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Upgrade to Release 1.7.13 from 1.7.09c


Version Information

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

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

See Technical Details section on the i2b2 Upgrades page.
Files to upgrade the i2b2 db instance  to 1.7.131.7.13              1.7.09ci2b2core-upgrade-1.7.13.zip
Files to upgrade the webclient          1.7.13
 i2b2webclient-1713.zip

 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 against your db instance.
  • Improved patient counting scripts
  • Log4J upgrade to latest 2.17.1 version to address security vulnerabilities
  • Code changes as per  veracode scan  to make i2b2 more secure
  • 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

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.



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.

Stop WildFly

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


Backup your existing i2b2.war directory

Linux

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

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\ 

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/

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--9.2.0jre8.jar</driver>

<driver>postgresql42.3.2.jar</driver>

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.

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

  • 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 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

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

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

HIVE_CELL_PARAMS configuration

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

Steps to Upgrade i2b2 Webclient

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

Install the new webclient on your web server

Linux

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

Update  i2b2_config_data.json  using your existing i2b2_config_data.js from your backed up web directory. Details are provided here

Windows

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

Update  i2b2_config_data.json  using your existing i2b2_config_data.js from your backed up web directory. Details are provided here

Start WildFly 

You can either run WildFly standalone or as a service.


Linux Standalone Example 
$ /opt/wildfly-{version}.Final/bin/standalone.sh -b 0.0.0.0 &
Windows Standalone Example 
> \opt\wildfly-{version}.Final\bin\standalone start

Verify Your Upgrade

 your upgrade


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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