Anchor
_Toc64985944
_Toc64985944
1.7.

...

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

...

13 Release Notes

Contents
1.7.

...

Required:

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.

Image Removed

...

Required:

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

Image Removed

...

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

...

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

Image Removed

Click Test to verify connection

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

Image Removed

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

...

13 Release Notes
Highlight of Features

Backend Features

Easier Install
- Pre-built War file for easier distributions of the application
- Properties files are moved from static files to a table in the database
Authentication protocol support for OKTA and NTLM v2.
Database scripts to generate Totalnum counts for Ontology Terms for POSTGRESQL, ORACLE and SQL SERVER databases
REDCap data import into i2b2, with ontology creation from REDCap forms
Documentation updates for Apache Webserver timeout settings for previous queries run.

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)
Image Removed
Right-clicking on a term and then "Find Term in Tree" shows the entire hierarchy around the selected term.
Image Removed

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.
Image Removed

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

...

Image Removed

...

Easier-to-read counts

...

Nick Brown and Griffin Weber

Beth Israel Deaconess Medical Center

...

Image Removed

...

Extended query-by-value flags

...

Robert Bradford

University of North Carolina

...

Image Removed

...

Totalnum in find terms

...

Mauro Bucalo

University of Pavia

...

Image Removed

...

Visual Design of new Find Terms

...

Leaf Team

University of Washington

...

Image Removed

...

Totalnum Counter for Postgres

...

Dan Vianello

Center for Biomedical Informatics, Washington University in St. Louis

...

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.
Image Removed
Add a second parameter domain_controller as below. Parameter value will be your institution domain_controller value
Image Removed
Add the final parameter authentication_method as below. Parameter value will be OKTA
Image Removed
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.
  Image Removed
  Add a second parameter domain_controller as below. Parameter value will be your institution domain_controller value
Image Removed
Add the final parameter authentication_method as below. Parameter value will be NTLM2
  Image Removed

...

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)

Image Removed

- 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
  - RADIO BUTTON
  - DROPDOWN
  - YES-NO
  - TRUE-FALSE
  - SLIDER / VISUAL ANALOG SCALE
  - DESCRIPTIVE TEXT
  - NOTES BOX
  - SIGNATURE
  - DYNAMIC QUERY(SQL)
- 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)

REDCAP SETUP CONFIGURATION

1) Set Project Params (PM_PROJECT_PARAM)

...

Frontend Features
LOTS OF TABS!
P2
Community-Contributed Features
Backend Features
Improved Totalnum Scripts
I2b2-Synthea data Load
Improved db Upgrade Process
Changelog
Database Drivers
Supported Db Server versions
Supported software versions
i2b2 Database Changes
i2b2 Server and Client Changes
New Features and Improvements
Bug Fixes
Notes for Developers

Anchor
_Toc64985945
_Toc64985945
Highlight of Features

Anchor
_Toc64985946
_Toc64985946
Frontend Features

Anchor
_Toc64985947
_Toc64985947
LOTS OF TABS!

Anchor
_Toc64985948
_Toc64985948
P2

Anchor
_Toc64985949
_Toc64985949
Community-Contributed Features

Contribution	Contributor

Anchor
_Toc64985950
_Toc64985950
Backend Features

Anchor
_Toc64985951
_Toc64985951
Improved Totalnum Scripts

Totalnum Scripts for Postgres and MSSQL have been updated to improve the Totalnum counter performance on very large(>1.5 million) ontology elements such as ACT medications, Debug messages have also been added for troubleshoot purposes
Totalnum Scripts Setup

In the Release_1-7/NewInstall/Metadata/ run the ant script to create the stored procedures. ant ant -f data_build.xml create_metadata_procedures_release_1-7 7
Run the stored procedures on your database. This can be done in two ways.In the Release_1-7/NewInstall/Metadata/ run the ant script to create the stored procedures.

POSTGRESQL : ant -

...

f data_build.

...

xml db_metadata_run_total_count_postgresql
ORACLE : ant -f data_build.

