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    <h1 class="releaseHeading" id="upgradeVersion-current">Upgrade to Release 1.7.12 from 1.7.09c</h1>
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	i2b2-upgrade-v1711v1712-info
	i2b2-upgrade-v1711v1712-info

Version Information

Current Version:	1.7.

12

Release Date:
12a

October 31

May,

2019

2020
License:	Mozilla 2 Open Source License

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	i2b2-upgrade-v1711v1712-download
	i2b2-upgrade-v1711v1712-download

Download

Description	i2b2 Released Version	Minimum Version Required	Download Link	Requirements
Files to upgrade the i2b2 server to 1.7.

12

12a

1.7.

12

12a

1.7.09c

Image Modified

i2b2_upgrade_1.7.09c_to_1.7.12.

2b2core-war-1712a.zip

See Technical Details section on the i2b2 Upgrades page.

Files to upgrade the i2b2 Database to 1.7.121.7.12

Image Removed i2b2createdb-1712.zip

Files to upgrade the i2b2 Web Client to 1.7.121.7.12

Image Removed i2b2webclient-1712.zip

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	i2b2-upgrade-v1711v1712-note
	i2b2-upgrade-v1711v1712-note

Notes

Release 1.7.12 contains changes to the i2b2 core Server, database and Web Client.

Therefore in addition to the i2b2upgrade-1712.zip file you also need to download the i2b2createdb-1712.zip and i2b2webclient-1712.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.

If you are upgrading to 1.7.12 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.

Anchori2b2-upgrade-v1710-howToi2b2-upgrade-v1710-howTo

The upgrade process is now made easier using a pre-built war file and the properties files are now stored in the database.
The prebuilt-war file has all the core, web and database files packaged together and available as single download zip file.

Note: 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

Knowing some sites have remained on JBoss 7 while some have upgraded to WildFly 10, we have gone ahead and provided Below are 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 namesafter you have upgraded to Wildfly.

UI Expand

title	Example Paths to i2b2.war

Code Block

language	powershell
title	JBoss 7 path

/opt/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/

Code Block

language	powershell
title	WildFly 10 path

/opt/wildfly-10.0.0.Final/standalone/deployments/i2b2.war/

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	i2b2-upgrade-v1710-stepByStep-

JBoss

WildFly
	i2b2-upgrade-v1710-stepByStep-

JBoss

WildFly

Step-by-Step Instructions for

JBoss

WildFly

In the following instructions the variable { version } refers to your version of Wildfly installed. We have tested with Wildfly 10, 14, and 17.

UI Steps

size	small

UI Step
Stop

JBoss

WildFly

Code Block

language	powershell
title	Linux Example
collapse	true

$ /opt/

jboss-as-7.1.1.

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

UI Step

Backup your existing i2b2.war directory

UI Expand

title	Linux

On Linux,

make a copy of

move the /opt/

jboss-as-7.1.1.

wildfly-{version}.Final/standalone/deployments/

i2b2.war/

and save it to a different location outside of /opt/

jboss-as-7.1.1.

wildfly-{version}.Final/

UI Expand

title	Windows

On Windows,

make a copy of

move the c:\opt\

jboss-as-7.1.1.

wildfly-{version}.Final\standalone\deployments\

i2b2.war\

and save it to a different location outside of c:\opt\

jboss-as-7.1.1. UI StepBackup your existing i2b2.war directory

wildfly-{version}.Final\

UI Step

Delete i2b2.war.deployed file

Code Block

language	powershell
title	Linux Example
collapse	true

$ 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

language	powershell
title	Linux Example
collapse	true

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

UI Step

Start JBoss

Code Block

language	powershell
title	Linux Example
collapse	true

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

UI Step

Verify your upgrade

UI Expand

title	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.)

Anchori2b2-upgrade-v1710-stepByStep-WildFlyi2b2-upgrade-v1710-stepByStep-WildFly

Step-by-Step Instructions for WildFly

UI Steps

size	small

UI Step

Stop WildFly

Code Block

language	powershell
title	Linux Example
collapse	true

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

Extract the download file i2b2core-war-1712a.zip to a folder outside of wildfly folder.

UI Step
Copy all the files from the download war file deployment into your existing WildFly standalone directory.

UI Step

Upgrade Database

Run the following upgrade scripts on your i2b2 database instance, where {db} can be Oracle, sqlserver or postgresql

In data folder

1.7.09c

PmData/scripts/upgrade_{db}_i2b2pm_tables.sql

Crcdata/scripts/crc_create_query_{db}.sql

Hivedata/scripts/upgrade_{db}_i2b2hive_tables.sql

1.7.10

Metadata/scripts/ont_{db}.sql

Crcdata/scripts/crc_create_query_{db}.sql

Hivedata/scripts/upgrade_{db}_i2b2hive_tables.sql

1.7.11

1.7.12

Crcdata/scripts/crc_create_query_{db}.sql

Hivedata/scripts/upgrade_{db}_i2b2hive_tables.sql

Run the ant scripts for Metadata and Crcdata for releases 1.7.09C to 1.7.12.

If you are upgrading from 1.7.12 to 1.7.12a, run the ant script for Crcdata.

UI Step

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

Copy *-ds.xml files from the backup folder to wildfly-1#.0.1.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 1.7.12, 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

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.

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,

make a copy of /opt/wildfly-10.0.0.Final/standalone/deployments/i2b2.war/

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

opt/wildfly-10.0.0.Final/

var/wwww/html/webclient

UI Expand

title	Windows

On Windows,

make a copy of

move the folder c:\

opt\wildfly-10.0.0.Final\standalone\deployments\i2b2.war\

inetpub\webclient and save it to a different location outside of c:\

opt\wildfly-10.0.0.Final\ Code Blocklanguagepowershell

inetpub\webclient

UI Step

Delete i2b2.war.deployed file

Install the new webclient on your web server

UI Expand

title	Linux

Examplecollapsetrue

$ 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

language	powershell
title	Linux Example
collapse	true

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

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

title	Windows

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

language	powershell
title	Linux Example
collapse	true

$ /opt/wildfly-

10.0.0.

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

UI Step

Verify your upgrade

UI Expand

title	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.)

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

Contents of the Zip File

UI Expand

title	i2b2upgrade-1709c-to-1711.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

Metadata/

ont_oracle.sql

ony_postgresql.sql

ont_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

Versions Compared

Old Version 3

New Version Current

Key

Download

Notes

Upgrade Instructions

Step-by-Step Instructions for

WildFly

Step-by-Step Instructions for WildFly

Contents of the Zip File

Pages

Recently updated

Page History

Versions Compared

Old Version 3

New Version Current

Key

Download

Notes

Upgrade Instructions

Step-by-Step Instructions for

WildFly

Step-by-Step Instructions for WildFly

Contents of the Zip File

Pages

Recently updated