Bump dset from 3.1.2 to 3.1.4 in /server #550
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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@v4 | |
| - uses: docker/setup-buildx-action@v3 | |
| with: | |
| buildkitd-flags: --debug | |
| - uses: actions/cache@v4 | |
| with: | |
| path: /tmp/.buildx-cache | |
| key: ${{ runner.os }}-buildx-${{ github.sha }} | |
| restore-keys: | | |
| ${{ runner.os }}-buildx- | |
| - uses: actions/setup-node@v4 | |
| 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@v4 | |
| - uses: docker/setup-buildx-action@v3 | |
| with: | |
| buildkitd-flags: --debug | |
| - uses: actions/cache@v4 | |
| with: | |
| path: /tmp/.buildx-cache | |
| key: ${{ runner.os }}-buildx-${{ github.sha }} | |
| restore-keys: | | |
| ${{ runner.os }}-buildx- | |
| - uses: actions/setup-node@v4 | |
| 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@v4 | |
| - uses: docker/login-action@v1 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ github.token }} | |
| - name: Configure SSH | |
| id: configure | |
| # The self-hosted runner is not ephemeral, so we load the secret key into | |
| # an agent instead in memory. Keep track of it for further workflow steps | |
| # and so we can clean it up and not leave orphaned processes hanging around. | |
| # | |
| # https://docs.docker.com/engine/context/working-with-contexts/ | |
| # This avoids passing an -H parameter to every Docker CLI call. | |
| # | |
| # We use `tr` to trim newlines. GITHUB_OUTPUT doesn't like multi-line strings | |
| run: | | |
| SSH_AGENT_EVAL=$(ssh-agent -s | tr '\012\015' ' '; echo) | |
| eval "$SSH_AGENT_EVAL" | |
| ssh-add - <<< "${{ secrets.DEPLOY_PRIVATE_KEY }}" | |
| echo "ssh-agent-eval=$SSH_AGENT_EVAL" >> $GITHUB_OUTPUT | |
| echo "ssh-agent-pid=$SSH_AGENT_PID" >> $GITHUB_OUTPUT | |
| mkdir -p ~/.ssh | |
| echo "${{ 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 |