Admin Tools

Overview

Documents the available admin tools and how to run them.

Admin Scripts

These admin scripts are in the admin/loader/src/main/scripts folder and make certain tasks easier.

• load.bat, load.csh 
  
  • Used to create database, clear indexes, and load terminology data.
• loadDelta.bat, loadDelta.csh
  
  • Used to run the delta loader.
• truncate_all.sql
  • MySQL script for removing all tables.
  • The alternative is to drop and recreate the schema

Update DB

Used to create or update the schema to accommodate new builds/installations or updating of schema.

• For this mojo to run, the database must already be created (e.g. Create database tsdb; )
• Connection parameters for the database must be set in the config.properties file.

• When running, pass a run.config parameter whose value is the path to the config.properties file.

• Note, the default behavior is to run with the hibernate.hbm2ddl.auto setting set to "update".  
  
  • This can be overridden by running with a -Dhibernate.hbm2ddl.auto=create setting.

% cd admin/updatedb
% mvn [-Dhibernate.hbm2ddl.auto=create] -Drun.config=/home/user/data/config.properties clean install

Loader

Used to load terminologies.

• For this mojo to run, the database must already be created (e.g. Create database tsdb; )
• Connection parameters for the database must be set in the config.properties file.

• When running, pass a run.config parameter whose value is the path to the config.properties file.

• When running, the name of the profile to be run must be indicated (see admin/loader/pom.xml for current options), e.g.  -P SNOMEDCT, -P ICD9CM
• The location of the RF2 formatted files must be supplied as an input parameter in config.properties, e.g. loader.SNOMEDCT.input.data=C:/data/snomedct-20140131-mini  and loader.ICD9CM.input.data=C:/data/icd9cm_2013.xml
• The parameters used to determine the defaultPreferredName for Concepts must be provided in the config.properties file. Current values are:
  

  • loader.defaultPreferredNames.typeId=900000000000013009

  • loader.defaultPreferredNames.refSetId=900000000000509007

  • loader.defaultPreferredNames.acceptabilityId=900000000000548007

% cd admin/loader
% mvn -Drun.config=/home/user/data/config.properties -PICD9CM clean install

Remover

Used to remove terminologies.

• For this mojo to run, the database must already be created (e.g. Create database tsdb; )
• Connection parameters for the database must be set in a the config.;properties file.

• When running, pass a run.config parameter whose value is the path to the config.;properties file.

• When running, the name of the profile to be run must be indicated (see admin/loader/pom.xml for current options), e.g. -P SNOMEDCT, -P ICD9CM.

% cd admin/remover
% mvn -Drun.config=/home/user/data/config.properties -PICD9CM clean install

Reindex

Used to create lucene indexes to facilitate searching.  Indexes are created based on the hibernate-search annotations such as @Indexed, @IndexedEmbedded, @Field, @ContainedInetc.

• Indexes are written into the directory specified by the hibernate.search.default.indexBase property

• When running, pass a run.config parameter whose value is the path to the config.properties file.

References/Links

• n/a