Informatics for Integrating Biology and the Bedside

Clinical Research Chart Cell Installation Guide (Linux)

Document Version 15

i2b2 Software Version 13

ii

Table of Contents

About this Guide _______________________________________________________ iii

Document Version History _______________________________________________ iii

Prerequisites ___________________________________________________________ 1 Required Software __________________________________________________________ 1

Install ________________________________________________________________ 4 Installing the Clinical Research Chart Application ________________________________ 4 Changing Server log level____________________________________________________ 10

Verify Installation _____________________________________________________ 11 CRC Cell Sanity Test via the i2b2Workbench ___________________________________ 11

License ______________________________________________________________ 15

iii

About this Guide Informatics for Integrating Biology and the Bedside (i2b2) is one of the sponsored initiatives of the NIH Roadmap National Centers for Biomedical Computing (httpwwwbistinihgovncbc) One of the goals of i2b2 is to provide clinical investigators broadly with the software tools necessary to collect and manage project-related clinical research data in the genomics age as a cohesive entitymdasha software suite to construct and manage the modern clinical research chart This guide with the provided source code will help you deploy an i2b2 cell

Document Version History Date Revision Description Author(s)

10262007 10 Version 10 Rajesh Kuttan Lori Phillips

06302008 11 Added multiple data source lookup configuration based on domain project and user JBoss data source configuration change (XA to Local transaction) CRCApplicationContextxml property change

Rajesh Kuttan

8202008 12 Uploader service install added Rajesh Kuttan 8272008 13 Updated JBOSS version Lori Phillips 9242008 14 File Repository integration with

CRC Uploader added

Rajesh Kuttan

10202008 15 Added info for two projects Lori Phillips

ii

Table of Contents

About this Guide _______________________________________________________ iii

Document Version History _______________________________________________ iii

Prerequisites ___________________________________________________________ 1 Required Software __________________________________________________________ 1

Install ________________________________________________________________ 4 Installing the Clinical Research Chart Application ________________________________ 4 Changing Server log level____________________________________________________ 10

Verify Installation _____________________________________________________ 11 CRC Cell Sanity Test via the i2b2Workbench ___________________________________ 11

License ______________________________________________________________ 15

iii

About this Guide Informatics for Integrating Biology and the Bedside (i2b2) is one of the sponsored initiatives of the NIH Roadmap National Centers for Biomedical Computing (httpwwwbistinihgovncbc) One of the goals of i2b2 is to provide clinical investigators broadly with the software tools necessary to collect and manage project-related clinical research data in the genomics age as a cohesive entitymdasha software suite to construct and manage the modern clinical research chart This guide with the provided source code will help you deploy an i2b2 cell

Document Version History Date Revision Description Author(s)

10262007 10 Version 10 Rajesh Kuttan Lori Phillips

06302008 11 Added multiple data source lookup configuration based on domain project and user JBoss data source configuration change (XA to Local transaction) CRCApplicationContextxml property change

Rajesh Kuttan

8202008 12 Uploader service install added Rajesh Kuttan 8272008 13 Updated JBOSS version Lori Phillips 9242008 14 File Repository integration with

CRC Uploader added

Rajesh Kuttan

10202008 15 Added info for two projects Lori Phillips

iii

About this Guide Informatics for Integrating Biology and the Bedside (i2b2) is one of the sponsored initiatives of the NIH Roadmap National Centers for Biomedical Computing (httpwwwbistinihgovncbc) One of the goals of i2b2 is to provide clinical investigators broadly with the software tools necessary to collect and manage project-related clinical research data in the genomics age as a cohesive entitymdasha software suite to construct and manage the modern clinical research chart This guide with the provided source code will help you deploy an i2b2 cell

Document Version History Date Revision Description Author(s)

10262007 10 Version 10 Rajesh Kuttan Lori Phillips

06302008 11 Added multiple data source lookup configuration based on domain project and user JBoss data source configuration change (XA to Local transaction) CRCApplicationContextxml property change

Rajesh Kuttan

8202008 12 Uploader service install added Rajesh Kuttan 8272008 13 Updated JBOSS version Lori Phillips 9242008 14 File Repository integration with

CRC Uploader added

Rajesh Kuttan

10202008 15 Added info for two projects Lori Phillips

1 Prerequisites

Required Software If you installed the prerequisite software from the Hive Installation Guide you may skip this section

a Java JDK JDK 50 (recommended) Download JDK 50 Update 11 (jdk-1_5_0_11-linux-i586bin) from httpjavasuncomproductsarchive

b JBoss 422GA Download ldquojboss-422GAziprdquo from httplabsjbosscomjbossasdownloads

a) Unzip jboss-422GAzip into a directory of your choice (optjboss-422GA or YOUR_JBOSS_HOME_DIR)

b) Set JBoss JVM to run with 1GB extended memory

Edit ldquoYOUR_JBOSS_HOME_DIRbinrunconfrdquo and change the JAVA_OPTS memory settings to that shown below (-Xms512m -Xmx1024m)

