Server: implement support for Pagination API on CMH #523
Workflow file for this run
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| name: Build, test, and deploy backend to staging | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| paths: | |
| - .github/workflows/node.yml | |
| - server/** | |
| - test-node/** | |
| pull_request: | |
| branches: | |
| - develop | |
| paths: | |
| - .github/workflows/node.yml | |
| - server/** | |
| - test-node/** | |
| workflow_dispatch: | |
| inputs: | |
| logLevel: | |
| description: "Log level" | |
| required: true | |
| default: "warning" | |
| type: choice | |
| options: | |
| - info | |
| - warning | |
| - debug | |
| jobs: | |
| build-server: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| working-directory: server | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: docker/setup-buildx-action@v1 | |
| with: | |
| buildkitd-flags: --debug | |
| - uses: actions/cache@v3 | |
| with: | |
| path: /tmp/.buildx-cache | |
| key: ${{ runner.os }}-buildx-${{ github.sha }} | |
| restore-keys: | | |
| ${{ runner.os }}-buildx- | |
| - uses: actions/setup-node@v3 | |
| with: | |
| node-version: 16 | |
| cache: yarn | |
| cache-dependency-path: server/yarn.lock | |
| - if: github.event_name == 'pull_request' | |
| run: yarn | |
| - if: github.event_name == 'pull_request' | |
| run: yarn lint | |
| - if: github.event_name == 'pull_request' | |
| run: yarn check-format | |
| - if: github.event_name == 'pull_request' | |
| run: yarn test | |
| - uses: docker/login-action@v1 | |
| if: github.event_name == 'push' | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ github.token }} | |
| - name: Build and push staging image | |
| if: github.event_name == 'push' | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: server | |
| push: true | |
| tags: ghcr.io/ccmbioinfo/osmp:latest | |
| cache-from: type=local,src=/tmp/.buildx-cache | |
| cache-to: type=local,dest=/tmp/.buildx-cache,mode=max | |
| build-test-node: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| working-directory: test-node | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: docker/setup-buildx-action@v1 | |
| with: | |
| buildkitd-flags: --debug | |
| - uses: actions/cache@v3 | |
| with: | |
| path: /tmp/.buildx-cache | |
| key: ${{ runner.os }}-buildx-${{ github.sha }} | |
| restore-keys: | | |
| ${{ runner.os }}-buildx- | |
| - uses: actions/setup-node@v3 | |
| with: | |
| node-version: 16 | |
| cache: yarn | |
| cache-dependency-path: test-node/yarn.lock | |
| - if: github.event_name == 'pull_request' | |
| run: yarn | |
| - if: github.event_name == 'pull_request' | |
| continue-on-error: true | |
| run: yarn lint | |
| - if: github.event_name == 'pull_request' | |
| run: yarn check-format | |
| - uses: docker/login-action@v1 | |
| if: github.event_name == 'push' | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ github.token }} | |
| - name: Build and push staging image | |
| if: github.event_name == 'push' | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: test-node | |
| push: true | |
| tags: ghcr.io/ccmbioinfo/osmp-test-node | |
| cache-from: type=local,src=/tmp/.buildx-cache | |
| cache-to: type=local,dest=/tmp/.buildx-cache,mode=max | |
| deploy: | |
| runs-on: [cheo-ri] | |
| needs: | |
| - build-server | |
| - build-test-node | |
| if: github.ref == 'refs/heads/develop' | |
| environment: SSMP_SERVER_DEV | |
