The 1.7.08 Release Notes have been updated to include information on the property files that need to be updated if a site chooses to use their existing JBoss instance instead of upgrading to WildFly.
i2b2 Release 1.7.08
Release Date: October 7, 2016
1.7.08 Release Summary
Release 1.7.08 contains a number of new features as well as bug fixes. Below are a few highlights of the changes included in this release. Information about the other changes can be found in the sections that follow this one.
JBoss Updated to WildFly
In order to address some of the security vulnerabilities that exist in some JBoss installations, the i2b2 Server has been upgraded to use WildFly. In 2014 Red Hat renamed their JBoss Application Server to WildFly and their latest version (WildFly 10) addresses the known security vulnerabilities.
Note
The Third Party Software Changes section contains additional information on upgrading WildFly as well as other 3rd party software.
Although we recommend upgrading to WildFly, we do recognize that some sites may not be in a position to upgrade their existing JBoss 7. In the section labeled i2b2 Property Settings for WildFly 10 and JBoss 7 we have documented all the places you will need to modify the paths in order to use 1.7.08 with your existing JBoss 7. We have also included some additional information that you will need to be aware of before using 1.7.08 with your existing JBoss,
SQL Server: Option to Improve Query Performance
New parameter to use temp table constraint instead of 'WITH' clause.
Large data warehouses that contain broad and deep ontologies run the risk of CRC queries having a slow response time. In this release (1.7.08) a new parameter has been added to the crc.properties file. This new parameter allows a site to use a temp table instead of a 'WITH' clause when running a CRC query.
Improvements to the Processing of Queueing Queries
In the Previous Query display, new statuses provide users with additional information that accurately reflects the current status and location of the query. The new statuses are:
SMALL_QUEUE
SMALL_QUEUE_RUNNING
MEDIUM_QUEUE
MEDIUM_QUEUE_RUNNING
LARGE_QUEUE
LARGE_QUEUE_RUNNING
In addition to updating the status of queries, an additional feature was added to the Web Client that makes these statuses visible to users. The query status can be seen in Previous Queries as well as in Show Query Status.
SHRINE Release 1.21.2 has been tested with i2b2 1.7.08 Release and has been approved by the SHRINE Team
Installation Notes
This release note applies to you if you are upgrading to 1.7.08 from an earlier version of i2b2.
If you are installing 1.7.08 from a computer running the i2b2 Workbench, ensure that the workbench and all eclipse applications are closed prior to installing this release.
If you are installing a new instance of i2b2 we recommend you refer to the installation documentation found on the i2b2 community wiki. This documentation will guide you through the entire installation process.
Upgrade Notes
i2b2 Release 1.7.08 contains changes to the following software components:
Database Scripts
i2b2 Server
i2b2 Web Client
Third Party Software Changes
In release 1.7.08 the i2b2 Server has been updated to use the following versions of third party software. These updates were done to address some security concerns with the third party software used by the i2b2
Apache Ant has been upgraded to 1.9
Apache Axis2 has been upgraded to 1.7.1
Java JDK has been upgraded to 8.0
JBoss has been upgraded to WildFly 10
3rd Party Software Versions and Links
The following table contains all the information needed to update your 3rd party software. In addition to the version information, the table contains links both to the Vendor's documentation as well as the appropriate chapter in the i2b2 Installation Guide located on the i2b2 Community Wiki.
Warning As stated earlier, the i2b2 team made the decision to upgrade to WildFly 10 and JDK 8 in order to address known security vulnerabilities with JBoss. In order for the i2b2 server (1.7.08) to work correctly, we recommend you update your environment to use WildFly 10 and JDK 8. However, if you are currently using JBoss 7 and do not want to upgrade your environment to use WildFly there are a few things you need to be aware of.
Release 1.7.08 was not tested with JBoss 7, therefore we cannot guarantee the stability of the release if you continue to use JBoss 7. We can however confirm the i2b2 server (1.7.08) was tested with WildFly 10 and JDK 8 and does work correctly.
JDK 8 does not work with JBoss 7. If you are upgrading to JDK8 then you have to upgrade to WildFly
If you are upgrading to WildFly and JDK 8 you need to do these upgrades before you upgrade your i2b2 server code.
The property settings delivered with i2b2 version 1.7.08 are pointing to WildFly. For those sites that are currently using JBoss 7 and are not ready to upgrade to WildFly 10 you will need to change the path information to point to JBoss 7. The files and properties that need to be modified are in the next section.
Change Summary - i2b2 Community Plugins - Release 1.7.08
Bug Fixes
[PLUGINS-17] - Plugins manifest is pointing to the wrong URL
Improvement / New Feature Details
View and Update the DB_LOOKUP Tables
JIRA ISSUES:
[CORE-218] - New web service to retrieve the db lookup settings in the configuration files
[WEBCLIENT-191] - ADMIN: Add the ability to view DB_LOOKUP settings for each cell
Release 1.7.08 added the ability to view current database connections defined in the DB_LOOKUP tables for each i2b2 cells. Administrators can also edit existing values and add new entries into the tables. This new feature resides within the i2b2 Admin Module. The DB_LOOKUP tables are specific to each i2b2 cell. To access the list of values in a specific cell you need to expand Manage Cells in the Navigation Tree on the left of the page. Then select the cell to expand further, once this is done you will see DB-Lookup as an option. Clicking on DB-Lookup will display the DBLookup List page. This page will display all the values in a table format.
The following screen shot shows all the entries in the CRC_DB_LOOKUP table.
To add a new entry into the DB_LOOKUP table simply click on the Add New DBLookup button that appears above the table of existing values. The page will be updated to a form with fields to capture the information to be stored in the DB_LOOKUP table.
