added option to override biostudies submission in order to make point… #422
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| name: Lint and Test Charts | |
| on: | |
| push: | |
| branches: | |
| - main | |
| workflow_run: | |
| workflows: ["Publish Docker"] | |
| branches: [main] | |
| types: | |
| - completed | |
| jobs: | |
| helm-lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install chart-testing | |
| uses: helm/chart-testing-action@v2.6.0 | |
| - run: helm repo add bitnami https://charts.bitnami.com/bitnami | |
| - name: Run chart-testing (lint) | |
| run: ct lint --charts ./api/helm-chart --debug | |
| api-test: | |
| runs-on: ubuntu-latest | |
| environment: | |
| name: test | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - uses: azure/setup-helm@v4.2.0 | |
| - uses: azure/setup-kubectl@v3 | |
| - name: Start minikube - if this breaks on local do a 'minikube delete' | |
| id: minikube | |
| uses: medyagh/setup-minikube@master | |
| with: | |
| cpus: 4 | |
| memory: 4G # 'wait' below times out on Actions with 2G | |
| start-args: '--force' | |
| - run: helm repo add bitnami https://charts.bitnami.com/bitnami | |
| - name: Get helm dependencies | |
| run: helm dependency build ./api/helm-chart | |
| - name: Start everything | |
| run: | | |
| helm install bia-api-local ./api/helm-chart \ | |
| --set "api_env.mongoTimeoutMs=${{ vars.MONGO_TIMEOUT_MS }}" \ | |
| --set "api_env.mongoRootUser=${{ vars.MONGO_INITDB_ROOT_USERNAME }}" \ | |
| --set "api_env.mongoRootPassword=${{ secrets.MONGO_INITDB_ROOT_PASSWORD }}" \ | |
| --set "api_env.jwtSecretKey=${{ secrets.JWT_SECRET_KEY }}" \ | |
| --set "api_env.userCreateSecretToken=${{ secrets.USER_CREATE_SECRET_TOKEN }}" \ | |
| --set "mongodb.enabled=true" \ | |
| --set "mongodb.auth.rootUser=${{ vars.MONGO_INITDB_ROOT_USERNAME }}" \ | |
| --set "mongodb.auth.rootPassword=${{ secrets.MONGO_INITDB_ROOT_PASSWORD }}" | |
| - name: Wait for api to start and health-check | |
| run: kubectl wait --for=condition=ready pod -l app.kubernetes.io/name=api --timeout=180s | |
| - name: Run tests | |
| run: helm test bia-api-local --logs | |
| - name: List pods for CI minikube debug | |
| run: | | |
| kubectl get pods | |
| kubectl describe pods -l app.kubernetes.io/name=api | |
| kubectl logs -l app.kubernetes.io/name=api | |
| if: ${{ failure() }} | |
| - name: Cleanup | |
| run: | | |
| minikube delete | |
| if: ${{ always() }} |