Release Management
Space shortcuts
Space Tools

Versions Compared

Old Version 37

changes.mady.by.user Reeta Metta

Saved on

compared with

New Version 38

changes.mady.by.user Reeta Metta

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

Anchor
i2b2-upgrade-v1713-info
i2b2-upgrade-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

Descriptioni2b2 Released VersionMinimum Version RequiredDownload LinkRequirements
Files to upgrade the i2b2 server to 1.7.131.7.131.7.09c

i2b2core-upgrade-1.7.13.zip ( downloadable)

See Technical Details section on the i2b2 Upgrades page.
Files to upgrade the i2b2 db instance  to 1.7.131.7.13              1.7.09ci2b2 data-source1.7.13.zip
Files to upgrade the webclient          1.7.13
 i2b2webclient-source1713.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 single data_build.xml
  • 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
nopaneltrue

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.


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.

UI Steps
sizesmall


UI Step

Stop WildFly

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


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



UI Step

Backup existing deployment directory containing i2b2.war file

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


Code Block
titleWindows
collapsetrue
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 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-1713\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

Edit the following files crc-ds.xml, ont-ds.xml, pm-ds.xml, work-ds.xml

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

Oracle

SQL Server

PostgreSQL

<driver>ojdbc8.jar</driver>

<driver>mssql-jdbc--9.2.0jre8.jar</driver>

<driver>postgresql42.3.2.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.

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-1713\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-7\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  ant commands.
  • In datafolder\Release_1-7\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

  • 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
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-1713.zip 
  • Replace your existing webclient folder on your web server with the  extracted webclient folder
  • Update  i2b2_config_data.js  using your existing i2b2_config_data.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
languagepowershell
titleLinux Standalone Example
collapsetrue
$ /opt/wildfly-{version}.Final/bin/standalone.sh -b 0.0.0.0 &


Code Block
languagepowershell
titleWindows Standalone Example
collapsetrue
> \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.)