fix(mimic-iv): exclude C4A from Charlson malignant_cancer mapping

.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"
+          input: "./annotations.json"
+          ignore-unauthorized-error: true

mimic-iv/concepts/comorbidity/charlson.sql

@@ -15,6 +15,12 @@
 -- (3) Quan H, Sundararajan V, Halfon P, et al. Coding algorithms for
 -- defining Comorbidities in ICD-9-CM and ICD-10 administrative data.
 -- Med Care. 2005 Nov; 43(11): 1130-9.
+--
+-- ICD-10-CM extensions (C4A, C7A, C7B) are not part of WHO ICD-10 and
+-- were not defined in Quan et al. (2005). The malignant_cancer mapping
+-- below follows Quan by excluding skin malignancy (C4A Merkel cell) and
+-- by not mapping C7A/C7B neuroendocrine categories, which fall outside
+-- the WHO ICD-10 code ranges used in the publication.
 -- ------------------------------------------------------------------
 
 WITH diag AS (
@@ -302,7 +308,12 @@ WITH diag AS (
             OR
             SUBSTR(icd10_code, 1, 3) BETWEEN 'C37' AND 'C41'
             OR
-            SUBSTR(icd10_code, 1, 3) BETWEEN 'C45' AND 'C58'
+            -- Split C45-C58 to exclude C4A (Merkel cell carcinoma), which
+            -- lexically falls inside BETWEEN 'C45' AND 'C58' but is skin
+            -- malignancy excluded by Quan et al. (2005).
+            SUBSTR(icd10_code, 1, 3) BETWEEN 'C45' AND 'C49'
+            OR
+            SUBSTR(icd10_code, 1, 3) BETWEEN 'C50' AND 'C58'
             OR
             SUBSTR(icd10_code, 1, 3) BETWEEN 'C60' AND 'C76'
             OR

mimic-iv/concepts_duckdb/comorbidity/charlson.sql

@@ -275,7 +275,8 @@ WITH diag AS (
         OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C00' AND 'C26'
         OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C30' AND 'C34'
         OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C37' AND 'C41'
-        OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C45' AND 'C58'
+        OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C45' AND 'C49'
+        OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C50' AND 'C58'
         OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C60' AND 'C76'
         OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C81' AND 'C85'
         OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C90' AND 'C97'

mimic-iv/concepts_postgres/comorbidity/charlson.sql

@@ -1,6 +1,6 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
 DROP TABLE IF EXISTS mimiciv_derived.charlson; CREATE TABLE mimiciv_derived.charlson AS
-/* ------------------------------------------------------------------ */ /* This query extracts Charlson Comorbidity Index (CCI) based on the */ /* recorded ICD-9 and ICD-10 codes. */ /* Reference for CCI: */ /* (1) Charlson ME, Pompei P, Ales KL, MacKenzie CR. (1987) A new method */ /* of classifying prognostic comorbidity in longitudinal studies: */ /* development and validation.J Chronic Dis; 40(5):373-83. */ /* (2) Charlson M, Szatrowski TP, Peterson J, Gold J. (1994) Validation */ /* of a combined comorbidity index. J Clin Epidemiol; 47(11):1245-51. */ /* */ /* Reference for ICD-9-CM and ICD-10 Coding Algorithms for Charlson */ /* Comorbidities: */ /* (3) Quan H, Sundararajan V, Halfon P, et al. Coding algorithms for */ /* defining Comorbidities in ICD-9-CM and ICD-10 administrative data. */ /* Med Care. 2005 Nov; 43(11): 1130-9. */ /* ------------------------------------------------------------------ */
+/* ------------------------------------------------------------------ */ /* This query extracts Charlson Comorbidity Index (CCI) based on the */ /* recorded ICD-9 and ICD-10 codes. */ /* Reference for CCI: */ /* (1) Charlson ME, Pompei P, Ales KL, MacKenzie CR. (1987) A new method */ /* of classifying prognostic comorbidity in longitudinal studies: */ /* development and validation.J Chronic Dis; 40(5):373-83. */ /* (2) Charlson M, Szatrowski TP, Peterson J, Gold J. (1994) Validation */ /* of a combined comorbidity index. J Clin Epidemiol; 47(11):1245-51. */ /* */ /* Reference for ICD-9-CM and ICD-10 Coding Algorithms for Charlson */ /* Comorbidities: */ /* (3) Quan H, Sundararajan V, Halfon P, et al. Coding algorithms for */ /* defining Comorbidities in ICD-9-CM and ICD-10 administrative data. */ /* Med Care. 2005 Nov; 43(11): 1130-9. */ /* ICD-10-CM extensions (C4A, C7A, C7B) are not part of WHO ICD-10 and */ /* were not defined in Quan et al. (2005). The malignant_cancer mapping */ /* below follows Quan by excluding skin malignancy (C4A Merkel cell) and */ /* by not mapping C7A/C7B neuroendocrine categories, which fall outside */ /* the WHO ICD-10 code ranges used in the publication. */ /* ------------------------------------------------------------------ */
 WITH diag AS (
   SELECT
     hadm_id,
@@ -276,7 +276,8 @@ WITH diag AS (
         OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C00' AND 'C26'
         OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C30' AND 'C34'
         OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C37' AND 'C41'
-        OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C45' AND 'C58'
+        OR SUBSTRING(icd10_code FROM 1 FOR 3) /* Split C45-C58 to exclude C4A (Merkel cell carcinoma), which */ /* lexically falls inside BETWEEN 'C45' AND 'C58' but is skin */ /* malignancy excluded by Quan et al. (2005). */ BETWEEN 'C45' AND 'C49'
+        OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C50' AND 'C58'
         OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C60' AND 'C76'
         OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C81' AND 'C85'
         OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C90' AND 'C97'