Create efo #88
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| name: Create NXOntology | |
| run-name: Create ${{ inputs.source }} | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| source: | |
| type: choice | |
| description: 'Which data source to generate.' | |
| options: | |
| - efo | |
| - hgnc | |
| - mesh | |
| - pubchem | |
| - test # for testing this action | |
| overwrite: | |
| type: boolean | |
| description: 'Overwrite output on an existing branch.' | |
| default: false | |
| permissions: | |
| contents: write | |
| jobs: | |
| create-runner: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| label: ${{ steps.create-runner.outputs.label }} | |
| steps: | |
| - id: create-runner | |
| uses: related-sciences/gce-github-runner@main | |
| with: | |
| token: ${{ secrets.GH_SA_TOKEN }} | |
| project_id: ${{ secrets.GCP_PROJECT_ID }} | |
| runner_service_account: ${{ secrets.GCP_SA }} | |
| service_account_key: ${{ secrets.GCP_SA_KEY }} | |
| machine_type: n2-highmem-8 | |
| image_project: ubuntu-os-cloud | |
| image_family: ubuntu-2004-lts | |
| ephemeral: true | |
| no_external_address: true | |
| export: | |
| needs: create-runner | |
| runs-on: ${{ needs.create-runner.outputs.label }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Setup dependencies | |
| uses: ./.github/actions/setup | |
| - name: Set parameters | |
| id: params | |
| shell: bash | |
| run: | | |
| CURRENT_DATE=$(date --utc --iso) | |
| echo "Setting parameter current_date=$CURRENT_DATE" | |
| echo "current_date=$CURRENT_DATE" >> $GITHUB_OUTPUT | |
| OUTPUT_PATH="output/${{ github.event.inputs.source }}" | |
| 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: Create output | |
| id: extract | |
| if: steps.params.outputs.export == 'true' | |
| run: poetry run nxontology_data ${{ github.event.inputs.source }} | |
| - name: Deploy | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| if: steps.params.outputs.export == 'true' | |
| with: | |
| folder: ./${{ steps.params.outputs.output_path }} | |
| branch: ${{ steps.params.outputs.output_path }} | |
| commit-message: | | |
| Export ${{ github.event.inputs.source }} on ${{ steps.params.outputs.current_date }} | |
| Ontology generated from source code at ${{ github.sha }}. | |
| Run in https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }} | |
| Triggered by @${{ github.actor }}. |