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i2b2 Release 1.7.12

Release Date: October 31, 2019

Release Summary

Release 1.7.12  contains  solutions for providing an easier install solution of i2b2, supporting various Authentication protocols, integration of REDCAP. Also included are  enhancements to i2b2Weblcient, new database scripts and bug fixes

Highlight of Features

  • Easier Install  with  using the  prebuilt WAR file  on a existing  widlfly instance.
  • Incorporate authenthication protocol support for OKTA, NTLM v2
  • Provide database scripts to update Totalnum counts for Ontology Terms for POSTGESSQL, ORACLE and SQL SERVER databases.
  • Enhanced Webclient Find Terms functionality-
  • Improved view of Left Pane in a maximized mode
  • Larger Query Results Panel view after Query run
  • Integration of REDCAP data entry  into i2b2 for Ontology creation 
  • Documentation updates for Apache Webserver timeout settings for previous queries run.

Installation Note

The 1.7.11 Release Notes apply to you if you are upgrading your existing i2b2 system from an earlier version of the i2b2 software.

Type of InstallWhere you need to go next

Upgrading an existing i2b2 (currently installed at your site)

Please go to the  Upgrade Notes section for the details about upgrading your i2b2 software.

Upgrading your i2b2 in a SHRINE network

Please read the information in the  SHRINE Networks section before proceeding.

Installing a new instance of i2b2. (Never installed it before)

We recommend you refer to the i2b2 Installation Guide found on the i2b2 Community Wiki
The install guide will take you through the entire installation process.

Upgrade Notes

Information about upgrading i2b2 to version 1.7.12 can be found in this section of the release notes.

i2b2 Components

In release 1.7.12 the following i2b2 components contain changes and therefore need to be updated when upgrading your i2b2 environment.

  • i2b2 Database
  • i2b2 Server (kernel)
  • i2b2 Web Client

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

Upgrade Paths

The i2b2 now provides two options for upgrading your i2b2 server.

  1. Continue to download the source code provided in the zip file released on
  2. Install the precompiled JAR files onto your existing i2b2 server to upgrade it to 1.7.11.

Both are acceptable paths to upgrade your i2b2 server and depending on which you choose will determine where you need to go to obtain the appropriate files. The location of the upgrade files for each component is outlined below.

Upgrade Software

DescriptionWhere to find itRequirements
Upgrade i2b2 database to 1.7.12

Software page (i2b2 Website)

Download file under Source Code
Upgrade i2b2 Web Client to 1.7.12

Software page (i2b2 Website)

Download file under Source Code
Upgrade i2b2 Server to 1.7.12 (Source Code)

Software page (i2b2 Website)

Download file under Source Code
Upgrade i2b2 Server to 1.7.12 (JAR files) Upgrade to latest version page (Community Wiki) See Technical Details section on the i2b2 Upgrades page and upgrade documentation on Upgrade to latest version page.

Database Changes

Release 1.7.12 involves a few changes to the i2b2 Database.  Included  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.

Change Summary - Release 1.7.12

Did you know?

  • Changes to the i2b2 server & database are listed under i2b2 Kernel (Core) Software
  • Changes to the i2b2 Web Client are listed under i2b2 Web Client Software
  • Additional information about the new features can be found in the Feature Details - Release 1.7.11 section located this Change Summary section.

i2b2 Kernel (Core Software)

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-278] - GetPDOFromInputList_requestType Fails on Postgresql
  • [CORE-307] - Fix internal key expiration date assigned when changing password
  • [CORE-308] - Full Request XML message is stored in the QT_PDO_QUERY_MASTER table
  • [CORE-313] - CRC-PDO: AverageObservationPageMethod doesnt work
  • [CORE-315] - Idenitified Data Plan- Demo_Oracle- Ontology term with No Protected access- is not visible if User role not Protected
  • [CORE-331] - GetCodeInfo- not finding codes with an '_'
  • [WEBCLIENT-231] - Able to set Date constraint on previous queries/ptset as concept
  • [WEBCLIENT-247] - bad image filename
  • [WEBCLIENT-248] - previousqueries panel-date option-'>' button not dispalying records after the specific date- same with '<' buttton
  • [WEBCLIENT-249] - previous queries panel- date option- datetime stamp not consistent with previous queries date stamp
  • [WEBCLIENT-252] - Ontology Options for Finding Terms- hidden Terms option is not validating hidden Terms
  • [WEBCLIENT-256] - previous queries - pagination by date- buttons don't work after the last pagination
  • [WEBCLIENT-259] - worplacefolder drag&drop- not working at subfolder level contents
  • [WEBCLIENT-260] - Drag and drop of folder with multiple concepts appears stuck on group panel
  • [WEBCLIENT-261] - Querytool- Ontology terms query run with breakdowns erroring out
  • [WEBCLIENT-262] - Querytool- query run with query ( run as patientset)-erroring out
  • [WEBCLIENT-263] - workplace folder drag and drop into simple temporal query events box - cannot drag and drop
  • [WEBCLIENT-264] - worplacefolder drag&drop- query report not displaying individual patient name and subfolder naming and path?
  • [WEBCLIENT-265] - Query run with individual pt is returning 0 results on rerun
  • [WEBCLIENT-266] - Individual pt query run with Timeline option - not drawing the timeline, causing unresponsive webpage
  • [WEBCLIENT-267] - Individual pt in Simple temporal query not working
  • [WEBCLIENT-268] - Query run with a ptset is errorin gout on rerun
  • [WEBCLIENT-269] - Individual Pt drag and drop- After query run, query not displaying the patient in panel
  • [WEBCLIENT-270] - worplacefolder drag&drop- queryname gets '@' by default instead of name of the folder on run
  • [WEBCLIENT-271] - workplace folder with empty contents is checked as zero pt instead of ignoring
  • [WEBCLIENT-272] - temporal query with workplace contents in constraint population panel not running
  • [WEBCLIENT-276] - workplace folder with multiple concepts taking long time to load in the query panel after drag and drop
  • [WEBCLIENT-277] - after workplace is deleted from the query panel Query run successful with empty contents

