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i2b2-upgrade-v1709c-info
i2b2-upgrade-v1709c-info

Version Information

Current Version:1.7.09c
Release Date:December 6, 2017
License:i2b2 Open Source License

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i2b2-upgrade-v1709c-download
i2b2-upgrade-v1709c-download

Download

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

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i2b2-upgrade-v1709c-note
i2b2-upgrade-v1709c-note

Upgrade 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 from the i2b2.org/software website. 
  • 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.

 

 

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i2b2-upgrade-v1709c-howTo
i2b2-upgrade-v1709c-howTo

Upgrade Instructions

Excerpt Include
i2b2 Upgrades
i2b2 Upgrades
nopaneltrue

 

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.

UI Expand
titleExample Paths to i2b2.war
Code Block
languagepowershell
titleJBoss 7 path
/opt/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/
Code Block
languagepowershell
titleWildFly 10 path
/opt/wildfly-10.0.0.Final/standalone/deployments/i2b2.war/

 

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i2b2-upgrade-v1709c-stepByStep-JBoss
i2b2-upgrade-v1709c-stepByStep-JBoss

Step-by-Step Instructions for JBoss

UI Steps
UI Step

Stop JBoss

Code Block
languagepowershell
titleLinux Example
collapsetrue
$ /opt/jboss-as-7.1.1.Final/bin/jboss-cli.sh --connect command=:shutdown
UI Step

Backup your existing i2b2.war directory

UI Expand
titleLinux

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/ 

UI Expand
titleWindows

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\ 

UI Step

Delete i2b2.war.deployed file

Code Block
languagepowershell
titleLinux Example
collapsetrue
$ rm /opt/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war.deployed
UI Step

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

UI Expand
titleContents of Zip File

i2b2 Upgrade Instructions for 1.7.05+ to 1.7.09c.pdf

configuration/
configuration/crcapp/
configuration/crcapp/crc.properties-1709

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/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

admin/

UI Step

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

Code Block
languagepowershell
titleLinux Example
collapsetrue
$ cp -r deployments /opt/jboss-as-7.1.1.Final/standalone
UI Step

Modify the crc.propertiesCopy the contents of the

UI Expand
titleUpdate 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.

 

Warning

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.

UI Step

Backup your existing admin directory

UI Expand
titleLinux Example

/var/www/html/admin

UI Expand
titleWindows Example

C:\inetpub\wwwroot\admin

UI Step

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

Warning

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.

UI Step

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

UI Step

Start JBoss

Code Block
languagepowershell
titleLinux Example
collapsetrue
$ /opt/jboss-as-7.1.1.Final/bin/standalone.sh -b 0.0.0.0 &
UI Step

Verify your upgrade

UI Expand
titleTest 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.)

 

 


 

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i2b2-upgrade-v1709c-stepByStep-WildFly
i2b2-upgrade-v1709c-stepByStep-WildFly

Step-by-Step Instructions for WildFly

projectdoc

 

macro
ui-steps
ui-
step

Stop

WidlFly

WildFly

Code Block
languagepowershell
titleLinux Example
collapsetrue
$ /opt/wildfly-10.0.0.Final/bin/jboss-cli.sh --connect command=:shutdown
UI Step

Backup your existing i2b2.war directory

ui-
text-box
Expand
titleLinux

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/

jboss

wildfly-

as-7

10.

1

0.

1

0.Final/ 

ui-
text-box
Expand
titleWindows

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\

jboss

wildfly-

as-7

10.

1

0.

1

0.Final

UI Step

Delete i2b2.war.deployed file

Code Block
languagepowershell
titleLinux Example
collapsetrue
$ rm /opt/wildfly-10.0.0.Final/standalone/deployments/i2b2.war.deployed

 

 

UI Step

Extract / copy the files from the upgrade zip file to your

WildFly

JBoss deployments directory

ui-
text-boxThe upgrade zip file contains the following files:
Expand
titleContents of Zip File

i2b2 Upgrade Instructions for 1.7.05+ to 1.7.09c.pdf

configuration/
configuration/crcapp/
configuration/crcapp/crc.properties-1709

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

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

ProjectManagement

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

Workplace

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

i2b2Common

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

FR

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

IM

Workplace-core.jar
deployments/i2b2.war/WEB-INF/services/
deployments/i2b2.war/WEB-INF/services/CRC.aar
deployments/i2b2.war/WEB-INF/services/

IM

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

FR

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

Ontology

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

ProjectManagement

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

Start WildFly

admin/

UI Step

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

Code Block
languagepowershell
titleLinux Example
collapsetrue
$ cp -r deployments /opt/jboss-as-7.1.1.Final/standalone
UI Step

Modify the crc.properties

UI Expand
titleUpdate 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.

Warning

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.

UI Step

Backup your existing admin directory

UI Expand
titleLinux Example

/var/www/html/admin

UI Expand
titleWindows Example

C:\inetpub\wwwroot\admin

UI Step

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

Warning

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.

UI Step

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

UI Step

Start JBoss

Code Block
languagepowershell
titleLinux Example
collapsetrue
$ /opt/wildfly-10.0.0.Final/bin/standalone.sh -b 0.0.0.0 &
UI Step

Verify your upgrade

UI Expand
titleTest 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.)