Run Paper Ranking Script and Update Issue #8
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| name: Run Paper Ranking Script and Update Issue | |
| on: | |
| schedule: | |
| - cron: '0 0 1 * *' # runs on the first day of every month | |
| workflow_dispatch: | |
| jobs: | |
| paper-ranking: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.12" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r src/bioregistry/analysis/paper_ranking_requirements.txt | |
| - name: Set Date Variables | |
| id: set-date-variables | |
| run: | | |
| end_date=$(date +'%Y-%m-%d') | |
| start_date=$(date -d "$end_date - 30 days" +'%Y-%m-%d') | |
| echo "START_DATE=$start_date" >> $GITHUB_ENV | |
| echo "END_DATE=$end_date" >> $GITHUB_ENV | |
| - name: Set PYTHONPATH | |
| run: | | |
| echo "PYTHONPATH=$PWD/src" >> $GITHUB_ENV | |
| - name: Run Paper Ranking Script | |
| id: run-ranking-script | |
| run: | | |
| echo "PYTHONPATH=$PYTHONPATH" # Verify PYTHONPATH | |
| python src/bioregistry/analysis/paper_ranking.py --start-date ${{ env.START_DATE }} --end-date ${{ env.END_DATE }} | |
| - name: Upload Full List as Artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: full-predictions-list-${{ env.START_DATE }}-to-${{ env.END_DATE }} | |
| path: exports/analyses/paper_ranking/predictions_${{ env.START_DATE }}_to_${{ env.END_DATE }}.tsv | |
| - name: Find Existing Issue | |
| id: find-issue | |
| uses: actions/github-script@v6 | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| script: | | |
| const { data: issues } = await github.rest.issues.listForRepo({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| state: 'open', | |
| labels: 'paper-ranking-results' | |
| }); | |
| const issue = issues.find(issue => issue.title === 'Potentially relevant papers ranked for curation'); | |
| return issue ? issue.number : null; | |
| - name: Create or Update Issue with Comment | |
| id: create-or-update-issue | |
| uses: actions/github-script@v6 | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| script: | | |
| const fs = require('fs'); | |
| const issueNumber = ${{ steps.find-issue.outputs.result }}; | |
| const startDate = process.env.START_DATE; | |
| const endDate = process.env.END_DATE; | |
| const content = fs.readFileSync(`exports/analyses/paper_ranking/predictions_${startDate}_to_${endDate}.tsv`, 'utf8'); | |
| const lines = content.split('\n').slice(1, 21); | |
| const rows = lines.map(line => { | |
| const [pubmed, title] = line.split('\t'); | |
| const link = `https://bioregistry.io/pubmed:${pubmed}`; | |
| return `| [${pubmed}](${link}) | ${title} |`; | |
| }); | |
| const tableHeader = '| PubMed ID | Title |\n| --- | --- |\n'; | |
| const commentBody = `This issue contains monthly updates to an automatically ranked list of PubMed papers as candidates for curation in the Bioregistry. Papers may be relevant in at least three ways: \n(1) as a new prefix for a resource that can be added to the Bioregistry,\n(2) as a provider for an existing prefix, or\n(3) as a new publication for an existing prefix already in the Bioregistry.\n\nThese curations can happen in separate issues and pull requests. The full list of ranked papers can be found [here](https://github.com/${{ github.repository }}/blob/main/exports/analyses/paper_ranking/predictions_${startDate}_to_${endDate}.tsv). If you review any of these papers for relevance, you should edit the curated papers file [here](https://github.com/${{ github.repository }}/blob/main/src/bioregistry/data/curated_papers.tsv); these curations are taken into account when retraining the ranking model.\n\n**New entries for ${startDate} to ${endDate}:**\n\n${tableHeader}${rows.join('\n')}`; | |
| if (issueNumber) { | |
| await github.rest.issues.createComment({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| issue_number: issueNumber, | |
| body: commentBody, | |
| }); | |
| } else { | |
| const response = await github.rest.issues.create({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| title: 'Potentially relevant papers ranked for curation', | |
| body: `${commentBody}`, | |
| labels: ['paper-ranking-results'], | |
| }); | |
| core.setOutput('issue-number', response.data.number); | |
| } |