Export #121
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name: Export | |
on: | |
schedule: | |
# https://crontab.guru/#05_11_*_*_2 | |
- cron: '05 11 * * 2' | |
workflow_dispatch: | |
inputs: | |
release: | |
description: 'Ensembl release number (e.g. 104 or latest)' | |
required: true | |
default: 'latest' | |
overwrite: | |
type: boolean | |
description: 'Overwrite output on an existing branch.' | |
default: false | |
jobs: | |
export: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
species: | |
- human | |
- mouse | |
- rat | |
steps: | |
- name: Checkout repository | |
uses: actions/checkout@v4 | |
- name: Setup dependencies | |
uses: ./.github/actions/setup | |
- name: Set parameters | |
id: params | |
shell: bash | |
run: | | |
DATE_ISO=$(date --utc --iso) | |
echo "Setting parameter date_iso=$DATE_ISO" | |
echo "date_iso=$DATE_ISO" >> $GITHUB_OUTPUT | |
ENSEMBL_RELEASE=${{ github.event.inputs.release || 'latest' }} | |
ENSEMBL_RELEASE=$(poetry run ensembl_genes ensembl_release --release="$ENSEMBL_RELEASE") | |
echo "Setting parameter release=$ENSEMBL_RELEASE" | |
echo "release=$ENSEMBL_RELEASE" >> $GITHUB_OUTPUT | |
ENSEMBL_DATABASE=$(poetry run ensembl_genes ensembl_database --species="${{ matrix.species }}" --release="$ENSEMBL_RELEASE") | |
echo "Setting parameter database=$ENSEMBL_DATABASE" | |
echo "database=$ENSEMBL_DATABASE" >> $GITHUB_OUTPUT | |
# output_path doubles as a hierarchical branch name | |
OUTPUT_PATH="output/${ENSEMBL_DATABASE}" | |
echo "Setting parameter output_path=$OUTPUT_PATH" | |
echo "output_path=$OUTPUT_PATH" >> $GITHUB_OUTPUT | |
OUTPUT_EXISTS="true" | |
git ls-remote --exit-code origin $OUTPUT_PATH || OUTPUT_EXISTS="false" | |
echo "$OUTPUT_PATH branch exists on origin: $OUTPUT_EXISTS" | |
echo "output_exists=$OUTPUT_EXISTS" >> $GITHUB_OUTPUT | |
OVERWRITE=${{ github.event.inputs.overwrite || 'false' }} | |
echo "Setting parameter overwrite=$OVERWRITE" | |
echo "overwrite=$OVERWRITE" >> $GITHUB_OUTPUT | |
EXPORT="false" | |
if [[ $OUTPUT_EXISTS = "false" || $OVERWRITE = "true" ]]; then | |
EXPORT="true" | |
fi | |
echo "Setting parameter export=$EXPORT" | |
echo "export=$EXPORT" >> $GITHUB_OUTPUT | |
- name: Extract tables | |
id: extract | |
if: steps.params.outputs.export == 'true' | |
run: poetry run ensembl_genes all --species="${{ matrix.species }}" --release=${{ steps.params.outputs.release }} | |
- name: Output artifact | |
# upload outputs to artifact only when the extraction fails | |
if: always() && steps.extract.outcome == 'failure' | |
uses: actions/upload-artifact@v3 | |
with: | |
name: failed_output_${{ steps.params.outputs.database }} | |
path: ${{ steps.params.outputs.output_path }} | |
- name: Deploy | |
uses: peaceiris/actions-gh-pages@v3 | |
if: steps.params.outputs.export == 'true' | |
with: | |
github_token: ${{ secrets.GITHUB_TOKEN }} | |
publish_branch: ${{ steps.params.outputs.output_path }} | |
publish_dir: ${{ steps.params.outputs.output_path }} | |
# Won't actually enable jekyll because we're not using GitHub Pages. | |
# https://github.com/peaceiris/actions-gh-pages/issues/660 | |
enable_jekyll: true | |
full_commit_message: | | |
export ${{ steps.params.outputs.database }} on ${{ steps.params.outputs.date_iso }} | |
code version ${{ github.sha }} | |
built by <${{ github.event.repository.html_url }}/actions/runs/${{ github.run_id }}> | |
allow_empty_commit: true |