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ontology.sh
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Created
Fri, Sep 27, 12:00
Size
2 KB
Mime Type
text/x-shellscript
Expires
Sun, Sep 29, 12:00 (2 d)
Engine
blob
Format
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Handle
21140443
Attached To
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: "
${
I2B2_DB_SHRINE_ONT_USER
}
interpolate_file ./skel/ontology_create_user.sql
"I2B2_DB_SHRINE_ONT_USER"
"${I2B2_DB_SHRINE_ONT_USER}"
|
\
interpolate
"I2B2_DB_SHRINE_ONT_PASSWORD"
"${I2B2_DB_SHRINE_ONT_PASSWORD}"
|
\
interpolate
"I2B2_DB_SHRINE_ONT_DATABASE"
"${I2B2_DB_SHRINE_ONT_DATABASE}"
|
\
interpolate
"I2B2_DB_SCHEMA"
"${I2B2_DB_SCHEMA}"
> ontology_create_user.sql.interpolated
#sudo -u postgres psql ${I2B2_DB_ONT_USER} < ontology_create_user.sql.interpolated
java -cp ../../:../../sqljdbc.jar tsql ontology_create_user.sql.interpolated
\
${
I2B2_DB_ONT_SERVER
}
${
I2B2_DB_ONT_USER
}
${
I2B2_DB_ONT_PASSWORD
}
${
I2B2_DB_ONT_DATABASE
}
# we interpolate ontology_create_tables for Postgres in order to correctly set owner/grants
interpolate_file ./skel/ontology_create_tables.sql
"I2B2_DB_SCHEMA"
"${I2B2_DB_SCHEMA}"
\
> ontology_create_tables.sql.interpolated
#sudo -u postgres psql ${I2B2_DB_ONT_USER} < ontology_create_tables.sql.interpolated
java -cp ../../:../../sqljdbc.jar tsql ontology_create_tables.sql.interpolated
\
${
I2B2_DB_ONT_SERVER
}
${
I2B2_DB_ONT_USER
}
${
I2B2_DB_ONT_PASSWORD
}
${
I2B2_DB_ONT_DATABASE
}
interpolate_file ./skel/ontology_table_access.sql
"I2B2_DB_SCHEMA"
"${I2B2_DB_SCHEMA}"
> ontology_table_access.sql.interpolated
#sudo -u postgres psql ${I2B2_DB_ONT_USER} < ontology_table_access.sql.interpolated
java -cp ../../:../../sqljdbc.jar tsql ontology_table_access.sql.interpolated
\
${
I2B2_DB_ONT_SERVER
}
${
I2B2_DB_ONT_USER
}
${
I2B2_DB_ONT_PASSWORD
}
${
I2B2_DB_ONT_DATABASE
}
#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
}
${
SHRINE_ONTOLOGY_SQL_FILE_URL
}
#NOTE: this is not needed for MSSQL
# temporary workaround to make sure all insert statements use the proper schema
#sed -i '1s/^/SET search_path TO '"${I2B2_DB_SHRINE_ONT_USER}"';\n/' ${SHRINE_ONTOLOGY_SQL_FILE}
#####
echo
"[i2b2/ontology.sh] Inserting shrine ontology."
#sudo -u postgres psql ${I2B2_DB_ONT_USER} < ${SHRINE_ONTOLOGY_SQL_FILE}
java -cp ../../:../../sqljdbc.jar tsql
${
SHRINE_ONTOLOGY_SQL_FILE
}
\
${
I2B2_DB_ONT_SERVER
}
${
I2B2_DB_ONT_USER
}
${
I2B2_DB_ONT_PASSWORD
}
${
I2B2_DB_ONT_DATABASE
}
#####
echo
"[i2b2/ontology.sh] Done."
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