Add spatial #6047
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| name: Build and Deploy the UI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| release: | |
| types: | |
| - released | |
| pull_request_target: | |
| branches: | |
| - master | |
| types: | |
| - labeled | |
| - unlabeled | |
| - opened | |
| - synchronize | |
| - reopened | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| id-token: write | |
| contents: read | |
| jobs: | |
| is-safe-to-run: | |
| name: Sensitive jobs are safe to be run | |
| runs-on: ubuntu-20.04 | |
| if: (github.event_name == 'pull_request_target' && contains(github.event.pull_request.labels.*.name, 'safe to run')) || github.event_name == 'release' || github.event_name == 'push' | |
| steps: | |
| - id: is-safe-to-run | |
| name: Is safe to run | |
| run: |- | |
| echo "Safe to run, checks will proceed" | |
| is-not-safe-to-run: | |
| name: Sensitive jobs aren't labeled safe to be run | |
| runs-on: ubuntu-20.04 | |
| if: (github.event_name == 'pull_request_target' && !contains(github.event.pull_request.labels.*.name, 'safe to run')) | |
| steps: | |
| - id: is-not-safe-to-run | |
| name: The pull request hasn't been labeled safe to run | |
| run: |- | |
| echo "Pull request not labeled safe to run" | |
| exit 1 | |
| uncheck-integration-test: | |
| name: Mark integration test as not run | |
| runs-on: ubuntu-20.04 | |
| needs: is-safe-to-run | |
| if: github.event_name == 'pull_request_target' | |
| steps: | |
| - id: get-pr-body | |
| name: Get the current PR body | |
| uses: jwalton/gh-find-current-pr@v1 | |
| with: | |
| state: open | |
| - id: create-unchecked-pr-body | |
| name: Create unchecked PR body | |
| run: |- | |
| UNCHECKED_BODY=$(sed 's/- \[[Xx]\] Started end-to-end tests on the latest commit./- \[ \] Started end-to-end tests on the latest commit./' <<\EOF | |
| ${{ steps.get-pr-body.outputs.body }} | |
| EOF | |
| ) | |
| echo "Unchecked PR body" | |
| echo $UNCHECKED_BODY | |
| # This sets multiline strings into the output variable | |
| # See https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions#example-of-a-multiline-string | |
| echo "body<<EOF" >> "$GITHUB_OUTPUT" | |
| echo "$UNCHECKED_BODY" >> "$GITHUB_OUTPUT" | |
| echo "EOF" >> "$GITHUB_OUTPUT" | |
| - id: uncheck-integration-checkbox | |
| if: steps.create-unchecked-pr-body.outputs.body != '' | |
| name: Uncheck the integration checkbox | |
| uses: tzkhan/pr-update-action@v2 | |
| with: | |
| repo-token: ${{ secrets.API_TOKEN_GITHUB }} | |
| head-branch-regex: ${{ github.head_ref }} | |
| lowercase-branch: false | |
| body-template: ${{ steps.create-unchecked-pr-body.outputs.body }} | |
| body-update-action: replace | |
| test: | |
| name: Run unit tests | |
| # TODO: the permissions here are too broad and need narrowing down | |
| # They are needed because so that upload-coverage can upload the coverage report | |
| # and post comments. | |
| permissions: write-all | |
| runs-on: ubuntu-20.04 | |
| needs: is-safe-to-run | |
| env: | |
| CI: true | |
| steps: | |
| - id: checkout | |
| name: Check out source code | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{github.head_ref}} | |
| repository: ${{github.event.pull_request.head.repo.full_name}} | |
| - id: setup-node | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: '20.18.0' | |
| cache: 'npm' | |
| - id: install | |
| name: Install dependencies | |
| run: |- | |
| echo "Running CI with " | |
| echo "Node version: $(node --version)" | |
| echo "NPM version: $(npm --version)" | |
| git config --global url."https://".insteadOf ssh:// | |
