1.22.8-medco

ontology.sh
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			#!/bin/bash

			echo "[i2b2/ontology.sh] Begin."

			#########
			# I2B2 Ontology Setup for SHRINE
			#
			#########
			source ./i2b2.rc
			#########

			#####
			echo "[i2b2/ontology.sh] Creating shrine_ont user."

			interpolate_file ./skel/ontology_create_user.sql "I2B2_DB_SHRINE_ONT_USER" "${I2B2_DB_SHRINE_ONT_USER}" \| \
			interpolate "I2B2_DB_SHRINE_ONT_PASSWORD" "${I2B2_DB_SHRINE_ONT_PASSWORD}" > ontology_create_user.sql.interpolated

			sqlplus system/${I2B2_ORACLE_SYSTEM_PASSWORD}@${I2B2_ORACLE_SID} < ontology_create_user.sql.interpolated

			sqlplus ${I2B2_DB_SHRINE_ONT_USER}/${I2B2_DB_SHRINE_ONT_PASSWORD}@${I2B2_ORACLE_SID} < ontology_create_tables.sql
			sqlplus ${I2B2_DB_SHRINE_ONT_USER}/${I2B2_DB_SHRINE_ONT_PASSWORD}@${I2B2_ORACLE_SID} < ontology_table_access.sql

			#echo "NEED TO DO SCHEMES"
			#echo "select distinct c_key, c_name from i2b2demodata.schemes"

			#########
			echo "[i2b2/ontology.sh] Downloading shrine ontology."

			SHRINE_ONTOLOGY_SQL_FILE="Shrine.sql"
			SHRINE_ONTOLOGY_SQL_FILE_URL=`perl ../determine-shrine-sql-url.pl`
			wget --no-clobber -O ${SHRINE_ONTOLOGY_SQL_FILE} ${SHRINE_ONTOLOGY_SQL_FILE_URL}

			#####
			echo "[i2b2/ontology.sh] Inserting shrine ontology."

			sqlplus ${I2B2_DB_SHRINE_ONT_USER}/${I2B2_DB_SHRINE_ONT_PASSWORD}@${I2B2_ORACLE_SID} < ${SHRINE_ONTOLOGY_SQL_FILE}

			#####

			echo "[i2b2/ontology.sh] Done."