change column definitions to match csv data

Author: JackieMium

mimic-ed/buildmimic/postgres/create.sql

@@ -60,7 +60,7 @@ CREATE TABLE mimic_ed.medrecon
   charttime TIMESTAMP(0) NOT NULL,
   name VARCHAR(255) NOT NULL,
   gsn VARCHAR(11) NOT NULL,
-  ndc VARCHAR(6) NOT NULL,
+  ndc VARCHAR(12) NOT NULL,
   etc_rn INT NOT NULL,
   etccode VARCHAR(8),
   etcdescription VARCHAR(255)
@@ -97,8 +97,8 @@ CREATE TABLE mimic_ed.triage
   o2sat DOUBLE PRECISION,
   sbp DOUBLE PRECISION,
   dbp DOUBLE PRECISION,
-  pain INT,
-  acuity INT,
+  pain DOUBLE PRECISION,
+  acuity DOUBLE PRECISION,
   chiefcomplaint VARCHAR(255)
 ) ;
 
@@ -118,6 +118,6 @@ CREATE TABLE mimic_ed.vitalsign
   o2sat DOUBLE PRECISION,
   sbp DOUBLE PRECISION,
   dbp DOUBLE PRECISION,
-  rhythm VARCHAR(50),
-  pain INT
-);
+  rhythm TEXT,
+  pain TEXT
+);

mimic-ed/buildmimic/postgres/load.sql

@@ -15,7 +15,7 @@
 \cd :mimic_data_dir
 
 -- If running scripts individually, you can set the schema where all tables are created as follows:
--- SET search_path TO mimicived;
+SET search_path TO mimic_ed;
 -- Restoring the search path to its default value can be accomplished as follows:
 -- SET search_path TO "$user",public;
 
@@ -29,35 +29,48 @@
 --------------------------------------------------------
 --  Load Data for Table diagnosis
 --------------------------------------------------------
-
+\echo '######################'
+\echo 'Copying diagnosis.....'
 \copy diagnosis FROM 'diagnosis.csv' DELIMITER ',' CSV HEADER NULL ''
+\echo 'Table diagnosis successfully generated.'
 
 --------------------------------------------------------
 --  Load Data for Table edstays
 --------------------------------------------------------
-
+\echo '###################'
+\echo 'Copying edstay.....'
 \copy edstays from 'edstays.csv' delimiter ',' csv header NULL ''
-
+\echo 'Table edstay successfully generated.'
 --------------------------------------------------------
 --  Load Data for Table medrecon
 --------------------------------------------------------
-
+\echo '#####################'
+\echo 'Copying medrecon.....'
 \copy medrecon from 'medrecon.csv' delimiter ',' csv header NULL ''
+\echo 'Table medrecon successfully generated.'
 
 --------------------------------------------------------
 --  Load Data for Table pyxis
 --------------------------------------------------------
-
+\echo '##################'
+\echo 'Copying pyxis.....'
 \copy pyxis from 'pyxis.csv' delimiter ',' csv header NULL ''
+\echo 'Table pyxis successfully generated.'
 
 --------------------------------------------------------
 --  Load Data for Table triage
 --------------------------------------------------------
-
+\echo '###################'
+\echo 'Copying triage.....'
 \copy triage from 'triage.csv' delimiter ',' csv header NULL ''
+\echo 'Table triage successfully generated.'
 
 --------------------------------------------------------
 --  Load Data for Table vitalsign
 --------------------------------------------------------
-
-\copy vitalsign from 'vitalsign.csv' delimiter ',' csv header NULL ''
+\echo '######################'
+\echo 'Copying vitalsign.....'
+\copy vitalsign from 'vitalsign.csv' delimiter ',' csv header NULL ''
+\echo 'Table vitalsign successfully generated.'
+\echo 'All tables generated.'
+\echo 'THE END.'

mimic-ed/buildmimic/postgres/load_gz.sql

@@ -15,7 +15,7 @@
 \cd :mimic_data_dir
 
 -- If running scripts individually, you can set the schema where all tables are created as follows:
--- SET search_path TO mimicived;
+SET search_path TO mimic_ed;
 -- Restoring the search path to its default value can be accomplished as follows:
 -- SET search_path TO "$user",public;
 
@@ -29,35 +29,49 @@
 --------------------------------------------------------
 --  Load Data for Table diagnosis
 --------------------------------------------------------
-
+\echo '######################'
+\echo 'Copying diagnosis.....'
 \copy diagnosis FROM PROGRAM 'gzip -dc diagnosis.csv.gz' DELIMITER ',' CSV HEADER NULL ''
+\echo 'Table diagnosis successfully generated.'
 
 --------------------------------------------------------
 --  Load Data for Table edstays
 --------------------------------------------------------
-
-\copy edstays from edstays 'gzip -dc edstays.csv.gz' delimiter ',' csv header NULL ''
+\echo '###################'
+\echo 'Copying edstay.....'
+\copy edstays from PROGRAM 'gzip -dc edstays.csv.gz' delimiter ',' csv header NULL ''
+\echo 'Table edstay successfully generated.'
 
 --------------------------------------------------------
 --  Load Data for Table medrecon
 --------------------------------------------------------
-
+\echo '#####################'
+\echo 'Copying medrecon.....'
 \copy medrecon from PROGRAM 'gzip -dc medrecon.csv.gz' delimiter ',' csv header NULL ''
+\echo 'Table medrecon successfully generated.'
 
 --------------------------------------------------------
 --  Load Data for Table pyxis
 --------------------------------------------------------
-
+\echo '##################'
+\echo 'Copying pyxis.....'
 \copy pyxis from PROGRAM 'gzip -dc pyxis.csv.gz' delimiter ',' csv header NULL ''
+\echo 'Table pyxis successfully generated.'
 
 --------------------------------------------------------
 --  Load Data for Table triage
 --------------------------------------------------------
-
+\echo '###################'
+\echo 'Copying triage.....'
 \copy triage from PROGRAM 'gzip -dc triage.csv.gz' delimiter ',' csv header NULL ''
+\echo 'Table triage successfully generated.'
 
 --------------------------------------------------------
 --  Load Data for Table vitalsign
 --------------------------------------------------------
-
-\copy vitalsign from PROGRAM 'gzip -dc vitalsign.csv.gz' delimiter ',' csv header NULL ''
+\echo '######################'
+\echo 'Copying vitalsign.....'
+\copy vitalsign from PROGRAM 'gzip -dc vitalsign.csv.gz' delimiter ',' csv header NULL ''
+\echo 'Table vitalsign successfully generated.'
+\echo 'All tables generated.'
+\echo 'THE END.'