| npm ci --legacy-peer-deps | |
| - id: test | |
| name: Run unit tests | |
| uses: mattallty/jest-github-action@v1 | |
| env: | |
| AWS_DEFAULT_REGION: ${{ secrets.AWS_REGION }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| test-command: 'npm run coverage' | |
| coverage-comment: false | |
| - id: upload-coverage | |
| name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v1 | |
| - id: check-licenses | |
| name: Check licenses | |
| env: | |
| ALLOWED_LICENSES: 'MIT;Apache-2.0;BSD-3-Clause;ISC;BSD-2-Clause;BSD;CC0-1.0;0BSD;Unlicense;(MIT AND Zlib);(Unlicense OR Apache-2.0);BSD-3-Clause OR MIT;(MIT OR Apache-2.0);CC-BY-4.0;Apache-Style;(Apache-2.0 OR MPL-1.1);WTFPL;(WTFPL OR MIT);EPL-1.0;(MIT AND BSD-3-Clause);(MIT OR CC0-1.0);Custom: https://github.com/aws-amplify/amplify-js;SGI-B-2.0' | |
| EXCLUDE_PACKAGES: '[email protected];[email protected];[email protected];[email protected];[email protected]' | |
| run: |- | |
| npm install -g license-checker | |
| license-checker --production --json --onlyAllow="${ALLOWED_LICENSES}" --excludePackages="${EXCLUDE_PACKAGES}" | |
| build-docker: | |
| name: Build Docker container | |
| runs-on: ubuntu-20.04 | |
| needs: is-safe-to-run | |
| outputs: | |
| ref-id: ${{ steps.ref.outputs.ref-id }} | |
| image-tag: ${{ steps.ref.outputs.image-tag }} | |
| steps: | |
| - id: checkout | |
| name: Check out source code | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{github.head_ref}} | |
| repository: ${{github.event.pull_request.head.repo.full_name}} | |
| - id: setup-node | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: '20.18.0' | |
| cache: 'npm' | |
| - id: install | |
| name: Install dependencies | |
| run: |- | |
| echo "Running CI with " | |
| echo "Node version: $(node --version)" | |
| echo "NPM version: $(npm --version)" | |
| git config --global url."https://".insteadOf ssh:// | |
| npm ci --legacy-peer-deps | |
| - id: next-cache-seek | |
| name: Look up the Next.js build cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ github.workspace }}/.next/cache | |
| key: ${{ runner.os }}-nextjs-${{ hashFiles('**/package-lock.json') }} | |
| - id: build | |
| name: Build project | |
| run: |- | |
| npm run build | |
| - id: upload-build-out | |
| name: Upload Next.js build output | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: next-build-out | |
| path: | | |
| .next/ | |
| !.next/cache | |
| include-hidden-files: true | |
| - id: download-build-out | |
| name: Download Next.js build output | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: next-build-out | |
| path: .next/ | |
| - id: ref | |
| name: Format docker tag and repository name. | |
| run: |- | |
| if [ "${{ github.event_name }}" = "pull_request_target" ]; then | |
| # Construct the PR_GITHUB_REF for our pull request copying GITHUB_REF's format | |
| # We can't use GITHUB_REF because it is set to master in this event | |
| # More info: https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#pull_request_target | |
| PR_GITHUB_REF="refs/pull/${{ github.event.pull_request.number }}/merge" | |
| REF_ID=$(echo $PR_GITHUB_REF | sed 's/\//-/g') | |
| else | |
| # This will take a ref like `refs/heads/master` | |
| # and turn it into `refs-heads-master` | |
| REF_ID=$(echo $GITHUB_REF | sed 's/\//-/g') | |
| fi | |
| echo "ref-id=$REF_ID" >> $GITHUB_OUTPUT | |
| # the final tag is something like: | |
| # refs-heads-master-a4f8bc313dae | |
| # this is what we push to ECR | |
| # we will also take semver'd tags like `1.0.0` and use them for releases | |
| # In push & PR events we want the tag to contain the latest commit on the branch: | |
