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).
Release Date: December, 2019
Included in the client and also on the Webclient Community Wiki page.
In maximized mode, the left pane now makes all tabs accessible.
When a query with breakdowns has finished, the results panel temporarily expands slightly to accommodate the breakdown graphs display.
Contribution | Contributor | |
|---|---|---|
ACT Technology and Data Harmonization Team University of Pittsburgh |
| |
Easier-to-read counts | Nick Brown and Griffin Weber Beth Israel Deaconess Medical Center |
|
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.) |
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.
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
Currently, the following REDCAP Features are supported in i2b2.
REDCAP SETUP CONFIGURATION
1) Set Project Params (PM_PROJECT_PARAM)
| Name | Value | Description |
|---|---|---|
| REDCAP_TOKEN_PID_{pid} | (7B42348B7C51123432048B51EAA) | Required:
|
| REDCAP_SURVEY_PROJECT | (pid) | Required: Set the Value parameter to the pid value from the Redcap project url.
|
| REDCAP_ONTOLOGY_REFRESH | Y | Optional, Defaults to Y 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. |
| REDCAP_ROOT_ONTOLOGY | \REDCAP\ | Optional, Defaults to \REDCAP\ |
| REDCAP_ONTOLOGY_FORMAT | tree | Optional, Defaults to tree 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_ROLE | DATA_PROT | Optional, Defaults to DATA_PROT If this redcap form has the identified value set to true, then 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) Give Editor role to the project for AGG_SERVICE_ACCOUNT( optional DATA_PROT, DEID, LDS)
4) Submit a form and check to see if the ontology was created.
ant -f data_build.xml create_metadata_procedures_release_1-7 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 visible in the ontology browser in the web client.
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.
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.
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.
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 |
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:
[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
[WEBCLIENT-328] - Webclient behaves oddly when splitter is moved to make left panel very small
[CORE-389] - Totalnum performance improvements on Postgres and SQLServer
[CORE-393] - REDcap import does not work in Postgres