Last Updated: 05/26/2011

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From: Wei,Xintao Sent: Thursday, May 26, 2011 3:04 PM To: i2b2 AUG Members
Subject: add user to project
Hi,
I2B2 1.5.2 has been installed on Windows server 2008.
Errors were reported when I added users to I2B2 demo project:
Error:
14:51:19,377 ERROR [ServicesHandler] not updated, does it exist?
14:51:19,377 ERROR [STDERR] edu.harvard.i2b2.common.exception.I2B2DAOException: not udated, does it exist?
14:51:19,378 ERROR [STDERR] at edu.harvard.i2b2.pm.delegate.ServicesHandler.execute(Unknown Source)
14:51:19,378 ERROR [STDERR] at edu.harvard.i2b2.pm.delegate.ServicesHandler.runDeleteParam(Unknown Source)
14:51:19,378 ERROR [STDERR] at edu.harvard.i2b2.pm.delegate.ServicesHandler.execute(Unknown Source)
14:51:19,379 ERROR [STDERR] at edu.harvard.i2b2.pm.ws.ExecutorRunnable.run(Unknown Source)
14:51:19,379 ERROR [STDERR] at java.lang.Thread.run(Thread.java:595)
Even though the user has no problem to use I2B2.
Any suggestions?
Xintao


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From: Phillips, Lori C. Sent: Thursday, May 26, 2011 1:07 PM To: Lusted, Jeff; i2b2 AUG Members
Subject: PDO
xsd/hive/pdo_1.1 is the latest and most current

From: Lusted, Jeff Sent: Thursday, May 26, 2011 12:56 PM To: i2b2 AUG Members
Subject: PDO
Hi!
I notice in the i2b2 distribution for v1.5.2, within the edu.harvard.i2b2.xml project, there are various versions of different objects...
I'm interested in studying the PDO. Which should I concentrate upon: xsd/hive/pdo or xsd/hive/pdo_1.1?
Regards
Jeff
Jeff Lusted, Senior Programmer (RCS, IT Services) University of Leicester Mob: 07941599062
Elite Without Being Elitist
Times Higher Awards Winner 2007, 2008, 2009, 2010


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From: Wei,Xintao Sent: Thursday, May 26, 2011 11:45 AM To: Mendis, Michael E.; i2b2 AUG Members
Subject: i2b2 workbench
Dear Mike,
It is about the "set value" feature using text. I will create a ticket as you described.
Thank you!
Xintao

From: Mike Mendis Sent: Thursday, May 26, 2011 11:36 AM To: Wei,Xintao; i2b2 AUG Members
Subject: i2b2 workbench
Thanks! The best would be to create a ticket in the jira bug tracker (jira.i2b2.org) and post the bug and the bugfix.
What was the bug?
Thanks again
mike

On 5/26/11 10:38 AM, Wei,Xintao wrote:
Hi,
If I fixed a i2b2 workbench bug, what do I need to do?
Thank you!
Xintao


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From: Phillip Reeder Sent: Thursday, May 26, 2011 11:24 AM To: i2b2 AUG Members
Subject: Issue with Query by Age at Visit
On 1.6, I tried to run a query against the demodata and got an error about a table not existing. I took a look at it and noticed that the schema name is hard coded into the c_dimcode.
For example:
((select birth_date from i2b2demodata.patient_dimension where patient_num = i2b2demodata.visit_dimension.patient_num) + (365.25 * 10))
I fixed it for me by just doing a replace on the dimcode for i2b2demodata with my schema name, but I'll have to do that for each and every project.
Phillip Reeder
Manager, Systems Analyst Services
The University of Texas Health Science Center at Houston Center for Clinical and Translational Sciences School of Biomedical Informatics


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From: Phillips, Lori C. Sent: Wednesday, May 25, 2011 2:04 PM To: Phillip Reeder Cc: i2b2 AUG Members
Subject: i2b2 1.6 and Patient_Dimension
Phillip, This feature is available in the 'Age at visit' and 'Age' metadata folders. Beyond that, I dont know if the demo data will change to accommodate this feature.
Just a guess on my part, but maybe you need an index on the pat_dim table to support the query? I dont know if anyone is using this feature.
Lori

From: Phillip Reeder Sent: Wednesday, May 25, 2011 12:35 PM To: Phillips, Lori C.
Subject: i2b2 1.6 and Patient_Dimension
Got it. Having some performance issues though where it's taking a long time for the query to run on our oracle server. Do you know if anyone else is using that feature yet? The demodata that we have loaded still had the gender, race, etc loaded into the observation_fact.
Phillip

From: Phillips, Lori C. Sent: Tuesday, May 24, 2011 2:55 PM To: Phillip Reeder
Subject: i2b2 1.6 and Patient_Dimension
Phillip,
I am reading between the lines of your question.
As long as the patient_dim table has (race_cd) populated you do not have to add anything extra to your obs_fact table.
The (patient) set finder query becomes:
select patient_num from observation_fact where patient_num in
(select patient_num from patient_dimension where race_cd = 'white')
In other words, no need to add a race_cd column to obs_Fact.

Lori

From: Phillips, Lori C. Sent: Tuesday, May 24, 2011 3:42 PM To: Phillip Reeder; i2b2 AUG Members
Subject: i2b2 1.6 and Patient_Dimension
Definitely; the metadata has to be specified in a certain way to make this happen. This document explains. (see page 6)
For the example where we search by 'race_cd = white' the metadata entry would have:
c_facttablecolumnname = patient_num c_tablename = patient_dimension c_columnname = race_cd c_operator = '=' c_dimcode = white

From: Phillip Reeder Sent: Tuesday, May 24, 2011 3:29 PM To: i2b2 AUG Members
Subject: i2b2 1.6 and Patient_Dimension
Is it possible to use the race_cd, language_cd, religion_cd, etc. columns from the patient_dimension in a query? I'm working on loading our data into the 1.6 schema and wanted to verify the functionality before I create observation_fact rows from all the columns.
Thanks,
Phillip Reeder Manager, Systems Analyst Services
The University of Texas Health Science Center at Houston Center for Clinical and Translational Sciences School of Biomedical Informatics


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From: Audrey Hureau Sent: Wednesday, May 25, 2011 10:33 AM To: i2b2 AUG Members
Subject: Users management
Hello everyone,
I am wondering what kind of parameter can we add as project user parameters? Besides, I would like to know if it is possible to give access to one specific user to specific data from the ontology. For example, to run queries, a user specialized in the cardiac area doesn't need to access to dermatological data. I don't know if I am clear.
Thank you for help.
Audrey


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From: Wei,Xintao Sent: Tuesday, May 24, 2011 1:13 PM To: Phillips, Lori C.; i2b2 AUG Members
Subject: workbench in eclipse
Dear Lori,
You are right. My execution order is wrong! Should be clean first then build-all.
Thank you very much!
Xintao

From: Phillips, Lori C. Sent: Tuesday, May 24, 2011 1:09 PM To: Wei,Xintao; i2b2 AUG Members
Subject: workbench in eclipse
BuildAssist automatically builds all these folders. Look at BuildAssist/build.xml target = build-all
1.) it builds edu.harvard.i2b2.common
which creates dist/i2b2Common-core.jar
Then it copies this file to a genlib dir in each of the projects.
Sometimes the build gets out of sync and you need to do a clean-all followed by a build-all.
See target execution order
Lori

From: Wei,Xintao Sent: Tuesday, May 24, 2011 12:57 PM To: i2b2 AUG Members
Subject: workbench in eclipse
The errors were reported after running ant-build and refresh all the projects:
Description Resource Path Location Type
Project 'edu.harvard.i2b2.common' is missing required source folder: 'gensrc' edu.harvard.i2b2.common Build path Build Path Problem
Project 'edu.harvard.i2b2.eclipse.plugins.analysis' is missing required library: 'genlib/i2b2Commoncore.jar' edu.harvard.i2b2.eclipse.plugins.analysis Build path Build Path Problem
Project 'edu.harvard.i2b2.eclipse.plugins.explorer' is missing required library: 'genlib/i2b2Commoncore.jar' edu.harvard.i2b2.eclipse.plugins.explorer Build path Build Path Problem
Project 'edu.harvard.i2b2.eclipse.plugins.ontology' is missing required library: 'genlib/i2b2Commoncore.jar' edu.harvard.i2b2.eclipse.plugins.ontology Build path Build Path Problem
Project 'edu.harvard.i2b2.eclipse.plugins.previousQuery' is missing required library: 'genlib/i2b2Common-core.jar' edu.harvard.i2b2.eclipse.plugins.previousQuery
Build path Build Path Problem
Project 'edu.harvard.i2b2.eclipse.plugins.query' is missing required library: 'genlib/i2b2Commoncore.jar' edu.harvard.i2b2.eclipse.plugins.query Build path Build Path Problem
Project 'edu.harvard.i2b2.eclipse.plugins.workplace' is missing required library: 'genlib/i2b2Commoncore.jar' edu.harvard.i2b2.eclipse.plugins.workplace Build path Build Path Problem
Project 'edu.harvard.i2b2.eclipse' is missing required library: 'genlib/i2b2Common-core.jar' edu.harvard.i2b2.eclipse Build path Build Path Problem I don't have "gensrc" in common folder. All other "gensrc" folders are empty.
I am using eclipse 3.5 with java 1.6. Did I miss any eclipse setups?
Thank you!
Xintao


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From: Davis, Michael (Oncology) Sent: Tuesday, May 24, 2011 8:11 AM To: Yves Thorrez; Travis Nagler; i2b2 AUG Members
Subject: Any 1.5.2 installs around?
Travis,
This is definitely good advice from Yves (thanks!!), here's were my steps to getting it to work
To run the webclient
Install XAMPP http://www.apachefriends.org/en/xampp.html
YOU MUST Enable curl (Client for URLs)
To enable curl library with XAMPP we need to modify the php.ini files in our xampp folder.
1) Locate the following files: C:\Program Files\xampp\apache\bin\php.ini
C:\Program Files\xampp\php\php.ini
C:\Program Files\xampp\php\php4\php.ini
2) Uncomment the following line on your php.ini file by removing the semicolon.
;extension=php_curl.dll
3) Restart your apache server.
4) Check your phpinfo if curl was properly enabled.

Regards,
Michael

From: Yves Thorrez Sent: Tuesday, May 24, 2011 2:04 AM To: Travis Nagler; i2b2 AUG Members
Subject: Any 1.5.2 installs around?
Hi Travis,
This one seems to bite a lot of folks. Here's what I suggested to Michael a few days ago. Hope it helps.
Yves

From: Yves Thorrez Sent: vrijdag 20 mei 2011 8:51 To: 'Davis, Michael (Oncology)'; i2b2 AUG Members
Subject: Web client not connecting
Michael,
You may want to check if cURL is configured in your installation. I use XAMPP in my local installation, where it's just a matter of uncommenting a line in php.ini. Otherwise, you may find this link useful:
http://www.tonyspencer.com/2003/10/22/curl-with-php-and-apache-on-windows/

Regards,
Yves
Yves Thorrez
Medische Informatieverwerking
Laarbeeklaan 101 - 1090 Brussel
www.uzbrussel.be

From: Davis, Michael (Oncology) Sent: donderdag 19 mei 2011 17:02 To: i2b2 AUG Members
Subject: Web client not connecting
I've installed i2b2 onto my local system and got the workbench working properly. However I'm having problems with getting the web client working using Apache 2.2. After installing the web client, it brings up the login dialog just fine but upon trying to login it gives we the following message "Your account does not have access to any i2b2 projects". I'm using the standard login accounts. Is there an easy way to debug the web client to see if it's communicating with my JBoss services (running my on Jboss 8080)?

From: Travis Nagler Sent: dinsdag 24 mei 2011 0:39 To: i2b2 AUG Members
Subject: Any 1.5.2 installs around?
We are installing version 1.5.2. I have been able to upload the data fine, the required software is installed with no apparent problems (Ant, JBoss, etc.), and I have followed the given instructions to the letter.
However, when I go to the webclient login page (for us, it's http://i2b2dev02.ucdmc.ucdavis.edu/admin/) and login using username "i2b2" and password "demouser", I get an error saying "Your account does not have access to any i2b2 accounts."
I have gone over the details, everything has been checked and rechecked, I have even received some other, much appreciated individual help for config files, etc. The data was loaded without error using the given i2b2 scripts, nothing was manually inputted. The whole process went very smoothly, except for the fact that I can't login as an admin user.
If you have any suggestions, I would greatly appreciate anything at this point. And if someone does have a running version of 1.5.2, I would VERY much appreciate hearing from you.
Thanks,
Travis
Travis H. Nagler
Senior Database Programmer
American Burn Assoc. - Data Coordinating Center UC Davis Division of Burn Surgery UC Davis Health System 2921 Stockton Blvd., Suite 1470 Sacramento, CA, 95817


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From: Michael.C.Ford Sent: Monday, May 23, 2011 7:07 PM To: Jeremy.Nix Cc: i2b2 AUG Members
Subject: Reset user id - member
Thanks for the response problem is in PM_USER_PARAMS I have zero records. none at all.

Jeremy Nix 05/23/2011 03:52 AM To Michael C Ford/CA/KAIPERM beninato, i2b2 AUG Members
Subject Reset user id – member
User lockout information is stored in pm_project_user_params. To unlock, just execute this:
DELETE FROM pm_project_user_params WHERE user_id=[your user] AND param_name_cd='LOCKEDOUT'
As for your log entries. That is simply a debug statement and can be ignored. You can adjust logging verbosity by editing the log4j file heJBOSS_HOME\server\default\conf\jboss-log4j.xml.
Jeremy Nix
Senior Application Developer
Cincinnati Children's Hospital Medical Center

On 05/20/2011 06:00 PM, Michael.C.Ford wrote:
I checked the PM_USER_DATA there is only status-cd and it's "A" I cleared PM_USER_SESSION and restarted but I got the same result.
looking at the log I find a lot of entries like the following 2011-05-20 13:23:17,314 DEBUG [org.springframework.jdbc.core.StatementCreatorUtils] Setting SQL statement parameter value: column index 1, parameter value [CRC], value class [java.lang.String], SQL type unknown

Peter Beninato 05/19/2011 11:24 AM To Michael C Ford/CA/KAIPERM cc
Subject Reset user id - member
You might want to look at some of the user tables in the PM schema, I know there is an "active" flag, maybe it is set to "LOCK"?

From: Michael.C.Ford Sent: Thursday, May 19, 2011 11:20 AM To: Mike Mendis Cc: i2b2 AUG Members
Subject: Reset user id - member
This is on Oracle

Mendis, Michael E. 05/19/2011 09:38 AM To Michael C Ford/CA/KAIPERM i2b2 AUG Members
Subject Reset user id - member
This is i2b2 1.4? If so than the lockout I was talking about was notimplemented until 1.5.
I am wondering if the lockout is on the database side with the database user.Is this a sql server or oracle db?
thanks
mike

From: Michael.C.Ford Sent: Thu 5/19/2011 12:15 PMTo: Mendis, Michael E.Cc: i2b2 AUG Members
Subject: Reset user id - member
I missed something.I clicked users -> the user ID but I did not find any parameters.
or is that the empty block that has Name, Datatype Value ?

Mike Mendis 05/18/2011 11:20 AM To Michael C Ford/CA/KAIPERM, i2b2 AUG Members cc
Subject: Reset user id - member
If you logon to the pm admin, than in the left navigation click on ManagedProjects, find the proiect that user is in, click on Users than click onthe user, last click on params. You should see a param liked PM_LOCKED_OUT, either clear it or delete it. Than try to login again.
What happened is this user is a obfuscated user and tried to run the samequery more than 7 times. And doing so you can figure out what the real patient count is by the way of the obfuscator works. So this lockout is done to prevent that.
mike

On 5/18/11 12:42 PM, Michael.C.Ford wrote:
I am rebuilding an I2b2 region.
Currently I am getting the following error message.edu.harvard.i2b2.common.exception.I2B2DAOException: LOCKEDOUT error: Useraccount locked on how do I unlock a user account?
I also see an error org.apache.axis2.AxisFault: Two services can not have same name, aservice with anonService171170011305149076532 already exists in the system but I don't know what service this is in reference to and if this is a real issue.


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From: Travis Nagler Sent: Monday, May 23, 2011 6:39 PM To: i2b2 AUG Members
Subject: Any 1.5.2 installs around?
We are installing version 1.5.2. I have been able to upload the data fine, the required software is installed with no apparent problems (Ant, JBoss, etc.), and I have followed the given instructions to the letter.
However, when I go to the webclient login page (for us, it's http://i2b2dev02.ucdmc.ucdavis.edu/admin/) and login using username "i2b2" and password "demouser", I get an error saying "Your account does not have access to any i2b2 accounts."
I have gone over the details, everything has been checked and rechecked, I have even received some other, much appreciated individual help for config files, etc. The data was loaded without error using the given i2b2 scripts, nothing was manually inputted. The whole process went very smoothly, except for the fact that I can't login as an admin user.
If you have any suggestions, I would greatly appreciate anything at this point. And if someone does have a running version of 1.5.2, I would VERY much appreciate hearing from you.
Thanks,
Travis
Travis H. Nagler
Senior Database Programmer
American Burn Assoc. - Data Coordinating Center
UC Davis Division of Burn Surgery
UC Davis Health System
2921 Stockton Blvd., Suite 1470
Sacramento, CA, 95817 http://www.ucdmc.ucdavis.edu

From: Jeremy Nix To: Michael.C.Ford Cc: beninato, i2b2 AUG Members Date: 05/23/2011 03:52 AM
Subject: Reset user id - member
User lockout information is stored in pm_project_user_params. To unlock, just execute this:
DELETE FROM pm_project_user_params WHERE user_id=[your user] AND param_name_cd='LOCKEDOUT'
As for your log entries. That is simply a debug statement and can be ignored. You can adjust logging verbosity by editing the log4j file heJBOSS_HOME\server\default\conf\jboss-log4j.xml.
Jeremy Nix
Senior Application Developer
Cincinnati Children's Hospital Medical Center

On 05/20/2011 06:00 PM, Michael.C.Ford wrote:
I checked the PM_USER_DATA there is only status-cd and it's "A" I cleared PM_USER_SESSION and restarted but I got the same result.
looking at the log I find a lot of entries like the following 2011-05-20 13:23:17,314 DEBUG [org.springframework.jdbc.core.StatementCreatorUtils] Setting SQL statement parameter value: column index 1, parameter value [CRC], value class [java.lang.String], SQL type unknown

Peter Beninato 05/19/2011 11:24 AM To Michael C Ford/CA/KAIPERM cc
Subject Reset user id - member
You might want to look at some of the user tables in the PM schema, I know there is an "active" flag, maybe it is set to "LOCK"?

From: Michael.C.Ford Sent: Thursday, May 19, 2011 11:20 AM To: Mike Mendis Cc: i2b2 AUG Members Subject: Reset user id - member
This is on Oracle

Mendis, Michael E. 05/19/2011 09:38 AM To Michael C Ford/CA/KAIPERM i2b2 AUG Members
Subject Reset user id - member
This is i2b2 1.4? If so than the lockout I was talking about was notimplemented until 1.5.
I am wondering if the lockout is on the database side with the database user.Is this a sql server or oracle db?
Thanks
mike

From: Michael.C.Ford Sent: Thu 5/19/2011 12:15 PM To: Mendis, Michael E.Cc: i2b2 AUG Members
Subject: Reset user id - member
I missed something.I clicked users -> the user ID but I did not find any parameters.
or is that the empty block that has Name, Datatype Value ?

Mike Mendis 05/18/2011 11:20 AM To Michael C Ford/CA/KAIPERM, i2b2 AUG Members
SubjectReset user id - member
If you logon to the pm admin, than in the left navigation click on ManagedProjects, find the proiect that user is in, click on Users than click onthe user, last click on params. You should see a param liked PM_LOCKED_OUT, either clear it or delete it. Than try to login again.
What happened is this user is a obfuscated user and tried to run the samequery more than 7 times. And doing so you can figure out what the real patient count is by the way of the obfuscator works. So this lockout is done to prevent that.
mike

On 5/18/11 12:42 PM, Michael.C.Ford wrote:
I am rebuilding an I2b2 region.
Currently I am getting the following error message.edu.harvard.i2b2.common.exception.I2B2DAOException:
LOCKEDOUT error : Useraccount locked on how do I unlock a user account ?
I also see an error org.apache.axis2.AxisFault: Two services can not have same name, aservice with anonService171170011305149076532 already exists in the system
but I don't know what service this is in reference to and if this is a real issue.


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From: Murphy, Shawn N. Sent: Friday, May 20, 2011 4:07 PM To: Dan Connolly; Phillips, Lori C. Cc: i2b2 AUG Members
Subject: long-running queries trigger crazy loop (or is it empty item_key?)
I think it should be OK. Oktousevalues is either "Y", or anything else (which is basically a No). The anything else in this case is a message that explains the why not part.
Thanks, Shawn.

From: Dan Connolly Sent: Friday, May 20, 2011 4:00 PM To: Phillips, Lori C. Cc: i2b2 AUG Members
Subject: long-running queries trigger crazy loop (or is it empty item_key?)
We didn't make that up; that's the way the Demodata comes out of the box:
edu.harvard.i2b2.data/Release_1-4/NewInstall$ grep 'The units in this set of tests are notequivalent' Metadata/scripts/oracle/labs_insert_data.sql |head -1
VALUES(4, '\i2b2\Labtests\LAB(LLB6) Coagulation(LLB14) Routine Coagulation\FIB\','Fibrinogen (Group:FIB)', 'N', 'FA', NULL, 'LOINC:3255-7', '<?xmlversion="1.0"?><ValueMetadata><Version>3.02</Version><CreationDateTime>04/15/200701:22:11</CreationDateTime><TestID>FIB</TestID><TestName>Fibrinogen</TestName><DataType>PosInteger</DataType><CodeType>GRP</CodeType><Loinc>3255-7</Loinc><Flagstouse>HL</Flagstouse><Oktousevalues>The units in this set of tests are not equivalent, thereforenumeric comparisons between the tests are notpossible.</Oktousevalues><MaxStringLength></MaxStringLength><LowofLowValue></LowofLowValue><HighofLowValue></HighofLowValue><LowofHighValue></LowofHighValue><HighofHighValue></HighofHighValue><LowofToxicValue></LowofToxicValue><HighofToxicValue></HighofToxicValue><EnumValues></EnumValues><CommentsDeterminingExclusion><Com></Com></CommentsDeterminingExclusion><UnitValues><NormalUnits>mg/dl</NormalUnits><NormalUnits>mg</NormalUnits><NormalUnits>%</NormalUnits><EqualUnits>mg/dl</EqualUnits><EqualUnits>mg</EqualUnits><EqualUnits>%</EqualUnits><ExcludingUnits></ExcludingUnits><ConvertingUnits><Units></Units><MultiplyingFactor></MultiplyingFactor></ConvertingUnits></UnitValues><Analysis><Enums /><Counts /><New /></Analysis></ValueMetadata>', 'concept_cd','concept_dimension', 'concept_path', 'T', 'like', '\i2b2\Labtests\LAB(LLB6) Coagulation(LLB14) Routine Coagulation\FIB\', NULL, 'Labtests \ Coagulation \ Routine Coagulation \Fibrinogen (Group:FIB)', TO_DATE('17/04/2006 12:00:00 AM','DD/MM/YYYY HH12:MI:SS PM'),TO_DATE('17/04/2006 12:00:00 AM','DD/MM/YYYY HH12:MI:SS PM'), TO_DATE('17/04/2006 12:00:00AM','DD/MM/YYYY HH12:MI:SS PM'), 'RPDR', NULL);edu.harvard.i2b2.data/Release_1-4/NewInstall$ grep 'The units in this set of tests are not
equivalent' Metadata/scripts/oracle/labs_insert_data.sql |wc123 9676 218814

On Fri, 2011-05-20 at 13:49 -0400, Phillips, Lori C. wrote:
I dont know if this is causing the problem or not, but your <ValueMetadata> , <Oktousevalues> is not going to be recognized in its current state.
<Oktousevalues>
Indicates if it is OK to use values (Y/N).
Y indicates value is a number (numeric types)
N or empty indicates value is not a number


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From: Phillips, Lori C. Sent: Friday, May 20, 2011 1:50 PM To: Dan Connolly Cc: i2b2 AUG Members
Subject: long-running queries trigger crazy loop (or is it empty item_key?)
I dont know if this is causing the problem or not, but your <ValueMetadata> , <Oktousevalues> is not going to be recognized in its current state.
<Oktousevalues>
Indicates if it is OK to use values (Y/N).
Y indicates value is a number (numeric types)
N or empty indicates value is not a number

From: Dan Connolly Sent: Thursday, May 19, 2011 12:43 PM To: Phillips, Lori C. Cc: i2b2 AUG Members
Subject: long-running queries trigger crazy loop (or is it empty item_key?)
I can't seem to drag the concept xml out of the browser window (firefox on Ubuntu linux).
What I can see in the XML Message History looks right:
<message_body>
<ns3:concepts>
<concept><level>5</level><key>\\i2b2\i2b2\Flowsheet\MODEL\ED I&O T:16003\INTAKE GROUP G:50 I#1
\ORAL INTAKE M:51 I#1\</key><name>001- #51 P.O. [735,227 facts; 32,645 patients]</name><synonym_cd>N</synonym_cd><visualattributes>LA </visualattributes><totalnum>0</totalnum><basecode>KUH|FLO_MEAS_ID:51</basecode><metadataxml>
<ValueMetadata> <Version>3.02</Version><CreationDateTime>26-APR-11</CreationDateTime><TestID>KUH|FLO_MEAS_ID:51</TestID><TestName>001- #51 P.O.</TestName><DataType>PosFloat</DataType><CodeType>GRP</CodeType><Loinc>Dummy2019-8@@</Loinc><Flagstouse>HL</Flagstouse><Oktousevalues>The units in this set of tests are not equivalent,
therefore numeric comparisons between the tests are not possible.</Oktousevalues><MaxStringLength /><LowofLowValue /><HighofLowValue /><LowofHighValue /><HighofHighValue /><LowofToxicValue /><HighofToxicValue /><EnumValues /><CommentsDeterminingExclusion>
<Com /> </CommentsDeterminingExclusion>
<UnitValues> <NormalUnits>mL</NormalUnits><ConvertingUnits>
<Units /><MultiplyingFactor /> </ConvertingUnits> </UnitValues>
<Analysis><Enums /><Counts /><New /> </Analysis>
</ValueMetadata></metadataxml><facttablecolumn>concept_cd</facttablecolumn><tablename>concept_dimension</tablename><columnname>concept_path</columnname><columndatatype>T</columndatatype><operator>like</operator><dimcode>\i2b2\Flowsheet\MODEL\ED I&O T:16003\INTAKE GROUP G:50 I#1
\ORAL INTAKE M:51 I#1\</dimcode>
<tooltip>001- #51 P.O.</tooltip></concept>

On Thu, 2011-05-19 at 09:06 -0400, Phillips, Lori C. wrote:
Dan
When you drag the concept from the Navigate terms to the Query Tool panel
there is XML that is being dragged over with the concept. What ends up as item_key
originates there as '<key>'. You can also drop the concept xml into a text document.
This xml should look something like this:
<?xml version="1.0" encoding="UTF-8" standalone="yes"?> <ns2:plugin_drag_drop xmlns:ns2="http://www.i2b2.org/xsd/hive/plugin/" xmlns:ns4 ="http://www.i2b2.org/xsd/hive/msg/1.1/" xmlns:ns3="http://www.i2b2.org/xsd/cell/crc/psm/1.1/" xmlns:ns5 ="http://www.i2b2.org/xsd/hive/msg/result/1.1/" xmlns:ns6="http://www.i2b2.org/xsd/cell/ont/1.1/" xmlns:ns7 ="http://www.i2b2.org/xsd/cell/crc/psm/querydefinition/1.1/">
<ns6:concepts>
<concept> <level>2</level> <key>\\i2b2_DIAG\i2b2\Diagnoses\Circulatory system (390-459)\</key> <name>Circulatory system</name> <synonym_cd>N</synonym_cd> <visualattributes>FA</visualattributes> <totalnum>66</totalnum> <tooltip>Diagnoses \ Circulatory system</tooltip>
</concept> </ns6:concepts> </ns2:plugin_drag_drop>
If you send us the xml we may be able to figure out why <item_key> is empty.
Thanks
Lori

From: Dan Connolly Sent: Wednesday, May 18, 2011 3:58 PM To: i2b2 AUG Members
Subject: long-running queries trigger crazy loop (or is it empty item_key?)
I'm not sure long-running is the issue.
I discovered the item_key element in the query definition is empty. I checked the metadata tables and all looks OK there.
Any clues how the item_key could come to be empty? The item_name looks right:
<query_definition><query_name>001- #51 P.O. [@14:54:48</query_name><specificity_scale>0</specificity_scale><panel>
<panel_number>1</panel_number><invert>0</invert><total_item_occurrences>1</total_item_occurrences><item>
<hlevel>5</hlevel><item_name>001- #51 P.O. [735,227 facts; 32,645
patients]</item_name> <item_key /><tooltip>001- #51 P.O.</tooltip><class>ENC</class><constrain_by_date></constrain_by_date><item_icon>LA</item_icon><item_is_synonym>false</item_is_synonym>
</item></panel></query_definition>

On Wed, 2011-05-18 at 13:40 +0000, Dan Connolly wrote:
I gather that i2b2 handles queries that take more than a few seconds differently. Can anybody point me to documentation on the difference? Or just explain it?
We're trying to test performance of i2b2 using solid state disks, but long-running queries are going haywire. The client goes in some sort of loop, making network requests one after the other, and I'm struggling to make sense of the jboss logs.
2011-05-18 08:14:10,957 INFO [edu.harvard.i2b2.crc.dao.DataSourceLookupHelper]Located DataSource for hiveId=[i2b2demo] projectId=[/BlueHeron/]2011-05-18 08:14:10,957 INFO [edu.harvard.i2b2.crc.dao.OracleDAOFactory] Usingdatasource java:QueryToolBlueHeronDS2011-05-18 08:14:10,975 INFO [edu.harvard.i2b2.crc.dao.DataSourceLookupHelper]Located DataSource for hiveId=[i2b2demo] projectId=[/BlueHeron/]2011-05-18 08:14:10,975 INFO [edu.harvard.i2b2.crc.dao.OracleDAOFactory] Usingdatasource java:QueryToolBlueHeronDS2011-05-18 08:14:11,274 INFO [edu.harvard.i2b2.crc.dao.DataSourceLookupHelper]Located DataSource for hiveId=[i2b2demo] projectId=[/BlueHeron/]2011-05-18 08:14:11,274 INFO [edu.harvard.i2b2.crc.dao.OracleDAOFactory] Usingdatasource java:QueryToolBlueHeronDS2011-05-18 08:14:11,379 INFO [edu.harvard.i2b2.crc.dao.DataSourceLookupHelper]Located DataSource for hiveId=[i2b2demo] projectId=[/BlueHeron/]2011-05-18 08:14:11,379 INFO [edu.harvard.i2b2.crc.dao.OracleDAOFactory] Usingdatasource java:QueryToolBlueHeronDS
I'm poring over the reams of debug logs.
I suspect there's something we missed in setting up this new i2b2 instance. Even quick queries weren't working at first, until we remembered to configure the OBFSC_SERVICE_ACCOUNT. I hope somebody can point me to something similar that will clear up this problem.

Dan Connolly
KUMC Medical Informatics


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From: Mendis, Michael E. Sent: Friday, May 20, 2011 11:26 AM To: Yves Thorrez; i2b2 AUG Members
Subject: Query-by-value bug using EnumValues?
Got send out before I could finish....
We found a issue with the webclient and fixing that.
I have tested on 1.6 using the webclient and workbench and they both working as designed.
But, using 1.5, I did notice the double single quotes. Looking into the issue on this.
Thanks
mike

On 5/20/11 11:14 AM, Mike Mendis wrote:
Hi Yves,
We looked into this and did find a issue with the webclient, the fix is being tested in QA and should be released soon.

On 5/17/11 10:27 AM, Yves Thorrez wrote:
Hi,
For our medication ontology, we need to discriminate between home medication at intake of patient and home medication at discharge of patient. Instead of having 2 folders in the ontology browser ("medication intake" and "medication discharge") with duplicate subtrees, we prefer the modifier way and let the user query-by-value based on an enum with values "at intake" and "at discharge".
C_METADATAXML: ... <EnumValues>
<Val description="">Intake</Val>
<Val description="">Discharge</Val> </EnumValues> ...
I found in the email repository that Peter already reported that the filter does not work with the web client of i2b2 1.5.2 (see extract below), which has also been my experience: the query does not take the set values into account.
The i2b2 workbench client on the other hand does consider the value(s), but consistently reports a patient count of 0. It turns out the selected value is surrounded by a rundant pair of single quotes:
SELECT /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num
FROM i2b2demodata.dbo.observation_fact WITH(NOLOCK) WHERE ( (
( concept_cd IN (
SELECT concept_cd FROM i2b2demodata.dbo.concept_dimension c WITH(NOLOCK) WHERE concept_path LIKE '\i2b2\UZB\Medicatie\Gastro?intestinaal stelsel\Antidiarreca
\Probiotica(BFB)\APB2183069%' )
) AND valtype_cd = 'T' AND tval_char IN ('''Intake''') )
) GROUP BY patient_num HAVING COUNT >=1 )
After removing the redundant quotes, the query reports the correct number of patients. Maybe this has already been fixed in one of the 1.6 RCs?
Thanks,
Yves

On 10/29/10 6:18 PM, Peter Beninato wrote:
Hi,
Working on trying to allow a Query-by-Value to work for Text Values. I'm using the demo and I can't say I have ever seen it work. (I have query-by NUMERIC Value working) I have noticed the use of Enum Values in the ontology c_metadataxml field. By way of example I'm using I2b2.c_basecode = 'LOINC:9317-9' Or select * from i2b2 where c_basecode LIKE 'LOINC:9317-9%' In the c_metadataxml there is a datatype of ENUM as in <DataType>Enum</DataType> I have used Query-by-Value before with "NUMBER" data. In those cases the DataType is set to "PosFloat" and in the observation the valtype_cd is set to 'N'. In the example for = 'LOINC:9317-9', The valtype_cd is set to 'T' and the XML Datatype is "ENUM" However, when I run for different values that are shown in the ENUM like 'NL', 'NORMAL' , these values *ARE NOT* included in the SQL found in qt_query_master, so it is like no filter is being applied. What does the XML need to be to get a text/enum query-by-value to work? How do the fields in observation_fact need to be set? Is there a "LAB" in the demo that does work for ENUM values? Thanks.
Yves
Thorrez Medische Informatieverwerking
Laarbeeklaan 101 - 1090 Brussel
www.uzbrussel.be


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From: Davis, Michael (Oncology) Sent: Friday, May 20, 2011 10:27 AM To: Yves Thorrez; i2b2 AUG Members
Subject: Web client not connecting
Yves,
Problem solved, installing the XAMPP worked great. Thanks for the help.
Regards,
Mike

From: Yves Thorrez Sent: Friday, May 20, 2011 2:51 AM To: Davis, Michael (Oncology); i2b2 AUG Members
Subject: Web client not connecting
Michael,
You may want to check if cURL is configured in your installation. I use XAMPP in my local installation, where it's just a matter of uncommenting a line in php.ini. Otherwise, you may find this link useful:
http://www.tonyspencer.com/2003/10/22/curl-with-php-and-apache-on-windows/
Regards,
Yves
Yves Thorrez
Medische Informatieverwerking
Laarbeeklaan 101 - 1090 Brussel
www.uzbrussel.be

From: Davis, Michael (Oncology) Sent: donderdag 19 mei 2011 17:02 To: i2b2 AUG Members
Subject: Web client not connecting
I've installed i2b2 onto my local system and got the workbench working properly. However I'm having problems with getting the web client working using Apache 2.2. After installing the web client, it brings up the login dialog just fine but upon trying to login it gives we the following message "Your account does not have access to any i2b2 projects". I'm using the standard login accounts. Is there an easy way to debug the web client to see if it's communicating with my JBoss services (running my on Jboss 8080)?
Heres my i2b2_config_data.js. (note
{
urlProxy: "index.php",
urlFramework: "js-i2b2/",
//
// THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO
lstDomains: [
{ name: "local",
domain: "i2b2demo",
debug: true,
urlCellPM: "http://localhost:8080/i2b2/rest/PMService/"
},
{ name: "i2b2.org",
domain: "HarvardDemo",
debug: true,
urlCellPM: "http://webservices.i2b2.org/i2b2/rest/PMService/"
} ] //
}
And part of the index.php
$pmURL = "http://127.0.0.1:8080/i2b2/rest/PMService/getServices"; $pmCheckAllRequests = false;
$WHITELIST = array( "http://", "http://127.0.0.1:8080/axis2/rest/", "http://localhost:8080/axis2/rest/", "http://127.0.0.1:7070/i2b2/rest/", "http://localhost:7070/i2b2/rest/", "http://webservices.i2b2.org", "https://webservices.i2b2.org"
);
$BLACKLIST = array( "http://127.0.0.1:9090/test", "http://localhost:9090/test", "http://127.0.0.1:7070/test", "http://localhost:7070/test"
);
Thanks
Michael Davis
University of Pittsburgh Cancer Institute


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From: Wei,Xintao Sent: Thursday, May 19, 2011 2:52 PM To: Murphy, Shawn N.; Peter Beninato Cc: i2b2 AUG Members
Subject: set value
Dear Peter and Shawn,
My partner can use the function on our local server on his computer with workbench 1.52, however, I cannot use it on both of my computers (Windowns PC and Mac). I even downloaded the i2b2workbench 1.52 again. The "set value" function is still gray to me.
Thank you!
Xintao

From: Murphy, Shawn N. Sent: Thursday, May 19, 2011 2:34 PM To: Peter Beninato; Wei,Xintao; i2b2 AUG Members
Subject: set value
Yes, or there may be an error in the c_metadata XML.
Thanks,
Shawn.

From: Peter Beninato Sent: Thursday, May 19, 2011 2:29 PM To: Wei,Xintao; i2b2 AUG Members
Subject: set value
Please check the c_metadataxml column in the i2b2 table for ontology items that you are trying to "set value".
The content of that field drives the pop up, if that is null then that is likely why you can not set the value.

From: Wei,Xintao Sent: Thursday, May 19, 2011 11:27 AM To: i2b2 AUG Members
Subject: set value
Hi,
I am trying to use the "Set Value" function in I2B2 Workbench 1.52 and 1.6. However, the "set value" function is always displayed in gray. I tried it on the Harvard I2B2 remote demo server, our local I2B2 server with demo data and our local server with our data. The "set value" in the drop down menu is always shown in gray.
Any suggestions?
Thank you!
Xintao


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From: Peter Beninato Sent: Thursday, May 19, 2011 12:04 PM To: Niveditha Thota; i2b2 AUG Members Cc: Robert Curtis Hendrickson
Subject: Question about 'Set Value' feature
Right, Yves Thorrez commented on this recently, and actually referred to an email I had sent some time ago.
Query by Value works for NUMERIC values.
Query by Value *DOES NOT* work for text values ( yet).
As you can see by error "NEG" needs to be single quoted for sql to work, and app is not quoting properly. If you look at i2b2.c_metadataxml, the "NEG" is probably in an ENUM tab.
Basically, what I do for text values is create separate entries in the ontolology for concept_code: (made up example)
LAB:1234_Negative
LAB:1234_Positive
Etc. for each text value of interest.
Peter

From: Niveditha Thota Sent: Thursday, May 19, 2011 8:58 AM To: Peter Beninato; i2b2 AUG Members Cc: Robert Curtis Hendrickson
Subject: Question about 'Set Value' feature
Thanks Peter.
Checked the generated queries in QT_query_master table Here is how they look:
The query with no criteria: INSERT INTO i2b2demodata.QUERY_GLOBAL_TEMP (patient_num, panel_count) SELECT patient_num, 1 FROM ( SELECT /*+ index(observation_fact fact_cnpt_pat_enct_idx) */patient_num FROM
i2b2demodata.observation_fact WHERE (((concept_cd IN (select concept_cd from i2b2demodata.concept_dimension c where concept_path like '\i2b2\Labtests\LAB(LLB48) Urinalysis (LLB49) Urinalysis\UA-BLD%')) ))
group by patient_num having count >=1) t <*> INSERT INTO i2b2demodata.DX (patient_num) SELECT * FROM ( SELECT DISTINCT t.patient_num FROM i2b2demodata.QUERY_GLOBAL_TEMP t WHERE
panel_count = 1 ) q
The query with NEG criteria: INSERT INTO i2b2demodata.QUERY_GLOBAL_TEMP (patient_num, panel_count) SELECT patient_num, 1 FROM ( SELECT /*+ index(observation_fact fact_cnpt_pat_enct_idx) */patient_num FROM
i2b2demodata.observation_fact WHERE (((concept_cd IN (select concept_cd from i2b2demodata.concept_dimension c where concept_path like '\i2b2\Labtests\LAB(LLB48) Urinalysis (LLB49) Urinalysis\UA-BLD%')) AND valtype_cd = 'T' and tval_char IN NEG))
group by patient_num having count >=1) t <*> INSERT INTO i2b2demodata.DX (patient_num) SELECT * FROM ( SELECT DISTINCT t.patient_num FROM i2b2demodata.QUERY_GLOBAL_TEMP t WHERE
panel_count = 1
) q
Please note that in the query with criteria the WHERE clause - (((concept_cd IN (select concept_cd from i2b2demodata.concept_dimension c where concept_path like '\i2b2\Labtests\LAB(LLB48) Urinalysis(LLB49) Urinalysis\UA-BLD%')) AND valtype_cd = 'T' and tval_char IN NEG)) - has NEG without quotes and hence is not treated as a string. This is causing the problem.
Executing
SELECT /*+ index(observation_fact fact_cnpt_pat_enct_idx) */patient_num FROM i2b2demodata.observation_fact WHERE (((concept_cd IN (select concept_cd from i2b2demodata.concept_dimension c where concept_path like '\i2b2\Labtests\LAB(LLB48) Urinalysis (LLB49) Urinalysis\UA-BLD%')) AND valtype_cd = 'T' and tval_char IN NEG))
group by patient_num having count >=1
Gives error
ORA-00904: "NEG": invalid identifier
00904. 00000 -"%s: invalid identifier"
Any idea why the selected criteria is not being treated as a string?
Nivi

From: Peter Beninato Sent: Thursday, May 19, 2011 10:17 AM To: Niveditha Thota; i2b2 AUG Members Cc: Robert Curtis Hendrickson
Subject: Question about 'Set Value' feature
You could look at the sql that the query created in QT_query_master table, that should give you some idea how the criteria is being applied.

From: Niveditha Thota Sent: Wednesday, May 18, 2011 2:30 PM To: i2b2 AUG Members Cc: Robert Curtis Hendrickson
Subject: Question about 'Set Value' feature
Hi,
Does the 'Set Value' feature in I2B2 work?
I executed a query which searches for concept 'Occult Blood' and this resulted in 104 patients using the demo data supplied by I2B2.
I ran a second query with the same concept 'Occult Blood' with a modification. Introduced 'Set value' -by value – 'NEG' and this also resulted in 104 results.
The second query should only give results for patients with tval_char equal to 'NEG' and the count in the demo database for this is 71.
Am I understanding this feature incorrectly and expecting it to behave differently?
Did anyone else in the group work with set value feature? If yes, did it yield the expected results.
Regards,
Nivi


NEXT EMAIL
From: Mendis, Michael E. Sent: Wednesday, May 18, 2011 3:20 PM To: Jack London Cc: i2b2 AUG Members members
Subject: VM Oracle version
Most likely will be at 10g xe for 1.6 They have just released 11g xe in beta this month. For the VM, we can only distribute the eXpress Edition (free one) in the VM. Also need to verify that the new 11g has the same license as did 10g.
mike

On 5/18/11 3:13 PM, Jack London wrote:
Mike,
It looks like the VM downloads for the v1.6 RC's have Oracle 10. Any plans to provide them with Oracle 11?
Jack
Jack London, Ph.D.
Research Professor Cancer Biology
Thomas Jefferson University Director, Informatics Shared Resource Kimmel Cancer Center 808 BLSB, 233 S. 10th St. Philadelphia, PA 19107


NEXT EMAIL
From: Dan Connolly Sent: Wednesday, May 18, 2011 9:40 AM To: i2b2 AUG Members
Subject: long-running queries trigger crazy loop
I gather that i2b2 handles queries that take more than a few seconds differently. Can anybody point me to documentation on the difference? Or just explain it?
We're trying to test performance of i2b2 using solid state disks, but long-running queries are going haywire. The client goes in some sort of loop, making network requests one after the other, and I'm struggling to make sense of the jboss logs.
2011-05-18 08:14:10,957 INFO [edu.harvard.i2b2.crc.dao.DataSourceLookupHelper] LocatedDataSource for hiveId=[i2b2demo] projectId=[/BlueHeron/]2011-05-18 08:14:10,957 INFO [edu.harvard.i2b2.crc.dao.OracleDAOFactory] Using datasourcejava:QueryToolBlueHeronDS2011-05-18 08:14:10,975 INFO [edu.harvard.i2b2.crc.dao.DataSourceLookupHelper] LocatedDataSource for hiveId=[i2b2demo] projectId=[/BlueHeron/]2011-05-18 08:14:10,975 INFO [edu.harvard.i2b2.crc.dao.OracleDAOFactory] Using datasourcejava:QueryToolBlueHeronDS2011-05-18 08:14:11,274 INFO [edu.harvard.i2b2.crc.dao.DataSourceLookupHelper] LocatedDataSource for hiveId=[i2b2demo] projectId=[/BlueHeron/]2011-05-18 08:14:11,274 INFO [edu.harvard.i2b2.crc.dao.OracleDAOFactory] Using datasourcejava:QueryToolBlueHeronDS2011-05-18 08:14:11,379 INFO [edu.harvard.i2b2.crc.dao.DataSourceLookupHelper] LocatedDataSource for hiveId=[i2b2demo] projectId=[/BlueHeron/]2011-05-18 08:14:11,379 INFO [edu.harvard.i2b2.crc.dao.OracleDAOFactory] Using datasourcejava:QueryToolBlueHeronDS
I'm poring over the reams of debug logs.
I suspect there's something we missed in setting up this new i2b2 instance. Even quick queries weren't working at first, until we remembered to configure the OBFSC_SERVICE_ACCOUNT. I hope somebody can point me to something similar that will clear up this problem.
Dan Connolly


NEXT EMAIL
From: Zapletal Eric Sent: Tuesday, May 17, 2011 12:45 PM To: Mendis, Michael E. Cc: Audrey Hureau; i2b2 AUG Members
Subject: Cell's AJAX library error
Hi everybody,
in the web client, I have the "An error has occurred in the Cell's AJAX library. Press F12 for more information" error, after the "Choose project" dialog (cf screenshot) in only one case:
if I press the "return" key in the "Choose project" dialog, the error dialogs pop-up (several times).
if I click the "Go" button in the "Choose project" dialog, everything is ok (no AJAX error) This can be repeated at each login (always the same behaviour) I don't know if it is related to the situation that Audrey exposed...
Eric

Le 17.05.2011 17:53, Mike Mendis a écrit :
Sounds like one of the cells is down. Does the web client come up at all?
When you start the workbench is the upper right icon yellow or red or green, also if you hover over the icon it should tell you which is down (if yellow or red)

On 5/17/11 11:25 AM, Audrey Hureau wrote:
I have some issue when I run the JBOSS but I don't know how to resolve it. Besides, the workbench works correctly even with these errors. The webclient configuration seems ok.


NEXT EMAIL
From: Audrey Hureau Sent: Tuesday, May 17, 2011 11:25 AM To: Mendis, Michael E.; i2b2 AUG Members
Subject: Cell's AJAX library error
I have some issue when I run the JBOSS but I don't know how to resolve it. Besides, the workbench works correctly even with these errors. The webclient configuration seems ok.
Audrey Hureau

2011/5/17 Mike Mendis
Verify that the setting in the webclient is correct, also that jboss is up running correctly.
mike

On 5/17/11 11:08 AM, Audrey Hureau wrote:
Hi everyone,
I saw on the internet that some people already had the same problem as mine but I didn't see any solutions to it. When I am connecting to the web client, an error message appears saying "An error has occured in the Cell's AJAX livrary. Press F12 for more information". When I press F12, nothing happens. Besides, I never had this problem before but now I have this message everytime I am trying tu access to the webclient. Does anyone know how to fix it? Thank you.


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From: Arnold, Garth Sent: Monday, May 16, 2011 12:18 PM To: i2b2 AUG Members
Subject: autorun jboss or I2B2 server
Hello Xintao - I'm using javaservice (v2.0.10) to run jboss as a service on Windows 2003 and 2008 servers. In a separate email I'll send you notes for how I set this up.
Garth
Garth Arnold | MANAGER, TECHNICAL INFRASTRUCTURE Group Health Research Institute

From: Wei,Xintao Sent: Monday, May 16, 2011 9:10 AM To: i2b2 AUG Members
Subject: autorun jboss or I2B2 server
Hi,
I installed an I2B2 server on Windows server 2008 with jboss-4.2.2.GA. The JBoss had to be restarted manually every time the machine restarted.
Do you have any experiences to autorun the jboss for I2B2 server or auto-restart the I2B2 server?
Thank you!
Xintao


NEXT EMAIL
From: Wei,Xintao Sent: Monday, May 16, 2011 12:10 PM To: i2b2 AUG Members
Subject: autorun jboss or I2B2 server
Hi,
I installed an I2B2 server on Windows server 2008 with jboss-4.2.2.GA. The JBoss had to be restarted manually every time the machine restarted.
Do you have any experiences to autorun the jboss for I2B2 server or auto-restart the I2B2 server?
Thank you!
Xintao


NEXT EMAIL
From: STEPHANE MEYSTRE Sent: Thursday, May 12, 2011 10:18 PM To: McMurry, Andrew J. Cc: Daniel Sullivan; i2b2 AUG Members
Subject: HIPAA-18 Location and Age
Actually, ages over 89 should be removed, not 90. For a complete reference, you should refer to the HIPAA Safe Harbor definition. This is one of the methods to have data considered de-identified, the other one being statistical, and doesn't define any specific PHI. Removal of some ages below 89 because of a higher risk of re-identification would therefore be a local decision, added to the HIPAA Safe Harbor.
You'll find some information about that and examples of systems in the attached paper.
Stephane
Stephane M. Meystre, MD, PhD Assistant Professor Department of Biomedical Informatics University of Utah 26 South 2000 East, HSEB suite 5700 Salt Lake City, UT 84112


NEXT EMAIL
From: McMurry, Andrew J. Sent: Thursday, May 12, 2011 10:08 PM To: Daniel Sullivan Cc: i2b2 AUG Members
Subject: HIPAA-18 Location and Age
Location technically IS an identifier, even if you are asking institution A for data and it reports (no surprise) institution A.
DOB is considered PHI whereas age (in years) is not. Ages over 90 should be removed. HIPAA Ages are also a problem if the subset of patients is < 10.
This paper from Beckwith et all should keep you in safe standing
http://open.med.harvard.edu/display/SCRUBBER/Publications
hope this helps,
andy

On May 12, 2011, at 6:45 PM, Daniel Sullivan wrote:
These are less i2b2 questions and more like de-id questions:
Would facility location or institution be considered a protected location under HIPAA-18?
If facility or institution is, what strategies are folks using to deal with this? Our current use cases are very institution/facility specific.
Also, I noticed that some 'versions' of the HIPAA 18 rules cover old age and some don't. See link below, but basically I went ahead and decided to bucket ages >89 à [dem|age:>89] based on statistical assumptions, however I came across one version of the de-id/phi/hipaa rules which addresses this issue specifically:
http://www.cdc.gov/mmwr/preview/mmwrhtml/m2e411a1.htm#box2
My question is this: are other institutions bucketing age groups that have a low enough statistical likelihood as to be 'very identifying' information?
Any responses are appreciated.
Daniel John Sullivan
Research Scientist ITHS Biomedical Informatics University of Washington Box 358051 815 Mercer St. Seattle, WA 98109


NEXT EMAIL
From: Phillips, Lori C. Sent: Thursday, May 12, 2011 1:41 PM To: i2b2 AUG Members
Subject: Find Terms functionality in the Web Client and Work Bench, do the trees need to include
to search on?
Peter is correct; it runs against any/all metadata tables that you have. Search by name runs against the c_name column Search by code runs against the c_basecode column.
There is no way to search or query for a concept that does not appear in the navigatation windows.

From: Peter Beninato Sent: Thursday, May 12, 2011 12:47 PM To: Daniel Sullivan; i2b2 AUG Members
Subject: Find Terms functionality in the Web Client and Work Bench, do the trees need to include to search on?
I think it runs against neither, but rather in the meta table schema, the i2b2 table, the column c_name.

From: Daniel Sullivan Sent: Thursday, May 12, 2011 9:43 AM To: i2b2 AUG Members
Subject: Find Terms functionality in the Web Client and Work Bench, do the trees need to include to search on?
I have a question, I hope it is an easy one:
When you search in the web client or work bench using the 'find terms' tab, does this search look at the Concept_Dimension, the actual raw concept codes in the Observation_Fact table, or both? I'm trying to determine if the 'orphan concept code' that does not have a closure on the concept trees is still searchable / queryable and I haven't had a chance yet to dig very deep into the relevant java beans or the web/workbench UI.
Daniel John Sullivan
Research Scientist ITHS Biomedical Informatics University of Washington Box 358051 815 Mercer St. Seattle, WA 98109


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From: Zapletal Eric Sent: Tuesday, May 10, 2011 4:05 AM To: Audrey Hureau Cc: Phillips, Lori C.; i2b2 AUG Members
Subject: Patient data insertion
Hi,
what is the result of the sub-request , ie
select concept_cd from i2b2demodata.concept_dimension c where concept_path LIKE '\onto \Diagnostiques\XXI-facteurs influant sur l etat de sante et motifs de recours aux services de sante \sujets ayant recours aux services de sante pour des motifs lies a la reproduction\resultat de l accouchement\naissance unique, enfant vivant%'

Le 09.05.2011 15:34, Audrey Hureau a écrit :
Lori,
The I2B2 metadata dimcode match with the concept_dimension concept_path because I insert my concept_path in the concept_dimension by getting the c_dimcode from the I2B2 metata table. Here is the query that I copied/pasted in the SQL editor:
"SELECT patient_num, 1 FROM ( SELECT /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num FROM i2b2demodata.observation_fact WHERE (((concept_cd IN (select concept_cd from i2b2demodata.concept_dimension c where concept_path LIKE '\onto\Diagnostiques\XXI- facteurs influant sur l etat de sante et motifs de recours aux services de sante\sujets ayant recours aux services de sante pour des motifs lies a la reproduction\resultat de l accouchement \naissance unique, enfant vivant%')) ))
group by patient_num having count >=1) t"

2011/5/9 Phillips, Lori C.
Audrey,
Additionally, the dimcode field in the i2b2 metadata table needs to match the concept_path field in the concept dimension table. What does the query that you copied/pasted in the SQL editor look like?
Lori

From: Audrey Hureau Sent: Monday, May 09, 2011 9:09 AM To: i2b2 AUG Members
Subject: Fwd: Patient data insertion
Eric,
When I copy/past the content of my query in a simple SQL editor, none results are found.
Daniel, The Observation_Fact's concept codes exist un the concept dimension. However, I didn't test a join between both tables but I don't know how to do it. Can you help me with it?
Audrey Hureau

2011/5/6 Daniel Sullivan
I am pretty certain the concept dimension has to link to the concept_cd field via a join. Do you know if Observation_Fact's concept codes exist in the concept dimension? Have you tested a join between concept_dimension and observation fact?

From: Audrey Hureau Sent: Friday, May 06, 2011 1:57 AM To: i2b2 AUG Members
Subject: Patient data insertion
Hi everyone,
I tried to insert my own patient data in i2b2. I implemented concept_dimension, observation_fact, patient_dimension and visit_dimension tables. But when I run a query about a diagnose which should return a lot of patients, i2b2 doesn't find any patient. My question is simple. Is there any other table that I have to affect? Does it matter if I didn't add data in the provider_dimension table corresponding to the ones I added ?
Thank you all.
Audrey Hureau


NEXT EMAIL
From: Audrey Hureau Sent: Monday, May 09, 2011 9:34 AM To: Phillips, Lori C.; i2b2 AUG Members
Subject: Re: Patient data insertion
Lori,
The I2B2 metadata dimcode match with the concept_dimension concept_path because I insert my concept_path in the concept_dimension by getting the c_dimcode from the I2B2 metata table. Here is the query that I copied/pasted in the SQL editor:
"SELECT patient_num, 1 FROM ( SELECT /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num FROM i2b2demodata.observation_fact WHERE (((concept_cd IN (select concept_cd from i2b2demodata.concept_dimension c where concept_path LIKE '\onto\Diagnostiques\XXIfacteurs influant sur l etat de sante et motifs de recours aux services de sante\sujets ayant recours aux services de sante pour des motifs lies a la reproduction\resultat de l accouchement\naissance unique, enfant vivant%')) ))
group by patient_num having count >=1) t"

2011/5/9 Phillips, Lori C.
Audrey,
Additionally, the dimcode field in the i2b2 metadata table needs to match the concept_path field in the concept dimension table. What does the query that you copied/pasted in the SQL editor look like?
Lori

From: Audrey Hureau Sent: Monday, May 09, 2011 9:09 AM To: i2b2 AUG Members
Subject: Fwd: Patient data insertion
Eric,
When I copy/past the content of my query in a simple SQL editor, none results are found.

Daniel,
The Observation_Fact's concept codes exist un the concept dimension. However, I didn't test a join between both tables but I don't know how to do it. Can you help me with it?
Audrey Hureau

2011/5/6 Daniel Sullivan
I am pretty certain the concept dimension has to link to the concept_cd field via a join. Do you know if Observation_Fact's concept codes exist in the concept dimension? Have you tested a join between concept_dimension and observation fact?

From: Audrey Hureau Sent: Friday, May 06, 2011 1:57 AM To: i2b2 AUG Members Subject: Patient data insertion
Hi everyone,
I tried to insert my own patient data in i2b2. I implemented concept_dimension, observation_fact, patient_dimension and visit_dimension tables. But when I run a query about a diagnose which should return a lot of patients, i2b2 doesn't find any patient. My question is simple. Is there any other table that I have to affect? Does it matter if I didn't add data in the provider_dimension table corresponding to the ones I added ?
Thank you all.
Audrey Hureau



NEXT EMAIL
From: Peter Beninato Sent: Friday, May 06, 2011 12:06 PM To: i2b2 AUG Members
Subject: i2b2 - v1.6 RC3 - query reuse
Hi,
On a local install working off of the demo data, it seems that re-using a query from previous queries is not working.
For instance, if you run a query for diagnosis Asthma, unspecified, it returns like 133 patients.
If you Clear and Drag that query up from the Previous queries it runs and throws a message box: The cell's status message could not be understood.
This is just a "patient count" query. The error might be reproducible.
Here is some of the jboss log: isOperation.java:295)
at org.apache.axis2.client.ServiceClient.sendReceive(ServiceClient.java: 579)
at org.apache.axis2.client.ServiceClient.sendReceive(ServiceClient.java: 508)
at edu.harvard.i2b2.crc.delegate.ontology.CallOntologyUtil.callOntology( Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.SortPanel.sortedPanel List(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.QueryToolUtilNew.gene rateSqlForGroupedPanelList(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.QueryToolUtilNew.getS etfinderSqlForQueryDefinition(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.RecursiveBuild.execQu ery(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.RecursiveBuild.startS qlBuild(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.QueryRequestSpringDao.buildSql(Unk
nown Source)
at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorDao.executeSQL(Unknow n Source)
at edu.harvard.i2b2.crc.ejb.ExecRunnable.processQueryRequest(Unknown Sou rce)
at edu.harvard.i2b2.crc.ejb.ExecRunnable.execute(Unknown Source)
at edu.harvard.i2b2.crc.ejb.QueryExecutorMDB.onMessage(Unknown Source)
at edu.harvard.i2b2.crc.ejb.QuerySmallExecutorMDB.onMessage(Unknown Sour ce)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl. java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces sorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.invocation.Invocation.performCall(Invocation.java:359)
at org.jboss.ejb.MessageDrivenContainer$ContainerInterceptor.invoke(Mess ageDrivenContainer.java:495)
at org.jboss.resource.connectionmanager.CachedConnectionInterceptor.invo ke(CachedConnectionInterceptor.java:158)
at org.jboss.ejb.plugins.CallValidationInterceptor.invoke(CallValidation Interceptor.java:63)
at org.jboss.ejb.plugins.AbstractTxInterceptor.invokeNext(AbstractTxInte rceptor.java:121)
at org.jboss.ejb.plugins.AbstractTxInterceptorBMT.invokeNext(AbstractTxI nterceptorBMT.java:173)
at org.jboss.ejb.plugins.MessageDrivenTxInterceptorBMT.invoke(MessageDri
venTxInterceptorBMT.java:47)
at org.jboss.ejb.plugins.MessageDrivenInstanceInterceptor.invoke(Message DrivenInstanceInterceptor.java:116)
at org.jboss.ejb.plugins.RunAsSecurityInterceptor.invoke(RunAsSecurityIn terceptor.java:109)
at org.jboss.ejb.plugins.LogInterceptor.invoke(LogInterceptor.java:205)
at org.jboss.ejb.plugins.ProxyFactoryFinderInterceptor.invoke(ProxyFacto ryFinderInterceptor.java:138)
at org.jboss.ejb.MessageDrivenContainer.internalInvoke(MessageDrivenCont ainer.java:402)
at org.jboss.ejb.Container.invoke(Container.java:960)
at org.jboss.ejb.plugins.jms.JMSContainerInvoker.invoke(JMSContainerInvo ker.java:987)
at org.jboss.ejb.plugins.jms.JMSContainerInvoker$MessageListenerImpl.onM essage(JMSContainerInvoker.java:1287)
at org.jboss.jms.asf.StdServerSession.onMessage(StdServerSession.java:26 6)
at org.jboss.mq.SpyMessageConsumer.sessionConsumerProcessMessage(SpyMess ageConsumer.java:891)
at org.jboss.mq.SpyMessageConsumer.addMessage(SpyMessageConsumer.java:17 0)
at org.jboss.mq.SpySession.run(SpySession.java:323)
at org.jboss.jms.asf.StdServerSession.run(StdServerSession.java:194)
at EDU.oswego.cs.dl.util.concurrent.PooledExecutor$Worker.run(PooledExec utor.java:761)
at java.lang.Thread.run(Thread.java:619)
09:02:12,978 ERROR [ExecRunnable] Error while fetching metadata [query_master_id
:249] from ontology org.apache.axis2.AxisFault: Incoming message input stream is null
at org.apache.axis2.transport.TransportUtils.createSOAPMessage(Transport Utils.java:64)
at org.apache.axis2.description.OutInAxisOperationClient.send(OutInAxisO peration.java:381)
at org.apache.axis2.description.OutInAxisOperationClient.execute(OutInAx isOperation.java:295)
at org.apache.axis2.client.ServiceClient.sendReceive(ServiceClient.java: 579)
at org.apache.axis2.client.ServiceClient.sendReceive(ServiceClient.java: 508)
at edu.harvard.i2b2.crc.delegate.ontology.CallOntologyUtil.callOntology( Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.SortPanel.sortedPanel List(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.QueryToolUtilNew.gene rateSqlForGroupedPanelList(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.QueryToolUtilNew.getS etfinderSqlForQueryDefinition(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.RecursiveBuild.execQu ery(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.RecursiveBuild.startS qlBuild(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.QueryRequestSpringDao.buildSql(Unk nown Source)
at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorDao.executeSQL(Unknow n Source)
at edu.harvard.i2b2.crc.ejb.ExecRunnable.processQueryRequest(Unknown Sou rce)
at edu.harvard.i2b2.crc.ejb.ExecRunnable.execute(Unknown Source)
at edu.harvard.i2b2.crc.ejb.QueryExecutorMDB.onMessage(Unknown Source)
at edu.harvard.i2b2.crc.ejb.QuerySmallExecutorMDB.onMessage(Unknown Sour ce)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl. java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces sorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.invocation.Invocation.performCall(Invocation.java:359)
at org.jboss.ejb.MessageDrivenContainer$ContainerInterceptor.invoke(Mess ageDrivenContainer.java:495)
at org.jboss.resource.connectionmanager.CachedConnectionInterceptor.invo ke(CachedConnectionInterceptor.java:158)
at org.jboss.ejb.plugins.CallValidationInterceptor.invoke(CallValidation Interceptor.java:63)
at org.jboss.ejb.plugins.AbstractTxInterceptor.invokeNext(AbstractTxInte rceptor.java:121)
at org.jboss.ejb.plugins.AbstractTxInterceptorBMT.invokeNext(AbstractTxI nterceptorBMT.java:173)
at org.jboss.ejb.plugins.MessageDrivenTxInterceptorBMT.invoke(MessageDri
venTxInterceptorBMT.java:47)
at org.jboss.ejb.plugins.MessageDrivenInstanceInterceptor.invoke(Message DrivenInstanceInterceptor.java:116)
at org.jboss.ejb.plugins.RunAsSecurityInterceptor.invoke(RunAsSecurityIn terceptor.java:109)
at org.jboss.ejb.plugins.LogInterceptor.invoke(LogInterceptor.java:205)
at org.jboss.ejb.plugins.ProxyFactoryFinderInterceptor.invoke(ProxyFacto ryFinderInterceptor.java:138)
at org.jboss.ejb.MessageDrivenContainer.internalInvoke(MessageDrivenCont ainer.java:402)
at org.jboss.ejb.Container.invoke(Container.java:960)
at org.jboss.ejb.plugins.jms.JMSContainerInvoker.invoke(JMSContainerInvo ker.java:987)
at org.jboss.ejb.plugins.jms.JMSContainerInvoker$MessageListenerImpl.onM essage(JMSContainerInvoker.java:1287)
at org.jboss.jms.asf.StdServerSession.onMessage(StdServerSession.java:26 6)
at org.jboss.mq.SpyMessageConsumer.sessionConsumerProcessMessage(SpyMess ageConsumer.java:891)
at org.jboss.mq.SpyMessageConsumer.addMessage(SpyMessageConsumer.java:17 0)
at org.jboss.mq.SpySession.run(SpySession.java:323)
at org.jboss.jms.asf.StdServerSession.run(StdServerSession.java:194)
at EDU.oswego.cs.dl.util.concurrent.PooledExecutor$Worker.run(PooledExec utor.java:761)
at java.lang.Thread.run(Thread.java:619)
edu.harvard.i2b2.crc.dao.setfinder.querybuilder.OntologyException: Error while f
etching metadata [query_master_id:249] from ontology org.apache.axis2.AxisFault: Incoming message input stream is null
at org.apache.axis2.transport.TransportUtils.createSOAPMessage(Transport Utils.java:64)
at org.apache.axis2.description.OutInAxisOperationClient.send(OutInAxisO peration.java:381)
at org.apache.axis2.description.OutInAxisOperationClient.execute(OutInAx isOperation.java:295)
at org.apache.axis2.client.ServiceClient.sendReceive(ServiceClient.java: 579)
at org.apache.axis2.client.ServiceClient.sendReceive(ServiceClient.java: 508)
at edu.harvard.i2b2.crc.delegate.ontology.CallOntologyUtil.callOntology( Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.SortPanel.sortedPanel List(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.QueryToolUtilNew.gene rateSqlForGroupedPanelList(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.QueryToolUtilNew.getS etfinderSqlForQueryDefinition(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.RecursiveBuild.execQu ery(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.RecursiveBuild.startS qlBuild(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.QueryRequestSpringDao.buildSql(Unk
nown Source)
at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorDao.executeSQL(Unknow n Source)
at edu.harvard.i2b2.crc.ejb.ExecRunnable.processQueryRequest(Unknown Sou rce)
at edu.harvard.i2b2.crc.ejb.ExecRunnable.execute(Unknown Source)
at edu.harvard.i2b2.crc.ejb.QueryExecutorMDB.onMessage(Unknown Source)
at edu.harvard.i2b2.crc.ejb.QuerySmallExecutorMDB.onMessage(Unknown Sour ce)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl. java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces sorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.invocation.Invocation.performCall(Invocation.java:359)
at org.jboss.ejb.MessageDrivenContainer$ContainerInterceptor.invoke(Mess ageDrivenContainer.java:495)
at org.jboss.resource.connectionmanager.CachedConnectionInterceptor.invo ke(CachedConnectionInterceptor.java:158)
at org.jboss.ejb.plugins.CallValidationInterceptor.invoke(CallValidation Interceptor.java:63)
at org.jboss.ejb.plugins.AbstractTxInterceptor.invokeNext(AbstractTxInte rceptor.java:121)
at org.jboss.ejb.plugins.AbstractTxInterceptorBMT.invokeNext(AbstractTxI nterceptorBMT.java:173)
at org.jboss.ejb.plugins.MessageDrivenTxInterceptorBMT.invoke(MessageDri
venTxInterceptorBMT.java:47)
at org.jboss.ejb.plugins.MessageDrivenInstanceInterceptor.invoke(Message DrivenInstanceInterceptor.java:116)
at org.jboss.ejb.plugins.RunAsSecurityInterceptor.invoke(RunAsSecurityIn terceptor.java:109)
at org.jboss.ejb.plugins.LogInterceptor.invoke(LogInterceptor.java:205)
at org.jboss.ejb.plugins.ProxyFactoryFinderInterceptor.invoke(ProxyFacto ryFinderInterceptor.java:138)
at org.jboss.ejb.MessageDrivenContainer.internalInvoke(MessageDrivenCont ainer.java:402)
at org.jboss.ejb.Container.invoke(Container.java:960)
at org.jboss.ejb.plugins.jms.JMSContainerInvoker.invoke(JMSContainerInvo ker.java:987)
at org.jboss.ejb.plugins.jms.JMSContainerInvoker$MessageListenerImpl.onM essage(JMSContainerInvoker.java:1287)
at org.jboss.jms.asf.StdServerSession.onMessage(StdServerSession.java:26 6)
at org.jboss.mq.SpyMessageConsumer.sessionConsumerProcessMessage(SpyMess ageConsumer.java:891)
at org.jboss.mq.SpyMessageConsumer.addMessage(SpyMessageConsumer.java:17 0)
at org.jboss.mq.SpySession.run(SpySession.java:323)
at org.jboss.jms.asf.StdServerSession.run(StdServerSession.java:194)
at EDU.oswego.cs.dl.util.concurrent.PooledExecutor$Worker.run(PooledExec utor.java:761)
at java.lang.Thread.run(Thread.java:619)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.SortPanel.sortedPanel List(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.QueryToolUtilNew.gene rateSqlForGroupedPanelList(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.QueryToolUtilNew.getS etfinderSqlForQueryDefinition(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.RecursiveBuild.execQu ery(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.RecursiveBuild.startS qlBuild(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.QueryRequestSpringDao.buildSql(Unk nown Source)
at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorDao.executeSQL(Unknow n Source)
at edu.harvard.i2b2.crc.ejb.ExecRunnable.processQueryRequest(Unknown Sou rce)
at edu.harvard.i2b2.crc.ejb.ExecRunnable.execute(Unknown Source)
at edu.harvard.i2b2.crc.ejb.QueryExecutorMDB.onMessage(Unknown Source)
at edu.harvard.i2b2.crc.ejb.QuerySmallExecutorMDB.onMessage(Unknown Sour ce)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl. java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces sorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
38
at org.jboss.invocation.Invocation.performCall(Invocation.java:359)
at org.jboss.ejb.MessageDrivenContainer$ContainerInterceptor.invoke(Mess ageDrivenContainer.java:495)
at org.jboss.resource.connectionmanager.CachedConnectionInterceptor.invo ke(CachedConnectionInterceptor.java:158)
at org.jboss.ejb.plugins.CallValidationInterceptor.invoke(CallValidation Interceptor.java:63)
at org.jboss.ejb.plugins.AbstractTxInterceptor.invokeNext(AbstractTxInte rceptor.java:121)
at org.jboss.ejb.plugins.AbstractTxInterceptorBMT.invokeNext(AbstractTxI nterceptorBMT.java:173)
at org.jboss.ejb.plugins.MessageDrivenTxInterceptorBMT.invoke(MessageDri venTxInterceptorBMT.java:47)
at org.jboss.ejb.plugins.MessageDrivenInstanceInterceptor.invoke(Message DrivenInstanceInterceptor.java:116)
at org.jboss.ejb.plugins.RunAsSecurityInterceptor.invoke(RunAsSecurityIn terceptor.java:109)
at org.jboss.ejb.plugins.LogInterceptor.invoke(LogInterceptor.java:205)
at org.jboss.ejb.plugins.ProxyFactoryFinderInterceptor.invoke(ProxyFacto ryFinderInterceptor.java:138)
at org.jboss.ejb.MessageDrivenContainer.internalInvoke(MessageDrivenCont ainer.java:402)
at org.jboss.ejb.Container.invoke(Container.java:960)
at org.jboss.ejb.plugins.jms.JMSContainerInvoker.invoke(JMSContainerInvo ker.java:987)
at org.jboss.ejb.plugins.jms.JMSContainerInvoker$MessageListenerImpl.onM
essage(JMSContainerInvoker.java:1287)
at org.jboss.jms.asf.StdServerSession.onMessage(StdServerSession.java:26 6)
at org.jboss.mq.SpyMessageConsumer.sessionConsumerProcessMessage(SpyMess ageConsumer.java:891)
at org.jboss.mq.SpyMessageConsumer.addMessage(SpyMessageConsumer.java:17 0)
at org.jboss.mq.SpySession.run(SpySession.java:323)
at org.jboss.jms.asf.StdServerSession.run(StdServerSession.java:194)
at EDU.oswego.cs.dl.util.concurrent.PooledExecutor$Worker.run(PooledExec utor.java:761)
at java.lang.Thread.run(Thread.java:619) 09:02:13,452 INFO [QueryManagerBeanUtil] RESULT INSTANCE ID 395 09:02:13,481 INFO [DataSourceLookupHelper] Located DataSource for hiveId=[i2b2d emo] projectId=[/Demo/] 09:02:13,481 INFO [OracleDAOFactory] Using datasource java:QueryToolDemoDS

