[MOMSI_G:00000] Update The Sequence Ontology #31
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| name: Process submission | |
| on: | |
| issues: | |
| types: [labeled] | |
| concurrency: 'main' | |
| jobs: | |
| validation: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| authorised-actor: ${{ steps.authorised-actor-check.outputs.valid && github.event.label.name == 'merge' }} | |
| has-genomics: ${{ contains(github.event.issue.labels.*.name, 'genomics') }} | |
| has-proteomics: ${{ contains(github.event.issue.labels.*.name, 'proteomics') }} | |
| has-metabolomics: ${{ contains(github.event.issue.labels.*.name, 'metabolomics') }} | |
| has-universal: ${{ contains(github.event.issue.labels.*.name, 'universal') }} | |
| steps: | |
| - name: Check if actor is authorised | |
| id: authorised-actor-check | |
| shell: bash | |
| run: | | |
| if [ "${{ contains(fromJSON(secrets.AUTHORISED_MERGE), github.triggering_actor) }}" ]; then | |
| echo "valid=true" >> $GITHUB_OUTPUT; | |
| else | |
| echo "valid=false" >> $GITHUB_OUTPUT; | |
| fi | |
| genomics: | |
| runs-on: ubuntu-latest | |
| needs: [validation] | |
| outputs: | |
| data_string: ${{ steps.set-data.outputs.data }} | |
| if: fromJSON(needs.validation.outputs.authorised-actor) && fromJSON(needs.validation.outputs.has-genomics) | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: '16' | |
| - uses: stefanbuck/github-issue-parser@v3 | |
| id: issue-parser | |
| with: | |
| template-path: .github/ISSUE_TEMPLATE/01-genomics-standards.yml | |
| - run: echo '${{ steps.issue-parser.outputs.jsonString }}' > submission.json | |
| - run: cat submission.json | |
| - name: Upload submission result | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: submission_data | |
| path: submission.json | |
| proteomics: | |
| runs-on: ubuntu-latest | |
| needs: [validation] | |
| outputs: | |
| data_string: ${{ steps.set-data.outputs.data }} | |
| if: fromJSON(needs.validation.outputs.authorised-actor) && fromJSON(needs.validation.outputs.has-proteomics) | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: '16' | |
| - uses: stefanbuck/github-issue-parser@v3 | |
| id: issue-parser | |
| with: | |
| template-path: .github/ISSUE_TEMPLATE/02-proteomics-standards.yml | |
| - run: echo '${{ steps.issue-parser.outputs.jsonString }}' > submission.json | |
| - run: cat submission.json | |
| - name: Upload submission result | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: submission_data | |
| path: submission.json | |
| metabolomics: | |
| runs-on: ubuntu-latest | |
| needs: [validation] | |
| outputs: | |
| data_string: ${{ steps.set-data.outputs.data }} | |
| if: fromJSON(needs.validation.outputs.authorised-actor) && fromJSON(needs.validation.outputs.has-metabolomics) | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: '16' | |
| - uses: stefanbuck/github-issue-parser@v3 | |
| id: issue-parser | |
| with: | |
| template-path: .github/ISSUE_TEMPLATE/03-metabolomics-standards.yml | |
| - run: echo '${{ steps.issue-parser.outputs.jsonString }}' > submission.json | |
| - run: cat submission.json | |
| - name: Upload submission result | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: submission_data | |
| path: submission.json | |
| universal: | |
| runs-on: ubuntu-latest | |
| needs: [validation] | |
| outputs: | |
| data_string: ${{ steps.set-data.outputs.data }} | |
| if: fromJSON(needs.validation.outputs.authorised-actor) && fromJSON(needs.validation.outputs.has-universal) | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: '16' | |
| - uses: stefanbuck/github-issue-parser@v3 | |
| id: issue-parser | |
| with: | |
| template-path: .github/ISSUE_TEMPLATE/04-universal-standards.yml | |
| - run: echo '${{ steps.issue-parser.outputs.jsonString }}' > submission.json | |
| - run: cat submission.json | |
| - name: Upload submission result | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: submission_data | |
| path: submission.json | |
| completion: | |
| runs-on: ubuntu-latest | |
| needs: [genomics, proteomics, metabolomics, universal] | |
| if: | | |
| !failure() | |
| && !cancelled() | |
| && (success('genomics') || success('proteomics') || success('metabolomics') || success('universal')) | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: '20' | |
| cache: "yarn" | |
| - name: Download submission result | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: submission_data | |
| - name: Restore data | |
| id: set-completion-data | |
| shell: bash | |
| run: | | |
| data=`cat submission.json` | |
| echo $data > submission.json | |
| - name: Set variables | |
| id: set-variables | |
| shell: bash | |
| run: | | |
| if [[ "${{ needs.genomics.result }}" == "success" ]]; then | |
| echo "genomics" > submitter.txt | |
| elif [[ "${{ needs.proteomics.result }}" == "success" ]]; then | |
| echo "proteomics" > submitter.txt | |
| elif [[ "${{ needs.metabolomics.result }}" == "success" ]]; then | |
| echo "metabolomics" > submitter.txt | |
| elif [[ "${{ needs.universal.result }}" == "success" ]]; then | |
| echo "universal" > submitter.txt | |
| fi | |
| - run: cat submitter.txt | |
| - run: node ./process-submission.cjs | |
| - name: Commit changes | |
| shell: bash | |
| run: | | |
| git config --global user.email "github-actions[bot]@users.noreply.github.com" && \ | |
| git config --global user.name "github-actions[bot]" && \ | |
| git add ./src/data/database.json && \ | |
| git add ./src/data/vizibase.json && \ | |
| git add ./src/data/typebase.json && \ | |
| git commit -m 'Update Standards' && \ | |
| git push | |
| - name: Install dependencies | |
| run: yarn --frozen-lockfile | |
| - name: Build | |
| run: npm run build | |
| - name: Upload artifact | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: ./dist | |
| - name: Close Issue | |
| run: gh issue close --comment "Auto-closing issue" ${{ github.event.issue.number }} | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| deploy: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| pages: write | |
| id-token: write | |
| needs: [genomics, proteomics, metabolomics, universal, completion] | |
| if: | | |
| !failure() | |
| && !cancelled() | |
| && (success('genomics') || success('proteomics') || success('metabolomics') || success('universal')) | |
| && success('completion') | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 |