To edit an existing entry, click on its Name located in the Navigation Tree on the left. The page will be updated to show the values currently filed in the DB_LOOKUP table. Make any changes and click on Save to save your edits.
Improvements to the Processing of Queueing Queries
JIRA ISSUES:
[CORE-221] - Improvements to the queuing process when running a query
[WEBCLIENT-192] - Improvements to queued queries in status window
In the i2b2, there are three queues a query may be placed into when it is run. The length of time a query waits in each queue is defined in the crc.properties file.
Small Queue
Medium Queue
Large Queue
In the Web Client, the status of a query can be seen in Previous Queries. The status would be PROCESSING, ERROR, or COMPLETED. None of these statuses would provide information on which queue the query was in. Database administrators would have to view the query in the QT_QUERY_INSTANCE table to see the queue information. The statuses and queue information were often ambiguous which would make it challenging to trouble shoot any issues.
To address this issue, new statuses have been added in Release 1.7.08. These new statuses provide users with additional information that accurately reflects the current status and location of the query. The new statuses are:
In addition to updating the status of queries, an additional feature was added to the Web Client that makes these statuses visible to users. The query status can be seen in Previous Queries as well as in Show Query Status.
SQL Server: Option to Improve Query Performance
JIRA ISSUES: [CORE-226] - New parameter to use temp table constraint instead of 'WITH' clause
Large data warehouses that contain broad and deep ontologies run the risk of CRC queries having a slow response time. In this release (1.7.08) a new parameter has been added to the crc.properties file. This new parameter allows a site to use a temp table instead of a 'WITH' clause when running a CRC query. In some environments, using a temp table allows the query to run more efficiently and process the request faster.
Parameter Name: edu.harvard.i2b2.crc.setfinderquery.constraintlogic
Located in: crc.properties file
Behavior:
Value
Behavior
TEMP or TEMPTABLES
Temp tables will be used when building queries.
WITH
Current query logic is used
If the parameter is missing from the crc.properties file, the system will current query logic (WITH clause).
Important This change only affects SQL Server databases. Both PostgreSQL and Oracle do not have the capabilities of using temp tables. They will continue to use the WITH clause.
Date Constraint Improvements
JIRA ISSUES: [WEBCLIENT-133] - Restrict ability to add Date Constraint if a panel contains any age concepts.
In the i2b2, the CRC will use the START_DATE in the OBSERVATION_FACT table when running a query with a date constraint defined on a panel. This can present a problem if at least one of the items in the panel is an age concept and the patient demographics are stored in the PATIENT_DIMENSION table. The problem is ages that are stored in the PATIENT_DIMENSION table will not have a START_DATE and therefore the date constraint is not valid.
General i2b2 users do not know whether or not an age has a start date and if they select a date constraint their query may not return the expected results. This becomes a bigger issue when you are using the i2b2 in a larger network in which some sites may store it in the PATIENT_DIMENSION and others in the OBSERVATION_FACT. This scenario will definitely result in misleading results and the user will be unaware of the discrepancy.
To avoid any confusion or misleading results, users can no longer add a date constraint if at least one item in the panel is an age concept. The following message will appear when attempting to set a date constraint on a panel with an age concept:
Date constraints are not allowed for age related concepts. This panel contains at least one age related concepts, therefore a date constraint can not be set for this panel."
Web Client Configurations
JIRA ISSUES: [
WEBCLIENT-198] - Parameters/Configurations for Web Client
In Release 1.7.08, a new configuration file has been added to the i2b2 Web Client. This file allows site administrators to customize the text on the login screens, default user id and password values, as well as how obfuscated results display in the i2b2 Web Client.
Logo that appears in toolbar when logged into the i2b2 Web Client.
"assets/images/title.gif"
loginHeaderText
Text in the header bar of the login box
"i2b2 Login"
loginUsernameText
Text for the username input of the login box.
"Username:"
loginDefaultUsername
Default text inside the username input.
"demo"
loginPasswordText
Text for the password input of the login box.
"Password:"
loginDefaultPassword
Default text inside the password input.
"demouser"
loginHostText
Text for the PM cell dropdown of the login box.
"i2b2 Host:"
obfuscatedDisplayNumber
The number to display after the plus/minus for obfuscated results.
Please see the important note at end of this table.
3
useFloorThreshold
If true, any result below floorThresholdNumber shows as '{floorThresholdText} {floorThresholdNumber}'
If false, floor threshold will not be used when displaying values in the i2b2 Web Client.
false
floorThresholdNumber
Threshold for the low number of results
10
floorThresholdText
Text that is prefixed before {floorThresholdNumber} (include trailing space)
"Less Than "
Important The calculation for the real obfuscation value continues to be controlled by the server and is based on the value defined in the CRC properties file. The obfuscatedDisplayNumber parameter in the i2b2_ui_config.js simply defines what number to display to the user when viewing the query results.
SQL Server: New Connection Parameter to Pass in String Based Variables
JIRA ISSUES: [CORE-227] - Add ability to send parameters with string based variables as varchar instead of nvarchar
Prior to release 1.7.08, parameters are sent in as Unicode (nvarchar) instead of varchar. SQL Server then has to explicitly convert the nvarchar to varchar in the query. The effect is that SQL Server optimizer may have to use an index scan instead of an index seek (which is faster).
To address this issue, we have added a new connection parameter to be used when i2b2 uses PreparedStatements to pass in string based variables in SQL Server. The following connection parameter is to be added to the datasource definition.