Specify options to pass to the Java VM if [ ldquox$JAVA_OPTSrdquo = ldquoxrdquo ] then JAVA_OPTS=-Xms512m ndashXmx1024m

-DsunrmidgcclientgcInterval=3600000 -DsunrmidgcservergcInterval=3600000

fi

c) If default port 8080 is unavailable (another application is using this port) edit ldquoYOUR_JBOSS_HOME_DIRserverdefaultdeployjboss-webdeployer

2

serverxmlrdquo file to reconfigure the non-SSL HTTP11 Connector to another port such as 9090

ltmdashDefine a non-SSL HTTP11 Connector on port 9090 ltConnector port=9090 address=$jbossbindaddress maxThreads=250 maxHttpHeaderSize=8192 emptySessionPath=true protocol=HTTP11 enableLookups=false redirectPort=8443 acceptCount=100 connectionTimeout=20000

disableUploadTimeout=true gt

ltmdashDefine an AJP 13 Connector on port 9009 ltConnector port=9009 address=$jbossbindaddress maxThreads=250 maxHttpHeaderSize=8192 protocol=AJP13 emptySessionPath=true enableLookups=rdquofalserdquo redirectPort=rdquo8443rdquogt

c Apache Ant 165

Download ldquoApache Ant version 165rdquo (apache-ant-165-binzip) from httparchiveapacheorgdistantbinaries a) Unzip into a directory of your choice (optapache-ant-165 or YOUR_ANT_HOME_DIR)

d Apache Axis2 11 Download ldquoApache Axis2 version 11rdquo from httpwsapacheorgaxis2download1_1downloadcgi and select the download type WAR (Web Archive) Distribution (axis2war) a) Create folder i2b2war inside ldquoYOUR_JBOSS_HOME_DIRserverdefaultdeployrdquo b) Unzip axis2war inside ldquoYOUR_JBOSS_HOME_DIRserverdefaultdeployi2b2warrdquo folder

3

e Oracle Express Edition

a) Download Oracle Database 10gExpress Edition (Universal) ldquooracle 10g EErdquo ldquooracle-xe-univ-10201-10i386rpmrdquo from httpwwworaclecomtechnologysoftwareproductsdatabasexehtdocs102xelinsofthtml

b) Run ldquorpm -i oracle-xe-univ-10201-10i386rpmrdquo as root Run ldquoetcinitdoracle-xe configurerdquo as root to configure the database Select HTTP and listener ports (use defaults 80801521 if they are available)

Select ldquoYrdquoes to start on boot when asked c) To verify that Oracle was properly installed open a browser and enter

httpyourHostyourPortapex You should see an Oracle Database Express Edition login screen

f CVS client If installing application source code from CVS make sure $CVSROOT variable is pointed to phsi2b2appdevrsquos cvsrepository (exttomcatphsi2b2appdevmghharvardeducvsrepository)

g Update your environment variables Be sure to set the JAVA_HOME ANT_HOME and JBOSS_HOME variables to the JAVA ANT and JBOSS home directories you set up in steps a-c respectively Examples are shown below

Sample environment variables JAVA_HOME=optjavajdk150_11 ANT_HOME=optapache-ant-165 JBOSS_HOME=optjboss-420GA PATH=$PATH$ANT_HOMEbin$JAVA_HOMEbin export JBOSS_HOME export ANT_HOME export JAVA_HOME h Data installation or upgrade has already been performed

4

2 Install

Installing the Clinical Research Chart Application

1 Download and extract the core server source code to a target area If this has been downloaded in a previous installation (eg PM or ONT) there is no need to repeat this step

a) Set up a target source_directory

b) Extract core server source code to the target source_directory

2 Ensure that JBOSS is not running a) $JBOSS_HOMEbinshutdownsh -S 3 Deploy eduharvardi2b2common

If this has been deployed in a previous installation (eg ONT) there is no need to repeat this step

a) ldquocd source_directoryeduharvardi2b2commonrdquo

b) Edit the buildproperties file and set jbosshome and axis2warname properties jbosshome=YOUR_JBOSS_HOME_DIR axis2warname=i2b2war