| # in push events, the latest commit of the master branch is GITHUB_SHA | |
| # in PR synch the latest commit of the branch is found in github.sha instead | |
| TIMESTAMP=$(date +%s) | |
| if [ "${{ github.event_name }}" = "release" ] && [ "${{ github.event.action }}" = "released" ]; then | |
| COMMIT_SHA="" | |
| IMAGE_TAG="${REF_ID/refs-tags-/}" | |
| elif [ "${{ github.event_name }}" = "pull_request_target" ]; then | |
| COMMIT_SHA="${{ github.sha }}" | |
| IMAGE_TAG="$REF_ID-$COMMIT_SHA-$TIMESTAMP" | |
| else | |
| COMMIT_SHA=$GITHUB_SHA | |
| IMAGE_TAG="$REF_ID-$COMMIT_SHA-$TIMESTAMP" | |
| fi | |
| # IMAGE_TAG is used in the Build Docker Image step. | |
| # We can easily build the image-tag from REF_ID and COMMIT_SHA for non-production releases. | |
| # But we can not easily create the image tag for production releases, so we're bulding it here | |
| echo "image-tag=$IMAGE_TAG" >> $GITHUB_OUTPUT | |
| # This will take a GitHub repo name like `hms-dbmi-cellenics/releases` | |
| # and turns it into `releases`. This will be the name of the | |
| # ECR repository. | |
| IMAGE_REPO_NAME=$(echo $GITHUB_REPOSITORY | awk -F '/' '{print $2}') | |
| echo "repo-name=$IMAGE_REPO_NAME" >> $GITHUB_OUTPUT | |
| - id: setup-aws | |
| name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::${{ secrets.AWS_ACCOUNT_ID }}:role/ci-role-ui | |
| aws-region: ${{ secrets.AWS_REGION }} | |
| - id: login-ecr | |
| name: Login to Amazon ECR | |
| uses: aws-actions/amazon-ecr-login@v1 | |
| - id: create-ecr-registry | |
| name: Create an ECR repository (if needed) | |
| # This will fail if the registry already exists, which is fine. If there is some other | |
| # error, the `push` step will fail instead. | |
| continue-on-error: true | |
| run: |- | |
| aws ecr create-repository --repository-name $REPO_NAME --image-tag-mutability IMMUTABLE | |
| env: | |
| REPO_NAME: ${{ steps.ref.outputs.repo-name }} | |
| - id: setup-buildx | |
| name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - id: build-docker-image | |
| name: Build Docker image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| file: ./Dockerfile | |
| platforms: linux/amd64 | |
| tags: ${{ format('{0}/{1}:{2}', steps.login-ecr.outputs.registry, steps.ref.outputs.repo-name, steps.ref.outputs.image-tag) }} | |
| push: true | |
| provenance: false | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| deploy: | |
| name: Deploy to Kubernetes | |
| runs-on: ubuntu-20.04 | |
| needs: [build-docker, is-safe-to-run] | |
| strategy: | |
| max-parallel: 1 | |
| matrix: | |
| environment: ['production', 'staging', 'develop'] | |
| steps: | |
| - id: checkout | |
| name: Check out source code | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{github.head_ref}} | |
| repository: ${{github.event.pull_request.head.repo.full_name}} | |
| - id: setup-aws | |
| name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::${{ secrets.AWS_ACCOUNT_ID }}:role/ci-role-ui | |
| aws-region: ${{ secrets.AWS_REGION }} | |
| - id: login-ecr | |
| name: Login to Amazon ECR | |
| uses: aws-actions/amazon-ecr-login@v1 | |
| - id: fill-metadata | |
| name: Fill out a new HelmRelease resource | |
| run: |- | |
| export DEPLOYMENT_NAME=$(echo $GITHUB_REPOSITORY | awk -F '/' '{print $2}') | |
| echo "deployment-name=$DEPLOYMENT_NAME" >> $GITHUB_OUTPUT | |
| if [ "${{ matrix.environment }}" = "production" ]; then | |
| export SANDBOX_ID="default" | |
| export KUBERNETES_ENV="production" | |
| export CHART_REF="master" | |
| export IMAGE_PATTERN="^(?P<version>[0-9]+\.[0-9]+\.[0-9]+)$" | |
| export IMAGE_EXTRACT='$version' | |