Connection Parameter: connection-property name="sendStringParametersAsUnicode"
Added To: datasource definition
Behavior:
Value
Behavior
false
String based variable will be sent as varchar
true
Current logic is used; String based variable will be sent in Unicode (nvarchar)
JIRA ISSUES: [CORE-229] - Provide updated JDBC drivers used by Oracle, PostgreSQL, and SQL Server
Included in release 1.7.08 are updated JDBC drivers for Oracle, PostgreSQL and SQL Server. The new version of JDBC drivers are optional and will not be installed automatically.
Important Sites that choose to upgrade their JDBC drivers will be required to also updated the datasource files for all of their cells.
Information on Updating Drivers
This section contains some general information and key points to keep in mind when updating your JDBC drivers.
Location of JDBC Jar files
Your current JDBC jar files reside in the following directories:
There are three new jar files, one for each type of supported databases.
Oracle = ojdbc7.jar
PostgreSQL = postgresql-9.4-1209.jar
SQL Server = sqljdbc42.jar
Update Existing i2b2 Instance
A script to deploy the new jar files has been included in the 1.7.08 Release. Once you have updated your server with the latest code you can run one of the following commands to deploy the new jdbc jar files:
Linux Command ant copy_new_jdbc_jar
Windows Command %ANT_HOME%\bin\ant.bat copy_new_jdbc_jar
Warning If you choose to install the new JDBC jar files you also need to update your datasource files with the new driver information. This needs to be done for each cell in the i2b2 hive.
i2b2 Release 1.7.07c
Release Date: June 7, 2016
Installation Notes
This release note applies to you if you are upgrading to 1.7.07c from an earlier version of i2b2.
If you are installing 1.7.07c from a computer running the i2b2 Workbench, ensure that the workbench and all eclipse applications are closed prior to installing this release.
If you are installing a new instance of i2b2 we recommend you refer to the installation documentation found on the i2b2 community wiki. This documentation will guide you through the entire installation process.
SHRINE Approval
Release 1.7.07c does not include any server changes and therefore does not affect SHRINE installations. This release does not need to be tested with the latest version of the SHRINE Software.
Upgrade Notes
i2b2 Release 1.7.07c contains changes to the following software components:
i2b2 Web Client
i2b2 Server - Admin code only
Important The Admin changes can be found in the i2b2core-src-1707c zip file located on the software page of the i2b2.org website. Please note that the other server components are included in this file. If you are upgrading from 1.7.07 then you do not need to update your i2b2 server as there are no changes. If you are upgrading from a release prior to 1.7.07 then you do need to install these other components.
Third Party Software Changes
No changes to third party software are included in release 1.7.07c
Change Summary - i2b2 Web Client Software - Release 1.7.07c
Bug Fixes
[WEBCLIENT-186] - Timeout message not returned when query runs longer than the defined 180 secs
i2b2 Release 1.7.07b
Release Date: March 1, 2016
Installation Notes
This release note applies to you if you are upgrading to 1.7.07b from an earlier version of i2b2.
If you are installing 1.7.07b from a computer running the i2b2 Workbench, ensure that the workbench and all eclipse applications are closed prior to installing this release.
If you are installing a new instance of i2b2 we recommend you refer to the installation documentation found on the i2b2 community wiki. This documentation will guide you through the entire installation process.
SHRINE Approval
Release 1.7.07b does not include any server changes and therefore does not affect SHRINE installations. This release does not need to be tested with the latest version of the SHRINE Software.
Upgrade Notes
i2b2 Release 1.7.07b contains changes to the following software components:
i2b2 Web Client
i2b2 Server - Admin code only
Important The Admin changes can be found in the i2b2core-src-1707b zip file located on the software page of the i2b2.org website. Please note that the other server components are included in this file. If you are upgrading from 1.7.07 then you do not need to update your i2b2 server as there are no changes. If you are upgrading from a release prior to 1.7.07 then you do need to install these other components.
Third Party Software Changes
No changes to third party software are included in release 1.7.07b
Change Summary - i2b2 Web Client Software - Release 1.7.07b
[WEBCLIENT-178] - Error returned when reloading the i2b2 Web Client after it times out
i2b2 Release 1.7.07
Release Date: January 15, 2016
Installation Notes
This release note applies to you if you are upgrading to 1.7.07 from an earlier version of i2b2.
If you are installing 1.7.07 from a computer running the i2b2 Workbench, ensure that the workbench and all eclipse applications are closed prior to installing this release.
If you are installing a new instance of i2b2 we recommend you refer to the installation documentation found on the i2b2 community wiki. This documentation will guide you through the entire installation process.
SHRINE Approval
SHRINE Release 1.20.1 has been tested with i2b2 1.7.07 Release and has been approved by the SHRINE Team
Upgrade Notes
i2b2 Release 1.7.07 contains changes to the following software components:
i2b2 Community Plugins
i2b2 Data
i2b2 Server
i2b2 Web Client
Third Party Software Changes
No changes to third party software are included in release 1.7.07
[PLUGINS-11] - CARE-Observation: Marital Statuses are not displaying
[PLUGINS-16] - Fix issue with double quotes in the manifests for several plugins
i2b2 Release 1.7.06
Release Date: August 12, 2015
Installation Notes
This release note applies to you if you are upgrading to 1.7.06 from an earlier version of i2b2.
If you are installing 1.7.06 from a computer running the i2b2 Workbench, ensure that the workbench and all eclipse applications are closed prior to installing this release.
If you are installing a new instance of i2b2 we recommend you refer to the installation documentation found on the i2b2 community wiki. This documentation will guide you through the entire installation process.
