Skip to content

TASK-7883 - Modify OpenCGA - CellBase dependency #121

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 8 commits into from
Sep 3, 2025
Merged

TASK-7883 - Modify OpenCGA - CellBase dependency #121

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
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
f3ef06b
Merge branch 'release-6.x.x' into TASK-7883
juanfeSanahuja Sep 3, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .github/workflows/pull-request-approved.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
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: ${{ github.event.pull_request.head.ref }}
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/test-analysis.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -39,4 +39,4 @@ jobs:
check_name: "Surefire tests report"
report_paths: './**/surefire-reports/TEST-*.xml'
commit: '${{ github.sha }}'
fail_on_test_failures: true
fail_on_test_failures: true
15 changes: 2 additions & 13 deletions .github/workflows/test-xetabase-workflow.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
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:
Expand Down
Loading