mimic-iv/concepts_postgres: apply updates from bigquery code

Re-run `convert_bigquery_to_postgres.sh` to update the Postgres
concepts. In particular, remove an old include..

```
\i measurement/differential_detailed.sql
```

..that leads to the following error:

```
psql:postgres-make-concepts.sql:35: error: measurement/differential_detailed.sql: No such file or directory
```

Author: schu

mimic-iv/concepts_postgres/firstday/first_day_gcs.sql

@@ -15,15 +15,25 @@ DROP TABLE IF EXISTS first_day_gcs; CREATE TABLE first_day_gcs AS
 WITH gcs_final AS
 (
     SELECT
-        gcs.*
+        ie.subject_id, ie.stay_id
+        , g.gcs
+        , g.gcs_motor
+        , g.gcs_verbal
+        , g.gcs_eyes
+        , g.gcs_unable
         -- This sorts the data by GCS
         -- rn = 1 is the the lowest total GCS value
         , ROW_NUMBER () OVER
         (
-            PARTITION BY gcs.stay_id
-            ORDER BY gcs.GCS
+            PARTITION BY g.stay_id
+            ORDER BY g.GCS
         ) as gcs_seq
-    FROM mimiciv_derived.gcs gcs
+    FROM mimiciv_icu.icustays ie
+    -- Only get data for the first 24 hours
+    LEFT JOIN mimiciv_derived.gcs g
+        ON ie.stay_id = g.stay_id
+        AND g.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
+        AND g.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
 )
 SELECT
     ie.subject_id

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

@@ -11,7 +11,7 @@
 
 -- NOTE: many scripts *require* you to use mimic_derived as the schema for outputting concepts
 -- change the search path at your peril!
-SET search_path TO mimiciv_derived, mimiciv_core, mimiciv_hosp, mimiciv_icu, mimiciv_ed;
+SET search_path TO mimiciv_derived, mimiciv_hosp, mimiciv_icu, mimiciv_ed;
 
 -- dependencies
 \i demographics/icustay_times.sql
@@ -32,7 +32,6 @@ SET search_path TO mimiciv_derived, mimiciv_core, mimiciv_hosp, mimiciv_icu, mim
 \i measurement/coagulation.sql
 \i measurement/complete_blood_count.sql
 \i measurement/creatinine_baseline.sql
-\i measurement/differential_detailed.sql
 \i measurement/enzyme.sql
 \i measurement/gcs.sql
 \i measurement/height.sql
@@ -65,8 +64,8 @@ SET search_path TO mimiciv_derived, mimiciv_core, mimiciv_hosp, mimiciv_icu, mim
 \i treatment/ventilation.sql
 
 -- firstday
-\i firstday/first_day_bg.sql
 \i firstday/first_day_bg_art.sql
+\i firstday/first_day_bg.sql
 \i firstday/first_day_gcs.sql
 \i firstday/first_day_height.sql
 \i firstday/first_day_lab.sql

mimic-iv/concepts_postgres/sepsis/suspicion_of_infection.sql

@@ -29,7 +29,13 @@ WITH ab_tbl AS
     , CAST(MAX(chartdate) AS DATE) AS chartdate
     , MAX(charttime) AS charttime
     , MAX(spec_type_desc) AS spec_type_desc
-    , max(case when org_name is not null and org_name != '' then 1 else 0 end) as PositiveCulture
+    -- identify negative cultures as NULL organism or a specific itemid saying "NEGATIVE"
+    , MAX(
+        CASE  WHEN org_name IS NOT NULL
+              AND org_itemid != 90856
+              AND org_name != ''
+        THEN 1 ELSE 0
+      END) as PositiveCulture
   from mimiciv_hosp.microbiologyevents
   group by micro_specimen_id
 )