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ontology.sh
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Created
Thu, Oct 17, 01:30
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1 KB
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text/x-shellscript
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Sat, Oct 19, 01:30 (1 d, 23 h)
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R2664 SHRINE MedCo Fork
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."
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