diff --git a/.github/workflows/lint_sqlfluff.yml b/.github/workflows/lint_sqlfluff.yml index 0986785b..d6e1c3f0 100644 --- a/.github/workflows/lint_sqlfluff.yml +++ b/.github/workflows/lint_sqlfluff.yml @@ -1,11 +1,17 @@ name: SQLFluff +# Lints changed mimic-iv/concepts/*.sql on pull requests and posts GitHub +# annotations. Fork PRs skip Annotate — GITHUB_TOKEN cannot create check runs +# from forks (Resource not accessible by integration / 403). on: - pull_request jobs: lint-mimic-iv: runs-on: ubuntu-latest + permissions: + contents: read + checks: write steps: - name: checkout uses: actions/checkout@v7 @@ -35,8 +41,14 @@ jobs: shell: bash run: sqlfluff lint --format github-annotation --annotation-level failure --nofail ${{ steps.get_files_to_lint.outputs.lintees }} > annotations.json - name: Annotate + # Same-repo PRs only: fork tokens get 403 creating check runs, and + # ignore-unauthorized-error does not treat that as unauthorized. + if: > + steps.get_files_to_lint.outputs.lintees != '' && + github.event.pull_request.head.repo.full_name == github.repository uses: yuzutech/annotations-action@v0.6.0 with: repo-token: "${{ secrets.GITHUB_TOKEN }}" title: "SQLFluff Lint" - input: "./annotations.json" \ No newline at end of file + input: "./annotations.json" + ignore-unauthorized-error: true diff --git a/mimic-iii/concepts/severityscores/lods.sql b/mimic-iii/concepts/severityscores/lods.sql index b5c3a7cb..bdb640ca 100644 --- a/mimic-iii/concepts/severityscores/lods.sql +++ b/mimic-iii/concepts/severityscores/lods.sql @@ -134,7 +134,7 @@ left join `physionet-data.mimiciii_derived.labs_first_day` labs ( select cohort.* - -- Below code calculates the component scores needed for SAPS + -- Below code calculates the component scores needed for LODS -- neurologic , case diff --git a/mimic-iii/concepts_postgres/severityscores/lods.sql b/mimic-iii/concepts_postgres/severityscores/lods.sql index 55422d67..a879dfdb 100644 --- a/mimic-iii/concepts_postgres/severityscores/lods.sql +++ b/mimic-iii/concepts_postgres/severityscores/lods.sql @@ -102,7 +102,7 @@ WITH cpap AS ( ON ie.icustay_id = labs.icustay_id ), scorecomp AS ( SELECT - cohort.*, /* Below code calculates the component scores needed for SAPS */ /* neurologic */ + cohort.*, /* Below code calculates the component scores needed for LODS */ /* neurologic */ CASE WHEN mingcs IS NULL THEN NULL diff --git a/mimic-iv/concepts/score/lods.sql b/mimic-iv/concepts/score/lods.sql index bc105402..f6c74ba3 100644 --- a/mimic-iv/concepts/score/lods.sql +++ b/mimic-iv/concepts/score/lods.sql @@ -128,7 +128,7 @@ WITH cpap AS ( , scorecomp AS ( SELECT cohort.* - -- Below code calculates the component scores needed for SAPS + -- Below code calculates the component scores needed for LODS -- neurologic , CASE diff --git a/mimic-iv/concepts_postgres/score/lods.sql b/mimic-iv/concepts_postgres/score/lods.sql index db27acc2..edaa0c74 100644 --- a/mimic-iv/concepts_postgres/score/lods.sql +++ b/mimic-iv/concepts_postgres/score/lods.sql @@ -101,7 +101,7 @@ WITH cpap AS ( ON ie.stay_id = labs.stay_id ), scorecomp AS ( SELECT - cohort.*, /* Below code calculates the component scores needed for SAPS */ /* neurologic */ + cohort.*, /* Below code calculates the component scores needed for LODS */ /* neurologic */ CASE WHEN gcs_min IS NULL THEN NULL