Merge branch 'develop' into TASK-4810

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

@@ -51,6 +51,5 @@ jobs:
     uses: ./.github/workflows/test-analysis.yml
     with:
       test_profile: ${{ needs.get_profiles.outputs.profiles }}
-      report_context: development
       mvn_opts: ${{ inputs.mvn_opts }}
     secrets: inherit

.github/workflows/develop.yml

@@ -9,34 +9,26 @@ on:
 
 jobs:
   build:
-    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x
+    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'
 
-  deploy-docker-ext-tools:
-    uses: opencb/java-common-libs/.github/workflows/[email protected]
-    needs: build
-    with:
-      cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }}
-    secrets: inherit
-
   test:
     uses: ./.github/workflows/test-analysis.yml
-    needs: deploy-docker-ext-tools
-    secrets: inherit
+    needs: build
     with:
       test_profile: runShortTests,runMediumTests
-      report_context: development
+    secrets: inherit
 
   deploy-maven:
-    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.9.x
+    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: test
     with:
       maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga
     secrets: inherit
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x
+    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,init

.github/workflows/docker-aws-emr.yml

@@ -8,15 +8,13 @@ on:
 
 jobs:
   build:
-    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
       maven_opts: -P storage-hadoop,emr6.1 -Dopencga.war.name=opencga
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x
+    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
     secrets: inherit
-#      DOCKER_HUB_USER: ${{ secrets.DOCKER_HUB_USER }}
-#      DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}

.github/workflows/docker-tools.yml → .github/workflows/docker-ext-tools.yml

@@ -1,4 +1,4 @@
-name: Deploy Docker Tools
+name: Deploy Docker Ext-Tools
 
 on:
   push:
@@ -12,13 +12,12 @@ on:
 
 jobs:
   build:
-    uses: opencb/java-common-libs/.github/workflows/[email protected]
-    with:
-      maven_opts:
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
 
   deploy-docker-ext-tools:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x
+    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 ${{ needs.build.outputs.version }}
     secrets: inherit
+

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

@@ -1,15 +1,17 @@
 name: Long test for run only on weekend
 
-#Every Saturday at 01:10
+
+## Every Saturday at 01:10
 on:
   schedule:
     - cron: '10 1 * * 6'
+  workflow_dispatch:
 
 jobs:
   test:
     uses: ./.github/workflows/test-analysis.yml
     secrets: inherit
     with:
-      test_profile: runLongTests,runMediumTests,runShortTests
-      report_context: development
+      test_profile: runShortTests,runMediumTests,runLongTests,
+
 

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

@@ -3,14 +3,17 @@ name: "Pull Request Merge Workflow"
 on:
   pull_request:
     branches:
-      - "develop"
-      - "release-*"
+      - develop
+      - release-*
     types:
       - closed
 
 jobs:
+  build:
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+
   delete-docker:
-    uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@release-4.9.x
+    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: inherit

.github/workflows/release.yml

@@ -8,52 +8,35 @@ on:
 
 jobs:
   build:
-    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x
+    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'
 
-  deploy-docker-ext-tools:
-    uses: opencb/java-common-libs/.github/workflows/[email protected]
-    needs: build
-    with:
-      cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }}
-    secrets: inherit
-
-  test:
-    uses: ./.github/workflows/test-analysis.yml
-    needs: deploy-docker-ext-tools
-    secrets: inherit
-    with:
-      test_profile: runShortTests,runMediumTests
-      report_context: xetabase
-
   deploy-maven:
-    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.9.x
-    needs: test
+    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
+    needs: build
     with:
       maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga
     secrets: inherit
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x
-    needs: test
+    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
     secrets: inherit
 
-
-
   deploy-python:
-    uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@release-4.9.x
-    needs: test
+    uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop
+    needs: build
     with:
       cli: ./clients/python/python-build.sh push
       artifact: build-folder
     secrets: inherit
 
   release:
-    uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@release-4.9.x
-    needs: [ build,test ]
+    uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop
+    needs: [ build, deploy-maven, deploy-docker, deploy-python ]
     with:
       artifact: build-folder
       file: |

