Check ClinVar FTP #539
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| 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 |