Merge branch 'release-3.2.x' into TASK-6708

.github/workflows/check-junit-test.yml

@@ -1,8 +1,36 @@
 name: Check junits
+run-name: "Check Junit. Hadoop ${{ inputs.hadoop }} ${{ inputs.module == 'all' && ' ' || format(':{0}. ', inputs.module ) }}${{ inputs.short_tests && 'Short ' || '' }}${{ inputs.medium_tests && 'Medium ' || '' }}${{ inputs.long_tests && 'Long ' || '' }}${{ ! ( inputs.short_tests || inputs.medium_tests || inputs.long_tests ) && 'Short Medium Long ' || '' }}tests."
 
 on:
   workflow_dispatch:
     inputs:
+      hadoop:
+        type: choice
+        description: 'Hadoop flavour.'
+        required: false
+        default: "hdp3.1"
+        options:
+          - "all"
+          - "hdp3.1"
+          - "hdi5.1"
+          - "emr6.1"
+          - "emr6.13"
+      module:
+        type: choice
+        description: 'OpenCGA module to test.'
+        required: false
+        default: "all"
+        options:
+          - "all"
+          - "opencga-analysis"
+          - "opencga-app"
+          - "opencga-catalog"
+          - "opencga-client"
+          - "opencga-core"
+          - "opencga-master"
+          - "opencga-server"
+          - "opencga-storage"
+          - "opencga-test"
       short_tests:
         type: boolean
         required: false
@@ -25,31 +53,49 @@ jobs:
     name: Test JUnit
     runs-on: ubuntu-22.04
     outputs:
-      profiles: ${{ steps.getter.outputs.profiles }}
+      profiles: ${{ steps.validate.outputs.profiles }}
+      modules: ${{ steps.validate.outputs.modules }}
+      hadoop: ${{ steps.validate.outputs.hadoop }}
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: '10'
       - name: Building string profiles to run
-        id: getter
+        id: validate
         run: |
           if [ -f "./.github/workflows/scripts/get_profiles.sh" ]; then
             chmod +x ./.github/workflows/scripts/get_profiles.sh
-            echo "profiles=$(./.github/workflows/scripts/get_profiles.sh ${{ inputs.short_tests }} ${{ inputs.medium_tests }} ${{ inputs.long_tests }})" >> $GITHUB_OUTPUT
+            profiles=$(./.github/workflows/scripts/get_profiles.sh ${{ inputs.short_tests }} ${{ inputs.medium_tests }} ${{ inputs.long_tests }})
+            modules='["${{ inputs.module }}"]'
+            hadoop='["${{ inputs.hadoop }}"]'
+          
+            if [ "${{ inputs.hadoop }}" == "all" ]; then
+              hadoop='["hdp3.1", "hdi5.1", "emr6.1", "emr6.13"]'
+            elif [ "${{ inputs.module }}" == "all" ]; then
+              # Only execute modules with matrix strategy if we are testing one single hadoop profile
+              modules='["opencga-analysis", "opencga-app", "opencga-catalog", "opencga-client", "opencga-core", "opencga-master", "opencga-server", "opencga-storage", "opencga-test"]'
+            fi
+            echo "profiles=[\"$profiles\"]" >> $GITHUB_OUTPUT
+            echo "modules=$modules" >> $GITHUB_OUTPUT
+            echo "hadoop=$hadoop" >> $GITHUB_OUTPUT
+            echo "Executing testing profiles -> $profiles" >> $GITHUB_STEP_SUMMARY
+            echo "Modules -> $modules" >> $GITHUB_STEP_SUMMARY
+            echo "Hadoop -> $hadoop" >> $GITHUB_STEP_SUMMARY
+            #echo "matrix={\"hadoop\": $hadoop, \"modules\": $modules}" >> $GITHUB_OUTPUT
           fi
-
-  echo_log:
-    needs: get_profiles
-    runs-on: ubuntu-22.04
-    steps:
-      - name: Echo profiles
-        id: log
-        run: echo "Executing testing profiles -> ${{ needs.get_profiles.outputs.profiles }}"
-
   test:
-    needs: [ get_profiles, echo_log ]
+    strategy:
+      fail-fast: false
+      matrix:
+        hadoop: ${{ fromJson(needs.get_profiles.outputs.hadoop) }}
+        module: ${{ fromJson(needs.get_profiles.outputs.modules) }}
+        profile: ${{ fromJson(needs.get_profiles.outputs.profiles) }}
+    needs: [ get_profiles ]
     uses: ./.github/workflows/test-analysis.yml
     with:
-      test_profile: ${{ needs.get_profiles.outputs.profiles }}
+      test_profile: ${{ matrix.profile }}
+      hadoop: ${{ matrix.hadoop }}
+      module: ${{ matrix.module }}
       mvn_opts: ${{ inputs.mvn_opts }}
+      sonar: false
     secrets: inherit