Peter Beninato - OCTRI DW Developer Oregon Health & Science University


NEXT EMAIL
From: Jeremy Nix Sent: Friday, May 06, 2011 11:53 AM To: Daniel Sullivan Cc: i2b2 AUG Members
Subject: Re: Navigate Terms Tree and observation term existence
The ontology does not dynamically show concepts/terms based on what is utilized in the observation_fact table. I believe that many institutions (including our own), choose to implement ETL processes to change a folder/leaf's c_visualattributes value based on whether there are fact records. The 2nd character in this value is generally "A" for active. If you wish to hide that folder/leaf, then set the value to "H". Hidden concepts are typically not returned to the client (though, this can be a client side option).
Jeremy Nix Senior Application Developer Cincinnati Children's Hospital Medical Center

On 05/06/2011 11:29 AM, Daniel Sullivan wrote:
Does anyone know yet, from experience with i2b2, if the Navigate Terms tree in the Web client or Work Bench limit or prune the tree based on 'existing' values? Another way of phrasing it, if there is a diagnostic category available under the diagnoses branch does this imply the value exists in the i2b2 instance observation_fact data?



NEXT EMAIL
From: zapletal eric Sent: Friday, May 06, 2011 6:18 AM To: Audrey Hureau Cc: i2b2 AUG Members
Subject: Re : Patient data insertion
Hi Audrey,
may be you can test this :
copy/paste the content or your query (which is stored is the QT_QUERY_MASTER table) in a simple SQL editor.
(suppress INSERT extra-statement of the stored query)
When you run it in a SQL editor you can check the database response in a very simple manner.
Eric

Message d'origine De: Audrey Hureau Date: Vendredi, Mai 6, 2011 10:57 am À: i2b2 AUG Members
Objet: Patient data insertion
Hi everyone,
I tried to insert my own patient data in i2b2. I implemented concept_dimension, observation_fact, patient_dimension and visit_dimension tables. But when I run a query about a diagnose which should return a lot of patients, i2b2 doesn't find any patient. > My question is simple. Is there any other table that I have to affect? Does it matter if I didn't add data in the provider_dimension table corresponding to the ones I added ?
Thank you all.
Audrey Hureau



NEXT EMAIL
From: Daniel Sullivan Sent: Thursday, May 05, 2011 9:52 AM To: Murphy, Shawn N. Cc: Daniel Sullivan; i2b2 AUG Members
Subject: RE: Table Usage/Deployment Documentation for i2b2
Ok

On Thu, 5 May 2011, Murphy, Shawn N. wrote:
Hi Dan,
It is used to persist the patient sets that are created by queries (when specified).
Thanks,
Shawn.

From: Daniel Sullivan Sent: Wednesday, May 04, 2011 6:33 PM To: i2b2 AUG Members
Subject: Table Usage/Deployment Documentation for i2b2
Does anyone have a good document or white paper or link that would describe the purpose of this entity?
[i2b2demodata].[QT_PATIENT_SET_COLLECTION]
I can dig into the JAVA code, but I wouldn't mind getting a high level (one or two sentence) description if someone knows. It looks like a query tool related table, but beyond that I feel like I would be guessing the purpose.
Any help is appreciated.
Dan



NEXT EMAIL
From: Jeremy Nix Sent: Thursday, May 05, 2011 7:53 AM To: Daniel Sullivan Cc: i2b2 AUG Members
Subject: Re: Table Usage/Deployment Documentation for i2b2
The qt_patient_set_collection is the table that stores the patient cohort created by your query. Your query results are stored as such:
qt_query_master: Stores high level query request, with query definition information.
qt_query_instance (1-many): Stores information regarding when the query was ran. A given query definition will soon (as I have been told) have the ability to be scheduled, so for each time the query runs, a new instance will be created.
qt_query_result_instance (1-many): When you run a query, you have the choice of creating multiple outputs. Outputs could be simple patient counts, patient sets, or patient encounter sets. This table stores what outputs were requested for the given query instance.
qt_patient_set_collection: If you choose to generate a patient cohort (meaning your interested in seeing more than a simple patient count), then the patients will be mapped to your query in this table.
qt_patient_enc_collection: If you choose to generate a patient encounter cohort, which not only keeps track of the patients that matched you criteria, but also keeps tracks of the encounters that matched you criteria, then those patients + encounters would be stored in this table.

Jeremy Nix Senior Application Developer Cincinnati Children's Hospital Medical Center

On 05/04/2011 06:33 PM, Daniel Sullivan wrote:
Does anyone have a good document or white paper or link that would describe the purpose of this entity?
[i2b2demodata].[QT_PATIENT_SET_COLLECTION]
I can dig into the JAVA code, but I wouldn't mind getting a high level (one or two sentence) description if someone knows. It looks like a query tool related table, but beyond that I feel like I would be guessing the purpose.
Any help is appreciated.
Dan



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From: Daniel Sullivan Sent: Wednesday, May 04, 2011 6:23 PM To: i2b2 AUG Members
Subject: Data Storage needs estimating
We have a current active instance of i2b2 and we are building a new instance for our bio-repository project. For planning purposes, I have been doing growth/size analysis and I was wondering if others have noticed similar numbers to those in the attached work sheet (keep in mind, these are just counts/sizes and there is NO actual healthcare data in the spreadsheet – so this is HIPAA safe to look at!).
I am seeing a size increase factor of 5.7 going from the source system data to i2b2, I know this is also related to specific peculiarities of our data, but I was wondering what size/factor others have noticed so I can get a sense of how far this estimate may be off and what factor I should use for estimating growth.
Any information regarding the data growth (or decrease) going from source data would be appreciated.
Thanks,
Dan


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From: Daniel Sullivan Sent: Wednesday, May 04, 2011 5:11 PM To: Cowall, Jeff Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Good info, I figured as much. Although (and I hate to admit this) when I first started working in healthcare informatics I 'assumed' that this information (procedure codes) would be available for use without a fee (I have learned the evil truth since then). Just as screw driver manufacturers don't own the metric or English system of measurement, I don't think it is reasonable for Docs/AMA to own this – manage, yes, but not own. Something weird about for profit standards orgs... Very weird (especially in a field – medicine – that is supposed to be about the 'care' and not the 'money').

From: Cowall, Jeff Sent: Wednesday, May 04, 2011 11:12 AM To: 'Daniel Sullivan'; 'Robert Curtis Hendrickson' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
The codes and ontology are copywritten property of the AMA...you won't find a decent freebie.
We pay an annual fee to Ingenix for their CPT4 Category Code product, which has an (up to) five node deep "path" for each code as well as description fields.
It's something like $2500 base license + $15/per user annually.
We wrote some java code to generate sql from it. It's pretty ad hoc, but I think we'd be glad to share it.
Daniel, I think James Law also write you, too. We're in the same group.

Cheers, Jeff

From: Daniel Sullivan Sent: Wednesday, May 04, 2011 1:59 PM To: 'Robert Curtis Hendrickson' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
I've been down that road too. I call it 'poor man's categorization'. Don't beat yourself up, if I find something I will make it available. So far, I have gotten some really good lede's from the community.
Cheers!

From: Robert Curtis Hendrickson Sent: Wednesday, May 04, 2011 9:01 AM To: 'Daniel Sullivan'
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Daniel,
If someone provides one, we could really use it, too!
Right now we use a ghastly and useless ontology based on 1st, 2nd, 3rd, letters of the procedure name.
Totally impractical for browsing, but keeps the gui from breaking....
Regards,
Curtis
From: Daniel Sullivan Sent: Wednesday, May 04, 2011 10:34 AM To: i2b2 AUG Members
Subject: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Has anyone built a custom ontology for CPT/HCPC codes? If so, is it something proprietary or something I could get? In i2b2 speak, I am looking for records that would have been loaded into i2b2metadata.I2B2 for CPT/HCPC query paths... This is NOT a request for an icd9 procedure tree (we already have one).
Any help is appreciated.
Cheers!
Daniel Sullivan


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From: Daniel Sullivan Sent: Wednesday, May 04, 2011 5:11 PM To: 'Mobed, Ketty'; 'Cowall, Jeff'; 'Robert Curtis Hendrickson' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
That sounds right, wouldn't we already have paid the AMA/Ingenix for this?

