Project: CT image based prediction model in head and neck cancer: contribution to MHub #581
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: Project Page Pull Request Creation | |
| on: | |
| issues: | |
| types: [ labeled ] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| if: github.event.label.name == 'project:create' | |
| runs-on: ubuntu-latest | |
| permissions: | |
| issues: write | |
| pull-requests: write | |
| steps: | |
| - name: Fetch the project issue info | |
| id: project_issue | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| run: | | |
| title=$(gh issue view ${{ github.event.issue.number }} --repo ${{ github.repository }} --json title --jq '.title') | |
| echo "title [$title]" | |
| # If any, remove"Project:" prefix | |
| title=$(echo "$title" | sed 's/^Project:\s*//') | |
| echo "title [$title]" | |
| echo "title=$title" >> $GITHUB_OUTPUT | |
| - name: Find project issue comment | |
| uses: peter-evans/find-comment@v2.4.0 | |
| id: fc | |
| with: | |
| issue-number: ${{ github.event.issue.number }} | |
| comment-author: 'github-actions[bot]' | |
| body-includes: Project Page Pull Request Creation | |
| - name: Create or update comment ⌛ | |
| id: couc | |
| uses: peter-evans/create-or-update-comment@v3 | |
| with: | |
| comment-id: ${{ steps.fc.outputs.comment-id }} | |
| issue-number: ${{ github.event.issue.number }} | |
| body: | | |
| ## Project Page Pull Request Creation | |
| :hourglass: **IN PROGRESS**:  | |
| edit-mode: replace | |
| - name: Extract event info | |
| id: event_info | |
| run: | | |
| # TODO: Extract event name from "event:NAME" label | |
| event_name="PW41_2024_MIT" | |
| echo "name=$event_name" >> $GITHUB_OUTPUT | |
| - uses: actions/checkout@v3 | |
| - name: Generate project directory name | |
| id: project_directory | |
| run: | | |
| title=$(echo ${{ steps.project_issue.outputs.title }}) | |
| echo "title [$title]" | |
| # Convert to title case | |
| title_cased=$(echo "$title" | sed 's/.*/\L&/; s/[a-z]*/\u&/g') | |
| echo "title_cased [$title_cased]" | |
| # Sanitize string to use as a directory name | |
| directory_name=$(echo "$title_cased" | tr -cs '[:alnum:]' '_' | sed 's/_//g') | |
| echo "directory_name [$directory_name]" | |
| echo "name=$directory_name" >> $GITHUB_OUTPUT | |
| - name: Check if project already exists | |
| id: check_project_exists | |
| run: | | |
| event_name=${{ steps.event_info.outputs.name }} | |
| project_directory=${{ steps.event_info.outputs.name }}/Projects/${{ steps.project_directory.outputs.name }} | |
| if [ -d "$project_directory" ]; then | |
| echo "::error::Project already exist" | |
| exit 1 | |
| fi | |
| - name: Create or update comment 🛑 | |
| if: ${{ failure() && steps.check_project_exists.outcome == 'failure' }} | |
| uses: peter-evans/create-or-update-comment@v3 | |
| with: | |
| comment-id: ${{ steps.couc.outputs.comment-id }} | |
| issue-number: ${{ github.event.issue.number }} | |
| body: | | |
| ## Project Page Pull Request Creation | |
| :stop_sign: **STOPPED**: Project already exists | |
| edit-mode: replace | |
| - name: Create project directory | |
| run: | | |
| event_name=${{ steps.event_info.outputs.name }} | |
| directory_name=${{ steps.project_directory.outputs.name }} | |
| mkdir $event_name/Projects/$directory_name | |
| - name: Bulk issue body | |
| id: bulk | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| run: | | |
| body=$(gh issue view ${{ github.event.issue.number }} --repo ${{ github.repository }} --json body --jq '.body') | |
| echo "$body" > ${{ runner.temp }}/bulk.txt | |
| - name: Display bulk.txt | |
| run: | | |
| cat ${{ runner.temp }}/bulk.txt | |
| - name: Split bulk | |
| run: | | |
| csplit ${{ runner.temp }}/bulk.txt \ | |
| '/^### Project Description/' \ | |
| '/^### Objective/' \ | |
| '/^### Approach and Plan/' \ | |
| '/^### Progress and Next Steps/' \ | |
| '/^### Illustrations/' \ | |
| '/^### Background and References/' \ | |
| -f ${{ runner.temp }}/project_pull_request_part_ -b "%02d.md" | |
| - name: Cleanup files | |
| run: | | |
| cat ${{ runner.temp }}/project_pull_request_part_01.md | sed "1 d" > ${{ runner.temp }}/description.md | |
| cat ${{ runner.temp }}/project_pull_request_part_02.md | sed "1 d" > ${{ runner.temp }}/objective.md | |
| cat ${{ runner.temp }}/project_pull_request_part_03.md | sed "1 d" > ${{ runner.temp }}/approach.md | |
| cat ${{ runner.temp }}/project_pull_request_part_04.md | sed "1 d" > ${{ runner.temp }}/progress.md | |
| cat ${{ runner.temp }}/project_pull_request_part_05.md | sed "1 d" > ${{ runner.temp }}/illustrations.md | |
| cat ${{ runner.temp }}/project_pull_request_part_06.md | sed "1 d" > ${{ runner.temp }}/background.md | |
