fix: retry schema-migration sfn on Batch.AWSBatchException #20554
Workflow file for this run
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| name: Push Tests | |
| on: | |
| pull_request: | |
| branches: | |
| - "*" | |
| push: | |
| branches: | |
| - "main" | |
| workflow_call: | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| DEPLOYMENT_STAGE: test | |
| # Force using BuildKit instead of normal Docker, required so that metadata | |
| # is written/read to allow us to use layers of previous builds as cache. | |
| DOCKER_BUILDKIT: 1 | |
| COMPOSE_DOCKER_CLI_BUILD: 1 | |
| DOCKER_REPO: ${{ secrets.ECR_REPO }}/ | |
| permissions: | |
| id-token: write | |
| contents: read | |
| jobs: | |
| lint: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 1800 | |
| - name: Login to ECR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.ECR_REPO }} | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 2 | |
| - uses: actions/setup-python@v5 | |
| - name: check backend | |
| uses: pre-commit/[email protected] | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version-file: "frontend/.nvmrc" | |
| cache: "npm" | |
| cache-dependency-path: "frontend/package-lock.json" | |
| - name: check frontend | |
| run: | | |
| cd frontend | |
| npm ci | |
| cp src/configs/local.js src/configs/configs.js | |
| npm run lint | |
| - uses: 8398a7/action-slack@v3 | |
| with: | |
| status: ${{ job.status }} | |
| fields: repo,commit,author,eventName,workflow,job,mention | |
| mention: "here" | |
| env: | |
| SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
| if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
| backend-unit-test: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 1800 | |
| - name: Login to ECR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.ECR_REPO }} | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 2 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/[email protected] | |
| with: | |
| files: | | |
| Dockerfile* | |
| **/Dockerfile | |
| requirements*.txt | |
| **/requirements*.txt | |
| - name: Check if containers need to be rebuilt | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-rebuild-backend | |
| - name: Run unit tests | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-unit-test-backend | |
| - name: Upload coverage results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
| retention-days: 3 | |
| - name: Upload Allure results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: allure-results | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
| retention-days: 20 | |
| - uses: 8398a7/[email protected] | |
| with: | |
| status: ${{ job.status }} | |
| fields: repo,commit,author,eventName,workflow,job,mention | |
| mention: "here" | |
| env: | |
| SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
| if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
| backend-wmg-unit-test: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 1800 | |
| - name: Login to ECR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.ECR_REPO }} | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 2 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/[email protected] | |
| with: | |
| files: | | |
| Dockerfile* | |
| **/Dockerfile | |
| requirements*.txt | |
| **/requirements*.txt | |
| - name: Check if containers need to be rebuilt | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-rebuild-wmg-backend | |
| - name: Run unit tests | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-unit-test-wmg-backend | |
| - name: Upload coverage results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
| retention-days: 3 | |
| - name: Upload Allure results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: allure-results | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
| retention-days: 20 | |
| - uses: 8398a7/[email protected] | |
| with: | |
| status: ${{ job.status }} | |
| fields: repo,commit,author,eventName,workflow,job,mention | |
| mention: "here" | |
| env: | |
| SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
| if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
| backend-de-unit-test: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 1800 | |
| - name: Login to ECR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.ECR_REPO }} | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 2 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/[email protected] | |
| with: | |
| files: | | |
| Dockerfile* | |
| **/Dockerfile | |
| requirements*.txt | |
| **/requirements*.txt | |
| - name: Check if containers need to be rebuilt | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-rebuild-de-backend | |
| - name: Run unit tests | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-unit-test-de-backend | |
| - name: Upload coverage results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
| retention-days: 3 | |
| - name: Upload Allure results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: allure-results | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
| retention-days: 20 | |
| - uses: 8398a7/[email protected] | |
| with: | |
| status: ${{ job.status }} | |
| fields: repo,commit,author,eventName,workflow,job,mention | |
| mention: "here" | |
| env: | |
| SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
| if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
| processing-unit-test: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 1800 | |
| - name: Login to ECR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.ECR_REPO }} | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 2 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/[email protected] | |
| with: | |
| files: | | |
| Dockerfile* | |
| **/Dockerfile* | |
| requirements*.txt | |
| **/requirements*.txt | |
| - name: Check if containers need to be rebuilt | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-rebuild-processing | |
| - name: Run tests in docker-compose | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-unit-test-processing | |
| - name: Upload coverage results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
| retention-days: 3 | |
| - name: Upload Allure results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: allure-results | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
| retention-days: 20 | |
| - uses: 8398a7/[email protected] | |
| with: | |
| status: ${{ job.status }} | |
| fields: repo,commit,author,eventName,workflow,job,mention | |
| mention: "here" | |
| env: | |
| SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
| if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
| wmg-processing-unit-test: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 1800 | |
| - name: Login to ECR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.ECR_REPO }} | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 2 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/[email protected] | |
| with: | |
| files: | | |
| Dockerfile* | |
| **/Dockerfile* | |
| requirements*.txt | |
| **/requirements*.txt | |
