Add HiRID v1.1.1 dataset to Postgres

N.B. This is for the raw data rather than the merged or imputed.

1 Download database and SQL scripts

1. Get permission to use HiRID dataset from here. https://physionet.org/content/hirid/1.1.1
2. Download the raw data files.

wget -r -N -c -np --user physionet user --ask-password https://physionet.org/files/hirid/1.1.1/raw_stage/observation_tables_csv.tar.gz
wget -r -N -c -np --user physionet user --ask-password https://physionet.org/files/hirid/1.1.1/raw_stage/pharma_records_csv.tar.gz

3. Unzip the .tar.gz files using e.g. tarball (Linux/Mac OS) or 7zip (windows)
4. Download the scripts from this repository.

2 Install Postgres

sudo apt-get install postgresql # (Linux)
brew install postgres           # (Mac OS)

or http://www.postgresql.org/download/ (Any Operating System incl Windows)

3 Create a user, database and schema in Postgres

sudo -u postgres psql # enter into postgres

# in postgres pay attention to the semicolons!
ALTER USER postgres PASSWORD 'myPassword'; # create password
#ALTER ROLE
CREATE DATABASE hirid; # create database
#CREATE DATABASE
\c hirid  # connect to database
#you are now connected to database "hirid" as user "postgres"
CREATE SCHEMA hirid; 
# CREATE SCHEMA
\q # quit

4 Load data into postgres

cd /folder/containing/data/and/scripts
psql -U postgres -h 127.0.0.1 -f create_tables.sql 'dbname=hirid options=--search_path=hirid password = myPassword'      # create tables 
psql -U postgres -h 127.0.0.1  -f load_data.sql 'dbname=hirid options=--search_path=hirid password = myPassword'         # load hirid data into tables. This may take a while
psql -U postgres -h 127.0.0.1  -f postgres_check.sql 'dbname=hirid options=--search_path=hirid password = myPassword'    # checks if the data has been loaded corrected

References

1. Hyland, S.L., Faltys, M., Hüser, M. et al. Early prediction of circulatory failure in the intensive care unit using machine learning. Nat Med 26, 364–373 (2020). https://doi.org/10.1038/s41591-020-0789-4
2. CircEWS Github repository https://github.com/ratschlab/circEWS