New metabolite ID mapping database #51
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| name: Generate webpage content | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: ["main"] | |
| paths: | |
| - '*.json' | |
| # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages | |
| permissions: | |
| contents: write | |
| pages: write | |
| id-token: write | |
| # Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued. | |
| # However, do NOT cancel in-progress runs as we want to allow these production deployments to complete. | |
| concurrency: | |
| group: "pages" | |
| cancel-in-progress: false | |
| jobs: | |
| webpage: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| modified: ${{ steps.commit.outputs.modified }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| fetch-depth: 0 | |
| - name: Install groovy | |
| run: sudo apt install groovy | |
| - name: Generate website | |
| run: | | |
| groovy update.groovy > docs/gene_database/readme.md | |
| cp *.json docs/. | |
| - name: Generate BridgeDb Webservice config files | |
| run: | | |
| groovy makeGDBconfig.groovy | |
| - name: Commit report | |
| id: commit | |
| run: | | |
| git config --global user.name 'GitHub Action' | |
| git config --global user.email 'action@github.com' | |
| git add docs | |
| if git diff --exit-code --staged; then | |
| echo "No changes" | |
| echo "modified=" >> $GITHUB_OUTPUT | |
| else | |
| git commit -m 'Converted JSON content into markdown ' | |
| git push | |
| echo "modified=$(git diff --name-only --diff-filter=AM ${{ github.event.before }} -- docs/*.json | xargs)" >> $GITHUB_OUTPUT | |
| fi | |
| # Build Jeckyll Website job | |
| build: | |
| runs-on: ubuntu-latest | |
| needs: webpage | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: main | |
| - name: Setup Pages | |
| uses: actions/configure-pages@v5 | |
| - name: Build with Jekyll | |
| uses: actions/jekyll-build-pages@v1 | |
| with: | |
| source: ./docs | |
| destination: ./_site | |
| - name: Upload artifact | |
| uses: actions/upload-pages-artifact@v3 | |
| # Jeckyll Website Deployment job | |
| deploy: | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 | |
| # Pinging jobs | |
| pingDocker: | |
| runs-on: ubuntu-latest | |
| needs: [webpage, deploy] | |
| if: ${{needs.webpage.outputs.modified}} | |
| steps: | |
| - name: Trigger docker release | |
| uses: peter-evans/repository-dispatch@v3 | |
| with: | |
| token: ${{ secrets.pat_external_workflow }} | |
| repository: bridgedb/docker | |
| event-type: update-event | |
| pingWikiPathways: | |
| runs-on: ubuntu-latest | |
| needs: [webpage, deploy] | |
| if: ${{needs.webpage.outputs.modified}} | |
| steps: | |
| - name: Trigger WikiPathways BridgeDb Cache Reset | |
| uses: peter-evans/repository-dispatch@v3 | |
| with: | |
| token: ${{ secrets.PAT_WORKFLOW_WIKIPATHWAYS_BRIDGEDB_CACHE }} | |
| repository: wikipathways/wikipathways-database | |
| event-type: bridgedb-data-update-event | |
| # see https://github.com/wikipathways/wikipathways-database/blob/main/.github/workflows/scheduled_bridge_cache.yml#L4-L5 |