move search_path into make concepts call

Author: alistairewj

mimic-iv/concepts_postgres/README.md

@@ -3,14 +3,12 @@
 This folder contains scripts to generate useful abstractions of raw MIMIC-IV data ("concepts"). The
 scripts are intended to be run against the MIMIC-IV data in a PostgreSQL database.
 
-**Most of these scripts are automatically generated by a shell script in the parent folder.** If you would like to contribute a correction, please look at the conversion shell script to ensure you edit the right script!
+**These scripts are automatically generated by a shell script in the concepts folder.**
+If you would like to contribute a correction, please look at the conversion shell script to ensure you edit the right script!
 
 To generate concepts, change to this directory and run `psql`. Then within psql, run:
 
 ```sql
--- NOTE: many scripts *require* you to use mimiciv_derived as the schema for outputting concepts
--- change the search path at your peril!
-set search_path to mimiciv_derived, mimiciv_hosp, mimiciv_icu, mimiciv_ed;
 \i postgres-functions.sql -- only needs to be run once
 \i postgres-make-concepts.sql
 ```

mimic-iv/concepts_postgres/postgres-functions.sql

@@ -2,6 +2,9 @@
 --  FROM table CROSS JOIN UNNEST(table.column) AS col -> ????  (see icustay-hours)
 --  ???(column) -> PERCENTILE_CONT(0.5) WITHIN GROUP (ORDER BY column)    (not sure how to do median in BQ)
 
+-- Set the search_path so all functions are generated on the mimiciv_derived schema
+SET search_path TO mimiciv_derived, mimiciv_core, mimiciv_hosp, mimiciv_icu, mimiciv_ed;
+
 CREATE OR REPLACE FUNCTION REGEXP_EXTRACT(str TEXT, pattern TEXT) RETURNS TEXT AS $$
 BEGIN
 RETURN substring(str from pattern);

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

@@ -6,6 +6,13 @@
 \echo '==='
 \echo ''
 
+-- Set the search_path, i.e. the location at which we generate tables.
+-- postgres looks at schemas sequentially, so this will generate tables on the mimiciv_derived schema
+
+-- 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;
+
 -- dependencies
 \i demographics/icustay_times.sql
 \i demographics/weight_durations.sql