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, 1.7.13" />
<!--    <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>

Anchor

	i2b2-upgrade-

v1712

v1713-info
	i2b2-upgrade-

v1712

v1713-info

Version Information

Current Version:	1.7.13
Release Date:	June 2022
License:	Mozilla 2 Open Source License

Anchor

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

Download

Description	i2b2 Released Version	Minimum Version Required	Download Link	Requirements
Files to upgrade the i2b2 server to 1.7.13	1.7.13	1.7.09c	i2b2core-upgrade-1.7.13.zip ( downloadable)	See Technical Details section on the i2b2 Upgrades page.
Files to upgrade the i2b2 db instance to 1.7.13	11.7.13	1.7.09c	i2b2core-upgrade-1i2b2 data-source1.7.13.zip
Files to upgrade the webclient	1.7.13		i2b2webclient-1713source1713.zip

Anchor

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

Notes

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

User login using SAML Authentication
User Account Registration Tool for local and SAML users
Updated ACT Ontology v4
Automated db upgrade process using
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:

Improved patient counting scripts
Log4J upgrade to latest 2.17.1 version to address security vulnerabilities
Code changes as per veracode scan making i2b2 more secure
i2b2-Synthea 1K syntheaMass data set in i2b2 format
i2b2-Synthea data load scripts for loading Synthea data from scratch

Note

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

.

Upgrade Instructions

Excerpt Include

	Upgrade i2b2
	Upgrade i2b2
nopanel	true

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

Initial Steps:

Download the i2b2core the binary upgrade distribution from i2b2core-upgrade-1713.zip from
Extract the download file i2b2core-upgrade-1713.zip to a folder outside of your existing i2b2 installation folder

Then, follow the steps below to upgrade i2b2 server, database instance and the webclient.

Anchor

	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.

i2b2-upgrade-zip-contentsi2b2-upgrade-zip-contents

UI Steps

size	small

UI Step

Stop WildFly

Code Block

language	powershell
title	Linux Example
collapse	true

$ /opt/wildfly-{version}.Final/bin/jboss-cli.sh --connect command=:shutdown

Code Block

language	powershell
title	Windows Standalone Example
collapse	true

> \opt\wildfly-{version}.Final\bin\standalone stop

UI Step

Backup your existing deployment directory containing i2b2.war directoryfile

UI Expandcode

title	Linux
collapse	true

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

UI Expandcode

title	Windows
collapse	true

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

Upgrade deployments folder

Copy all the files from the extracted downloaded war file downloaded deployment into folder into your existing WildFly standalone standalone/deployments directory.The folder includes the upgraded war file and jdbc driver files

Example your deployments folder: /opt/<wildfly-17.0.0.Final and above version>/standalone/deployments/

Example extracted deployments folder: i2b2core-upgrade-1713\i2b2\deployments

Info
The folder includes the upgraded war file and upgraded jdbc driver files.

UI Step

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

In your deployment directory

Copy

, 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

Replace ALL the <driver>{something}.jar</driver> with latest drivers as below

Oracle	SQL Server	PostgreSQL
<driver>ojdbc8.jar</driver>	<driver>mssql-jdbc-7-9.42.10jre8.jre8.jar</driver>	<driver>postgresql42.3.2.8.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.

uiprojectdoc-box-expandinfo

title	Example

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

UI Step

Steps to perform db upgrade:

Backup your existing data folder

Copy

Copy all the folders

from the extracted download data folder into

created by extracting the latest version into your existing data Upgrade folder

. Example .\2b2core-upgrade-1712a_ext

. This will replace existing Crcdata, Hivedata, Metadata, PMdata folders. Example: Downloads\i2b2core-upgrade-1713\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-7\Upgrade\.

This will replace the existing Crcdata, Hivedata, Metadata, PMdata folders .

Copy the db.properties files from your

data

back up into the respective locations (namely Crcdata, Hivedata, Metadata, PMdata )

Run

Open the command prompt and navigate to each cell folder and run the following upgrade ant commands on your i2b2 database instance, where {db}

can

can be Oracle, sqlserver or postgresql.

