i2b2 Release 1.7.12
Release Date: October 31, 2019
Release 1.7.12 contains solutions for providing an easier install solution of i2b2, supporting various Authentication protocols and integration of REDCAP. Also included are enhancements to i2b2Weblcient, new database scripts and bug fixes
Highlight of Features
- Easier Install 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.
The 1.7.12 Release Notes apply to you if you are upgrading your existing i2b2 system from an earlier version of the i2b2 software.
|Type of Install||Where 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.
Information about upgrading i2b2 to version 1.7.12 can be found in this section of the release notes.
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
The JDBC drivers were updated to the following versions.
|mssql-jdbc-7.0.0.jre8.jar||MS Sql Server 7.0.0|
The i2b2 now provides two options for upgrading your i2b2 server.
- Continue to download the source code provided in the zip file released on www.i2b2.org/software
- Install the precompiled JAR files onto your existing i2b2 server to upgrade it to 1.7.12.
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.
|Description||Where to find it||Requirements|
|Upgrade i2b2 database to 1.7.12|
Software page (i2b2 Website)
|Download i2b2createdb-1712.zip file under Source Code |
|Upgrade i2b2 Web Client to 1.7.12|
Software page (i2b2 Website)
|Download i2b2webclient-1712.zip file under Source Code |
|Upgrade i2b2 Server to 1.7.12 (Source Code) |
Software page (i2b2 Website)
|Download i2b2core-src-1712.zip 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.|
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 1.7.12 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
- [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 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
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
New Feature: More authentication protocol support (okta, NTLM v2)
- Support for NTLM2 is supported. Instead of using authentication_method - NTML use NTML2
- Support for OKTA
New Feature: RedCap
1) Set Project Params (PM_PROJECT_PARAM)
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.
This is the name of the Data Collection Instruments to associate this project with, in this example it is set to the 'Profile'
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.
Optional, Defaults to \REDCAP\
What the root ontology is
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_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:
Click Test to verify connection
3) Submit a form and check to see if the ontology was created.
New Feature: Enhanced Find Terms
Find terms gives a sense of the hierarchy, and terms that are children of other search results are not returned.
New Feature: Improved Maximized Left Pane
In maximized mode, the left pane now makes all tabs accessible.
New Feature: Totalnum scripts
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
- 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
New Feature: ACT Ontology
- In the Release_1-7/NewInstall/Metadata/db.properties file change the db.project from demo to act.
- Than run the ant script against create_metadata_tables_release_1-7 and db_metadata_load_data