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juanfeSanahujajuanfeSanahuja
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Merge branch 'release-5.2.x'
2 parents 717f469 + 67acad1 commit b0812f6

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‎.github/workflows/build-java-app-workflow.yml

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@@ -6,6 +6,10 @@ on:
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maven_opts:
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type: string
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required: false
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build_folder:
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type: string
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required: false
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default: "build-folder"
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outputs:
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version:
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description: "Project version"
@@ -34,10 +38,10 @@ jobs:
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./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }}
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fi
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- name: Maven Build (skip tests)
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run: mvn -T 2 clean install -DskipTests ${{ inputs.maven_opts }}
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run: mvn -T 2 clean install -DskipTests ${{ inputs.maven_opts }} --no-transfer-progress
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- uses: actions/upload-artifact@v4
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with:
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name: build-folder
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name: ${{ inputs.build_folder }}
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path: build
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- id: get_project_version
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name: Get project version

‎.github/workflows/deploy-docker-hub-workflow.yml

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branch:
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type: string
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required: false
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build_folder:
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type: string
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required: false
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default: "build-folder"
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secrets:
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DOCKER_HUB_USER:
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required: true
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ref: ${{ inputs.branch }}
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- uses: actions/download-artifact@v4
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with:
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name: build-folder
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name: ${{ inputs.build_folder }}
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path: build
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- name: Chmod
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run: "find build -regex '.*sh' | while read file ; do chmod u+x $file ; done"

‎.github/workflows/deploy-maven-repository-workflow.yml

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@@ -37,17 +37,17 @@ jobs:
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gpg-private-key: ${{ secrets.MAVEN_GPG_PRIVATE_KEY }} # Value of the GPG private key to import
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gpg-passphrase: MAVEN_GPG_PASSPHRASE # env variable for GPG private key passphrase
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- name: Deploy to Maven Central repository
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run: mvn clean deploy -DskipTests -P deploy-maven ${{ inputs.maven_opts }}
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run: mvn clean deploy -DskipTests -P deploy-maven ${{ inputs.maven_opts }} --no-transfer-progress
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env:
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MAVEN_NEXUS_USER: ${{ secrets.MAVEN_NEXUS_USER }}
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MAVEN_NEXUS_PASSWORD: ${{ secrets.MAVEN_NEXUS_PASSWORD }}
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MAVEN_NEXUS_USER: ${{ secrets.MAVEN_USER_TOKEN }}
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MAVEN_NEXUS_PASSWORD: ${{ secrets.MAVEN_PASSWORD_TOKEN }}
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MAVEN_GPG_PASSPHRASE: ${{ secrets.MAVEN_GPG_PASSPHRASE }}
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- name: Set up Java for publishing to GitHub Packages
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uses: actions/setup-java@v4
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with:
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distribution: 'temurin'
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java-version: '8'
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- name: Deploy to GitHub Packages repository
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run: mvn clean deploy -DskipTests -P deploy-github ${{ inputs.maven_opts }}
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run: mvn clean deploy -DskipTests -P deploy-github ${{ inputs.maven_opts }} --no-transfer-progress
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/manual-deploy-maven.yml

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name: Manual maven deploy workflow
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on:
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workflow_dispatch:
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inputs:
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branch:
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description: "The branch, tag or SHA of the source code to build docker."
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type: string
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required: true
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jobs:
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checkout:
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name: Build Java app
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runs-on: ubuntu-22.04
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: '10'
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ref: "${{ inputs.branch }}"
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deploy-maven:
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uses: ./.github/workflows/deploy-maven-repository-workflow.yml
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needs: checkout
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secrets: inherit

‎.github/workflows/publish-test-report-workflow.yml

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name: Reusable workflow to push in DockerHub
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on:
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workflow_call:
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inputs:
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target_path:
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type: string
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required: true
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content:
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type: string
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required: false
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secrets:
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SSH_TESTING_SERVER_HOST:
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required: true
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SSH_TESTING_SERVER_PASSWORD:
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required: true
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SSH_TESTING_SERVER_PORT:
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required: true
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SSH_TESTING_SERVER_USER:
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required: true
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jobs:
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publish-test-report:
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name: Publish test report
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runs-on: ubuntu-22.04
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steps:
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- uses: actions/download-artifact@v4
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with:
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name: ${{ inputs.content }}
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path: report
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- name: Deploy tests web recursively to remote
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run: |
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set -e
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set -x
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export SSHPASS=${{ secrets.SSH_TESTING_SERVER_PASSWORD }}
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SSH_OPTS="-o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -o ServerAliveInterval=60"
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sshpass -e ssh ${SSH_OPTS} ${{ secrets.SSH_TESTING_SERVER_USER }}@${{ secrets.SSH_TESTING_SERVER_HOST }} -p ${{ secrets.SSH_TESTING_SERVER_PORT }} "mkdir -p ${{ inputs.target_path }}"
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echo "Copying report tests to remote path ${{ inputs.target_path }}"
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sshpass -e scp ${SSH_OPTS} -r -P ${{ secrets.SSH_TESTING_SERVER_PORT }} report ${{ secrets.SSH_TESTING_SERVER_USER }}@${{ secrets.SSH_TESTING_SERVER_HOST }}:${{ inputs.target_path }}

‎.github/workflows/pull-request-approved.yml

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name: Pull request approve workflow
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run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}'
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on:
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pull_request_review:
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types: [ submitted ]
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jobs:
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build:
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uses: ./.github/workflows/build-java-app-workflow.yml
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test:
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name: "Run all tests before merging"
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uses: ./.github/workflows/test-analysis.yml
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needs: build
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secrets: inherit

