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Merge pull request #9856 from obophenotype/issue-9579-2
Documenting differences in ontology files (attempt 2)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,139 @@ | ||
| name: 'Create OAK diffs on Pull requests' | ||
|
|
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| on: | ||
| # Triggers the workflow on pull request events for the master branch | ||
| pull_request: | ||
| branches: [ master ] | ||
|
|
||
| # Allows you to run this workflow manually from the Actions tab | ||
| workflow_dispatch: | ||
|
|
||
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | ||
| jobs: | ||
| build_branch: | ||
| runs-on: ubuntu-latest | ||
| container: obolibrary/odkfull:v1.5 | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - name: Build ontology | ||
| run: | | ||
| cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE hp.obo -B | ||
| cp hp.obo tmp/hp-branch.obo | ||
| - name: Upload tmp/hp-branch.obo | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: hp-branch.obo | ||
| path: src/ontology/tmp/hp-branch.obo | ||
| retention-days: 1 | ||
| build_main: | ||
| runs-on: ubuntu-latest | ||
| container: obolibrary/odkfull:v1.5 | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| with: | ||
| ref: master | ||
| - name: Classify ontology | ||
| run: | | ||
| cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE hp.obo -B | ||
| cp hp.obo tmp/hp-main.obo | ||
| - name: Upload tmp/hp-main.obo | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: hp-main.obo | ||
| path: src/ontology/tmp/hp-main.obo | ||
| retention-days: 1 | ||
| diff: | ||
| needs: | ||
| - build_branch | ||
| - build_main | ||
| runs-on: ubuntu-latest | ||
| container: obolibrary/odkfull:v1.5 | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - name: Download main build | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: hp-main.obo | ||
| path: src/ontology/tmp/ | ||
| - name: Download branch build | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: hp-branch.obo | ||
| path: src/ontology/tmp/ | ||
| - name: Diff classification | ||
| run: | | ||
| pip install -U oaklib | ||
| cd src/ontology; | ||
| runoak -i simpleobo:tmp/hp-main.obo diff -X simpleobo:tmp/hp-branch.obo -o reports/difference_main-branch_base.md --output-type md | ||
| - name: Upload diff | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: difference_main-branch_base.md | ||
| path: src/ontology/reports/difference_main-branch_base.md | ||
| post_comment: | ||
| needs: diff | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Download reasoned diff | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: difference_main-branch_base.md | ||
| path: src/ontology/reports/ | ||
| # - name: Prepare reasoned comment | ||
| # run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology: </summary> \n\" >comment.md; cat src/ontology/reports/difference_main-branch_base.md >>comment.md" | ||
| # - name: Post reasoned comment | ||
| # env: | ||
| # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| # uses: NejcZdovc/[email protected] | ||
| # with: | ||
| # github_token: ${{ secrets.GITHUB_TOKEN }} | ||
| # file: "../../comment.md" | ||
| # identifier: "REASONED" | ||
| # Post or update comment on pull request if difference_md.md exists | ||
| - name: Post or update comment on pull request | ||
| uses: actions/github-script@v7 | ||
| with: | ||
| script: | | ||
| const fs = require('fs'); | ||
| const path = 'src/ontology/reports/difference_main-branch_base.md'; | ||
| if (fs.existsSync(path)) { | ||
| let content = fs.readFileSync(path, 'utf8'); | ||
| if (content) { | ||
| // GitHub's max issue body size is approximately 65536 characters | ||
| const maxBodySize = 65536; | ||
| const truncateMsg = '\n</details>\n\n ### WARNING: This diff is too large and has been truncated. For full diff see [here](https://github.com/${{ github.repository }}/blob/${{ github.head_ref }}/src/ontology/reports/difference_main-branch_base.md).'; | ||
| if (content.length > maxBodySize) { | ||
| // Truncate the content to fit within the GitHub comment size limit | ||
| content = content.substring(0, maxBodySize - truncateMsg.length) + truncateMsg; | ||
| } | ||
| const { owner, repo } = context.repo; | ||
| const { number } = context.issue; | ||
| const existingComments = await github.rest.issues.listComments({ | ||
| owner, | ||
| repo, | ||
| issue_number: number | ||
| }); | ||
| const existingComment = existingComments.data.find(comment => comment.user.login === 'github-actions[bot]'); | ||
| if (existingComment) { | ||
| await github.rest.issues.updateComment({ | ||
| owner, | ||
| repo, | ||
| comment_id: existingComment.id, | ||
| body: content | ||
| }); | ||
| } else { | ||
| await github.rest.issues.createComment({ | ||
| owner, | ||
| repo, | ||
| issue_number: number, | ||
| body: content | ||
| }); | ||
| } | ||
| } else { | ||
| console.log("The markdown file is empty."); // Debug print if the file is empty | ||
| } | ||
| } else { | ||
| console.log("The markdown file does not exist."); // Debug print if the file does not exist | ||
| } |
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