Last Updated: 07/27/2011

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From: Michael.C.Ford.kp Sent: Wednesday, July 27, 2011 5:52 PM To: peter.kenah.duke Cc: i2b2 AUG MembersSubject: Re: Cloning a Jboss installation
I just did somthing like that. only changed *-ds.xml files in the deploy folder crc-ds.xml ont-ds.xml
etc.

From: Peter Kenah peter.kenah.duke Sent: 07/27/2011 01:44 PM To: members.i2b2aug Subject: Cloning a Jboss installation
I have working i2b2 server and we coped all the tables to another schema and then did the following:

Copy the entire jboss directory to a new location
We then edited all the config files in the new jboss home to change the usernames and password to the new schema
We were able to start jboss at the new location and it started. But when we use the workbench we get the following errors:
[jkhan.phl-dwetl06 dwgadmin]$ 17:09:21,020 ERROR [ServicesHandler] Environment group has not been setup 17:09:21,021 ERROR [STDERR] java.lang.Exception: Environment group has not been setup 17:09:21,022 ERROR [STDERR] at edu.harvard.i2b2.pm.delegate.ServicesHandler.execute(Unknown Source) 17:09:21,022 ERROR [STDERR] at edu.harvard.i2b2.pm.ws.ExecutorRunnable.run(Unknown Source) 17:09:21,022 ERROR [STDERR] at java.lang.Thread.run(Thread.java:662) 17:09:31,830 INFO [PropertiesFactoryBean] Loading properties file from class path resource [crc_application_directory.properties] 17:09:31,894 ERROR [TimerImpl] Error invoking ejbTimeout: javax.ejb.EJBException: java.lang.IllegalArgumentException: dataSource is required 17:09:31,935 INFO [XmlBeanDefinitionReader] Loading XML bean definitions from URL [file:/opt/jboss-4.2.2.GA/server/default/conf/crcapp/CRCApplicationContext.xml] 17:09:31,994 INFO [CollectionFactory] JDK 1.4+ collections available 17:09:32,009 INFO [CollectionFactory] Commons Collections 3.x available 17:09:32,012 INFO [FileSystemXmlApplicationContext] Bean factory for application context [org.springframework.context.support.FileSystemXmlApplicationContext;hashCode=217882540]: org.springframework.beans.factory.support.DefaultListableBeanFactory defining beans [jaxbPackage,appType,message_header,TestDataSourceLookup,TestDataSource,CRCDataSourceLookup,defau ltSetfinderResultType,setFinderResultGeneratorMap]; root of BeanFactory hierarchy 17:09:32,024 INFO [FileSystemXmlApplicationContext] 8 beans defined in application context [org.springframework.context.support.FileSystemXmlApplicationContext;hashCode=217882540]
17:09:32,031 INFO [FileSystemXmlApplicationContext] Unable to locate MessageSource with name 'messageSource': using default [org.springframework.context.support.DelegatingMessageSource.12e60a94] 17:09:32,034 INFO [FileSystemXmlApplicationContext] Unable to locate ApplicationEventMulticaster with name 'applicationEventMulticaster': using default [org.springframework.context.event.SimpleApplicationEventMulticaster.6ac6b7ee] 17:09:32,035 INFO [DefaultListableBeanFactory] Pre-instantiating singletons in factory [org.springframework.beans.factory.support.DefaultListableBeanFactory defining beans [jaxbPackage,appType,message_header,TestDataSourceLookup,TestDataSource,CRCDataSourceLookup,defau ltSetfinderResultType,setFinderResultGeneratorMap]; root of BeanFactory hierarchy]
Questions:
Is this the best method to point jboss to different schemas?
What can I do to fix the errors I am getting


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From: Churchill, Susanne E. Sent: Wednesday, July 27, 2011 2:09 PM To: i2b2 AUG MembersSubject: AUG slides
The slides from the full AUG meeting are now all posted on your webpage: https://www.i2b2.org/work/aug.html as well as a link to the post conference website for the SHRINE Meeting. Slides from the NLP Workshop presentations by the core i2b2 team are also posted.
Susanne


