update tcga pathway results based on integrated assoication analysis #84
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Data Directory Audit | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| # Allow manual triggering | |
| workflow_dispatch: | |
| permissions: | |
| contents: write # needed for issues.create | |
| issues: write # needed for issues.create and issues.createComment | |
| jobs: | |
| check-data-directories: | |
| name: Check for committed data files | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| # TODO:: this whole markdown that gets generated is verbose to have in this github action | |
| # We should consider moving this to a jinja template that gets rendered | |
| # with variables passed in from the action | |
| - name: Check for data files in protected directories | |
| id: data-check | |
| run: | | |
| echo "Checking for committed data files in protected directories..." | |
| # Define the directories to check | |
| PROTECTED_DIRS=("data/rawdata" "data/procdata" "data/results") | |
| FOUND_FILES=0 | |
| # Create a detailed markdown report | |
| echo "# Data Directory Audit Report" > data_audit.md | |
| echo "" >> data_audit.md | |
| echo "⚠️ Data files have been detected in protected directories that should not be committed to Git. ⚠️" >> data_audit.md | |
| echo "" >> data_audit.md | |
| echo "## Detected Files" >> data_audit.md | |
| echo "" >> data_audit.md | |
| for DIR in "${PROTECTED_DIRS[@]}"; do | |
| # Check if the directory exists | |
| if [ -d "$DIR" ]; then | |
| # Get a list of all files in the directory, excluding README.md and .gitignore | |
| FILE_LIST=$(find "$DIR" -type f -not -name "README.md" -not -name ".gitignore") | |
| FILE_COUNT=$(echo "$FILE_LIST" | grep -v "^$" | wc -l) | |
| if [ "$FILE_COUNT" -gt 0 ]; then | |
| echo "::warning::Found $FILE_COUNT files in $DIR directory!" | |
| echo "### $DIR" >> data_audit.md | |
| echo "" >> data_audit.md | |
| echo "Found $FILE_COUNT file(s):" >> data_audit.md | |
| echo "" >> data_audit.md | |
| echo '```' >> data_audit.md | |
| echo "$FILE_LIST" >> data_audit.md | |
| echo '```' >> data_audit.md | |
| echo "" >> data_audit.md | |
| FOUND_FILES=$((FOUND_FILES + FILE_COUNT)) | |
| else | |
| echo "✅ No data files found in $DIR" | |
| fi | |
| else | |
| echo "Directory $DIR not found, skipping check." | |
| fi | |
| done | |
| if [ "$FOUND_FILES" -gt 0 ]; then | |
| echo "## Recommended Actions" >> data_audit.md | |
| echo "" >> data_audit.md | |
| echo "1. Remove these files from the repository using git commands" >> data_audit.md | |
| echo "2. Add them to your .gitignore file" >> data_audit.md | |
| echo "3. Document data sources in docs/data_sources.md" >> data_audit.md | |
| echo "" >> data_audit.md | |
| echo "**Remember:** Data files should never be committed to Git. See the README files in data directories for proper data management guidelines." >> data_audit.md | |
| echo "" >> data_audit.md | |
| echo "For detailed instructions on how to properly ignore data files, visit:" >> data_audit.md | |
| echo "https://bhklab.github.io/bhklab-project-template/gitignore/" >> data_audit.md | |
| echo "FOUND_DATA_FILES=true" >> $GITHUB_ENV | |
| echo "FOUND_FILE_COUNT=$FOUND_FILES" >> $GITHUB_ENV | |
| echo "::error::Found $FOUND_FILES total files in protected data directories!" | |
| cat data_audit.md | |
| else | |
| echo "✅ All protected data directories are clean (only contain README.md and .gitignore files)" | |
| echo "FOUND_DATA_FILES=false" >> $GITHUB_ENV | |
| fi | |
| # If this is a pull request and we found data files, comment on the PR | |
| - name: Comment on Pull Request | |
| if: github.event_name == 'pull_request' && env.FOUND_DATA_FILES == 'true' | |
| uses: actions/github-script@v6 | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| script: | | |
| const fs = require('fs'); | |
| const reportContent = fs.readFileSync('data_audit.md', 'utf8'); | |
| await github.rest.issues.createComment({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| issue_number: context.issue.number, | |
| body: reportContent | |
| }); | |
| # If this is a push to main and we found data files, create an issue | |
| - name: Create Issue for Data Files | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/main' && env.FOUND_DATA_FILES == 'true' | |
| uses: actions/github-script@v6 | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| script: | | |
| const fs = require('fs'); | |
| const reportContent = fs.readFileSync('data_audit.md', 'utf8'); | |
| await github.rest.issues.create({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| title: `🚨 Data files detected in protected directories: ${process.env.FOUND_FILE_COUNT} files`, | |
| body: reportContent, | |
| labels: ['data-management', 'needs-attention'] | |
| }); |