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