‎.github/workflows/test-analysis.yml

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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any
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SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
32-
run: mvn -B verify surefire-report:report --fail-never org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=opencb_java-common-libs
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run: mvn -B verify surefire-report:report --fail-never org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=opencb_java-common-libs --no-transfer-progress
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- name: Publish Test Report
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uses: scacap/action-surefire-report@v1
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## Skip cancelled()

‎.github/workflows/test-xetabase-workflow.yml

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name: TEST Xetabase and publish report workflow
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on:
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workflow_call:
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inputs:
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task:
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type: string
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required: true
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branch:
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type: string
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required: true
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workflow_dispatch:
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inputs:
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task:
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type: string
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description: 'Task ID to be tested.'
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required: true
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branch:
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type: string
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description: 'Branch of opencga-enterprise to be tested and built.'
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required: true
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env:
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AZCOPY_SPA_CLIENT_SECRET: ${{ secrets.AZCOPY_SPA_CLIENT_SECRET }}
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AZCOPY_AUTO_LOGIN_TYPE: "SPN"
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AZCOPY_SPA_APPLICATION_ID: ${{ secrets.AZCOPY_SPA_APPLICATION_ID }}
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AZCOPY_TENANT_ID: ${{ secrets.AZCOPY_TENANT_ID }}
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jobs:
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test:
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name: Execute JUnit and Jacoco tests
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runs-on: ubuntu-22.04
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steps:
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- name: Clone OpenCGA Enterprise branch '${{ github.event.inputs.branch }}'
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uses: actions/checkout@v4
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with:
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repository: zetta-genomics/opencga-enterprise
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ref: ${{ github.event.inputs.branch }}
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token: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
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path: opencga-enterprise
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fetch-depth: "10"
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- id: get_opencga_branch
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name: Get OpenCGA branch from 'pom.xml' property
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run: |
44+
pwd
45+
chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh
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opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh ${{ github.event.inputs.task }})
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echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT
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- uses: actions/checkout@v4
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with:
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repository: opencb/opencga
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ref: ${{ steps.get_opencga_branch.outputs.opencga_branch }}
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path: opencga
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fetch-depth: '10'
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- name: Set up JDK 8
55+
uses: actions/setup-java@v4
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with:
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distribution: 'temurin'
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java-version: '8'
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cache: 'maven'
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- name: Install Samtools
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run: sudo apt-get install samtools python3-deeptools
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- name: Start MongoDB v6.0
63+
uses: supercharge/[email protected]
64+
with:
65+
mongodb-version: 6.0
66+
mongodb-replica-set: rs-test
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- name: K8s Tunnel MongoDB
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run: |
69+
wget https://dl.k8s.io/release/v1.28.2/bin/linux/amd64/kubectl
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chmod +x ./kubectl
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echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf
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./kubectl -n cellbase-db port-forward services/cellbase-rs0-svc 27018:27017 --kubeconfig ./admin.conf &
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- name: Install Azure AZCOPY
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uses: kheiakiyama/install-azcopy-action@v1
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with:
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version: 'v10'
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- name: DockerHub login
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uses: docker/login-action@v3
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with:
80+
username: ${{ secrets.DOCKER_HUB_USER }}
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password: ${{ secrets.DOCKER_HUB_PASSWORD }}
82+
- name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise
83+
run: |
84+
ln -s opencga opencga-enterprise/opencga-home
85+
cd opencga-enterprise
86+
./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ github.event.inputs.task }} -c localhost:27018 -H hdp3.1
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- name: Upload reports results to Github
88+
uses: actions/upload-artifact@v4
89+
with:
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name: report-test
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path: /home/runner/work/testing-environment/testing-environment/opencga-enterprise/reports/test
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- name: Upload log
93+
uses: actions/upload-artifact@v4
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with:
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name: build-log
96+
path: /home/runner/work/testing-environment/testing-environment/opencga-enterprise/build.log
97+
- name: Upload junit reports to a remote scp server
98+
uses: garygrossgarten/github-action-scp@release
99+
with:
100+
local: opencga-enterprise/reports/test
101+
remote: /var/www/html/reports/xetabase/${{ github.event.inputs.task }}/
102+
host: ${{ secrets.SSH_TESTING_SERVER_HOST}}
103+
port: ${{ secrets.SSH_TESTING_SERVER_PORT}}
104+
username: ${{ secrets.SSH_TESTING_SERVER_USER }}
105+
password: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }}
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concurrency: 2
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108+

‎.github/workflows/testkeeper.yml

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name: Test Keeper Secrets integration with Github Actions
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on:
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workflow_dispatch:
5+
6+
jobs:
7+
buildexecutable:
8+
runs-on: ubuntu-22.04
9+
name: Build with Keeper secrets
10+
steps:
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- name: Retrieve secrets from Keeper
12+
id: ksecrets
13+
uses: Keeper-Security/ksm-action@master
14+
with:
15+
keeper-secret-config: ${{ secrets.KEEPER_SM_GH_OPENCB }}
16+
secrets: |
17+
AZURE_KUBE_CONFIG/field/Secret Value > env:KEEPERTOKEN
18+
19+
- name: Print Login & Password & URL
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run: |
21+
echo "Login is ${{ env.KEEPERTOKEN }}"

‎commons-datastore/commons-datastore-core/pom.xml

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<parent>
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<groupId>org.opencb.commons</groupId>
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<artifactId>commons-datastore</artifactId>
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<version>5.1.0</version>
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<version>5.2.0</version>
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<relativePath>../pom.xml</relativePath>
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</parent>
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