c) ldquoant clean dist deploy jboss_pre_deployment_setuprdquo

5

4 Deploy eduharvardi2b2crc and eduharvardi2b2crcloader 41 Build eduharvardi2b2crcloader

The Uploader service is added to the CRC as part of the Release 13 The source for the Uploader resides in eduharvardi2b2crcloader project and it uses the CRCrsquos datasource setup

a) ldquocd source_directoryeduharvardi2b2crcloaderrdquo

b) Edit the buildproperties file and set jbosshome and axis2warname properties

jbosshome=YOUR_JBOSS_HOME_DIR axis2warname=i2b2war c) Edit the etcspringcrc_loader_application_directoryproperties file and

specify a location for the application properties directory This location can be anything you desire but must be a directory path that your linux user has access permission for

eduharvardi2b2crcapplicationdir= YOUR_JBOSS_HOME_DIR serverdefaultconfcrcloaderapp d) Edit the etcspringeduharvardi2b2crcloaderproperties file and set project

management properties Set Project Management property settings

eduharvardi2b2crcloaderwspmurl=httplocalhost7070axis2restPMServicegetServices Flag to bypass project management cell eduharvardi2b2crcloaderwspmbypass=false eduharvardi2b2crcloaderwspmbypassrole=ADMIN eduharvardi2b2crcloaderwspmbypassproject=Demo

If you are using file repository cell and want to connect the CRC loader to it then set the FileRepository cell property setting File Management Cell eduharvardi2b2crcloaderwsfrurl=httplocalhost9090 i2b2servicesFRService

6

CRCLoaderApplicationContextxml Specify the jdbc properties to locate the ldquoCRC_DB_LOOKUPrdquo table ltbean id=LoaderLookupDS class=orgapachecommonsdbcpBasicDataSource destroy-method=closegt ltproperty name=driverClassName value= oraclejdbcdriverOracleDrivergt ltproperty name=url value=jdbcoraclethinlocalhost1521xegt ltproperty name=username value=i2b2hivegt ltproperty name=password value=i2b2hive_pswdgt ltbeangt Update entry in eduharvardi2b2crcloaderproperties to reflect the above change Datasource Lookup properties eduharvardi2b2crcloaderdslookupdatasource=LoaderLookupDS eduharvardi2b2crcloaderdslookupservertype=ORACLE eduharvardi2b2crcloaderdslookupschemaname=i2b2hive h) ldquoant -f buildxml clean distrdquo Note No ldquodeployrdquo target is used The loader will be deployed as part of eduharvardi2b2crc project

42 Build and deploy eduharvardi2b2crc and eduharvardi2b2crcloader a) ldquocd source_directoryeduharvardi2b2crcrdquo

b) Edit the buildproperties file and set jbosshome and axis2warname properties

jbosshome=YOUR_JBOSS_HOME_DIR axis2warname=i2b2war jms persistance could be either oracle or mssql jbossjmspersistance=oracle c) Edit the etcspringcrc_application_directoryproperties file and specify a

location for the application properties directory This location can be anything you desire but must be a directory path that your linux user has access permission for

eduharvardi2b2crcapplicationdir= YOUR_JBOSS_HOME_DIR serverdefaultconfcrcapp

7

d) Edit the etcspringcrcproperties file and set project management properties Set Project Management property settings queryprocessorwspmurl=httplocalhost7070axis2restPMServicegetServices Flag to bypass project management cell queryprocessorwspmbypass=false queryprocessorwspmbypassrole=ADMIN queryprocessorwspmbypassproject=Demo Set Ontology property settings change the hostname and port queryprocessorwsontologyurl=httplocalhost9090axis2restOntologyServicegetTermInfo e) Set data source lookup by domain project and user The following steps tells CRC where the ldquoCRC_DB_LOOKUPrdquo table is located

code_lookup

PK c_domain_id varchar(255) PK c_project_path varchar(255) PK c_owner_id varchar(255)

c_db_fullschema varchar(255) c_db_datasource varchar(255) c_db_servertype varchar(255) c_db_nicename varchar(255) c_db_tooltip varchar(255) c_comment text c_entry_date datetime c_change_date datetime c_status_cd char(1)

CRCApplicationContextxml ltbean id=CRCDataSourceLookup class=orgapachecommonsdbcpBasicDataSource destroy-method=closegt ltproperty name=driverClassName value= oraclejdbcdriverOracleDrivergt ltproperty name=url value=jdbcoraclethinlocalhost1521xegt ltproperty name=username value=i2b2hivegt ltproperty name=password value=i2b2hive_pswdgt ltbeangt Update entry in crcproperties to reflect the above change