| - name: Check if containers need to be rebuilt | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-rebuild-wmg-processing | |
| - name: Run tests in docker-compose | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-unit-test-wmg-processing | |
| - name: Upload coverage results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
| retention-days: 3 | |
| - name: Upload Allure results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: allure-results | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
| retention-days: 20 | |
| - uses: 8398a7/[email protected] | |
| with: | |
| status: ${{ job.status }} | |
| fields: repo,commit,author,eventName,workflow,job,mention | |
| mention: "here" | |
| env: | |
| SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
| if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
| cellguide-pipeline-unit-test: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 1800 | |
| - name: Login to ECR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.ECR_REPO }} | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 2 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/[email protected] | |
| with: | |
| files: | | |
| Dockerfile* | |
| **/Dockerfile* | |
| requirements*.txt | |
| **/requirements*.txt | |
| - name: Check if containers need to be rebuilt | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-rebuild-cellguide-pipeline | |
| - name: Run tests in docker-compose | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-unit-test-cellguide-pipeline | |
| - name: Upload coverage results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
| retention-days: 3 | |
| - name: Upload Allure results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: allure-results | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
| retention-days: 20 | |
| - uses: 8398a7/[email protected] | |
| with: | |
| status: ${{ job.status }} | |
| fields: repo,commit,author,eventName,workflow,job,mention | |
| mention: "here" | |
| env: | |
| SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
| if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
| cxg-admin-unit-test: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 1800 | |
| - name: Login to ECR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.ECR_REPO }} | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 2 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/[email protected] | |
| with: | |
| files: | | |
| Dockerfile* | |
| **/Dockerfile | |
| requirements*.txt | |
| **/requirements*.txt | |
| - name: Check if containers need to be rebuilt | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-rebuild-backend | |
| - name: Run unit tests | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-unit-test-cxg-admin | |
| - name: Upload coverage results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
| retention-days: 3 | |
| - name: Upload Allure results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: allure-results | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
| retention-days: 20 | |
| - uses: 8398a7/[email protected] | |
| with: | |
| status: ${{ job.status }} | |
| fields: repo,commit,author,eventName,workflow,job,mention | |
| mention: "here" | |
| env: | |
| SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
| if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
| backend-integration-test: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 1800 | |
| - name: Login to ECR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.ECR_REPO }} | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 2 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/[email protected] | |
| with: | |
| files: | | |
| Dockerfile* | |
| **/Dockerfile | |
| requirements*.txt | |
| **/requirements*.txt | |
| - name: Check if containers need to be rebuilt | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-rebuild-backend | |
| - name: Run tests against postgres instance | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make local-integration-test-backend | |
| - name: Upload coverage results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
| retention-days: 3 | |
| - name: Upload Allure results as an artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: allure-results | |
| path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
| retention-days: 20 | |
| - uses: 8398a7/[email protected] | |
| with: | |
| status: ${{ job.status }} | |
| fields: repo,commit,author,eventName,workflow,job,mention | |
| mention: "here" | |
| env: | |
| SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
| if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
| submit-codecoverage: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| needs: | |
| - backend-unit-test | |
| - backend-integration-test | |
| - backend-wmg-unit-test | |
| - wmg-processing-unit-test | |
| - processing-unit-test | |
| - cellguide-pipeline-unit-test | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 1800 | |
| - name: Login to ECR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.ECR_REPO }} | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 2 | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: coverage | |
| path: . | |
| - name: coverage report | |
| run: | | |
| echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
| make coverage/report-xml | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| env_vars: OS,PYTHON | |
| files: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| publish-test-report: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| needs: | |
| - backend-unit-test | |
| - backend-wmg-unit-test | |
| - backend-integration-test | |
| - wmg-processing-unit-test | |
| - processing-unit-test | |
| - cellguide-pipeline-unit-test | |
| runs-on: ubuntu-22.04 | |
| permissions: | |
| contents: write | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: allure-results | |
| path: allure-results | |
| # Checkout gh-pages branch and get Allure result history | |
| - name: Get Allure history | |
| uses: actions/checkout@v3 | |
| if: always() | |
| continue-on-error: true | |
| with: | |
| ref: gh-pages | |
| path: gh-pages | |
| fetch-depth: 2 | |
| # Create test results history as an Allure report | |
| - name: Create test results history as an Allure report | |
| uses: simple-elf/allure-report-action@master | |
| if: always() | |
| id: allure-report | |
| with: | |
| allure_results: allure-results | |
| gh_pages: gh-pages | |
| allure_report: allure-report | |
| allure_history: allure-history | |
| # Deploy Allure report to github pages | |
| - name: Deploy report to Github Pages | |
| if: always() | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_branch: gh-pages | |
| publish_dir: allure-history | |
| # Output the link to the github page for this current run | |
| - name: Post the link to the report in summary | |
| run: "echo 'Test Results Dashboard (Run #${{ github.run_number }}): https://chanzuckerberg.github.io/single-cell-data-portal/${{ github.run_number }}' >> $GITHUB_STEP_SUMMARY" |