| - name: Display clean files | |
| run: | | |
| echo "Description:" | |
| cat ${{ runner.temp }}/description.md | |
| echo "Objective:" | |
| cat ${{ runner.temp }}/objective.md | |
| echo "Approach:" | |
| cat ${{ runner.temp }}/approach.md | |
| echo "Progress:" | |
| cat ${{ runner.temp }}/progress.md | |
| echo "Illustrations:" | |
| cat ${{ runner.temp }}/illustrations.md | |
| echo "Background:" | |
| cat ${{ runner.temp }}/background.md | |
| - name: Issue Forms Body Parser | |
| id: parse | |
| uses: zentered/issue-forms-body-parser@v2.0.0 | |
| - name: Extract issue fields | |
| id: extract | |
| run: | | |
| echo ${{ toJSON(steps.parse.outputs.data) }} | \ | |
| jq --arg title "${{ steps.project_issue.outputs.title }}" \ | |
| --rawfile description "${{ runner.temp }}/description.md" \ | |
| --rawfile objective "${{ runner.temp }}/objective.md" \ | |
| --rawfile illustrations "${{ runner.temp }}/illustrations.md" \ | |
| --rawfile approach "${{ runner.temp }}/approach.md" \ | |
| --rawfile progress "${{ runner.temp }}/progress.md" \ | |
| --rawfile background "${{ runner.temp }}/background.md" '{ | |
| "title": $title, | |
| "category": .category.text, | |
| "presenter_location": .["presenter-location"].text, | |
| "description": $description, | |
| "objective": $objective, | |
| "approach": $approach, | |
| "progress": $progress, | |
| "illustrations": $illustrations, | |
| "background": $background, | |
| "investigators": [.["key-investigators"].list[].text | | |
| capture("(?<name>[^\\s]+(?:\\s[^\\s]+)*?)\\s*\\((?<affiliation>[^,]*)(?:,\\s*(?<country>[^)]*))?\\)") | | |
| {name, affiliation: (.affiliation // ""), country: (.country // "")}], | |
| }' > ${{ runner.temp }}/template-data.json | |
| - name: Display template-data.json | |
| run: | | |
| cat ${{ runner.temp }}/template-data.json | |
| - uses: actions/setup-python@v4.6.0 | |
| with: | |
| python-version: "3.x" | |
| - name: Install jinja2 | |
| run: | | |
| python -m pip install jinja2 | |
| # Provide the cli interface | |
| python -m pip install jinja2_cli | |
| # Install the package providing the "to_yaml" and "regex_replace" filters. | |
| python -m pip install jinja2-ansible-filters | |
| - name: Generate Project README.md | |
| run: | | |
| jinja2 \ | |
| ${{ steps.event_info.outputs.name }}/Projects/Template/README.md.j2 \ | |
| ${{ runner.temp }}/template-data.json \ | |
| --format json \ | |
| -e "jinja2_ansible_filters.AnsibleCoreFiltersExtension" \ | |
| -o ${{ steps.event_info.outputs.name }}/Projects/${{ steps.project_directory.outputs.name }}/README.md | |
| - uses: tibdex/github-app-token@v1 | |
| id: generate-token | |
| with: | |
| app_id: ${{ secrets.APP_ID }} | |
| private_key: ${{ secrets.APP_PRIVATE_KEY }} | |
| - name: Create Pull Request | |
| id: cpr | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| token: ${{ steps.generate-token.outputs.token }} | |
| commit-message: | | |
| ${{ steps.event_info.outputs.name }}: Add project ${{ steps.project_directory.outputs.name }} | |
| committer: GitHub <noreply@github.com> | |
| author: ${{ github.actor }} <${{ github.actor }}@users.noreply.github.com> | |
| branch: ${{ steps.event_info.outputs.name }}/${{ steps.project_directory.outputs.name }} | |
| delete-branch: true | |
| title: Add project "${{ steps.project_issue.outputs.title }}" to "${{ steps.event_info.outputs.name }}" | |
| body: | | |
| Fixes #${{ github.event.issue.number }} | |
| labels: | | |
| project | |
| event:${{ steps.event_info.outputs.name }} | |
| - name: Create or update comment ❌ | |
| if: ${{ failure() && steps.check_project_exists.outcome == 'success' }} | |
| uses: peter-evans/create-or-update-comment@v3 | |
| with: | |
| comment-id: ${{ steps.couc.outputs.comment-id }} | |
| issue-number: ${{ github.event.issue.number }} | |
| body: | | |
| ## Project Page Pull Request Creation | |
| :x: **FAILED**: See ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} | |
| edit-mode: replace | |
| - name: Create or update comment ✅ | |
| if: ${{ success() }} | |
| uses: peter-evans/create-or-update-comment@v3 | |
| with: | |
| comment-id: ${{ steps.couc.outputs.comment-id }} | |
| issue-number: ${{ github.event.issue.number }} | |
| body: | | |
| ## Project Page Pull Request Creation | |
| :white_check_mark: **COMPLETED**: See ${{ steps.cpr.outputs.pull-request-url }} | |
| edit-mode: replace | |
| - name: Remove "project:create" label | |
| if: ${{ always() }} | |
| uses: actions/github-script@v6 | |
| with: | |
| script: | | |
| github.rest.issues.removeLabel({ | |
| issue_number: context.payload.issue.number, | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| name: ["project:create"] | |
| }) | |