| concurrency: SSMP_SERVER_DEV | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: docker/login-action@v1 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ github.token }} | |
| - name: Configure SSH | |
| id: configure | |
| # The self-hosted runner is not ephemeral, so we load the secret key into | |
| # an agent instead in memory. Keep track of it for further workflow steps | |
| # and so we can clean it up and not leave orphaned processes hanging around. | |
| # | |
| # https://docs.docker.com/engine/context/working-with-contexts/ | |
| # This avoids passing an -H parameter to every Docker CLI call. | |
| run: | | |
| SSH_AGENT_EVAL=$(ssh-agent -s) | |
| eval "$SSH_AGENT_EVAL" | |
| ssh-add - <<< "${{ secrets.DEPLOY_PRIVATE_KEY }}" | |
| echo "::set-output name=ssh-agent-eval::$SSH_AGENT_EVAL" | |
| echo "::set-output name=ssh-agent-pid::$SSH_AGENT_PID" | |
| mkdir -p ~/.ssh | |
| echo "${{ secrets.DEPLOY_HOST_KEY }}" > ~/.ssh/known_hosts | |
| chmod -R g-rwx,o-rwx ~/.ssh | |
| docker context create deploy-target --docker host=ssh://${{ secrets.DEPLOY_SSH_HOST }} | |
| docker context use deploy-target | |
| - name: Deploy | |
| # Even though this is deploying to a remote Docker Engine, | |
| # Compose uses the registry credentials of the client | |
| env: | |
| COMPOSE_FILE: docker-compose.staging.yaml | |
| PROJECT_ROOT: /home/ubuntu/osmp | |
| # Server | |
| G4RD_AUTH_METHOD: ${{ secrets.G4RD_AUTH_METHOD }} | |
| G4RD_PASSWORD: ${{ secrets.G4RD_PASSWORD }} | |
| G4RD_URL: ${{ secrets.G4RD_URL }} | |
| G4RD_USERNAME: ${{ secrets.G4RD_USERNAME }} | |
| G4RD_REALM: ${{ secrets.G4RD_REALM }} | |
| G4RD_GRANT_TYPE: ${{ secrets.G4RD_GRANT_TYPE }} | |
| G4RD_TOKEN_URL: ${{ secrets.G4RD_TOKEN_URL }} | |
| G4RD_CLIENT_ID: ${{ secrets.G4RD_CLIENT_ID }} | |
| CMH_AZURE_CLIENT_ID: ${{ secrets.CMH_AZURE_CLIENT_ID }} | |
| CMH_AZURE_CLIENT_SECRET: ${{ secrets.CMH_AZURE_CLIENT_SECRET }} | |
| CMH_TOKEN_URL: ${{ secrets.CMH_TOKEN_URL }} | |
| CMH_RESOURCE: ${{ secrets.CMH_RESOURCE }} | |
| CMH_SCOPE: ${{ secrets.CMH_SCOPE }} | |
| CMH_GRANT_TYPE: ${{ secrets.CMH_GRANT_TYPE }} | |
| CMH_GENE42_SECRET: ${{ secrets.CMH_GENE42_SECRET }} | |
| CMH_URL: ${{ secrets.CMH_URL }} | |
| KEYCLOAK_AUTH_URL: ${{ secrets.KEYCLOAK_AUTH_URL }} | |
| KEYCLOAK_REALM: ${{ secrets.KEYCLOAK_REALM }} | |
| KEYCLOAK_CLIENT_ID: ${{ secrets.KEYCLOAK_CLIENT_ID }} | |
| SERVER_SESSION_SECRET: ${{ secrets.SERVER_SESSION_SECRET }} | |
| # Test Node | |
| TEST_DATA_DB: ${{ secrets.TEST_DATA_DB }} | |
| TEST_DATA_DB_USER: ${{ secrets.TEST_DATA_DB_USER }} | |
| TEST_DATA_DB_PASSWORD: ${{ secrets.TEST_DATA_DB_PASSWORD }} | |
| # Test Node MySQL | |
| TEST_DATA_DB_ROOT_PASSWORD: ${{ secrets.TEST_DATA_DB_ROOT_PASSWORD }} | |
| # Keycloak | |
| KEYCLOAK_DB_ADDR: ${{ secrets.KEYCLOAK_DB_ADDR }} | |
| KEYCLOAK_DB: ${{ secrets.KEYCLOAK_DB }} | |
| KEYCLOAK_DB_USER: ${{ secrets.KEYCLOAK_DB_USER }} | |
| KEYCLOAK_DB_PASSWORD: ${{ secrets.KEYCLOAK_DB_PASSWORD }} | |
| # Mongo | |
| MONGO_CONNECTION_STRING: ${{ secrets.MONGO_CONNECTION_STRING }} | |
| run: | | |
| eval "${{ steps.configure.outputs.ssh-agent-eval }}" | |
| docker-compose pull | |
| docker-compose up -d --remove-orphans | |
| - name: Clean up | |
| if: always() | |
| run: | | |
| docker context rm -f deploy-target | |
| eval "${{ steps.configure.outputs.ssh-agent-eval }}" | |
| SSH_AGENT_PID="${{ steps.configure.outputs.ssh-agent-pid }}" ssh-agent -k |