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 Weblclient, the ACT ontology, and bug fixes
Release Date: October 31, 2019
Type of Install | Where you need to go next |
---|---|
Upgrading an existing i2b2 (currently installed at your site) | Please go to the Upgrade Notes page for the details about upgrading your i2b2 software. |
Upgrading your i2b2 in a SHRINE network | TODO: This needs to be added to this release's notes. |
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. When finished, browse the Upgrade Notes page for information on configuring new features. |
TODO: It'd be great to add links to the sections of the release notes that talk about each of these...
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.) |
Find terms shows the terms' contextual hierarchy, and terms that are children of other search results are not returned.
Right-clicking on a term and then "Find Term in Tree" shows the entire hierarchy around the selected term.
In maximized mode, the left pane now makes all tabs accessible.
Included in the client and also on the Webclient Community Wiki page.
Featuring:
The i2b2 server can now be installed in four steps:
TODO: We need some documentation on what features are supported and what aren't.
1) Set Project Params (PM_PROJECT_PARAM)
Name | Value | Description |
---|---|---|
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_FORM | (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_REFRESH | Y | Optional, Defaults to Y 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\ |
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, 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.
In the Release_1-7/NewInstall/Metadata/ run the ant script
ant -f data_build.xml create_metadata_tables_release_1-7
This will create the stored procedures:
Next, execute the RunTotalNum stored procedure on your database. This can take several hours. 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.
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.