3388 allow organisms without consensus sequences #100
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
| name: Integration tests | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| paths: | |
| - "backend/**" | |
| - "keycloak/**" | |
| - "kubernetes/**" | |
| - "website/**" | |
| - "deploy.py" | |
| - "integration-tests/**" | |
| - ".github/scripts/**" | |
| - ".github/workflows/**" | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| integration-tests: | |
| permissions: | |
| packages: read | |
| contents: read | |
| checks: read | |
| actions: read # Required by workflow-telemetry-action | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 45 | |
| env: | |
| sha: ${{ github.event.pull_request.head.sha || github.sha }} | |
| steps: | |
| - name: Shorten sha | |
| run: echo "sha=${sha::7}" >> $GITHUB_ENV | |
| - name: Collect Workflow Telemetry | |
| uses: catchpoint/workflow-telemetry-action@v2 | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install k3d | |
| run: | | |
| curl -s https://raw.githubusercontent.com/rancher/k3d/main/install.sh | bash | |
| k3d version | |
| - uses: azure/setup-helm@v4 | |
| - name: Create k3d cluster | |
| run: | | |
| ./deploy.py --verbose cluster | |
| - name: Deploy with helm | |
| run: | | |
| ./deploy.py --verbose helm --branch ${{ github.ref_name }} --sha ${{ env.sha }} --for-e2e --enablePreprocessing | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version-file: ./website/.nvmrc | |
| - name: Cache .npm | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.npm | |
| key: ${{ runner.os }}-node-${{ hashFiles('integration-tests/**/package-lock.json') }} | |
| - name: Install dependencies | |
| run: cd integration-tests && npm i | |
| - name: Get Installed Playwright Version | |
| id: playwright-version | |
| run: cd integration-tests && echo "PLAYWRIGHT_VERSION=$(node -e "console.log(require('./package-lock.json').packages['node_modules/@playwright/test'].version)")" >> $GITHUB_ENV | |
| - name: Cache Playwright Browsers | |
| uses: actions/cache@v4 | |
| id: playwright-cache | |
| with: | |
| path: ~/.cache/ms-playwright | |
| key: ${{ runner.os }}-playwright-${{ env.PLAYWRIGHT_VERSION }} | |
| - name: Install Playwright Browsers and System Dependencies | |
| run: cd integration-tests && npx playwright install --with-deps | |
| if: steps.playwright-cache.outputs.cache-hit != 'true' | |
| - name: Install only System Dependencies | |
| run: cd website && npx playwright install-deps | |
| if: steps.playwright-cache.outputs.cache-hit == 'true' | |
| - name: Wait for the pods to be ready | |
| run: ./.github/scripts/wait_for_pods_to_be_ready.py --timeout 190 | |
| - name: Sleep for 10 secs | |
| run: sleep 10 | |
| - name: Run Integration test | |
| run: | | |
| set -o pipefail | |
| cd integration-tests && npx playwright test 2>&1 | tee output.txt | |
| EXIT_CODE=$? | |
| echo '```' >> $GITHUB_STEP_SUMMARY | |
| sed -n '/Running [0-9]\+ tests/,$p' output.txt >> $GITHUB_STEP_SUMMARY | |
| echo '```' >> $GITHUB_STEP_SUMMARY | |
| exit $EXIT_CODE | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: playwright-report | |
| path: integration-tests/playwright-report/ | |
| retention-days: 30 | |
| - name: List running pods | |
| if: ${{ !cancelled() }} | |
| run: kubectl get pods --all-namespaces | |
| - name: Describe pods | |
| if: ${{ !cancelled() }} | |
| run: kubectl describe pods -l app=loculus | |
| - name: Show events | |
| if: ${{ !cancelled() }} | |
| run: kubectl get events | |
| - name: Save logs from all containers to file | |
| if: ${{ !cancelled() }} | |
| run: ./.github/scripts/collect_kubernetes_logs.sh | |
| - name: Upload Kubernetes logs | |
| if: ${{ !cancelled() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: kubernetes-logs | |
| path: kubernetes_logs/ |