| export IMAGE_POLICY_TYPE="semver" | |
| export IMAGE_POLICY_KEY="range" | |
| export IMAGE_POLICY_VALUE=">=0.0.0" | |
| export REPLICA_COUNT="4" | |
| export MANIFEST_PATH="./production" | |
| fi | |
| if [ "${{ matrix.environment }}" = "develop" ]; then | |
| export SANDBOX_ID="default" | |
| export KUBERNETES_ENV="staging" | |
| export CHART_REF="master" | |
| export IMAGE_PATTERN="^$REF_ID-[a-f0-9]+-(?P<timestamp>[0-9]+)$" | |
| export IMAGE_EXTRACT='$timestamp' | |
| export IMAGE_POLICY_TYPE="numerical" | |
| export IMAGE_POLICY_KEY="order" | |
| export IMAGE_POLICY_VALUE="asc" | |
| export REPLICA_COUNT="2" | |
| export MANIFEST_PATH="./staging" | |
| fi | |
| if [ "${{ matrix.environment }}" = "staging" ]; then | |
| # The chart template for the UI repo is stored in IAC branch master | |
| # If you are working on the chart for UI/API, you can modify this value manualy in in your PR's release | |
| export CHART_REF="master" | |
| export SANDBOX_ID="STAGING_SANDBOX_ID" | |
| export KUBERNETES_ENV="staging" | |
| export IMAGE_PATTERN="^$REF_ID-[a-f0-9]+-(?P<timestamp>[0-9]+)$" | |
| export IMAGE_EXTRACT='$timestamp' | |
| export IMAGE_POLICY_TYPE="numerical" | |
| export IMAGE_POLICY_KEY="order" | |
| export IMAGE_POLICY_VALUE="asc" | |
| export REPLICA_COUNT="1" | |
| export MANIFEST_PATH="./staging" | |
| fi | |
| echo "kubernetes-env=$KUBERNETES_ENV" >> $GITHUB_OUTPUT | |
| export NAMESPACE="$DEPLOYMENT_NAME-$SANDBOX_ID" | |
| export CHART_SOURCE_NAME="$DEPLOYMENT_NAME-chart" | |
| export IMAGE_POLICY_TAG="{\"\$imagepolicy\": \"$NAMESPACE:$DEPLOYMENT_NAME:tag\"}" | |
| yq ' | |
| select(di == 0).metadata.name = strenv(NAMESPACE) | | |
| select(di == 0).metadata.labels.sandboxId = strenv(SANDBOX_ID) | | |
| select(di == 1).metadata.name = strenv(CHART_SOURCE_NAME) | | |
| select(di == 1).metadata.namespace = strenv(NAMESPACE) | | |
| select(di == 1).spec.url = "https://github.com/" + strenv(GITHUB_OWNER) + "/iac" | | |
| select(di == 1).spec.ref.branch = strenv(CHART_REF) | | |
| select(di == 2).metadata.name = strenv(DEPLOYMENT_NAME) | | |
| select(di == 2).metadata.namespace = strenv(NAMESPACE) | | |
| select(di == 2).spec.image = strenv(REGISTRY) + "/" + strenv(DEPLOYMENT_NAME) | | |
| select(di == 3).metadata.name = strenv(DEPLOYMENT_NAME) | | |
| select(di == 3).metadata.namespace = strenv(NAMESPACE) | | |
| select(di == 3).spec.imageRepositoryRef.name = strenv(DEPLOYMENT_NAME) | | |
| select(di == 3).spec.imageRepositoryRef.namespace = strenv(NAMESPACE) | | |
| select(di == 3).spec.filterTags.pattern = strenv(IMAGE_PATTERN) | | |
| select(di == 3).spec.filterTags.extract = strenv(IMAGE_EXTRACT) | | |
| select(di == 3).spec.policy.[strenv(IMAGE_POLICY_TYPE)].[strenv(IMAGE_POLICY_KEY)] = strenv(IMAGE_POLICY_VALUE) | | |
| select(di == 4).metadata.name = strenv(DEPLOYMENT_NAME) + "-image-update" | | |
| select(di == 4).metadata.namespace = strenv(NAMESPACE) | | |
| select(di == 4).spec.update.path = strenv(MANIFEST_PATH) | | |
| select(di == 5).metadata.name = strenv(DEPLOYMENT_NAME) | | |
| select(di == 5).metadata.namespace = strenv(NAMESPACE) | | |
| select(di == 5).metadata.labels.sandboxId = strenv(SANDBOX_ID) | | |
| select(di == 5).spec.releaseName = strenv(DEPLOYMENT_NAME) | | |
| select(di == 5).spec.chart.spec.sourceRef.name = strenv(CHART_SOURCE_NAME) | | |
| select(di == 5).spec.chart.spec.sourceRef.namespace = strenv(NAMESPACE) | | |
| select(di == 5).spec.values.kubernetes.env = strenv(KUBERNETES_ENV) | | |
| select(di == 5).spec.values.biomageCi.repo = strenv(GITHUB_REPOSITORY) | | |
