Error with "rare" subset annotation for Hematologic Diseases that may also be propagating into 'inferred rare' assignments #2463
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| name: Create new pull request | |
| on: | |
| workflow_dispatch: | |
| issues: | |
| types: [opened, edited] | |
| issue_comment: | |
| types: [created, edited] | |
| jobs: | |
| check: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| phraseExists: ${{ steps.check-body.outputs.phraseExists }} | |
| commentId: ${{ steps.check-body.outputs.commentId }} | |
| steps: | |
| - name: Check if issue body contains 'Hey ontobot' | |
| id: check-body | |
| uses: actions/github-script@v6 | |
| with: | |
| script: | | |
| const issue = await github.rest.issues.get({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| issue_number: context.issue.number | |
| }); | |
| let bodyText = issue.data.body ? issue.data.body.toLowerCase() : ''; | |
| let commentId = null; | |
| // Fetch all comments for the issue | |
| const comments = await github.rest.issues.listComments({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| issue_number: context.issue.number | |
| }); | |
| // Function to check for the phrase in bodyText and comments | |
| function checkForPhrase(bodyText, comments) { | |
| const phrase = 'hey ontobot'; | |
| // Check if bodyText includes the phrase | |
| let result = bodyText.includes(phrase); | |
| // If not found in bodyText, check each comment | |
| for (let comment of comments.reverse()) { // Reverse to give precedence to the latest comment | |
| if (comment.body.toLowerCase().includes(phrase)) { | |
| result = true; | |
| commentId = comment.id; | |
| break; | |
| } | |
| } | |
| return { | |
| result: result, | |
| commentId: result ? commentId : null | |
| }; | |
| } | |
| const checkResult = checkForPhrase(bodyText, comments.data); | |
| console.log(`Result: ${checkResult.result}`); | |
| console.log(`Comment ID: ${checkResult.commentId}`); | |
| console.log(`Check Result: ${JSON.stringify(checkResult)}`); | |
| core.setOutput('phraseExists', checkResult.result); | |
| core.setOutput('commentId', checkResult.commentId); | |
| - name: Log phraseExists output | |
| run: | | |
| echo "phraseExists: ${{ steps.check-body.outputs.phraseExists }}" | |
| echo "commentId: ${{ steps.check-body.outputs.commentId }}" | |
| echo "Outputs: $(echo '${{ toJSON(steps.check-body.outputs) }}')" | |
| - name: Conditional step based on result | |
| if: ${{ steps.check-body.outputs.phraseExists == 'true' }} | |
| run: echo "The phrase 'Hey ontobot' was found." | |
| build: | |
| needs: check | |
| if: needs.check.outputs.phraseExists == 'true' | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python-version: ["3.9"] | |
| os: [ubuntu-latest] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Return issue number | |
| id: gh-script-issue | |
| uses: actions/github-script@v6 | |
| with: | |
| script: | | |
| const issue_number = context.issue.number; | |
| return issue_number | |
| - name: Return repository name | |
| id: gh-script-repo | |
| uses: actions/github-script@v6 | |
| with: | |
| script: | | |
| const repo = context.repo.owner + "/" + context.repo.repo; | |
| return repo; | |
| - name: Set branch name | |
| id: vars | |
| run: | | |
| echo "resource=src/ontology/mondo-edit.obo" >> $GITHUB_ENV | |
| echo "branch-name=ochange_automation_"${{ steps.gh-script-issue.outputs.result }} >> $GITHUB_ENV | |
| - name: Install dependencies | |
| run: | | |
| pip install ontobot-change-agent | |
| - name: Run ochange | |
| id: ochange | |
| run: | | |
| cmd="ochange process-issue ${{ env.resource }} \ | |
| -r ${{ steps.gh-script-repo.outputs.result }} \ | |
| -n ${{ steps.gh-script-issue.outputs.result }} \ | |
| -g ${{ secrets.GH_TOKEN }} \ | |
| -p MONDO" | |
| if [ "${{ needs.check.outputs.commentId }}" != "" ]; then | |
| cmd="$cmd -c ${{ needs.check.outputs.commentId }}" | |
| fi | |
| echo "Running command: $cmd" | |
| eval $cmd | |
| - uses: actions/create-github-app-token@v1 | |
| id: app-token | |
| with: | |
| app-id: ${{ vars.ONTOBOT_APP_ID }} | |
| private-key: ${{ secrets.ONTOBOT_APP_PRIVATE_KEY }} | |
| - name: Create Pull Request | |
| uses: peter-evans/create-pull-request@v4 | |
| if: ${{ env.PR_TITLE }} | |
| with: | |
| branch-suffix: short-commit-hash | |
| labels: Automated | |
| author: ${{ env.ISSUE_CREATOR }} <${{ env.ISSUE_CREATOR }}@users.noreply.github.com> | |
| committer: ${{ env.ISSUE_CREATOR }} <${{ env.ISSUE_CREATOR }}@users.noreply.github.com> | |
| body: ${{ env.PR_BODY }} | |
| title: ${{ env.PR_TITLE }} | |
| base: ${{ github.head_ref }} | |
| branch: ${{ env.branch-name }} | |
| token: ${{ steps.app-token.outputs.token }} |