Upgrade Notes
i2b2 Release 1.7.06 contains changes to the following software components:
i2b2 Server
i2b2 Web Client
i2b2 Workbench
Third Party Software Changes
No changes to third party software are included in release 1.7.06
[CORE-149] - JDBC calls to interrupted threads throw sqlexceptions - Queries do not leave medium queue
[CORE-165] - Timeline filter not working if database is SQL Server
[CORE-180] - SHRINE queries will not run once i2b2 is updated to 1.7.05
Documentation Updates
[CORE-179] - Difference between documentation and table concept_dimension
Change Summary - i2b2 Web Client Software - Release 1.7.06
Bug Fixes
[WEBCLIENT-110] - Temporal queries do not print unless a population is defined
[WEBCLIENT-115] - IE Compatibility tag missing end tag and not within the header
[WEBCLIENT-116] - Graph Results display as "undefined" for obfuscated users
[WEBCLIENT-117] - Query Tool displays behind Query Status and Graph Results tabs
[WEBCLIENT-120] - Print query does not work in Internet Explorer for Previous Temporal Queries
[WEBCLIENT-121] - Previous temporal queries do not run in Internet Explorer
[WEBCLIENT-123] - Order of events not maintained when running a previous temporal query
[WEBCLIENT-124] - Clear in Query Tool does not clear correctly for Temporal Queries
[WEBCLIENT-126] - Only able to view the first two events when previous temporal query is added to the query tool
i2b2 Release 1.7.05
Release Date: May 6, 2015
Installation Notes
This release note applies to you if you are upgrading to 1.7.05 from an earlier version of i2b2.
If you are installing 1.7.05 from a computer running the i2b2 Workbench, ensure that the workbench and all eclipse applications are closed prior to installing this release.
If you are installing a new instance of i2b2 we recommend you refer to the installation documentation found on the i2b2 community wiki. This documentation will guide you through the entire installation process.
Upgrade Notes
i2b2 Release 1.7.05 contains changes to the following software components:
Database Scripts
i2b2 Server
i2b2 Web Client
i2b2 Workbench
Third Party Software Changes
No changes to third party software are included in release 1.7.05
[WEBCLIENT-89] - New Graph Results view to display patient breakdowns in a graph
Improvements
[WEBCLIENT-85] - Display error message to user in Find for previous queries
[WEBCLIENT-86] - Indicator needed to inform users the system is searching when doing a Find
[WEBCLIENT-88] - Category names in Find (Previous Queries) can be misleading
[WEBCLIENT-103] - Add text wrapping capabilities to the i2b2 Web Client
Bug Fixes
[WEBCLIENT-73] - Wrong name displays when renaming a previous query in Workplace
[WEBCLIENT-76] - Update the I.E. Emulation that is defined in the Web Client <meta> tag
[WEBCLIENT-81] - Not able to select item from pop-up menu in Previous Queries
[WEBCLIENT-83] - Need message to say no results found
[WEBCLIENT-84] - Not able to search Previous Queries if "Any Categories" is selected
[WEBCLIENT-90] - Query Results not cleared when clear query in Query Tool
[WEBCLIENT-91] - Items are not staying with the pointer when dragged to another i2b2 view (Firefox only)
[WEBCLIENT-92] - Refresh icon needs to updated to one with transparent background
[WEBCLIENT-93] - Update the message that appears to users in Graph Results if using I.E. 7 or 8
[WEBCLIENT-94] - ONT - Containers Dragable by Default
[WEBCLIENT-95] - Help is not displaying in the Web Client
[WEBCLIENT-97] - Selecting temporal constraint selection "Same encounter" is not changing selection at the individiual group level
[WEBCLIENT-99] - Find view is not resizing properly
[WEBCLIENT-101] - Date picker calendar does not close unless you choose a date
[WEBCLIENT-105] - Previous Queries appear to be missing value constraints when dropped in Query Tool
[WEBCLIENT-106] - Observation details are missing when viewed in Timeline
[WEBCLIENT-107] - Graph Results panel temporarily attached to bottom of Show Query Status panel
[WEBCLIENT-108] - Value constraint window doesn't open in I.E. 11
[WEBCLIENT-109] - Web Client may be using the wrong cell data when multiple projects and cells defined
[WEBCLIENT-112] - Find Terms: Search by Code does not display results returned
i2b2 Release 1.7.04
Release Date: November 13, 2014
Installation Notes
This release note applies to you if you are upgrading to 1.7.04 from an earlier version of i2b2.
If you are installing 1.7.04 from a computer running the i2b2 Workbench, ensure that the workbench and all eclipse applications are closed prior to installing this release.
If you are installing a new instance of i2b2 we recommend you refer to the installation documentation found on the i2b2 community wiki. This documentation will guide you through the entire installation process.
Upgrade Notes
i2b2 Release 1.7.04 contains changes to the following software components:
Database Scripts
i2b2 Server
i2b2 Web Client
i2b2 Workbench
Third Party Software Changes
No changes to third party software are included in release 1.7.04
This release note applies to you if you are upgrading to 1.7.03a from an earlier version of i2b2.
If you are installing 1.7.03a from a computer running the i2b2 Workbench, ensure that the workbench and all eclipse applications are closed prior to installing this release.
If you are installing a new instance of i2b2 we recommend you refer to the installation documentation found on the i2b2 community wiki. This documentation will guide you through the entire installation process.
Upgrade Notes
i2b2 Release 1.7.03a contains changes to the following software components:
i2b2 Web Client
Third Party Software Changes
No changes to third party software are included in release 1.7.03a
Change Summary - i2b2 Web Client Software - Release 1.7.03a
Bug Fixes
[WEBCLIENT-68] - Panel timing on anchoring observations can be changed to treat independently or same encounter
[WEBCLIENT-69] - Print Query is only including the information for the first group / panel
[WEBCLIENT-70] - The concept associated with a modifier is not printing when you print the query
i2b2 Release 1.7.03
Release Date: August 20, 2014
Installation Notes
This release note applies to you if you are upgrading to 1.7.03 from an earlier version of i2b2.
