Check ClinVar FTP #507
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |