On Pull Request #20
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| name: On Pull Request | |
| on: | |
| workflow_dispatch: | |
| #pull_request: | |
| #paths: | |
| # - '**/*.gpml' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.head_ref || github.ref }} | |
| cancel-in-progress: false # to allow multiple runs to queue up rather than clobber | |
| jobs: | |
| # Retrieves GPML file and PR number associated with incoming Pull Request and creates | |
| # global variables that can accessed by subsequent jobs: | |
| # * pr-number = the unique number that identifies a Pull Request | |
| # * add-modified = a GPML file that is being added or modified in the wikipathways database | |
| # * deleted = a GPML file that is being deleted from the wikipathways database | |
| get-gpml-pr: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| pr-number: ${{ steps.changes.outputs.pr-number }} | |
| added-modified: ${{ steps.changes.outputs.added-modified }} | |
| deleted: ${{ steps.changes.outputs.deleted }} | |
| steps: | |
| # Make sure we have some code to diff. | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Get PR and GPML | |
| id: changes | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} #only need to support TESTING | |
| run: | | |
| echo "GPML files were changed in pull request ${{ github.event.before }} -> ${{ github.event.after }}" | |
| #echo "pr-number=${{ github.event.pull_request.number }}" >> $GITHUB_OUTPUT | |
| echo "pr-number=4" >> $GITHUB_OUTPUT #TESTING | |
| #echo "added-modified=$(git diff --name-only --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$ | xargs)" >> $GITHUB_OUTPUT | |
| echo "added-modified=$(gh pr view 4 --json files --jq '.files.[].path' | grep '.gpml$')" >> $GITHUB_OUTPUT #TESTING | |
| if git diff --name-only --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$; then | |
| echo 'added or modified:' | |
| git diff --name-only --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$ | |
| fi | |
| echo "deleted=$(git diff --name-only --diff-filter=D ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$ | xargs)" >> $GITHUB_OUTPUT | |
| if git diff --name-only --diff-filter=D ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$; then | |
| echo 'deleted:' | |
| git diff --name-only --diff-filter=D ${{ github.event.before }} ${{ github.event.after }} | grep .gpml$ | |
| fi | |
| check_gpml: | |
| needs: [get-gpml-pr] | |
| if: ${{needs.get-gpml-pr.outputs.added-modified}} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - name: Check GPML file | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| GPML_FILE=${{needs.get-gpml-pr.outputs.added-modified}} | |
| echo "Found .gpml file: $GPML_FILE" | |
| org="$(sed -n '/<Pathway /s/.*Organism=\(.*\)[^\n]*/\1/p' $GPML_FILE | tr -d '"' | tr -d '>' | tr -d '\r')" | |
| name="$(sed -n '/<Pathway /s/.*Name=\(.*\)[^\n]*/\1/p' $GPML_FILE | tr -d '"' | tr -d '>' | tr -d '\r')" | |
| desc="$(sed -n '/<Comment Source="WikiPathways-description">\(.*\)<\/Comment>/\1/p' $GPML_FILE | tr -d '"')" | |
| # Start PR description | |
| NEW_DESCRIPTION=" | |
| # Pathway Information | |
| Title: $name | |
| Organism: $org | |
| Description: $desc | |
| --- | |
| " | |
| PR_NUMBER=${{needs.get-gpml-pr.outputs.pr-number}} | |
| gh pr edit $PR_NUMBER --body "$NEW_DESCRIPTION" | |
| metadata: | |
| needs: [check_gpml] | |
| if: ${{needs.changed-gpmls.outputs.added-modified}} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v3 | |
| - name: Run meta-data-action | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| echo "TODO: Run meta-data-action and attach output JSON and TSV to PR" | |
| # Update PR description | |
| PR_NUMBER=${{needs.get-gpml-pr.outputs.pr-number}} | |
| CURRENT_DESCRIPTION=$(gh pr view $PR_NUMBER --json body -q ".body") | |
| NEW_DESCRIPTION="$CURRENT_DESCRIPTION | |
| # Generate Metadata Files | |
| - [x] info.json generated | |
| - [x] datanodes.tsv generated | |
| " | |
| gh pr edit $PR_NUMBER --body "$NEW_DESCRIPTION" | |
| pubmed: | |
| needs: [metadata] | |
| if: ${{needs.changed-gpmls.outputs.added-modified}} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v3 | |
| - name: Run generate-references | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| echo "TODO: Run generate-references and attach output TSV to PR" | |
| # Update PR description | |
| PR_NUMBER=${{needs.get-gpml-pr.outputs.pr-number}} | |
| CURRENT_DESCRIPTION=$(gh pr view $PR_NUMBER --json body -q ".body") | |
| NEW_DESCRIPTION="$CURRENT_DESCRIPTION | |
| - [x] references.tsv generated | |
| " | |
| gh pr edit $PR_NUMBER --body "$NEW_DESCRIPTION" | |
| frontmatter: | |
| needs: [pubmed] | |
| if: ${{needs.changed-gpmls.outputs.added-modified}} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v3 | |
| - name: Run create_pathway_frontmatter.py | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| echo "TODO: Run create_pathway_frontmatter.py and attach output MD to PR" | |
| # Update PR description | |
| PR_NUMBER=${{needs.get-gpml-pr.outputs.pr-number}} | |
| CURRENT_DESCRIPTION=$(gh pr view $PR_NUMBER --json body -q ".body") | |
| NEW_DESCRIPTION="$CURRENT_DESCRIPTION | |
| - [x] .md generated | |
| " | |
| gh pr edit $PR_NUMBER --body "$NEW_DESCRIPTION" | |
| json-svg: | |
| needs: [frontmatter] | |
| if: ${{needs.changed-gpmls.outputs.added-modified}} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v3 | |
| - name: Run generate-svgs | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| echo "TODO: Run generate-svgs and attach output JSON, SVG and PNG to PR" | |
| # Update PR description | |
| PR_NUMBER=${{needs.get-gpml-pr.outputs.pr-number}} | |
| CURRENT_DESCRIPTION=$(gh pr view $PR_NUMBER --json body -q ".body") | |
| NEW_DESCRIPTION="$CURRENT_DESCRIPTION | |
| - [x] .json generated | |
| - [x] .svg generated | |
| - [x] .png generated | |
| * TODO: insert PNG here * | |
|  | |
| " | |
| gh pr edit $PR_NUMBER --body "$NEW_DESCRIPTION" | |
| testing: | |
| needs: [frontmatter] | |
| if: ${{needs.changed-gpmls.outputs.added-modified}} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v3 | |
| - name: Perform automatic test | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| # TODO: perform testing | |
| # Update PR description | |
| PR_NUMBER=${{needs.get-gpml-pr.outputs.pr-number}} | |
| CURRENT_DESCRIPTION=$(gh pr view $PR_NUMBER --json body -q ".body") | |
| NEW_DESCRIPTION="$CURRENT_DESCRIPTION | |
| --- | |
| # Automated Testing | |
| - [x] Test one PASSED | |
| ```diff | |
| - Test two FAILED | |
| ``` | |
| - [x] Test three PASSED | |
| - [ ] Interactions are connected | |
| - [ ] Datanodes are annotated with database references | |
| - [ ] Decription, consisting of 2-3 sentence overview of processes described in the pathway | |
| - [ ] At least one literature reference | |
| - [ ] At least one pathway ontology term | |
| - [ ] Pathway title conforms to the [guidelines](https://github.com/wikipathways/wikipathways-faq/discussions/24) | |
| --- | |
| " | |
| gh pr edit $PR_NUMBER --body "$NEW_DESCRIPTION" |