrets:
-      SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+    secrets: inherit
+#      SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+#      SSH_TESTING_SERVER_HOST: ${{ secrets.SSH_TESTING_SERVER_HOST}}
+#      SSH_TESTING_SERVER_PORT: ${{ secrets.SSH_TESTING_SERVER_PORT}}
+#      SSH_TESTING_SERVER_USER: ${{ secrets.SSH_TESTING_SERVER_USER }}
+#      SSH_TESTING_SERVER_PASSWORD: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }}
 
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: test
     with:
       maven_opts: -Dcheckstyle.skip -DCELLBASE.WAR.NAME=cellbase
-    secrets:
-      MAVEN_NEXUS_USER: ${{ secrets.MAVEN_NEXUS_USER }}
-      MAVEN_NEXUS_PASSWORD: ${{ secrets.MAVEN_NEXUS_PASSWORD }}
-      MAVEN_GPG_PASSPHRASE: ${{ secrets.MAVEN_GPG_PASSPHRASE }}
-      MAVEN_GPG_PRIVATE_KEY: ${{ secrets.MAVEN_GPG_PRIVATE_KEY }}
+    secrets: inherit
+#      MAVEN_NEXUS_USER: ${{ secrets.MAVEN_NEXUS_USER }}
+#      MAVEN_NEXUS_PASSWORD: ${{ secrets.MAVEN_NEXUS_PASSWORD }}
+#      MAVEN_GPG_PASSPHRASE: ${{ secrets.MAVEN_GPG_PASSPHRASE }}
+#      MAVEN_GPG_PRIVATE_KEY: ${{ secrets.MAVEN_GPG_PRIVATE_KEY }}
 
   deploy-docker:
     uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
     needs: test
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base
-    secrets:
-      DOCKER_HUB_USER: ${{ secrets.DOCKER_HUB_USER }}
-      DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
-
-#  deploy:
-#    name: Build and Deploy CellBase libs, Javadocs and Docker images in Maven Central and DockerHub repositories
-#    runs-on: ubuntu-20.04
-#    needs: test
-#    steps:
-#      - uses: actions/checkout@v2
-#        with:
-#          fetch-depth: '10'
-#      - name: Set up JDK 1.8
-#        uses: actions/setup-java@v1
-#        with:
-#          java-version: 1.8
-#          server-id: ossrh                        # Value of the distributionManagement/repository/id field of the pom.xml
-#          server-username: MAVEN_NEXUS_USER       # env variable for username in deploy
-#          server-password: MAVEN_NEXUS_PASSWORD   # env variable for token in deploy
-#
-#      ## IMPORTANT: this creates the 'build' installation folder and must be the FIRST action!
-#      ## Deploy in Maven repository
-#      - name: Copy GPG Private key
-#        run: echo "${{ secrets.MAVEN_GPG_PRIVATE_KEY }}" > private-key.txt && gpg --import --no-tty --batch --yes private-key.txt
-#      - name: Deploy to Maven Central respository
-#        env:
-#          MAVEN_NEXUS_USER: ${{ secrets.MAVEN_NEXUS_USER }}
-#          MAVEN_NEXUS_PASSWORD: ${{ secrets.MAVEN_NEXUS_PASSWORD }}
-#        run: mvn clean deploy -Dgpg.passphrase=${{ secrets.MAVEN_GPG_PASSPHRASE }} -DskipTests -P deploy
-#
-#      ## making requests via Python needs special package
-#      - name: Install Python package
-#        run: pip3 install requests
-#
-#      ## Build and deploy Docker images to DockerHub
-#      - name: Login to dockerhub
-#        run: docker login -u ${{ secrets.DOCKER_HUB_USER }} -p ${{ secrets.DOCKER_HUB_PASSWORD }}
-#      - name: Build and publish Docker images to DockerHub
-#        run: python3 ./build/cloud/docker/docker-build.py push
-#
-#      ## Generate and deploy Javadocs
-#      - name: Get CellBase version
-#        id: get_version
-#        run: echo ::set-output name=VERSION::$(grep '<cellbase.version>' pom.xml | sed 's/cellbase.version//g' | sed 's/[<>/ ]//g')
-#      - name: Generate Javadocs
-#        run: mvn javadoc:aggregate
-#      - name: Deploy to server
-#        id: deploy
-#        uses: Pendect/[email protected]
-#        env:
-#          DEPLOY_KEY: ${{secrets.SCP_PRIVATE_KEY}}
-#        with:
-#          flags: '-avzr --delete'
-#          options: ''
-#          ssh_options: ''
-#          src: 'target/site/apidocs/*'
-#          dest: '${{ secrets.SCP_SITE_USER }}@128.232.224.128:/mnt/resources/opencb/cellbase/javadocs/${{ steps.get_version.outputs.VERSION }}'
-#      - name: Display status from deploy
-#        run: echo "${{ steps.deploy.outputs.status }}"
+    secrets: inherit
+#      DOCKER_HUB_USER: ${{ secrets.DOCKER_HUB_USER }}
+#      DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
diff --git a/.github/workflows/pull-request-merge.yml b/.github/workflows/pull-request-merge.yml
@@ -0,0 +1,18 @@
+name: "Merge Workflow"
+
+on:
+  pull_request:
+    branches:
+      - "develop"
+      - "release-*"
+    types:
+      - closed
+
+jobs:
+  delete-docker:
+    uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@develop
+    with:
+      cli: python3 ./build/cloud/docker/docker-build.py delete --images base --tag ${{ github.head_ref }}
+    secrets:
+      DOCKER_HUB_USER: ${{ secrets.DOCKER_HUB_USER }}
+      DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -9,184 +9,47 @@ on:
 jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
-    with:
-      maven_opts: -Dcheckstyle.skip -DCELLBASE.WAR.NAME=cellbase
 
