lint_sqlfluff.yml

name: SQLFluff

on:
  - pull_request

jobs:
  lint-mimic-iv:
    runs-on: ubuntu-latest
    steps:
      - name: checkout
        uses: actions/checkout@v4
      - name: Install Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.12"
      - name: install sqlfluff
        run: "pip install sqlfluff==3.5.0"
      - name: Get changed files
        id: get_file_changes
        uses: trilom/file-changes-action@v1.2.4
        with:
          output: ' '
      - name: Get changed .sql files in mimic-iv concepts folder
        id: get_files_to_lint
        shell: bash
        run: |
          # Compose list of changed SQL files under mimic-iv/concepts and export to step output
          raw="${{ steps.get_file_changes.outputs.files_modified }} ${{ steps.get_file_changes.outputs.files_added }}"
          # Check for mimic-iv SQL files which may have changed
          filtered="$(printf '%s' "$raw" | tr -s ' ' '\n' | grep -E '^mimic-iv/concepts/.*[.]sql$' || true)"
          # Turn this into a space separated list for the next step
          files="$(printf '%s' "$filtered" | tr -s '\n' ' ')"
          echo "lintees=${files}" >> "$GITHUB_OUTPUT"

      - name: Lint SQL files
        id: sqlfluff_json
        if: steps.get_files_to_lint.outputs.lintees != ''
        shell: bash
        run: sqlfluff lint --format github-annotation --annotation-level failure --nofail ${{ steps.get_files_to_lint.outputs.lintees }} > annotations.json
      - name: Annotate
        uses: yuzutech/annotations-action@v0.5.0
        with:
          repo-token: "${{ secrets.GITHUB_TOKEN }}"
          title: "SQLFluff Lint"
          input: "./annotations.json"