diff --git a/.github/workflows/lint_sqlfluff.yml b/.github/workflows/lint_sqlfluff.yml index 0986785b..0b338395 100644 --- a/.github/workflows/lint_sqlfluff.yml +++ b/.github/workflows/lint_sqlfluff.yml @@ -35,8 +35,12 @@ jobs: shell: bash run: sqlfluff lint --format github-annotation --annotation-level failure --nofail ${{ steps.get_files_to_lint.outputs.lintees }} > annotations.json - name: Annotate + # Fork PRs cannot create check runs with GITHUB_TOKEN; lint already ran. + continue-on-error: true + if: steps.get_files_to_lint.outputs.lintees != '' uses: yuzutech/annotations-action@v0.6.0 with: repo-token: "${{ secrets.GITHUB_TOKEN }}" title: "SQLFluff Lint" - input: "./annotations.json" \ No newline at end of file + input: "./annotations.json" + ignore-missing-file: true diff --git a/mimic-iv/concepts/score/oasis.sql b/mimic-iv/concepts/score/oasis.sql index 2add3b93..bc2ec87d 100644 --- a/mimic-iv/concepts/score/oasis.sql +++ b/mimic-iv/concepts/score/oasis.sql @@ -89,7 +89,9 @@ WITH surgflag AS ( , uo.urineoutput , CASE - WHEN adm.admission_type = 'ELECTIVE' AND sf.surgical = 1 + WHEN adm.admission_type IN ( + 'ELECTIVE', 'SURGICAL SAME DAY ADMISSION' + ) AND sf.surgical = 1 THEN 1 WHEN adm.admission_type IS NULL OR sf.surgical IS NULL THEN NULL diff --git a/mimic-iv/concepts/score/sapsii.sql b/mimic-iv/concepts/score/sapsii.sql index 08902658..3f6c3f9a 100644 --- a/mimic-iv/concepts/score/sapsii.sql +++ b/mimic-iv/concepts/score/sapsii.sql @@ -326,9 +326,13 @@ WITH co AS ( , comorb.mets , CASE - WHEN adm.admission_type = 'ELECTIVE' AND sf.surgical = 1 + WHEN adm.admission_type IN ( + 'ELECTIVE', 'SURGICAL SAME DAY ADMISSION' + ) AND sf.surgical = 1 THEN 'ScheduledSurgical' - WHEN adm.admission_type != 'ELECTIVE' AND sf.surgical = 1 + WHEN adm.admission_type NOT IN ( + 'ELECTIVE', 'SURGICAL SAME DAY ADMISSION' + ) AND sf.surgical = 1 THEN 'UnscheduledSurgical' ELSE 'Medical' END AS admissiontype diff --git a/mimic-iv/concepts_duckdb/score/oasis.sql b/mimic-iv/concepts_duckdb/score/oasis.sql index 8b5f8f3b..dd11728a 100644 --- a/mimic-iv/concepts_duckdb/score/oasis.sql +++ b/mimic-iv/concepts_duckdb/score/oasis.sql @@ -60,7 +60,9 @@ WITH surgflag AS ( vent.vent AS mechvent, uo.urineoutput, CASE - WHEN adm.admission_type = 'ELECTIVE' AND sf.surgical = 1 + WHEN adm.admission_type IN ( + 'ELECTIVE', 'SURGICAL SAME DAY ADMISSION' + ) AND sf.surgical = 1 THEN 1 WHEN adm.admission_type IS NULL OR sf.surgical IS NULL THEN NULL diff --git a/mimic-iv/concepts_duckdb/score/sapsii.sql b/mimic-iv/concepts_duckdb/score/sapsii.sql index 0ec63dfb..f0cf7c62 100644 --- a/mimic-iv/concepts_duckdb/score/sapsii.sql +++ b/mimic-iv/concepts_duckdb/score/sapsii.sql @@ -254,9 +254,13 @@ WITH co AS ( comorb.hem, comorb.mets, CASE - WHEN adm.admission_type = 'ELECTIVE' AND sf.surgical = 1 + WHEN adm.admission_type IN ( + 'ELECTIVE', 'SURGICAL SAME DAY ADMISSION' + ) AND sf.surgical = 1 THEN 'ScheduledSurgical' - WHEN adm.admission_type <> 'ELECTIVE' AND sf.surgical = 1 + WHEN adm.admission_type NOT IN ( + 'ELECTIVE', 'SURGICAL SAME DAY ADMISSION' + ) AND sf.surgical = 1 THEN 'UnscheduledSurgical' ELSE 'Medical' END AS admissiontype diff --git a/mimic-iv/concepts_postgres/score/oasis.sql b/mimic-iv/concepts_postgres/score/oasis.sql index e1e680f6..f8a127b5 100644 --- a/mimic-iv/concepts_postgres/score/oasis.sql +++ b/mimic-iv/concepts_postgres/score/oasis.sql @@ -61,7 +61,9 @@ WITH surgflag AS ( vent.vent AS mechvent, uo.urineoutput, CASE - WHEN adm.admission_type = 'ELECTIVE' AND sf.surgical = 1 + WHEN adm.admission_type IN ( + 'ELECTIVE', 'SURGICAL SAME DAY ADMISSION' + ) AND sf.surgical = 1 THEN 1 WHEN adm.admission_type IS NULL OR sf.surgical IS NULL THEN NULL diff --git a/mimic-iv/concepts_postgres/score/sapsii.sql b/mimic-iv/concepts_postgres/score/sapsii.sql index 3daf3794..87cf8043 100644 --- a/mimic-iv/concepts_postgres/score/sapsii.sql +++ b/mimic-iv/concepts_postgres/score/sapsii.sql @@ -249,9 +249,13 @@ WITH co AS ( comorb.hem, comorb.mets, CASE - WHEN adm.admission_type = 'ELECTIVE' AND sf.surgical = 1 + WHEN adm.admission_type IN ( + 'ELECTIVE', 'SURGICAL SAME DAY ADMISSION' + ) AND sf.surgical = 1 THEN 'ScheduledSurgical' - WHEN adm.admission_type <> 'ELECTIVE' AND sf.surgical = 1 + WHEN adm.admission_type NOT IN ( + 'ELECTIVE', 'SURGICAL SAME DAY ADMISSION' + ) AND sf.surgical = 1 THEN 'UnscheduledSurgical' ELSE 'Medical' END AS admissiontype