   test:
-    name: CellBase Test
-    runs-on: ubuntu-20.04
+    uses: opencb/cellbase/.github/workflows/test-analysis.yml@develop
     needs: build
-    strategy:
-      matrix:
-        mongodb: ["4.2"]
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: '10'
-      - name: Set up JDK 8
-        uses: actions/setup-java@v3
-        with:
-          distribution: 'temurin'
-          java-version: '8'
-          cache: 'maven'
-      - name: Start MongoDB v${{ matrix.mongodb }}
-        uses: supercharge/[email protected]
-        with:
-          mongodb-version: ${{ matrix.mongodb }}
-          mongodb-replica-set: rs-test
-      - name: Build with Maven
-        run: mvn -T 2 clean install -DskipTests -Dcheckstyle.skip
-
-  sonar:
-    uses: opencb/java-common-libs/.github/workflows/sonar-analysis-workflow.yml@develop
-    needs: test
-    with:
-      sonarProjectKey: opencb_cellbase
-    secrets:
-      SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+    secrets: inherit
+#      SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+#      SSH_TESTING_SERVER_HOST: ${{ secrets.SSH_TESTING_SERVER_HOST}}
+#      SSH_TESTING_SERVER_PORT: ${{ secrets.SSH_TESTING_SERVER_PORT}}
+#      SSH_TESTING_SERVER_USER: ${{ secrets.SSH_TESTING_SERVER_USER }}
+#      SSH_TESTING_SERVER_PASSWORD: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }}
 
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: test
     with:
       maven_opts: -Dcheckstyle.skip -DCELLBASE.WAR.NAME=cellbase
-    secrets:
-      MAVEN_NEXUS_USER: ${{ secrets.MAVEN_NEXUS_USER }}
-      MAVEN_NEXUS_PASSWORD: ${{ secrets.MAVEN_NEXUS_PASSWORD }}
-      MAVEN_GPG_PASSPHRASE: ${{ secrets.MAVEN_GPG_PASSPHRASE }}
-      MAVEN_GPG_PRIVATE_KEY: ${{ secrets.MAVEN_GPG_PRIVATE_KEY }}
+    secrets: inherit
+#      MAVEN_NEXUS_USER: ${{ secrets.MAVEN_NEXUS_USER }}
+#      MAVEN_NEXUS_PASSWORD: ${{ secrets.MAVEN_NEXUS_PASSWORD }}
+#      MAVEN_GPG_PASSPHRASE: ${{ secrets.MAVEN_GPG_PASSPHRASE }}
+#      MAVEN_GPG_PRIVATE_KEY: ${{ secrets.MAVEN_GPG_PRIVATE_KEY }}
 
   deploy-docker:
     uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
     needs: test
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base
-    secrets:
-      DOCKER_HUB_USER: ${{ secrets.DOCKER_HUB_USER }}
-      DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
+    secrets: inherit
+#      DOCKER_HUB_USER: ${{ secrets.DOCKER_HUB_USER }}
+#      DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
 
   deploy-python:
     uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop
     needs: test
     with:
       cli: bash ./clients/python/python-build.sh push
       artifact: build-folder
-    secrets:
-      PYPI_TWINE_USER: ${{ secrets.PYPI_TWINE_USER }}
-      PYPI_TWINE_PASSWORD: ${{ secrets.PYPI_TWINE_PASSWORD }}
+    secrets: inherit
+#      PYPI_TWINE_USER: ${{ secrets.PYPI_TWINE_USER }}
+#      PYPI_TWINE_PASSWORD: ${{ secrets.PYPI_TWINE_PASSWORD }}
 
