Refactor build pipeline and add synonyms to some translations #179
Workflow file for this run
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: '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 | |
| } |