change mimic_ schema prefix to mimiciv_ in duckdb

Author: alistairewj

mimic-iv/buildmimic/duckdb/import_duckdb.sh

@@ -67,9 +67,9 @@ fi
 # with the following changes:
 # 1. Remove optional precision value from TIMESTAMP(NN) -> TIMESTAMP
 #    duckdb does not support this.
-# 2. Remove NOT NULL constraint from mimic_hosp.microbiologyevents.spec_type_desc
+# 2. Remove NOT NULL constraint from mimiciv_hosp.microbiologyevents.spec_type_desc
 #    as there is one (!) zero-length string which is treated as a NULL by the import.
-# 3. Remove NOT NULL constraint from mimic_hosp.prescriptions.drug
+# 3. Remove NOT NULL constraint from mimiciv_hosp.prescriptions.drug
 #    as there are zero-length strings which are treated as NULLs by the import.
 try duckdb "$OUTFILE" <<EOSQL
 -------------------------------------------
@@ -80,17 +80,17 @@ try duckdb "$OUTFILE" <<EOSQL
 -- Creating schemas --
 ----------------------
 
-DROP SCHEMA IF EXISTS mimic_hosp CASCADE;
-CREATE SCHEMA mimic_hosp;
-DROP SCHEMA IF EXISTS mimic_icu CASCADE;
-CREATE SCHEMA mimic_icu;
+DROP SCHEMA IF EXISTS mimiciv_hosp CASCADE;
+CREATE SCHEMA mimiciv_hosp;
+DROP SCHEMA IF EXISTS mimiciv_icu CASCADE;
+CREATE SCHEMA mimiciv_icu;
 
 ---------------------
 -- Creating tables --
 ---------------------
 
-DROP TABLE IF EXISTS mimic_hosp.admissions;
-CREATE TABLE mimic_hosp.admissions
+DROP TABLE IF EXISTS mimiciv_hosp.admissions;
+CREATE TABLE mimiciv_hosp.admissions
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -109,8 +109,8 @@ CREATE TABLE mimic_hosp.admissions
   hospital_expire_flag SMALLINT
 );
 
-DROP TABLE IF EXISTS mimic_hosp.patients;
-CREATE TABLE mimic_hosp.patients
+DROP TABLE IF EXISTS mimiciv_hosp.patients;
+CREATE TABLE mimiciv_hosp.patients
 (
   subject_id INTEGER NOT NULL,
   gender CHAR(1) NOT NULL,
@@ -120,8 +120,8 @@ CREATE TABLE mimic_hosp.patients
   dod DATE
 );
 
-DROP TABLE IF EXISTS mimic_hosp.transfers;
-CREATE TABLE mimic_hosp.transfers
+DROP TABLE IF EXISTS mimiciv_hosp.transfers;
+CREATE TABLE mimiciv_hosp.transfers
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER,
@@ -134,17 +134,17 @@ CREATE TABLE mimic_hosp.transfers
 
 -- hosp schema
 
-DROP TABLE IF EXISTS mimic_hosp.d_hcpcs;
-CREATE TABLE mimic_hosp.d_hcpcs
+DROP TABLE IF EXISTS mimiciv_hosp.d_hcpcs;
+CREATE TABLE mimiciv_hosp.d_hcpcs
 (
   code CHAR(5) NOT NULL,
   category SMALLINT,
   long_description TEXT,
   short_description VARCHAR(180)
 );
 
-DROP TABLE IF EXISTS mimic_hosp.diagnoses_icd;
-CREATE TABLE mimic_hosp.diagnoses_icd
+DROP TABLE IF EXISTS mimiciv_hosp.diagnoses_icd;
+CREATE TABLE mimiciv_hosp.diagnoses_icd
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -153,33 +153,33 @@ CREATE TABLE mimic_hosp.diagnoses_icd
   icd_version SMALLINT
 );
 
-DROP TABLE IF EXISTS mimic_hosp.d_icd_diagnoses;
-CREATE TABLE mimic_hosp.d_icd_diagnoses
+DROP TABLE IF EXISTS mimiciv_hosp.d_icd_diagnoses;
+CREATE TABLE mimiciv_hosp.d_icd_diagnoses
 (
   icd_code CHAR(7) NOT NULL,
   icd_version SMALLINT NOT NULL,
   long_title VARCHAR(255)
 );
 
-DROP TABLE IF EXISTS mimic_hosp.d_icd_procedures;
-CREATE TABLE mimic_hosp.d_icd_procedures
+DROP TABLE IF EXISTS mimiciv_hosp.d_icd_procedures;
+CREATE TABLE mimiciv_hosp.d_icd_procedures
 (
   icd_code CHAR(7) NOT NULL,
   icd_version SMALLINT NOT NULL,
   long_title VARCHAR(222)
 );
 
