fix: correct SIRS comment typos in mimic-iii and mimic-iv

.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-iii/concepts/severityscores/sirs.sql

@@ -88,7 +88,7 @@ left join `physionet-data.mimiciii_derived.labs_first_day` l
   , case
       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 bands_max > 10 then 1 -- > 10% immature neutrophils (band forms)
       when coalesce(wbc_min, bands_max) is null then null
       else 0
     end as wbc_score
@@ -97,7 +97,7 @@ left join `physionet-data.mimiciii_derived.labs_first_day` l
 )
 select
   ie.subject_id, ie.hadm_id, ie.icustay_id
-  -- Combine all the scores to get SOFA
+  -- Combine all component scores to get SIRS
   -- Impute 0 if the score is missing
   , coalesce(temp_score,0)
   + coalesce(heartrate_score,0)

mimic-iii/concepts_duckdb/severityscores/sirs.sql

@@ -1,5 +1,5 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
-DROP TABLE IF EXISTS mimiciii_derived.sirs; CREATE TABLE mimiciii_derived.sirs AS
+DROP TABLE IF EXISTS mimiciv_derived.sirs; CREATE TABLE mimiciv_derived.sirs AS
 WITH bg AS (
   SELECT
     bg.icustay_id,

mimic-iii/concepts_postgres/severityscores/sirs.sql

@@ -1,5 +1,5 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
-DROP TABLE IF EXISTS mimiciii_derived.sirs; CREATE TABLE mimiciii_derived.sirs AS
+DROP TABLE IF EXISTS mimiciv_derived.sirs; CREATE TABLE mimiciv_derived.sirs AS
 /* ------------------------------------------------------------------ */ /* Title: Systemic inflammatory response syndrome (SIRS) criteria */ /* This query extracts the Systemic inflammatory response syndrome (SIRS) criteria */ /* The criteria quantify the level of inflammatory response of the body */ /* The score is calculated on the first day of each ICU patients' stay. */ /* ------------------------------------------------------------------ */ /* Reference for SIRS: */ /*    American College of Chest Physicians/Society of Critical Care Medicine Consensus Conference: */ /*    definitions for sepsis and organ failure and guidelines for the use of innovative therapies in sepsis" */ /*    Crit. Care Med. 20 (6): 864–74. 1992. */ /*    doi:10.1097/00003246-199206000-00025. PMID 1597042. */ /* Variables used in SIRS: */ /*  Body temperature (min and max) */ /*  Heart rate (max) */ /*  Respiratory rate (max) */ /*  PaCO2 (min) */ /*  White blood cell count (min and max) */ /*  the presence of greater than 10% immature neutrophils (band forms) */ /* The following views required to run this query: */ /*  1) vitals_first_day - generated by vitals-first-day.sql */ /*  2) labs_first_day - generated by labs-first-day.sql */ /*  3) blood_gas_first_day_arterial - generated by blood-gas-first-day-arterial.sql */ /* Note: */ /*  The score is calculated for *all* ICU patients, with the assumption that the user will subselect appropriate ICUSTAY_IDs. */ /*  For example, the score is calculated for neonates, but it is likely inappropriate to actually use the score values for these patients. */
 WITH bg AS (
   /* join blood gas to ventilation durations to determine if patient was vent */
@@ -58,7 +58,7 @@ WITH bg AS (
       WHEN wbc_max > 12.0
       THEN 1
       WHEN bands_max > 10
-      THEN 1 /* > 10% immature neurophils (band forms) */
+      THEN 1 /* > 10% immature neutrophils (band forms) */
       WHEN COALESCE(wbc_min, bands_max) IS NULL
       THEN NULL
       ELSE 0
@@ -68,7 +68,7 @@ WITH bg AS (
 SELECT
   ie.subject_id,
   ie.hadm_id,
-  ie.icustay_id, /* Combine all the scores to get SOFA */ /* Impute 0 if the score is missing */
+  ie.icustay_id, /* Combine all component scores to get SIRS */ /* Impute 0 if the score is missing */
   COALESCE(temp_score, 0) + COALESCE(heartrate_score, 0) + COALESCE(resp_score, 0) + COALESCE(wbc_score, 0) AS sirs,
   temp_score,
   heartrate_score,

mimic-iv/concepts/score/sirs.sql

@@ -76,7 +76,7 @@ WITH scorecomp AS (
         , CASE
             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 bands_max > 10 THEN 1 -- > 10% immature neutrophils (band forms)
             WHEN COALESCE(wbc_min, bands_max) IS NULL THEN NULL
             ELSE 0
         END AS wbc_score
@@ -86,7 +86,7 @@ WITH scorecomp AS (
 
 SELECT
     ie.subject_id, ie.hadm_id, ie.stay_id
-    -- Combine all the scores to get SOFA
+    -- Combine all component scores to get SIRS
     -- Impute 0 if the score is missing
     , COALESCE(temp_score, 0)
     + COALESCE(heart_rate_score, 0)

mimic-iv/concepts_postgres/score/sirs.sql

@@ -54,7 +54,7 @@ WITH scorecomp AS (
       WHEN wbc_max > 12.0
       THEN 1
       WHEN bands_max > 10
-      THEN 1 /* > 10% immature neurophils (band forms) */
+      THEN 1 /* > 10% immature neutrophils (band forms) */
       WHEN COALESCE(wbc_min, bands_max) IS NULL
       THEN NULL
       ELSE 0
@@ -64,7 +64,7 @@ WITH scorecomp AS (
 SELECT
   ie.subject_id,
   ie.hadm_id,
-  ie.stay_id, /* Combine all the scores to get SOFA */ /* Impute 0 if the score is missing */
+  ie.stay_id, /* Combine all component scores to get SIRS */ /* Impute 0 if the score is missing */
   COALESCE(temp_score, 0) + COALESCE(heart_rate_score, 0) + COALESCE(resp_score, 0) + COALESCE(wbc_score, 0) AS sirs,
   temp_score,
   heart_rate_score,