From 19e2c2383152638a5570eb4e46077a1a71c4d390 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 14 Aug 2025 10:30:06 +0200 Subject: [PATCH 1/6] Delete cellbase references in Xetabase test #TASK-7884 --- .github/workflows/test-xetabase-workflow.yml | 17 ++--------------- 1 file changed, 2 insertions(+), 15 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 0b060f58..cf3ff216 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -70,24 +70,11 @@ jobs: distribution: 'temurin' java-version: '8' cache: 'maven' - - name: Install Samtools - run: sudo apt-get install samtools python3-deeptools - name: Start MongoDB v6.0 uses: supercharge/mongodb-github-action@1.8.0 with: mongodb-version: 6.0 mongodb-replica-set: rs-test - - name: K8s Tunnel MongoDB - run: | - wget https://dl.k8s.io/release/v1.28.2/bin/linux/amd64/kubectl - chmod +x ./kubectl - echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf - ./kubectl -n cellbase-db port-forward services/cellbase-rs0-svc 27018:27017 --kubeconfig ./admin.conf & - - name: DockerHub login - uses: docker/login-action@v3 - with: - username: ${{ env.DOCKER_HUB_USER }} - password: ${{ env.DOCKER_HUB_PASSWORD }} - name: Install sshpass run: sudo apt-get install sshpass - name: Add SSH Host to known_hosts @@ -97,11 +84,11 @@ jobs: env: SSH_HOST: ${{ env.SSH_HOST }} SSH_PORT: ${{ env.SSH_PORT }} - - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise + - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, opencga and opencga-enterprise run: | cd opencga-enterprise ln -s ../opencga opencga-home - ./build.sh -t -l runShortTests -b -s -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 + ./build.sh -t -l runShortTests -b -s -T ${{ inputs.task }} - name: Upload reports results to Github uses: actions/upload-artifact@v4 with: From 4b1e90a60dfd3093cabd5ac1ca3eab8e1d8ca5f0 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 14 Aug 2025 10:30:06 +0200 Subject: [PATCH 2/6] Delete cellbase references in Xetabase test #TASK-7883 --- .github/workflows/test-xetabase-workflow.yml | 17 ++--------------- 1 file changed, 2 insertions(+), 15 deletions(-) diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index 0b060f58..cf3ff216 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -70,24 +70,11 @@ jobs: distribution: 'temurin' java-version: '8' cache: 'maven' - - name: Install Samtools - run: sudo apt-get install samtools python3-deeptools - name: Start MongoDB v6.0 uses: supercharge/mongodb-github-action@1.8.0 with: mongodb-version: 6.0 mongodb-replica-set: rs-test - - name: K8s Tunnel MongoDB - run: | - wget https://dl.k8s.io/release/v1.28.2/bin/linux/amd64/kubectl - chmod +x ./kubectl - echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf - ./kubectl -n cellbase-db port-forward services/cellbase-rs0-svc 27018:27017 --kubeconfig ./admin.conf & - - name: DockerHub login - uses: docker/login-action@v3 - with: - username: ${{ env.DOCKER_HUB_USER }} - password: ${{ env.DOCKER_HUB_PASSWORD }} - name: Install sshpass run: sudo apt-get install sshpass - name: Add SSH Host to known_hosts @@ -97,11 +84,11 @@ jobs: env: SSH_HOST: ${{ env.SSH_HOST }} SSH_PORT: ${{ env.SSH_PORT }} - - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise + - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, opencga and opencga-enterprise run: | cd opencga-enterprise ln -s ../opencga opencga-home - ./build.sh -t -l runShortTests -b -s -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1 + ./build.sh -t -l runShortTests -b -s -T ${{ inputs.task }} - name: Upload reports results to Github uses: actions/upload-artifact@v4 with: From 024ed22c66a6138dabb12c8d3562ae952ff2f2da Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 14 Aug 2025 13:14:04 +0200 Subject: [PATCH 3/6] Update test reference to use the current branch workflow #TASK-7883 --- .github/workflows/pull-request-approved.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 0c489fd7..e61ad207 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -35,7 +35,7 @@ jobs: test: name: "Run all tests before merging" needs: calculate-xetabase-branch - uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop + uses: ./.github/workflows/test-xetabase-workflow.yml@develop with: branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }} task: ${{ github.event.pull_request.head.ref }} From 4a2a035df64fd4bc92e3a4845551fa29c1210896 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 14 Aug 2025 13:20:18 +0200 Subject: [PATCH 4/6] Update test reference to use the current branch workflow #TASK-7883 --- .github/workflows/pull-request-approved.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index e61ad207..7e34cf39 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -35,7 +35,7 @@ jobs: test: name: "Run all tests before merging" needs: calculate-xetabase-branch - uses: ./.github/workflows/test-xetabase-workflow.yml@develop + uses: ./.github/workflows/test-xetabase-workflow.yml with: branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }} task: ${{ github.event.pull_request.head.ref }} From 8f7668316922ea1b4295c165a084967d3437b77c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 14 Aug 2025 13:32:20 +0200 Subject: [PATCH 5/6] Add sam tolls because it is necessary for test #TASK-7883 --- .github/workflows/test-analysis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 487cbb35..eadc89ad 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -20,6 +20,8 @@ jobs: distribution: 'temurin' java-version: '11' cache: 'maven' + - name: Install Samtools + run: sudo apt-get install samtools python3-deeptools - name: Start MongoDB v6.0 uses: supercharge/mongodb-github-action@1.8.0 with: From 5b05d3663c071381049303fe6c664860ff78caa3 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 14 Aug 2025 14:14:37 +0200 Subject: [PATCH 6/6] Add sam tolls because it is necessary for test #TASK-7883 --- .github/workflows/test-analysis.yml | 4 +--- .github/workflows/test-xetabase-workflow.yml | 2 ++ 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index eadc89ad..3af76372 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -20,8 +20,6 @@ jobs: distribution: 'temurin' java-version: '11' cache: 'maven' - - name: Install Samtools - run: sudo apt-get install samtools python3-deeptools - name: Start MongoDB v6.0 uses: supercharge/mongodb-github-action@1.8.0 with: @@ -41,4 +39,4 @@ jobs: check_name: "Surefire tests report" report_paths: './**/surefire-reports/TEST-*.xml' commit: '${{ github.sha }}' - fail_on_test_failures: true + fail_on_test_failures: true \ No newline at end of file diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml index cf3ff216..3720d93c 100644 --- a/.github/workflows/test-xetabase-workflow.yml +++ b/.github/workflows/test-xetabase-workflow.yml @@ -70,6 +70,8 @@ jobs: distribution: 'temurin' java-version: '8' cache: 'maven' + - name: Install Samtools + run: sudo apt-get install samtools python3-deeptools - name: Start MongoDB v6.0 uses: supercharge/mongodb-github-action@1.8.0 with: