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Release Date: December 14, 2016
=20Release 1.7.08b fixes a bug in the CRC regarding when a query finishes r= unning the BATCH_MODE in the QT_QUERY_INSTANCE table says PROCESSING INSTEA= D OF FINISHED.
=20i2b2 Release 1.7.08b contains changes to the following software compone= nts:
=20Release Date: November 23, 2016
=20Release 1.7.08a is primarily focused on fixing and improving the queuein= g process. The main issue addressed in this release is a fix for an issue t= hat was introduced in 1.7.08; An error was returned when a query timed out = and moved on to the medium queue. Although the query continued to run it wa= s misleading to users as they were informed it generated an error an was th= erefore no longer running. A number of other issues were uncovered during t= he development and testing of this release. A complete list of each issue c= an be found in the section titled Change Summary - i2b2 Core Software
=20 =20 =20i2b2 Release 1.7.08a contains changes to the following software compone= nts:
=20=20 | Important The changes to the queuein= g process were thoroughly tested against an Oracle and SQL Server database.= Minimal testing was done against a PostgreSQL database. | =20
=20 | Note The Web Client contains only on= e minor fix to the wording of an error message. Upgrading to the new Web Cl= ient is not essential for this release. Please see the Change Summary - i2b2 Web Client Software= section to see what was changed. | =20
Release Date: October 7, 2016
=20Release 1.7.08 contains a number of new features as well as bug fixes. B= elow are a few highlights of the changes included in this release. Informat= ion about the other changes can be found in the sections that follow this o= ne.
=20In order to address some of the security vulnerabilities that exist in s= ome 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.<= /p>=20
=20 | Note The Third Party Software Changes sectio= n 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 existi= ng JBoss 7. In the section labeled i2b2 Property Settings for WildFly 10 and JBoss 7 we ha= ve 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 additiona= l information that you will need to be aware of before using 1.7.08 with yo= ur existing JBoss, | =20
New parameter to use temp table constraint instead of 'WITH' clause.
=20Large data warehouses that contain broad and deep ontologies run the ris= k of CRC queries having a slow response time. In this release (1.7.08) a ne= w parameter has been added to the crc.properties file. This new para= meter allows a site to use a temp table instead of a 'WITH' clause w= hen running a CRC query.
=20Additional information about this new feature can be found in the= Improvement / New F= eature Details section under the SQL Server: Option to Improve Query Performance<= /a> heading.
=20In the Previous Query display, new statuses provide users with additiona= l information that accurately reflects the current status and location of t= he query. The new statuses are:
=20In addition to updating the status of queries, an additional feature was= added to the Web Client that makes these statuses visible to users. The qu= ery status can be seen in Previous Queries as well as in Show Que= ry Status.
=20A complete list of all the statuses as well as additional informat= ion about this new feature can be found in the Improvement / New Feature Details section un= der the Impro= vements to the Processing of Queueing Queries heading.
=20SHRINE Release 1.21.2 has been tested w= ith i2b2 1.7.08 Release and has been approved by the SHRINE T= eam
=20i2b2 Release 1.7.08 contains changes to the following software componen= ts:
=20In release 1.7.08 the i2b2 Server has been updated to use the fol= lowing versions of third party software. These updates were done to address= some security concerns with the third party software used by the i2b2
= =20The following table contains all the information needed to update your 3= rd party software. In addition to the version information, the table contai= ns links both to the Vendor's documentation as well as the appropriate chap= ter in the i2b2 Install= ation Guide located on the i2b2 Community Wiki.
=203rd Party Software | =20Version | =20Download Link | =20Vendor Documentation | =20i2b2 Installation Guide | =20i2b2 Notes | =20
---|---|---|---|---|---|
Apache Ant | =201.9 | =20Apache Ant 1.9 Softwar= e | =20Ant's manual and API documentation is in= cluded in the binary distribution. | =20=20 | =20 |
Apache Axis2 | =201.7.1 | =20Axi= s2 1.7.1 Software | =20Installation Guide | =20Apache Axis2 | =20Download the WAR Distribution File | = =20
Java JDK | =208.0 | =20JDK 8 Software | =20=20 | Java JDK | =20Reminder: Update your JAVA_HOME environm= ent variable to point to JDK 8.0 | =20
WildFly | =2010 | =20WildFly 10 Software | =20Getting Started Guide | =20=20 | =20 |
=20 | Warning As stated earlier, the i2b2 = team made the decision to upgrade to WildFly 10 and JDK 8 in order to addre= ss 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 n= ot want to upgrade your environment to use WildFly there are a few things y= ou need to be aware of.=20
If you are upgrading to WildFly and JDK 8 you need to do these up= grades before you upgrade your i2b2 server code. | =20
The property settings delivered with i2b2 version 1.7.08 are pointing t= o WildFly. For those sites that are currently using JBoss 7 and are not rea= dy 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.
=20 File Name: crc_application_director=
y.properties
Location: edu.harvard.i2b2.crc/etc/spring/
WildFly 10 path: | = =20e= du.harvard.i2b2.crc.applicationdir=3D/opt/wildfly-10.0.0.Final/stand= alone/configuration/crcapp | =20
JBoss 7 path: | =20e= du.harvard.i2b2.crc.applicationdir=3D/opt/jboss-as-7.1.1.Final/stand= alone/configuration/crcapp | =20
File Name: build.properties
Location: edu.harvard.i2b2.crc/
WildFly 10 path: | = =20j= boss.home=3D/opt/wildfly-10.0.0.Final | =20
JBoss 7 path: | =20j= boss.home=3D/opt/jboss-as-7.1.1.Final | =20
File Name: fr_application_directory=
.properties
Location: edu.harvard.i2b2.fr/etc/spring/
WildFly 10 path: | = =20e= du.harvard.i2b2.fr.applicationdir=3D/opt/wildfly-10.0.0.Final/standa= lone/configuration/frapp | =20
JBoss 7 path: | =20e= du.harvard.i2b2.fr.applicationdir=3D/opt/jboss-as-7.1.1.Final/standa= lone/configuration/frapp | =20
File Name: build.properties
Location: edu.harvard.i2b2.fr/
WildFly 10 path: | = =20j= boss.home=3D/opt/wildfly-10.0.0.Final | =20
JBoss 7 path: | =20j= boss.home=3D/opt/jboss-as-7.1.1.Final | =20
File Name: im_application_directory=
.properties
Location: edu.harvard.i2b2.im/etc/spring/
WildFly 10 path: | = =20e= du.harvard.i2b2.im.applicationdir=3D/opt/wildfly-10.0.0.Final/standa= lone/configuration/imapp | =20
JBoss 7 path: | =20e= du.harvard.i2b2.im.applicationdir=3D/opt/jboss-as-7.1.1.Final/standa= lone/configuration/imapp | =20
File Name: build.properties
Location: edu.harvard.i2b2.im/
WildFly 10 path: | = =20j= boss.home=3D/opt/wildfly-10.0.0.Final | =20
JBoss 7 path: | =20j= boss.home=3D/opt/jboss-as-7.1.1.Final | =20
File Name: ontology_application_dir=
ectory.properties
Location: edu.harvard.i2b2.ontology/etc/sprin=
g/
WildFly 10 path: | = =20e= du.harvard.i2b2.ontology.applicationdir=3D/opt/wildfly-10.0.0.Final/= standalone/configuration/ontologyapp | =20
JBoss 7 path: | =20e= du.harvard.i2b2.ontology.applicationdir=3D/opt/jboss-as-7.1.1.Final/= standalone/configuration/ontologyapp | =20
File Name: build.properties
Location: edu.harvard.i2b2.ontology/
WildFly 10 path: | = =20j= boss.home=3D/opt/wildfly-10.0.0.Final | =20
JBoss 7 path: | =20j= boss.home=3D/opt/jboss-as-7.1.1.Final | =20
File Name: build.properties
Location: edu.harvard.i2b2.pm/
WildFly 10 path: | = =20j= boss.home=3D/opt/wildfly-10.0.0.Final | =20
JBoss 7 path: | =20j= boss.home=3D/opt/jboss-as-7.1.1.Final | =20
File Name: build.properties
Location: edu.harvard.i2b2.server-common/
WildFly 10 path: | = =20j= boss.home=3D/opt/wildfly-10.0.0.Final | =20
JBoss 7 path: | =20j= boss.home=3D/opt/jboss-as-7.1.1.Final | =20
File Name: workplace_application_di=
rectory.properties
Location: edu.harvard.i2b2.workplace/etc/spr=
ing/
WildFly 10 path: | = =20e= du.harvard.i2b2.workplace.applicationdir=3D/opt/wildfly-10.0.0.Final= /standalone/configuration/workplaceapp | =20
JBoss 7 path: | =20e= du.harvard.i2b2.workplace.applicationdir=3D/opt/jboss-as-7.1.1.Final= /standalone/configuration/workplaceapp | =20
File Name: build.properties
Location: edu.harvard.i2b2.workplace/
WildFly 10 path: | = =20j= boss.home=3D/opt/wildfly-10.0.0.Final | =20
JBoss 7 path: | =20j= boss.home=3D/opt/jboss-as-7.1.1.Final | =20
JIRA ISSUES:
 =
;[CORE-218] - New web service to retrieve the =
db lookup settings in the configuration files
&=
nbsp; [WEBCLIENT-191] - ADMIN: Add t=
he ability to view DB_LOOKUP settings for each cell
Release 1.7.08 added the ability to view current database connections d= efined 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 t= o 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. T= his page will display all the values in a table format.
=20The following screen shot shows all the entries in the CRC_DB_LOOKUP ta= ble.
=20 =20To 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. Th= e page will be updated to a form with fields to capture the information to = be stored in the DB_LOOKUP table.
=20 =20To 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 fil= ed in the DB_LOOKUP table. Make any changes and click on Save to sav= e your edits.
=20 =20 =20JIRA ISSUES:
 =
;[CORE-221] - Improvements to the queuing proc=
ess 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 cr= c.properties file.
=20In the Web Client, the status of a query can be seen in Previous Querie= s. 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_QUE= RY_INSTANCE table to see the queue information. The statuses and queue info= rmation were often ambiguous which would make it challenging to trouble sho= ot any issues.
=20To address this issue, new statuses have been added in Release 1.7.08. = These new statuses provide users with additional information that accuratel= y reflects the current status and location of the query. The new statuses a= re:
=20In addition to updating the status of queries, an additional feature wa= s added to the Web Client that makes these statuses visible to users. The q= uery status can be seen in Previous Queries as well as in Show Qu= ery Status.
=20 =20JIRA ISSUES: [CORE-226]= - New parameter to use temp table constraint instead of 'WITH' clause
= =20Large data warehouses that contain broad and deep ontologies run the ri= sk of CRC queries having a slow response time. In this release (1.7.08) a n= ew parameter has been added to the crc.properties file. This new par= ameter 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 t= he query to run more efficiently and process the request faster.
=20 Parameter Name: edu.harvard.i2b2.crc.setfinderquery.constraintlo=
gic
Located in: crc.properties file
Behavior:
Value | =20Behavior | =20
---|---|
TEMP or TEMPTABLES | =20Temp tables will be used when building q= ueries. | =20
WITH | =20Current query logic is used | =20
If the parameter is missing from the crc.properties file, the system wi= ll current query logic (WITH clause).
=20=20 | Important This change only affects SQ= L Server databases. Both PostgreSQL and Oracle do not have the capabilities= of using temp tables. They will continue to use the WITH clause. | =20
JIRA ISSUES: [WEBCLIEN= T-133] - Restrict ability to add Date Constraint if a panel contains an= y age concepts.
=20In the i2b2, the CRC will use the START_DATE in the OBSERVATION_FACT ta= ble when running a query with a date constraint defined on a panel. This ca= n present a problem if at least one of the items in the panel is an age con= cept and the patient demographics are stored in the PATIENT_DIMENSION table= . The problem is ages that are stored in the PATIENT_DIMENSION table will n= ot have a START_DATE and therefore the date constraint is not valid.
= =20General i2b2 users do not know whether or not an age has a start date a= nd 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 larg= er network in which some sites may store it in the PATIENT_DIMENSION and ot= hers in the OBSERVATION_FACT. This scenario will definitely result in misle= ading results and the user will be unaware of the discrepancy.
=20To 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 f= ollowing message will appear when attempting to set a date constraint on a = panel with an age concept: Date constraints are not allowed for age rel= ated concepts. This panel contains at least one age related concepts, there= fore a date constraint can not be set for this panel."
=20 =20JIRA ISSUES: [ WEBCLIE= NT-198] - Parameters/Configurations for Web Client
=20In 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 t= he login screens, default user id and password values, as well as how obfus= cated results display in the i2b2 Web Client.
=20File Name: i2b2_ui_config.j= s File Location: /webclient/js= -i2b2/
=20Parameter | =20Description | =20Default Value | =20
---|---|---|
titleLogoSrc | =20Logo that appears in toolbar when logged= into the i2b2 Web Client. | =20"assets/images/title.gif" | =20
loginHeaderText | =20Text in the header bar of the login box<= /td>=20 | "i2b2 Login" | =20
loginUsernameText | =20Text for the username input of the login= box. | =20"Username:" | =20
loginDefaultUsername | =20Default text inside the username input.<= /td>=20 | "demo" | =20
loginPasswordText | =20Text for the password input of the login= box. | =20"Password:" | =20
loginDefaultPassword | =20Default text inside the password input.<= /td>=20 | "demouser" | =20
loginHostText | =20Text for the PM cell dropdown of the log= in box. | =20"i2b2 Host:" | =20
obfuscatedDisplayNumber | =20The number to display after the plus/min=
us for obfuscated results. Please see the important note at end of t= his table. | =20
3 | =20
useFloorThreshold | =20If true, any result below floorTh=
resholdNumber shows as '{floorThresholdText} {floorThresholdNumber}' If= false, floor threshold will not be used when displaying values in t= he i2b2 Web Client. | =20
false | =20
floorThresholdNumber | =20Threshold for the low number of results<= /td>=20 | 10 | =20
floorThresholdText | =20Text that is prefixed before {floorThres= holdNumber} (include trailing space) | =20"Less Than " | =20
=20 | Important The calculation for the rea= l obfuscation value continues to be controlled by the server and is based o= n the value defined in the CRC properties file. The obfuscatedDisplayNum= ber parameter in the i2b2_ui_config.js simply defines what numbe= r to display to the user when viewing the query results. | =20
JIRA ISSUES: [CORE-227]= - Add ability to send parameters with string based variables as varchar in= stead of nvarchar
=20Prior to release 1.7.08, parameters are sent in as Unicode (nvarchar) i= nstead of varchar. SQL Server then has to explicitly convert the nvarchar t= o 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).
=20To address this issue, we have added a new connection parameter to be u= sed when i2b2 uses PreparedStatements to pass in string based variables in = SQL Server. The following connection parameter is to be added to the dataso= urce definition.
=20 Connection Parameter: connection-property name=3D"sendStringPara=
metersAsUnicode"
Added To: datasource definition
Behavi=
or:
Value | =20Behavior | =20
---|---|
false | =20String based variable will be sent as va= rchar | =20
true | =20Current logic is used; String based vari= able will be sent in Unicode (nvarchar) | =20
Example: <connect= ion-property name=3D"sendStringParametersAsUnicode" >false</connectio= n-property>
=20 =20JIRA ISSUES: [CORE-229]= - Provide updated JDBC drivers used by Oracle, PostgreSQL, and SQL Server<= /p>=20
Included in release 1.7.08 are updated JDBC drivers for Oracle, Postgre= SQL and SQL Server. The new version of JDBC drivers are optional and will n= ot be installed automatically.
=20=20 | Important Sites that choose to upgrad= e their JDBC drivers will be required to also updated the datasource files = for all of their cells. | =20
This section contains some general information and key points to keep i= n mind when updating your JDBC drivers.
=20Your current JDBC jar files reside in the following directories:
= =20There are three new jar files, one for each type of supported databases.=
=20A script to deploy the new jar files has been included in the 1.7.08 Re= lease. Once you have updated your server with the latest code you can run o= ne of the following commands to deploy the new jdbc jar files:
=20 Linux Command &nbs= p; ant copy_new_jdbc_jar | =20
Windows Command &n= bsp; %ANT_HOME%\bin\ant.bat copy_new_jdbc_jar | =20
=20 | Warning If you choose to install the = new JDBC jar files you also need to update your datasource files wit= h the new driver information. This needs to be done for each cell in the i2= b2 hive. | =20
Release Date: June 7, 2016
=20Release 1.7.07c does not include any server changes and therefore does n= ot affect SHRINE installations. This release does not need to be tested wit= h the latest version of the SHRINE Software.
=20i2b2 Release 1.7.07c contains changes to the following software compone= nts:
=20=20 | Important The Admin changes can be f= ound 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 include= d in this file. If you are upgrading from 1.7.07 then you do not need to up= date 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.= | =20
No changes to third party software are included in release 1.7.07c
= =20Release Date: March 1, 2016
=20Release 1.7.07b does not include any server changes and therefore does n= ot affect SHRINE installations. This release does not need to be tested wit= h the latest version of the SHRINE Software.
=20i2b2 Release 1.7.07b contains changes to the following software compone= nts:
=20=20 | Important The Admin changes can be f= ound 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 include= d in this file. If you are upgrading from 1.7.07 then you do not need to up= date 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.= | =20
No changes to third party software are included in release 1.7.07b
= =20Release Date: January 15, 2016
=20SHRINE Release 1.20.1 has been tested = with i2b2 1.7.07 Release and has been approved by the SHRINE = Team
=20i2b2 Release 1.7.07 contains changes to the following software componen= ts:
=20No changes to third party software are included in release 1.7.07
=20Release Date: August 12, 2015
=20i2b2 Release 1.7.06 contains changes to the following software componen= ts:
=20No changes to third party software are included in release 1.7.06
=20Release Date: May 6, 2015
=20i2b2 Release 1.7.05 contains changes to the following software componen= ts:
=20No changes to third party software are included in release 1.7.05
=20Release Date: November 13, 2014
=20i2b2 Release 1.7.04 contains changes to the following software componen= ts:
=20No changes to third party software are included in release 1.7.04
=20Release Date: August 28, 2014
=20i2b2 Release 1.7.03a contains changes to the following software compone= nts:
=20No changes to third party software are included in release 1.7.03a
= =20Release Date: August 20, 2014
=20i2b2 Release 1.7.03 contains changes to the following software componen= ts:
=20No changes to third party software are included in release 1.7.03
=20JIRA ISSUES: [CORE-135]=
=20In the i2b2 metadata table there are two columns (C_PATH and C_SYMBOL) t= hat 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 n= ow be populated with the appropriate data when creating a new container, fo= lder, term, or modifier from within the Edit Terms view.
=20JIRA ISSUES: [CORE-141]=
=20In the Edit Terms view users can create terms that have values associate= d to them. These values are stored in the C_METADATAXML column in the custo= m 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 wi= th carriage returns / line feeds. This change improves the way the metadata= xml if filed into the table by removing all line feeds from the data before= filing it into the C_METADATAXML column
=20Release Date: July 1, 2014
=20i2b2 Release 1.7.02 contains changes to the following software componen= ts:
=20No changes to third party software are included in release 1.7.02
=20JIRA ISSUES: [CORE-95] a= nd [WEBCLIENT-56]
=20In 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, user= s 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 i2b= 2 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.
=20=20 | 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 wi= ll need to contact their site administrator and follow the protocols establ= ished at their institution. This feature is only available f= or those users that log in with the standard i2b2 Authentication method. | =20
In the i2b2 Web Client, a new option called Change Password now a= ppears in the Web Client's toolbar.
=20 =20Clicking on Change Password will open the i2b2 Change Password= window.
=20 =20In the i2b2 Workbench, a new button labeled Password has been add= ed to the i2b2 desktop title bar.
=20 =20Clicking on Password will open the Set Password window.
=20 =20The functionality to change your password is the same regardless of whet= her you access the change password window from within the i2b2 Web Client o= r the workbench. There are basically three steps:
=20Once 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.
=20=20 | Note Once you change your password y= ou will need to log out of the Web Client or Workbench and log back in usin= g your new password. | =20
Release Date: February 4, 2014
=20i2b2 Release 1.7.01 contains changes to the following software component= s:
=20No changes to third party software are included in release 1.7.01
=20Release Date: December 20, 2013
=20i2b2 Release 1.7 contains changes to the following software components:=
=20In release 1.7 the i2b2 Server has been updated to use the follow= ing versions of third party software.
=20=20 | Warning Only the i2b2 Server was upg= raded to use the above versions of JBoss, Ant, and Axis2. The i2b2 Workbenc= h 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 co= mmons. Server edu.harvard.i2b2.server-common= p> Client edu.harvard.i2b2.common | =20
The temporal query is a new type of query introduced in re= lease 1.7. There are two components to these queries that make them a littl= e more complex than the type of queries available prior to 1.7 (classic i2b= 2 queries).
=20The first component to these queries is the list of events defined by th= e user.
=20The second component is the relationship between the events. This relati= onship is referred to a Temporal Relationship, which is best described as h= ow the different events relate in regards to the time in which the event(s)= occurred.
=20Users can also define a patient or event population in which they wish t= o run the temporal query against. This step is optional and is not required= in order to run the temporal query.
=20The 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 e= xisting Query Tool view has been modified to accommodate Temporal Queries w= hile a new view called Temporal Query Tool view has been created for the i2= b2 Workbench.
=20The new Temporal Query Tool view and the modifications to the existing Q= uery Tool view extend the query functionalities provided by the classic Que= ry Tool view.
=20It is important to note that while the manner in which users setup a tem= poral query is different in each of the clients the overall functionality i= s the same.
=20The following two sections will describe how to run Temporal Queries in = the i2b2 Web Client and the i2b2 Workbench.
=20In the i2b2 Web Client there are five basic steps in defining a tempo= ral query in the Query Tool view.
=20=20 | Note For detailed information about = creating Temporal Queries please see the Temporal Query help file located o= n-line from within the i2b2 Web Client. | =20
The first step is to change the Temporal Constraint to Define sequenc= e of Events.
=20 =20Once you have changed the Temporal constraint to be Define sequence o= f 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= .
=20 =20The events are the first component of a temporal query. There are no res= trictions on the number of events you wish to define. The only requirement = is that you have to define at least two events.
=20To define the events simply click on the Page selection box and s= elect Event 1 from the drop-down list.
=20 =20The groups and constraints for the events work in the same manner as the= y did for a traditional i2b2 query. Simply drag the items you want to inclu= de in Event 1 to the appropriate groups.
=20Once you have added your items to the groups you can click on the Pag= e selection box and select Event 2 from the drop-down list. This= will change the page to display the groups for Event 2.
=20If you need to add a third event you can click on the New Event butto= n located next to the Page selection box.
=20As stated earlier the second component of a temporal query is the relati= onship between the events (temporal relationship). In the i2b2 Web Client t= his 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.
=20The page will display as follows:
=20 =20In the Web Client running a query works the same regardless of whether o= r 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.
=20In the i2b2 Workbench there are three pages or steps in defining and run= ning a temporal query in the new Temporal Query Tool view.
=20Each page as well as defining constraints is further defined in the next= few sections.
=20=20 | 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. | =20
On this page you will define your population requirements.
=20 =20As stated earlier there are two components to a temporal query= ; (1) List of events and (2) the relationship between the events.
= =20The second page is where you will define both the events and their relat= ionship.
=20 =20On this page the name of the query will default and if you wish to renam= e 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.
=20 =20There are some minor differences in terminology or layout that needs to = be noted in this release note.
=20In the classic Query Tool view you can only define date constraints on t= he group / panel level. In the new Temporal Query TOol view you can now def= ine 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 gr= oups and the date constraint on the panel level will not be available for s= election.
=20If 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.
=20 =20The ability to exclude all items in a group does exist in the new Tempor= al Query Tool view. However, the method in which it is defined differs betw= een the classic Query Tool view and the Temporal Query Tool view.
=20In the existing Query Tool view ("Classic") the exclusion constra= int was defined by clicking on the button labeled Exclude.
=20 =20In the Temporal Query Tool view (New) the exclusion constraint wa= s rolled into the window for defining the Occurrence constraint.
=20 =20The Specify Occurrence Constraints windows will open when you cli= ck on the box that displays the occurrence constraint. To set the exclusion= constraint you need to select "=3D 0 (No Occurrences)" from the drop-down = list.
=20 =20The above option is equivalent to the Exclude feature in the clas= sic Query Tool view.
=20New 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 ca= lled 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 disp= lay the drop-down list. Once you select the user and click on OK, th= e Previous Queries view will refresh and display only those previous querie= s created by the selected user.