If you are installing 1.7.03 from a computer running the i2b2 Workbench, ensure that the workbench and all eclipse applications are closed prior to installing this release.
If you are installing a new instance of i2b2 we recommend you refer to the installation documentation found on the i2b2 community wiki. This documentation will guide you through the entire installation process.
Upgrade Notes
i2b2 Release 1.7.03 contains changes to the following software components:
i2b2 Server
i2b2 Web Client
Third Party Software Changes
No changes to third party software are included in release 1.7.03
Change Summary - i2b2 Core Software - Version 1.7.03
Bug Fixes
[CORE-143] - Do not require M_APPLIED_PATH when retrieving modifier information from the Ontology Cell
Improvements
[CORE-135] - Edit tool to file C_PATH and C_SYMBOL when adding new item
[CORE-141] - Remove carriage returns / line feeds from metadataxml when filing a term in Edit Terms view
Change Summary - i2b2 Web Client Software - Release 1.7.03
Bug Fixes
[WEBCLIENT-63] - Temporal Queries: Wrong description is displaying in the list of constraints for "On or After"
[WEBCLIENT-66] - Wrong operator sent for some temporal relationships
Improvement / New Feature Details
Edit tool to file C_PATH and C_SYMBOL when adding new item
In the i2b2 metadata table there are two columns (C_PATH and C_SYMBOL) that are used exclusively by the Ontology Mapping tool. Prior to release 1.7.03 these columns were not populated when you added a new term via the Edit Terms view. This situation has been rectified in that these columns will now be populated with the appropriate data when creating a new container, folder, term, or modifier from within the Edit Terms view.
Edit Tool view: Line feeds removed from Metadataxml
In the Edit Terms view users can create terms that have values associated to them. These values are stored in the C_METADATAXML column in the custom metadata table. Prior to release 1.7.03 when you created or edited a term with values in the Edit Tool view, the metadata was stored in the table with carriage returns / line feeds. This change improves the way the metadataxml if filed into the table by removing all line feeds from the data before filing it into the C_METADATAXML column
i2b2 Release 1.7.02
Release Date: July 1, 2014
Installation Notes
This release note applies to you if you are upgrading to 1.7.02 from an earlier version of i2b2.
If you are installing 1.7.02 from a computer running the i2b2 Workbench, ensure that the workbench and all eclipse applications are closed prior to installing this release.
If you are installing a new instance of i2b2 we recommend you refer to the installation documentation found on the i2b2 community wiki. This documentation will guide you through the entire installation process.
Upgrade Notes
i2b2 Release 1.7.02 contains changes to the following software components:
Database Scripts
i2b2 Server
i2b2 Web Client
i2b2 Workbench
Third Party Software Changes
No changes to third party software are included in release 1.7.02
Change Summary - i2b2 Core Software - Version 1.7.02
[WEBCLIENT-46] - Renaming shared folders doesn't work in the webclient
[WEBCLIENT-47] - "Delete Concept" in I2B2 web app deletes the first occurrence of the concept, not the one selected
[WEBCLIENT-51] - Only 1 temporal relationship sent in xml even though multiple are defined
[WEBCLIENT-52] - Modifier folders/containers don't work with i2b2 v1.7 and PostgreSQL
[WEBCLIENT-54] - When an item in the Term Navigator has more than a certain number of elements underneath, the arithmetic in the 'Need more items' dialog box is incorrect
[WEBCLIENT-55] - With error in data source the client runs on forever
[WEBCLIENT-58] - Operators do not default correctly when adding a temporal relationship
[WEBCLIENT-59] - Print Query not working in Chrome browser
Tasks
[WEBCLIENT-61] - Disable changing passwords on the demo site
In release 1.7.02, i2b2 users are now able to change their password from within the i2b2 Web Client and Workbench. Previously to this release, users did not have the ability to change their own password. They would have to notify their administrator who would have to change it for them in the i2b2 administration module. This new feature adds a layer of security in that the user can manage their own password and not have the added risk of other users (i.e. the admin) knowing their password.
Important If a user is setup to log into the i2b2 using either Active Directory or LDAP authentication methods then they will not be able to change their password from within the i2b2 Web Client or Workbench. If they need to change their password they will need to contact their site administrator and follow the protocols established at their institution.
This feature is only available for those users that log in with the standard i2b2 Authentication method.
In the i2b2 Web Client, a new option called Change Password now appears in the Web Client's toolbar.
Clicking on Change Password will open the i2b2 Change Password window.
In the i2b2 Workbench, a new button labeled Password has been added to the i2b2 desktop title bar.
Clicking on Password will open the Set Password window.
The functionality to change your password is the same regardless of whether you access the change password window from within the i2b2 Web Client or the workbench. There are basically three steps:
Enter your current password.
Enter a new password for your user.
Retype your password.
Once you do the above three steps and click on OK the system will verify you entered your "current" password correctly and the password you entered at the New Password and Retype Password fields match. Provided everything is correct your new password will be saved.
Note Once you change your password you will need to log out of the Web Client or Workbench and log back in using your new password.
i2b2 Release 1.7.01
Release Date: February 4, 2014
Installation Notes
This release note applies to you if you are upgrading to 1.7.01 from an earlier version of i2b2.
If you are installing 1.7.01 from a computer running the i2b2 Workbench, ensure that the workbench and all eclipse applications are closed prior to installing this release.
