prepare.sh
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prepare.sh
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			#!/bin/bash

			#########
			echo "[i2b2/prepare.sh] begin."
			#########
			#
			# I2B2 Configuration for SHRINE
			#
			# Steps
			# 1. hive: creates the shrine project
			# 2. ontology: loads up the shrine ontology
			#
			#
			# @see i2b2.rc
			# @see called scripts.
			#
			#########
			rm ~/i2b2.rc
			cp i2b2.rc ~/i2b2.rc
			cp ../../common.rc ~/common.rc
			cp i2b2-aliases.sh ~
			chmod 640 ~/common.rc
			chmod 640 ~/i2b2.rc
			chmod 750 ~/i2b2-aliases.sh
			source ./i2b2.rc
			#########

			chmod +x *.sh

			#########
			# echo "[i2b2/prepare.sh] Shutting down JBOSS, just to be on the safe side."
			# i2b2_jboss_shutdown
			# TODO: make cleaner

			#########
			echo "[i2b2/prepare.sh] Your I2B2 Environment Variables (see i2b2.rc)"

			export \| grep I2B2

			##########

			#Complie the java class to execute jdbc scripts
			javac ../../tsql.java

			../install_prereqs.sh
			./configure_hive.sh
			./configure_pm.sh
			./ontology.sh
			./reconfigure-i2b2.sh
			./disable-update-cells.sh
			./post-install.sh

			##########
			echo "[i2b2/prepare.sh] done."
			##########

			# echo "[i2b2/prepare.sh] Clean start of JBOSS"
			# i2b2_jboss_startup