Remove debugging output from custom marshaler #215
Workflow file for this run
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| # 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. | |
| # | |
| # Example: | |
| # Web shell: https://tmate.io/t/q8FU3U9SvmMVxAhMHRyExNhr8 | |
| # SSH: ssh q8FU3U9SvmMVxAhMHRyExNhr8@sfo2.tmate.io | |
| # | |
| # - 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: ^1.18 | |
| - name: Check out code | |
| uses: actions/checkout@v2 | |
| - name: Build | |
| run: make build | |
| - name: Store funnel | |
| uses: actions/upload-artifact@v2 | |
| 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@v3 | |
| 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 $FLAGS &> funnel.logs & | |
| - uses: actions/checkout@v3 | |
| with: | |
| repository: lbeckman314/tes-compliance-suite | |
| ref: feature/tesv1.1 | |
| path: tes-compliance-suite | |
| - name: Install TES compliance suite | |
| run: | | |
| cd tes-compliance-suite | |
| /root/.pyenv/shims/python3 -m venv venv | |
| source venv/bin/activate | |
| pip install -r requirements.txt | |
| python setup.py install | |
| mkdir reports | |
| - name: Test compliance | |
| run: | | |
| cd tes-compliance-suite | |
| source venv/bin/activate | |
| tes-compliance-suite report --version "${{ 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 }} | |