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i2b2-upgrade-

v180

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i2b2-upgrade-

v180

v181-info

Version Information

Current Version:1.8.
0
1
Release Date:
December 2023
June 2024
License:Mozilla 2 Open Source License




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i2b2-upgrade-v180v181-download
i2b2-upgrade-v180v181-download

Download

Descriptioni2b2 Released Release VersionMinimum Version RequiredDownload LinkRequirements
Files to upgrade the i2b2 server to 1.8.011.8.011.7.09c

i2b2core-upgrade-1.8.0181.zip ( downloadable)

See Technical Details section on the i2b2 Upgrades page.
Files to upgrade the i2b2 db instance  to 1.8.011.8.01              1.7.09ci2b2 data-source1.8.01.zip
Files to upgrade the webclient         1.8.01
i2b2webclient-source180181.zip


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i2b2-upgrade-v180v181-note
i2b2-upgrade-v180v181-note

 Notes

Info

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
nopaneltrue

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

Initial Steps:

  • Download  the binary upgrade distribution from  i2b2core-upgrade-180181.zip
  • Extract the download file i2b2core-upgrade-180181.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-v180-stepByStep-WildFly
i2b2-upgrade-v180-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
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$ /opt/wildfly-{version}.Final/bin/jboss-cli.sh --connect command=:shutdownstop


Code Block
languagepowershell
titleWindows Standalone Example
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> \opt\wildfly-{version}.Final\bin\standalone stop



UI Step

Backup existing deployment directory containing i2b2.war file

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


Code Block
titleWindows
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On Windows, movecopy 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 deployment folder into your existing WildFly standalone/deployments directory.

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

Example extracted deployments folder: i2b2core-upgrade-180181\i2b2\deployments

Info

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



UI Step

Update  datasource (*-ds.xml) files   

In your deployment directory, copy *-ds.xml files from the backup folder to wildfly-17.0.#.Final/standalone/deployments

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

Edit the following files crc-ds.xml, ont-ds.xml, pm-ds.xml, work-ds.xmlReplace ALL the <driver>{something}.jar</driver> with latest drivers as belowxml  with the above jar file name

Oracle

SQL Server

PostgreSQL

<driver>ojdbc8.jar</driver>

<driver>mssql-jdbc--912.4.2jre8.0jre8.jar</driver><driver>postgresql42

<driver>postgresql42.37.2.1jar</driver>



UI Step

Migrate cell properties to 1.8.0 1 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.

Info Box

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 all the folders created by extracting the latest version into your existing  data Upgrade folder. This will replace existing Crcdata, Hivedata, Metadata, PMdata folders. Example:  Downloads\i2b2core-upgrade-180181\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-8\Upgrade\.
  • 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 each cell folder 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  of ant commands.
  • In datafolder\Release_1-8\Upgrade\  run the ant commands under each individual cell folder as below
Upgrade From BuildUpgrade to Latest build

1.7.09c

In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-09c upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a

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

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10  upgrade_tables_release_1-7-12a

In the Pmdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-09c  

1.7.10

In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a

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

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-12a

1.7.11


In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11  upgrade_table_release_1-7-12a

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

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a

1.7.12a

In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a

In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a

1.7.13

For Oracle and Postgres, no database upgrade is required. If using SQL Server, reload the following stored procedures:

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

1.8.0

In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-8-0

In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-8-0

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


Info
titleHIVE_CELL_PARAMS configuration

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


Steps to Upgrade i2b2 Webclient

UI Step

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


UI Step

Install new webclient 

  • Extract the i2b2webclient-180181.zip 
  • Replace your existing webclient folder on your web server with the  extracted new webclient folder

  • i2b2_config_data.js has been renamed to i2b2_config_domain.json. Edit the i2b2_config_domain.json  using your existing i2b2_config_data.js from your backed up web directory. Details are provided here

Info Box

Backup your entire webclient folder  folder before proceeding with webclient upgrade



UI Step

Start WildFly 

You can either run WildFly standalone or as a service.

Code Block
languagepowershell
titleLinux Standalone Example
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$ /opt/wildfly-{version}.Final/bin/standalone.sh -b 0.0.0.0 &


Code Block
languagepowershell
titleWindows Standalone Example
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> \opt\wildfly-{version}.Final\bin\standalone start


Verify Your Upgrade

UI Step

Test 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.)





Release Management RM