chore(deps): update docker.io/obiba/opal docker tag to v5 #2402
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| name: ci | |
| on: | |
| pull_request: | |
| branches: | |
| - master | |
| push: | |
| branches: | |
| - master | |
| release: | |
| types: | |
| - created | |
| permissions: read-all | |
| env: | |
| ONCO_ANALYTICS_NAMESPACE_NAME: bzkf-onco-analytics | |
| jobs: | |
| build-decompose-xml-image: | |
| name: build decompose-xmls container image | |
| uses: miracum/.github/.github/workflows/standard-build.yaml@3a6d6e823363d6a7b39daaadc24566130bddef38 # v1.12.10 | |
| permissions: | |
| contents: write | |
| id-token: write | |
| packages: write | |
| pull-requests: write | |
| actions: read | |
| security-events: write | |
| with: | |
| image: ghcr.io/${{ github.repository }}/decompose-xmls | |
| build-context: src/decompose_xmls | |
| enable-build-test-layer: false | |
| secrets: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| build-obds-fhir-to-opal-image: | |
| name: build obds-fhir-to-opal container image | |
| uses: miracum/.github/.github/workflows/standard-build.yaml@3a6d6e823363d6a7b39daaadc24566130bddef38 # v1.12.10 | |
| permissions: | |
| contents: write | |
| id-token: write | |
| packages: write | |
| pull-requests: write | |
| actions: read | |
| security-events: write | |
| with: | |
| image: ghcr.io/${{ github.repository }}/obds-fhir-to-opal | |
| build-context: src/obds_fhir_to_opal | |
| enable-build-test-layer: false | |
| secrets: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| lint: | |
| uses: miracum/.github/.github/workflows/standard-lint.yaml@3a6d6e823363d6a7b39daaadc24566130bddef38 # v1.12.10 | |
| permissions: | |
| contents: read | |
| pull-requests: write | |
| issues: write | |
| security-events: write | |
| actions: read | |
| with: | |
| enable-validate-gradle-wrapper: false | |
| codeql-languages: '["python"]' | |
| enable-codeql: false | |
| enable-verify-base-image-signature: false | |
| secrets: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| tests: | |
| strategy: | |
| matrix: | |
| # Python versions to run tests for | |
| python-version: ["3.11"] | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| cd src/decompose_xmls | |
| pip install pytest | |
| pip install -r requirements.txt | |
| pip install -r requirements-test.txt | |
| - name: Run decompose_xmls tests | |
| run: | | |
| cd src/decompose_xmls | |
| pytest | |
| test-k8s: | |
| runs-on: ubuntu-22.04 | |
| # disabled since the major deployment platform is currently | |
| # docker compose anyways | |
| if: ${{ false }} | |
| # run tests only on PRs | |
| # ${{ github.event_name == 'pull_request' }} | |
| needs: | |
| - build-decompose-xml-image | |
| - build-obds-fhir-to-opal-image | |
| steps: | |
| - name: install k3s | |
| run: | | |
| curl -sfL https://get.k3s.io | INSTALL_K3S_VERSION=v1.28.3+k3s2 sh - | |
| - name: setup .kube/config | |
| run: | | |
| mkdir ~/.kube | |
| sudo k3s kubectl config view --raw | tee ~/.kube/config > /dev/null | |
| chmod 600 ~/.kube/config | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
| - name: install dependencies | |
| run: | | |
| kubectl get node | |
| # via <https://stackoverflow.com/a/65411733> | |
| kubectl create namespace "${ONCO_ANALYTICS_NAMESPACE_NAME}" --dry-run=client -o yaml | kubectl apply -f - | |
| kubectl config set-context --current --namespace="${ONCO_ANALYTICS_NAMESPACE_NAME}" | |
| kubectl config view | |
| helm dependency build charts/prerequisites | |
| helm upgrade --install --wait --timeout=10m --set strimzi-kafka-operator.generateNetworkPolicy=false onco-analytics-on-fhir-prerequisites charts/prerequisites | |
| kubectl apply -f k8s/ | |
| kubectl wait kafka/bzkf-dizbox-cluster --for=condition=Ready --timeout=600s | |
| kubectl apply -f k8s/kafka-bridge.yaml | |
| kubectl wait kafkabridge/bzkf-dizbox-bridge --for=condition=Ready --timeout=600s | |
| kubectl get all -A | |
| - name: install onco-analytics-on-fhir | |
| run: | | |
| helm repo add miracum https://miracum.github.io/charts | |
| helm repo add akhq https://akhq.io/ | |
| helm repo add hapi-fhir-jpaserver-starter https://hapifhir.github.io/hapi-fhir-jpaserver-starter | |
| helm dependency build charts/onco-analytics-on-fhir | |
| helm upgrade --install --wait --timeout=10m onco-analytics-on-fhir charts/onco-analytics-on-fhir | |
| kubectl get all -A | |
| - name: test deployments | |
| run: | | |
| helm test onco-analytics-on-fhir | |
| kubectl wait deployment/onco-analytics-on-fhir-stream-processors-obds-to-fhir --for=condition=Available --timeout=300s | |
| kubectl wait deployment/onco-analytics-on-fhir-stream-processors-fhir-to-server --for=condition=Available --timeout=300s | |
| - 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@ff15f0306b3f739f7b6fd43fb5d26cd321bd4de5 # v3.2.1 | |
| with: | |
| name: kind-cluster-dump.txt | |
| path: | | |
| kind-cluster-dump.txt | |
| build-air-gapped-installer: | |
| runs-on: ubuntu-22.04 | |
| if: ${{ github.event_name == 'pull_request' }} | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
| - run: | | |
| ./build-air-gapped-installer.sh | |
| release: | |
| if: ${{ startsWith(github.ref, 'refs/tags/') }} | |
| permissions: | |
| actions: read | |
| contents: write | |
| id-token: write | |
| packages: write | |
| needs: | |
| - build-decompose-xml-image | |
| - build-obds-fhir-to-opal-image | |
| uses: ./.github/workflows/release.yaml |