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From: Phillips, Lori C. Sent: Wednesday, July 27, 2011 9:26 AM To: i2b2 AUG MembersSubject: RE: Some information
Addtional information on the date problem. It appears it may be an internationalization issue. I was wondering if any of our other European members using oracle has experienced something like this and what the resolution was.
The sql generated is:
"Select patient_num from i2b2demodata.observation_fact where (((concept_cd in (select concept_cd from i2b2demodata.concept_dimension c where concept_path like '\onto \Diagnostiques\IX-maladies de l appareil circulatoire%')) AND start_date between to_date('10-janv.-2010 01:00:00','DD-MON-YYYY HH24.MIN.SS') AND to_date('25-déc.-2010 01:00:00','DD-MON-YYYY HH24:MI:SS') ))"

From: Audrey Hureau [audrey.hureau.gmail] Sent: Tuesday, July 26, 2011 5:04 AM To: i2b2 AUG MembersSubject: Some information
Hello everyone,
I am wondering something about the workbench.
First at all, I would like to know what the date constrain refers to in the workbench?
Does it refer to the observation's start and end date or to the visit's dates?
Secondly, I would like to know how can I add some features? When I try to add new features from the workbench, i2b2 searches for new features but I have an error message after a few second which says : "Network connection problems encountered during search". When I clik on details I can see :
"Unable to access "https://www.i2b2.org/updatesSites". Error parsing site stream. [Prematured end of file.] Prematured end of file."
Is someone already has had this problem? Do I have to install the features first?
Audrey Hureau


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From: Phillips, Lori C. Sent: Tuesday, July 26, 2011 4:22 PM To: Yves Thorrez Cc: i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] Update patient count information
Recapping for AUG members:
A number of issues were found using a sqlserver database.
1. A user validation bug was found in the ONT cell. It was erroneously looking at the PM response project name instead of project id when validating users. A work around for users hitting this bug today is to rename your projects so that the name matches the id. This bug will be resolved in RC4.
2. The sqlserver QT_BREAKDOWN_PATH entries were incorrect causing the Analysis types gender/race/etc breakdowns to fail and the patient count to fail.

The New Install data scripts for the demodata will be corrected and provided in RC4.
Users having this problem should (SQLSERVER) update your QT_BREAKDOWN_PATH table.
First delete the rows associated with the names below and update with this script:
insert into QT_BREAKDOWN_PATH(name,value,create_date) values ('PATIENT_GENDER_COUNT_XML','
i2b2 _DEMO\i2b2\Demographics\Gender\',getdate())
insert into QT_BREAKDOWN_PATH(name,value,create_date) values ('PATIENT_RACE_COUNT_XML','
i2b2_DEMO \i2b2\Demographics\Race\',getdate())
insert into QT_BREAKDOWN_PATH(name,value,create_date) values ('PATIENT_VITALSTATUS_COUNT_XML','
i2b2 _DEMO\i2b2\Demographics\VitalStatus\',getdate())
insert into QT_BREAKDOWN_PATH(name,value,create_date) values ('PATIENT_AGE_COUNT_XML','
i2b2_DEMO \i2b2\Demographics\Age\',getdate())