From: Mobed, Ketty Sent: Wednesday, May 04, 2011 11:22 AM To: 'Cowall, Jeff'; 'Daniel Sullivan'; 'Robert Curtis Hendrickson' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
I'm just wondering, since most of us work at clinical institutions that already have CPT licenses wouldn't it be already available for us to develop the CPT ontology?
Thanks for the brainstorm. Ketty

From: Cowall, Jeff Sent: Wednesday, May 04, 2011 11:12 AM To: 'Daniel Sullivan'; 'Robert Curtis Hendrickson' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
The codes and ontology are copywritten property of the AMA...you won't find a decent freebie.
We pay an annual fee to Ingenix for their CPT4 Category Code product, which has an (up to) five node deep "path" for each code as well as description fields. It's something like $2500 base license + $15/per user annually. We wrote some java code to generate sql from it. It's pretty ad hoc, but I think we'd be glad to share
it.
Daniel, I think James Law also write you, too. We're in the same group.
Cheers, Jeff

From: Daniel Sullivan Sent: Wednesday, May 04, 2011 1:59 PM To: 'Robert Curtis Hendrickson' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
I've been down that road too. I call it 'poor man's categorization'. Don't beat yourself up, if I find something I will make it available. So far, I have gotten some really good lede's from the community.
Cheers!

From: Robert Curtis Hendrickson Sent: Wednesday, May 04, 2011 9:01 AM To: 'Daniel Sullivan'
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Daniel,
If someone provides one, we could really use it, too!
Right now we use a ghastly and useless ontology based on 1st, 2nd, 3rd, letters of the procedure name.
Totally impractical for browsing, but keeps the gui from breaking....
Regards,
Curtis

From: Daniel Sullivan Sent: Wednesday, May 04, 2011 10:34 AM To: i2b2 AUG Members
Subject: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Has anyone built a custom ontology for CPT/HCPC codes? If so, is it something proprietary or something I could get? In i2b2 speak, I am looking for records that would have been loaded into i2b2metadata.I2B2 for CPT/HCPC query paths... This is NOT a request for an icd9 procedure tree (we already have one).
Any help is appreciated.
Cheers!
Daniel Sullivan


NEXT EMAIL
From: Mobed, Ketty Sent: Wednesday, May 04, 2011 3:23 PM To: 'Cowall, Jeff'; 'Daniel Sullivan'; 'Robert Curtis Hendrickson' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Thanks Jeff.
But I am still perplexed that there isn't already a one-tier less granular CPT ontology available, as I am thinking that nodes at the top wouldn't change that dramatically from version to version, only codes at the most granular level and those could be revised on an annual basis.
Is there a way to work with the AMA folks to create the CPT ontology for common use or does this cut into their purse string? It just makes so much more sense to me, as we are all trying to bring this into our i2b2 work benches.
Ketty

From: Cowall, Jeff Sent: Wednesday, May 04, 2011 11:36 AM To: Mobed, Ketty; 'Daniel Sullivan'; 'Robert Curtis Hendrickson' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
I wish...
What I found here was that there were/are many lookup table copies floating around, but that nobody had the official "tree". Makes sense actually, from an infrastructure development point of view. Ultimately, we decided that having an authoritative reference for the research community had value, and that the annual fee was more cost-effective than the staff resources that would be used to develop one.
Besides, the data does indeed change...codes do fall out of use, and new codes are generated each year. Last I looked, "h1n1 virus" had been added recently, for example. Versioning references will certainly be a source of lively (if obscure) discussions in the future, I'm sure.
Beyond that, makes me yearn for effective Master Data Management at the enterprise level...
jeff

From: Mobed, Ketty Sent: Wednesday, May 04, 2011 2:22 PM To: Cowall, Jeff; 'Daniel Sullivan'; 'Robert Curtis Hendrickson' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
I'm just wondering, since most of us work at clinical institutions that already have CPT licenses wouldn't it be already available for us to develop the CPT ontology?
Thanks for the brainstorm.
Ketty

From: Cowall, Jeff Sent: Wednesday, May 04, 2011 11:12 AM To: 'Daniel Sullivan'; 'Robert Curtis Hendrickson' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
The codes and ontology are copywritten property of the AMA...you won't find a decent freebie.
We pay an annual fee to Ingenix for their CPT4 Category Code product, which has an (up to) five node deep "path" for each code as well as description fields. It's something like $2500 base license + $15/per user annually.
We wrote some java code to generate sql from it. It's pretty ad hoc, but I think we'd be glad to share it.
Daniel, I think James Law also write you, too. We're in the same group.
Cheers, Jeff

From: Daniel Sullivan Sent: Wednesday, May 04, 2011 1:59 PM To: 'Robert Curtis Hendrickson' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
I've been down that road too. I call it 'poor man's categorization'. Don't beat yourself up, if I find something I will make it available. So far, I have gotten some really good lede's from the community.
Cheers!

From: Robert Curtis Hendrickson Sent: Wednesday, May 04, 2011 9:01 AM To: 'Daniel Sullivan'
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Daniel,
If someone provides one, we could really use it, too!
Right now we use a ghastly and useless ontology based on 1st, 2nd, 3rd, letters of the procedure name.
Totally impractical for browsing, but keeps the gui from breaking....
Regards,
Curtis

From: Daniel Sullivan Sent: Wednesday, May 04, 2011 10:34 AM To: i2b2 AUG Members
Subject: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Has anyone built a custom ontology for CPT/HCPC codes? If so, is it something proprietary or something I could get? In i2b2 speak, I am looking for records that would have been loaded into i2b2metadata.I2B2 for CPT/HCPC query paths... This is NOT a request for an icd9 procedure tree (we already have one).
Any help is appreciated.
Cheers!
Daniel Sullivan


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From: Chan, Wayne Sent: Wednesday, May 04, 2011 2:59 PM To: 'i2b2 AUG Members'
Subject: problem with i2b2 Desktop VMWare Image 1.4
I downloaded the i2b2 Desktop VMWare Image 1.4 and unzipped it on my linux host. I then added it (Add Virtual Machine to Inventory) to my VMware Server 2, powered it on. However, there appear to be at least these following 2 problems with it:
1) Failed IP set up for eth0 – as a result, there is no IP addr configured
2) Unable to start eclipse (error msg: Failed to execute child process "eclipse" (No such file or directory)



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From: Arvinder Choudhary Sent: Wednesday, May 04, 2011 2:59 PM To: i2b2 AUG Members; Russ Waitman; Daniel Sullivan Cc: Dan Connolly
Subject: Re: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Daniel and Fellow i2b2tians
I am more than happy to share the scripts that I modified after receiving it from - Phillips Reeder (University of THSC at houston) to extract data from UMLS.
Regards
Arvinder Choudhary
BE MS PMP Medical informatics Project Director University of Kansas Medical Center 3901 Rainbow Blvd, KS 66160

Russ Waitman 5/4/2011 10:46 AM
Daniel, If you're academic use, you can download the concept ontologies from the UMLS and then process them into an i2b2 ontology. Arvinder Choudhary on our team lead that effort. He can probably comment more but some of our code is on our trac site at http://informatics.kumc.edu/work/browser/heron_load/cpt_build
You can also browse more details if you search "CPT" on that site.
Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center http://informatics.kumc.edu

Daniel Sullivan 5/4/2011 10:33 AM
Has anyone built a custom ontology for CPT/HCPC codes? If so, is it something proprietary or something I could get? In i2b2 speak, I am looking for records that would have been loaded into i2b2metadata.I2B2 for CPT/HCPC query paths... This is NOT a request for an icd9 procedure tree (we already have one).
Any help is appreciated.
Cheers!
Daniel Sullivan


NEXT EMAIL
From: Key, Dustin Sent: Wednesday, May 04, 2011 2:36 PM To: 'Daniel Sullivan' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Dan,
I'd be happy to share the SAS code that builds the ontology from the UMLS sources. I just can't send the metadata itself, due to my understanding of the UMLS licensing which has language such as
LICENSEE is prohibited from distributing the UMLS Metathesaurus or subsets of it, including individual vocabulary sources within the Metathesaurus, except (a) as an integral part of computer applications developed by LICENSEE for a purpose other than redistribution of vocabulary sources contained in the UMLS Metathesaurus and (b) if permitted by paragraph 12 of this agreement.

From: Daniel Sullivan Sent: Wednesday, May 04, 2011 10:55 AM To: Key, Dustin Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
I would be interested in looking at it. I've built hierarchies for CPT before, so this is not a huge concern. I just don't want to re-invent the wheel if the 'processed' (ready for the i2b2 tables) version is already done and I just need to download it.
Separate note, this community seems very responsive to questions and help – very good sign considering I am new to it (i2b2) J
Thanks for the help!

From: Key, Dustin Sent: Wednesday, May 04, 2011 9:24 AM To: 'Russ Waitman'; i2b2 AUG Members; Daniel Sullivan Cc: Arvinder Choudhary; Dan Connolly
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Daniel,
Also, if you are looking for SAS code to build the hierarchy and the concept_dimension data from UMLS for HCPCS and CPT4, I may be able to help you --I have some code.

Dustin

From: Russ Waitman Sent: Wednesday, May 04, 2011 8:46 AM To: i2b2 AUG Members; Daniel Sullivan Cc: Arvinder Choudhary; Dan Connolly
Subject: Re: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Daniel,
If you're academic use, you can download the concept ontologies from the UMLS and then process them into an i2b2 ontology. Arvinder Choudhary on our team lead that effort. He can probably comment more but some of our code is on our trac site at http://informatics.kumc.edu/work/browser/heron_load/cpt_build
You can also browse more details if you search "CPT" on that site.
Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center http://informatics.kumc.edu

Daniel Sullivan 5/4/2011 10:33 AM
Has anyone built a custom ontology for CPT/HCPC codes? If so, is it something proprietary or something I could get? In i2b2 speak, I am looking for records that would have been loaded into i2b2metadata.I2B2 for CPT/HCPC query paths... This is NOT a request for an icd9 procedure tree (we already have one).
Any help is appreciated.
Cheers!
Daniel Sullivan


NEXT EMAIL
From: Justin Prosser Sent: Wednesday, May 04, 2011 2:30 PM To: Mobed, Ketty Cc: 'Cowall, Jeff'; 'Daniel Sullivan'; 'Robert Curtis Hendrickson'; i2b2 AUG Members
Subject: Re: An i2b2 Style concept/ontology tree for CPT/HCPC codes
I think the details are here: http://www.ama-assn.org/ama/pub/physician-resources/solutions-managing-your-practice/coding-billing-insurance/cpt/frequentlyasked-questions.page?
Q: I just want to incorporate CPT material into my information management system. What kind of license do I need?
A: You need an end user or "internal use" license. An internal use license gives permission when CPT will only be used within a company and will not be redistributed. The royalty fee for an internal use license is $80 per legal entity plus $13.50 per user. The CPT data file is included in the license fee.
So I'd assume your institution would need to pay per user in this case and they also have wording "per user per product" for the distribution license which sounds a bit aggressive. -Justin

On May 4, 2011, at 11:22 AM, Mobed, Ketty wrote:
I'm just wondering, since most of us work at clinical institutions that already have CPT licenses wouldn't it be already available for us to develop the CPT ontology?
Thanks for the brainstorm.
Ketty

From: Cowall, Jeff Sent: Wednesday, May 04, 2011 11:12 AM To: 'Daniel Sullivan'; 'Robert Curtis Hendrickson' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
The codes and ontology are copywritten property of the AMA...you won't find a decent freebie. > We pay an annual fee to Ingenix for their CPT4 Category Code product, which has an (up to) five node deep "path" for each code as well as description fields.
It's something like $2500 base license + $15/per user annually.
We wrote some java code to generate sql from it. It's pretty ad hoc, but I think we'd be glad to share it.
Daniel, I think James Law also write you, too. We're in the same group.
Cheers,
Jeff

From: Daniel Sullivan Sent: Wednesday, May 04, 2011 1:59 PM To: 'Robert Curtis Hendrickson' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
I've been down that road too. I call it 'poor man's categorization'. Don't beat yourself up, if I find something I will make it available. So far, I have gotten some really good lede's from the community.
Cheers!

