Update bwmd_concepts.owl (aligned BWMD import/mappings) #2
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| # ============================================================================== | |
| # WORKFLOW: Refresh Ontology Imports | |
| # ============================================================================== | |
| # Purpose: Updates external ontology import modules to maintain consistency | |
| # with upstream ontologies | |
| # | |
| # This workflow: | |
| # 1. Detects changes to import-related files or receives trigger from setup-repo | |
| # 2. Runs ODK make targets to refresh external ontology modules | |
| # 3. Commits updated import files back to the repository | |
| # 4. Triggers the QC workflow to continue the automation chain | |
| # | |
| # External imports are OWL files that include terms from other ontologies | |
| # (e.g., BFO, PATO, CHEBI). Keeping them updated ensures consistency. | |
| # | |
| # Execution Chain Position: | |
| # setup-repo → [REFRESH-IMPORTS] → qc → docs | |
| # | |
| # Read more about ODK imports: | |
| # https://github.com/INCATools/ontology-development-kit#imports | |
| # ============================================================================== | |
| name: Refresh Ontology Imports | |
| # ============================================================================== | |
| # WORKFLOW TRIGGERS | |
| # ============================================================================== | |
| # This workflow can be triggered in three ways: | |
| # 1. Via repository_dispatch from setup-repo workflow (initial setup) | |
| # 2. Automatically on pushes that modify import-related files | |
| # 3. Manually via workflow_dispatch for forced refresh | |
| # | |
| # Path filters ensure the workflow only runs when relevant files change, | |
| # preventing unnecessary executions on unrelated commits. | |
| # | |
| # IMPORTANT: Push triggers skip commits made by github-actions[bot] to prevent | |
| # duplicate runs when the workflow chain is triggered via repository_dispatch. | |
| # ============================================================================== | |
| on: | |
| # ============================================================================ | |
| # TRIGGER 1: Repository Dispatch (from setup-repo workflow) | |
| # ============================================================================ | |
| # Listens for 'trigger-refresh-imports' event dispatched by setup-repo.yml | |
| # This ensures imports are refreshed immediately after initial ontology setup | |
| # ============================================================================ | |
| repository_dispatch: | |
| types: [trigger-refresh-imports] | |
| # ============================================================================ | |
| # TRIGGER 2: Push Events (for regular development) | |
| # ============================================================================ | |
| # Triggers when import-related files are modified and pushed | |
| # | |
| # Monitored paths: | |
| # - src/ontology/imports/** : Import module definitions and OWL files | |
| # - src/ontology/*-edit.owl : Main edit file (may contain import declarations) | |
| # | |
| # Why these paths? | |
| # - Changes to import definitions require re-fetching external ontology terms | |
| # - Edit file changes may add/remove imports that need processing | |
| # | |
| # Note: This trigger is skipped for commits made by github-actions[bot] | |
| # to prevent duplicate runs when triggered via repository_dispatch | |
| # ============================================================================ | |
| push: | |
| branches: ["main"] # Triggers only on main branch | |
| paths: | |
| # - 'src/ontology/imports/**' | |
| # - 'src/ontology/*-edit.owl' | |
| - 'src/ontology/**' | |
| # ============================================================================ | |
| # TRIGGER 3: Pull Request Events (for PR validation) | |
| # ============================================================================ | |
| # Same as push trigger, but for pull requests | |
| # Allows validation of import changes during code review | |
| # Note: Commits are skipped for PRs (see commit step conditions) | |
| # ============================================================================ | |
| pull_request: | |
| branches: ["main"] | |
| paths: | |
| # - 'src/ontology/imports/**' | |
| # - 'src/ontology/*-edit.owl' | |
| - 'src/ontology/**' | |
| # ============================================================================ | |
| # TRIGGER 4: Manual Trigger (for forced refresh) | |
| # ============================================================================ | |
| # Allows manual execution via GitHub UI | |
| # Useful for: | |
| # - Testing import refresh without code changes | |
| # - Forcing refresh after upstream ontology updates | |
| # - Troubleshooting import issues | |
| # ============================================================================ | |
| workflow_dispatch: | |
| # ============================================================================== | |
