New Upgrade Path: Precompied JARs

Introduction

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. If you installed i2b2 from source originally, the general upgrade path would follow:

1. Install WildFly 10 and migrate your configurations to it
2. Upgrade to JDK 8
3. Build i2b2 from source and deploy into WildFly 10

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 1.7.08b by providing drop-in JARs.

Technical Details

We are providing a zip file containing a pre-compiled version of i2b2 1.7.08b 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
• You are on i2b2 versions 1.7.05, 1.7.06, or 1.7.07
• You either installed i2b2 from source or are using the i2b2 VMWare virtual machine (1.7.05, 1.7.06, or 1.7.07 only)

Step-by-step Instructions

1. Stop JBoss

For example, on Linux:

$ /opt/jboss-as-7.1.1.Final/bin/jboss-cli.sh --connection :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 1.7.08b.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/services/
deployments/i2b2.war/WEB-INF/services/CRC.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

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_1.7.08b.zip
$ cp -r deployments /opt/jboss-as-7.1.1.Final/standalone/

5. Start JBoss

For example, on Linux:

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

6. 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.)

Notes

• These upgrade instructions are to upgrade the server software of i2b2 only. You will want to grab the i2b2 1.7.08b 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 commons-collections-3.2.1.jar shipped with JBoss 7.

Documentation

Description	Download / View Link
Current Release Notes	1.7.08b Release Notes
Installation Guide	i2b2 Installation Guide
VMWare Installation Guide
i2b2 Workbench Documentation

Download Software Files

i2b2 Source Code

Description	Software Version	Download Link	Additional Documentation
i2b2 Core Source Code	1.7.08b	i2b2core-src-1708b.zip
i2b2 Web Client Source Code	1.7.08a	i2b2webclient-1708a.zip
i2b2 Workbench Source

JAR Files

Description	Software Version	Download Link	Additional Documentation
	1.7.08b

VMWare Images

Description	Software Version	Download Link	Additional Documentation
Complete VMware i2b2 server installed on CentOS	i2b2 server = 1.7.08b Web client = 1.7.08a	i2b2vmware-1708b.zip

Client Desktop Application

Description	Software Version	Download Link	Additional Documentation
i2b2 Workbench for Windows	1.7.07
i2b2 Workbench for Mac	1.7.07