Release 1.7.12  contains solutions for providing an easier install of i2b2, redesigned Find Terms, totalnum counting scripts, new Authentication protocols, and REDCAP import. Also included are other enhancements to the i2b2 Webclient, the ACT ontology, and bug fixes. Release 1.7.12a includes several bugfixes, including a very important query queueing improvement.

After reading this documentation, please go to the Quick Upgrade Guide for the details about upgrading your i2b2 software. If you are installing from scratch, refer instead to the Quick Install Guide (and optionally the full i2b2 Installation Guide).

i2b2 Release 1.7.12

Release Date: December, 2019

Highlight of Features

Backend Features

Frontend Features

Redesigned Find Terms By Name

New Webclient Documentation

Improved view of Left Pane in maximized mode

Larger Query Results Panel view after Query run

When a query with breakdowns has finished, the results panel temporarily expands slightly to accommodate the breakdown graphs display.

Community-Contributed Features



ACT Ontology

ACT Technology and Data Harmonization Team

University of Pittsburgh

Easier-to-read counts

Nick Brown and Griffin Weber

Beth Israel Deaconess Medical Center

Extended query-by-value flags

Robert Bradford

University of North Carolina

Totalnum in find terms

Mauro Bucalo

University of Pavia

Visual Design of new Find Terms

Leaf Team

University of Washington

Totalnum Counter for Postgres

Dan Vianello

Center for Biomedical Informatics, Washington University in St. Louis

(Part of overall totalnum scripts in this release.)

Feature Configuration

Easier i2b2 Install

The i2b2 server can now be installed using a pre-built war file instead of having to build it from source, or the war file can be built from source much more easily. More information is in the updated Installation Guide. The properties files are now stored in the database.

Authentication Protocol Support for NTLM2/OKTA

RedCap Import Setup

Currently,  the following  REDCAP Features  are supported in i2b2.



1) Set Project Params (PM_PROJECT_PARAM)



  • Get the pid value from the Redcap project url. Set the pid parameter name to this value

  • Get the API Key from Redcap.  Logon to Redcap, and on the right side under applications click API.   Then, select Generate token, and use this token for the value for the parameter.




Set the Value parameter to the pid value from the Redcap project url. 


Optional, Defaults to Y
Y - Every time a form is submitted the i2b2 metadata ontology gets regenerated

N - Do Not regenerate the metadata ontology.   

NOTE:  When first setting up i2b2/redcap this needs to be set to Y at least once or the ontology will not be created.


Optional, Defaults to \REDCAP\
This is the key for the root of the REDCap ontology.


Optional, Defaults to tree
This is how the ontology will be created

tree - All enumerated values, Yes/No will be children on the ontology

The only exception is items with checkbox, which will always be a popup

If this redcap form has the identified value set to true, then this ontology will be protected and only users with the following i2b2 access role will be able to access it.

2) On the redcap side, set the Data Entry Trigger, it is under Project Setup → in Enable optional modules and customizations, select Additional customizations → Data Entry Trigger, and enter:

http://{i2b2 url}/i2b2/services/QueryToolService/redcapPush

Click Test to verify connection

3) Give Editor role to the project for AGG_SERVICE_ACCOUNT( optional DATA_PROT, DEID, LDS)

4) Submit a form and check to see if the ontology was created.

Totalnum Scripts Setup

  1. In the Release_1-7/NewInstall/Metadata/ run the ant script to create the stored procedures.
    1. POSTGRESQL : ant -f data_build.xml db_metadata_run_total_count_postgresql
    2. ORACLE : ant -f data_build.xml db_metadata_run_total_count_oracle
    3. SQL SERVER : ant -f data_build.xml db_metadata_run_total_count_sqlserver        
  2. Execute the RunTotalNum stored procedure on your database. This can take several hours. 

                 Example Usage:    


                                          Note: If you get the error as: ERROR at line 1: ORA-01031: insufficient privilege, then run the command:
                                          grant create table to (DB USER)

                                          SQL server:              
                                          exec RUNTOTALNUM

                                          select RUNTOTALNUM('observation_fact','public')
                                      -- (replace 'public' by the schema name for the fact table)
                                      -- I
f using a schema other than public for metadata, you might need to run "set search_path to 'i2b2metadata','public' " first as well


             3.  When finished, verify it is complete by checking that c_totalnum columns in your ontology tables contain numbers (not nulls).

                These total counts will be visible in the ontology browser in the web client.

ACT Ontology Setup

This will allow you to install the ACT ontology as a separate project in i2b2. Note that this will create a project with ONLY the ontology - no data. At this time, using the demodata with the ACT ontology is not supported. You will need to load your own data to run queries using the ontology.



                     This will create  the new  ACT Ontology structure under project ACT.


Using Extended Query-By-Value Flags

This is a community contributed feature, turned off by default, and has only been minimally tested by the core i2b2 team.

An expanded set of lab flag values can be easily modified by users to support their needs or expanded to the full set of HL7/LOINC flag values. The expanded list is toggleable via an added config setting in the i2b2_ui_config.js. (Note: Only numeric lab results have the flag functionality included.)

With the expanded set of lab values, the base 'A','L','H' are omitted to prevent collisions with things like "CH" (Critical High) or "CL" (Critical Low) due to the indexOf function call to determine if a flag is in the list.

To use the expanded lab flag set, make ETL changes to accommodate the expanded list of values you would like to use and modify i2b2_ui_config.js to match.

Configuring the Expanded Webclient Left Pane

To set the webclient to start with the left pane in the new expanded mode, make sure this new parameter is added to i2b2_config.js. 

startZoomed: true

The .zip file for this release defaults to this mode.


Database Drivers

The JDBC drivers were updated to the following versions.

DriverNew Version
postgresql-42.2.5.jarPostgreSQL 42.2.5
mssql-jdbc-7.0.0.jre8.jarMS Sql Server 7.0.0

i2b2 Database Changes

i2b2 Server and Client Changes

New Features and Improvements

Bug Fixes

i2b2 Release 1.7.12a

Release Date: May, 2020

Release 1.7.12a  includes fixes for the i2b2 Web Client, i2b2 Core Server, and  Postgres and SQLServer database Stored Procedures. The notable changes in this release are:

i2b2 Server Side Fixes:

[CORE-392] - Queueing is not working as designed

[CORE-393] - REDcap import does not work in Postgres

[CORE-387] - Hierarchical view turns off if there are >1000 results, even if only a few hundred are returned
                       Full Request XML message is stored in the QT_PDO_QUERY_MASTER table

i2b2 Web Client Fixes:

[WEBCLIENT-328] - Webclient behaves oddly when splitter is moved to make left panel very small

i2b2 Database Fixes:

[CORE-389] - Totalnum performance improvements on Postgres and SQLServer

[CORE-393] - REDcap import does not work in Postgres