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load_7z.sql
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-----------------------------------------
-- Load data into the MIMIC-IV schemas --
-----------------------------------------
-- To run from a terminal:
-- psql "dbname=<DBNAME> user=<USER>" -v mimic_data_dir=<PATH TO DATA DIR> -f load_gz.sql
\cd :mimic_data_dir
-- making sure that all tables are emtpy and correct encoding is defined -utf8-
SET CLIENT_ENCODING TO 'utf8';
-- hosp schema
\cd hosp
\COPY mimiciv_hosp.admissions FROM PROGRAM '7z e -so admissions.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.d_hcpcs FROM PROGRAM '7z e -so d_hcpcs.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.diagnoses_icd FROM PROGRAM '7z e -so diagnoses_icd.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.d_icd_diagnoses FROM PROGRAM '7z e -so d_icd_diagnoses.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.d_icd_procedures FROM PROGRAM '7z e -so d_icd_procedures.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.d_labitems FROM PROGRAM '7z e -so d_labitems.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.drgcodes FROM PROGRAM '7z e -so drgcodes.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.emar_detail FROM PROGRAM '7z e -so emar_detail.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.emar FROM PROGRAM '7z e -so emar.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.hcpcsevents FROM PROGRAM '7z e -so hcpcsevents.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.labevents FROM PROGRAM '7z e -so labevents.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.microbiologyevents FROM PROGRAM '7z e -so microbiologyevents.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.omr FROM PROGRAM '7z e -so omr.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.patients FROM PROGRAM '7z e -so patients.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.pharmacy FROM PROGRAM '7z e -so pharmacy.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.poe_detail FROM PROGRAM '7z e -so poe_detail.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.poe FROM PROGRAM '7z e -so poe.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.prescriptions FROM PROGRAM '7z e -so prescriptions.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.procedures_icd FROM PROGRAM '7z e -so procedures_icd.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.provider FROM PROGRAM '7z e -so provider.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.services FROM PROGRAM '7z e -so services.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_hosp.transfers FROM PROGRAM '7z e -so transfers.csv.gz' DELIMITER ',' CSV HEADER NULL '';
-- icu schema
\cd ../icu
\COPY mimiciv_icu.caregiver FROM PROGRAM '7z e -so caregiver.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_icu.chartevents FROM PROGRAM '7z e -so chartevents.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_icu.datetimeevents FROM PROGRAM '7z e -so datetimeevents.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_icu.d_items FROM PROGRAM '7z e -so d_items.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_icu.icustays FROM PROGRAM '7z e -so icustays.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_icu.ingredientevents FROM PROGRAM '7z e -so ingredientevents.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_icu.inputevents FROM PROGRAM '7z e -so inputevents.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_icu.outputevents FROM PROGRAM '7z e -so outputevents.csv.gz' DELIMITER ',' CSV HEADER NULL '';
\COPY mimiciv_icu.procedureevents FROM PROGRAM '7z e -so procedureevents.csv.gz' DELIMITER ',' CSV HEADER NULL '';