OSP-based-publications-and-content/.github/workflows/find-missing-journal-publications.yml at master · Open-Systems-Pharmacology/OSP-based-publications-and-content · GitHub

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name: Find Missing Journal Publications

# Searches scientific literature sources for recently published articles / book
# chapters that mention "PK-Sim" or "Open Systems Pharmacology" and are not yet
# listed in journal-publications.md. The resulting markdown table is uploaded as
# an artifact, published as an annotation and e-mailed to MAIL_MISSING_PUBS.
#
# Required repository secret:
#   * MAIL_MISSING_PUBS - recipient e-mail address for the report.
# Required secrets for the SMTP server used to send the e-mail:
#   * MAIL_SERVER   - SMTP server address (e.g. smtp.gmail.com).
#   * MAIL_PORT     - SMTP server port (e.g. 465).
#   * MAIL_USERNAME - SMTP user name.
#   * MAIL_PASSWORD - SMTP password / app token.
# Optional secrets to raise rate limits / unlock extra sources:
#   * NCBI_API_KEY, NCBI_EMAIL, SEMANTIC_SCHOLAR_API_KEY, CORE_API_KEY.

on:
  workflow_dispatch:
    inputs:
      days:
        description: 'The number of days that the search time interval for new publications is set at.'
        required: false
        type: number
        default: 14
  schedule:
    # 23:00 CET on Sundays. GitHub cron runs in UTC, and CET is UTC+1, so the
    # job is scheduled at 22:00 UTC. (During CEST / summer time this maps to
    # 00:00, which is acceptable for a weekly report.)
    - cron: '0 22 * * 0'

permissions:
  contents: read

jobs:
  find:
    runs-on: ubuntu-latest
    env:
      MAIL_MISSING_PUBS: ${{ secrets.MAIL_MISSING_PUBS }}
    steps:
      - name: Check out repository
        uses: actions/checkout@v6
        with:
          persist-credentials: false

      - name: Set up Python
        uses: actions/setup-python@v6
        with:
          python-version: '3.x'

      - name: Find missing journal publications
        id: find
        env:
          NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}
          NCBI_EMAIL: ${{ secrets.NCBI_EMAIL }}
          SEMANTIC_SCHOLAR_API_KEY: ${{ secrets.SEMANTIC_SCHOLAR_API_KEY }}
          CORE_API_KEY: ${{ secrets.CORE_API_KEY }}
        run: >-
          python .github/scripts/find-missing-journal-publications.py
          --existing journal-publications.md
          --output find-missing-journal-publications.md
          --days ${{ inputs.days || 14 }}

      - name: Upload report artifact
        uses: actions/upload-artifact@v7
        with:
          name: find-missing-journal-publications
          path: find-missing-journal-publications.md

      - name: Send report by e-mail
        if: ${{ steps.find.outputs.has_results == 'true' && env.MAIL_MISSING_PUBS != '' }}
        # Pinned to the v17 commit SHA for supply-chain safety.
        uses: dawidd6/action-send-mail@42942bc2f8fba4e611b459a018967a6a7c78c68c
        with:
          server_address: ${{ secrets.MAIL_SERVER }}
          server_port: ${{ secrets.MAIL_PORT }}
          username: ${{ secrets.MAIL_USERNAME }}
          password: ${{ secrets.MAIL_PASSWORD }}
          subject: "Missing OSP journal publications (${{ steps.find.outputs.count }})"
          to: ${{ secrets.MAIL_MISSING_PUBS }}
          from: OSP Publication Finder <${{ secrets.MAIL_USERNAME }}>
          html_body: file://find-missing-journal-publications.md
          convert_markdown: true
          attachments: find-missing-journal-publications.md