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ontology.sh
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Created
Sat, Sep 14, 17:16
Size
1 KB
Mime Type
text/x-shellscript
Expires
Mon, Sep 16, 17:16 (2 d)
Engine
blob
Format
Raw Data
Handle
20782340
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."
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
sudo -u postgres psql
${
I2B2_DB_ONT_USER
}
< ontology_create_user.sql.interpolated
# we interpolate ontology_create_tables for Postgres in order to correctly set owner/grants
interpolate_file ./skel/ontology_create_tables.sql
"I2B2_DB_ONT_USER"
"${I2B2_DB_ONT_USER}"
|
\
interpolate
"I2B2_DB_SHRINE_ONT_USER"
"${I2B2_DB_SHRINE_ONT_USER}"
> ontology_create_tables.sql.interpolated
sudo -u postgres psql
${
I2B2_DB_ONT_USER
}
< ontology_create_tables.sql.interpolated
interpolate_file ./skel/ontology_table_access.sql
"I2B2_DB_SHRINE_ONT_USER"
"${I2B2_DB_SHRINE_ONT_USER}"
> ontology_table_access.sql.interpolated
sudo -u postgres psql
${
I2B2_DB_ONT_USER
}
< ontology_table_access.sql.interpolated
#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
}
${
SHRINE_ONTOLOGY_SQL_FILE_URL
}
# temporary workaround to make sure all insert statements use the proper schema
sed -i
'1s/^/SET search_path TO '
"${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
}
#####
echo
"[i2b2/ontology.sh] Done."
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