Merge pull request #1210 from MIT-LCP/fix_make

syntax fixes

.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

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

@@ -3,7 +3,10 @@ DROP TABLE IF EXISTS vasopressin; CREATE TABLE vasopressin AS
 -- This query extracts dose+durations of vasopressin administration
 select
   stay_id, linkorderid
-  , rate as vaso_rate
+  -- three rows in units/min, rest in units/hour
+  -- the three rows in units/min look reasonable and fit with the patient course
+  , CASE WHEN rateuom = 'units/min' THEN rate * 60.0
+    ELSE rate END AS vaso_rate
   , amount as vaso_amount
   , starttime
   , endtime

mimic-iv/concepts/postgres/postgres-make-concepts.sql

@@ -44,10 +44,13 @@
 \i medication/dobutamine.sql
 \i medication/dopamine.sql
 \i medication/epinephrine.sql
+\i medication/milrinone.sql
 \i medication/neuroblock.sql
 \i medication/norepinephrine.sql
 \i medication/phenylephrine.sql
 \i medication/vasopressin.sql
+\i medication/vasoactive_agent.sql
+\i medication/norepinephrine_equivalent_dose.sql
 
 -- treatment
 \i treatment/crrt.sql

mimic-iv/concepts/postgres/score/apsiii.sql

@@ -52,7 +52,7 @@ with pa as
   -- and fio2 < 50, or if no fio2, assume room air
   AND coalesce(fio2, fio2_chartevents, 21) < 50
   AND bg.po2 IS NOT NULL
-  AND bg.specimen_pred = 'ART.'
+  AND bg.specimen = 'ART.'
 )
 , aa as
 (
@@ -74,7 +74,7 @@ with pa as
   WHERE vd.stay_id is not null -- patient is ventilated
   AND coalesce(fio2, fio2_chartevents) >= 50
   AND bg.aado2 IS NOT NULL
-  AND bg.specimen_pred = 'ART.'
+  AND bg.specimen = 'ART.'
 )
 -- because ph/pco2 rules are an interaction *within* a blood gas, we calculate them here
 -- the worse score is then taken for the final calculation
@@ -132,7 +132,7 @@ with pa as
     ON bg.hadm_id = ie.hadm_id
     AND bg.charttime >= ie.intime AND bg.charttime < ie.outtime
   where ph is not null and pco2 is not null
-  AND bg.specimen_pred = 'ART.'
+  AND bg.specimen = 'ART.'
 )
 , acidbase_max as
 (

mimic-iv/concepts/postgres/score/sapsii.sql

@@ -117,7 +117,7 @@ select hadm_id
   from co
   LEFT JOIN mimic_derived.bg bg
     ON co.subject_id = bg.subject_id
-    AND bg.specimen_pred = 'ART.'
+    AND bg.specimen = 'ART.'
     AND bg.charttime > co.starttime
     AND bg.charttime <= co.endtime
   left join mimic_derived.ventilation vd

mimic-iv/concepts/postgres/score/sofa.sql

@@ -53,7 +53,7 @@ WITH co AS
     and bg.charttime >= vd.starttime
     and bg.charttime <= vd.endtime
     and vd.ventilation_status = 'InvasiveVent'
-  WHERE specimen_pred = 'ART.'
+  WHERE specimen = 'ART.'
 )
 , vs AS
 (

mimic-iv/concepts/postgres/treatment/ventilation.sql

@@ -203,6 +203,7 @@ WITH tm AS
 , vd2 as
 (
     SELECT vd1.stay_id, vd1.charttime
+    , vd1.charttime_lead, vd1.ventilation_status
     , ventduration, new_ventilation_event
     -- create a cumulative sum of the instances of new ventilation
     -- this results in a monotonically increasing integer assigned 

mimic-iv/concepts/score/apsiii.sql

@@ -50,7 +50,7 @@ with pa as
   -- and fio2 < 50, or if no fio2, assume room air
   AND coalesce(fio2, fio2_chartevents, 21) < 50
   AND bg.po2 IS NOT NULL
-  AND bg.specimen_pred = 'ART.'
+  AND bg.specimen = 'ART.'
 )
 , aa as
 (
@@ -72,7 +72,7 @@ with pa as
   WHERE vd.stay_id is not null -- patient is ventilated
   AND coalesce(fio2, fio2_chartevents) >= 50
   AND bg.aado2 IS NOT NULL
-  AND bg.specimen_pred = 'ART.'
+  AND bg.specimen = 'ART.'
 )
 -- because ph/pco2 rules are an interaction *within* a blood gas, we calculate them here
 -- the worse score is then taken for the final calculation
@@ -130,7 +130,7 @@ with pa as
     ON bg.hadm_id = ie.hadm_id
     AND bg.charttime >= ie.intime AND bg.charttime < ie.outtime
   where ph is not null and pco2 is not null
-  AND bg.specimen_pred = 'ART.'
+  AND bg.specimen = 'ART.'
 )
 , acidbase_max as
 (

mimic-iv/concepts/score/sapsii.sql

@@ -115,7 +115,7 @@ select hadm_id
   from co
   LEFT JOIN `physionet-data.mimic_derived.bg` bg
     ON co.subject_id = bg.subject_id
-    AND bg.specimen_pred = 'ART.'
+    AND bg.specimen = 'ART.'
     AND bg.charttime > co.starttime
     AND bg.charttime <= co.endtime
   left join `physionet-data.mimic_derived.ventilation` vd

mimic-iv/concepts/score/sofa.sql

@@ -51,7 +51,7 @@ WITH co AS
     and bg.charttime >= vd.starttime
     and bg.charttime <= vd.endtime
     and vd.ventilation_status = 'InvasiveVent'
-  WHERE specimen_pred = 'ART.'
+  WHERE specimen = 'ART.'
 )
 , vs AS
 (

mimic-iv/concepts/treatment/ventilation.sql

@@ -201,6 +201,7 @@ WITH tm AS
 , vd2 as
 (
     SELECT vd1.stay_id, vd1.charttime
+    , vd1.charttime_lead, vd1.ventilation_status
     , ventduration, new_ventilation_event
     -- create a cumulative sum of the instances of new ventilation
     -- this results in a monotonically increasing integer assigned