.github/workflows/task.yml

@@ -5,10 +5,12 @@ on:
     branches:
       - TASK-*
   workflow_dispatch:
-#WARNING Develop branch needed for prod
+
+# WARNING Develop branch needed for prod
+
 jobs:
   build:
-    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x
+    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'
 
@@ -18,10 +20,9 @@ jobs:
     secrets: inherit
     with:
       test_profile: runShortTests
-      report_context: development
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x
+    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,init --tag ${{ github.ref_name }}

.github/workflows/test-analysis.yml

@@ -1,30 +1,19 @@
 name: Build and test the project
+
 on:
   workflow_call:
     inputs:
       test_profile:
         type: string
         required: true
-      report_context:
-        type: string
-        required: true
       mvn_opts:
         type: string
         required: false
         default: ""
     secrets:
       SONAR_TOKEN:
         required: true
-      SSH_TESTING_SERVER_HOST:
-        required: true
-      SSH_TESTING_SERVER_PORT:
-        required: true
-      SSH_TESTING_SERVER_USER:
-        required: true
-      SSH_TESTING_SERVER_PASSWORD:
-        required: true
-env:
-  xb_version: "1.7.2"
+
 jobs:
   analysis:
     name: Execute Sonar Analysis
@@ -52,6 +41,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
         run: mvn -T 2 clean install -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -DskipTests -Dcheckstyle.skip org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=opencb_opencga
+
   test:
     name: Execute JUnit and Jacoco tests
     runs-on: ubuntu-22.04
@@ -81,31 +71,14 @@ jobs:
           mongodb-version: 6.0
           mongodb-replica-set: rs-test
       - name: Run Junit tests
-        run: mvn -B verify surefire-report:report -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' ${{ inputs.mvn_opts }}
-      - name: Upload result dir
-        uses: actions/upload-artifact@v3
-        with:
-          name: workdir
-          path: "**/target/site"
-  publish-test:
-    name: Publish test results
-    runs-on: ubuntu-22.04
-    needs: test
-    strategy:
-      matrix:
-        module: ["opencga-app", "opencga-catalog", "opencga-client", "opencga-clinical", "opencga-core", "opencga-master", "opencga-server", "opencga-storage", "opencga-storage/opencga-storage-app", "opencga-storage/opencga-storage-benchmark", "opencga-storage/opencga-storage-core", "opencga-storage/opencga-storage-hadoop", "opencga-storage/opencga-storage-server", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps"]
-    steps:
-      - name: Download result dir
-        uses: actions/download-artifact@v3
-        with:
-          name: workdir
-      - name: Deploy unit tests web recursively to remote
-        uses: garygrossgarten/github-action-scp@release
+        run: mvn -B verify surefire-report:report --fail-never -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' ${{ inputs.mvn_opts }}
+      - name: Publish Test Report
+        uses: scacap/action-surefire-report@v1
+        ## Skip cancelled()
+        ## https://docs.github.com/en/actions/learn-github-actions/expressions#cancelled
+        if: success() || failure()
         with:
-          local: ${{ matrix.module }}/target/site
-          remote: /var/www/html/reports/${{ inputs.report_context }}/${{ env.xb_version }}/${{ github.ref_name }}/opencga/${{ github.sha }}/unit/${{ matrix.module }}
-          host: ${{ secrets.SSH_TESTING_SERVER_HOST}}
-          port: ${{ secrets.SSH_TESTING_SERVER_PORT}}
-          username: ${{ secrets.SSH_TESTING_SERVER_USER }}
-          password: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }}
-          concurrency: 2
+          check_name: "Surefire tests report"
+          report_paths: './**/surefire-reports/TEST-*.xml'
+          commit: '${{ github.sha }}'
+          fail_on_test_failures: true

opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/hrdetect/HRDetectAnalysis.java

@@ -59,7 +59,7 @@ public class HRDetectAnalysis extends OpenCgaToolScopeStudy {
     public static final String ID = "hr-detect";
     public static final String DESCRIPTION = "Run HRDetect analysis for a given somatic sample.";
 
-    public final static String HRDETECT_SCORES_FILENAME_DEFAULT = "data_matrix.tsv";
+    public final static String HRDETECT_SCORES_FILENAME_DEFAULT = "hrdetect_output.tsv";
 
     @ToolParams
     private HRDetectAnalysisParams hrdetectParams = new HRDetectAnalysisParams();