chinotype

General purpose script for looking for over and under represented EHR facts in an i2b2 patient-set. Can be used for finding healthcare outcomes disparities, comorbidities, and who knows what else. The name is a portmanteau of Chi-squared and phenotype.

Also includes a web plugin to call the script from i2b2.

Note: you may need to edit cgi-bin/chi2.cgi to have the correct LD_LIBRARY_PATH for your system. Note: this assumes you have already deployed apache, java, wildfly, and i2b2

Packages needed:

CentOS

Oracle Instant Client (download current latest version from oracle.com)

rpm -ivh ~/oracle-instantclient12.2-basic-12.2.0.1.0-1.i386.rpm
rpm -ivh ~/oracle-instantclient12.2-devel-12.2.0.1.0-1.i386.rpm

echo 'export ORACLE_VERSION="12.2"' >> $HOME/.bashrc
echo 'export ORACLE_HOME="/usr/lib/oracle/$ORACLE_VERSION/client"'>> $HOME/.bashrc
echo 'export PATH=$PATH:"$ORACLE_HOME/bin"' >> $HOME/.bashrc
echo 'export LD_LIBRARY_PATH="$ORACLE_HOME/lib"' >> $HOME/.bashrc

Development Environment

yum install epel-release
yum install python-pip
yum install gcc
yum install python-devel

Additional Python Modules

I don't know why yet, but you need to do these before you do pip install -r requirements.txt

pip install argh
pip install argparse
pip install cx_Oracle

Create Directories (assuming that your cgi scripts run with apache's permissions)

mkdir /var/log/chi2; chgrp apache /var/log/chi2; chmod g+w /var/log/chi2
cp -r chi2 /usr/local/chi2; chgrp -r apache /usr/local/chi2; chmod -R g+w /usr/local/chi2

cp cgi-bin/chi2.cgi /var/www/cgi-bin

mkdir /var/www/html/webclient/js-i2b2/cells/plugins/uthscsa/
cp -r webclient/js-i2b2/cells/plugins/uthscsa/chi2 /var/www/html/webclient/js-i2b2/cells/plugins/uthscsa