If you are installing a new instance of i2b2 we recommend you refer to the installation documentation found on the i2b2 community wiki. This documentation will guide you through the entire installation process.
Upgrade Notes
i2b2 Release 1.7.01 contains changes to the following software components:
Database Scripts
i2b2 Server
i2b2 Web Client
Third Party Software Changes
No changes to third party software are included in release 1.7.01
Change Summary - i2b2 Core Software - Version 1.7.01
Improvements
[CORE-88] - Confusing error message logged for non-Oracle users
Bug Fixes
[CORE-83] - Trying to build and compile i2b2 Server on Fedora Core 20 with Wildfly 8.0.0
[CORE-85] - Fresh install fails on PM Module and admin screen
[CORE-87] - Installation process needs to put database drivers in i2b2.war/WEB-INF/lib
Data Install: The stored procedures for PostgreSQL for the CRC Loader was enhanced and optimized.
Server Install: JDBC Drivers not copied correctly. When installing i2b2 server-common, the JDBC drivers were not copied into the i2b2.war/WEB-INF/lib directory.
CRC-Loader: Importing Visit Dimension Data. When using the CRC Loader, some primary key data such as inout_cd, location_cd, length_of_visit, etc, was not being imported correctly.
[CORE-90] - Install Documentation: Wrong schema configurations documented for a PostgreSQL database
Change Summary - i2b2 Web Client Software - Release 1.7.01
Bug Fixes
[WEBCLIENT-48] - Web client gets into non-functional state
Clicking on the Clear button does not return the Query Tool to the default settings. When a temporal query is created, and a user clicks on the clear button to start a new query, the Temporal Constraint is changed to "Define sequence of events" and it should default to "Treat all groups independently.
Date constraints not being stored with the previous query. When a date constraint was defined on a query the previous query would not maintain the constraint when you would use it to run another query.
i2b2 Release 1.7
Release Date: December 20, 2013
Installation Notes
This release note applies to you if you are upgrading to 1.7 from an earlier version of i2b2.
If you are installing 1.7 from a computer running the i2b2 Workbench, ensure that the workbench and all eclipse applications are closed prior to installing this release.
If you are installing a new instance of i2b2 we recommend you refer to the installation documentation found on the i2b2 community wiki. This documentation will guide you through the entire installation process.
Upgrade Notes
i2b2 Release 1.7 contains changes to the following software components:
Database Scripts
i2b2 Server
i2b2 Web Client
i2b2 Workbench
Third Party Software Changes
In release 1.7 the i2b2 Server has been updated to use the following versions of third party software.
JBoss has been upgraded to 7.1.1
Apache Ant has been upgraded to 1.8.2
Apache Axis2 has been upgraded to 1.6.2
Warning Only the i2b2 Server was upgraded to use the above versions of JBoss, Ant, and Axis2. The i2b2 Workbench will continue to use the previous versions. As a result, the source codes for the server and the workbench client have different plug-ins for the commons.
Server edu.harvard.i2b2.server-common
Client edu.harvard.i2b2.common
Change Summary - i2b2 Core Software - Release 1.7
Improvements
Find Terms: New feature called "Jump to Term in Tree"
Previous Query: Filter list by user
Previous Query: Search Previous Queries View
Previous Query: Page through previous queries by date
Database: PROJECT_ID Column added to PATIENT_MAPPING and ENCOUNTER_MAPPING tables (support for new IM cell)
Demo Data: Updated PATIENT_MAPPING table to support the new IM cell.
New Features
Temporal Queries (New Temporal Query Tool View)
Identity Management Cell (IM)
Identity Management Tables
Managers Tool View
OpenEMPI Support
Patient Mapping View
Patient Sets View
PostgreSQL Database Support
Workplace Find View
Bug Fixes
[CORE-5] - CRC build from source deposits i2b2Common-core.jar in wrong directory
[CORE-74] - Typo in i2b2_config_data.js of admin interface
[CORE-81] - No PATIENT_NUM in OBSERVATION_FACT_PK (conflict with documentation)
Documentation
Architecture, design and messaging documents for the new Identity Management (IM) Cell.
Design documentation for the new Temporal Query Tool plug-in.
User guide for the new Temporal Query view.
Documentation for the new views (Patient Set, Patient Mapping, Managers Tool, and Find in Workplace).
[CORE-8] - Suggestions for improvements to installation documents
[CORE-75] - CRC_Design.pdf page numbers are broken, all page numbers are set to 1 of 1, 2 of 2, etc. instead of 1 of xx
[CORE-78] - Errors in I2B2 Hive Installation Guide v 1.7.0
Tasks
[CORE-45] - Establish CRCLoader project (eclipse) from exiting ant build file failed
Change Summary - i2b2 Web Client Software - Release 1.7
New Features
Temporal Queries (Modification made to existing Query Tool)
Documentation
[WEBCLIENT-40] - Webclient: documentation should state that php and curl are prerequisites for the webclient
Improvement / New Feature Details
Temporal Queries
The temporal query is a new type of query introduced in release 1.7. There are two components to these queries that make them a little more complex than the type of queries available prior to 1.7 (classic i2b2 queries).
The first component to these queries is the list of events defined by the user.
The second component is the relationship between the events. This relationship is referred to a Temporal Relationship, which is best described as how the different events relate in regards to the time in which the event(s) occurred.
Users can also define a patient or event population in which they wish to run the temporal query against. This step is optional and is not required in order to run the temporal query.
The process in which temporal queries are defined is slightly different in the i2b2 Web Client and the i2b2 Workbench. In the i2b2 Web Client the existing Query Tool view has been modified to accommodate Temporal Queries while a new view called Temporal Query Tool view has been created for the i2b2 Workbench.