.github/workflows/develop.yml

@@ -11,25 +11,26 @@ jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
-      maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6'
+      maven_opts: -Phdp3.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip
 
-  test:
-    uses: ./.github/workflows/test-analysis.yml
-    needs: build
-    with:
-      test_profile: runShortTests,runMediumTests
-    secrets: inherit
+## TASK-4970: remove the test job from the develop.yml workflow because it is not needed anymore.
+#  test:
+#    uses: ./.github/workflows/test-analysis.yml
+#    needs: build
+#    with:
+#      test_profile: runShortTests,runMediumTests
+#    secrets: inherit
 
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
-    needs: test
+    needs: build
     with:
-      maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga
+      maven_opts: -P hdp3.1 -Dopencga.war.name=opencga
     secrets: inherit
 
   deploy-docker:
     uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
-    needs: test
+    needs: build
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base,init
     secrets: inherit

.github/workflows/long-test-analysis.yml

@@ -9,9 +9,13 @@ on:
 
 jobs:
   test:
+    strategy:
+      fail-fast: false
+      matrix:
+        hadoop: [ "hdp3.1", "hdi5.1", "emr6.1", "emr6.13" ]
     uses: ./.github/workflows/test-analysis.yml
-    secrets: inherit
     with:
-      test_profile: runShortTests,runMediumTests,runLongTests,
-
+      test_profile: runShortTests,runMediumTests,runLongTests
+      hadoop: ${{ matrix.hadoop }}
+    secrets: inherit
 

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

@@ -10,6 +10,16 @@ on:
         description: "The tag for the new docker."
         type: string
         required: true
+      hadoop:
+        type: choice
+        description: 'Hadoop flavour. Any of: [hdp3.1, hdi5.1, emr6.1, emr6.13]'
+        required: false
+        default: hdp3.1
+        options:
+          - hdp3.1
+          - hdi5.1
+          - emr6.1
+          - emr6.13
 
 jobs:
   build:
@@ -32,19 +42,18 @@ jobs:
         run: |
           if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then
             chmod +x ./.github/workflows/scripts/get_same_branch.sh
-            ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }}
+            ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} ${{ inputs.hadoop }}
           fi
       - name: Maven Build (skip tests)
-        run: mvn -T 2 clean install -DskipTests -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6'
+        run: mvn -T 2 clean install -DskipTests -P${{ inputs.hadoop }} -Dopencga.war.name=opencga -Dcheckstyle.skip
       - uses: actions/upload-artifact@v4
         with:
           name: build-folder
           path: build
 
-
   deploy-docker:
     uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
     needs: build
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ inputs.tag }}
-    secrets: inherit
+    secrets: inherit

.github/workflows/manual-deploy-ext-tools.yml

@@ -10,6 +10,11 @@ on:
         description: "The tag for the new docker."
         type: string
         required: true
+      hadoop:
+        type: string
+        description: 'Hadoop flavour. Any of: [hdp3.1, hdi5.1, emr6.1, emr6.13]'
+        required: false
+        default: "hdp3.1"
 
 jobs:
   build:
@@ -32,7 +37,7 @@ jobs:
         run: |
           if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then
             chmod +x ./.github/workflows/scripts/get_same_branch.sh
-            ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }}
+            ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} ${{ inputs.hadoop }}
           fi
       - name: Maven Build (skip tests)
         run: mvn -T 2 clean install -DskipTests
@@ -41,11 +46,9 @@ jobs:
           name: build-folder
           path: build
 
-
   deploy-docker-ext-tools:
     uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
     needs: build
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ inputs.tag }}
     secrets: inherit
-

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

@@ -0,0 +1,35 @@
+name: Pull request approve workflow
+run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}'
+
+on:
+  pull_request_review:
+    types: [ submitted ]
+
+jobs:
+  calculate-xetabase-branch:
+    name: Calculate Xetabase branch
+    runs-on: ubuntu-22.04
+    outputs:
+      xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }}
+    steps:
+      - name: Clone project
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: '10'
+      - id: get_xetabase_branch
+        name: "Get current branch for Xetabase from target branch"
+        run: |
+          chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh
+          xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.base.ref }})
+          echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY}
+          echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT
+
+  test:
+    name: "Run all tests before merging"
+    needs: calculate-xetabase-branch
+    uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@TASK-6399
+    with:
+      branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }}
+      task: ${{ github.event.pull_request.head.ref }}
+    secrets: inherit
+

.github/workflows/pull-request-merge.yml → .github/workflows/pull-request-merged.yml

@@ -13,7 +13,7 @@ jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
-      maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6'
+      maven_opts: -P hdp3.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip
 
   delete-docker:
     uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@develop