Support for ingest of imaging data - DICOM #814
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| # Copyright (c) University College London Hospitals NHS Foundation Trust | |
| # | |
| # Licensed under the Apache License, Version 2.0 (the "License"); | |
| # you may not use this file except in compliance with the License. | |
| # You may obtain a copy of the License at | |
| # | |
| # http://www.apache.org/licenses/LICENSE-2.0 | |
| # | |
| # Unless required by applicable law or agreed to in writing, software | |
| # distributed under the License is distributed on an "AS IS" BASIS, | |
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
| # See the License for the specific language governing permissions and | |
| # limitations under the License. | |
| --- | |
| name: PR comment | |
| on: | |
| issue_comment: | |
| types: [created] # only run on new comments | |
| # https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#issue_comment | |
| # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#issue_comment | |
| permissions: | |
| checks: write | |
| jobs: | |
| pr_comment: | |
| name: PR comment | |
| # https://docs.github.com/en/graphql/reference/enums#commentauthorassociation | |
| # (and https://docs.github.com/en/rest/reference/issues#comments) | |
| # only allow commands where: | |
| # - the comment is on a PR | |
| # - the commenting user has write permissions (i.e. is OWNER or COLLABORATOR) | |
| if: ${{ github.event.issue.pull_request }} | |
| runs-on: ubuntu-latest | |
| outputs: | |
| command: ${{ steps.check_command.outputs.command }} | |
| prRef: ${{ steps.check_command.outputs.prRef }} | |
| prHeadSha: ${{ steps.check_command.outputs.prHeadSha }} | |
| prRefId: ${{ steps.check_command.outputs.prRefId }} | |
| branchRefId: ${{ steps.check_command.outputs.branchRefid }} | |
| ciGitRef: ${{ steps.check_command.outputs.ciGitRef }} | |
| makeCommand: ${{ steps.set_make_command.outputs.makeCommand }} | |
| steps: | |
| # Ensure we have the script file for the github-script action to use | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| token: ${{ secrets.FLOWEHR_REPOSITORIES_GH_TOKEN }} | |
| fetch-depth: 0 # entire history is needed for paths filter | |
| persist-credentials: false | |
| # Determine whether the comment is a command | |
| - id: check_command | |
| name: Check for a command using GitHub script | |
| uses: actions/github-script@v6 | |
| with: | |
| github-token: ${{ secrets.FLOWEHR_REPOSITORIES_GH_TOKEN }} | |
| script: | | |
| const script = require('./.github/scripts/build.js') | |
| await script.getCommandFromComment({core, context, github}); | |
| - name: Output PR details | |
| run: | | |
| echo "PR Details" | |
| echo "==========" | |
| echo "prRef : ${{ steps.check_command.outputs.prRef }}" | |
| echo "prHeadSha : ${{ steps.check_command.outputs.prHeadSha }}" | |
| echo "prRefId : ${{ steps.check_command.outputs.prRefId }}" | |
| echo "ciGitRef : ${{ steps.check_command.outputs.ciGitRef }}" | |
| - uses: dorny/paths-filter@v2 | |
| id: changes | |
| with: | |
| token: ${{ secrets.FLOWEHR_REPOSITORIES_GH_TOKEN }} | |
| base: main | |
| ref: ${{ steps.check_command.outputs.prHeadSha }} | |
| filters: | | |
| core: | |
| - 'infrastructure/core/**' | |
| transform: | |
| - 'infrastructure/transform/**' | |
| serve: | |
| - 'infrastructure/serve/**' | |
| apps: | |
| - 'apps/**' | |
| devcontainer: | |
| - '.devcontainer/**' | |
| - id: set_make_command | |
| run: | | |
| if [ ${{ steps.check_command.outputs.command }} = "test-all" ]; then | |
| make_command="test" | |
| elif [ ${{ steps.check_command.outputs.command }} = "destroy" ]; then | |
| make_command="destroy" | |
| elif [ ${{ steps.check_command.outputs.command }} = "destroy-no-terraform" ]; then | |
| make_command="destroy-no-terraform" | |
| elif [ ${{ steps.changes.outputs.core }} = "true" ]; then | |
| make_command="test" | |
| elif [ ${{ steps.changes.outputs.transform }} = "true" ] && \ | |
| [ ${{ steps.changes.outputs.serve }} = "true" ]; then | |
| make_command="test" | |
| elif [ ${{ steps.changes.outputs.transform }} = "true" ]; then | |
| make_command="test-transform" | |