   release:
     uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop
     needs: [deploy-maven, deploy-docker, deploy-python]
-
-#  deploy:
-#    name: Build and deploy CellBase libs, Java docs and Docker images in Maven Central and DockerHub repositories
-#    runs-on: ubuntu-18.04
-##    needs: test
-#    steps:
-#      - uses: actions/checkout@v2
-#        with:
-#          fetch-depth: '10'
-#      - name: Set up JDK 1.8
-#        uses: actions/setup-java@v1
-#        with:
-#          java-version: 1.8
-#          server-id: ossrh                        # Value of the distributionManagement/repository/id field of the pom.xml
-#          server-username: MAVEN_NEXUS_USER       # env variable for username in deploy
-#          server-password: MAVEN_NEXUS_PASSWORD   # env variable for token in deploy
-#
-#      ## IMPORTANT: this creates the 'build' installation folder and must be the FIRST action!
-#      ## Deploy in Maven repository
-#      - name: Copy GPG Private key
-#        run: echo "${{ secrets.MAVEN_GPG_PRIVATE_KEY }}" > private-key.txt && gpg --import --no-tty --batch --yes private-key.txt
-#      - name: Deploy to Maven Central respository
-#        env:
-#          MAVEN_NEXUS_USER: ${{ secrets.MAVEN_NEXUS_USER }}
-#          MAVEN_NEXUS_PASSWORD: ${{ secrets.MAVEN_NEXUS_PASSWORD }}
-#        run: mvn clean deploy -Dgpg.passphrase=${{ secrets.MAVEN_GPG_PASSPHRASE }} -DskipTests -DCELLBASE.WAR.NAME=cellbase -P deploy
-#
-#      ## set tag name
-#      - name: Get tag
-#        id: get_tag
-#        run: echo ::set-output name=TAG_NAME::${GITHUB_REF/refs\/tags\//}
-#
-#      ## Build and deploy Docker images to DockerHub
-#      - name: Login to dockerhub
-#        run: docker login -u ${{ secrets.DOCKER_HUB_USER }} -p ${{ secrets.DOCKER_HUB_PASSWORD }}
-#      - name: Build and publish Docker images to DockerHub
-#        run: python3 ./build/cloud/docker/docker-build.py push --tag ${{ steps.get_tag.outputs.TAG_NAME }}
-#
-#      ## Delete snapshot
-#      - name: Delete SNAPSHOT image on dockerhub, if present
-#        env:
-#          SNAPSHOT_TAG: "${{ steps.get_tag.outputs.TAG_NAME }}-SNAPSHOT"
-#        run: python3 ./build/cloud/docker/docker-build.py delete --username ${{ secrets.DOCKER_HUB_USER }} --password ${{ secrets.DOCKER_HUB_PASSWORD}} --tag ${SNAPSHOT_TAG}
-#
-#      ## Publish GitHub release
-#      - name: Create GitHub Release
-#        id: create_release
-#        uses: actions/create-release@master
-#        env:
-#          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
-#        with:
-#          tag_name: ${{ github.ref }}
-#          release_name: Release ${{ github.ref }}
-#          body: |
-#            See http://docs.opencb.org/display/cellbase/Release+Notes for the full list of features and fixes in this release.
-#          draft: false
-#          prerelease: false
-#
-#      ## Tar the build directory
-#      - name: zip
-#        id: zip
-#        run: tar -zcf cellbase-${{ steps.get_tag.outputs.TAG_NAME }}.tar.gz build --transform s/build/cellbase-${{ steps.get_tag.outputs.TAG_NAME }}/
-#
-#      ## Upload tarball
-#      - name: Upload Release Asset
-#        id: upload-release-asset
-#        uses: actions/[email protected]
-#        env:
-#          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-#        with:
-#          upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
-#          asset_path: ./cellbase-${{ steps.get_tag.outputs.TAG_NAME }}.tar.gz
-#          asset_name: cellbase-${{ steps.get_tag.outputs.TAG_NAME }}.tar.gz
-#          asset_content_type: application/tar+gzip
-
-#  site:
-#    name: Generate Maven site
-#    runs-on: ubuntu-18.04
-#    needs: build
-#    steps:
-#      - uses: actions/checkout@v2
-#        with:
-#          fetch-depth: '10'
-#      - name: Set up JDK 1.8
-#        uses: actions/setup-java@v1
-#        with:
-#          java-version: 1.8
-#      - name: Generate Site with Maven CLI
-#        run: mvn site
-#      - name: Prepare Maven Site submodules
-#        run: cp -r cellbase-app/target/site target/site/cellbase-app &&
-#          cp -r cellbase-client/target/site target/site/cellbase-client &&
-#          cp -r cellbase-core/target/site target/site/cellbase-core &&
-#          cp -r cellbase-lib/target/site target/site/cellbase-lib &&
-#          cp -r cellbase-server/target/site target/site/cellbase-server
-#      - name: Get CellBase version
-#        id: get_version
-#        run: echo ::set-output name=VERSION::$(grep '<cellbase.version>' pom.xml | sed 's/cellbase.version//g' | sed 's/[<>/ ]//g')
-#      - name: Get current date in YYMMDD format
-#        id: get_date
-#        run: echo ::set-output name=YYMMDD::$(date +%Y%m%d)
-#      - name: Get current date in HHMMSS format
-#        id: get_time
-#        run: echo ::set-output name=HHMMSS::$(date +%H%M%S)
-#      - name: Deploy Site web recursively to remote
-#        uses: garygrossgarten/github-action-scp@release
-#        with:
-#          local: target/site
-#          remote: /mnt/resources/opencb/cellbase/site/${{ steps.get_tag.outputs.TAG_NAME }}/${{ steps.get_date.outputs.YYMMDD }}/${{ steps.get_time.outputs.HHMMSS }}-${{ github.sha }}
-#          host: 128.232.224.128
-#          username: ${{ secrets.SCP_SITE_USER }}
-#          password: ${{ secrets.SCP_SITE_PASSWORD }}