merge cidc-api-gae/pull/815 #978
Workflow file for this run
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| name: Continuous Integration | |
| on: | |
| push: | |
| branches: ["*"] | |
| pull_request: | |
| branches: ["*"] | |
| jobs: | |
| test: | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.9] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.dev.txt | |
| - name: Check code format with black | |
| run: | | |
| black --check functions main.py --target-version=py37 | |
| - name: Test with pytest | |
| run: | | |
| pytest | |
| deploy: | |
| runs-on: ubuntu-latest | |
| needs: test | |
| if: ${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/production' }} | |
| strategy: | |
| matrix: | |
| include: | |
| - name: ingest_upload | |
| topic: uploads | |
| timeout: 540 | |
| memory: 2048 | |
| - name: send_email | |
| topic: emails | |
| timeout: 60 | |
| memory: 512 | |
| - name: store_auth0_logs | |
| topic: daily_cron | |
| timeout: 120 | |
| memory: 1024 | |
| - name: disable_inactive_users | |
| topic: daily_cron | |
| timeout: 120 | |
| memory: 1024 | |
| - name: refresh_download_permissions | |
| topic: daily_cron | |
| timeout: 120 | |
| memory: 1024 | |
| - name: vis_preprocessing | |
| topic: artifact_upload | |
| timeout: 540 | |
| memory: 1024 | |
| max_instances: 10 | |
| - name: derive_files_from_manifest_upload | |
| topic: patient_sample_update | |
| timeout: 60 | |
| memory: 1024 | |
| - name: derive_files_from_assay_or_analysis_upload | |
| topic: assay_or_analysis_upload_complete | |
| timeout: 540 | |
| memory: 1024 | |
| - name: update_cidc_from_csms | |
| topic: csms_trigger | |
| timeout: 540 | |
| memory: 1024 | |
| - name: grant_download_permissions | |
| topic: grant_download_perms | |
| timeout: 540 | |
| memory: 1024 | |
| - name: worker | |
| topic: worker | |
| timeout: 540 | |
| memory: 1024 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Cloud SDK | |
| uses: google-github-actions/setup-gcloud@v0 | |
| with: | |
| project_id: ${{ github.ref == 'refs/heads/production' && 'cidc-dfci' || 'cidc-dfci-staging' }} | |
| service_account_key: ${{ github.ref == 'refs/heads/production' && secrets.GCP_SA_KEY_PROD || secrets.GCP_SA_KEY_STAGING }} | |
| export_default_credentials: true | |
| - name: Deploy ${{ matrix.name }} to Cloud Functions | |
| env: | |
| ENV_VARS_FILE: ${{ github.ref == 'refs/heads/production' && '.env.prod.yaml' || '.env.staging.yaml' }} | |
| run: | | |
| gcloud functions deploy ${{ matrix.name }} \ | |
| --trigger-topic ${{ matrix.topic }} \ | |
| --timeout ${{ matrix.timeout }} \ | |
| --memory ${{ matrix.memory }} \ | |
| --env-vars-file $ENV_VARS_FILE \ | |
| --runtime python37 \ | |
| ${{ matrix.max_instances && format('--max-instances {0}', matrix.max_instances) || ''}} |