Update deprecated GitHub Actions #518
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Workflow for running the TES compliance suite against Funnel | |
| # This includes the following steps: | |
| # 1. Build Funnel and store the resulting binary artifact | |
| # 2. Install tes-compliance-suite and run against every version of TES simultaneously | |
| # 3. start-report-deployment: Send a dispatch to the funnel-compliance repository to generate and publish | |
| # the tes-compliance-suite report to https://ohsu-comp-bio.github.io/funnel-compliance/ | |
| # Optionally debug via SSH | |
| # Ref: https://fleetdm.com/engineering/tips-for-github-actions-usability | |
| # | |
| # To use this step uncomment and place anywhere in the build steps. The build will pause on this step and | |
| # output a ssh address associated with the Github action worker. Helpful for debugging build steps and | |
| # and intermediary files/artifacts. | |
| # | |
| # - name: "Debug: Package dependancies for tmate (CentOS)" | |
| # run: | | |
| # yum install -y xz | |
| # ln -s /bin/true /bin/apt-get | |
| # | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| name: Compliance Test | |
| on: | |
| push: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| container: quay.io/ohsu-comp-bio/slurm | |
| steps: | |
| - name: Set up Go 1.x | |
| uses: actions/setup-go@v2 | |
| with: | |
| go-version: 1.21 | |
| - name: Check out code | |
| uses: actions/checkout@v2 | |
| - name: Build | |
| run: make build | |
| - name: Store funnel | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: funnelBin | |
| path: funnel | |
| compliance: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| version: [1.0.0, 1.1.0] | |
| db: ["boltdb", "mongodb"] | |
| compute: ["local", "slurm"] | |
| needs: build | |
| runs-on: ubuntu-latest | |
| container: | |
| image: quay.io/ohsu-comp-bio/slurm | |
| options: --hostname slurmctl --cap-add sys_admin | |
| steps: | |
| # Required to access the 'tests/mongo.config.yml' file | |
| # Perhaps uploading it as an artifact would be more efficient? | |
| - name: Check out code | |
| uses: actions/checkout@v2 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: funnelBin | |
| - name: Start Funnel server | |
| run: | | |
| touch config.yml | |
| if [ ${{ matrix.db }} = "mongodb" ]; then | |
| make start-mongodb | |
| cat `pwd`/tests/mongo.config.yml >> config.yml | |
| # Required for Funnel to connect MongoDB | |
| echo "172.17.0.1 localhost" >> /etc/hosts | |
| elif [ ${{ matrix.compute }} = "slurm" ]; then | |
| cat `pwd`/tests/slurm.config.yml >> config.yml | |
| cp config.yml /opt/funnel_config.yml | |
| # Start Slurm | |
| /usr/local/bin/docker-entrypoint.sh | |
| fi | |
| chmod +x funnel | |
| FLAGS="--config `pwd`/config.yml" | |
| ./funnel server run $FLAGS &> funnel.logs & | |
| - name: Run OpenAPI Test Runner | |
| run: | | |
| # Clone the 'upstream' OpenAPI Test Runner when PR #65 is merged | |
| # https://github.com/elixir-cloud-aai/openapi-test-runner/pull/65 | |
| # git clone https://github.com/elixir-cloud-aai/openapi-test-runner | |
| git clone https://github.com/ohsu-comp-bio/openapi-test-runner -b fix/create-and-filter-task | |
| cd openapi-test-runner | |
| python3 -m venv venv | |
| source venv/bin/activate | |
| pip install -r requirements.txt | |
| python setup.py install | |
| openapi-test-runner report --version "${{ matrix.version }}" --server "http://localhost:8000/" | |
| - name: Install TES compliance suite | |
| run: | | |
| git clone https://github.com/lbeckman314/tes-compliance-suite -b feature/tesv1.1 | |
| cd tes-compliance-suite | |
| /root/.pyenv/shims/python3 -m venv venv | |
| source venv/bin/activate | |
| pip install -r requirements.txt | |
| python setup.py install | |
| mkdir reports | |
| - name: Test compliance (Report Publishing) | |
| run: | | |
| cd tes-compliance-suite | |
| source venv/bin/activate | |
| tes-compliance-suite report --version "${{ matrix.version }}" --server "http://localhost:8000/" | |
| start-report-deployment: | |
| needs: compliance | |
| runs-on: ubuntu-latest | |
| steps: | |
| # https://docs.github.com/en/rest/repos/repos?apiVersion=2022-11-28#create-a-repository-dispatch-event | |
| - name: Start report generation | |
| uses: passeidireto/trigger-external-workflow-action@main | |
| env: | |
| PAYLOAD_AUTHOR: "Funnel" | |
| PAYLOAD_REVISION: "3" | |
| with: | |
| repository: ohsu-comp-bio/funnel-compliance | |
| event: start-report | |
| github_pat: ${{ secrets.ACTIONS_TOKEN }} | |