cron.yml

name: Check ClinVar FTP

on:
  workflow_dispatch:
  schedule:
    #         ┌───────────── minute (0 - 59)
    #         │ ┌───────────── hour (0 - 23)
    #         │ │ ┌───────────── day of the month (1 - 31)
    #         │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
    #         │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
    #         │ │ │ │ │
    #         │ │ │ │ │
    #         │ │ │ │ │
    #         * * * * *
    #
    # Human-readable: "At minute 37 past every 3rd hour on Monday."
    #
    # This is sufficient as there are only releases on Mondays.
    - cron: '37 */3 * * 1'

jobs:
  Check-ClinVar-FTP:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          ref: main
          fetch-depth: 0

      - name: setup git config
        run: |
          git config user.name "GitHub Actions Bot"
          git config user.email "<>"

      - name: Create new PR if necessary
        env:
          GITHUB_TOKEN: ${{ secrets.BOT_PAT }}
        run: |
          set -x

          # Download ClinVar XML listing
          curl https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/weekly_release/ \
          > /tmp/lst.html

          # Look for date of the "*-latest_weekly.xml.gz"
          grep 'latest_weekly.xml.gz"' /tmp/lst.html \
          | head -n 1 \
          | cut -d '>' -f 21- \
          | cut -d '<' -f 1 \
          | cut -d ' ' -f 1 \
          | tr -d '-' \
          > /tmp/release-name.txt
          release_name=$(cat /tmp/release-name.txt)

          set +e

          # Check whether we already have a tag for this
          tag_name=clinvar-weekly-$release_name
          git tag | grep "${tag_name}$" >/dev/null
          tag_needed=$?
          # Check whether we already have a branch for this
          branch_name=release-${tag_name}
          git branch -a | grep "${branch_name}$" >/dev/null
          branch_needed=$?

          # Only create a new branch if no tag and no branch exist yet.  The
          # tag will be created together with the release on the main branch.
          if [[ "$tag_needed" -eq 1 ]]; then
            # The tag does not exist yet.  We may need to create a new branch
            # and PR.
            if [[ "$branch_needed" -eq 1 ]]; then
              >&2 echo "Neither the tag nor the branch exist; create branch and PR"
              git checkout -b $branch_name

              cp /tmp/release-name.txt release-name.txt
              git add release-name.txt

              git commit -m "chore: weekly ClinVar release $release_name"
              git push --set-upstream origin $branch_name
            else
              >&2 echo "The tag is missing but the branch exists"
              git checkout $branch_name
            fi

            # If necessary, create new pull request and set it to auto-merge.
            gh pr view >/dev/null
            pr_needed=$?
            if [ "$pr_needed" -eq 1 ]; then
              >&2 echo "The tag is missing, branch exists here, now creating PR"

              # Enforce that the "autorelease" ticket is present.
              gh label create "autorelease" --color EDEDED --force

              # Creat epull request and set to auto-merge.
              set -e
              gh pr create --fill --base main --head $branch_name --label autorelease
              gh pr merge --auto --squash
            else
              set -e
              >&2 echo "The tag is missing but the PR already exists"
            fi
          else
            set -e
            >&2 echo "The tag already exist, move on; nothing to do"
          fi