Health Ontology Mapper Installation Document (1.0)

Table of Contents

Table of Contents

Document Version History

OntoMapper Installation Instructions

Mapping Interpreter Install and Execution Instructions

Document Version History

OntoMapper Installation Instructions

• Download OntoMapper source from Recom SVN repository:

http://svn.recomdata.com/osr/OntologyMapper/trunk/IDR

• Create I2B2-OntoMapper schema per your database environment.

  http://wiki.recomdata.com/download/attachments/3866908/IDR_Schema_v1.5.gif

Execute the following scripts for Sybase IQ:

http://wiki.recomdata.com/download/attachments/3866908/I2B2DEMODATA_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2METADATA_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2WORKDATA_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2HIVE_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/Alter_I2B2DEMODATA_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2_Metadata_Insert_IQ.sql

http://wiki.recomdata.com/download/attachments/3866908/OntoMapper_Metadata_Insert_IQ.sql

Execute the following scripts for Oracle:

http://wiki.recomdata.com/download/attachments/3866908/I2B2DEMODATA_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2METADATA_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2WORKDATA_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2HIVE_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/Alter_I2B2DEMODATA_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/I2B2_Metadata_Insert_Oracle.sql

http://wiki.recomdata.com/download/attachments/3866908/OntoMapper_Metadata_Insert_Oracle.sql

• Configure dataSource properties per your environment in applicationContext.xml.  Both ‘dataSource’ and ‘i2b2MetadataDataSource’ needs to be modified.

WebContent\WEB-INF\applicationContext.xml

• Change the file (IRB & IACUC Approval file) upload folder in upload.properties per your environment.

src\upload.properties

• Configure the logger properties in log4j.properties.

src\log4j.properties

• Build the OntoMapper application by executing the ANT build file buildIDR.xml located under the root directory.

ant -f buildIDR.xml

• Deploy the generated IDR.war (found under root directory) onto any web server preferably Glassfish v2.1 server and restart the same. 

• Access the OntoMapper application via the URL:

http://localhost:8080/IDR/jsp/Login.jsf

Mapping Interpreter Install and Execution Instructions

• Configure the database properties per your environment in db.properties found under the root directory.

• Change the file (mapper instance xml file) upload folder in upload.properties per your environment.

src\upload.properties

• Configure the logger properties in log4j.properties.

src\log4j.properties

• Build the Mapping Interpreter by executing the ANT build file build.xml found under the root directory.

ant -f build.xml

• Execute the generated Mapper.jar (found under the root directory) by passing requisite parameters.  The Mapping Interpreter takes an xml file (mapper instance file) as input.

java -jar Mapper.jar file=xml\HSDB_Mapper.xml

• Once a mapper instance file is executed it could be re-run by supplying its id found in MAP_DIMENSION table of I2B2DEMODATA schema.

java -jar Mapper.jar id=1