fix: make proWES run locally #91
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| name: proWES checks | |
| on: | |
| push: | |
| branches: [ dev ] | |
| pull_request: | |
| branches: [ dev ] | |
| jobs: | |
| lint: | |
| name: Run static code analysis | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install requirements | |
| run: | | |
| pip install -r requirements_dev.txt | |
| pip install . | |
| - name: Lint with Flake8 | |
| run: flake8 | |
| - name: Lint with Pylint | |
| run: pylint pro_wes/ setup.py | |
| - name: Check code format with Black | |
| run: black --check setup.py pro_wes/ tests/ | |
| - name: Check types with mypy | |
| run: mypy setup.py pro_wes/ | |
| test: | |
| name: Run tests | |
| runs-on: ubuntu-latest | |
| env: | |
| PROBE_ENDPOINT: localhost:8090/ga4gh/wes/v1/service-info | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install yq | |
| run: pip install yq | |
| - name: Update configuration hosts | |
| run: | | |
| yq -y --in-place '.db.host = "mongodb"' pro_wes/config.yaml | |
| yq -y --in-place '.jobs.host = "rabbitmq"' pro_wes/config.yaml | |
| - name: Deploy app | |
| run: docker compose up -d --build | |
| - name: Wait for app startup | |
| run: sleep 20 | |
| - name: Probe endpoint | |
| run: | | |
| test $( \ | |
| curl \ | |
| -sL \ | |
| -v \ | |
| -o /dev/null \ | |
| -w '%{http_code}' \ | |
| -X GET \ | |
| --header 'Accept: application/json' \ | |
| "${PROBE_ENDPOINT}" \ | |
| ) == '200' || exit 1 | |
| publish: | |
| name: Build and publish app image | |
| runs-on: ubuntu-latest | |
| if: ${{ github.event_name == 'push' }} | |
| needs: [lint, test] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Generate tag | |
| run: | | |
| echo "TAG=$(date '+%Y%m%d')" >> $GITHUB_ENV | |
| - name: Build and publish image | |
| id: docker | |
| uses: philips-software/[email protected] | |
| with: | |
| dockerfile: . | |
| image-name: "prowes" | |
| tags: "latest ${{ env.TAG }}" | |
| push-branches: "${{ github.event.repository.default_branch }}" | |
| env: | |
| REGISTRY_USERNAME: ${{ secrets.DOCKERHUB_LOGIN }} | |
| REGISTRY_TOKEN: "${{ secrets.DOCKERHUB_TOKEN }}" | |
| DOCKER_ORGANIZATION: ${{ secrets.DOCKERHUB_ORG }} | |
| GITHUB_ORGANIZATION: ${{ github.repository_owner }} | |
| - name: Verify that image was pushed | |
| run: | | |
| echo "Push indicator: ${{ steps.docker.outputs.push-indicator }}" | |
| echo "# Set to 'true' if image was pushed, empty string otherwise" | |
| test "${{ steps.docker.outputs.push-indicator }}" == "true" |