Alternative to above Step

5

, you can run individual SQL scripts on your db instance in place of ant commands.
In

data folder

datafolder\Release_1-7\Upgrade\ run the ant commands under each individual cell

subfolder

folder as below

Upgrade From Build	Upgrade to Latest build

.


1.7.09c	In the Crcdata folder run the following ant command: ant -f data_build.

xml

xml upgrade_

table

tables_release_1-7-09c upgrade_

table

tables_release_1-7-10 upgrade_

table

tables_release_1-7-11 upgrade_

table

tables_release_1-7-

12

12a

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

hive_

tables_release_1-7-

09c upgrade

11 upgrade_

hive_

tables_release_1-7-

10 upgrade_hive_tables_release_1-7-11 upgrade_hive_tables_release_1-7-12

12a

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

09c

10 upgrade_tables_release_1-7-

10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12

12a

In the

PMdata

Pmdata folder run the following ant command: ant -f data_build.xml upgrade_

pm_

tables_release_1-7-

09c upgrade_pm_tables_release_1-7-10 upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12

09c
1.7.10	In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-10 upgrade_

table

tables_release_1-7-11 upgrade_

table

tables_release_1-7-

12

12a

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

upgrade_hive_tables_release_1-7-10

upgrade_

hive_

tables_release_1-7-11 upgrade_

hive_

tables_release_1-7-

12

12a

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-

11 upgrade_tables_release_1-7-12
In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-10 upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12

12a

1.7.11

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

table

tables_release_1-7-

11

11 upgrade_table_release_1-7-

12

12a

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

hive_

tables_release_1-7-

11 upgrade_hive

11 upgrade_tables_release_1-7-

12

12a

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

11 upgrade_tables_release_1-7-12
In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12

12a

1.7.

12

12a	In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_

table

tables_release_1-7-

12

12a

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

_hive

_tables_release_1-7-

12

12a

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

12In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-12

12a

Upgrade stored procedures

Run the below CRC and metadata Sql Procedures if your db instance is Postgres.

In Crcdata/scripts/procedures/<db instance>/*.sql

In Metadata/scripts/procedures/<db instance>/*.sql

Info

title	HIVE_CELL_PARAMS configuration

Check HIVE_CELL_PARAMS table is updated with cell properties parameters as detailed here

Steps to Upgrade i2b2 Webclient

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

existing webclient folder to a different location outside of your current webclient installation folder

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

title	Linux 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

title	Windows

On Linux, extract

new webclient

Extract the i2b2webclient-1713.

zip to the folder /var/www/html/webclient/ and copy the backup

zip
Replace your existing webclient folder on your web server with the extracted webclient folder
Update i2b2_config_data.

js to /var/wwww/html/webclient
On Windows, extract the i2b2webclient-1713.zip c:\inetpub\webclient and copy the backup

js using your existing i2b2_config_data.

js to c:\inetpub\webclient

UI Step

Install the new webclient on your web server

UI Expand

title	Linux

UI Expand

title	Windows

Start WildFly

js from your backed up web directory. Details are provided here

Info Box
Backup your entire webclient folder before proceeding with webclient upgrade

UI Step

Start WildFly

You can either run WildFly standalone or as a service.

Code Block

language	powershell
title	Linux Standalone Example
collapse	true

$ /opt/wildfly-{version}.Final/bin/standalone.sh -b 0.0.0.0 &

Code Block

language	powershell
title	Windows Standalone Example
collapse	true

> \opt\wildfly-{version}.Final\bin\standalone start

Verify

Your Upgrade

your upgrade

title

UI Step

UI Expand

Test

Web Client

Webclient

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

Versions Compared

Old Version 15

New Version Current

Key

Download

Notes

Upgrade Instructions

Initial Steps:

Steps to Upgrade

i2b2 Server

Steps to Upgrade i2b2 database

Steps to Upgrade i2b2 Webclient

Start WildFly

Verify

Your Upgrade

Pages

Recently updated

Page History

Versions Compared

Old Version 15

New Version Current

Key

Download

Notes

Upgrade Instructions

Initial Steps:

Steps to Upgrade

i2b2 Server

Steps to Upgrade i2b2 database

Steps to Upgrade i2b2 Webclient

Start WildFly

Verify

Your Upgrade

Pages

Recently updated