The new Temporal Query Tool view and the modifications to the existing Query Tool view extend the query functionalities provided by the classic Query Tool view.
It is important to note that while the manner in which users setup a temporal query is different in each of the clients the overall functionality is the same.
The following two sections will describe how to run Temporal Queries in the i2b2 Web Client and the i2b2 Workbench.
i2b2 Web Client: Temporal Queries
In the i2b2 Web Client there are five basic steps in defining a temporal query in the Query Tool view.
Change Temporal Constraint to Define sequence of Events.
Define Population in which events occur (optional step).
Define Events
Define order of events (temporal relationships)
Run the query
Note For detailed information about creating Temporal Queries please see the Temporal Query help file located on-line from within the i2b2 Web Client.
Step 1: Change Temporal Constraint
The first step is to change the Temporal Constraint to Define sequence of Events.
Step 2: Define Population in which events occur
Once you have changed the Temporal constraint to be Define sequence of Events a new Page selection box will appear below the Temporal Constraint section. The default page will be Population in which events occur. It is on this page you will define your population requirements.
Step 3: Define Events
The events are the first component of a temporal query. There are no restrictions on the number of events you wish to define. The only requirement is that you have to define at least two events.
To define the events simply click on the Page selection box and select Event 1 from the drop-down list.
The groups and constraints for the events work in the same manner as they did for a traditional i2b2 query. Simply drag the items you want to include in Event 1 to the appropriate groups.
Once you have added your items to the groups you can click on the Page selection box and select Event 2 from the drop-down list. This will change the page to display the groups for Event 2.
If you need to add a third event you can click on the New Event button located next to the Page selection box.
Step 4: Define Order of Events (Temporal Relationship)
As stated earlier the second component of a temporal query is the relationship between the events (temporal relationship). In the i2b2 Web Client this is done on the Define order of events page, which is accessed by clicking on the Page selection box and selecting Define order of events from the drop-down list.
The page will display as follows:
Step 5: Run Query
In the Web Client running a query works the same regardless of whether or not it is a Temporal Query or a traditional i2b2 query. By clickin on the Run Query button, the i2b2 client will send the request to the i2b2 server which will run the query as defined.
i2b2 Workbench: New Temporal Query Tool View
In the i2b2 Workbench there are three pages or steps in defining and running a temporal query in the new Temporal Query Tool view.
Page 1: Define Population
Page 2: Define Temporal Relationships
Page 3: Review and Submit Query
i2b2 Workbench: New Temporal Query Tool View
Define Date Constraints and Exclusions in Temporal Query Tool View
Defining the Date Constraints
Exclude Panel
Each page as well as defining constraints is further defined in the next few sections.
Note For detailed information about using the Temporal Query Tool view, please see the help file for this view which is available on-line from within the i2b2 Workbench.
Page 1: Define Population
On this page you will define your population requirements.
Page 2: Define Temporal Relationships
As stated earlier there are two components to a temporal query; (1) List of events and (2) the relationship between the events.
The second page is where you will define both the events and their relationship.
Page 3: Review and Submit
On this page the name of the query will default and if you wish to rename it you can do so at this point. Whatever is entered here will be the name given to the query when it is run. In addition you can select the Analysis Types that you want when running the query.
Defining Date Constraints and Exclusions in Temporal Query Tool View
There are some minor differences in terminology or layout that needs to be noted in this release note.
Defining the Date Constraints
In the classic Query Tool view you can only define date constraints on the group / panel level. In the new Temporal Query TOol view you can now define a date constraint on either the query or group levels. If you define it on the query level it will default the same date constraint for all the groups and the date constraint on the panel level will not be available for selection.
If you want to define it on the panel level select Group-Specific. Go to the group you wish to define the constraint and click on the column that displays No Date Constraints.
Exclude Panel
The ability to exclude all items in a group does exist in the new Temporal Query Tool view. However, the method in which it is defined differs between the classic Query Tool view and the Temporal Query Tool view.
In the existing Query Tool view ("Classic") the exclusion constraint was defined by clicking on the button labeled Exclude.
In the Temporal Query Tool view (New) the exclusion constraint was rolled into the window for defining the Occurrence constraint.
The Specify Occurrence Constraints windows will open when you click on the box that displays the occurrence constraint. To set the exclusion constraint you need to select "= 0 (No Occurrences)" from the drop-down list.
The above option is equivalent to the Exclude feature in the classic Query Tool view.
Previous Query: Filter list by user
New in release 1.7 is the ability to filter the list of previous queries by the user who created the query. In the options dialog () window there is a new field called Get previous queries for user. The default is all users and can be changed to a specific user by clicking on the down arrow to display the drop-down list. Once you select the user and click on OK, the Previous Queries view will refresh and display only those previous queries created by the selected user.
Important In i2b2 only managers are allowed to view queries for another user, therefore this feature is only available to those users who have the role of MANAGER defined for the project. If a user does not have the manager role then this field will be inactive and unavailable for selection.
Previous Query: Search Previous Queries View
In release 1.7 the ability to search the Previous Queries view has been added. The functionality is very similar to Find Terms view except it will search the Previous Queries view instead of Navigate Terms view. Users can search any of the three levels;
Previous Query (name)
Previous Query Result
Patient
Previous Query: Page through previous queries by date
Users can now retrieve the next or previous grouping of previous queries by the date in which the query was created.
The Previous button() will retrieve the group of previous queries that occur prior to the date displayed in the date / time field.
The Next button() will retrieve the group of previous queries that occur after the date displayed in the date / time field.
