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<!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, 1.7.13" />
<!--    <link rel="stylesheet" type="text/css" media="all" href="/stylesheets/i2b2-wiki.css" /> -->
</head>
<body>
    <h1 class="releaseHeading" id="upgradeVersion-current">Upgrade to Release 1.7.13 from 1.7.09c</h1>
</body>
</html>


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i2b2-upgrade-v1712-info
i2b2-upgrade-v1712-info

Version Information

Current Version:1.7.13
Release Date:
License:Mozilla 2 Open Source License


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i2b2-upgrade-v1713-download
i2b2-upgrade-v1713-download

Download

Descriptioni2b2 Released VersionMinimum Version RequiredDownload LinkRequirements
Files to upgrade the i2b2 server to 1.7.131.7.131.7.09c
See Technical Details section on the i2b2 Upgrades page.
Files to upgrade the i2b2 db instance  to 1.7.13 1.7.13              1.7.09c


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i2b2-upgrade-v1713-note
i2b2-upgrade-v1713-note

 Notes

Release 1.7.13 contains changes to the i2b2 core Server, database and Web Client.

  • The db upgrade process is now automated to reduce the workload of manually running each individual sql script against your db instance.
  • All the SQL script executions are incorporated into a single data_build.xml which can easily be run using ant commands.

Note: If you are running your application on JBoss, please upgrade to Wildfly before proceeding with the upgrade.


Upgrade Instructions

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Upgrade i2b2
Upgrade i2b2
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Below are Step-by-Step Instructions after you have  upgraded to Wildfly.



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

Steps to Upgrade i2b2 Server

In the following instructions the variable { version } refers to your version of Wildfly installed.  We now support Wildfly 17 version.

UI Steps
sizesmall





UI Step

Stop WildFly

Code Block
languagepowershell
titleLinux Example
collapsetrue
$ /opt/wildfly-{version}.Final/bin/jboss-cli.sh --connect command=:shutdown



UI Step

Backup your existing i2b2.war directory

UI Expand
titleLinux

On Linux, move the /opt/wildfly-{version}.Final/standalone/deployments/ and save it to a different location outside of /opt/wildfly-{version}.Final/ 



UI Expand
titleWindows

On Windows, move the c:\opt\wildfly-{version}.Final\standalone\deployments\ and save it to a different location outside of c:\opt\wildfly-{version}.Final\ 





UI Step

Extract the download file i2b2core-upgrade-1713.zip to a folder outside of wildfly folder.




UI Step

Copy all the files from the downloaded  war file deployment into your existing WildFly standalone directory. This includes the upgraded war file and jdbc driver files

/opt/<wildfly-17.0.0.Final and above version>/standalone/deployments/


UI Step

Update the datasource (*-ds.xml) files in your  deployment directory

Copy *-ds.xml files from the backup folder to wildfly-17.0.#.Final/standalone/deployments

Edit the following files crc-ds.xml, ont-ds.xml, pm-ds.xml, work-ds.xml
and replace ALL the <driver>{something}.jar</driver> with

Oracle

SQL Server

PostgreSQL

<driver>ojdbc8.jar</driver>

<driver>mssql-jdbc-7.4.1.jre8.jar</driver>

<driver>postgresql42.2.8.jar</driver>



UI Step

Migrate cell properties to 1.7.13, if needed. In 1.7.12, cell properties have been moved to the database, in a table called hive_cell_params. If any cell properties were previously changed, they will need to be manually updated in the database. After this, the properties files can be deleted to prevent confusion.

More documentation on setting cell properties is available at this page. Most commonly, the AGG_SERVICE_ACCOUNT password will need to be updated. Generally, the cell URLs do not need to be configured anymore, as the hostname and port is now auto-detected.

UI Expand
titleExample

Properties files are stored at /opt/wildfly-{version}.Final/standalone/configuration/ on Linux and c:\opt\wildfly-{version}.Final\standalone\configuration\ on Windows. The table can be edited with a SQL editor in hive_cell_params.


Steps to Upgrade i2b2 database

Update the datasource (*-ds.xml) files in your  deployment directory

Copy *-ds.xml files from the backup folder to wildfly-17.0.#.Final/standalone/deployments

Edit the following files crc-ds.xml, ont-ds.xml, pm-ds.xml, work-ds.xml
and replace ALL the <driver>{something}.jar</driver> with

Migrate cell properties to 1.7.13, if needed. In 1.7.12, cell properties have been moved to the database, in a table called hive_cell_params. If any cell properties were previously changed, they will need to be manually updated in the database. After this, the properties files can be deleted to prevent confusion.

More documentation on setting cell properties is available at this page. Most commonly, the AGG_SERVICE_ACCOUNT password will need to be updated. Generally, the cell URLs do not need to be configured anymore, as the hostname and port is now auto-detected.

Properties files are stored at /opt/wildfly-{version}.Final/standalone/configuration/ on Linux and c:\opt\wildfly-{version}.Final\standalone\configuration\ on Windows. The table can be edited with a SQL editor in hive_cell_params.
UI Step
  1. Backup your existing data folder
  2.  Download and extract the i2b2core-upgrade-1.7.13.zip   to a folder outside of your existing data folder.
  3.  Copy all the folders from the downloaded data folder   into your data Upgrade folder.

                    Example .\2b2core-upgrade-1712a_ext\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-7\Upgrade\. This will replace the existing Crcdata, Hivedata, Metadata, PMdata folders .

  1. Copy the db.properties files from your data back up into the respective locations(namely Crcdata, Hivedata, Metadata, PMdata )
  2.  Run the following upgrade ant commands on your i2b2 database instance, where {db} can be Oracle, sqlserver or postgresql .

                    Alternative to Step 5, you can run individual SQL scripts on your db instance in place of  ant commands.

In  data folder\Release_1-7\Upgrade\  run the ant commands under each individual cell subfolder as below.

1.7.09c


1.7.10


1.7.11

1.7.12




1.7.13

In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7

In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7

In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7

UI Step

Oracle

SQL Server

PostgreSQL

<driver>ojdbc8.jar</driver>

<driver>mssql-jdbc-7.4.1.jre8.jar</driver>

<driver>postgresql42.2.8.jar</driver>

UI Step
UI Expand
titleExample



Steps to Upgrade i2b2 WebClient

UI Step

Backup your existing i2b2_config_data.js from your web server

On your webclient backup your existing i2b2_config_data.js to a folder outside of your web server.

UI Expand
titleLinux Example

On Linux, move the folder /var/www/html/webclient/ and save it to a different location outside of /var/wwww/html/webclient


UI Expand
titleWindows

On Windows, move the folder c:\inetpub\webclient and save it to a different location outside of c:\inetpub\webclient




UI Step

Install the new webclient on your web server

UI Expand
titleLinux

On Linux, extract the i2b2webclient-1712a.zip to the folder /var/www/html/webclient/ and copy the backup i2b2_config_data.js  to /var/wwww/html/webclient


UI Expand
titleWindows

On Windows, extract the i2b2webclient-1712a.zip c:\inetpub\webclient and copy the backup i2b2_config_data.js  to c:\inetpub\webclient




UI Step

Start WildFly

Code Block
languagepowershell
titleLinux Example
collapsetrue
$ /opt/wildfly-{version}.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-zip-contents
i2b2-upgrade-zip-contents







Release Management RM