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Release 1.7.12  contains solutions for providing an easier install solution of i2b2, redesigned Find Terms, totalnum counting scripts, new Authentication protocols, and REDCAP import. Also included are  are other enhancements to the i2b2 Webclient, the ACT ontology, and bug fixes.

After reading this documentation, please go to the Upgrade Notes page the Quick Upgrade Guide for the details about upgrading your i2b2 software. If you are installing from scratch, additionally refer to the refer instead to the Quick Install Guide (and optionally the full i2b2 Installation Guide on the i2b2 Community Wiki. The install guide will take you through the entire installation process.






i2b2 Release 1.7.12





Release Date: November 21 December, 2019

Table of Contents

Highlight of Features

Backend Features

Frontend Features

Redesigned Find Terms By Name


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.)



Easier i2b2 Install

The i2b2 server can now be installed in three or four steps:

  1. (Optional) Build the war from source. Run in the edu.harvard.i2b2.server-common folder:
          ant clean dist war
  2. Copy the i2b2.war from the dist folder (or the binary release zip file) to /opt/wildfly-VERSION-Final/standalone/deployments/ folder.
  3. Run the data build for all the cell (PM, HIVE, ONT and CRC) . In the Hive there is a new table called HIVE_CELL_PARAM which contains all the previous XML and properties file.
  4. Modify the *-ds.xml in the deployment folder to point to the database

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.

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

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

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  •   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.

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

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

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RedCap Import Setup

TODO: We need some documentation on what features are supported and what aren't.

Currently,  the following  REDCAP Features  are supported in i2b2.

  • Project level :
    •  Only one unique redcap project id  can be assigned to  each i2b2 project( system finds the first project it encounters and assigns it, so two projects cannot have same REDCAP project id:
  •  Form level:
    • Renaming a Form in Redcap will create a new record in table access instead of updating the original record which means in i2b2 the original survey will still show in Ontology in addition to creating the renamed survey as a new Ontology item.
    • On adding a new Field/editing a field in the REDCAP form, the form needs to be explicitly associated with the record again to take effect in i2b2
    • Data triggers happen only on Form SAVE button.
    • Only Form  SAVE as a URL survey or Admin edit/add record Saves, triggers i2b2 Ontology creation. Other forms of Form creation in REDCAP- by Data import tool, API format, will not trigger Ontology creation in i2b2)
    • Ontology is only displayed in Tree structure format in i2b2. Pop up display (sometimes called query-by-value) is not supported. (example as below)   

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    • There is no mapping of records submitted in REDCAP to existing patient_ids in i2b2. The scope of this release is limited to adding new record rows in Observation_fact table and Updating the fields of records added.
  • Field level:
    • The following project fields from REDCAP  are supported in i2b2.
      • TEXT BOX
      • CHECKBOX
      • DROPDOWN
      • YES-NO
      • TRUE-FALSE
      • NOTES BOX
    • Text box (Short text)Number and Date/Time ) with Validation capability in REDCAP - validation  will work only as a simple text String search in i2b2
    • Check box, Multiple Choice , Yes-No, True-False Form fields will appear as a Tree format in i2b2 ( Popup display is not supported)


1) Set Project Params (PM_PROJECT_PARAM)

REDCP_TOKEN REDCAP_TOKEN_PID_{pid}(7B42348B7C51123432048B51EAA)


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

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This is the name of the Data Collection Instruments to associate this project with, in this example it is set to the 'Profile'

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

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

N - Do Not regenerate the metadata ontology.   

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


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


Optional, Defaults to tree
How 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, than then this ontology will be protected and only users with the following i2b2 access role will be able to access it.


Click Test to verify connection

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

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


  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.

  • In the Release_1-7/NewInstall/Metadata/ file change the db.project from demo to


  • act   

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  •  Create new Project ACT  in the Admin tool
  • Add  AGG SERVICE Account to the Project
  • Add new dblookup-row  with parameters  under CRC, Ontology and workplace to set up the project path( example as in below)   

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  •   Run the ant script against create_metadata_tables_release_1-7 and db_metadata_load_data

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

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Using Extended Query-By-Value Flags


  • 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