fix(mimic-iv): include phenylephrine infusion variants

.github/workflows/transpile.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Install package
         run: pip install -e . --no-deps
       - name: Run transpiler unit tests
-        run: pytest tests/test_transpile.py -q
+        run: pytest tests/test_transpile.py tests/test_phenylephrine.py -q
 
   generated-up-to-date:
     name: Check cross-dialect concepts match BQ

mimic-iv/concepts/medication/phenylephrine.sql

@@ -9,4 +9,10 @@ SELECT
     , starttime
     , endtime
 FROM `physionet-data.mimiciv_icu.inputevents`
-WHERE itemid = 221749 -- phenylephrine
+WHERE itemid IN (
+    221749 -- Phenylephrine
+    , 229630 -- Phenylephrine (50/250)
+    , 229631 -- Phenylephrine (200/250)_OLD_1
+    , 229632 -- Phenylephrine (200/250)
+)
+-- Exclude 229789 (Phenylephrine (Intubation)), which is bolus dosing.

mimic-iv/concepts_duckdb/medication/phenylephrine.sql

@@ -9,4 +9,4 @@ SELECT
   endtime
 FROM mimiciv_icu.inputevents
 WHERE
-  itemid = 221749
+  itemid IN (221749, 229630, 229631, 229632)

mimic-iv/concepts_postgres/medication/phenylephrine.sql

@@ -1,6 +1,7 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
 DROP TABLE IF EXISTS mimiciv_derived.phenylephrine; CREATE TABLE mimiciv_derived.phenylephrine AS
-/* This query extracts dose+durations of phenylephrine administration */ /* Local hospital dosage guidance: 0.5 mcg/kg/min (low) - 5 mcg/kg/min (high) */
+/* This query extracts dose+durations of phenylephrine administration */
+/* Local hospital dosage guidance: 0.5 mcg/kg/min (low) - 5 mcg/kg/min (high) */
 SELECT
   stay_id,
   linkorderid, /* one row in mcg/min, the rest in mcg/kg/min */
@@ -14,4 +15,9 @@ SELECT
   endtime
 FROM mimiciv_icu.inputevents
 WHERE
-  itemid = 221749 /* phenylephrine */
+  itemid IN (
+    221749, /* Phenylephrine */
+    229630, /* Phenylephrine (50/250) */
+    229631, /* Phenylephrine (200/250)_OLD_1 */
+    229632 /* Phenylephrine (200/250) */
+  ) /* Exclude 229789 (Phenylephrine (Intubation)), which is bolus dosing. */

tests/test_phenylephrine.py

@@ -0,0 +1,71 @@
+"""Synthetic regression coverage for phenylephrine concentration variants (#2159)."""
+from pathlib import Path
+
+import pytest
+
+from mimic_utils.transpile import transpile_query
+
+duckdb = pytest.importorskip("duckdb")
+ROOT = Path(__file__).resolve().parents[1] / "mimic-iv"
+
+
+@pytest.mark.parametrize("sql_source", ["bigquery", "committed_duckdb"])
+def test_infusion_variants_reach_norepinephrine_equivalent_dose(sql_source):
+    with duckdb.connect() as con:
+        con.execute("CREATE SCHEMA mimiciv_icu; CREATE SCHEMA mimiciv_derived")
+        con.execute("""
+            CREATE TABLE mimiciv_icu.inputevents (
+                stay_id BIGINT, linkorderid BIGINT, itemid INTEGER,
+                rate DOUBLE, rateuom VARCHAR, patientweight DOUBLE,
+                amount DOUBLE, starttime TIMESTAMP, endtime TIMESTAMP
+            )
+        """)
+        # All four infusion labels, the intubation bolus label, and an unrelated drug.
+        # Each infusion has a distinct stay so a missing item cannot be masked.
+        for stay_id, itemid, rate, unit in [
+            (1, 221749, 1.0, "mcg/kg/min"),
+            (2, 229630, 2.0, "mcg/kg/min"),
+            (3, 229631, 3.0, "mcg/kg/min"),
+            (4, 229632, 200.0, "mcg/min"),
+            (5, 229789, None, None),
+            (6, 999999, 9.0, "mcg/kg/min"),
+        ]:
+            con.execute("""
+                INSERT INTO mimiciv_icu.inputevents VALUES
+                (?, ?, ?, ?, ?, 50, 10, '2150-01-01 00:00:00', '2150-01-01 02:00:00')
+            """, [stay_id, stay_id, itemid, rate, unit])
+
+        def build(name):
+            if sql_source == "bigquery":
+                sql = (ROOT / "concepts" / "medication" / f"{name}.sql").read_text()
+                con.execute(
+                    f"CREATE TABLE mimiciv_derived.{name} AS "
+                    + transpile_query(sql, "bigquery", "duckdb")
+                )
+            else:
+                con.execute((ROOT / "concepts_duckdb" / "medication" / f"{name}.sql").read_text())
+
+        build("phenylephrine")
+        assert con.execute("""
+            SELECT stay_id, vaso_rate FROM mimiciv_derived.phenylephrine ORDER BY stay_id
+        """).fetchall() == [(1, 1.0), (2, 2.0), (3, 3.0), (4, 4.0)]
+
+        for name in ("dobutamine", "dopamine", "epinephrine", "norepinephrine", "vasopressin", "milrinone"):
+            con.execute(
+                f"CREATE TABLE mimiciv_derived.{name} AS "
+                "SELECT * FROM mimiciv_derived.phenylephrine WHERE FALSE"
+            )
+        # A variant also contributes when another vasopressor is already present.
+        con.execute("""
+            INSERT INTO mimiciv_derived.norepinephrine
+            SELECT stay_id, linkorderid, 0.1, vaso_amount, starttime, endtime
+            FROM mimiciv_derived.phenylephrine WHERE stay_id = 2
+        """)
+        build("vasoactive_agent")
+        build("norepinephrine_equivalent_dose")
+        rows = con.execute("""
+            SELECT stay_id, norepinephrine_equivalent_dose
+            FROM mimiciv_derived.norepinephrine_equivalent_dose ORDER BY stay_id
+        """).fetchall()
+        assert [r[0] for r in rows] == [1, 2, 3, 4]
+        assert [float(r[1]) for r in rows] == pytest.approx([0.1, 0.3, 0.3, 0.4])