fix(mimic-iv): filter lab concepts by expected valueuom

.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/measurement/complete_blood_count.sql

@@ -8,7 +8,11 @@ SELECT
     , MAX(CASE WHEN itemid = 51221 THEN valuenum ELSE NULL END) AS hematocrit
     , MAX(CASE WHEN itemid = 51222 THEN valuenum ELSE NULL END) AS hemoglobin
     , MAX(CASE WHEN itemid = 51248 THEN valuenum ELSE NULL END) AS mch
-    , MAX(CASE WHEN itemid = 51249 THEN valuenum ELSE NULL END) AS mchc
+    , MAX(
+        CASE
+            WHEN itemid = 51249 AND valueuom = 'g/dL' THEN valuenum ELSE NULL
+        END
+    ) AS mchc
     , MAX(CASE WHEN itemid = 51250 THEN valuenum ELSE NULL END) AS mcv
     , MAX(CASE WHEN itemid = 51265 THEN valuenum ELSE NULL END) AS platelet
     , MAX(CASE WHEN itemid = 51279 THEN valuenum ELSE NULL END) AS rbc
@@ -30,6 +34,8 @@ WHERE le.itemid IN
         , 51301  -- WBC
     )
     AND valuenum IS NOT NULL
+    -- MCHC (51249) is sometimes recorded with valueuom '%' in error; keep g/dL only
+    AND (itemid != 51249 OR valueuom = 'g/dL')
     -- lab values cannot be 0 and cannot be negative
     AND valuenum > 0
 GROUP BY le.specimen_id

mimic-iv/concepts/measurement/inflammation.sql

@@ -4,14 +4,20 @@ SELECT
     , MAX(charttime) AS charttime
     , le.specimen_id
     -- convert from itemid into a meaningful column
-    , MAX(CASE WHEN itemid = 50889 THEN valuenum ELSE NULL END) AS crp
+    , MAX(
+        CASE
+            WHEN itemid = 50889 AND valueuom = 'mg/L' THEN valuenum ELSE NULL
+        END
+    ) AS crp
 FROM `physionet-data.mimiciv_hosp.labevents` le
 WHERE le.itemid IN
     (
         -- 51652 -- high sensitivity CRP
         50889 -- crp
     )
     AND valuenum IS NOT NULL
+    -- CRP (50889) rows with missing valueuom are excluded; mg/L is the expected unit
+    AND (itemid != 50889 OR valueuom = 'mg/L')
     -- lab values cannot be 0 and cannot be negative
     AND valuenum > 0
 GROUP BY le.specimen_id

mimic-iv/concepts_duckdb/measurement/complete_blood_count.sql

@@ -8,7 +8,7 @@ SELECT
   MAX(CASE WHEN itemid = 51221 THEN valuenum ELSE NULL END) AS hematocrit,
   MAX(CASE WHEN itemid = 51222 THEN valuenum ELSE NULL END) AS hemoglobin,
   MAX(CASE WHEN itemid = 51248 THEN valuenum ELSE NULL END) AS mch,
-  MAX(CASE WHEN itemid = 51249 THEN valuenum ELSE NULL END) AS mchc,
+  MAX(CASE WHEN itemid = 51249 AND valueuom = 'g/dL' THEN valuenum ELSE NULL END) AS mchc,
   MAX(CASE WHEN itemid = 51250 THEN valuenum ELSE NULL END) AS mcv,
   MAX(CASE WHEN itemid = 51265 THEN valuenum ELSE NULL END) AS platelet,
   MAX(CASE WHEN itemid = 51279 THEN valuenum ELSE NULL END) AS rbc,
@@ -19,6 +19,9 @@ FROM mimiciv_hosp.labevents AS le
 WHERE
   le.itemid IN (51221, 51222, 51248, 51249, 51250, 51265, 51279, 51277, 52159, 51301)
   AND NOT valuenum IS NULL
+  AND (
+    itemid <> 51249 OR valueuom = 'g/dL'
+  )
   AND valuenum > 0
 GROUP BY
   le.specimen_id

mimic-iv/concepts_duckdb/measurement/inflammation.sql

@@ -5,9 +5,14 @@ SELECT
   MAX(hadm_id) AS hadm_id,
   MAX(charttime) AS charttime,
   le.specimen_id,
-  MAX(CASE WHEN itemid = 50889 THEN valuenum ELSE NULL END) AS crp
+  MAX(CASE WHEN itemid = 50889 AND valueuom = 'mg/L' THEN valuenum ELSE NULL END) AS crp
 FROM mimiciv_hosp.labevents AS le
 WHERE
-  le.itemid IN (50889) AND NOT valuenum IS NULL AND valuenum > 0
+  le.itemid IN (50889)
+  AND NOT valuenum IS NULL
+  AND (
+    itemid <> 50889 OR valueuom = 'mg/L'
+  )
+  AND valuenum > 0
 GROUP BY
   le.specimen_id

mimic-iv/concepts_postgres/measurement/complete_blood_count.sql

@@ -9,7 +9,7 @@ SELECT
   MAX(CASE WHEN itemid = 51221 THEN valuenum ELSE NULL END) AS hematocrit,
   MAX(CASE WHEN itemid = 51222 THEN valuenum ELSE NULL END) AS hemoglobin,
   MAX(CASE WHEN itemid = 51248 THEN valuenum ELSE NULL END) AS mch,
-  MAX(CASE WHEN itemid = 51249 THEN valuenum ELSE NULL END) AS mchc,
+  MAX(CASE WHEN itemid = 51249 AND valueuom = 'g/dL' THEN valuenum ELSE NULL END) AS mchc,
   MAX(CASE WHEN itemid = 51250 THEN valuenum ELSE NULL END) AS mcv,
   MAX(CASE WHEN itemid = 51265 THEN valuenum ELSE NULL END) AS platelet,
   MAX(CASE WHEN itemid = 51279 THEN valuenum ELSE NULL END) AS rbc,
@@ -31,6 +31,9 @@ WHERE
     51301 /* WBC */
   )
   AND NOT valuenum IS NULL
+  AND /* MCHC (51249) is sometimes recorded with valueuom '%' in error; keep g/dL only */ (
+    itemid <> 51249 OR valueuom = 'g/dL'
+  )
   AND /* lab values cannot be 0 and cannot be negative */ valuenum > 0
 GROUP BY
   le.specimen_id

mimic-iv/concepts_postgres/measurement/inflammation.sql

@@ -5,11 +5,14 @@ SELECT
   MAX(hadm_id) AS hadm_id,
   MAX(charttime) AS charttime,
   le.specimen_id, /* convert from itemid into a meaningful column */
-  MAX(CASE WHEN itemid = 50889 THEN valuenum ELSE NULL END) AS crp
+  MAX(CASE WHEN itemid = 50889 AND valueuom = 'mg/L' THEN valuenum ELSE NULL END) AS crp
 FROM mimiciv_hosp.labevents AS le
 WHERE
   le.itemid IN (50889 /* 51652 -- high sensitivity CRP */ /* crp */)
   AND NOT valuenum IS NULL
+  AND /* CRP (50889) rows with missing valueuom are excluded; mg/L is the expected unit */ (
+    itemid <> 50889 OR valueuom = 'mg/L'
+  )
   AND /* lab values cannot be 0 and cannot be negative */ valuenum > 0
 GROUP BY
   le.specimen_id