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medco-deployment/docker-images/i2b2/sql/05-i2b2-orig-data.sh
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05-i2b2-orig-data.sh
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#!/bin/bash
set -Eeuo pipefail
# load the structure and data of i2b2 database (including some bug fixes)
function loadI2b2Data {
DB_NAME="$1"
IS_ADDITIONAL_DB="$2"
# ---------- CRC data ----------
cd "$I2B2_DATA_DIR/edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata"
cat > db.properties <<EOL
db.type=postgresql
db.username=$I2B2_DB_USER
db.password=$I2B2_DB_PW
db.driver=org.postgresql.Driver
db.url=jdbc:postgresql://$I2B2_DB_HOST:$I2B2_DB_PORT/$DB_NAME?currentSchema=i2b2demodata_i2b2
db.project=demo
EOL
ant -f data_build.xml create_crcdata_tables_release_1-7
ant -f data_build.xml create_procedures_release_1-7
if ! ${IS_ADDITIONAL_DB}
then
ant -f data_build.xml db_demodata_load_data
fi
# ---------- Hive data ----------
cd "$I2B2_DATA_DIR/edu.harvard.i2b2.data/Release_1-7/NewInstall/Hivedata"
cat > db.properties <<EOL
db.type=postgresql
db.username=$I2B2_DB_USER
db.password=$I2B2_DB_PW
db.driver=org.postgresql.Driver
db.url=jdbc:postgresql://$I2B2_DB_HOST:$I2B2_DB_PORT/$DB_NAME?currentSchema=i2b2hive
EOL
if ! ${IS_ADDITIONAL_DB}
then
ant -f data_build.xml create_hivedata_tables_release_1-7
ant -f data_build.xml db_hivedata_load_data
fi
# ---------- IM data ----------
cd "$I2B2_DATA_DIR/edu.harvard.i2b2.data/Release_1-7/NewInstall/Imdata"
cat > db.properties <<EOL
db.type=postgresql
db.username=$I2B2_DB_USER
db.password=$I2B2_DB_PW
db.driver=org.postgresql.Driver
db.url=jdbc:postgresql://$I2B2_DB_HOST:$I2B2_DB_PORT/$DB_NAME?currentSchema=i2b2imdata
db.project=demo
EOL
ant -f data_build.xml create_imdata_tables_release_1-7
if ! ${IS_ADDITIONAL_DB}
then
ant -f data_build.xml db_imdata_load_data
fi
# ---------- Metadata ----------
cd "$I2B2_DATA_DIR/edu.harvard.i2b2.data/Release_1-7/NewInstall/Metadata"
cat > db.properties <<EOL
db.type=postgresql
db.username=$I2B2_DB_USER
db.password=$I2B2_DB_PW
db.driver=org.postgresql.Driver
db.url=jdbc:postgresql://$I2B2_DB_HOST:$I2B2_DB_PORT/$DB_NAME?currentSchema=i2b2metadata_i2b2
db.project=demo
EOL
ant -f data_build.xml create_metadata_tables_release_1-7
if ! ${IS_ADDITIONAL_DB}
then
ant -f data_build.xml db_metadata_load_data
fi
# ---------- PM data ----------
cd "$I2B2_DATA_DIR/edu.harvard.i2b2.data/Release_1-7/NewInstall/Pmdata"
cat > db.properties <<EOL
db.type=postgresql
db.username=$I2B2_DB_USER
db.password=$I2B2_DB_PW
db.driver=org.postgresql.Driver
db.url=jdbc:postgresql://$I2B2_DB_HOST:$I2B2_DB_PORT/$DB_NAME?currentSchema=i2b2pm
EOL
if ! ${IS_ADDITIONAL_DB}
then
ant -f data_build.xml create_pmdata_tables_release_1-7
ant -f data_build.xml create_triggers_release_1-7
ant -f data_build.xml db_pmdata_load_data
fi
# ---------- Work data ----------
cd "$I2B2_DATA_DIR/edu.harvard.i2b2.data/Release_1-7/NewInstall/Workdata"
cat > db.properties <<EOL
db.type=postgresql
db.username=$I2B2_DB_USER
db.password=$I2B2_DB_PW
db.driver=org.postgresql.Driver
db.url=jdbc:postgresql://$I2B2_DB_HOST:$I2B2_DB_PORT/$DB_NAME?currentSchema=i2b2workdata
db.project=demo
EOL
ant -f data_build.xml create_workdata_tables_release_1-7
ant -f data_build.xml db_workdata_load_data
# ---------- Data bug fixes ----------
if ! ${IS_ADDITIONAL_DB}
then
psql $PSQL_PARAMS -d "$DB_NAME" <<-EOSQL
update i2b2hive.crc_db_lookup set c_db_fullschema = 'i2b2demodata_i2b2' where c_domain_id = 'i2b2demo';
update i2b2hive.im_db_lookup set c_db_fullschema = 'i2b2imdata' where c_domain_id = 'i2b2demo';
update i2b2hive.ont_db_lookup set c_db_fullschema = 'i2b2metadata_i2b2' where c_domain_id = 'i2b2demo';
update i2b2hive.work_db_lookup set c_db_fullschema = 'i2b2workdata' where c_domain_id = 'i2b2demo';
EOSQL
fi
}
loadI2b2Data $I2B2_DB_NAME false
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