-DROP TABLE IF EXISTS mimic_hosp.d_labitems;
-CREATE TABLE mimic_hosp.d_labitems
+DROP TABLE IF EXISTS mimiciv_hosp.d_labitems;
+CREATE TABLE mimiciv_hosp.d_labitems
 (
   itemid INTEGER NOT NULL,
   label VARCHAR(50),
   fluid VARCHAR(50),
   category VARCHAR(50)
 );
 
-DROP TABLE IF EXISTS mimic_hosp.drgcodes;
-CREATE TABLE mimic_hosp.drgcodes
+DROP TABLE IF EXISTS mimiciv_hosp.drgcodes;
+CREATE TABLE mimiciv_hosp.drgcodes
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -190,8 +190,8 @@ CREATE TABLE mimic_hosp.drgcodes
   drg_mortality SMALLINT
 );
 
-DROP TABLE IF EXISTS mimic_hosp.emar_detail;
-CREATE TABLE mimic_hosp.emar_detail
+DROP TABLE IF EXISTS mimiciv_hosp.emar_detail;
+CREATE TABLE mimiciv_hosp.emar_detail
 (
   subject_id INTEGER NOT NULL,
   emar_id VARCHAR(25) NOT NULL,
@@ -228,8 +228,8 @@ CREATE TABLE mimic_hosp.emar_detail
   non_formulary_visual_verification VARCHAR(1)
 );
 
-DROP TABLE IF EXISTS mimic_hosp.emar;
-CREATE TABLE mimic_hosp.emar
+DROP TABLE IF EXISTS mimiciv_hosp.emar;
+CREATE TABLE mimiciv_hosp.emar
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER,
@@ -244,8 +244,8 @@ CREATE TABLE mimic_hosp.emar
   storetime TIMESTAMP NOT NULL
 );
 
-DROP TABLE IF EXISTS mimic_hosp.hcpcsevents;
-CREATE TABLE mimic_hosp.hcpcsevents
+DROP TABLE IF EXISTS mimiciv_hosp.hcpcsevents;
+CREATE TABLE mimiciv_hosp.hcpcsevents
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -255,8 +255,8 @@ CREATE TABLE mimic_hosp.hcpcsevents
   short_description VARCHAR(180)
 );
 
-DROP TABLE IF EXISTS mimic_hosp.labevents;
-CREATE TABLE mimic_hosp.labevents
+DROP TABLE IF EXISTS mimiciv_hosp.labevents;
+CREATE TABLE mimiciv_hosp.labevents
 (
   labevent_id INTEGER NOT NULL,
   subject_id INTEGER NOT NULL,
@@ -275,8 +275,8 @@ CREATE TABLE mimic_hosp.labevents
   comments TEXT
 );
 
-DROP TABLE IF EXISTS mimic_hosp.microbiologyevents;
-CREATE TABLE mimic_hosp.microbiologyevents
+DROP TABLE IF EXISTS mimiciv_hosp.microbiologyevents;
+CREATE TABLE mimiciv_hosp.microbiologyevents
 (
   microevent_id INTEGER NOT NULL,
   subject_id INTEGER NOT NULL,
@@ -304,8 +304,8 @@ CREATE TABLE mimic_hosp.microbiologyevents
   comments TEXT
 );
 
-DROP TABLE IF EXISTS mimic_hosp.omr;
-CREATE TABLE mimic_hosp.omr
+DROP TABLE IF EXISTS mimiciv_hosp.omr;
+CREATE TABLE mimiciv_hosp.omr
 (
   subject_id INTEGER NOT NULL,
   chartdate TIMESTAMP NOT NULL,
@@ -314,8 +314,8 @@ CREATE TABLE mimic_hosp.omr
   result_value VARCHAR(255) NOT NULL
 );
 
-DROP TABLE IF EXISTS mimic_hosp.pharmacy;
-CREATE TABLE mimic_hosp.pharmacy
+DROP TABLE IF EXISTS mimiciv_hosp.pharmacy;
+CREATE TABLE mimiciv_hosp.pharmacy
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -346,8 +346,8 @@ CREATE TABLE mimic_hosp.pharmacy
   fill_quantity VARCHAR(50)
 );
 
-DROP TABLE IF EXISTS mimic_hosp.poe_detail;
-CREATE TABLE mimic_hosp.poe_detail
+DROP TABLE IF EXISTS mimiciv_hosp.poe_detail;
+CREATE TABLE mimiciv_hosp.poe_detail
 (
   poe_id VARCHAR(25) NOT NULL,
   poe_seq INTEGER NOT NULL,
@@ -356,8 +356,8 @@ CREATE TABLE mimic_hosp.poe_detail
   field_value TEXT
 );
 
-DROP TABLE IF EXISTS mimic_hosp.poe;
-CREATE TABLE mimic_hosp.poe
+DROP TABLE IF EXISTS mimiciv_hosp.poe;
+CREATE TABLE mimiciv_hosp.poe
 (
   poe_id VARCHAR(25) NOT NULL,
   poe_seq INTEGER NOT NULL,
@@ -372,8 +372,8 @@ CREATE TABLE mimic_hosp.poe
   order_status VARCHAR(15)
 );
 
