WIP - Dependency updates to fix vulnerabilities from security scans #6254
Workflow file for this run
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| name: Test | |
| on: | |
| pull_request: | |
| branches: | |
| - develop | |
| - dev-[0-9]+.[0-9]+.[0-9]+ | |
| types: | |
| # defaults + 'edited', to handle changes to flags like ___REQUIRES_GATEWAY_PR___ in the PR body | |
| [ opened, synchronize, reopened, edited ] | |
| push: | |
| branches: | |
| - develop | |
| tags: | |
| - v* | |
| workflow_dispatch: | |
| env: | |
| AERIE_USERNAME: "${{secrets.AERIE_USERNAME}}" | |
| AERIE_PASSWORD: "${{secrets.AERIE_PASSWORD}}" | |
| HASURA_GRAPHQL_ADMIN_SECRET: "${{secrets.HASURA_GRAPHQL_ADMIN_SECRET}}" | |
| HASURA_GRAPHQL_JWT_SECRET: "${{secrets.HASURA_GRAPHQL_JWT_SECRET}}" | |
| POSTGRES_USER: "${{secrets.POSTGRES_USER}}" | |
| POSTGRES_PASSWORD: "${{secrets.POSTGRES_PASSWORD}}" | |
| GATEWAY_USERNAME: "${{secrets.GATEWAY_USERNAME}}" | |
| GATEWAY_PASSWORD: "${{secrets.GATEWAY_PASSWORD}}" | |
| MERLIN_USERNAME: "${{secrets.MERLIN_USERNAME}}" | |
| MERLIN_PASSWORD: "${{secrets.MERLIN_PASSWORD}}" | |
| SCHEDULER_USERNAME: "${{secrets.SCHEDULER_USERNAME}}" | |
| SCHEDULER_PASSWORD: "${{secrets.SCHEDULER_PASSWORD}}" | |
| SEQUENCING_USERNAME: "${{secrets.SEQUENCING_USERNAME}}" | |
| SEQUENCING_PASSWORD: "${{secrets.SEQUENCING_PASSWORD}}" | |
| PR_BODY: "${{github.event.pull_request.body}}" | |
| jobs: | |
| unit-test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v6 | |
| - name: Load NPM Cache | |
| uses: ./.github/actions/load-node-cache | |
| - name: Setup Java | |
| uses: actions/setup-java@v5 | |
| with: | |
| distribution: "temurin" | |
| java-version: "21" | |
| - name: Setup Gradle | |
| uses: gradle/actions/setup-gradle@v5 | |
| with: | |
| # This action defaults to matching on "main" and "master" as the branches allowed to write to the cache | |
| cache-read-only: ${{ github.ref != 'refs/heads/develop' }} | |
| - name: Assemble | |
| # Don't generate docs for tests | |
| run: ./gradlew assemble -x javadoc -x javadocJar -x generateDocumentation --parallel | |
| - name: Run Unit Tests | |
| run: ./gradlew test --parallel | |
| - name: Upload Test Results as XML and HTML | |
| if: always() | |
| uses: actions/upload-artifact@v7 | |
| with: | |
| name: Unit Test Results | |
| path: | | |
| **/build/test-results/test | |
| **/build/reports/tests/test | |
| action-unit-tests: | |
| runs-on: ubuntu-latest | |
| environment: e2e-test | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v6 | |
| - name: Setup NPM | |
| uses: actions/setup-node@v6 | |
| with: | |
| node-version-file: ./action-server/.nvmrc | |
| cache: npm | |
| cache-dependency-path: ./action-server/package-lock.json | |
| - name: Install Dependencies | |
| run: npm ci | |
| working-directory: ./action-server | |
| - name: Run Action Server Unit Tests | |
| run: npm --silent run test | |
| working-directory: ./action-server | |
| - name: Upload Test Results | |
| if: always() | |
| uses: actions/upload-artifact@v7 | |
| with: | |
| name: Action Server Test Results | |
| path: | | |
| **/action-server/action-server-test-report.log | |
| db-tests: | |
| runs-on: ubuntu-latest | |
| environment: e2e-test | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v6 | |
| - name: Setup Postgres Client (psql) | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install --yes postgresql-client | |
| - name: Setup Java | |
| uses: actions/setup-java@v5 | |
| with: | |
| distribution: "temurin" | |
| java-version: "21" | |
| - name: Setup Gradle | |
| uses: gradle/actions/setup-gradle@v5 | |
| with: | |
| # This action defaults to matching on "main" and "master" as the branches allowed to write to the cache | |
| cache-read-only: ${{ github.ref != 'refs/heads/develop' }} | |
| - name: Start Services | |
| run: | | |
| docker compose -f ./e2e-tests/docker-compose-test.yml up postgres -d --quiet-pull | |
| - name: Sleep for 5 Seconds | |
| run: sleep 5s | |
| shell: bash | |
| - name: Run DB Tests | |
| run: ./gradlew db-tests:e2eTest | |
| - name: Upload DB Test Results | |
| if: always() | |
| uses: actions/upload-artifact@v7 | |
| with: | |
| name: DB Test Results | |
| path: | | |
| **/db-tests/build/reports/tests/e2eTest | |
| - name: Shutdown Backend | |
| uses: ./.github/actions/shutdown-test-backend | |
| sequencing-e2e-tests: | |
| runs-on: ubuntu-latest | |
| environment: e2e-test | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v6 | |
| - name: Setup Java | |
| uses: actions/setup-java@v5 | |
| with: | |
| distribution: "temurin" | |
| java-version: "21" | |
| - name: Setup Gradle | |
| uses: gradle/actions/setup-gradle@v5 | |
| with: | |
| # This action defaults to matching on "main" and "master" as the branches allowed to write to the cache | |
| cache-read-only: ${{ github.ref != 'refs/heads/develop' }} | |
| - name: Start E2E Test Backend | |
| uses: ./.github/actions/start-test-backend | |
| - name: Run Sequencing E2E Tests | |
| run: ./gradlew sequencing-server:e2eTest | |
| - name: Upload Sequencing E2E Test Results | |
| if: always() | |
| uses: actions/upload-artifact@v7 | |
| with: | |
| name: Sequencing E2E Test Results | |
| path: | | |
| **/sequencing-server/test-report.* | |
| - name: Shutdown E2E Test Backend | |
| uses: ./.github/actions/shutdown-test-backend | |
| java-e2e-test: | |
| runs-on: ubuntu-latest | |
| environment: e2e-test | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v6 | |
| - name: Setup Java | |
| uses: actions/setup-java@v5 | |
| with: | |
| distribution: "temurin" | |
| java-version: "21" | |
| - name: Setup Gradle | |
| uses: gradle/actions/setup-gradle@v5 | |
| with: | |
| # This action defaults to matching on "main" and "master" as the branches allowed to write to the cache | |
| cache-read-only: ${{ github.ref != 'refs/heads/develop' }} | |
| - name: Start E2E Test Backend | |
| uses: ./.github/actions/start-test-backend | |
| - name: Build scheduling procedure jars for testing | |
| run: ./gradlew e2e-tests:buildAllProcedureJars | |
| - name: Run E2E Tests | |
| run: ./gradlew e2e-tests:e2eTest | |
| - name: Upload E2E Test Results | |
| if: always() | |
| uses: actions/upload-artifact@v7 | |
| with: | |
| name: E2E Test Results | |
| path: | | |
| **/e2e-tests/build/reports/tests/e2eTest | |
| - name: Shutdown Backend | |
| uses: ./.github/actions/shutdown-test-backend |