Export #125
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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 |