| elif [ ${{ steps.changes.outputs.serve }} = "true" ]; then | |
| make_command="test-serve" | |
| elif [ ${{ steps.changes.outputs.apps }} = "true" ]; then | |
| make_command="test-apps" | |
| elif [ ${{ steps.changes.outputs.devcontainer }} = "true" ]; then | |
| make_command="test" | |
| else | |
| make_command="none" | |
| fi | |
| echo "makeCommand=${make_command}" >> $GITHUB_OUTPUT | |
| - name: Report check status start | |
| if: ${{ steps.check_command.outputs.command == 'test' || steps.check_command.outputs.command == 'test-all' }} | |
| uses: LouisBrunner/checks-action@v1.5.0 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} # Needs the auto-generated token | |
| sha: ${{ steps.check_command.outputs.prHeadSha }} | |
| name: "Deploy PR" | |
| status: "in_progress" | |
| details_url: "https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}" | |
| # If we don't run the actual deploy (see the run_test job below) we won't receive | |
| # a check-run status, and will have to send it "manually" | |
| - name: Bypass E2E check-runs status | |
| if: | | |
| (steps.check_command.outputs.command == 'test-force-approve') || | |
| (steps.set_make_command.outputs.makeCommand == 'none') | |
| uses: LouisBrunner/checks-action@v1.5.0 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} # Needs the auto-generated token | |
| # the name must be identical to the one received by the real job | |
| sha: ${{ steps.check_command.outputs.prHeadSha }} | |
| name: "Deploy PR" | |
| status: "completed" | |
| conclusion: "success" | |
| destroy_pr_env: # Destroy all resources deployed by PR | |
| needs: [pr_comment] | |
| if: | | |
| (needs.pr_comment.outputs.command == 'destroy') || | |
| (needs.pr_comment.outputs.command == 'destroy-no-terraform') | |
| name: Destroy PR | |
| uses: ./.github/workflows/devcontainer_make_command.yml | |
| with: | |
| suffix_override: flwr-${{ needs.pr_comment.outputs.prRefId }} | |
| environment: infra-test | |
| command: ${{ needs.pr_comment.outputs.makeCommand }} | |
| sha: ${{ needs.pr_comment.outputs.prHeadSha }} | |
| secrets: inherit | |
| destroy_cleanup: # Clean up state and dev container if destroy successful | |
| needs: [pr_comment, destroy_pr_env] | |
| name: Clean-up | |
| uses: ./.github/workflows/clean_state.yml | |
| with: | |
| suffix_override: flwr-${{ needs.pr_comment.outputs.prRefId }} | |
| environment: infra-test | |
| secrets: inherit | |
| run_test: | |
| needs: [pr_comment] | |
| if: | | |
| (needs.pr_comment.outputs.command == 'test' || needs.pr_comment.outputs.command == 'test-all') && | |
| (needs.pr_comment.outputs.makeCommand != 'none') | |
| name: Deploy PR | |
| uses: ./.github/workflows/devcontainer_make_command.yml | |
| with: | |
| suffix_override: flwr-${{ needs.pr_comment.outputs.prRefId }} | |
| environment: infra-test | |
| command: ${{ needs.pr_comment.outputs.makeCommand }} | |
| sha: ${{ needs.pr_comment.outputs.prHeadSha }} | |
| secrets: inherit | |
| test_cleanup: # Clean up state and dev container if test successful | |
| needs: [pr_comment, run_test] | |
| name: Clean-up | |
| uses: ./.github/workflows/clean_state.yml | |
| with: | |
| suffix_override: flwr-${{ needs.pr_comment.outputs.prRefId }} | |
| environment: infra-test | |
| secrets: inherit | |
| summary: | |
| name: Summary | |
| needs: [pr_comment, run_test] | |
| if: always() && needs.run_test.result != 'skipped' # Run even on test failure | |
| runs-on: ubuntu-latest | |
| environment: infra-test | |
| steps: | |
| # For PR builds triggered from comment builds, the GITHUB_REF is set to main | |
| # so the checks aren't automatically associated with the PR | |
| # If prHeadSha is specified then explicitly mark the checks for that SHA | |
| - name: Report check status | |
| uses: LouisBrunner/checks-action@v1.5.0 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} # Needs the auto-generated token | |
| sha: ${{ needs.pr_comment.outputs.prHeadSha }} | |
| name: "Deploy PR" | |
| status: "completed" | |
| conclusion: ${{ needs.run_test.result }} | |
| details_url: "https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}" |