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juanfeSanahujajuanfeSanahuja
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First version of pull-request #TASK-8067
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‎.github/actions/prepare-opencga-enterprise/action.yml‎

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name: "Prepare OpenCGA Enterprise"
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description: "Checkout enterprise, resolve OpenCGA ref, optionally clone java-common-libs/biodata and compute dependencies_sha"
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inputs:
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enterprise_ref:
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description: "Branch, tag or SHA of opencga-enterprise to checkout"
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required: true
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clone_dependencies:
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description: "Clone java-common-libs and biodata on the same branch for SNAPSHOT builds"
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required: false
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default: "true"
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outputs:
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enterprise_version:
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description: "project.version from opencga-enterprise"
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value: ${{ steps.project_version.outputs.enterprise_version }}
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is_release:
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description: "true if project.version is a release (no SNAPSHOT)"
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value: ${{ steps.project_version.outputs.is_release }}
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opencga_branch:
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description: "Resolved OpenCGA branch, tag or ref"
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value: ${{ steps.opencga_branch.outputs.opencga_branch }}
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dependencies_sha:
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description: "SHA representing the combination of OpenCGA/java-common-libs/biodata commits"
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value: ${{ steps.dependencies_sha.outputs.dependencies_sha }}
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runs:
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using: "composite"
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steps:
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- name: Checkout opencga-enterprise
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uses: actions/checkout@v4
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with:
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ref: ${{ inputs.enterprise_ref }}
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repository: zetta-genomics/opencga-enterprise
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token: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
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path: opencga-enterprise
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fetch-depth: 10
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- id: project_version
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name: Read project.version and determine release flag
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shell: bash
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run: |
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version=$(mvn -q -Dexpression=project.version -DforceStdout help:evaluate)
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echo "enterprise_version=$version" >> "$GITHUB_OUTPUT"
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echo "enterprise_version=$version" >> "$GITHUB_OUTPUT"
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if [[ "$version" == *SNAPSHOT ]]; then
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echo "is_release=false" >> "$GITHUB_OUTPUT"
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else
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echo "is_release=true" >> "$GITHUB_OUTPUT"
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fi
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- id: opencga_branch
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name: Resolve OpenCGA branch or tag from opencga.version and branch
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shell: bash
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run: |
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if [ ! -f "./.github/workflows/scripts/opencga_branch.sh" ]; then
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echo "ERROR: .github/workflows/scripts/opencga_branch.sh not found" >&2
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exit 1
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fi
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chmod +x ./.github/workflows/scripts/opencga_branch.sh
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branch=$(
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./.github/workflows/scripts/opencga_branch.sh \
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"${{ steps.project_version.outputs.is_release }}"
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)
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echo "opencga_branch=$branch" >> "$GITHUB_OUTPUT"
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- name: Checkout OpenCGA
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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: ${{ steps.opencga_branch.outputs.opencga_branch }}
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path: opencga-home
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fetch-depth: 10
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- id: dependencies_sha
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name: Compute dependencies SHA for OpenCGA/java-common-libs/biodata
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shell: bash
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run: |
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base_sha="${GITHUB_SHA}"
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if [[ "${{ inputs.clone_dependencies }}" == "true" && "${{ steps.project_version.outputs.is_release }}" == "false" ]]; then
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if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then
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echo "::group::Clone java-common-libs and biodata and compute dependencies SHA"
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chmod +x ./.github/workflows/scripts/get_same_branch.sh
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export DEPENDENCIES_SHA="$base_sha"
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export WORKSPACE="${WORKSPACE:-/home/runner/work}"
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./.github/workflows/scripts/get_same_branch.sh "${{ inputs.enterprise_ref }}"
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echo "::endgroup::"
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exit 0
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else
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echo "get_same_branch.sh not found, skipping dependency cloning."
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fi
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fi
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echo "dependencies_sha=$base_sha" >> "$GITHUB_OUTPUT"

‎.github/actions/setup-java-maven/action.yml‎

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java_version:
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description: "Java version to use"
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required: false
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default: "11"
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default: "8"
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storage_hadoop:
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description: "Hadoop flavour, used as part of the Maven cache key"
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required: false

‎.github/workflows/build.yml‎

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- name: Maven Build (skip tests)
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if: ${{ !inputs.deploy_maven }}
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run: mvn -T 2 clean install -DskipTests ${{ inputs.maven_opts }} --no-transfer-progress
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- name: Maven Deploy (skip tests, deploy to Maven Central y GitHub Packages)
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if: ${{ inputs.deploy_maven }}
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run: mvn -T 2 clean deploy -DskipTests -Pdeploy-maven,deploy-github ${{ inputs.maven_opts }} --no-transfer-progress
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- name: Get project version
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id: get_project_version
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# This step extracts the Maven project version and exposes it as an output.
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run: |
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echo "version=$(mvn help:evaluate -q -Dexpression=project.version -DforceStdout)" >> "$GITHUB_OUTPUT"

