Build caTIES

• cancer Text Information and Extraction Service loads the surgical pathology reports and associates them to the Participants and Specimen collection groups in the Suite database. caTIES offers

1. pathology report loading service
2. de-ID service
3. concept coding the pathology reports against NCI MetaThesaurus

• Right now, we will configure caTIES to support pathology report loading and concept coding services. Steps to deploy caTIES:
• Make sure Jboss service is up and running. If its not, start the service as root

  service jboss-catissue-webapp start
  

• Open file remoteService.xml at the following location:

  su - catissue
  pushd src/caTissueSuite_11_installer/caTissueSuite_Client/conf
  

• Change the host name and port in remoteService.xml to look as follows:

  <property name="serviceUrl">
     <value>http://your.new.host.name:38080/catissuecore/http/remoteService</value>
  </property>
  

• Switch to catissueSuiteInstaller

  popd
  
  pushd src/caTissueSuite_11_installer
  

• Deploy Gate Library

  ant -f deploy.xml deploy_gate
  

• Deploy caTIES

  ant -f deploycaties.xml deploy_caties
  
  popd
  

• We have configured the caTIES for the report loading and concept coding services. Both these services are ad-hoc services i.e., they do not run the background always, they are invoked only when there are HL7 reports to be loaded into the caTissueSuite. To make use of these two services, first need to run the report loader and later, the concept coder service.
• Run the Report Loader Service

  pushd ~/reportLoader
  
  ant run_report_loader_server
  

• The above service can be stopped with ant stop_report_loader_server from the same directory
• Run the Concept Coder Service

  popd
  
  pushd ~/conceptCoder
  
  ant run_concept_code_server
  
  popd
  

• The above service can be stopped with ant stop_concept_code_server from the same directory
• Please refer to Chapter 3 from the caTissueSuite Deployment Manual for further details

Inject Test Data into caTissueSuite Database

• caTissueSuite database can be populated with test data by running the test cases.

• Change directory to the following location

  su - catissue
  
  pushd src/caTissueSuite_11_installer/caTissueSuite_Client/src/edu/wustl/catissuecore/bizlogic/test/
  

• Open file CaTissueBaseTestCase.java from the above location and do the following:
  • change the default username (admin@admin.com) to the value specified in /home/catissue/src/caTissueSuite_11_installer/caTissueInstall.properties for the property first.admin.emailAddress
  • change the default password (Test123) to the value specified in /home/catissue/src/caTissueSuite_11_installer/caTissueInstall.properties file for the property first.admin.password NOTE: If you have changed your password, after logging into the caTissueSuite web application for the first time, you should change the password here with the same.
• Compile and run the test cases

  popd
  
  pushd src/caTissueSuite_11_installer/caTissueSuite_Client
  
  ant runNightlyBuild
  
  popd