Merge pull request #1656 from notwarn/keyan

Add the 'load_7z.sql' script to enable the loading of 'ed' module dat…

Author: alistairewj

mimic-iv-ed/buildmimic/postgres/load_7z.sql

@@ -0,0 +1,77 @@
+-- -------------------------------------------------------------------------------
+--
+-- Load data into the MIMICIVED schema
+--
+-- -------------------------------------------------------------------------------
+
+--------------------------------------------------------
+--  File created - Tue 08 Jun 2023
+--------------------------------------------------------
+
+-- To run from a terminal:
+--  psql "dbname=<DBNAME> user=<USER>" -v mimic_data_dir=<PATH TO DATA DIR> -f load_7z.sql
+
+-- Change to the directory containing the data files
+\cd :mimic_data_dir
+
+-- If running scripts individually, you can set the schema where all tables are created as follows:
+SET search_path TO mimiciv_ed;
+-- Restoring the search path to its default value can be accomplished as follows:
+-- SET search_path TO "$user",public;
+
+/* Set the mimic_data_dir variable to point to directory containing
+   all .csv files. If using Docker, this should not be changed here.
+   Rather, when running the docker container, use the -v option
+   to have Docker mount a host volume to the container path /mimic_data
+   as explained in the README file
+*/
+
+--------------------------------------------------------
+--  Load Data for Table diagnosis
+--------------------------------------------------------
+\echo '######################'
+\echo 'Copying diagnosis.....'
+\copy diagnosis FROM PROGRAM '7z e -so diagnosis.csv.gz' DELIMITER ',' CSV HEADER NULL ''
+\echo 'Table diagnosis successfully generated.'
+
+--------------------------------------------------------
+--  Load Data for Table edstays
+--------------------------------------------------------
+\echo '###################'
+\echo 'Copying edstays.....'
+\copy edstays from PROGRAM '7z e -so edstays.csv.gz' delimiter ',' csv header NULL ''
+\echo 'Table edstays successfully generated.'
+
+--------------------------------------------------------
+--  Load Data for Table medrecon
+--------------------------------------------------------
+\echo '#####################'
+\echo 'Copying medrecon.....'
+\copy medrecon from PROGRAM '7z e -so 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 '7z e -so 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 '7z e -so triage.csv.gz' delimiter ',' csv header NULL ''
+\echo 'Table triage successfully generated.'
+
+--------------------------------------------------------
+--  Load Data for Table vitalsign
+--------------------------------------------------------
+\echo '######################'
+\echo 'Copying vitalsign.....'
+\copy vitalsign from PROGRAM '7z e -so vitalsign.csv.gz' delimiter ',' csv header NULL ''
+\echo 'Table vitalsign successfully generated.'
+\echo 'All tables generated.'
+\echo 'THE END.'