=20 =20=20 | Important In i2b2 only managers are = allowed to view queries for another user, therefore this feature is only av= ailable 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 i= nactive and unavailable for selection. | =20
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 Term= s view. Users can search any of the three levels;
=20Users can now retrieve the next or previous grouping of previous queries= by the date in which the query was created.
=20 =20The Previous button () will retrieve the group of previous queries that occ= ur prior to the date displayed in the date / time field.
=20The Next button () will retrieve the group of previous queries that occur after= the date displayed in the date / time field.
=20A new cell called the Identity Management (IM) Cell was developed in rel= ease 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.= p>=20
The full functionality of the IM cell will be developed in stages. The i= nitial framework and key services are released as part of the 1.7 release. = Some of the key features being released in 1.7 are:
=20In addition to the above features, the i2b2 Worbench (eclipse client) ha= s two new views that were created to support the new IM cell. These new vie= ws, called Patient Mapping and Admin Tool are further defined= in the following two sections called Patient Mapping View and Ad= min Tool View.
=20The Managers Tool view was developed in release 1.7 and works in = conjunction with the IM Cell. It currently has two main functions.
=20=20 | Important If you are using the IM ce= ll and your patient identifiers are encyrpted the you need to set the Proje= ct key in the IM cell. It is important to note that if you restart your i2b= 2 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 th= e i2b2 demo project is: i2b2demodatakey1 In the VM image yo= u need to log into the i2b2 Workbench as the i2b2 Admin user. User ID: i2b2 | =20
Patient Sets View=20
In release 1.7 a new view called Patient Sets was created. This n=
ew 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 d=
isplays 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 patie=
nt. A new view called Find in Workplace was created in release 1.7. T=
his view is very similar to the Find Terms view except it will searc=
h the Workplace view instead of the Navigate Terms view. A new feature called Jump to Term in Tree has been added to the <=
i>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. S=
electing "Jump to Term in Tree" from the pop-up menu will bring the Navi=
gate Terms view into focus and the hierarchical tree will automatically=
open to the location of the term selected in the Find Terms view.=
p>=20
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/ The ability to use a PostgreSQL database as an i2b2 database has been ad=
ded to release 1.7. Both the create and insert data database scripts for Po=
stgreSQL are included in this release. The following new tables were created as part of the new IM cell. A new column called Project_ID has been added to both the PATI=
ENT_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 pr=
oject a patient is part of. The PATIENT_MAPPING table in the CRC has been updated to include =
the following: Demo data has been added to all of the new IM tables except the AUDIT ta=
ble. This IM data was added to provide examples for using the new IM cell.<=
/p>=20
The i2b2 database scripts have been updated to include the table creatio=
n and data insert scripts for a PostgreSQL database. The i2b2 source code is licensed under the i2b2 Software License 2.1. Th=
is includes but is not limited to all code in the edu.harvard.i2b2.* packag=
e namespace. Microsoft, Windows, Windows 7, Windows Server 2003 and 2008 are either r=
egistered trademarks or trademarks of Microsoft Corporation in the United S=
tates 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.Workplace Find View
=
=20
Find Terms: New feature call=
ed "Jump to Term in Tree"
=20
OpenEMPISupport
=20
PostgreSQL Database Support<=
/h3>=20
Data: New Tables created fo=
r the IM Cell
=20
=20
=20
=20
Table Name =20
Description =20
=20
=20
IM_MPI_DEMOGRAPHICS =20
Contains General demographic information=
for the patients. =20
=20
=20
IM_MPI_MAPPING =20
Maps the patient"s i2b2 number an=
d the local MRN. =20
=20
=20
IM_PROJECT_SITES =20
Contains information about the different=
sites (Source Systems). =20
=20
=20
IM_PROJECT_PATIENTS =20
Stores the patients that are part of a p=
roject(s). =20
=20
=20
IM_AUDIT =20
Stores the audit details of patients acc=
essed in the IM cell. This includes; the user, site, and project requesting=
the access as well as the date in which it was accessed. =20
Data: New Columns added =
to support IM cell
=20
Data: Improved Patient Mappin=
g Data
=20
=20
=20
=20
=20
=20
=20
Important =20
The mapping information add=
ed to the CRC and IM tables is strictly for demonstration purposes and does=
NOT contain real patient information.New PostgreSQL Databa=
se Scripts
=20
=20
Licensing
=20
Trademarks
=20