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Release 1.7.

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Release Date: October 31, 2019

Release Summary

Release 1.7.12  contains  12  contains solutions for providing an easier install solution of i2b2, supporting various Authentication protocols and integration of REDCAPredesigned Find Terms, totalnum counting scripts, new Authentication protocols, and REDCAP import. Also included are  other enhancements to i2b2Weblcient, new database scripts the i2b2 Weblclient, the ACT ontology, 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.

Installation Note

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i2b2 Release 1.7.12

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Release Date: October 31, 2019

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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)

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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.Image Removed

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Required:

This is the name of the Data Collection Instruments to associate this project with, in this example it is set to the 'Profile'

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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.

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Optional, Defaults to \REDCAP\
What the root ontology is

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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

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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

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Click Test to verify connection

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

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Upgrade Notes

Information about upgrading i2b2 to version 1.7.12 can be found in this section of the release notes.

i2b2 Components

In release 1.7.12 the following i2b2 components contain changes and therefore need to be updated when upgrading your i2b2 environment.

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Database Drivers

The JDBC drivers were updated to the following versions.

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Upgrade Paths

The i2b2 now provides two options for upgrading your i2b2 server.

1. Continue to download the source code provided in the zip file released on www.i2b2.org/software
   
2. Install the precompiled JAR files onto your existing i2b2 server to upgrade it to 1.7.12.

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Upgrade Software

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Software page (i2b2 Website)

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Software page (i2b2 Website)

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Software page (i2b2 Website)

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Database Changes

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

Bug Fixes

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Highlight of Features

Release Summary

• 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.

Community-Contributed Feature

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.

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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