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

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# .github/workflows/pull-request-approve.yml
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# Workflow to be triggered on PR approval, receives target_branch as input, checks out the repo,
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# computes the correct opencga-enterprise branch, and calls test-xetabase with the calculated branch and PR head as task.
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name: Xetabase PR Approve Entrypoint
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on:
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workflow_call:
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inputs:
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target_branch:
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description: 'Target branch of the PR (github.event.pull_request.base.ref)'
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required: true
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type: string
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head_ref:
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description: 'Source branch of the PR (github.event.pull_request.head.ref)'
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required: true
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type: string
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secrets:
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ZETTA_REPO_ACCESS_TOKEN:
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required: true
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THIRDPARTY_READ_TOKEN:
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required: false
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KEEPER_SM_GH_OPENCB:
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required: false
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jobs:
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resolve-and-test:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout triggering repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 10
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path: triggering-repo
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- name: Parse pom.xml to get project artifactId
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id: pom
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shell: bash
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working-directory: triggering-repo
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run: |
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artifactId=$(xmllint --xpath '/*[local-name()="project"]/*[local-name()="artifactId"]/text()' pom.xml)
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echo "artifactId=$artifactId" >> "$GITHUB_OUTPUT"
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- name: Compute opencga-enterprise branch
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id: compute_branch
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env:
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ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
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shell: bash
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working-directory: triggering-repo
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run: |
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chmod +x ../.github/workflows/scripts/get_opencga_enterprise_branch.sh
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branch=$( ../.github/workflows/scripts/get_opencga_enterprise_branch.sh "${{ steps.pom.outputs.artifactId }}" "${{ inputs.target_branch }}" "${{ inputs.head_ref }}" )
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echo "branch=$branch" | tee -a $GITHUB_STEP_SUMMARY
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echo "branch=$branch" >> $GITHUB_OUTPUT
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- name: Checkout opencga-enterprise
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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: ${{ steps.compute_branch.outputs.branch }}
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path: opencga-enterprise
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token: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
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- name: Call test-xetabase workflow with calculated branch
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uses: ./.github/workflows/test-xetabase.yml
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with:
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branch: ${{ steps.compute_branch.outputs.branch }}
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task: ${{ inputs.head_ref }}
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secrets:
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ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
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THIRDPARTY_READ_TOKEN: ${{ secrets.THIRDPARTY_READ_TOKEN }}
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KEEPER_SM_GH_OPENCB: ${{ secrets.KEEPER_SM_GH_OPENCB }}

