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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).

Table of Contents

i2b2 Release 1.7.12

Release Date: December, 2019

Highlight of Features

Backend Features

Frontend Features

Redesigned Find Terms By Name

  • Find terms shows the terms' contextual hierarchy, and terms that are children of other search results are not returned. Shown here: 1.7.11 (left) vs. 1.7.12 (right)
  • Right-clicking on a term and then "Find Term in Tree" shows the entire hierarchy around the selected term.

New Webclient Documentation

  • Included in the client and also on the Webclient Community Wiki page.

  • Featuring:
    • 3-minute screencast tutorial
    • Better overviews and guideposts
    • More task-oriented teaching

Improved view of Left Pane in maximized mode

  • In maximized mode, the left pane now makes all tabs accessible.

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

  •   User Set up with  OKTA Configuration:   On the Admin page, under Manage Users,

               Add a Parameter domain  and assign the values as below. Parameter value will be your institution domain name.


                 Add a second parameter domain_controller as below. Parameter value will be your institution domain_controller value


                  Add the final parameter authentication_method as below. Parameter value will be OKTA


  •   User Set up with  NTLM2 Configuration:   On the Admin page, under Manage Users,

                    Add a Parameter domain  and assign the values as below. Parameter value will be your institution domain name.


                      Add a second parameter domain_controller as below. Parameter value will be your institution domain_controller value


                  Add the final parameter authentication_method as below. Parameter value will be NTLM2


RedCap Import Setup

Currently,  the following  REDCAP Features  are supported in i2b2.


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. 


                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

Warning Box

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


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. 


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

  • Small changes to the i2b2 Database. 
    • Property files were moved into the database in the new Hive table HIVE_CELL_PARAMS.
    • Query type classname property moved from the properties file to the CRC table QT_QUERY_RESULT_TYPE in a new CLASSNAME field
  • Totalnum counts to Ontology Terms in the demo data that is delivered with the software along with the  Stored procedures used for creating the counts.
  • ACT Ontology

i2b2 Server and Client Changes

New Features and Improvements

  • [CORE-378] - Find Terms should display partial results when maximum is exceeded
  • [CORE-377] - Admin interface
  • [CORE-352] - Show hierarchy in Find Terms
  • [CORE-348] - Improve build process, auto-build entire WAR file
  • [CORE-347] - Refactor to remove XML config files
  • [CORE-346] - OKTA
  • [CORE-345] - Replace old Spring Libraries
  • [CORE-344] - Support for NTLM2
  • [CORE-345] - Replace old Spring Libraries
  • [CORE-343] - Replace old Spring Libraries
  • [CORE-345] - Provide totalnum counting scripts
  • [CORE-341] - Add a findByName filter for results inside other results
  • [WEBCLIENT-310] - Mauro Bucalo contribution: totalnum in find, improved date filters
  • [WEBCLIENT-309] - Find Terms should display partial results when maximum is exceeded
  • [WEBCLIENT-308] - UNC Contribution: Configurable extended lab result flags
  • [WEBCLIENT-306] - Beth Israel contribution: commas in counts, query option infrastructure
  • [WEBCLIENT-299] - Fully spell out words in tabs
  • [WEBCLIENT-298] - open web issue management for i2b2
  • [WEBCLIENT-287] - Improved term info panel
  • [WEBCLIENT-285] - New webclient documentation
  • [WEBCLIENT-282] - Improve find terms view
  • [WEBCLIENT-281] - Left side panels tabbed instead of stacked
  • [WEBCLIENT-279] - Query status window resize to show graphs
  • [WEBCLIENT-174] - Previous query run as a query-in-query containing unsupported concepts does not draw the timeline
  • [WEBCLIENT-104] - Add Print functionality to i2b2 web client help files

Bug Fixes

  • [CORE-367] - When a SHRINE query is rerun in i2b2 the date parameter seems to be lost.
  • [CORE-366] - Error on API request on endpoint /i2b2/services/QueryToolService/publishDataRequest
  • [CORE-308] - Full Request XML message is stored in the QT_PDO_QUERY_MASTER table
  • [CORE-362] - db_metadata_load_identified_data does not exist
  • [CORE-358] - Issues with 1.7.10 VM image
  • [CORE-353] - DBLookup pages - not all fields appear
  • [CORE-333] - Query run with Text search with words that contain a space and a dash is erroring out
  • [CORE-332] - OracleLarge db give db error for Ontology terms 'Encounters', 'Enrollment, 'VitalSigns'
  • [CORE-231] - CRC: PDO query does not escape characters
  • [CORE-224] - SQL Server: Database error when no start_date on a temporal query
  • [CORE-222] - Visit_Dimension event set in PDO not returning
  • [WEBCLIENT-312] - Find Term tab- context menu shows Find Term in Tree" item without any item selection
  • [WEBCLIENT-311] - Find Terms- Search by "Any Category" not displaying right msg if no match found
  • [WEBCLIENT-303] - Find Terms - Category Diagnosis ICD10 showing as Diagnosis
  • [WEBCLIENT-302] - Find Terms- Search by term matching more than 2000 count -resulting in application
  • [WEBCLIENT-294] - Webclient Reports "QUERY CANCELLED" While Query Is Still Running
  • [WEBCLIENT-293] - A large number of results when searching by name hangs the webclient
  • [WEBCLIENT-288] - Right Click on Find Terms Persists
  • [WEBCLIENT-273] - Query report displays individual pt as "undefined" on loading the previous query after run
  • [WEBCLIENT-272] - temporal query with workplace contents in constraint population panel not running
  • [WEBCLIENT-254] - 2b2 Admin page not displaying all the rows from dblookup table for the projects
  • [WEBCLIENT-231] - Able to set Date constraint on previous queries/ptset as concept
  • [WEBCLIENT-223] - Admin uses last URL from PM_CELL_DATA in getAllDbLookups call
  • [WEBCLIENT-159] - Run/Rerun a temporal query without events is not displaying msg that minimum 2 events are required


i2b2 Release 1.7.12a

Release Date: April May, 2020

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

  • Updated QueryProcessorUtility to improve handling of the Medium and Large Process Queues.
  • Added support for Find Terms to return results using the Hierarchical View even for very large result sets.
  • Fixed issues with Redcap import for Postgres database due to stored procedure INSERT_EID_MAP_FROMTEMP.
  • Improvement of Totalnum counting stored procedures computation for very large Ontologies (>1.5 million elements) and very large data, on Postgres and SQLServer.
  • Prevent  the left pane on the i2b2 webclient from becoming small when the splitter is dragged

i2b2 Server Side Fixes:

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


[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