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  other enhancements to the i2b2 Webclient, the ACT ontology, and bug fixes.

After reading this documentation, please go to the Upgrade Notes page for the details about upgrading your i2b2 software. If you are installing from scratch, additionally refer to the 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, 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

Contribution

Contributor


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 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

NOTE: If you are an existing user and have previously changed the properties files, you will need to modify the corresponding parameters in HIVE_CELL_PARAM.

RedCap Import Setup

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

1) Set Project Params (PM_PROJECT_PARAM)

NameValueDescription
REDCP_TOKEN (7B42348B7C51123432048B51EAA)

Required:

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

REDCAP_SURVEY_PROJECT(profile)

Required:

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

REDCAP_ONTOLOGY_REFRESHY

Optional, Defaults to Y
Y - Every time a form is submitted the i2b2 metadata ontology get 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 or the ontology will not be created.

REDCAP_ROOT_ONTOLOGY\REDCAP\

Optional, Defaults to \REDCAP\
What the root ontology is

REDCAP_ONTOLOGY_FORMATtree

Optional, Defaults to tree
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

RECAP_PROTECTED_ROLEDATA_PROTOptional, Defaults to DATA_PROT
If this redcap form has the identified value set to true, than 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) 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.
  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

  1. In the Release_1-7/NewInstall/Metadata/db.properties file change the db.project from demo to act.
  2. Run the ant script against create_metadata_tables_release_1-7 and db_metadata_load_data

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.

Changelog

Database Drivers

The JDBC drivers were updated to the following versions.

DriverNew Version
ojdbc8.jarOracle 12.2.0.1
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