Identity Management Cell (IM)
A new cell called the Identity Management (IM) Cell was developed in release 1.7. This new cell contains Protected Health Information (PHI), which can be used to identify patients. The IM cell is used to manage this PHI in a manner consistent with the HIPAA privacy rule. The patient data will be available only as a HIPAA defined "Limited Data Set" to most of the hive.
The full functionality of the IM cell will be developed in stages. The initial framework and key services are released as part of the 1.7 release. Some of the key features being released in 1.7 are:
New tables to store identifiers from different sites, and patients that are included in a project.
Audit controls are implemented that are in compliance with the HIPAA privacy rules.
Services developed to set and validated an AES key for encrypting and decrypting patient MRNs in the IM cell.
Unencrypted patient identifiers sent in the PDO can be processed through the IM cell to retrieve all site IDs for the patient and project.
In addition to the above features, the i2b2 Worbench (eclipse client) has two new views that were created to support the new IM cell. These new views, called Patient Mapping and Admin Tool are further defined in the following two sections called Patient Mapping View and Admin Tool View.
Managers Tool View
The Managers Tool view was developed in release 1.7 and works in conjunction with the IM Cell. It currently has two main functions.
Set and / or validate that the project key is defined in the IM Cell.
The project key is used by the IM cell to decrypte the patient id"s that are encrypted.
The Set Key is used to define the key in the IM cell.
The Validate Key is used to verify the key is set.
Important If you are using the IM cell and your patient identifiers are encyrpted the you need to set the Project key in the IM cell. It is important to note that if you restart your i2b2 server or in the case of the VM image restarting the virtual machine then you will need to re-enter the project key.
The project key for the i2b2 demo project is: i2b2demodatakey1
In the VM image you need to log into the i2b2 Workbench as the i2b2 Admin user.
User ID: i2b2
Password: demouser
View the audit information.
As part of the IM cell an audit table was created to track when a patient in the IM cell was accessed. This new view allows Project Managers or Administrators to run a report to see that audit information. The report can be run for a particular user, patient, or all audit information for the project you are logged into.
Patient Sets View
In release 1.7 a new view called Patient Sets was created. This new view will display a list of Patient sets that were created when a query was run. It is similar to the Previous Queries view except it only displays the patient sets and not the previous query or other result sets (i.e. Encounter sets, Number of patients, etc).
The patient sets can be expanded to display a list of patients.
Users can drag an entire patient set or a single patient to other views in the i2b2 Workbench.
Users can also perform a search in which they can search by the name of the patient set or for a list of patient sets that contain a specific patient.
Workplace Find View
A new view called Find in Workplace was created in release 1.7. This view is very similar to the Find Terms view except it will search the Workplace view instead of the Navigate Terms view.
Find Terms: New feature called "Jump to Term in Tree"
A new feature called Jump to Term in Tree has been added to the Find Terms view. Users can now easily jump directly to a term in the Navigate Terms view from the Find Terms view.
Once a term is found in the Find Terms view the user can click on the term using the right mouse button to display the pop-up menu. Selecting "Jump to Term in Tree" from the pop-up menu will bring the Navigate Terms view into focus and the hierarchical tree will automatically open to the location of the term selected in the Find Terms view.
OpenEMPISupport
OpenEMPI is an open source Enterprise Master Patient Index (EMPI) which is developed and supported by another community. The i2b2 IM cell has been developed to allow communication with OpenEMPI for those sites that choose to use it as their patient repository.
For additional information on OpenEMPI please see their website by going to the following location: https://openempi.kenai.com/
PostgreSQL Database Support
The ability to use a PostgreSQL database as an i2b2 database has been added to release 1.7. Both the create and insert data database scripts for PostgreSQL are included in this release.
Data: New Tables created for the IM Cell
The following new tables were created as part of the new IM cell.
Table Name
Description
IM_MPI_DEMOGRAPHICS
Contains General demographic information for the patients.
IM_MPI_MAPPING
Maps the patient"s i2b2 number and the local MRN.
IM_PROJECT_SITES
Contains information about the different sites (Source Systems).
IM_PROJECT_PATIENTS
Stores the patients that are part of a project(s).
IM_AUDIT
Stores the audit details of patients accessed in the IM cell. This includes; the user, site, and project requesting the access as well as the date in which it was accessed.
Data: New Columns added to support IM cell
A new column called Project_ID has been added to both the PATIENT_MAPPING and ENCOUNTER_MAPPING tables in the crc. The PROJECT_ID was added to support the IM cell. It will allow sites to track which project a patient is part of.
Data: Improved Patient Mapping Data
The PATIENT_MAPPING table in the CRC has been updated to include the following:
Mappings of existing patients to multiple site MRNs.
Project IDs added to patients.
Demo data has been added to all of the new IM tables except the AUDIT table. This IM data was added to provide examples for using the new IM cell.
Important The mapping information added to the CRC and IM tables is strictly for demonstration purposes and does NOT contain real patient information.
New PostgreSQL Database Scripts
The i2b2 database scripts have been updated to include the table creation and data insert scripts for a PostgreSQL database.
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 7, Windows Server 2003 and 2008 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.
SHRINE Release 1.21.2 has been tested with i2b2 1.7.08 Release and has been approved by the SHRINE Team
SHRINE Release 1.20.1 has been tested with i2b2 1.7.07 Release and has been approved by the SHRINE Team
) window there is a new field called Get previous queries for user. The default is all users and can be changed to a specific user by clicking on the down arrow to display the drop-down list. Once you select the user and click on OK, the Previous Queries view will refresh and display only those previous queries created by the selected user.
) will retrieve the group of previous queries that occur prior to the date displayed in the date / time field.
) will retrieve the group of previous queries that occur after the date displayed in the date / time field.
