Page History

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Community-Contributed Features

Contribution	Contributor
SAML Authentication	Kevin Bui Michelle Morris University of Pittsburgh Justin Prosser University of Washington Mike Mendis Jeff Klann Reeta Metta Mass General Brigham	i2b2 now includes support for SAML-based enterprise authentication via an institutional Identity Provider. See more information below.
Ability to specify user parameter defaults	Michael Horvath Wake Forest University	This change is meant to allowing user params to take precedence over hive params. Currently, it's the other way around. Particularly, if you have the situation where you have a large number of users who use an authentication method other than the default basic, but your service account (AGG_SERVICE_ACCOUNT) is using basic then you need to specify a user param for each of your users. With this change, you can set default authentication params in pm_hive_params for all users, and then set your service account specifically to be authentication_method = 'BASIC'. May seem like a small change, but it would be very welcome not to need to assign params for each new user at our institution. In the process of making this change, I re-organized basic authentication into its own package and removed some code duplication.
LDAP UPN Support	Michael Horvath Wake Forest	Active Directory enables other methods of binding which are more flexible besides just using the distinguished name. https://docs.microsoft.com/en-us/openspecs/windows_protocols/ms-adts/6a5891b8-928e-4b75-a4a5-0e3b77eaca52. This change is to enable binding the the User Principle Name form, which is very convenient when the distinguished names for users is not easily available (OU by department, etc.).
API to get all children of an ontology node	Kevin Bui Michelle Morris University of Pittsburgh	The metadata GetChildren API call, which returns information on the children of an ontology node, can now be configured to return multiple levels of children (e.g., children, children's children, etc.). This is done by specifying the numLevel parameters. By default, the function assumes numLevel = 1 and will return the direct descendants of the concept, which is one level of children. When the numLevel = -1 the function will return ALL descendants of the concept, otherwise the function will return up to and including the number of levels specified by numLevel (eg. numlevel=2 returns two levels of descendants, numLevel=4 returns four levels of descendants).
Totalnum Counter Performance Improvements	Darren Henderson University of Kentucky	Performance enhancements on SQL Server totalnum counting to not unnecessarily recompute temp tables.

Backend Features

SAML Authentication

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Backup your existing data folder
Copy all the folders from the extracted download data folder into your existing data Upgrade folder
Example: Downloads\2b2core-upgrade-1712a\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-7\Upgrade\. This will replace
existing Crcdata, Hivedata, Metadata, PMdata folders.
Alternative to above step, navigate to the edu.harvard.i2b2.data\Release_1-7\Upgrade\ directory of your extracted folder
Copy the db.properties files from your back up into the respective locations(namely Crcdata, Hivedata, Metadata, PMdata )
Open the command prompt and navigate to cell folders and run the following upgrade ant commands on your i2b2 database instance, where {db} can be Oracle, sqlserver or postgresql.
Alternative to above Step, you can run individual SQL scripts on your db instance in place of ant commands.

Upgrade From Build	Upgrade to Latest build
In data folder\Release_1-7\Upgrade\ run the ant commands under each individual cell subfolder as below.
1.7.09c	In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-09c upgrade_table_release_1-7-10 upgrade_table_release_1-7-11 upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-09c upgrade_hive_tables_release_1-7-10 upgrade_hive_tables_release_1-7-11 upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-09c upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-09c upgrade_pm_tables_release_1-7-10 upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12
1.7.10	In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-10 upgrade_table_release_1-7-11 upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-10 upgrade_hive_tables_release_1-7-11 upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-10 upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12
1.7.11	In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-11 upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-11 upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12
1.7.12	In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-12

Changelog

Database Drivers

The JDBC drivers were updated to the following versions.

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

Supported Db Server versions

Server Type	SQL Server	Oracle	Postgres
Supported Version/s	2012+ (tested with up to 2019)	12g+ and 21c	9 to 14

Supported software versions

Application Type	Java	Wildfly	Apache HTD	Apache Ant	Apache Axis2	PHP
Supported Version/s	8 or 11	17.0.0	2.4.17 or higher	1.9.6	1.7.1	7.2.27 or higher

i2b2 Database Changes

New db updates

DATA-7 QT_PATIENT_SET_ENC_COLLECTION should be a bigint
DATA-5 Synthea i2b2 data
DATA-8 Synthea data load test from Github files
DATA-6 improve i2b2 db upgrade process
DATA-12 Stored procedure to update concept dimension
DATA-11 Age in years updater during demodata install
DATA-9 ACT v4 ontology
CORE-389 Totalnum performance improvements
CORE-394 Obfuscated totalnum reporting tables
CORE-398 Multifact support for totalnums
CORE-400 Show totalnums in top level folders

i2b2 Server and Client Changes

New Features and Improvements

Webclient

Server-Side

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-343 Fix Veracode identified Security flaws in i2b2Webclient Code

CORE-399 Oracle index hints must use the table alias
CORE-382 Username / password errors should not specify which had the problem
CORE-402 Fix Veracode identified Security flaws in i2b2 Server-Side Code
CORE-404 Adding support for JDK 11. Now including the gensrc due to jaxb has been removed.
CORE-413 FetchAllChildren
CORE-414 SAML
CORE-415 Log4j upgraded to v2
CORE-416 User parameter precedence change (contributed by Michael Horvath)
CORE-417 LDAP UPN support (contributed by Michael Horvath)
CORE-419 i2b2 - redcap: ability to read from a file instead of from just a redcap api

Bug Fixes

Webclient

Server-Side

WEBCLIENT-351 Obfuscated User Not Showing Graph
WEBCLIENT-342 switch response status check from "OK" to 200 to handle lab value pop up in http/2 protocols
WEBCLIENT-335 temporal query in webclient with no anchoring events not running
WEBCLIENT-350 Unable to drag items in workplace
WEBCLIENT-325 Wayne's improvements to hierarchical find-by-name
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-291 Date constraints popup OK button disabled, maintains new date if canceled
WEBCLIENT-196 Temporal query more than 2 events is not populating query name in the query name textbox and displaying new event added msg
WEBCLIENT-156 switching from events grouppanel view to 'same financial encounter' selection is not switching to original concept group panel view

CORE-418 Local timestamps in sessions on Oracle - appserver /db server in diff time zones
CORE-282 Error returned when obfuscated user is locked out
CORE-281 Query continues to run after user receives lockout message
CORE-412 Disable login to agg service account
CORE-405 Upgrade JDBC Drivers
CORE-403 Add result path
CORE-399 use alias for index hint

Notes for Developers

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

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Versions Compared

Old Version 35

New Version 36

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