From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Friday, July 22, 2011 9:19 AM To: Yves Thorrez; Phillips, Lori C. Cc: i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] Update patient count information
I've reloaded the data in sqlserver, now the NPEs in the response are gone.
Here's the response message:
URL: http://localhost:9090/i2b2/rest/OntologyService/getProcessStatus ns5:response xmlns:ns2="http://www.i2b2/xsd/cell/fr/1.0/" xmlns:ns4 ="http://www.i2b2/xsd/cell/crc/psm/1.1/" xmlns:ns3="http://www.i2b2/xsd/cell/crc/loader/1.1/" xmlns:tns="http://ws.ontology.i2b2.harvard" xmlns:ns9="http://www.i2b2/xsd/cell/pm/1.1/" xmlns:ns5="http://www.i2b2/xsd/hive/msg/1.1/" xmlns:ns6="http://www.i2b2/xsd/cell/ont/1.1/" xmlns:ns7="http://www.i2b2/xsd/cell/crc/psm/querydefinition/1.1/" xmlns:ns8 ="http://www.i2b2/xsd/cell/crc/psm/analysisdefinition/1.1/"
message_header i2b2_version_compatible1.1/i2b2_version_compatible hl7_version_compatible2.4/hl7_version_compatible sending_application
application_nameOntology Cell/application_name
application_version1.5/application_version /sending_application sending_facility
facility_namei2b2 Hive/facility_name /sending_facility receiving_application
application_namei2b2 Workbench/application_name
application_version1.6/application_version /receiving_application receiving_facility
facility_namei2b2 Hive/facility_name /receiving_facility datetime_of_message2011-07-22T15:14:41.812+02:00/datetime_of_message security
domaini2b2demo/domain
usernamedemo/username
password token_ms_timeout="1800000" is_token="true"*********/password /security message_control_id
message_num2NHFcYwmq7sBp2GyTlhs/message_num
instance_num1/instance_num /message_control_id processing_id
processing_idP/processing_id
processing_modeI/processing_mode /processing_id accept_acknowledgement_typeAL/accept_acknowledgement_type application_acknowledgement_typeAL/application_acknowledgement_type country_codeUS/country_code project_idDemo/project_id
/message_header response_header result_status
status type="DONE"Ontology processing completed/status
/result_status /response_header message_body
ns6:ontology_process_status_list / /message_body /ns5:response
And when attempting to update patient count info:
URL: http://localhost:9090/i2b2/rest/OntologyService/updateConceptTotalNum ns5:response xmlns:ns2="http://www.i2b2/xsd/cell/fr/1.0/" xmlns:ns4 ="http://www.i2b2/xsd/cell/crc/psm/1.1/" xmlns:ns3="http://www.i2b2/xsd/cell/crc/loader/1.1/" xmlns:tns="http://ws.ontology.i2b2.harvard" xmlns:ns9="http://www.i2b2/xsd/cell/pm/1.1/" xmlns:ns5="http://www.i2b2/xsd/hive/msg/1.1/" xmlns:ns6="http://www.i2b2/xsd/cell/ont/1.1/" xmlns:ns7="http://www.i2b2/xsd/cell/crc/psm/querydefinition/1.1/" xmlns:ns8 ="http://www.i2b2/xsd/cell/crc/psm/analysisdefinition/1.1/"
message_header i2b2_version_compatible1.1/i2b2_version_compatible hl7_version_compatible2.4/hl7_version_compatible sending_application
application_nameOntology Cell/application_name
application_version1.5/application_version /sending_application sending_facility
facility_namei2b2 Hive/facility_name /sending_facility receiving_application
application_namei2b2 Workbench/application_name
application_version1.6/application_version /receiving_application receiving_facility
facility_namei2b2 Hive/facility_name /receiving_facility datetime_of_message2011-07-22T15:15:49.343+02:00/datetime_of_message security
domaini2b2demo/domain
usernamedemo/username
password token_ms_timeout="1800000" is_token="true"*********/password /security message_control_id
message_numpm9an16gAcQDA9xY4e9c/message_num
instance_num1/instance_num /message_control_id processing_id
processing_idP/processing_id
processing_modeI/processing_mode /processing_id accept_acknowledgement_typeAL/accept_acknowledgement_type application_acknowledgement_typeAL/application_acknowledgement_type country_codeUS/country_code project_idDemo/project_id
/message_header response_header result_status
status type="ERROR"User does not have correct privileges/status /result_status /response_header /ns5:response

