#334 - Re-enable CodeableConceptServiceIT (#417) #1480
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| name: Docker | |
| on: | |
| push: | |
| branches: | |
| - '**' | |
| tags: | |
| - v[0-9]+.[0-9]+.[0-9]+** | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Docker Meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: | | |
| ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | |
| tags: | | |
| type=ref,event=branch | |
| type=ref,event=pr | |
| type=semver,pattern={{version}} | |
| type=semver,pattern={{major}}.{{minor}} | |
| type=semver,pattern={{major}} | |
| type=sha | |
| labels: | | |
| maintainer=medizininformatik-initiative | |
| org.opencontainers.image.authors=medizininformatik-initiative | |
| org.opencontainers.image.source=https://github.com/medizininformatik-initiative/feasibility-backend | |
| org.opencontainers.image.vendor=medizininformatik-initiative | |
| org.opencontainers.image.title=dataportal backend | |
| org.opencontainers.image.description=The backend for the dataportal, including feasibility query execution as well as data selection and extraction. | |
| - name: Set up JDK 22 | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: 22 | |
| - name: Cache Local Maven Repo | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.m2/repository | |
| key: tests-maven-${{ hashFiles('pom.xml') }} | |
| - uses: s4u/[email protected] | |
| with: | |
| servers: | | |
| [{"id": "mii", "username": "${{ github.actor }}", "password": "${{ secrets.GITHUB_TOKEN }}"}] | |
| - name: Initialize CodeQL | |
| uses: github/codeql-action/init@v3 | |
| with: | |
| languages: java | |
| queries: security-and-quality | |
| - name: Run Tests | |
| run: mvn -Pdownload-ontology -B verify | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| with: | |
| fail_ci_if_error: true | |
| - name: Perform CodeQL Analysis | |
| uses: github/codeql-action/analyze@v3 | |
| - name: Upload Dataportal Backend Jar | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: backend-jar | |
| path: target/dataportalBackend.jar | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build and Export to Docker | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| tags: backend:latest | |
| outputs: type=docker,dest=/tmp/dataportalBackend.tar | |
| - name: Upload Dataportal Backend Image | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: backend-image | |
| path: /tmp/dataportalBackend.tar | |
| security-scan: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up JDK 21 | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'zulu' | |
| java-version: 21 | |
| - name: Cache Local Maven Repo | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.m2/repository | |
| key: security-scan-maven-${{ hashFiles('pom.xml') }} | |
| - uses: s4u/[email protected] | |
| with: | |
| servers: | | |
| [{"id": "mii", "username": "${{ github.actor }}", "password": "${{ secrets.GITHUB_TOKEN }}"}] | |
| - name: Maven Package | |
| run: mvn -Pdownload-ontology -B -DskipTests package | |
| - name: Build and push Docker image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| tags: security-scan-build:latest | |
| push: false | |
| - name: Run Trivy Vulnerability Scanner | |
| uses: aquasecurity/trivy-action@master | |
| with: | |
| image-ref: security-scan-build:latest | |
| format: sarif | |
| output: trivy-results.sarif | |
| severity: 'CRITICAL,HIGH' | |
| timeout: '15m0s' | |
| env: | |
| TRIVY_DB_REPOSITORY: public.ecr.aws/aquasecurity/trivy-db:2 | |
| TRIVY_JAVA_DB_REPOSITORY: public.ecr.aws/aquasecurity/trivy-java-db:1 | |
| - name: Upload Trivy Scan Results to GitHub Security Tab | |
| uses: github/codeql-action/upload-sarif@v3 | |
| with: | |
| sarif_file: trivy-results.sarif | |
| integration-test: | |
| needs: tests | |
| runs-on: ubuntu-latest | |
| env: | |
| ONTOLOGY_GIT_TAG: v3.0.1 | |
| ELASTIC_HOST: http://localhost:9200 | |
| ELASTIC_FILEPATH: https://github.com/medizininformatik-initiative/fhir-ontology-generator/releases/download/TAGPLACEHOLDER/ | |
| ELASTIC_FILENAME: elastic.zip | |
| OVERRIDE_EXISTING: true | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@v4 | |
| - name: Download Dataportal Backend Image | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: backend-image | |
| path: /tmp | |
| - name: Install jq | |
| uses: dcarbone/[email protected] | |
| - name: Load Dataportal Backend Image | |
| run: docker load --input /tmp/dataportalBackend.tar | |
| - name: Download ontology files from github | |
| run: .github/scripts/download-and-unpack-ontology.sh | |
| - name: Run Dataportal Backend with Database, Elasticsearch, Keycloak and Blaze | |
| run: docker compose -f .github/integration-test/docker-compose.yml up -d | |
| - name: Wait for Dataportal Backend | |
| run: .github/scripts/wait-for-url.sh http://localhost:8091/actuator/health | |
| - name: Check if Dataportal Backend is correctly running with the user with id 10001 | |
| run: .github/scripts/check-if-running-as-user-10001.sh | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8082/health | |
| - name: Load Data | |
| run: .github/scripts/load-test-data.sh | |
| - name: Wait for Keycloak | |
| run: .github/scripts/wait-for-url.sh http://localhost:8083/auth/ | |
| - name: Create Test User in Keycloak | |
| run: .github/scripts/create-keycloak-user.sh | |
| - name: Wait for Elastic | |
| run: .github/scripts/wait-for-url.sh http://localhost:9200/_cluster/health | |
| - name: Create indices and upload data to elastic | |
| run: .github/scripts/init-elasticsearch.sh | |
| - name: Wait for Flare | |
| run: .github/scripts/wait-for-url.sh http://localhost:8092/cache/stats | |
| - name: Post Test Query | |
| run: .github/scripts/post-test-query.sh | |
| - name: Post Elasticsearch Test Queries | |
| run: .github/scripts/post-elastic-test-queries.sh | |
| - name: Dump docker logs on failure | |
| if: failure() | |
| uses: jwalton/gh-docker-logs@v2 | |
| release: | |
| if: ${{ startsWith(github.ref, 'refs/tags/v') }} | |
| needs: | |
| - tests | |
| - integration-test | |
| - security-scan | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up JDK 22 | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: 22 | |
| - name: Cache Local Maven Repo | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.m2/repository | |
| key: release-maven-${{ hashFiles('pom.xml') }} | |
| - uses: s4u/[email protected] | |
| with: | |
| servers: | | |
| [{"id": "mii", "username": "${{ github.actor }}", "password": "${{ secrets.GITHUB_TOKEN }}"}] | |
| - name: Prepare Version | |
| id: prep | |
| run: | | |
| echo ::set-output name=repository::$(echo $GITHUB_REPOSITORY | tr '[:upper:]' '[:lower:]') | |
| echo ::set-output name=version::${GITHUB_REF#refs/tags/v} | |
| - name: Maven Package | |
| run: mvn -Pdownload-ontology -B -DskipTests package | |
| - name: Login to GitHub Docker Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build and push Docker image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| platforms: linux/amd64,linux/arm64 | |
| tags: | | |
| ghcr.io/${{ steps.prep.outputs.repository }}:latest | |
| ghcr.io/${{ steps.prep.outputs.repository }}:${{ steps.prep.outputs.version }} | |
| push: true |