Adding data preprocessing code for ITQM 2023 paper "Generation of Radiology Findings in Chest X-Ray by Leveraging Collaborative Knowledge" #61

	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/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 -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 ${{ steps.get_files_to_lint.outputs.lintees }} > annotations.json
	- name: Annotate
	uses: yuzutech/annotations-action@v0.3.0
	with:
	repo-token: "${{ secrets.GITHUB_TOKEN }}"
	title: "SQLFluff Lint"
	input: "./annotations.json"

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