paper_ranking.yml

name: Run Paper Ranking Script and Update Issue

on:
  schedule:
    - cron: '0 0 1 * *' # runs on the first day of every month
  workflow_dispatch:

permissions:
  contents: write
  issues: write

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: |
        # TODO update to using uv
        python -m pip install --upgrade pip
        pip install .[paper-ranking]

    - 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
        # TODO update to using python -m
        python src/bioregistry/analysis/paper_ranking.py --start-date ${{ env.START_DATE }} --end-date ${{ env.END_DATE }}

    - name: Configure Git
      run: |
        git config user.name "github-actions[bot]"
        git config user.email "41898282+github-actions[bot]@users.noreply.github.com"

    - name: Commit and Push Changes
      run: |
        git add exports/analyses/paper_ranking/predictions.tsv
        git commit -m "Update predictions file with papers between ${{ env.START_DATE }} and ${{ env.END_DATE }}"
        git push

    - name: Find Commit Hash
      id: get-commit-hash
      run: echo "COMMIT_HASH=$(git rev-parse HEAD)" >> $GITHUB_ENV

    - 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 = ${{ steps.find-issue.outputs.result }};
          const startDate = process.env.START_DATE;
          const endDate = process.env.END_DATE;
          const commitHash = process.env.COMMIT_HASH;
          const rankingFileLink = `https://github.com/${{ github.repository }}/blob/${commitHash}/exports/analyses/paper_ranking/predictions.tsv`;
          const content = fs.readFileSync(`exports/analyses/paper_ranking/predictions.tsv`, 'utf8');
          const lines = content.split('\n').slice(1, 21);
          const rows = lines.map(line => {
            const [pubmed, title] = line.split('\t');
            const link = `https://bioregistry.io/pubmed:${pubmed}`;
            return `| [${pubmed}](${link}) | ${title} |`;
          });
          const tableHeader = '| PubMed ID | Title |\n| --- | --- |\n';
          const commentBody = `This issue contains monthly updates to an automatically ranked list of PubMed papers as candidates for curation in the Bioregistry. Papers may be relevant in at least three ways: \n(1) as a new prefix for a resource that can be added to the Bioregistry,\n(2) as a provider for an existing prefix, or\n(3) as a new publication for an existing prefix already in the Bioregistry.\n\nThese curations can happen in separate issues and pull requests. The full list of ranked papers can be found [here](${rankingFileLink}). 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);
          }