Remove mesh xrefs from HPO #151
Workflow file for this run
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| name: 'Create OAK diffs on Pull requests' | |
| 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 | |
| } |