Release #60
Workflow file for this run
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| # This workflow builds a release version of Pathling and deploys it to Maven Central and PyPI. | |
| name: Release | |
| # This workflow is only run when a release is published. | |
| on: | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| env: | |
| # The add-exports and add-opens flags are required for Java 21 | |
| MAVEN_OPTS: --add-exports=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED | |
| permissions: | |
| id-token: write | |
| contents: write # Required to upload release assets | |
| jobs: | |
| release-maven: | |
| name: Release to Maven Central | |
| environment: maven-central | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| submodules: recursive | |
| - name: Set up JDK | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: 21 | |
| distribution: "zulu" | |
| - name: Install Bun | |
| uses: oven-sh/setup-bun@v2 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v6 | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: "4.1.3" | |
| use-public-rspm: true | |
| - name: Set up Pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Cache local Maven repository | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.m2/repository | |
| key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }} | |
| restore-keys: |- | |
| ${{ runner.os }}-maven- | |
| - name: Cache Python packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: /home/runner/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('lib/python/requirements/dev.txt', 'lib/python/requirements/package.txt') }} | |
| - name: Cache R packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ runner.temp }}/Library | |
| key: r-packages-${{ runner.os }}-${{ hashFiles('lib/R/DESCRIPTION.src') }} | |
| restore-keys: r-packages-${{ runner.os }}- | |
| - name: Cache SonarQube packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.sonar/cache | |
| key: ${{ runner.os }}-sonar | |
| restore-keys: ${{ runner.os }}-sonar | |
| - name: Install TinyTeX and libcurl | |
| # These are required for building the R package documentation. | |
| run: | | |
| wget -qO- "https://yihui.org/tinytex/install-bin-unix.sh" | sh | |
| echo "$HOME/bin" >> $GITHUB_PATH | |
| sudo apt-get install -y libcurl4-openssl-dev | |
| - name: Install GPG key | |
| env: | |
| GPG_KEY: ${{ secrets.GPG_KEY }} | |
| run: | | |
| echo "$GPG_KEY" | gpg --batch --import | |
| gpg --list-secret-keys --keyid-format LONG | |
| - name: Configure Maven settings | |
| uses: s4u/maven-settings-action@v3.1.0 | |
| with: | |
| servers: | | |
| [{ | |
| "id": "central", | |
| "username": "${{ secrets.OSSRH_USERNAME }}", | |
| "password": "${{ secrets.OSSRH_PASSWORD }}" | |
| }] | |
| # Release won't be possible if there are outstanding vulnerabilities of medium severity or | |
| # higher as reported by Trivy. | |
| - name: Run security scan | |
| uses: aquasecurity/trivy-action@0.32.0 | |
| with: | |
| scan-type: repo | |
| severity: "MEDIUM,HIGH,CRITICAL" | |
| scan-ref: . | |
| format: sarif | |
| output: trivy-results.sarif | |
| skip-files: examples/**/*,**/target/**/*,sql-on-fhir/sof-js/package-lock.json,licenses/**/*,site/package-lock.json | |
| # Upon release, the databases will be updated and scanned to make sure nothing has crept | |
| # in since the last daily update. | |
| cache: false | |
| - name: Run deploy goal | |
| env: | |
| PYSPARK_PYTHON: ${{ steps.python-install.outputs.python-path }} | |
| PYSPARK_DRIVER_PYTHON: ${{ steps.python-install.outputs.python-path }} | |
| R_KEEP_PKG_SOURCE: yes | |
| SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} | |
| MAVEN_GPG_PASSPHRASE: ${{ secrets.GPG_PASSPHRASE }} | |
| run: | | |
| mvn --batch-mode deploy \ | |
| org.sonarsource.scanner.maven:sonar-maven-plugin:sonar \ | |
| -Dsonar.projectKey=aehrc_pathling -Dsonar.organization=aehrc \ | |
| -Dsonar.host.url=https://sonarcloud.io \ | |
| -Dsonar.sarifReportPaths=trivy-results.sarif \ | |
| -pl '!benchmark' -Pdocs,mavenRelease,check | |
| timeout-minutes: 60 | |
| - name: Save test reports | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: surefire-reports | |
| path: "**/surefire-reports/" | |
| - name: Save coverage reports | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-reports | |
| path: | | |
| **/jacoco.xml | |
| **/target/site/jacoco | |
| **/target/site/jacoco-aggregate | |
| lib/python/**/coverage.xml | |
| - name: Save built JARs | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: jars | |