| select(di == 5).spec.values.biomageCi.sandboxId = strenv(SANDBOX_ID) | | |
| select(di == 5).spec.values.image.registry = strenv(REGISTRY) | | |
| select(di == 5).spec.values.image.repository = strenv(DEPLOYMENT_NAME) | | |
| select(di == 5).spec.values.image.tag = strenv(IMAGE_TAG) | | |
| select(di == 5).spec.values.image.tag line_comment = strenv(IMAGE_POLICY_TAG) | | |
| select(di == 5).spec.values.replicaCount = env(REPLICA_COUNT) | | |
| select(di == 5).spec.values.serviceAccount.iamRole = "ui-role-" + strenv(KUBERNETES_ENV) | |
| ' .flux.yaml > $DEPLOYMENT_NAME-without-host.yaml | |
| if [ "${{ matrix.environment }}" = "production" ] | |
| then | |
| yq ' | |
| select(di == 5).spec.values.service.additionalHosts = true | |
| ' $DEPLOYMENT_NAME-without-host.yaml > $DEPLOYMENT_NAME.yaml | |
| else | |
| yq ' | |
| select(di == 5).spec.values.service.additionalHosts = false | |
| ' $DEPLOYMENT_NAME-without-host.yaml > $DEPLOYMENT_NAME.yaml | |
| fi | |
| cat $DEPLOYMENT_NAME.yaml | |
| env: | |
| GITHUB_OWNER: ${{ github.repository_owner }} | |
| REF_ID: ${{ needs.build-docker.outputs.ref-id }} | |
| IMAGE_TAG: ${{ needs.build-docker.outputs.image-tag }} | |
| REGISTRY: ${{ steps.login-ecr.outputs.registry }} | |
| - name: Push production/develop template to releases repo for deployment | |
| if: (matrix.environment == 'production' && github.event_name == 'release' && github.event.action == 'released') || (matrix.environment == 'develop' && github.event_name == 'push') | |
| uses: dmnemec/[email protected] | |
| env: | |
| API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }} | |
| with: | |
| source_file: ${{ steps.fill-metadata.outputs.deployment-name }}.yaml | |
| destination_repo: ${{ github.repository_owner }}/releases | |
| destination_folder: ${{ steps.fill-metadata.outputs.kubernetes-env }} | |
| user_email: [email protected] | |
| user_name: Biomage CI/CD | |
| - name: Change name of deployment file for staging deployment | |
| if: (github.event_name == 'pull_request_target' || github.event_name == 'push') && matrix.environment == 'staging' | |
| env: | |
| DEPLOYMENT_NAME: ${{ steps.fill-metadata.outputs.deployment-name }} | |
| REF_ID: ${{ needs.build-docker.outputs.ref-id }} | |
| run: |- | |
| mv $DEPLOYMENT_NAME.yaml $REF_ID.yaml | |
| - name: Push staging deployment template to releases | |
| if: (github.event_name == 'pull_request_target' || github.event_name == 'push') && matrix.environment == 'staging' | |
| uses: dmnemec/[email protected] | |
| env: | |
| API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }} | |
| with: | |
| source_file: ${{ needs.build-docker.outputs.ref-id }}.yaml | |
| destination_repo: ${{ github.repository_owner }}/releases | |
| destination_folder: staging-candidates/${{ steps.fill-metadata.outputs.deployment-name }} | |
| user_email: [email protected] | |
| user_name: 'Biomage CI/CD' | |
| ready-to-merge: | |
| name: Ready for merging | |
| runs-on: ubuntu-20.04 | |
| needs: [deploy, is-safe-to-run] | |
| steps: | |
| - id: ready-to-merge | |
| name: Signal readiness to merge | |
| run: |- | |
| exit 0 | |
| report-if-failed: | |
| name: Report if workflow failed | |
| runs-on: ubuntu-20.04 | |
| needs: [test, build-docker, deploy, is-safe-to-run] | |
| if: failure() && github.ref == 'refs/heads/master' | |
| steps: | |
| - id: send-to-slack | |
| name: Send failure notification to Slack on failure | |
| env: | |
| SLACK_BOT_TOKEN: ${{ secrets.WORKFLOW_STATUS_BOT_TOKEN }} | |
| uses: voxmedia/github-action-slack-notify-build@v1 | |
| with: | |
| channel: workflow-failures | |
| status: FAILED | |
| color: danger |