chore: update docs location and link for seurat notice #6310
Workflow file for this run
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| name: Create/Update rdev for PR | |
| on: | |
| pull_request: | |
| branches-ignore: | |
| - "prod" | |
| types: | |
| - opened | |
| - synchronize | |
| - reopened | |
| env: | |
| # Force using BuildKit instead of normal Docker, required so that metadata | |
| # is written/read to allow us to use layers of previous builds as cache. | |
| DOCKER_BUILDKIT: 1 | |
| COMPOSE_DOCKER_CLI_BUILD: 1 | |
| DOCKER_REPO: ${{ secrets.ECR_REPO }}/ | |
| STACK_NAME: pr-${{ github.event.number }} | |
| permissions: | |
| id-token: write | |
| issues: write | |
| pull-requests: write | |
| contents: write | |
| jobs: | |
| get_previous_image_digests: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| runs-on: ubuntu-22.04 | |
| outputs: | |
| ecr_repos: ${{ steps.get_digests.outputs.ecr_repos }} | |
| image_digests: ${{ steps.get_digests.outputs.image_digests }} | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 1800 | |
| - name: Login to ECR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.ECR_REPO }} | |
| - name: Get previous image digests for each repo | |
| id: get_digests | |
| run: | | |
| ECR_REPOS=(corpora-frontend corpora-backend corpora-backend-de corpora-backend-wmg \ | |
| corpora-upload-failures corpora-upload-success \ | |
| dataset-submissions corpora-upload wmg-processing cellguide-pipeline) | |
| IMAGE_DIGESTS=() | |
| for ecr_repo in "${ECR_REPOS[@]}"; do | |
| IMAGE_DIGESTS+=(`aws ecr list-images --repository-name $ecr_repo --filter tagStatus=TAGGED \ | |
| | jq -r --arg STACK_NAME ${STACK_NAME} '[.imageIds[] \ | |
| | select(.imageTag==$STACK_NAME)][0].imageDigest'`) | |
| done | |
| echo "ECR_REPOS=${ECR_REPOS[@]}" >> $GITHUB_OUTPUT | |
| echo "IMAGE_DIGESTS=${IMAGE_DIGESTS[@]}" >> $GITHUB_OUTPUT | |
| build_images: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| uses: ./.github/workflows/build-images.yml | |
| secrets: inherit | |
| seed-wmg-cellguide-rdev: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 1800 | |
| - name: Checkout Repository | |
| uses: actions/checkout@v2 | |
| - name: Grant Execute Permission to Bash Script | |
| run: | | |
| chmod +x ./scripts/populate_rdev_with_cellguide_data.sh ./scripts/populate_rdev_with_wmg_data.sh | |
| - name: Seed cell guide data | |
| run: | | |
| ./scripts/populate_rdev_with_cellguide_data.sh ${{ env.STACK_NAME }} | |
| - name: Seed WMG data | |
| run: | | |
| ./scripts/populate_rdev_with_wmg_data.sh ${{ env.STACK_NAME }} | |
| deploy-rdev: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| runs-on: ubuntu-22.04 | |
| concurrency: | |
| group: pr-${{ github.event.number }}-happy | |
| cancel-in-progress: false | |
| needs: | |
| - build_images | |
| - get_previous_image_digests | |
| - seed-wmg-cellguide-rdev | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 2700 | |
| - name: Login to ECR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.ECR_REPO }} | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 1 | |
| - name: Update deployment | |
| uses: chanzuckerberg/github-actions/.github/actions/[email protected] | |
| with: | |
| tfe-token: ${{ secrets.TFE_TOKEN }} | |
| stack-name: ${{ env.STACK_NAME }} | |
| tag: ${{ needs.build_images.outputs.image_tag }} | |
| happy_version: "0.110.1" | |
| delete-previous-images: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| runs-on: ubuntu-22.04 | |
| needs: | |
| - get_previous_image_digests | |
| - deploy-rdev | |
| steps: | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-west-2 | |
| role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
| role-duration-seconds: 2700 | |
| - name: Login to ECR | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ secrets.ECR_REPO }} | |
| - name: Delete previous images | |
| run: | | |
| ECR_REPOS=(${{ needs.get_previous_image_digests.outputs.ecr_repos }}) | |
| IMAGE_DIGESTS=(${{ needs.get_previous_image_digests.outputs.image_digests }}) | |
| for ((i = 0; i < ${#ECR_REPOS[@]}; ++i)); do | |
| if [ ${IMAGE_DIGESTS[$i]} == "null" ]; then | |
| continue | |
| fi | |
| aws ecr batch-delete-image --repository-name ${ECR_REPOS[$i]} --image-ids imageDigest=${IMAGE_DIGESTS[$i]} | |
| done | |
| summarize: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') && github.event.action == 'opened' }} | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Summerize deployment | |
| id: summary | |
| run: | | |
| summary="## Deployment Summary" | |
| summary+="\n- backend_url: https://${{ env.STACK_NAME }}-backend.rdev.single-cell.czi.technology" | |
| summary+="\n- backend_de_url: https://${{ env.STACK_NAME }}-backend-de.rdev.single-cell.czi.technology" | |
| summary+="\n- backend_wmg_url: https://${{ env.STACK_NAME }}-backend-wmg.rdev.single-cell.czi.technology" | |
| summary+="\n- frontend_url: https://${{ env.STACK_NAME }}-frontend.rdev.single-cell.czi.technology" | |
| summary+="\n- delete_db_task_definition_arn: arn:aws:ecs:us-west-2:***:task-definition/dp-rdev-${{ env.STACK_NAME}}-deletion:1" | |
| summary+="\n- migrate_db_task_definition_arn: arn:aws:ecs:us-west-2:***:task-definition/dp-rdev-${{ env.STACK_NAME}}-migration:1" | |
| echo "SUMMARY=$summary" >> $GITHUB_OUTPUT | |
| - name: Post Comment | |
| uses: actions/github-script@v7 | |
| with: | |
| script: | | |
| github.rest.issues.createComment({ | |
| issue_number: context.issue.number, | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| body: "${{ steps.summary.outputs.summary}}" | |
| }) | |
| rdev-tests: | |
| if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
| uses: ./.github/workflows/rdev-tests.yml | |
| secrets: inherit | |
| needs: | |
| - deploy-rdev |