UTHSCSA-CIRD/chinotype

Name: chinotype

Owner: Clinical Informatics Research Division

Description: 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.

Created: 2015-07-17 01:00:41.0

Updated: 2017-03-20 21:04:56.0

Pushed: 2017-11-08 12:28:34.0

Homepage:

Size: 5201

Language: Python

GitHub Committers

User	Most Recent Commit	# Commits
Check your git settings!	2015-10-07 23:34:45.0	27
Alex F. Bokov, Ph.D.	2017-04-09 23:16:05.0	87
bos666	2016-05-18 21:27:26.0	8

Other Committers

User	Email	Most Recent Commit	# Commits
Alex F Bokov	bokov@i2b2-mi-web.v126.strf.uthscsa.edu	2015-07-17 02:17:43.0	3
Angela Bos	bos@deb-mi-staging.v126.strf.uthscsa.edu	2015-08-12 22:02:36.0	12

README

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)

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

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

Development Environment

install epel-release
install python-pip
install gcc
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

install argh
install argparse
install cx_Oracle

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

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

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

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