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