8

Datasource Lookup properties queryprocessordslookupdatasource=CRCDataSourceLookup queryprocessordslookupservertype=ORACLE queryprocessordslookupschemaname=i2b2hive

f) Configure JBoss Datasource CRC supports both Oracle and SqlServer Edit etcjbosscrc-dsxml and set the database connection properties For SqlServer data source please use the sample provided in the crc-dsxml The following steps show the configuring Oracle data source for two projects If your setup has multiple projects pointing to different data sources then copy ltlocal-tx-datasourcegt in ds-xml for each project data source

ltjndi-namegtQueryToolDemoDSltjndi-namegt ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2demodataltuser-namegt ltpasswordgti2b2demodata_passwordltpasswordgt

For example project Demo2 would have this entry

ltjndi-namegtQueryToolDemo2DSltjndi-namegt with connection-url

ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2demodata2ltuser-namegt ltpasswordgti2b2demodata2_passwordltpasswordgt

g) Edit etcjbosscrc-jms-dsxml and set JMS database connection properties If the data source going to be Sqlserver then comment the oracle section

and uncomment sqlserver datasource section Whether if it is Oracle or Sqlserver database keep the ltjndi-namegtDefaultDSltjndi-namegt

ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2hive_unameltuser-namegt ltpasswordgti2b2hive_passwordltpasswordgt h) ldquoant -f master_buildxml clean build-all deployrdquo

5 Start JBOSS

9

a) Run ldquo$JBOSS_HOMEbinrunsh ndashb 0000rdquo

6 Verify webservice is running a) Check url ldquohttpyourHost9090i2b2serviceslistServicesrdquo in a browser Verify that QueryToolService is listed as active

5

4 Deploy eduharvardi2b2crc and eduharvardi2b2crcloader 41 Build eduharvardi2b2crcloader

The Uploader service is added to the CRC as part of the Release 13 The source for the Uploader resides in eduharvardi2b2crcloader project and it uses the CRCrsquos datasource setup

a) ldquocd source_directoryeduharvardi2b2crcloaderrdquo

b) Edit the buildproperties file and set jbosshome and axis2warname properties

jbosshome=YOUR_JBOSS_HOME_DIR axis2warname=i2b2war c) Edit the etcspringcrc_loader_application_directoryproperties file and

specify a location for the application properties directory This location can be anything you desire but must be a directory path that your linux user has access permission for

eduharvardi2b2crcapplicationdir= YOUR_JBOSS_HOME_DIR serverdefaultconfcrcloaderapp d) Edit the etcspringeduharvardi2b2crcloaderproperties file and set project

management properties Set Project Management property settings

eduharvardi2b2crcloaderwspmurl=httplocalhost7070axis2restPMServicegetServices Flag to bypass project management cell eduharvardi2b2crcloaderwspmbypass=false eduharvardi2b2crcloaderwspmbypassrole=ADMIN eduharvardi2b2crcloaderwspmbypassproject=Demo

If you are using file repository cell and want to connect the CRC loader to it then set the FileRepository cell property setting File Management Cell eduharvardi2b2crcloaderwsfrurl=httplocalhost9090 i2b2servicesFRService

6

CRCLoaderApplicationContextxml Specify the jdbc properties to locate the ldquoCRC_DB_LOOKUPrdquo table ltbean id=LoaderLookupDS class=orgapachecommonsdbcpBasicDataSource destroy-method=closegt ltproperty name=driverClassName value= oraclejdbcdriverOracleDrivergt ltproperty name=url value=jdbcoraclethinlocalhost1521xegt ltproperty name=username value=i2b2hivegt ltproperty name=password value=i2b2hive_pswdgt ltbeangt Update entry in eduharvardi2b2crcloaderproperties to reflect the above change Datasource Lookup properties eduharvardi2b2crcloaderdslookupdatasource=LoaderLookupDS eduharvardi2b2crcloaderdslookupservertype=ORACLE eduharvardi2b2crcloaderdslookupschemaname=i2b2hive h) ldquoant -f buildxml clean distrdquo Note No ldquodeployrdquo target is used The loader will be deployed as part of eduharvardi2b2crc project