From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: vrijdag 22 juli 2011 14:08 To: Phillips, Lori C. Cc: i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] Update patient count information
Lori,
This is the request message; it has the project_id filled in. The response message (below) contains a bunch of NullPointerExceptions.
URL: http://localhost:9090/i2b2/rest/OntologyService/getProcessStatus ns4:request xmlns:ns2="http://www.i2b2/xsd/hive/pdo/1.1/" xmlns:ns4 ="http://www.i2b2/xsd/hive/msg/1.1/" xmlns:ns3="http://www.i2b2/xsd/hive/plugin/" xmlns:ns5 ="http://www.i2b2/xsd/cell/ont/1.1/"
message_header i2b2_version_compatible1.1/i2b2_version_compatible hl7_version_compatible2.4/hl7_version_compatible sending_application
application_namei2b2 Workbench/application_name
application_version1.6/application_version /sending_application sending_facility
facility_namei2b2 Hive/facility_name /sending_facility receiving_application
application_nameOntology Cell/application_name
application_version1.6/application_version /receiving_application receiving_facility
facility_namei2b2 Hive/facility_name
/receiving_facility datetime_of_message2011-07-22T13:53:52.562+02:00/datetime_of_message security
domaini2b2demo/domain usernamedemo/username password token_ms_timeout="1800000" is_token="true"*********/password
/security
message_control_id message_numyaDXyit5Gq4uuH41DyCE/message_num instance_num0/instance_num
/message_control_id
processing_id processing_idP/processing_id processing_modeI/processing_mode
/processing_id accept_acknowledgement_typeAL/accept_acknowledgement_type application_acknowledgement_typeAL/application_acknowledgement_type country_codeUS/country_code project_idDemo/project_id
/message_header request_header
result_waittime_ms120000/result_waittime_ms /request_header message_body
ns5:get_ont_process_status max_return_records="100"
process_type_cdONT_PATIENT_COUNT_UPDATE/process_type_cd
/ns5:get_ont_process_status /message_body /ns4:request
URL: http://localhost:9090/i2b2/rest/OntologyService/getProcessStatus ns5:response xmlns:ns2="http://www.i2b2/xsd/cell/fr/1.0/" xmlns:ns4 ="http://www.i2b2/xsd/cell/crc/psm/1.1/" xmlns:ns3="http://www.i2b2/xsd/cell/crc/loader/1.1/" xmlns:tns="http://ws.ontology.i2b2.harvard" xmlns:ns9="http://www.i2b2/xsd/cell/pm/1.1/" xmlns:ns5="http://www.i2b2/xsd/hive/msg/1.1/" xmlns:ns6="http://www.i2b2/xsd/cell/ont/1.1/" xmlns:ns7="http://www.i2b2/xsd/cell/crc/psm/querydefinition/1.1/" xmlns:ns8 ="http://www.i2b2/xsd/cell/crc/psm/analysisdefinition/1.1/"
message_header i2b2_version_compatible1.1/i2b2_version_compatible hl7_version_compatible2.4/hl7_version_compatible sending_application
application_nameOntology Cell/application_name
application_version1.5/application_version /sending_application sending_facility
facility_namei2b2 Hive/facility_name /sending_facility receiving_application
application_namei2b2 Workbench/application_name
application_version1.6/application_version /receiving_application receiving_facility
facility_namei2b2 Hive/facility_name /receiving_facility
datetime_of_message2011-07-22T13:53:52.984+02:00/datetime_of_message
security domaini2b2demo/domain usernamedemo/username password token_ms_timeout="1800000" is_token="true"*********/password
/security
message_control_id message_numyaDXyit5Gq4uuH41DyCE/message_num instance_num1/instance_num
/message_control_id
processing_id processing_idP/processing_id processing_modeI/processing_mode
/processing_id accept_acknowledgement_typeAL/accept_acknowledgement_type application_acknowledgement_typeAL/application_acknowledgement_type country_codeUS/country_code project_idDemo/project_id
/message_header response_header result_status
status type="DONE"Ontology processing completed/status
/result_status /response_header message_body
ns6:ontology_process_status_list