...

xml db_metadata_run_total_count_oracle
SQL SERVER : ant -f data_build.

...

xml db_metadata_run_total_count_

...

sqlserver

...

Execute the RunTotalNum stored procedure on your database. This can take several hours. Example Example Usage:

...

    Oracle:
begin
  RUNTOTALNUM('observation_fact','i2b2demodata');
  end;

...

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
PostgreSQL:

...

select RUNTOTALNUM('observation_fact','public')

...

– (replace 'public' by the schema name for the fact table)

...

– If 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 counts will be visible in the ontology browser in the web client.

...

Anchor

...

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/db.properties file change the db.project from demo to act

Image Removed

Do the same in Release_1-7/NewInstall/Pmdata/db.properties, or perform these two steps manually:
- Create new Project ACT in the Admin tool
- Add AGG SERVICE Account to the Project
The Hivedata install will add new dblookup-rows with parameters under CRC, Ontology and workplace to set up the project path, but this can also be configured manually in the Admin tool ( example as in below)

Image Removed

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.

Image Removed

...

Warning Box
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.

...

Image Removed

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

_Toc64985952
_Toc64985952
I2b2-Synthea data Load

A new option is now available for loading Synthea data files into i2b2. Synthetic patient data generated by Synthea is hosted on SyntheticMass..The Synthea sample files have been converted to i2b2-ACT format. The zipped data files can be downloaded from https://github.com/i2b2/i2b2-synthea
Synthea Load Process:

Create db Schema with name labeled synthea
Load Synthea data from the sample data files provided

Download the zipped flat files and extract to them to a local directory
Using SSMS, import the sample obs file into obvseration_fact table
Import the sample obs-pat file into patient dimension table.

Download latest stored procedures from github
Execute the stored procedures on your database to create the patientnum and encounternumbers.

Anchor
_Toc64985953
_Toc64985953
Improved db Upgrade Process

Currently i2b2 db upgrade process is tedious involving multiple manual steps of running upgrade scripts and stored procedures. This release provides a single upgrade script which will perform the complete db upgrade.

Anchor
_Toc64985954
_Toc64985954
Changelog

Anchor
_Toc64985955
_Toc64985955
Database Drivers

The JDBC drivers were updated to the following versions.

Driver	New Version
ojdbc8.jar	Oracle 12.2.0.1
postgresql-42.2.5.jar	PostgreSQL 42.2.5
mssql-jdbc-7.0.0.jre8.jar	MS 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

...

Anchor
_Toc64985956
_Toc64985956
Supported Db Server versions

Type	Version
SQL Server	2012+
Oracle	12g+
Postgres	9

Anchor
_Toc64985957
_Toc64985957
Supported software versions

Application

Version

Java

8

java

11

Wildfly

17.0.0

Apache HTD

2.4.17 or higher

Apache Ant

1.9.6

Apache Axis2

1.7.1

Anchor

	_GoBack
	_GoBack

PHP

7.2.27 or higher

Anchor
_Toc64985958
_Toc64985958
i2b2 Database Changes

New db updates include

Anchor
_Toc64985959
_Toc64985959
i2b2 Server and Client Changes

Anchor
_Toc64985960
_Toc64985960
New Features and Improvements

CORE-389 Totalnum performance improvements
CORE-399 Oracle index hints must use the table alias
CORE-400 CORE-389 Show totalnums in top-level folders
CORE-382 Username / password errors should not specify which had the problem
WEBCLIENT-334 Provide tabs for major plugins and temporal query
WEBCLIENT-344 Cleanup Analysis Tools list of Plugins to only Supported Items
WEBCLIENT-325 Wayne's improvements to hierarchical find-by-name
WEBCLIENT-320 Provide REFRESH ALL context menu in FindTerms panel
WEBCLIENT-307 Drag and drop in term info panel
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-342 switch response status check from "OK" to 200 to handle lab value pop up in http/2 protocols
CORE-402 Fix Veracode identified Security flaws in i2b2 Server-Side Code
WEBCLIENT-343 Fix Veracode identified Security flaws in i2b2Webclient Code
CORE-404 Adding support for JDK 11. Now including the gensrc due to jaxb has been removed.