42 Build and deploy eduharvardi2b2crc and eduharvardi2b2crcloader a) ldquocd source_directoryeduharvardi2b2crcrdquo

b) Edit the buildproperties file and set jbosshome and axis2warname properties

jbosshome=YOUR_JBOSS_HOME_DIR axis2warname=i2b2war jms persistance could be either oracle or mssql jbossjmspersistance=oracle c) Edit the etcspringcrc_application_directoryproperties file and specify a

location for the application properties directory This location can be anything you desire but must be a directory path that your linux user has access permission for

eduharvardi2b2crcapplicationdir= YOUR_JBOSS_HOME_DIR serverdefaultconfcrcapp

7

d) Edit the etcspringcrcproperties file and set project management properties Set Project Management property settings queryprocessorwspmurl=httplocalhost7070axis2restPMServicegetServices Flag to bypass project management cell queryprocessorwspmbypass=false queryprocessorwspmbypassrole=ADMIN queryprocessorwspmbypassproject=Demo Set Ontology property settings change the hostname and port queryprocessorwsontologyurl=httplocalhost9090axis2restOntologyServicegetTermInfo e) Set data source lookup by domain project and user The following steps tells CRC where the ldquoCRC_DB_LOOKUPrdquo table is located

code_lookup

PK c_domain_id varchar(255) PK c_project_path varchar(255) PK c_owner_id varchar(255)

c_db_fullschema varchar(255) c_db_datasource varchar(255) c_db_servertype varchar(255) c_db_nicename varchar(255) c_db_tooltip varchar(255) c_comment text c_entry_date datetime c_change_date datetime c_status_cd char(1)

CRCApplicationContextxml ltbean id=CRCDataSourceLookup class=orgapachecommonsdbcpBasicDataSource destroy-method=closegt ltproperty name=driverClassName value= oraclejdbcdriverOracleDrivergt ltproperty name=url value=jdbcoraclethinlocalhost1521xegt ltproperty name=username value=i2b2hivegt ltproperty name=password value=i2b2hive_pswdgt ltbeangt Update entry in crcproperties to reflect the above change

8

Datasource Lookup properties queryprocessordslookupdatasource=CRCDataSourceLookup queryprocessordslookupservertype=ORACLE queryprocessordslookupschemaname=i2b2hive

f) Configure JBoss Datasource CRC supports both Oracle and SqlServer Edit etcjbosscrc-dsxml and set the database connection properties For SqlServer data source please use the sample provided in the crc-dsxml The following steps show the configuring Oracle data source for two projects If your setup has multiple projects pointing to different data sources then copy ltlocal-tx-datasourcegt in ds-xml for each project data source

ltjndi-namegtQueryToolDemoDSltjndi-namegt ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2demodataltuser-namegt ltpasswordgti2b2demodata_passwordltpasswordgt

For example project Demo2 would have this entry

ltjndi-namegtQueryToolDemo2DSltjndi-namegt with connection-url

ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2demodata2ltuser-namegt ltpasswordgti2b2demodata2_passwordltpasswordgt

g) Edit etcjbosscrc-jms-dsxml and set JMS database connection properties If the data source going to be Sqlserver then comment the oracle section

and uncomment sqlserver datasource section Whether if it is Oracle or Sqlserver database keep the ltjndi-namegtDefaultDSltjndi-namegt

ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2hive_unameltuser-namegt ltpasswordgti2b2hive_passwordltpasswordgt h) ldquoant -f master_buildxml clean build-all deployrdquo

5 Start JBOSS

9

a) Run ldquo$JBOSS_HOMEbinrunsh ndashb 0000rdquo

6 Verify webservice is running a) Check url ldquohttpyourHost9090i2b2serviceslistServicesrdquo in a browser Verify that QueryToolService is listed as active

6

CRCLoaderApplicationContextxml Specify the jdbc properties to locate the ldquoCRC_DB_LOOKUPrdquo table ltbean id=LoaderLookupDS class=orgapachecommonsdbcpBasicDataSource destroy-method=closegt ltproperty name=driverClassName value= oraclejdbcdriverOracleDrivergt ltproperty name=url value=jdbcoraclethinlocalhost1521xegt ltproperty name=username value=i2b2hivegt ltproperty name=password value=i2b2hive_pswdgt ltbeangt Update entry in eduharvardi2b2crcloaderproperties to reflect the above change Datasource Lookup properties eduharvardi2b2crcloaderdslookupdatasource=LoaderLookupDS eduharvardi2b2crcloaderdslookupservertype=ORACLE eduharvardi2b2crcloaderdslookupschemaname=i2b2hive h) ldquoant -f buildxml clean distrdquo Note No ldquodeployrdquo target is used The loader will be deployed as part of eduharvardi2b2crc project

