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1.8.2 Release Notes

i2b2 1.8.2 Release introduces functionality of user-created data table definition and data download of limited data sets (LDS). The Data Request Management tool enables project managers to manage the data file exports. In addition, there are minor improvements in the Query tool, improvements to the fast "totalnum" patient counting scripts,  and some bug fixes.

Highlight of Features

Top New Features

Description

Export Extension: Create data table

The Create Data Table tool allows the i2b2 user to create their own data table definitions with ontology variables and then request data exports in the Run Query dialog.

Export Extension: Data Request Manager

The Data Request Manager tool allows an i2b2 manager to manage and process the user data requests. Both custom table exports and exports of pre-defined tables defined by domain can be run and managed using the new tools. 



ENACT Ontology v4.2

Upgraded to UMLS 2025AA:

  • Lab (Provisional)
  • Medications grouped alphabetically
  • Medications grouped by VA Classification
  • Diagnosis ICD10CM
  • Procedures CPT4
  • Procedures HCPCS
  • Procedures ICD10PCS

Other updates:

  • Lab (Common)
  • Demographics
  • Social Determinants of Health
  • Research Ontology
  • Vaccines

 Update to new secure versions of software

 

The new server uses Java 17, Wildfly 37.01, and Axis2 v2

Digital Twin Bundle (distributed separately) 

Tools for computing loyalty cohorts and computational phenotypes in i2b2. 

Bug fixes and minor feature updates



Totalnum (patient counting) scripts have been updated, and the PM cell has performance enhancements (a database trigger to rotate the pm_user_session table)

Detailed Documentation on New Features

Data Exporter extension for i2b2

i2b2 data exporter functionality is now enhanced the enable i2b2 users to create their own Data table definitions  from ontology elements. The data table definitions are displayed as options that can be selected in the Run Query dialog. Users can submit multiple data requests for with a query.  The Manager user can manage the data requests and generate data files using a Data Request Manager console.  Detailed documentation on set up can be found here: Data Exporter Set-up

The below steps describe the overall process:

  • User logs into i2b2 webclient and creates Data table definition using the Create Data Table tool, using desired Ontology elements
  • User runs a regular i2b2 query, checking the User-created Data request option(s) when running the query.
  • The manager logs in and views the data requests using the Data Request Manager Console.
  • Manager user generates the data export files using the Data Request Manager Console.
  • The generated data file is stored in a configurable location on the i2b2 server.

ENACT - V4.2 Ontology

The V4.2 Ontology includes 19 ontologies- 12 updated and 7 unchanged


Metadata and CRC zip files provided in the NewInstall  load the latest ENACT Version-4.2 ontology into your db schema using ANT scripts.

The CPT4 ontology table is not included with i2b2 due to AMA restrictions on redistribution of CPT code information. Contact the ENACT team to get a copy if your institution is an AMA member.

ENACT V4.2 data load process

  1. Download and extract the newinstall zip package from "Download Binary Distribution" in the top section of https://www.i2b2.org/software
  2. Edit the  edu.harvard.i2b2.data\Release_1-8\NewInstall\Metadata\db.properties file to update the project properties to 'ACT' ; db.project=ACT
  3. From the edu.harvard.i2b2.data\Release_1-8\NewInstall\Metadata folder, run the ant command: ant -f data_build.xml db_metadata_load_data. This will execute the SQL scripts from the edu.harvard.i2b2.data\Release_1-8NewInstall\Metadata\act\scripts\<db type> folder to create and load the metadata tables 
  4. From the edu.harvard.i2b2.data\Release_1-8\NewInstall\crcdata folder, run the ant command: ant -f data_build.xml db_demodata_load_data. This will execute the SQL scripts from the edu.harvard.i2b2.data\Release_1-8NewInstall\crcdata\act\scripts\<db type> folder to create and load the concept_dimension 
  5.  Run the scripts from the edu.harvard.i2b2.data\Release_1-8\NewInstall\Metadata \<dbtype>\scripts folder to load the Schemes, Table_access tables
  6. You can now verify the new Ontology by logging into the webclient

Note: the ENACT v4.2 ontology is distributed as a New Install only. If you are upgrading, install the v4.2 tables in a different schema from v4.1. Installing in the same schema will insert duplicate rows into the Ontology, Concept_dimension and Table_access tables


ACT Fast Totalnum Scripts

The 5x faster totalnum scripts (patient counting scripts) are now available for all three database platforms!

Patient Counting Scripts ("totalnum")

PM_USER_SESSION table rotation trigger

When a user logs in, the PM_USER_SESSION table size is now checked. If it has over 1000, all of the expired sessions after the first 100 are moved to a new PM_USER_SESSION_ARC table. A large PM_USER_SESSION table causes performance problems, and this is especially problematic when using SHRINE, which frequently starts new sessions.

Changelog

Database Drivers

The JDBC drivers were updated to the following versions.

Server Type

oracle

Postgresql

mssql

Driver Version

ojdbc11jar

postgresql-42.7.8.jar

mssql-jdbc-12.8.1.jre8.jar

Supported Db Server versions

Server Type

SQL Server

Oracle

PostgresSQL

Supported Version/s

2012+ (tested with up to 2022)

23.3

11 to 14 (9 and 10 work for querying, but not data export)

Supported software versions

Application Type

Java

Wildfly

Apache HTD

Apache Ant

Apache Axis2

PHP                                           

Supported Version/s

17

37.01

2.0 (RHEL 6) and 2.2 ( RHEL 7)

1.9.627.2.27 or higher                                              

Supported Operating Systems

 Rocky linux 8 and 9, CentOS versions 7

Windows 2016 -2019

Unofficially, MacOS and other flavors of Linux are likely to work.


i2b2 Server and Client Changes

New Features and Improvements

Web client

WEBCLIENT-368   1.8.2 Webclient update     

CORE-370 VERACODE Scan - 1.8.2 Webclient                                                                                                                                                                                                                   

Core-server

CORE-456 Data Export: agg table

CORE-455 Data Export: Request Management admin tool

CORE-451 Enhanced Data Export - download file generation

CORE-459 upgrade to wildfly 34 with axis2 version2

CORE-460 Upgrade to JAVA 17

CORE-454 Upgrade Spring jar to version 6

CORE-447 Update JDBC drivers

CORE-458 Software maintenance - drivers, libraries

CORE-445 java code folder structure for 1.7 should be changed to refer to 1.8.2       

CORE-473   VERACODE Scan - 1.8.2 Server code                                                                                                                                                                                                                                   

i2b2 Database Changes

New Features and Improvements

DATA-51     RPDO custom table export stored procedures    

DATA-51     Data exporter (v1.8.2) - Add RPDO_Table_Request and Qt_breakdown_path change- add column       

DATA-32     Faster Totalnum (patient counting) script!                                                                                                                                                                                                

Bug Fixes

Core-server / Data

CORE-450 html injection in Queryname and workplace

CORE-249 Search by code fails ungracefully



Notes for Developers

If you change the xsd (REST API message definitions), then you will need to regenerate gensrc via JAXB in Java 8. In the i2b2-core cell directory for which you're regenerating the XSD-Java, run the ant target "jaxb_gen" on Java 8 and then build as usual using Java 17.





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Release Management RM