Release Notes for i2b2 Version 1.6.02

These release notes address resolutions for issues found and information about the i2b2 version 1.6.02. Unless otherwise specified, these notes apply to the following operating systems:

• Apple Macintosh OS x 10.4/5
• Apple Macintosh OS x 10.6 (Snow Leopard)
• Microsoft Windows XP Professional
• Microsoft Windows Vista Professional
• Microsoft Windows 7
• Microsoft Windows Server 2003

Additional Information

Included in this document are the following sections:

Installation

This release note applies to you if you are upgrading to 1.6.02 from a computer running an earlier version of i2b2. This release contains web client, server and oracle database changes so it is important to update all that apply to you. Release 1.6.02 does not contain any changes to the i2b2 Workbench.

WHERE DO I START?
Prior to setting up the i2b2 server, workbench or VM Image it is highly recommended that you read one of the following documents located in the documentation folder.

All of these documents will explain what needs to be done during the setup and in what order.

Third Party Software

No changes to third party software are included in release 1.6.02

New Features

i2b2 release 1.6.02 contains new features that have been outlined below.

String Constraint

In the 1.6.02 release there is now an option to constrain a query by a string of text. Similar to other text and numeric constraints, a user can narrow down their search criteria when setting up the query in the query tool view. The main difference between this new constraint and the existing ones is the string constraint allows users to enter a string of text as opposed to an enumerated or numerical value.
The operators for a string constraint are defined below.

Defining the string constraint works the same way as other text and numeric constraints. Once you drag the concept or modifier to a panel in the query tool view the appropriate constraint window will open. The only requirement is that the concept or modifier has to have metadataxml entered in the metadata table for that item. This requirement has not changed. The only thing that has changed is a new data type has been added to the metadataxml. Information about this new data type can be found in the Data section of these release notes.

CDATA marker added to the xml message

The 1.6.02 release, the CDATA marker has been added to the xml messages being sent from the i2b2 Web Client and the Workbench. This new section will appear for those concepts and modifiers that can have a value constraint defined when running a query or generating a timeline. An example of the change is shown below.

<item>
    <hlevel>3</hlevel>
    <item_name>Social history [Contains: smokes]</item_name>
    <item_key>\\i2b2_REP\i2b2\Reports\Medical History\Social History{color:#0000ff}</item_key>
    <tooltip>i2b2 \ Reports \ Medical History \ Social History</tooltip>
    <class>ENC</class>
    <item_icon>LA</item_icon>
    <item_is_synonym>false</item_is_synonym>
    <constrain_by_value>
          <value_type>TEXT</value_type>
          <value_operator>LIKE[contains]</value_operator>
          <value_constraint><![CDATA[smokes]]></value_constraint>
    </constrain_by_value>
</item>

Lockout / Obfuscation Parameters

In the 1.6.02 new parameters were added to the crc.properties file to support the lockout process for obfuscated users as well as the obfuscation process itself.
In addition to the new parameters a modification was made to one of the existing parameters (edu.harvard.i2b2.crc.lockout.setfinderquery.count). The value of -1 is now supported, which means if this parameter is set to -1 then obfuscated users will not be locked out.
This modification as well as the new parameters is outlined below. More detailed information can be found on the i2b2 Community Wiki.

Updates

Data

In release 1.6.02, no changes were made to the structure of the database. The only change was to add examples to the metadata, concept_dimension, modifier_dimension, and observation_fact tables to support the new string constraint.
In addition to adding new data examples the metadataxml was updated with a new data type of "String". An example of this new metadataxml is as follows:

<?xml version="1.0" encoding="UTF-8"?>
<ValueMetadata>
     <Version>3.2</Version>
     <CreationDateTime>2011-10-19T13:32:16.198-04:00</CreationDateTime>
     <TestID>MED:SIG</TestID>
     <TestName>Rx Sig</TestName>
     <DataType>String</DataType>
     <MaxStringLength>50</MaxStringLength>
     <Flagstouse/>
     <Oktousevalues/>
</ValueMetadata>

Fixes:

The following fixes were added to this release.

Memory error: not able to load PDO

When running a query to obtain a patient list an out of memory error will occur if the database contains a large amount of data. In addition, the patient data object (PDO) is never fully created and will not open in the previous query view.
STATUS/RESOLUTION: This problem was introduced with the enhancement to allow for custom columns in the PDO and only affects large databases. This issue has been resolved. Creating and loading the PDO will no longer cause an out of memory error.

Not able to search for terms with an '&' in the name

In the i2b2 Web client users are not able to search for terms with an ampersand '&' in the name. The term would never be returned with the results.
STATUS/RESOLUTION: This issue has been resolved. Terms with an '&'in the name are now returned in the Find Terms View.

Demo Database Scripts: Passwords inconsistent

In the scripts for the i2b2 demo database the passwords for the user setup during the install process are inconsistent.
STATUS/RESOLUTION: This issue has been resolved. All of the above users now have the same password ('demouser').

• The password is only changed for the i2b2 demo database. Your individual administration and user passwords for your own databases will not change.

PM: Project-User parameters are not saved with the project

The project-user parameters entered into Admin are not being saved with the project id. Therefore they are being associated with all projects instead of the one intended.
STATUS/RESOLUTION: This issue has been resolved. Project-User parameters are now saved with the appropriate project id and are specific to the project and the user.

• If you have entered project-user parameters in version 1.6 or 1.6.01 then you will need to fix them after you upgrade to 1.6.02. Once you upgrade to 1.6.02 the parameters with 'undefined' as the project id will no longer appear in Admin. Therefore you will need to go into the PM_PROJECT_USER_PARAMS table and update the PROJECT_ID column with the correct project id.

Licensing

The i2b2 source code is licensed under the i2b2 Software License 2.1. This includes but is not limited to all code in the edu.harvard.i2b2.* package namespace.

Trademarks

Microsoft, Windows, Windows XP, Windows Vista, Windows 7 and Windows Server are either registered trademarks or trademarks of Microsoft Corporation in the United States and/or other countries.

Mac OS is a registered trademark of Apple, Inc.

Eclipse Galileo is a registered trademark of the Eclipse Foundation, Inc.

All other trademarks are the property of their respective owners.