42 Build and deploy eduharvardi2b2crc and eduharvardi2b2crcloader a) ldquocd source_directoryeduharvardi2b2crcrdquo

b) Edit the buildproperties file and set jbosshome and axis2warname properties

jbosshome=YOUR_JBOSS_HOME_DIR axis2warname=i2b2war jms persistance could be either oracle or mssql jbossjmspersistance=oracle c) Edit the etcspringcrc_application_directoryproperties file and specify a

location for the application properties directory This location can be anything you desire but must be a directory path that your linux user has access permission for

eduharvardi2b2crcapplicationdir= YOUR_JBOSS_HOME_DIR serverdefaultconfcrcapp

7

d) Edit the etcspringcrcproperties file and set project management properties Set Project Management property settings queryprocessorwspmurl=httplocalhost7070axis2restPMServicegetServices Flag to bypass project management cell queryprocessorwspmbypass=false queryprocessorwspmbypassrole=ADMIN queryprocessorwspmbypassproject=Demo Set Ontology property settings change the hostname and port queryprocessorwsontologyurl=httplocalhost9090axis2restOntologyServicegetTermInfo e) Set data source lookup by domain project and user The following steps tells CRC where the ldquoCRC_DB_LOOKUPrdquo table is located

code_lookup

PK c_domain_id varchar(255) PK c_project_path varchar(255) PK c_owner_id varchar(255)

c_db_fullschema varchar(255) c_db_datasource varchar(255) c_db_servertype varchar(255) c_db_nicename varchar(255) c_db_tooltip varchar(255) c_comment text c_entry_date datetime c_change_date datetime c_status_cd char(1)

CRCApplicationContextxml ltbean id=CRCDataSourceLookup class=orgapachecommonsdbcpBasicDataSource destroy-method=closegt ltproperty name=driverClassName value= oraclejdbcdriverOracleDrivergt ltproperty name=url value=jdbcoraclethinlocalhost1521xegt ltproperty name=username value=i2b2hivegt ltproperty name=password value=i2b2hive_pswdgt ltbeangt Update entry in crcproperties to reflect the above change

8

Datasource Lookup properties queryprocessordslookupdatasource=CRCDataSourceLookup queryprocessordslookupservertype=ORACLE queryprocessordslookupschemaname=i2b2hive

f) Configure JBoss Datasource CRC supports both Oracle and SqlServer Edit etcjbosscrc-dsxml and set the database connection properties For SqlServer data source please use the sample provided in the crc-dsxml The following steps show the configuring Oracle data source for two projects If your setup has multiple projects pointing to different data sources then copy ltlocal-tx-datasourcegt in ds-xml for each project data source

ltjndi-namegtQueryToolDemoDSltjndi-namegt ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2demodataltuser-namegt ltpasswordgti2b2demodata_passwordltpasswordgt

For example project Demo2 would have this entry

ltjndi-namegtQueryToolDemo2DSltjndi-namegt with connection-url

ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2demodata2ltuser-namegt ltpasswordgti2b2demodata2_passwordltpasswordgt

g) Edit etcjbosscrc-jms-dsxml and set JMS database connection properties If the data source going to be Sqlserver then comment the oracle section

and uncomment sqlserver datasource section Whether if it is Oracle or Sqlserver database keep the ltjndi-namegtDefaultDSltjndi-namegt

ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2hive_unameltuser-namegt ltpasswordgti2b2hive_passwordltpasswordgt h) ldquoant -f master_buildxml clean build-all deployrdquo

5 Start JBOSS

9

a) Run ldquo$JBOSS_HOMEbinrunsh ndashb 0000rdquo

6 Verify webservice is running a) Check url ldquohttpyourHost9090i2b2serviceslistServicesrdquo in a browser Verify that QueryToolService is listed as active

7

d) Edit the etcspringcrcproperties file and set project management properties Set Project Management property settings queryprocessorwspmurl=httplocalhost7070axis2restPMServicegetServices Flag to bypass project management cell queryprocessorwspmbypass=false queryprocessorwspmbypassrole=ADMIN queryprocessorwspmbypassproject=Demo Set Ontology property settings change the hostname and port queryprocessorwsontologyurl=httplocalhost9090axis2restOntologyServicegetTermInfo e) Set data source lookup by domain project and user The following steps tells CRC where the ldquoCRC_DB_LOOKUPrdquo table is located

code_lookup

PK c_domain_id varchar(255) PK c_project_path varchar(255) PK c_owner_id varchar(255)

c_db_fullschema varchar(255) c_db_datasource varchar(255) c_db_servertype varchar(255) c_db_nicename varchar(255) c_db_tooltip varchar(255) c_comment text c_entry_date datetime c_change_date datetime c_status_cd char(1)

CRCApplicationContextxml ltbean id=CRCDataSourceLookup class=orgapachecommonsdbcpBasicDataSource destroy-method=closegt ltproperty name=driverClassName value= oraclejdbcdriverOracleDrivergt ltproperty name=url value=jdbcoraclethinlocalhost1521xegt ltproperty name=username value=i2b2hivegt ltproperty name=password value=i2b2hive_pswdgt ltbeangt Update entry in crcproperties to reflect the above change

