Merge pull request #1210 from MIT-LCP/fix_make

syntax fixes

Author: alistairewj

.github/workflows/main.yml

@@ -22,4 +22,4 @@ jobs:
         run: |
             echo "Generating tables on BigQuery"
             cd mimic-iv/concepts
-            bash make_concepts.sh > /dev/null
+            bash make_concepts.sh

mimic-iv/concepts/make_concepts.sh

@@ -31,7 +31,7 @@ do
 
             # not skipping - so generate the table on bigquery
             echo "Generating ${TARGET_DATASET}.${tbl}"
-            bq query --use_legacy_sql=False --replace --destination_table=${TARGET_DATASET}.${tbl} < ${d}/${fn}
+            bq query --quiet --use_legacy_sql=False --replace --destination_table=${TARGET_DATASET}.${tbl} < ${d}/${fn}
         fi
     done
 done
@@ -43,5 +43,5 @@ do
   table=`echo $table_path | rev | cut -d/ -f1 | rev`
 
   echo "Generating ${TARGET_DATASET}.${table}"
-  bq query --use_legacy_sql=False --replace --destination_table=${TARGET_DATASET}.${table} < ${table_path}.sql
+  bq query --quiet --use_legacy_sql=False --replace --destination_table=${TARGET_DATASET}.${table} < ${table_path}.sql
 done

mimic-iv/concepts/medication/norepinephrine.sql

@@ -7,7 +7,6 @@ select
   -- below row is written for completion, but doesn't impact rows
   WHEN rateuom = 'mg/kg/min' THEN rate * 1000.0
   ELSE rate END AS vaso_rate
-  , rate as vaso_rate
   , amount as vaso_amount
   , starttime
   , endtime

mimic-iv/concepts/medication/norepinephrine_equivalent_dose.sql

@@ -14,7 +14,6 @@ SELECT stay_id, starttime, endtime
   , 4) AS norepinephrine_equivalent_dose
   -- angotensin_ii*10 -- angitensin ii rarely used, currently not incorporated
   -- (it could be included due to norepinephrine sparing effects)
-  AS norepinephrine_equivalent_dose
 FROM mimic_derived.vasoactive_agent
 WHERE norepinephrine IS NOT NULL
 OR epinephrine IS NOT NULL

mimic-iv/concepts/postgres/measurement/cardiac_marker.sql

@@ -7,16 +7,18 @@ SELECT
   , MAX(charttime) AS charttime
   , le.specimen_id
   -- convert from itemid into a meaningful column
-  , MAX(CASE WHEN itemid = 51002 THEN value ELSE NULL END) AS troponin_i
   , MAX(CASE WHEN itemid = 51003 THEN value ELSE NULL END) AS troponin_t
   , MAX(CASE WHEN itemid = 50911 THEN valuenum ELSE NULL END) AS ck_mb
+  , MAX(CASE WHEN itemid = 50963 THEN valuenum ELSE NULL END) AS ntprobnp
 FROM mimic_hosp.labevents le
 WHERE le.itemid IN
 (
     -- 51002, -- Troponin I (troponin-I is not measured in MIMIC-IV)
     -- 52598, -- Troponin I, point of care, rare/poor quality
     51003, -- Troponin T
-    50911  -- Creatinine Kinase, MB isoenzyme
+    50911,  -- Creatinine Kinase, MB isoenzyme
+    50963 -- N-terminal (NT)-pro hormone BNP (NT-proBNP) 
 )
+AND valuenum IS NOT NULL
 GROUP BY le.specimen_id
 ;

mimic-iv/concepts/postgres/medication/dobutamine.sql

@@ -3,6 +3,7 @@ DROP TABLE IF EXISTS dobutamine; CREATE TABLE dobutamine AS
 -- This query extracts dose+durations of dopamine administration
 select
 stay_id, linkorderid
+-- all rows in mcg/kg/min
 , rate as vaso_rate
 , amount as vaso_amount
 , starttime

mimic-iv/concepts/postgres/medication/dopamine.sql

@@ -3,6 +3,7 @@ DROP TABLE IF EXISTS dopamine; CREATE TABLE dopamine AS
 -- This query extracts dose+durations of dopamine administration
 select
 stay_id, linkorderid
+-- all rows in mcg/kg/min
 , rate as vaso_rate
 , amount as vaso_amount
 , starttime

mimic-iv/concepts/postgres/medication/epinephrine.sql

@@ -3,6 +3,7 @@ DROP TABLE IF EXISTS epinephrine; CREATE TABLE epinephrine AS
 -- This query extracts dose+durations of epinephrine administration
 select
 stay_id, linkorderid
+-- all rows in mcg/kg/min
 , rate as vaso_rate
 , amount as vaso_amount
 , starttime

mimic-iv/concepts/postgres/medication/norepinephrine.sql

@@ -3,7 +3,12 @@ DROP TABLE IF EXISTS norepinephrine; CREATE TABLE norepinephrine AS
 -- This query extracts dose+durations of norepinephrine administration
 select
   stay_id, linkorderid
-  , rate as vaso_rate
+  -- two rows in mg/kg/min... rest in mcg/kg/min
+  -- the rows in mg/kg/min are documented incorrectly
+  , CASE WHEN rateuom = 'mg/kg/min' AND patientweight = 1 THEN rate
+  -- below row is written for completion, but doesn't impact rows
+  WHEN rateuom = 'mg/kg/min' THEN rate * 1000.0
+  ELSE rate END AS vaso_rate
   , amount as vaso_amount
   , starttime
   , endtime

mimic-iv/concepts/postgres/medication/phenylephrine.sql

@@ -3,7 +3,9 @@ DROP TABLE IF EXISTS phenylephrine; CREATE TABLE phenylephrine AS
 -- This query extracts dose+durations of phenylephrine administration
 select
   stay_id, linkorderid
-  , rate as vaso_rate
+  -- one row in mcg/min, the rest in mcg/kg/min
+  , CASE WHEN rateuom = 'mcg/min' THEN rate / patientweight
+  ELSE rate END as vaso_rate
   , amount as vaso_amount
   , starttime
   , endtime