From: Robert Curtis Hendrickson Sent: Wednesday, May 04, 2011 9:01 AM To: 'Daniel Sullivan'
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Daniel,
If someone provides one, we could really use it, too!
Right now we use a ghastly and useless ontology based on 1st, 2nd, 3rd, letters of the procedure name.
Totally impractical for browsing, but keeps the gui from breaking....
Regards,
Curtis

From: Daniel Sullivan Sent: Wednesday, May 04, 2011 10:34 AM To: i2b2 AUG Members
Subject: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Has anyone built a custom ontology for CPT/HCPC codes? If so, is it something proprietary or something I could get? In i2b2 speak, I am looking for records that would have been loaded into i2b2metadata.I2B2 for CPT/HCPC query paths... This is NOT a request for an icd9 procedure tree (we already have one).
Any help is appreciated.
Cheers!
Daniel Sullivan


NEXT EMAIL
From: Mobed, Ketty Sent: Wednesday, May 04, 2011 2:18 PM To: 'Key, Dustin' Cc: i2b2 AUG Members
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Hi Dustin,
I build the terminology trees in Xcel and then transform the hierarchy into an .owl file using Protégé for visualization (e.g. the ICD9 tree http://bioportal.bioontology.org/visualize/45221 in BioPortal). That's why I wanted to know if you already had the CPT hierarchy (ontology tree) developed.
Thanks, Ketty

From: Key, Dustin Sent: Wednesday, May 04, 2011 10:47 AM To: Mobed, Ketty; 'Russ Waitman'; i2b2 AUG Members; Daniel Sullivan Cc: Arvinder Choudhary; Dan Connolly
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Hi Ketty,
I'm afraid I'm going to demonstrate some of my own ignorance in this matter and say that I don't know what owl files are. :+) I've been working with RRF extracts from UMLS, specifically sources MTHCH2010, MTHHH2010 , CPT2010, and HCPC2010, and using the MRHIER and MRCONSO tables from those sources to build the ontology tree for i2b2.
Dustin

From: Mobed, Ketty Sent: Wednesday, May 04, 2011 9:36 AM To: Key, Dustin; 'Russ Waitman'; i2b2 AUG Members; Daniel Sullivan Cc: Arvinder Choudhary; Dan Connolly
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Hi Dustin,
Have owl files already been created for CPT4 and HCPCS?
Thanks, Ketty
Ketty Mobed, PhD MSPH Research Analyst / Terminologist ITS - Academic Research Systems UCSF - Campus Box 0707

From: Key, Dustin Sent: Wednesday, May 04, 2011 9:24 AM To: 'Russ Waitman'; i2b2 AUG Members; Daniel Sullivan Cc: Arvinder Choudhary; Dan Connolly
Subject: RE: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Daniel,
Also, if you are looking for SAS code to build the hierarchy and the concept_dimension data from UMLS for HCPCS and CPT4, I may be able to help you --I have some code.
Dustin

From: Russ Waitman Sent: Wednesday, May 04, 2011 8:46 AM To: i2b2 AUG Members; Daniel Sullivan Cc: Arvinder Choudhary; Dan Connolly
Subject: Re: An i2b2 Style concept/ontology tree for CPT/HCPC codes
Daniel,
If you're academic use, you can download the concept ontologies from the UMLS and then process them into an i2b2 ontology. Arvinder Choudhary on our team lead that effort. He can probably comment more but some of our code is on our trac site at http://informatics.kumc.edu/work/browser/heron_load/cpt_build
You can also browse more details if you search "CPT" on that site.
Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center http://informatics.kumc.edu

Daniel Sullivan 5/4/2011 10:33 AM
Has anyone built a custom ontology for CPT/HCPC codes? If so, is it something proprietary or something I could get? In i2b2 speak, I am looking for records that would have been loaded into i2b2metadata.I2B2 for CPT/HCPC query paths... This is NOT a request for an icd9 procedure tree (we already have one).
Any help is appreciated.
Cheers!
Daniel Sullivan


NEXT EMAIL
From: Mendis, Michael E. Sent: Tuesday, May 03, 2011 2:45 PM To: Travis Nagler; i2b2 AUG Members
Subject: Re: 1.5.2 login problem
Take a look at some of the * ds.xml files in the jboss deploy diretory and make sure they point to a correct database.
mike

On 5/3/11 2:38 PM, Travis Nagler wrote:
Also, after starting JBOSS, I keep getting the following repeating error:
11:14:26,456 ERROR [TimerImpl] Error invoking ejbTimeout: javax.ejb.EJBException: org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get JDBC Connection; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Io exception: The Network Adapter could not establish the connection) 11:16:26,470 ERROR [TimerImpl] Error invoking ejbTimeout: javax.ejb.EJBException: org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get JDBC Connection; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Io exception: The Network Adapter could not establish the connection) 11:16:26,475 ERROR [TimerImpl] Error invoking ejbTimeout: javax.ejb.EJBException: org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get JDBC Connection; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Io exception: The Network Adapter could not establish the connection) 11:18:26,488 ERROR [TimerImpl] Error invoking ejbTimeout: javax.ejb.EJBException: org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get JDBC Connection; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Io exception: The Network Adapter could not establish the connection) 11:18:26,494 ERROR [TimerImpl] Error invoking ejbTimeout: javax.ejb.EJBException: org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get JDBC Connection; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Io exception: The Network Adapter could not establish the connection)
Would this be holding back on connecting to the db through the web client? What can I do to fix this?

Thanks,
Travis
Travis H. Nagler
Senior Database Programmer American Burn Assoc. Data Coordinating Center UC Davis Division of Burn Surgery UC Davis Health System 2921 Stockton Blvd., Suite 1470 Sacramento, CA, 95817 http://www.ucdmc.ucdavis.edu

From: Daniel Sullivan To: Travis Nagler, i2b2 AUG Members Date: 05/02/2011 01:04 PM
Subject: RE: 1.5.2 login problem
Have you tried looking at the whitelist/blacklist entries for the web?client (this is a php file). • index.php

From: Travis Nagler Sent: Monday, May 02, 2011 12:38 PM To: i2b2 AUG Members
Subject: 1.5.2 login problem
I have been following the instructions for a 1.5.2 install. I have also ran through this with the sys admin who runs the i2b2 server for us and has experience with our 1.3 install.
There have been no errors during the data import, setting up the required software (Ant, Java, etc.), or during any part of the initial PM install. However, when I get to Section 4 in the Project_Management_Installation_Guide_15.pdf instructions which says to login into the web client with an admin user/pwd (i2b2/demouser), no user name or password I have can get me into the client. I have tried demo, i2b2, i2b2demo, whatever. I keep getting the same error message (see below).
We have not been able to find any problems in the logs, and it actually looks like NOTHING is going to the logs right now. So we u ed the Workbench to see if we could get an error to work on. When I use the "i2b2workbench.exe" program on my computer, I am able to login using "i2b2" and "demouser", but get an immediate error once the workbench actually shows on the screen. It is a long message. The first portion of it is below, and I have attached the whole error in the text file below.
Time Thread Level Category Message
9250 main INFO edu.harvard.i2b2.eclipse.login.LoginDialog workbench message version=
1.1 10201 main INFO edu.harvard.i2b2.eclipse.login.LoginDialog http://i2b2dev02.ucdmc.ucdavis.edu:9090/i2b2/rest/PMService/getVersion
<http://i2b2dev02.ucdmc.ucdavis.edu:9090/i2b2/rest/PMService/getVersion>
10202 main INFO edu.harvard.i2b2.eclipse.login.LoginDialog version response: <ns3:response xmlns:ns2="http://www.i2b2.org/xsd/hive/msg/1.1/ <http://www.i2b2.org/xsd/hive/msg/1.1/> " xmlns:ns4="http://www.i2b2.org/xsd/cell/pm/1.1/ <http://www.i2b2.org/xsd/cell/pm/1.1/> " xmlns:ns3 ="http://www.i2b2.org/xsd/hive/msg/version/ <http://www.i2b2.org/xsd/hive/msg/version/> " xmlns:tns="http://ws.pm.i2b2.harvard.edu <http://ws.pm.i2b2.harvard.edu/> "> <message_body> <i2b2_message_version>1.1</i2b2_message_version> </message_body> </ns3:response> 18253 main INFO edu.harvard.i2b2.previousquery.ui.PreviousQueryPanel Previous Query plugin version 1.5.0 19679 main INFO org.apache.commons.httpclient.HttpMethodDirector I/O exception (java.net.ConnectException) caught when processing request: Connection refused: connect 19682 main INFO org.apache.commons.httpclient.HttpMethodDirector Retrying request 20695 main INFO org.apache.commons.httpclient.HttpMethodDirector I/O exception (java.net.ConnectException) caught when processing request: Connection refused: connect 20696 main INFO org.apache.commons.httpclient.HttpMethodDirector Retrying request 21699 main INFO org.apache.commons.httpclient.HttpMethodDirector I/O exception (java.net.ConnectException) caught when processing request: Connection refused: connect 21701 main INFO org.apache.commons.httpclient.HttpMethodDirector Retrying request 22703 main ERROR org.apache.axis2.transport.http.RESTSender Error in processing POST request
Also, following the instructions in Section 2.7 of the Data Installation Guide_1-5-1.pdf, we tested the connection to the client but got the following error there, as well.
Website: http://i2b2dev02.ucdmc.ucdavis.edu:9090/i2b2/rest/PMService
<http://i2b2dev02.ucdmc.ucdavis.edu:9090/i2b2/rest/PMService>
Error: "This XML file does not appear to have any style information associated with it. The document tree is shown below.
<soapenv:Fault> <faultcode/> <faultstring>
I can not find a service for this request to be serviced. Check the WSDL and the request URI; nested exception is: org.apache.axis2.AxisFault: I can not find a service for this request to be serviced. Check the WSDL and the request URI </faultstring> <detail/> </soapenv:Fault>"
I cannot seem to establish a connection to the db. I have been having this problem for over a week now and need to get this fixed. We have gone through the instructions in detail, but cannot get the connection to be established.
Does anyone have any thoughts of what I might try next to get logged in to the web client?

Thanks,
Travis
Travis H. Nagler
Senior Database Programmer American Burn Assoc. - Data Coordinating Center UC Davis Division of Burn Surgery UC Davis Health System 2921 Stockton Blvd., Suite 1470 Sacramento, CA, 95817 http://www.ucdmc.ucdavis.edu



NEXT EMAIL
From: Chan, Wayne Sent: Tuesday, May 03, 2011 9:18 AM To: 'i2b2 AUG Members' Cc: Sadasivam, Rajani
Subject: RE: REgine Cell Plugin..
Hi, all,
I haven't heard back from any one, so I assume the answer is no – so I'll try to narrow it to a question concerning general adaptation of earlier plugins (developed on earlier i2b2 versions) to the latest i2b2 versions (v.1.5 forward), as following:
These earlier plugins require that an .aar file be copied to "/opt/apachetomcat-5.5.23/webapps/axis2/WEB-INF/services", as well as a group of jaxb-. files (jaxb-api.jar, jaxb-impl.jar, jaxb-LICENSE.txt, and jaxb-xjc.jar) be copied to "/opt/apache-tomcat-5.5.23/webapps/axis2/WEB-INF/lib", respectively.
Since from v.1.5 (I believe) onward, i2b2 doesn't call for tomcat anymore, that presents somewhat of a problem of "legacy support".
I found that the other .aar files are located in " /opt/jboss-4.2.2.GA/server/default/deploy/i2b2.war/WEB-INF/" on my i2b2 v1.6 system. So, I copied the REninge.aar in "/opt/apache-tomcat-5.5.23/webapps/axis2/WEB-INF/services" over to " /opt/jboss-4.2.2.GA/server/default/deploy/i2b2.war/WEB-INF/services", and the jaxb-api.jar, jaxbimpl.jar, jaxb-LICENSE.txt, and jaxb-xjc.jar in "/opt/apache-tomcat-5.5.23/webapps/axis2/WEBINF/lib" over to "/opt/jboss-4.2.2.GA/server/default/deploy/i2b2.war/WEB-INF/lib" also.
Now, the REngine Service is finally displayed in the List Services, as expected. However, when I browsed to the web admin, there were several errors. The errors no longer appear after I removed those 4 jaxb-. files from "/opt/jboss-4.2.2.GA/server/default/deploy/i2b2.war/WEB-INF/lib".
However, that leaves me in the catch-22 situation – w/o these jaxb-. files in the right place for the REgine Cell plugin to marshall & unmarshall the xml messages, it doesn't work.
So, does anyone know where to place those jaxb-. files in v.1.5 onward?
Thanks.
Wayne

From: Chan, Wayne Sent: Monday, May 02, 2011 1:18 PM To: 'i2b2 AUG Members' Cc: Sadasivam, Rajani
Subject: REgine Cell Plugin..
Hi,
Has anybody successfully installed the REngine Cell plugin (http://code.google.com/p/i2b2-rengine-project/wiki/HowTo) to i2b2 v1.5 or later?
Thanks.
Wayne



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From: Daniel Sullivan Sent: Monday, May 02, 2011 1:06 PM To: 'Wei,Xintao'; i2b2 AUG Members
Subject: RE: Webclient problem
You need to check the JBoss log and the Apache log (assuming you are using Apache and Jboss) to get better precision around these errors. There are cases where the 'top level' error does not give you the real cause. I have found the JBoss log to be the most helpful, secondarily the apache log. Make sure you have the debug message/logging turned on for JBoss though. The web client is really just a thin Javascript/ajax app, so the 'real' action is happening in the middle tier and I don't think the EJB services bubble up very good error message via the web service response.

From: Wei,Xintao Sent: Monday, May 02, 2011 9:59 AM To: i2b2 AUG Members
Subject: Webclient problem
Hi,
We installed the I2B2 1.52 to our windows server 2008 with sql server 2005.
I have a problem about the webclient:
A "undefined" message will popup when our queries returns 0 hits. After closing the popup window, the "Query status" panel still showed that the query is running and the time still counting up, and no more queries can be run and no way to stop the query. The server didn't show any errors or warnings. If we logout the webclient and login again, the query stopped and new queries can be run again.
I tried the same queries that occur the problem on the WorkBench, no "undefined" message popup and everything looked fine to me. So this problem only happens in webclient.
We are running the webclient on IE 8. Does the IE 8 occur the problem?
I tested the webclient 1.52 and 1.6 with our queries. Both of them will have the problem with the "undefined" popup messages.
Not all queries with 0 hits will have the popup messages. We will not have popup messages if the queries with 0 hits only have one group of query term. However, we will have the popup messages if the queries with 0 hits contain terms in more than one group, for example, term1 in group1 AND term2 in group2.
Any suggestions?
Thank you!
Xintao



NEXT EMAIL
From: Churchill, Susanne E. Sent: Monday, May 02, 2011 9:39 AM To: i2b2 AUG Members
Subject: NLP Meeting Agenda
Please find attached the agenda for the AUG NLP Meeting scheduled for the morning of Tuesday, June 28, 2011 - just before the start of the full AUG meeting.
Please register with me if you plan to attentd.
REMINDER: PLEASE REGISTER WITH ME IF YOU WILL BE ATTENDING THE FULL AUG MEETING JUNE 28-29, 12PM-12PM.
Thanks,
Susanne