Merge pull request #498 from Raphael-Gazzotti/update-uberon-terms #269
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| name: Autopopulation | ||
| # Run the job if a PR was merged or a push occurred on main | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| permissions: | ||
| contents: write | ||
| jobs: | ||
| sync-instances: | ||
| if: github.repository == 'openMetadataInitiative/openMINDS_instances' && ${{ !contains(github.event.head_commit.message, '[ci skip-autopopulate]') }} | ||
|
Check warning on line 14 in .github/workflows/autopopulation.yml
|
||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| fetch-depth: 0 # Fetch full history for accurate diff comparisons | ||
| token: ${{ secrets.GITHUB_TOKEN }} | ||
| - name: Set up Python | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: '3.13' | ||
| - name: Process and Sync Changes in instance Files | ||
| id: process_sync_instances | ||
| run: | | ||
| # Identify modified or added .jsonld files | ||
| # Store them in changed_files.txt (fallback to true to prevent pipeline failure) | ||
| git checkout HEAD | ||
| git diff --name-only --diff-filter=AM HEAD^ HEAD | grep '\.jsonld$' > changed_files.txt || true | ||
| declare -A modified_jsons | ||
| declare -A file_versions | ||
| declare -A skip_files | ||
| # Process the list of changed .jsonld files | ||
| if [ -s changed_files.txt ]; then | ||
| while IFS= read -r file; do | ||
| FILE_MODULE=$(dirname "$file" | cut -d'/' -f3-) | ||
| FILE_NAME=$(basename "$file") | ||
| MODULE_NAME="$FILE_MODULE/$FILE_NAME" | ||
| FILE_VERSION=$(echo "$file" | cut -d'/' -f2) | ||
| # If the file appears in multiple versions on push, mark it for skipping | ||
| if [[ -n "${file_versions[$MODULE_NAME]}" ]]; then | ||
| skip_files[$MODULE_NAME]=1 | ||
| echo "Skipping all versions of $MODULE_NAME due to multiple versions detected." | ||
| # Store eligible .jsonld files for instance generation | ||
| else | ||
| file_versions[$MODULE_NAME]="$FILE_VERSION" | ||
| modified_jsons["$file"]="$FILE_VERSION" | ||
| fi | ||
| done < changed_files.txt | ||
| fi | ||
| # Process eligible .jsonld files for instance generation | ||
| if [ ${#modified_jsons[@]} -gt 0 ]; then | ||
| MAIN_FOLDER="instances" | ||
| # Fetch reference files required for instance generation | ||
| wget https://raw.githubusercontent.com/openMetadataInitiative/openMINDS/refs/heads/main/vocab/types.json -P .github/ | ||
| wget https://raw.githubusercontent.com/openMetadataInitiative/openMINDS/refs/heads/main/vocab/properties.json -P .github/ | ||
| wget https://raw.githubusercontent.com/openMetadataInitiative/openMINDS/refs/heads/pipeline/versions.json -P .github/ | ||
| # Loop through each modified .jsonld file | ||
| for FILE in "${!modified_jsons[@]}"; do | ||
| FILE_MODULE=$(dirname "$FILE" | cut -d'/' -f3-) | ||
| FILE_NAME=$(basename "$FILE") | ||
| MODULE_NAME="$FILE_MODULE/$FILE_NAME" | ||
| # Skip generation if marked for skipping | ||
| if [[ -n "${skip_files[$MODULE_NAME]}" ]]; then | ||
| echo "Skipping generation for $MODULE_NAME due to multiple versions in a merged PR/push." | ||
| continue | ||
| fi | ||
| # Retrieve version where the .jsonld file is located | ||
| FILE_VERSION="${modified_jsons[$FILE]}" | ||
| # Iterate over existing versions in the instances directory | ||
| for VERSION in $(ls "$MAIN_FOLDER"); do | ||
| if [ "$VERSION" != "$FILE_VERSION" ]; then | ||
| TARGET_FILE="$MAIN_FOLDER/$VERSION/$FILE_MODULE/$FILE_NAME" | ||
| TOP_LEVEL_DIR=$(echo "$FILE_MODULE" | cut -d'/' -f1) | ||
| # Target file does not exist in instances/VERSION/terminologies/terminology | ||
| if [[ "$FILE_MODULE" == "terminologies/terminology" ]] && [[ ! -e "$TARGET_FILE" ]]; then | ||
| echo "Skipping $TARGET_FILE: terminology file does not exist in $VERSION." | ||
| # Folder does not exist in instances/VERSION/terminologies/ | ||
| elif [[ "$FILE_MODULE" == terminologies/* ]] && [[ ! -d "$MAIN_FOLDER/$VERSION/$FILE_MODULE/" ]]; then | ||
| echo "Skipping $FILE_MODULE: folder does not exist in $VERSION." | ||
| # Top-level folder exists in instances/VERSION/ | ||
| elif [ -d "$MAIN_FOLDER/$VERSION/$TOP_LEVEL_DIR/" ]; then | ||
| mkdir -p "$MAIN_FOLDER/$VERSION/$FILE_MODULE/" | ||
| echo "Generating instance from $FILE to $TARGET_FILE." | ||
| python .github/scripts/sync_instances.py "$FILE" "$TARGET_FILE" "$VERSION" | ||
| # Top-level folder not in instances/VERSION/ | ||
| else | ||
| echo "Skipping $FILE_MODULE: top-level folder does not exist in $VERSION." | ||
| fi | ||
| fi | ||
| done | ||
| done | ||
| # Commit changes if any instances were modified | ||
| git config --global user.name "openMINDS pipeline" | ||
| git config --global user.email "support@openmetadatainitiative.org" | ||
| git add $MAIN_FOLDER/**/*.jsonld | ||
| git commit -m "Autopopulation of instance file." | ||
| git pull --rebase origin main | ||
| git push origin HEAD:main | ||
| else | ||
| echo "No JSON-LD files modified." | ||
| fi | ||
| shell: bash | ||