‎.github/workflows/scripts/get_opencga_enterprise_branch.sh‎

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#!/usr/bin/env bash
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# get_opencga_enterprise_branch.sh
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#
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# This script computes the correct opencga-enterprise branch to use for testing a PR in any Xetabase component repo.
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# It unifies the logic previously duplicated in java-common-libs, biodata, and opencga.
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#
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# Inputs:
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# 1. project (artifactId from pom.xml)
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# 2. base_ref (target branch of the PR)
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# 3. head_ref (source branch of the PR)
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#
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# Output:
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# Prints the resolved opencga-enterprise branch to stdout.
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# Exits with non-zero and error message if it cannot resolve a branch.
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set -euo pipefail
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project="$1"
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base_ref="$2"
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head_ref="$3"
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# Helper: check if a branch exists in the remote opencga-enterprise repo
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branch_exists() {
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local branch="$1"
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REPO_URI="https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git"
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git ls-remote --heads "$REPO_URI" "$branch" | grep -q refs/heads
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}
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# 1. TASK-* branch logic: if head_ref starts with TASK- and exists in opencga-enterprise, use it
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if [[ "$head_ref" =~ ^TASK- ]]; then
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if branch_exists "$head_ref"; then
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echo "$head_ref"
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exit 0
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fi
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fi
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# 2. develop branch logic: always map to develop
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if [[ "$base_ref" == "develop" ]]; then
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echo "develop"
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exit 0
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fi
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# 3. release-* branch logic
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if [[ "$base_ref" =~ ^release-([0-9]+)\. ]]; then
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major="${BASH_REMATCH[1]}"
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# Project-specific offset for release branch mapping
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case "$project" in
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java-common-libs)
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offset=3
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;;
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biodata|opencga)
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offset=1
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;;
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opencga-enterprise)
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# If the project is opencga-enterprise, use the branch as-is
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echo "$base_ref"
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exit 0
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;;
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*)
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echo "ERROR: Unknown project '$project' for release branch mapping" >&2
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exit 1
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;;
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esac
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new_major=$((major - offset))
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if (( new_major < 1 )); then
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echo "ERROR: Computed release branch version < 1 for $project (base_ref: $base_ref, offset: $offset)" >&2
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exit 1
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fi
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# Try to match release-x.x.x, fallback to release-x.x
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branch_pattern="release-${new_major}."
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# Find the latest matching branch in opencga-enterprise
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branch=$(git ls-remote --heads https://github.com/zetta-genomics/opencga-enterprise.git | grep "refs/heads/${branch_pattern}" | awk -F'refs/heads/' '{print $2}' | sort -Vr | head -n1)
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if [[ -n "$branch" ]]; then
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echo "$branch"
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exit 0
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else
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echo "ERROR: No matching release branch found in opencga-enterprise for $project (pattern: $branch_pattern)" >&2
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exit 1
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fi
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fi
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# 4. Fallback: fail with clear error
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echo "ERROR: Could not resolve opencga-enterprise branch for project '$project' (base_ref: $base_ref, head_ref: $head_ref)" >&2
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exit 1
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‎.github/workflows/test-xetabase.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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jobs:
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test:
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name: Execute JUnit and Jacoco tests
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runs-on: ${{ vars.UBUNTU_VERSION }}
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steps:
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- name: Retrieve secrets from Keeper
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id: ksecrets
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uses: Keeper-Security/ksm-action@master
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with:
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keeper-secret-config: ${{ secrets.KEEPER_SM_GH_OPENCB }}
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secrets: |
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AZURE_KUBE_CONFIG/field/Secret Value > env:AZURE_KUBE_CONFIG
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DOCKER_HUB_USER/field/Secret Value > env:DOCKER_HUB_USER
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DOCKER_HUB_PASSWORD/field/Secret Value > env:DOCKER_HUB_PASSWORD
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SSH_TESTING_SERVER_HOST/field/Secret Value > env:SSH_HOST
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SSH_TESTING_SERVER_PORT/field/Secret Value > env:SSH_PORT
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SSH_TESTING_SERVER_USER/field/Secret Value > env:SSH_USER
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SSH_TESTING_SERVER_PASSWORD/field/Secret Value > env:SSH_PASS
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- name: Prepare enterprise, OpenCGA and dependencies
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id: prepare
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uses: ./.github/actions/prepare-opencga-enterprise
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with:
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enterprise_ref: ${{ inputs.branch != '' && inputs.branch || github.ref_name }}
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clone_dependencies: "true"
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- name: Set up Java and Maven cache
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# Uses dependencies_sha to make the cache key sensitive to dependency commits
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uses: ./.github/actions/setup-java-maven-cache
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with:
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storage_hadoop: ${{ inputs.storage_hadoop }}
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dependencies_sha: ${{ steps.prepare.outputs.dependencies_sha }}
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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
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uses: supercharge/mongodb-github-action@1.8.0
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with:
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mongodb-version: 6.0
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mongodb-replica-set: rs-test
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- name: Install sshpass
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run: sudo apt-get install sshpass
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- name: Add SSH Host to known_hosts
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run: |
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mkdir -p ~/.ssh
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ssh-keyscan -p ${{ env.SSH_PORT }} ${{ env.SSH_HOST }} >> ~/.ssh/known_hosts
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env:
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SSH_HOST: ${{ env.SSH_HOST }}
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SSH_PORT: ${{ env.SSH_PORT }}
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- name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, opencga and opencga-enterprise
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run: |
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cd opencga-enterprise
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ln -s ../opencga opencga-home
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./build.sh --test --test-level runShortTests --prepare-branches --test-save-reports --task ${{ inputs.task }} --storage-hadoop ${{ vars.HADOOP_FLAVOUR }} --prepare-hadoop --github
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env:
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THIRDPARTY_READ_TOKEN: ${{ secrets.THIRDPARTY_READ_TOKEN }}
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- name: Upload reports results to Github
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uses: actions/upload-artifact@v4
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with:
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name: report-test
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path: ./opencga-enterprise/reports/
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if-no-files-found: error
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- name: Upload log
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uses: actions/upload-artifact@v4
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## Skip cancelled()
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## https://docs.github.com/en/actions/learn-github-actions/expressions#cancelled
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if: success() || failure()
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with:
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name: build-log
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path: |
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./opencga-enterprise/build.log
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./opencga-enterprise/reports/*.log.gz
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if-no-files-found: error
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- name: Log summary
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run: |
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cat ./opencga-enterprise/build.log | tee -a $GITHUB_STEP_SUMMARY
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