fix(mimic-iv): align lab measurement concepts on positive valuenum filter

.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/README.md

@@ -3,6 +3,10 @@
 This folder contains scripts to generate useful abstractions of raw MIMIC-IV data ("concepts").
 The scripts are written using the **BigQuery Standard SQL Dialect**. Concepts are categorized into folders if possible, otherwise they remain in the top-level directory. The [concepts_postgres](/mimic-iv/concepts_postgres) and [concepts_duckdb](/mimic-iv/concepts_duckdb) folders contain automatically generated PostgreSQL and DuckDB versions of these scripts; see the [top-level readme](/mimic-iv/README.md#generating-the-concepts) for how these were generated.
 
+Lab measurement concepts under `measurement/` generally exclude non-positive `valuenum` rows
+(`valuenum IS NOT NULL AND valuenum > 0`) and, where documented in the source SQL, filter
+`valueuom` to the expected unit for a given `itemid`.
+
 The concepts are organized into individual SQL scripts, with each script generating a table. The BigQuery `mimiciv_derived` dataset under `physionet-data` contains the concepts pregenerated. Access to this dataset is available to MIMIC-IV approved users: see the [cloud instructions](https://mimic.mit.edu/docs/gettingstarted/cloud/) on how to access MIMIC-IV on BigQuery (which includes the derived concepts).
 
 See the [top-level readme](/mimic-iv/README.md) for more information about generating the concepts.

mimic-iv/concepts/measurement/cardiac_marker.sql

@@ -18,5 +18,6 @@ WHERE le.itemid IN
         , 50963 -- N-terminal (NT)-pro hormone BNP (NT-proBNP) 
     )
     AND valuenum IS NOT NULL
+    AND valuenum > 0
 GROUP BY le.specimen_id
 ;

mimic-iv/concepts/measurement/coagulation.sql

@@ -27,5 +27,6 @@ WHERE le.itemid IN
         , 51275 -- PTT
     )
     AND valuenum IS NOT NULL
+    AND valuenum > 0
 GROUP BY le.specimen_id
 ;

mimic-iv/concepts_duckdb/measurement/cardiac_marker.sql

@@ -10,6 +10,6 @@ SELECT
   MAX(CASE WHEN itemid = 50963 THEN valuenum ELSE NULL END) AS ntprobnp
 FROM mimiciv_hosp.labevents AS le
 WHERE
-  le.itemid IN (51003, 50911, 50963) AND NOT valuenum IS NULL
+  le.itemid IN (51003, 50911, 50963) AND NOT valuenum IS NULL AND valuenum > 0
 GROUP BY
   le.specimen_id

mimic-iv/concepts_duckdb/measurement/coagulation.sql

@@ -13,6 +13,8 @@ SELECT
   MAX(CASE WHEN itemid = 51275 THEN valuenum ELSE NULL END) AS ptt
 FROM mimiciv_hosp.labevents AS le
 WHERE
-  le.itemid IN (51196, 51214, 51297, 51237, 51274, 51275) AND NOT valuenum IS NULL
+  le.itemid IN (51196, 51214, 51297, 51237, 51274, 51275)
+  AND NOT valuenum IS NULL
+  AND valuenum > 0
 GROUP BY
   le.specimen_id

mimic-iv/concepts_postgres/measurement/cardiac_marker.sql

@@ -17,5 +17,6 @@ WHERE
     50963 /* N-terminal (NT)-pro hormone BNP (NT-proBNP) */
   )
   AND NOT valuenum IS NULL
+  AND valuenum > 0
 GROUP BY
   le.specimen_id

mimic-iv/concepts_postgres/measurement/coagulation.sql

@@ -22,5 +22,6 @@ WHERE
     51275 /* PTT */
   )
   AND NOT valuenum IS NULL
+  AND valuenum > 0
 GROUP BY
   le.specimen_id