Feature Details - Release 1.7.12

New Feature: Easier i2b2 Install

  • If you are using a prebuilt WAR file: Copy the .war file into a wildfly 14 or 16 instance in the /opt/wildfly-VERSION-Final/standalone/deployments/ folder
  • If you are creating a new WAR file : 1) Run in the edu.harvard.i2b2.server-common folder
    2) ant clean dist war
    3) Copy the i2b2.war from the dist folder to /opt/wildfly-VERSION-Final/standalone/deployments/ folder.
  • 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.
  • Modify the *-ds.xml in the deployment folder to point to the database


If you wanted to create a root level folder in your ontology called "PHI Demonstration" and only wanted users with the DATA_PROT role to be able to see it, you would make the following changes to your TABLE_ACCESS table:

i2b2_LABSi2b2N1\i2b2\Labtests\Laboratory Tests...null
i2b2_PHIi2b2phiY1\i2b2\PHI\PHI Demonstration...DATA_PROT

New Feature: Workplace Folder drag and drop

Now you can drag a workplace folder to the query tool, the folder can contain sub folders.   All the concepts, previous queries, and individual patients will be displayed in the panel.

Below is the workplace with combination of available items


After the drag and drop to the query panel the list of all the items are displayed

New Feature: Individual Patient drag and drop from Previous Query Panel

Once a patient set is created, that patient can be dragged and dropped to the Query Tool Panel

Below is a patient set with 2 patients

After drag and drop of the individual patient to the query tool panel

New Feature: Previous Queries Upgrade in Web Client

The Previous Queries panel in the web client has been upgraded to accommodate three new options.

  • Filter Previous Queries List by User - Users with the MANAGER role will now see a drop down in the Previous Queries Options menu that allows them to filter previous queries by a specific user in the i2b2 project.
  • Auto Refresh Previous Queries - Users now have the ability to set an auto-refresh timer in the Previous Queries Options menu in which the Previous Queries list will auto-refresh in the specified time period (off, 10 seconds, 30 seconds, or 60 seconds).
  • Page through Previous Queries by Date - Users can navigate Previous Queries by a particular date.

New Feature: Support for WildFly 14

The i2b2 software now officially supports WildFly 14. The primary advantages are the faster install/upgrade of i2b2 as a pre-packaged collection (WAR) and managed data source connections/pooling.

New Feature: Inter-CELL SSL Setup

Create server and client certificates (Wildfly 10 & 14)

The keytool utility stores the keys and certificates in a file termed as keystore, a repository of certificates used for identifying a client or a server. Typically, a keystore contains one client or one server's identity, which are protected by using a password.

Create a Self Signed Certificate

You can create a certificate for your server using the following command:


$ keytool -genkey -keyalg RSA -keystore server.keystore -storepass secret -keypass secret -validity 365  -dname "cn=Partners Healtbcare,o=Partners,c=US"

Now let's copy this keystore into the configuration folder of the application server:


$ cp server.keystore $JBOSS_HOME/standalone/configuration

Now export the server certificate in a file called server.crt:


$ keytool -exportcert -keystore server.keystore -storepass secret -keypass secret -file server.crt

Certificate stored in file <server.crt>

Now import the cert into the CA for the Java JRE:


$ keytool -import -alias i2b2server -keystore  /usr/java/latest/jre/lib/security/cacerts -file server.crt

The password might be changeit

In /opt/{wildfly} in bin run to create user and select (a) management user

Wildfly 10 Setup

In Wildfly 10 run

Connect to the server



Start by creating a Security Realm which will contain the keystore and trustore references



Next, for one-way SSL, set the path to the keystore, along with the keystore path and password:


/core-service=management/security-realm=SSLRealm/server-identity=ssl:adJavathe2d(keystore-path="server.keystore", keystore-relative-to="jboss.server.config.dir", keystore-password="secret")

Finally, set the value of Undertow's https listener to your Security Realm:



If the above fails edit the standalone.xml and add right after http-listener

                <https-listener name="default-https" security-realm="SSLRealm" socket-binding="https"/>

Wildfly 14 Setup

In Wildfly 14 run

Connect to the server



Finally, set the value of Undertow's https listener to your Security Realm:



 Both Wildfly 10 and 14

Add the following to the axis2.xml file right after the   <transportReceiver name="http"


   <transportReceiver name="https"


Change the, and files to point to the https://localhost:8443

Database Changes

Change all the pm_cell_data within the PM Database to https://localhost:8443

After all the cells have been updated it should look like below.

Webclient Changes

Webclient, if using self-signed cert add the following to the index.php

        curl_setopt($proxyRequest, CURLOPT_SSL_VERIFYHOST, 0);

        curl_setopt($proxyRequest, CURLOPT_SSL_VERIFYPEER, 0);

Also into the index.php add the new url to the whitelist such as:


$WHITELIST = array(

        "http" . (($_SERVER['SERVER_PORT'] == '443') ? 's' : '' ) . "://" . $_SERVER['HTTP_HOST'],










Updated: i2b2 License

The i2b2 software is now made available under the terms of the Mozilla Public License (MPL) version 2.0. i2b2 is also distributed under the terms of the Healthcare Disclaimer addendum.

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