Anchor
_Toc64985961
_Toc64985961
Bug Fixes

WEBCLIENT-341 Toggle between <and > group panel buttons resulting in blank QueryResults view
WEBCLIENT-319 FindTerms- exceeding more than 200(default) return count - displaying server error
WEBCLIENT-316 Admin tool unresponsive in IE11
WEBCLIENT-305 Occasionally items in Find Terms by name are not draggable
WEBCLIENT-304 Hierarchical levels in Find Terms might not work in ontologies that have extra backslashes
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

...

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:

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-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

Anchor
_Toc64985962
_Toc64985962
Notes for Developers

For Java 11 install, if you change xsd, then modify the gensource.

...

Page History

Versions Compared

Old Version 1

New Version 2

Key

Anchor_Toc64985944_Toc649859441.7.

13 Release Notes

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

Community-Contributed Features

Feature Configuration

Easier i2b2 Install

Authentication Protocol Support for NTLM2/OKTA

Anchor_Toc64985945_Toc64985945Highlight of Features

Anchor_Toc64985946_Toc64985946Frontend Features

Anchor_Toc64985947_Toc64985947LOTS OF TABS!

Anchor_Toc64985948_Toc64985948P2

Anchor_Toc64985949_Toc64985949Community-Contributed Features

Anchor_Toc64985950_Toc64985950Backend Features

Anchor_Toc64985951_Toc64985951Improved Totalnum Scripts

Anchor

Changelog

_Toc64985952_Toc64985952I2b2-Synthea data Load

Anchor_Toc64985953_Toc64985953Improved db Upgrade Process

Anchor_Toc64985954_Toc64985954Changelog

Anchor_Toc64985955_Toc64985955Database Drivers

i2b2 Database Changes

i2b2 Server and Client Changes

New Features and Improvements

Anchor_Toc64985956_Toc64985956Supported Db Server versions

Anchor_Toc64985957_Toc64985957Supported software versions

Anchor_Toc64985958_Toc64985958i2b2 Database Changes

Anchor_Toc64985959_Toc64985959i2b2 Server and Client Changes

Anchor_Toc64985960_Toc64985960New Features and Improvements

Bug Fixes

Anchor_Toc64985961_Toc64985961Bug Fixes

i2b2 Server Side Fixes:

i2b2 Web Client Fixes:

i2b2 Database Fixes:

Anchor_Toc64985962_Toc64985962Notes for Developers

Pages

Recently updated

Anchor
_Toc64985944
_Toc64985944
1.7.

Anchor
_Toc64985945
_Toc64985945
Highlight of Features

Anchor
_Toc64985946
_Toc64985946
Frontend Features

Anchor
_Toc64985947
_Toc64985947
LOTS OF TABS!

Anchor
_Toc64985948
_Toc64985948
P2

Anchor
_Toc64985949
_Toc64985949
Community-Contributed Features

Anchor
_Toc64985950
_Toc64985950
Backend Features

Anchor
_Toc64985951
_Toc64985951
Improved Totalnum Scripts

_Toc64985952
_Toc64985952
I2b2-Synthea data Load

Anchor
_Toc64985953
_Toc64985953
Improved db Upgrade Process

Anchor
_Toc64985954
_Toc64985954
Changelog

Anchor
_Toc64985955
_Toc64985955
Database Drivers

Anchor
_Toc64985956
_Toc64985956
Supported Db Server versions

Anchor
_Toc64985957
_Toc64985957
Supported software versions

Anchor
_Toc64985958
_Toc64985958
i2b2 Database Changes

Anchor
_Toc64985959
_Toc64985959
i2b2 Server and Client Changes

Anchor
_Toc64985960
_Toc64985960
New Features and Improvements

Anchor
_Toc64985961
_Toc64985961
Bug Fixes

Anchor
_Toc64985962
_Toc64985962
Notes for Developers