8

Datasource Lookup properties queryprocessordslookupdatasource=CRCDataSourceLookup queryprocessordslookupservertype=ORACLE queryprocessordslookupschemaname=i2b2hive

f) Configure JBoss Datasource CRC supports both Oracle and SqlServer Edit etcjbosscrc-dsxml and set the database connection properties For SqlServer data source please use the sample provided in the crc-dsxml The following steps show the configuring Oracle data source for two projects If your setup has multiple projects pointing to different data sources then copy ltlocal-tx-datasourcegt in ds-xml for each project data source

ltjndi-namegtQueryToolDemoDSltjndi-namegt ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2demodataltuser-namegt ltpasswordgti2b2demodata_passwordltpasswordgt

For example project Demo2 would have this entry

ltjndi-namegtQueryToolDemo2DSltjndi-namegt with connection-url

ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2demodata2ltuser-namegt ltpasswordgti2b2demodata2_passwordltpasswordgt

g) Edit etcjbosscrc-jms-dsxml and set JMS database connection properties If the data source going to be Sqlserver then comment the oracle section

and uncomment sqlserver datasource section Whether if it is Oracle or Sqlserver database keep the ltjndi-namegtDefaultDSltjndi-namegt

ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2hive_unameltuser-namegt ltpasswordgti2b2hive_passwordltpasswordgt h) ldquoant -f master_buildxml clean build-all deployrdquo

5 Start JBOSS

9

a) Run ldquo$JBOSS_HOMEbinrunsh ndashb 0000rdquo

6 Verify webservice is running a) Check url ldquohttpyourHost9090i2b2serviceslistServicesrdquo in a browser Verify that QueryToolService is listed as active

8

Datasource Lookup properties queryprocessordslookupdatasource=CRCDataSourceLookup queryprocessordslookupservertype=ORACLE queryprocessordslookupschemaname=i2b2hive

f) Configure JBoss Datasource CRC supports both Oracle and SqlServer Edit etcjbosscrc-dsxml and set the database connection properties For SqlServer data source please use the sample provided in the crc-dsxml The following steps show the configuring Oracle data source for two projects If your setup has multiple projects pointing to different data sources then copy ltlocal-tx-datasourcegt in ds-xml for each project data source

ltjndi-namegtQueryToolDemoDSltjndi-namegt ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2demodataltuser-namegt ltpasswordgti2b2demodata_passwordltpasswordgt

For example project Demo2 would have this entry

ltjndi-namegtQueryToolDemo2DSltjndi-namegt with connection-url

ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2demodata2ltuser-namegt ltpasswordgti2b2demodata2_passwordltpasswordgt

g) Edit etcjbosscrc-jms-dsxml and set JMS database connection properties If the data source going to be Sqlserver then comment the oracle section

and uncomment sqlserver datasource section Whether if it is Oracle or Sqlserver database keep the ltjndi-namegtDefaultDSltjndi-namegt

ltconnection-urlgtjdbcoraclethinlocalhost1521xeltconnection-urlgt ltdriver-classgtoraclejdbcdriverOracleDriverltdriver-classgt ltuser-namegti2b2hive_unameltuser-namegt ltpasswordgti2b2hive_passwordltpasswordgt h) ldquoant -f master_buildxml clean build-all deployrdquo

5 Start JBOSS

9

a) Run ldquo$JBOSS_HOMEbinrunsh ndashb 0000rdquo

6 Verify webservice is running a) Check url ldquohttpyourHost9090i2b2serviceslistServicesrdquo in a browser Verify that QueryToolService is listed as active

9

a) Run ldquo$JBOSS_HOMEbinrunsh ndashb 0000rdquo

6 Verify webservice is running a) Check url ldquohttpyourHost9090i2b2serviceslistServicesrdquo in a browser Verify that QueryToolService is listed as active

10

Changing Server log level By default JBOSS log will be in DEBUG mode changing it to INFO mode will increase server performance

a) Edit $JBOSS_HOMEserverdefaultconfjboss-log4jxml file and add the ldquoThresholdrdquoltparamgt

ltappender name=FILE class=orgjbossloggingappenderDailyRollingFileAppendergt lterrorHandler class=orgjbossloggingutilOnlyOnceErrorHandlergt ltparam name=File value=$jbossserverhomedirlogserverloggt ltparam name=Append value=falsegt ltparam name=Threshold value=INFOgt lt-- Rollover at midnight each day --gt ltparam name=DatePattern value=yyyy-MM-ddgt ltlayout class=orgapachelog4jPatternLayoutgt lt-- The default pattern Date Priority [Category] Messagen --gt ltparam name=ConversionPattern value=d -5p [c] mngt ltlayoutgt ltappendergt

