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Upgrade i2b2 Server: 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

A zip file containing a precompiled version of i2b2 1.7.09c has been provided in the Download section of this document.  The contents of the zip file can be dropped into your existing instance of i2b2 to upgrade it. The JARs were compiled with JDK 7 and will run in your existing JBoss 7 or WildFly application server. The upgrade technique will work on both Linux and Windows environments.

The following requirements must be met in order to use this upgrade path:

JBoss 7 (tested on JBoss
html-text
<!DOCTYPE html>
<html>
<head>
    <title>Upgrade i2b2 Software</title>
    <meta charset="UTF-8">
    <meta name="description" content="Upgrading the i2b2 Software to the latest version" />
    <meta name="keywords" content="i2b2, release, upgrade, 1.7.10" />
<!--    <link rel="stylesheet" type="text/css" media="all" href="/stylesheets/i2b2-wiki.css" /> -->
</head>
<body>
    <h1 class="releaseHeading" id="upgradeVersion-current">Upgrade to Release 1.7.10 from 1.7.09c</h1>
</body>
</html>


Anchor
i2b2-upgrade-v1710-info
i2b2-upgrade-v1710-info

Version Information

Current Version:1.7.10
Release Date:May 14, 2018
License:i2b2 Open Source License


Anchor
i2b2-upgrade-v1710-download
i2b2-upgrade-v1710-download

Download

Descriptioni2b2 Released VersionMinimum Version RequiredDownload LinkRequirements
Files to upgrade the i2b2 server to 1.7.101.7.101.7.09cSee Technical Details section on the i2b2 Upgrades page.
Files to upgrade the i2b2 Database to 1.7.101.7.10
Image Added i2b2createdb-1710.zip
Files to upgrade the i2b2 Web Client to 1.7.101.7.10
Image Added i2b2webclient-1710.zip


Anchor
i2b2-upgrade-v1710-note
i2b2-upgrade-v1710-note

 Notes

    • Release 1.7.10 contains changes to the i2b2 database and Web Client. Therefore in addition to the i2b2upgrade-1710.zip file you also need to download the i2b2createdb-1710.zip and i2b2webclient-1710.zip files. 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.
    • The i2b2 Admin module no longer needs to be setup on the i2b2 server. This is due to a new feature introduced in release 1.7.10 that enables a single sign-on location for both the Web Client and Admin Module. Please see the 1.7.10 Release Notes for additional information.
    • If you are upgrading to 1.7.10 from a release prior to 1.7.09c it is important you read the upgrade documentation before upgrading your system because earlier upgrades had changes to properties files. When a release has a change to a property file as did 1.7.09 we will make note of it and outline the steps to merge the changes into your local properties file.

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i2b2-upgrade-v1710-howTo
i2b2-upgrade-v1710-howTo

Upgrade Instructions

Excerpt Include
Upgrade i2b2
Upgrade i2b2
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
) and JRE 7 or Wildfly10 and JRE 8 are running on your application server
  • Currently running i2b2 version 1.7.05 or higher
  • Existing i2b2 was installed from source or you are using the i2b2 VMWare virtual machine with release 1.7.05 or higher installed
  • Download

    Descriptioni2b2 Released VersionMinimum Version RequiredFile SizeDownload LinkRequirements
    Files to upgrade the i2b2 server from at least 1.7.05 to 1.7.09c.1.7.09c1.7.05 Image Removed i2b2upgrade-1705-to-1709c.zipSee Technical Details section.

    Notes

    • These upgrade instructions are to upgrade the software for only the i2b2 server. It does not include any changes to made to the i2b2 Database or the i2b2 Web Client software. Depending on the current version of your i2b2, you may need to also get the latest i2b2 Web Client and Data zip files to deploy. If you are upgrading from 1.7.09b you do not need these other components as release 1.7.09c contains server changes only.
    • 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.
    /standalone/deployments/i2b2.war/




    Code Block
    languagepowershell
    titleWildFly 10 path
    /opt/<wildfly-17.0.0.Final and above versions>/standalone/deployments/






    Anchor
    i2b2-upgrade-v1710-stepByStep-JBoss
    i2b2-upgrade-v1710-stepByStep-JBoss

    Step-by-Step Instructions for JBoss


    UI Steps
    sizesmall


    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



    Warning

    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.




    UI Step

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




    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

    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.)





    Anchor
    i2b2-upgrade-v1710-stepByStep-WildFly
    i2b2-upgrade-v1710-stepByStep-WildFly

    Step-by-Step Instructions for WildFly


    UI Steps
    sizesmall


    UI Step

    Stop 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 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/wildfly-10.0.0.Final/ 




    UI 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\wildfly-10.0.0.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



    Warning

    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.




    UI Step

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




    UI Step

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



    Code Block
    languagepowershell
    titleLinux Example
    collapsetrue
    $ cp -r deployments /opt/wildfly-10.0.0.Final/standalone




    UI Step

    Start WildFly



    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.)








    Anchor
    i2b2-upgrade-zip-contents
    i2b2-upgrade-zip-contents

    Contents of the Zip File


    UI Expand
    titlei2b2upgrade-1709c-to-1710.zip


    database/

    Crcdata/

    scripts/

    oracle/

    query_demo_insert_data.sql

    postgresql/

    query_demo_insert_data.sql

    sqlserver/

    query_demo_insert_data.sql

    crc_create_query_oracle.sql

    crc_create_query_postgresql.sql

    crc_create_qyert_sqlserver.sql

    Pmdata/

    upgrade_oracle_i2b2pm_tables.sql

    upgrade_postgresql_i2b2pm_tables.sql

    upgrade_sqlserver_i2b2pm_tables.sql


    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