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i2b2.rc
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Sun, Nov 10, 02:12

i2b2.rc
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#!/bin/bash
#########
# I2B2 Environment variables
#
# You can install by setting the i2b2 IP address and then using defaults.
# You MUST change the default passwords for production operation.
#
# To include this script for your logon, you can add a line to your bash profile like this
# vi ~/.bashrc
#########
COMMON_RC_FILE=common.rc
if [ -f ~/${COMMON_RC_FILE} ] ; then
source ~/${COMMON_RC_FILE}
elif [ -f ../../${COMMON_RC_FILE} ] ; then
source ../../${COMMON_RC_FILE}
else
echo "Either ~/${COMMON_RC_FILE} or ../../${COMMON_RC_FILE} must be present" ; exit -1
fi
# at-a-glance way to check whether we're using Oracle or Postgres or MSSQL
export I2B2_RDBMS=sqlserver
#
#WILL NEED TO CHANGE IF NOT IN I2B2 VM
#The i2b2 user Shrine should log in as.
export SHRINE_USER=shrine
#The plaintext password for the i2b2 user Shrine should log in as.
export SHRINE_OBFUSCATED_WEBCLIENT_PASSWORD=demouser
#SHRINE_OBFUSCATED_WEBCLIENT_PASSWORD hashed with i2b2's password-hashing algorithm
if [ -f ../I2b2PasswordCryptor.java ] ; then
export SHRINE_PASSWORD_CRYPTED=`javac ../I2b2PasswordCryptor.java && java -classpath ../ I2b2PasswordCryptor ${SHRINE_OBFUSCATED_WEBCLIENT_PASSWORD}`
fi
#The directory containing the JBoss application server that i2b2 runs in.
export JBOSS_HOME=/opt/jboss
if [ ! -d $JBOSS_HOME ] ; then
# try alternative versioned JBoss directory (used by newer VM images)
export JBOSS_HOME=( ${JBOSS_HOME}* )
fi
#A directory inside JBoss where important files will go.
export JBOSS_DEPLOY_DIR="${JBOSS_HOME}/standalone/deployments"
#ITL server address for the MSSQL server
#MUST CHANGE THIS OR IT WILL NOT WORK!
export I2B2_DB_SERVER=[MSSQL Server (ie. sql01.mydomain.edu)]
#ITL default username and password for the MSSQL server
#This value can be used if a single SQL account is
# used to connect to the i2b2 database(s)
# or it can be overridden below if different accounts are used for various cells
# NOTE: this account should already exist on the SQL Server
# and have permission to access the database(s) used for i2b2 and shrine
export I2B2_DB_USER=i2b2_dbo
export I2B2_DB_PASSWORD=demouser
export I2B2_DB_SCHEMA=dbo
#Postgres role for the i2b2 PM cell
export I2B2_DB_PM_SERVER=${I2B2_DB_SERVER}
export I2B2_DB_PM_USER=i2b2pm
export I2B2_DB_PM_PASSWORD=${I2B2_DB_PASSWORD}
export I2B2_DB_PM_DATABASE=i2b2pm
export I2B2_DB_PM_JDBC_URL=jdbc:sqlserver://${I2B2_DB_PM_SERVER}:1433;databaseName=${I2B2_DB_PM_DATABASE}
#ITL Configuration for the i2b2 Hive
#ITL server address for the MSSQL server
export I2B2_DB_HIVE_SERVER=${I2B2_DB_SERVER}
export I2B2_DB_HIVE_USER=i2b2hive
export I2B2_DB_HIVE_PASSWORD=${I2B2_DB_PASSWORD}
export I2B2_DB_HIVE_DATABASE=i2b2hive
#ITL modified to use MSSQL connection string
export I2B2_DB_HIVE_JDBC_URL=jdbc:sqlserver://${I2B2_DB_HIVE_SERVER}:1433;databaseName=${I2B2_DB_HIVE_DATABASE}
#Java DataSource name used by the i2b2 hive
export I2B2_DB_HIVE_DATASOURCE_NAME=OntologyBootStrapDS
#ITL Configuration for the i2b2 ontology cell
export I2B2_DB_ONT_SERVER=${I2B2_DB_SERVER}
export I2B2_DB_ONT_USER=i2b2metadata
export I2B2_DB_ONT_PASSWORD=${I2B2_DB_PASSWORD}
export I2B2_DB_ONT_DATABASE=i2b2metadata
export I2B2_DB_ONT_JDBC_URL=jdbc:sqlserver://${I2B2_DB_ONT_SERVER}:1433;databaseName=${I2B2_DB_ONT_DATABASE}
#Java DataSource name used by the i2b2 ontology cell
export I2B2_DB_ONT_DATASOURCE_NAME=OntologyDemoDS
#ITL Configuration for the Shrine ontology cell
#NOTE: defaults to the same connection information as the i2b2 ONT cel
export I2B2_DB_SHRINE_ONT_SERVER=${I2B2_DB_ONT_SERVER}
export I2B2_DB_SHRINE_ONT_USER=${I2B2_DB_ONT_USER}
export I2B2_DB_SHRINE_ONT_PASSWORD=${I2B2_DB_ONT_PASSWORD}
export I2B2_DB_SHRINE_ONT_DATABASE=${I2B2_DB_ONT_DATABASE}
export I2B2_DB_SHRINE_ONT_JDBC_URL=jdbc:sqlserver://${I2B2_DB_SERVER}:1433;databaseName=${I2B2_DB_SHRINE_ONT_DATABASE}
#Java DataSource name used by the Shrine ontology cell
export I2B2_DB_SHRINE_ONT_DATASOURCE_NAME=OntologyShrineDS
#ITL Configuration for the i2b2 CRC cell
export I2B2_DB_CRC_SERVER=${I2B2_DB_SERVER}
export I2B2_DB_CRC_USER=i2b2demodata
export I2B2_DB_CRC_PASSWORD=${I2B2_DB_PASSWORD}
export I2B2_DB_CRC_DATABASE=i2b2demodata
export I2B2_DB_CRC_JDBC_URL=jdbc:sqlserver://${I2B2_DB_CRC_SERVER}:1433;databaseName=${I2B2_DB_CRC_DATABASE}
#Java DataSource name used by the i2b2 CRC cell
export I2B2_DB_CRC_DATASOURCE_NAME=QueryToolDemoDS
#ITL Configuration for the i2b2 IM cell
export I2B2_DB_IM_SERVER=${I2B2_DB_SERVER}
export I2B2_DB_IM_USER=i2b2imdata
export I2B2_DB_IM_PASSWORD=${I2B2_DB_PASSWORD}
export I2B2_DB_IM_DATABASE=i2b2imdata
export I2B2_DB_IM_JDBC_URL=jdbc:sqlserver://${I2B2_DB_IM_SERVER}:1433;databaseName=${I2B2_DB_IM_DATABASE}
#ITL Configuration for the i2b2 WORK cell
export I2B2_DB_WORK_SERVER=${I2B2_DB_SERVER}
export I2B2_DB_WORK_USER=i2b2workdata
export I2B2_DB_WORK_PASSWORD=${I2B2_DB_PASSWORD}
export I2B2_DB_WORK_DATABASE=i2b2workdata
export I2B2_DB_WORK_JDBC_URL=jdbc:sqlserver://${I2B2_DB_WORK_SERVER}:1433;databaseName=${I2B2_DB_WORK_DATABASE}
#END THINGS THAT WILL NEED TO CHANGE

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