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    <h1 class="releaseHeading" id="upgradeVersion-current">Upgrade to Release 1.7.13 from 1.7.09c</h1>
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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

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	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	i2b2core-upgrade-1.7.13.zip
Files to upgrade the webclient	1.7.13		i2b2webclient-1713.zip

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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.

User login using SAML Authentication
User Account Registration Tool
Updated ACT Ontology v4
Automated db upgrade process using single data_build.xml executed by Ant command 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.
Improved patient counting scripts
Log4J upgrade to address security vulnerabilities
i2b2-Synthea 1K syntheaMass data set and data load scripts

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.

Initial Steps:

Download the binary upgrade distribution from i2b2core-upgrade-1713.zip
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.

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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

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UI Step

Stop WildFly

Code Block

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

UI Step

Backup your existing i2b2.war directory

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title	Linux

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

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title	Windows

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

Copy all the files from the extracted downloaded war file deployment into your existing WildFly standalone directory. The folder 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.

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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

Backup your existing data folder
Copy all the folders from the extracted download data folder into your existing data Upgrade folder
Example: Downloads\2b2core-upgrade-1712a\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-7\Upgrade\. This will replace
existing Crcdata, Hivedata, Metadata, PMdata folders.
Alternative to above step, navigate to the edu.harvard.i2b2.data\Release_1-7\Upgrade\ directory of your extracted folder
Copy the db.properties files from your back up into the respective locations(namely Crcdata, Hivedata, Metadata, PMdata )
Open the command prompt and navigate to cell folders and run the following upgrade ant commands on your i2b2 database instance, where {db} can be Oracle, sqlserver or postgresql.
Alternative to above Step, 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.
Upgrade From Build	Upgrade to Latest build
1.7.09c	In the Crcdata folder run the following ant command: ant -f data_build. xml upgrade_table_release_1-7-09c upgrade_table_release_1-7-10 upgrade_table_release_1-7-11 upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_ xml upgrade_tables_release_1-7-09c 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 Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7- 09c upgrade 11 upgrade_tables_release_1-7- 10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12 12a In the PMdata Metadata folder run the following ant command: ant -f data_build.xml upgrade _pm _tables_release_1-7- 09c 10 upgrade_ pm_ tables_release_1-7- 10 upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12 12a
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
1.7.1212a	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 Metadata folder run the following ant command: ant -f data_build.xml upgrade _hive _tables_release_1-7- 12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-12 12a

Upgrade stored procedures
Run the CRC Sql Procedures (ie for PostgreSQL) in Crcdata/scripts/procedures/postgresql/*.sql
Run the Metadata Sql Procedures (ie for PostgreSQL) in Metadata/scripts/procedures/postgresql/*.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.

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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

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title	Windows

UI Step

Install the new webclient on your web server

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title	Linux

On Linux, extract the i2b2webclient-1713.zip to the folder /var/www/html/webclient/ and copy the backup

Update i2b2_config_data.json using your existing i2b2_config_data.js to /var/wwww/html/webclient .js from your backed up web directory. Details are provided here

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title	Windows

On Windows, extract the i2b2webclient-1713.zip c:\inetpub\webclient and copy the backup webclient

Update i2b2_config_data.json using your existing i2b2_config_data.js to c:\inetpub\webclient js from your backed up web directory. Details are provided here

Start WildFly

UI Step

You can either run WildFly standalone or as a service.

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

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title	Windows Standalone Example
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> \opt\wildfly-{version}.Final\bin\standalone start

Verify Your Upgrade

your upgrade

UI Step

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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

Versions Compared

Old Version 20

New Version 21

Key

Download

Notes

Upgrade Instructions

Initial Steps:

Steps to Upgrade i2b2 Server

Steps to Upgrade i2b2 database

Start WildFly

Verify Your Upgrade

Pages

Recently updated

Page History

Versions Compared

Old Version 20

New Version 21

Key

Download

Notes

Upgrade Instructions

Initial Steps:

Steps to Upgrade i2b2 Server

Steps to Upgrade i2b2 database

Start WildFly

Verify Your Upgrade

Pages

Recently updated