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TASK-7883 - Modify OpenCGA - CellBase dependency #121

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TASK-7883 - Modify OpenCGA - CellBase dependency #121

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19e2c23
Delete cellbase references in Xetabase test #TASK-7884
juanfeSanahuja Aug 14, 2025
4b1e90a
Delete cellbase references in Xetabase test #TASK-7883
juanfeSanahuja Aug 14, 2025
a1c16f4
Merge branch 'TASK-7883' of github.com:opencb/java-common-libs into T…
juanfeSanahuja Aug 14, 2025
024ed22
Update test reference to use the current branch workflow #TASK-7883
juanfeSanahuja Aug 14, 2025
4a2a035
Update test reference to use the current branch workflow #TASK-7883
juanfeSanahuja Aug 14, 2025
8f76683
Add sam tolls because it is necessary for test #TASK-7883
juanfeSanahuja Aug 14, 2025
5b05d36
Add sam tolls because it is necessary for test #TASK-7883
juanfeSanahuja Aug 14, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/pull-request-approved.yml
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Expand Up @@ -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
with:
branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }}
task: ${{ github.event.pull_request.head.ref }}
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2 changes: 1 addition & 1 deletion .github/workflows/test-analysis.yml
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Expand Up @@ -39,4 +39,4 @@ jobs:
check_name: "Surefire tests report"
report_paths: './**/surefire-reports/TEST-*.xml'
commit: '${{ github.sha }}'
fail_on_test_failures: true
fail_on_test_failures: true
15 changes: 2 additions & 13 deletions .github/workflows/test-xetabase-workflow.yml
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Expand Up @@ -77,17 +77,6 @@ jobs:
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
Expand All @@ -97,11 +86,11 @@ 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:
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