feat: added gleason score and PSA mapping #461
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| name: ci | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - beta | |
| release: | |
| types: [created] | |
| pull_request: | |
| branches: | |
| - master | |
| - beta | |
| permissions: read-all | |
| jobs: | |
| build: | |
| uses: miracum/.github/.github/workflows/standard-build.yaml@6e79e87ffce2b28fa1052cbe3ac78f9ab7a2ea77 # v1.11.3 | |
| permissions: | |
| contents: read | |
| id-token: write | |
| packages: write | |
| pull-requests: write | |
| actions: read | |
| security-events: write | |
| with: | |
| enable-build-test-layer: true | |
| enable-upload-test-image: true | |
| secrets: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| add-test-coverage: | |
| runs-on: ubuntu-22.04 | |
| needs: | |
| - build | |
| permissions: | |
| # for add Coverage PR Comment | |
| pull-requests: write | |
| if: ${{ github.event_name == 'pull_request' }} | |
| steps: | |
| # <https://docs.docker.com/storage/containerd/> | |
| # via <https://github.com/docker/setup-buildx-action/issues/257> | |
| - name: Set up containerd image store | |
| shell: bash | |
| run: | | |
| jq '. | .+{"features": {"containerd-snapshotter": true}}' /etc/docker/daemon.json > /tmp/docker-daemon-with-containerd.json | |
| sudo mv /tmp/docker-daemon-with-containerd.json /etc/docker/daemon.json | |
| cat /etc/docker/daemon.json | |
| sudo systemctl restart docker | |
| docker info -f '{{ .DriverStatus }}' | |
| - name: Download test image | |
| uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4 | |
| with: | |
| name: ${{ needs.build.outputs.image-slug }}-test | |
| path: /tmp | |
| - name: Load test image | |
| run: | | |
| docker load --input /tmp/image-test.tar | |
| docker image ls | |
| - name: Copy unit test coverage reports from test container | |
| env: | |
| UNIT_TEST_IMAGE: ${{ fromJson(needs.build.outputs.test-image-meta-json).tags[0] }} | |
| run: | | |
| docker create --name=unit-test-container "${UNIT_TEST_IMAGE}" | |
| docker cp unit-test-container:/test ${{ github.workspace }}/test | |
| - name: Add coverage to PR | |
| id: jacoco | |
| uses: madrapps/jacoco-report@db72e7e7c96f98d239967958b0a0a6ca7d3bb45f # v1.6.1 | |
| with: | |
| paths: | | |
| ${{ github.workspace }}/test/jacoco/test/jacocoTestReport.xml | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| min-coverage-overall: 40 | |
| min-coverage-changed-files: 60 | |
| update-comment: true | |
| title: "## Code Coverage Report" | |
| test: | |
| name: run k8s smoke test | |
| runs-on: ubuntu-22.04 | |
| if: ${{ github.event_name == 'pull_request' || github.ref_name == 'beta' }} | |
| needs: | |
| - build | |
| permissions: | |
| contents: read | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7 | |
| - name: Create KinD cluster | |
| uses: helm/kind-action@0025e74a8c7512023d06dc019c617aa3cf561fde # v1.10.0 | |
| with: | |
| cluster_name: kind | |
| - name: Download image | |
| if: ${{ github.event_name == 'pull_request' }} | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7 | |
| with: | |
| name: ${{ needs.build.outputs.image-slug }} | |
| path: /tmp | |
| - name: Load image into KinD | |
| if: ${{ github.event_name == 'pull_request' }} | |
| run: | | |
| kind load image-archive /tmp/image.tar | |
| # list images in cluster | |
| docker exec kind-control-plane crictl images | |
| - name: Install test chart | |
| env: | |
| IMAGE_TAG: ${{ needs.build.outputs.image-version }} | |
| run: | | |
| helm dep up tests/k8s | |
| # start by first installing the Strimzi and Prometheus operators | |
| helm upgrade --install \ | |
| --set "stream-processors.enabled=false" \ | |
| --set "stream-processors.processors.obds-to-fhir.container.image.tag=${IMAGE_TAG}" \ | |
| --wait \ | |
| --timeout=10m \ | |
| obds-to-fhir-test \ | |
| tests/k8s | |
| kubectl wait kafka/obds-to-fhir-kafka --for=condition=Ready --timeout=300s | |
| # install the actual obds-to-fhir stream processor | |
| helm upgrade --install \ | |
| --set "stream-processors.enabled=true" \ | |
| --set "stream-processors.processors.obds-to-fhir.container.image.tag=${IMAGE_TAG}" \ | |
| --wait \ | |
| --timeout=10m \ | |
| obds-to-fhir-test \ | |
| tests/k8s | |
| - name: Run Helm test to make sure everything started correctly | |
| run: | | |
| helm test obds-to-fhir-test | |
| - name: Print cluster logs | |
| if: always() | |
| run: | | |
| kubectl cluster-info dump -o yaml | tee kind-cluster-dump.txt | |
| - name: Upload cluster dump | |
| if: always() | |
| uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4 | |
| with: | |
| name: kind-cluster-dump.txt | |
| path: | | |
| kind-cluster-dump.txt | |
| lint: | |
| uses: miracum/.github/.github/workflows/standard-lint.yaml@6e79e87ffce2b28fa1052cbe3ac78f9ab7a2ea77 # v1.11.3 | |
| permissions: | |
| contents: read | |
| pull-requests: write | |
| issues: write | |
| security-events: write | |
| actions: read | |
| with: | |
| codeql-languages: '["java"]' | |
| enable-codeql: true | |
| java-version: "21" | |
| secrets: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| release: | |
| uses: miracum/.github/.github/workflows/standard-release.yaml@6e79e87ffce2b28fa1052cbe3ac78f9ab7a2ea77 # v1.11.3 | |
| needs: | |
| - lint | |
| - build | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| issues: write | |
| secrets: | |
| semantic-release-token: ${{ secrets.MIRACUM_BOT_SEMANTIC_RELEASE_TOKEN }} |