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/sirs.sql b/mimic-iii/concepts/severityscores/sirs.sql index 9de5bcff..32a171ac 100644 --- a/mimic-iii/concepts/severityscores/sirs.sql +++ b/mimic-iii/concepts/severityscores/sirs.sql @@ -89,7 +89,7 @@ left join `physionet-data.mimiciii_derived.labs_first_day` l when wbc_min < 4.0 then 1 when wbc_max > 12.0 then 1 when bands_max > 10 then 1-- > 10% immature neurophils (band forms) - when coalesce(wbc_min, bands_max) is null then null + when coalesce(wbc_min, wbc_max, bands_max) is null then null else 0 end as wbc_score diff --git a/mimic-iii/concepts_duckdb/severityscores/sirs.sql b/mimic-iii/concepts_duckdb/severityscores/sirs.sql index 5a449b75..289ba2f3 100644 --- a/mimic-iii/concepts_duckdb/severityscores/sirs.sql +++ b/mimic-iii/concepts_duckdb/severityscores/sirs.sql @@ -56,7 +56,7 @@ WITH bg AS ( THEN 1 WHEN bands_max > 10 THEN 1 - WHEN COALESCE(wbc_min, bands_max) IS NULL + WHEN COALESCE(wbc_min, wbc_max, bands_max) IS NULL THEN NULL ELSE 0 END AS wbc_score diff --git a/mimic-iii/concepts_postgres/severityscores/sirs.sql b/mimic-iii/concepts_postgres/severityscores/sirs.sql index 1a34cc28..7c370c25 100644 --- a/mimic-iii/concepts_postgres/severityscores/sirs.sql +++ b/mimic-iii/concepts_postgres/severityscores/sirs.sql @@ -59,7 +59,7 @@ WITH bg AS ( THEN 1 WHEN bands_max > 10 THEN 1 /* > 10% immature neurophils (band forms) */ - WHEN COALESCE(wbc_min, bands_max) IS NULL + WHEN COALESCE(wbc_min, wbc_max, bands_max) IS NULL THEN NULL ELSE 0 END AS wbc_score diff --git a/mimic-iv/concepts/score/sirs.sql b/mimic-iv/concepts/score/sirs.sql index ca4a933e..40ae266b 100644 --- a/mimic-iv/concepts/score/sirs.sql +++ b/mimic-iv/concepts/score/sirs.sql @@ -77,7 +77,7 @@ WITH scorecomp AS ( WHEN wbc_min < 4.0 THEN 1 WHEN wbc_max > 12.0 THEN 1 WHEN bands_max > 10 THEN 1-- > 10% immature neurophils (band forms) - WHEN COALESCE(wbc_min, bands_max) IS NULL THEN NULL + WHEN COALESCE(wbc_min, wbc_max, bands_max) IS NULL THEN NULL ELSE 0 END AS wbc_score diff --git a/mimic-iv/concepts_duckdb/score/sirs.sql b/mimic-iv/concepts_duckdb/score/sirs.sql index a806e7c7..43e55784 100644 --- a/mimic-iv/concepts_duckdb/score/sirs.sql +++ b/mimic-iv/concepts_duckdb/score/sirs.sql @@ -53,7 +53,7 @@ WITH scorecomp AS ( THEN 1 WHEN bands_max > 10 THEN 1 - WHEN COALESCE(wbc_min, bands_max) IS NULL + WHEN COALESCE(wbc_min, wbc_max, bands_max) IS NULL THEN NULL ELSE 0 END AS wbc_score diff --git a/mimic-iv/concepts_postgres/score/sirs.sql b/mimic-iv/concepts_postgres/score/sirs.sql index b1b28667..65578a77 100644 --- a/mimic-iv/concepts_postgres/score/sirs.sql +++ b/mimic-iv/concepts_postgres/score/sirs.sql @@ -55,7 +55,7 @@ WITH scorecomp AS ( THEN 1 WHEN bands_max > 10 THEN 1 /* > 10% immature neurophils (band forms) */ - WHEN COALESCE(wbc_min, bands_max) IS NULL + WHEN COALESCE(wbc_min, wbc_max, bands_max) IS NULL THEN NULL ELSE 0 END AS wbc_score