| path: | | |
| utilities/target/utilities-*.jar | |
| encoders/target/encoders-*.jar | |
| terminology/target/terminology-*.jar | |
| fhirpath/target/fhirpath-*.jar | |
| library-api/target/library-api-*.jar | |
| library-runtime/target/library-runtime-*.jar | |
| lib/python/target/python-*.jar | |
| lib/R/target/r-*.jar | |
| if-no-files-found: "error" | |
| - name: Save Python wheel | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: python-wheel | |
| path: lib/python/target/py-dist/pathling-*.whl | |
| - name: Save R package | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: r-package | |
| path: lib/R/target/pathling_*.tar.gz | |
| - name: Save site | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: site | |
| path: site/target/site/ | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::865780493209:role/PathlingBenchmarkUpload | |
| aws-region: ap-southeast-2 | |
| - name: Extract major version | |
| id: extract-version | |
| run: | | |
| # Extract version from tag (e.g. v8.0.1 -> v8) | |
| VERSION_TAG="${{ github.ref_name }}" | |
| MAJOR_VERSION=$(echo "$VERSION_TAG" | sed -E 's/^(v[0-9]+).*/\1/') | |
| echo "major_version=${MAJOR_VERSION}" >> $GITHUB_OUTPUT | |
| echo "Extracted major version: ${MAJOR_VERSION}" | |
| - name: Upload SQL on FHIR test report to S3 | |
| run: aws s3 cp fhirpath/target/fhir-view-compliance-test.json s3://pathling-benchmark/test-reports/${{ steps.extract-version.outputs.major_version }}/sof-test-results.json | |
| - name: Upload release assets | |
| run: | | |
| gh release upload ${{ github.ref_name }} \ | |
| --clobber \ | |
| library-runtime/target/library-runtime-*.jar \ | |
| lib/python/target/py-dist/pathling-*.whl \ | |
| lib/R/target/pathling_*.tar.gz | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| release-pypi: | |
| name: Release to PyPI | |
| environment: pypi | |
| runs-on: ubuntu-latest | |
| needs: release-maven | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| # This is required so that git-commit-id-plugin can find the latest tag. | |
| fetch-depth: 0 | |
| submodules: recursive | |
| - name: Set up JDK | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: 21 | |
| distribution: "zulu" | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v6 | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: "4.1.3" | |
| use-public-rspm: true | |
| - name: Set up Pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Cache local Maven repository | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.m2/repository | |
| key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-maven- | |
| - name: Cache Python packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: /home/runner/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('lib/python/requirements/dev.txt', 'lib/python/requirements/package.txt') }} | |
| - name: Cache R packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ runner.temp }}/Library | |
| key: r-packages-${{ runner.os }}-${{ hashFiles('lib/R/DESCRIPTION.src') }} | |
| restore-keys: r-packages-${{ runner.os }}- | |
| - name: Install TinyTeX and libcurl | |
| # These are required for building the R package documentation. | |
| run: | | |
| wget -qO- "https://yihui.org/tinytex/install-bin-unix.sh" | sh | |
| echo "$HOME/bin" >> $GITHUB_PATH | |
| sudo apt-get install -y libcurl4-openssl-dev | |
| - name: Run deploy goal | |
| env: | |
| PYSPARK_PYTHON: ${{ steps.python-install.outputs.python-path }} | |
| PYSPARK_DRIVER_PYTHON: ${{ steps.python-install.outputs.python-path }} | |
| TWINE_USERNAME: ${{ secrets.TWINE_USERNAME }} | |
| TWINE_PASSWORD: ${{ secrets.TWINE_PASSWORD }} | |
| R_KEEP_PKG_SOURCE: yes | |
| run: | | |
| mvn --batch-mode deploy \ | |
| -pl lib/python -am \ | |
| -DskipTests -PpythonRelease | |
| timeout-minutes: 30 | |
| upload-to-dap: | |
| name: Upload source code to CSIRO DAP | |
| environment: csiro-dap | |
| runs-on: [self-hosted, Linux] | |
| needs: [release-maven, release-pypi] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Download source code and upload to CSIRO DAP | |
| run: python .github/scripts/dap_upload.py | |
| env: | |
| GITHUB_REPOSITORY: ${{ github.repository }} | |
| GITHUB_REF_NAME: ${{ github.ref_name }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| DAP_USERNAME: ${{ secrets.DAP_USERNAME }} | |
| DAP_PASSWORD: ${{ secrets.DAP_PASSWORD }} | |
| DAP_BASE_URL: https://data.csiro.au | |
| COLLECTION_PID: csiro:49524 | |
| timeout-minutes: 20 |