To switch back to DEBUG mode comment out the ldquoThresholdrdquo ltparamgt and wait a minute THERE IS NO NEED TO RESTART JBOSS

11

3 Verify Installation

CRC Cell Sanity Test via the i2b2Workbench

1 Configure the i2b2Workbench to communicate with your CRC cell

This step is addressed in section 5 Global Hive Data of the Project Management (PM) Cellgridsphere installation and set up Please refer to this document if the CRC Cell has not yet been configured

To verify this data go to the site httptomcatHosttomcatPortgridsphere Once logged on select ldquoGlobal Hive Datardquo from the primary navigation tab and ldquoRegistered Cellrdquo from the secondary navigation menu If the CRC Cell has been configured you will see the following

To verify cell data select cell name and click on Edit Cell Info

11

3 Verify Installation

CRC Cell Sanity Test via the i2b2Workbench

1 Configure the i2b2Workbench to communicate with your CRC cell

This step is addressed in section 5 Global Hive Data of the Project Management (PM) Cellgridsphere installation and set up Please refer to this document if the CRC Cell has not yet been configured

To verify this data go to the site httptomcatHosttomcatPortgridsphere Once logged on select ldquoGlobal Hive Datardquo from the primary navigation tab and ldquoRegistered Cellrdquo from the secondary navigation menu If the CRC Cell has been configured you will see the following

To verify cell data select cell name and click on Edit Cell Info

12

2 Launch the i2b2Workbench (double-click on i2b2Workbenchexe) Login to i2b2 a Select your target location (YourSite) b Enter a valid username and password that you set up in gridsphere (demodemouser) c The URL at the bottom of the login screen should be the address of your PM cell If not return to PM Cell installation procedures section 7 Verify Installation

13

3 Open the Query Tool Previous Queries and Timeline views in the workbench

If all is configured properly you will be greeted with the following

14

4 Possible problems

a Error message appears in view window - ldquoData repository cell is unavailablerdquo

CRC cell address in gridsphere is incorrect (see step 1 of this section) or CRC Cell may be down Check url ldquohttpyourHost9090i2b2serviceslistServicesrdquo in a browser Verify that QueryToolService is listed as active

- ldquoRemote server is unavailablerdquo Server may be down

Check url ldquohttpyourHost9090i2b2serviceslistServicesrdquo in a browser Verify that QueryToolServiceService is listed as active

- ldquoPM service is not respondingrdquo

Project Management Cell is down or its address was not configured properly in section 2 step 4d

- ldquoDatabase errorrdquo There are problems connecting to the database

Verify database configuration parameters in section 2 steps 4c-e

13

3 Open the Query Tool Previous Queries and Timeline views in the workbench

If all is configured properly you will be greeted with the following

14

4 Possible problems

a Error message appears in view window - ldquoData repository cell is unavailablerdquo

CRC cell address in gridsphere is incorrect (see step 1 of this section) or CRC Cell may be down Check url ldquohttpyourHost9090i2b2serviceslistServicesrdquo in a browser Verify that QueryToolService is listed as active

- ldquoRemote server is unavailablerdquo Server may be down

Check url ldquohttpyourHost9090i2b2serviceslistServicesrdquo in a browser Verify that QueryToolServiceService is listed as active

- ldquoPM service is not respondingrdquo

Project Management Cell is down or its address was not configured properly in section 2 step 4d

- ldquoDatabase errorrdquo There are problems connecting to the database

Verify database configuration parameters in section 2 steps 4c-e

14

4 Possible problems

a Error message appears in view window - ldquoData repository cell is unavailablerdquo

CRC cell address in gridsphere is incorrect (see step 1 of this section) or CRC Cell may be down Check url ldquohttpyourHost9090i2b2serviceslistServicesrdquo in a browser Verify that QueryToolService is listed as active

- ldquoRemote server is unavailablerdquo Server may be down

Check url ldquohttpyourHost9090i2b2serviceslistServicesrdquo in a browser Verify that QueryToolServiceService is listed as active

- ldquoPM service is not respondingrdquo

Project Management Cell is down or its address was not configured properly in section 2 step 4d

- ldquoDatabase errorrdquo There are problems connecting to the database

Verify database configuration parameters in section 2 steps 4c-e

15

4 License

The i2b2 source code is licensed under the i2b2 Software License Software This includes but not limited to all code in the eduharvardmghi2b2 package namespace