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Info
titleTo Get Support

For any general information about the application, application support, or to report a bug, contact Application Support.

To Print the Guide
You can create a PDF of the guide. For instructions refer to the tip Printing or exporting multiple pagesExporting Multiple Pages to PDF. If you want to print a single page, refer to Printing a pagePage.

Topics in this document include:

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  1. file.repository.dir:  A directory on the system that hosts the JBoss application server for storing uploaded files, for example, C:/apps/caNanoLab.
    NOTE: This directory should be writable by the user that starts the JBoss server, and this directory should be created prior to starting the application. Use either double-back slashes or a single forward slash / as the file separator if working on Windows platform.
  2. admin.email:  The email address that receives requests for new user accounts, for example, the NCICBIIT application support NCIAppSupport@nih.gov email for the NCICBIIT installation.
  3. ldap.authentication.enabled:  A Boolean flag to indicate whether or not to use LDAP for user authentication in caNanoLab, for example, true.
    NOTE: Please note that the default value is true. If you are not using LDAP for user authentication, set this value to false and leave properties 4) through 9) blank.
  4. ldap.host.url:  The URL of the LDAP server used for user authentication.
  5. ldap.searchable.base:  The location in the directory from which the LDAP search begins.
  6. ldap.userId.label:  The uid label for LDAP, for example, cn.
  7. superadmin.login.name:  The LDAP login name for the user account who is the super admin of the UPT tool. See User Provisioning Tool (UPT) for details on setting up UPT.
  8. superadmin.first.name:  The LDAP first name for the user account who is the super admin of the UPT tool.
  9. superadmin.last.name:  The LDAP last name for the user account who is the super admin of the UPT tool.
  10. database.server:  The name of the server hosting the database, for example, localhost.
  11. database.port:  The database port number, for example, 3306.
  12. database.user: The database user name used in the caNanoLab application, for example, cananolab_app.
  13. database.password: The password for the database user specified above, for example, go!234.
  14. database.system.user:  The system database user name with privileges to create a database, create tables, grant user accesses to a database, for example, root.
  15. database.system.password:  The password for the system database user specified above, for example, rootpass.
  16. jboss.server.dir:  The JBoss server directory, for example, C:/apps/jboss-5.1.0.GA/server/default.

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It is possible to configure Apache server to interface with the JBoss server and set up a virtual host for the caNanoLab application. If you need assistance, please contact NCICBIIT NCI CBIIT Application Support.

Installation and Deployment

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Step

Action

1

Set up an environment variable JBOSS_HOME to point to the JBoss installation directory.

Note: Use either double back slashes backslashes // or a single forward slash / as the file separator if working on Windows platform, for example, JBOSS_HOME=C:/jboss-5.1.0.GA (C:\jboss-5.1.0.GA would fail).

2

Execute the Ant build script build.xml located at <CANANOLAB_SOURCE>/build with the target deploy:cananolab-webpp.

Example: Issue the following commands to execute the Ant script:

C:\>cd C:\caNanoLab_2.0\build C:\caNanoLab_2.0\build>ant deploy:cananolab-webapp

Successful execution of the Ant script generates the following artifacts that include two deployable web archive war files, configuration files and libraries for running the web application in the JBoss environment, and also places these artifacts in the appropriate directories under <JBOSS_HOME>:

Code Block
 <CANANOLAB_SOURCE>/target/dist/exploded/cananolab- webapp/caNanoLab.war 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/Applica tionSecurityConfig.xml 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/csmupt. csm.new.hibernate.cfg.xml 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/csmupt4 23.csm.new.hibernate.cfg.xml 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/login- config.xml 
 <CANANOLAB_SOURCE>/target/dist/exploaded/common/mysql- connector-java-5.0.7.jar 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/upt- ds.xml 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/propert ies-service.xml 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/upt- ds.xml  
 <CANANOLAB_SOURCE>/target/dist/exploded/common/uptEAR. ear

3

We recommend increasing the JBoss JVM heap size to 1G bytes and permanent generation (permgen) memory space to 256M bytes by updating the file
<JBOSS_HOME>/bin/run.conf with the following JAVA_OPTS:

Code Block
JAVA_OPTS="-Xms512m -Xmx1024m -XX:PermSize=128m - XX:MaxPermSize=256m -Dsun.rmi.dgc.client.gcInterval=3600000 - Dsun.rmi.dgc.server.gcInterval=3600000"

This configuration file is read when JBoss server starts.

4

When deploying the caNanolab application in a production environment, we also recommend updating the default logging behavior of the JBoss server by turning off the unnecessary loggings thus reducing file system requirements for server log files.

Please locate the file <JBOSS_HOME>/server/default/conf/log4j.xml and add to the beginning of the section Limit categories the following text:

Code Block
<!-- ================ --> 
 <!-- Limit categories --> 
 <!-- ================ --> 
 
 <!-- edited for caNanoLab --> 
 <category name="org.hibernate">
<priority value="WARN"/> 
 </category> 
 <category name="org.springframework"> 
 <priority value="WARN"/> 
 </category> 
 <category name="org.globus"> 
 <priority value="WARN"/> 
 </category> 
 <category name="gov.nih.nci"> 
 <priority value="ERROR"/> 
 </category> 
 <category name="org.displaytag"> 
 <priority value="ERROR"/> 
 </category> 
 <category name="org.directwebremoting"> 
 <priority value="ERROR"/> 
 </category> 
 <category name="net.sf.ehcache"> 
 <priority value="INFO"/> 
 </category> 
 <category name="com.mchange.v2"> 
 <priority value="INFO"/> 
 </category> 
 <category name="org.jboss"> 
 <priority value="INFO"/> 
 </category> 
 <category name="CSM"> 
 <priority value="ERROR"/> 
 </category> 
 <category name="Authorization"> 
 <priority value="ERROR"/> 
 </category> 
 <!—end of edit for caNanoLab -->

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For more information about how to use the UPT tool for managing user accounts, contact NCICBIIT NCI CBIIT Application Support at  nciappsupport@nih.gov and request that the caNanoLab technical team gives you a demonstration of the UPT tool in the context of the caNanoLab application.

Contacting Application Support

NCICBIIT NCI CBIIT Application Support

nciappsupport@nih.gov

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