-DROP TABLE IF EXISTS mimic_hosp.prescriptions;
-CREATE TABLE mimic_hosp.prescriptions
+DROP TABLE IF EXISTS mimiciv_hosp.prescriptions;
+CREATE TABLE mimiciv_hosp.prescriptions
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -397,8 +397,8 @@ CREATE TABLE mimic_hosp.prescriptions
   route VARCHAR(50)
 );
 
-DROP TABLE IF EXISTS mimic_hosp.procedures_icd;
-CREATE TABLE mimic_hosp.procedures_icd
+DROP TABLE IF EXISTS mimiciv_hosp.procedures_icd;
+CREATE TABLE mimiciv_hosp.procedures_icd
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -408,8 +408,8 @@ CREATE TABLE mimic_hosp.procedures_icd
   icd_version SMALLINT
 );
 
-DROP TABLE IF EXISTS mimic_hosp.services;
-CREATE TABLE mimic_hosp.services
+DROP TABLE IF EXISTS mimiciv_hosp.services;
+CREATE TABLE mimiciv_hosp.services
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -420,8 +420,8 @@ CREATE TABLE mimic_hosp.services
 
 -- icu schema
 
-DROP TABLE IF EXISTS mimic_icu.chartevents;
-CREATE TABLE mimic_icu.chartevents
+DROP TABLE IF EXISTS mimiciv_icu.chartevents;
+CREATE TABLE mimiciv_icu.chartevents
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -435,8 +435,8 @@ CREATE TABLE mimic_icu.chartevents
   warning SMALLINT
 );
 
-DROP TABLE IF EXISTS mimic_icu.datetimeevents;
-CREATE TABLE mimic_icu.datetimeevents
+DROP TABLE IF EXISTS mimiciv_icu.datetimeevents;
+CREATE TABLE mimiciv_icu.datetimeevents
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -449,8 +449,8 @@ CREATE TABLE mimic_icu.datetimeevents
   warning SMALLINT
 );
 
-DROP TABLE IF EXISTS mimic_icu.d_items;
-CREATE TABLE mimic_icu.d_items
+DROP TABLE IF EXISTS mimiciv_icu.d_items;
+CREATE TABLE mimiciv_icu.d_items
 (
   itemid INTEGER NOT NULL,
   label VARCHAR(100) NOT NULL,
@@ -463,8 +463,8 @@ CREATE TABLE mimic_icu.d_items
   highnormalvalue FLOAT
 );
 
-DROP TABLE IF EXISTS mimic_icu.icustays;
-CREATE TABLE mimic_icu.icustays
+DROP TABLE IF EXISTS mimiciv_icu.icustays;
+CREATE TABLE mimiciv_icu.icustays
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -476,8 +476,8 @@ CREATE TABLE mimic_icu.icustays
   los FLOAT
 );
 
-DROP TABLE IF EXISTS mimic_icu.ingredientevents;
-CREATE TABLE mimic_icu.ingredientevents(
+DROP TABLE IF EXISTS mimiciv_icu.ingredientevents;
+CREATE TABLE mimiciv_icu.ingredientevents(
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
   stay_id INTEGER,
@@ -496,8 +496,8 @@ CREATE TABLE mimic_icu.ingredientevents(
   originalrate FLOAT
 );
 
-DROP TABLE IF EXISTS mimic_icu.inputevents;
-CREATE TABLE mimic_icu.inputevents
+DROP TABLE IF EXISTS mimiciv_icu.inputevents;
+CREATE TABLE mimiciv_icu.inputevents
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -526,8 +526,8 @@ CREATE TABLE mimic_icu.inputevents
   originalrate FLOAT
 );
 
-DROP TABLE IF EXISTS mimic_icu.outputevents;
-CREATE TABLE mimic_icu.outputevents
+DROP TABLE IF EXISTS mimiciv_icu.outputevents;
+CREATE TABLE mimiciv_icu.outputevents
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -539,8 +539,8 @@ CREATE TABLE mimic_icu.outputevents
   valueuom VARCHAR(20)
 );
 
-DROP TABLE IF EXISTS mimic_icu.procedureevents;
-CREATE TABLE mimic_icu.procedureevents
+DROP TABLE IF EXISTS mimiciv_icu.procedureevents;
+CREATE TABLE mimiciv_icu.procedureevents
 (
   subject_id INTEGER NOT NULL,
   hadm_id INTEGER NOT NULL,
@@ -567,7 +567,7 @@ CREATE TABLE mimic_icu.procedureevents
 EOSQL
 
 # goal: get path from find, e.g., ./1.0/icu/d_items
-# and return database table name for it, e.g., mimic_icu.d_items
+# and return database table name for it, e.g., mimiciv_icu.d_items
 make_table_name () {
     # strip leading directories (e.g., ./icu/hello.csv.gz -> hello.csv.gz)
     BASENAME=${1##*/}