daily fluid balance implementation #54
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| name: SQLFluff | |
| on: | |
| - pull_request | |
| jobs: | |
| lint-mimic-iv: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v3 | |
| - name: Install Python | |
| uses: "actions/setup-python@v2" | |
| with: | |
| python-version: "3.7" | |
| - name: install sqlfluff | |
| run: "pip install sqlfluff==1.4.5" | |
| - name: Get changed files | |
| id: get_file_changes | |
| uses: trilom/[email protected] | |
| with: | |
| output: ' ' | |
| - name: Get changed .sql files in mimic-iv concepts folder | |
| id: get_files_to_lint | |
| shell: bash -l {0} | |
| run: | | |
| # Set the command in the $() brackets as an output to use in later steps | |
| echo "lintees=$( | |
| echo \ | |
| $(echo ${{ steps.get_file_changes.outputs.files_modified }} | | |
| tr -s ' ' '\n' | | |
| grep -E '^mimic-iv/concepts/.*[.]sql$' | | |
| tr -s '\n' ' ') \ | |
| $(echo ${{ steps.get_file_changes.outputs.files_added }} | | |
| tr -s ' ' '\n' | | |
| grep -E '^mimic-iv/concepts/.*[.]sql$' | | |
| tr -s '\n' ' ') | |
| ) >> $GITHUB_OUTPUT" | |
| - name: Lint SQL files | |
| id: sqlfluff_json | |
| if: steps.get_files_to_lint.outputs.lintees != '' | |
| shell: bash -l {0} | |
| run: sqlfluff lint --format github-annotation --annotation-level failure --nofail ${{ steps.get_files_to_lint.outputs.lintees }} > annotations.json | |
| - name: Annotate | |
| uses: yuzutech/[email protected] | |
| with: | |
| repo-token: "${{ secrets.GITHUB_TOKEN }}" | |
| title: "SQLFluff Lint" | |
| input: "./annotations.json" |