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Version Information

i2b2 Version:1.7.09c
Release Date:January 12, 2017
License:i2b2 Open Source License

Download

Descriptioni2b2 Released VersionMinimum Version RequiredDownload LinkRequirements
Files to upgrade the i2b2 server to 1.7.09c1.7.09c1.7.05 i2b2upgrade-1705-to-1709c.zipSee Technical Details section on the i2b2 Upgrades page.
Files to upgrade the i2b2 Web Client to 1.7.09c1.7.09c  i2b2webclient-1709c.zip 

 Notes

    • Release 1.7.09 had changes to the crc.properties file. Since some sites might be upgrading from 1.7.08 or earlier, we have kept the steps to update the crc.properties files in these updgrade notes. However, if you are already on 1.7.09, 1.7.09a or higher you will skip the step to modify the crc.properties file as you have already done this step.
    • Release 1.7.09c contains changes to the i2b2 Web Client. Therefore in addition to the upgrade zip file you also need to download the i2b2webclient-1709c.zip file. The process of installing the i2b2 Web Client has not changed. If you have questions on how this is done you can find additional information in Chapter 7. i2b2 Web Client Install of the i2b2 Installation Guide.
    • Because this release contains Web Client changes, the i2b2 Admin module that resides on the i2b2 server will also need to be updated. The Web Client and Admin share code and although  none of the changes are specific to the Admin, this update in necessary to make sure the two applications remain in sync.

Upgrade Instructions

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 by providing drop-in JARs.

Knowing some sites have remained on JBoss 7 while some have upgraded to WildFly 10, we have gone ahead and provided Step-by-Step Instructions for both scenarios. For the most part the overall process is very similar. What is different, is the path in which the files reside. Expand the box below to see an example of the differences between the two path names.

Example Paths to i2b2.war
JBoss 7 path
/opt/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/

WildFly 10 path
/opt/wildfly-10.0.0.Final/standalone/deployments/i2b2.war/

 



Step-by-Step Instructions for JBoss

Stop JBoss

 

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

 

 

Backup your existing i2b2.war directory

Linux

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


Windows

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

Delete i2b2.war.deployed file

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

DO NOT delete your existing i2b2.war directory. The zip file contains only a subset of files to add/replace in your existing i2b2.war directory.

Extract / copy the deployment files from the upgrade zip file to your JBoss deployments directory

Copy the deployments directory into your existing JBoss standalone directory, replacing any existing files when prompted.

Linux Example
$ cp -r deployments /opt/jboss-as-7.1.1.Final/standalone

Modify the crc.properties

Update crc.properties

Open the crc.properties-1709 file and copy the contents from it into the crc.properties file located in the configuration directory on the i2b2 server.

DO NOT replace the crc.properties file with the new crc.properties-1709 file as the new file only contains the new parameters. If you replace the existing one you will lose all your current configurations and all the necessary parameters to run the crc.

Backup your existing admin directory

Linux Example

/var/www/html/admin


Windows Example

C:\inetpub\wwwroot\admin

Extract / Copy the admin directory from the update zip file to your web server directory

To prevent the loss of your current data configuration settings verify you can access the i2b2_config_data.js file in the backup copy of the admin directory you created in the previous step.

Copy your old i2b2_config_data.js file into the updated admin directory on your web server. Overwrite the existing file if prompted.

Start JBoss

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

Verify your upgrade

Test Web Client

Navigate to your local i2b2 Web Client in your preferred browser and verify you are able to log on and perform standard i2b2 functions. (e.g. Run queries, retrieve previous queries, view breakdowns, etc.)

Step-by-Step Instructions for WildFly

Stop WildFly

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

Backup your existing i2b2.war directory

Linux

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


Windows

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

Delete i2b2.war.deployed file

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

DO NOT delete your existing i2b2.war directory. The zip file contains only a subset of files to add/replace in your existing i2b2.war directory.

Extract / copy the deployment files from the upgrade zip file to your WildFly deployments directory

Copy the deployments directory into your existing WildFly standalone directory, replacing any existing files when prompted.

Linux Example
$ cp -r deployments /opt/wildfly-10.0.0.Final/standalone

Modify the crc.properties

Update crc.properties

Open the crc.properties-1709 file and copy the contents from it into the crc.properties file located in the configuration directory on the i2b2 server.

DO NOT replace the crc.properties file with the new crc.properties-1709 file as the new file only contains the new parameters. If you replace the existing one you will lose all your current configurations and all the necessary parameters to run the crc.

Backup your existing admin directory

Linux Example

/var/www/html/admin


Windows Example

C:\inetpub\wwwroot\admin

Extract / Copy the admin directory from the update zip file to your web server directory

To prevent the loss of your current data configuration settings verify you can access the i2b2_config_data.js file in the backup copy of the admin directory you created in the previous step.

Copy your old i2b2_config_data.js file into the updated admin directory on your web server. Overwrite the existing file if prompted.

Start WildFly

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

Verify your upgrade

Test Web Client

Navigate to your local i2b2 Web Client in your preferred browser and verify you are able to log on and perform standard i2b2 functions. (e.g. Run queries, retrieve previous queries, view breakdowns, etc.)

Contents of the Zip File

i2b2 Upgrade Instructions for 1.7.05+ to 1.7.09c.pdf

admin/

admin/...

configuration/

configuration/crcapp/

configuration/crcapp/crc.properties-1709

deployments/

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/FR-core.jar

deployments/i2b2.war/WEB-INF/lib/i2b2Common-core.jar

deployments/i2b2.war/WEB-INF/lib/IM-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/FR.aar

deployments/i2b2.war/WEB-INF/services/IM.aar

deployments/i2b2.war/WEB-INF/services/ProjectManagement.aar

deployments/i2b2.war/WEB-INF/services/Ontology.aar

deployments/i2b2.war/WEB-INF/services/Workplace.aar

deployments/i2b2.war.dodeploy

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