| # ENVIRONMENT VARIABLES | |
| # ============================================================================== | |
| # Global variables available to all jobs in this workflow | |
| # ============================================================================== | |
| env: | |
| # Default branch for git operations (used in some ODK make targets) | |
| DEFAULT_BRANCH: main | |
| # ============================================================================== | |
| # JOBS | |
| # ============================================================================== | |
| jobs: | |
| # ============================================================================ | |
| # JOB 1: check-ontology-dir | |
| # ============================================================================ | |
| # Pre-flight check to verify ontology directory exists | |
| # | |
| # Purpose: Prevents workflow failure in empty/misconfigured repositories | |
| # - Runs before main job (cheap safety check) | |
| # - Outputs boolean flag for conditional job execution | |
| # - Skips entire workflow if src/ontology/ doesn't exist | |
| # | |
| # Additional check: Skips workflow for bot commits on push events | |
| # - Prevents duplicate runs when workflow chain is active | |
| # - Bot commits happen when workflows commit their outputs | |
| # - Repository dispatch handles the workflow chain progression | |
| # ============================================================================ | |
| check-ontology-dir: | |
| runs-on: ubuntu-latest | |
| # CRITICAL: Skip this workflow if triggered by push from github-actions[bot] | |
| # This prevents duplicate runs in the workflow chain | |
| # The chain uses repository_dispatch, so push triggers from bot commits are redundant | |
| if: | | |
| github.event_name != 'push' || | |
| github.event.head_commit.author.name != 'github-actions[bot]' | |
| # Job outputs (available to dependent jobs via needs.check-ontology-dir.outputs) | |
| outputs: | |
| dir-exists: ${{ steps.check.outputs.exists }} | |
| steps: | |
| # ======================================================================== | |
| # STEP 1.1: Checkout Repository | |
| # ======================================================================== | |
| # Fetch repository code for directory check | |
| # Lightweight checkout (no full history needed for directory check) | |
| # ======================================================================== | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| # ======================================================================== | |
| # STEP 1.2: Check for Ontology Directory | |
| # ======================================================================== | |
| # Verifies src/ontology/ exists and sets output flag | |
| # ======================================================================== | |
| - name: Check for ontology directory | |
| id: check | |
| run: | | |
| if [ -d "src/ontology" ]; then | |
| echo "Ontology directory found." | |
| echo "exists=true" >> $GITHUB_OUTPUT | |
| else | |
| echo "No src/ontology directory found; skipping workflow." | |
| echo "exists=false" >> $GITHUB_OUTPUT | |
| fi | |
| # ============================================================================ | |
| # JOB 2: refresh-imports | |
| # ============================================================================ | |
| # Main job that performs import refresh operations | |
| # | |
| # Dependencies: Requires check-ontology-dir to pass | |
| # Condition: Only runs if src/ontology/ directory exists | |
| # Container: ODK full image with all necessary tools | |
| # ============================================================================ | |
| refresh-imports: | |
| runs-on: ubuntu-latest | |
| # Grant write permissions for committing updated imports | |
| permissions: | |
| contents: write | |
| # Job dependencies | |
| needs: check-ontology-dir | |
| # Conditional execution: only run if directory exists | |
| if: needs.check-ontology-dir.outputs.dir-exists == 'true' | |
| # Use ODK container for consistent tooling environment | |
| # Version v1.6 pinned for reproducibility | |
| # Includes: ROBOT, OWLTools, make, Java, Python | |
| container: obolibrary/odkfull:v1.6 | |
| steps: | |
| # ======================================================================== | |
| # STEP 2.1: Checkout Repository | |
| # ======================================================================== | |
| # Fetch complete repository with full git history | |
| # | |
| # Why fetch-depth: 0? | |
| # - Full history may be needed for ODK make targets | |
| # - Allows git operations that reference commits/branches | |
| # - Required for accurate import mirroring | |
| # ======================================================================== | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Full history | |
| # ======================================================================== | |
| # STEP 2.2: Refresh Imports via ODK | |
| # ======================================================================== | |
