New Upgrade Path: Precompiled JARs

The release of i2b2 1.7.08 introduced a major platform change in which the JBoss 7 application server was replaced with WildFly 10 (formerly known as “JBoss” 10), and JDK 8 became required.

With consideration that you may be using custom ports, proxies, HTTPS, and other custom configurations that must be re-setup in WildFly from scratch and/or may be incompatible with WildFly, we have introduced a new upgrade path for using your existing JBoss 7 with i2b2 1.7.09b by providing drop-in JARs.

Technical Details

We are providing a zip file containing a pre-compiled version of i2b2 1.7.09b that you can drop into your existing instance to upgrade i2b2. The JARs were compiled with JDK 7 and will run in your existing JBoss 7 application server. The upgrade technique will work on both Linux and Windows environments.

You should meet all of the following requirements to use this upgrade path:

  • You should be running JBoss 7 (tested on JBoss-as-7.1.1.Final) and JRE 7 or Wildfly 10 and JRE 8
  • You are on i2b2 versions 1.7.05, 1.7.06, 1.7.07, or 1.7.08
  • You either installed i2b2 from source or are using the i2b2 VMWare virtual machine (1.7.05, 1.7.06, 1.7.07, or 1.7.08)

Step-by-step Instructions for JBoss

1. Stop JBoss

For example, on Linux:

$ /opt/jboss-as-7.1.1.Final/bin/jboss-cli.sh --connect command=:shutdown

2. Backup your existing i2b2.war directory

On Linux, make a copy of /opt/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/ to a different location outside of /opt/jboss-as-7.1.1.Final/

On Windows, make a copy of c:\opt\jboss-as-7.1.1.Final\standalone\deployments\i2b2.war\ to a different location outside of c:\opt\jboss-as-7.1.1.Final\

3. Delete the i2b2.war.deployed file

For example, on Linux:

$ rm /opt/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war.deployed

4. Extract/copy the files from the zip file to your JBoss deployments directory

The zip file contains the following file structure:

i2b2 Upgrade Instructions for 1.7.05 to 1.7.09b.pdf
deployments/
deployments/i2b2.war.dodeploy
deployments/i2b2.war/
deployments/i2b2.war/WEB-INF/
deployments/i2b2.war/WEB-INF/lib/
deployments/i2b2.war/WEB-INF/lib/CRC-core.jar
deployments/i2b2.war/WEB-INF/lib/Ontology-core.jar
deployments/i2b2.war/WEB-INF/lib/ProjectManagement-core.jar
deployments/i2b2.war/WEB-INF/lib/Workplace-core.jar
deployments/i2b2.war/WEB-INF/lib/i2b2Common-core.jar
deployments/i2b2.war/WEB-INF/lib/FR-core.jar
deployments/i2b2.war/WEB-INF/lib/IM-core.jar
deployments/i2b2.war/WEB-INF/services/
deployments/i2b2.war/WEB-INF/services/CRC.aar
deployments/i2b2.war/WEB-INF/services/IM.aar
deployments/i2b2.war/WEB-INF/services/FR.aar
deployments/i2b2.war/WEB-INF/services/Ontology.aar
deployments/i2b2.war/WEB-INF/services/ProjectManagement.aar
deployments/i2b2.war/WEB-INF/services/Workplace.aar
configuration/crcapp/crc.properties-1709

 

You should copy the deployments directory into your existing JBoss standalone directory, replacing any existing file when prompted.

For example, on Linux:

$ unzip i2b2_upgrade_1.7.05_to_1.7.09b.zip
$ cp -r deployments /opt/jboss-as-7.1.1.Final/standalone/

5. Modify the crc.properties

Copy the contents of the crc.properties-1709 to crc.properties

6. Start JBoss

For example, on Linux:

$ /opt/jboss-as-7.1.1.Final/bin/standalone.sh -b 0.0.0.0 &

7. Verify your upgrade

Navigate to your local i2b2 web client in your browser and verify that i2b2 is working normally (e.g. confirm that queries can run and complete, and previous queries can be retrieved, etc.)

 

Step-by-step Instructions for Wildfly

 

1. Stop Wildfly

For example, on Linux:

$ /opt/wildfly-10.0.0.Final/bin/jboss-cli.sh --connect command=:shutdown

2. Backup your existing i2b2.war directory

On Linux, make a copy of /opt/wildfly-10.0.0.Final/standalone/deployments/i2b2.war/ to a different location outside of /opt/wildfly-10.0.0.Final/

On Windows, make a copy of c:\opt\wildfly-10.0.0.Final\standalone\deployments\i2b2.war\ to a different location outside of c:\opt\wildfly-10.0.0.Final\

3. Delete the i2b2.war.deployed file

For example, on Linux:

$ rm /opt/wildfly-10.0.0.Final/standalone/deployments/i2b2.war.deployed

4. Extract/copy the files from the zip file to your JBoss deployments directory

The zip file contains the following file structure:

i2b2 Upgrade Instructions for 1.7.05 to 1.7.09b.pdf
deployments/
deployments/i2b2.war.dodeploy
deployments/i2b2.war/
deployments/i2b2.war/WEB-INF/
deployments/i2b2.war/WEB-INF/lib/
deployments/i2b2.war/WEB-INF/lib/CRC-core.jar
deployments/i2b2.war/WEB-INF/lib/Ontology-core.jar
deployments/i2b2.war/WEB-INF/lib/ProjectManagement-core.jar
deployments/i2b2.war/WEB-INF/lib/Workplace-core.jar
deployments/i2b2.war/WEB-INF/lib/i2b2Common-core.jar
deployments/i2b2.war/WEB-INF/lib/FR-core.jar
deployments/i2b2.war/WEB-INF/lib/IM-core.jar
deployments/i2b2.war/WEB-INF/services/
deployments/i2b2.war/WEB-INF/services/CRC.aar
deployments/i2b2.war/WEB-INF/services/IM.aar
deployments/i2b2.war/WEB-INF/services/FR.aar
deployments/i2b2.war/WEB-INF/services/Ontology.aar
deployments/i2b2.war/WEB-INF/services/ProjectManagement.aar
deployments/i2b2.war/WEB-INF/services/Workplace.aar 
configuration/crcapp/crc.properties-1709
 

You should copy the deployments directory into your existing Wildfly standalone directory, replacing any existing file when prompted.

For example, on Linux:

$ unzip i2b2_upgrade_1.7.05_to_1.7.09b.zip
$ cp -r deployments /opt/wildfly-10.0.0.Final/standalone/

5. Modify the crc.properties

      Copy the contents of the crc.properties-1709 to crc.properties

6. Start Wildfly

For example, on Linux:

$ /opt/wildfly-10.0.0.Final/bin/standalone.sh -b 0.0.0.0 &

7. Verify your upgrade

Navigate to your local i2b2 web client in your browser and verify that i2b2 is working normally (e.g. confirm that queries can run and complete, and previous queries can be retrieved, etc.)

Download

Descriptioni2b2 VersionFile SizeDownload LinkRequirements
i2b2 1.7.05+ to 1.7.09b Server Upgrade1.7.09b3.5 MB i2b2_upgrade_1.7.05_to_1.7.09b.zipSee Technical Details section above.

Notes

  • These upgrade instructions are to upgrade the server software of i2b2 only. You will want to grab the latest i2b2 web client zip and deploy it as normal.
  • In April 2016, we provided instructions to patch a potential security vulnerability in JBoss 7, specifically in the commons-collections-3.2.1.jar shipped with JBoss 7.