| # Runs ODK make targets to update external ontology import modules | |
| # | |
| # Process: | |
| # 1. Attempt standard refresh-imports target (most common) | |
| # 2. If that fails, try per-import refresh (fallback for custom setups) | |
| # | |
| # Make variables: | |
| # - IMP=true : Enable import module generation | |
| # - MIR=true : Enable mirror mode (local caching of external ontologies) | |
| # - PAT=false : Disable patient profile generation (if applicable) | |
| # - -B : Force rebuild (treats all targets as needing update) | |
| # | |
| # What this does: | |
| # - Downloads latest versions of external ontologies | |
| # - Extracts only needed terms (defined in imports/*_terms.txt) | |
| # - Generates import module OWL files (imports/*_import.owl) | |
| # - Caches external ontologies locally (mirror/ directory) | |
| # | |
| # Fallback logic: | |
| # If refresh-imports target doesn't exist in Makefile, attempts to | |
| # refresh specific import files directly (e.g., imports/pmdco_import.owl) | |
| # ======================================================================== | |
| - name: Refresh imports via ODK | |
| working-directory: src/ontology | |
| run: | | |
| # ===== OPTION A: Standard Refresh Target ===== | |
| # Most ODK repositories have a refresh-imports target | |
| # This target processes all imports defined in *-odk.yaml | |
| echo "Attempting standard refresh-imports target..." | |
| make IMP=true MIR=true PAT=false refresh-imports -B || { | |
| echo "Standard refresh-imports target not found or failed." | |
| echo "Attempting per-import refresh (fallback)..." | |
| # ===== OPTION B: Per-Import Refresh (Fallback) ===== | |
| # If standard target fails, try refreshing specific imports | |
| # Customize this section based on your ontology's imports | |
| # Example: imports/pmdco_import.owl | |
| # | |
| # To find your import targets, check: | |
| # 1. src/ontology/imports/ directory | |
| # 2. project-odk.yaml import_group section | |
| # 3. src/ontology/Makefile IMPORTS variable | |
| make IMP=true MIR=true PAT=false imports/pmdco_import.owl -B || \ | |
| echo "Specific import target failed; no changes needed" | |
| } | |
| echo "Import refresh complete." | |
| # ======================================================================== | |
| # STEP 2.3: Commit Updated Imports | |
| # ======================================================================== | |
| # Commits refreshed import files back to the repository | |
| # | |
| # Conditions: | |
| # - Only runs for push/dispatch events (not pull requests) | |
| # - Only commits if changes detected (action skips empty commits) | |
| # | |
| # What gets committed: | |
| # - src/ontology/imports/*.owl : Updated import module files | |
| # | |
| # Why --force flag? | |
| # - Import OWL files are often in .gitignore | |
| # - --force overrides gitignore rules for these specific files | |
| # - Ensures generated imports are tracked in version control | |
| # | |
| # Commit metadata: | |
| # - Message: Descriptive message indicating automated refresh | |
| # - Author: github-actions[bot] (distinguishes from human commits) | |
| # ======================================================================== | |
| - name: Commit updated imports | |
| # Skip commits for pull requests (review changes manually in PR) | |
| if: github.event_name != 'pull_request' | |
| uses: EndBug/add-and-commit@v9 | |
| with: | |
| # Descriptive commit message for git history | |
| message: "Refresh imports via ODK" | |
| # Working directory (repository root) | |
| cwd: "." | |
| # Add only import OWL files, forcing inclusion despite .gitignore | |
| add: "src/ontology/imports/*.owl --force" | |
| # Use GitHub Actions bot as commit author | |
| default_author: github_actions | |
| # Push to current branch | |
| push: true | |
| # ======================================================================== | |
| # STEP 2.4: Trigger Next Workflow (QC) | |
| # ======================================================================== | |
| # Dispatches repository event to start the QC workflow | |
| # | |
| # Workflow Chain: | |
| # setup-repo → refresh-imports → [QC] → docs | |
| # | |
| # Why repository_dispatch? | |
| # - Allows explicit workflow chaining | |
| # - Maintains clear separation between workflow stages | |
| # - Prevents race conditions with concurrent triggers | |
| # | |
| # Condition: Only trigger for non-PR events (PRs don't auto-deploy) | |
| # | |
| # Event type: trigger-qc | |
| # Listened for by: qc.yml | |
| # ======================================================================== | |
| - name: Trigger QC Workflow | |
| # Skip for pull requests (QC will run via push trigger after PR merge) | |
| if: github.event_name != 'pull_request' | |
| uses: peter-evans/repository-dispatch@v3 | |
| with: | |
| # Use default GitHub token (automatically available) | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| # Event name that qc.yml listens for | |
| event-type: trigger-qc |