ontology_process_status process_id5/process_id process_type_cdONT_PATIENT_COUNT_UPDATE/process_type_cd process_step_cdPROCESSED 5513/135068/process_step_cd start_date2011-07-21T19:55:58.277+02:00/start_date end_date2011-07-21T21:17:17.133+02:00/end_date process_status_cdERROR/process_status_cd messagejava.lang.NullPointerException at
edu.harvard.i2b2.ontology.dao.CRCConceptTotalNumUpdateDao.updateConceptTotalNum(Unknown Source) at edu.harvard.i2b2.ontology.delegate.UpdateTotalNumRunnable.runnable(Unknown Source) at edu.harvard.i2b2.ontology.delegate.ExecutorRunnable.run(Unknown Source) at java.lang.Thread.run(Thread.java:662) /message /ontology_process_status ontology_process_status process_id6/process_id process_type_cdONT_PATIENT_COUNT_UPDATE/process_type_cd process_step_cdPROCESSED 0/129592/process_step_cd start_date2011-07-21T21:24:30.760+02:00/start_date end_date2011-07-21T21:24:34.277+02:00/end_date process_status_cdERROR/process_status_cd messagejava.lang.NullPointerException
at edu.harvard.i2b2.ontology.dao.CRCConceptTotalNumUpdateDao.updateConceptTotalNum(Unknown Source)
at edu.harvard.i2b2.ontology.delegate.UpdateTotalNumRunnable.runnable(Unknown
37
Source)
at edu.harvard.i2b2.ontology.delegate.ExecutorRunnable.run(Unknown Source) at java.lang.Thread.run(Thread.java:662)
/message /ontology_process_status ontology_process_status
process_id7/process_id process_type_cdONT_PATIENT_COUNT_UPDATE/process_type_cd process_step_cdPROCESSED 0/129592/process_step_cd start_date2011-07-21T21:25:51.540+02:00/start_date end_date2011-07-21T21:25:54.370+02:00/end_date process_status_cdERROR/process_status_cd messagejava.lang.NullPointerException at
edu.harvard.i2b2.ontology.dao.CRCConceptTotalNumUpdateDao.updateConceptTotalNum(Unknown Source) at edu.harvard.i2b2.ontology.delegate.UpdateTotalNumRunnable.runnable(Unknown Source) at edu.harvard.i2b2.ontology.delegate.ExecutorRunnable.run(Unknown Source) at java.lang.Thread.run(Thread.java:662) /message /ontology_process_status ontology_process_status process_id8/process_id process_type_cdONT_PATIENT_COUNT_UPDATE/process_type_cd process_step_cdPROCESSED 626/135068/process_step_cd start_date2011-07-21T21:27:33.620+02:00/start_date end_date2011-07-21T21:36:40.977+02:00/end_date
process_status_cdERROR/process_status_cd
messageedu.harvard.i2b2mon.exception.I2B2Exception: java.lang.NullPointerException
at org.jboss.ejb.plugins.local.BaseLocalProxyFactory.invokeHome(BaseLocalProxyFactory.java:342)
at org.jboss.ejb.plugins.local.LocalHomeProxy.invoke(LocalHomeProxy.java:133)
at $Proxy136.create(Unknown Source)
at edu.harvard.i2b2.crc.delegate.setfinder.DeleteQueryMasterHandler.execute(Unknown Source)
at edu.harvard.i2b2.crc.delegate.setfinder.QueryRequestDelegate.handleRequest(Unknown Source)
at edu.harvard.i2b2.crc.axis2.QueryService.handleRequest(Unknown Source)
at edu.harvard.i2b2.crc.axis2.QueryService.request(Unknown Source)
at sun.reflect.GeneratedMethodAccessor116.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.axis2.receivers.RawXMLINOutMessageReceiver.invokeBusinessLogic(RawXMLINOutMe ssageReceiver.java:88)
at org.apache.axis2.receivers.AbstractInOutSyncMessageReceiver.receive(AbstractInOutSyncMessage Receiver.java:39)
at org.apache.axis2.engine.AxisEngine.receive(AxisEngine.java:493)
at org.apache.axis2.transport.http.util.RESTUtil.invokeAxisEngine(RESTUtil.java:153)
at org.apache.axis2.transport.http.util.RESTUtil.processPostRequest(RESTUtil.java:102)
at org.apache.axis2.transport.http.AxisRESTServlet.doPost(AxisRESTServlet.java:66)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:710)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:96) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)/me ssage /ontology_process_status /ns6:ontology_process_status_list /message_body /ns5:response

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: vrijdag 22 juli 2011 13:32 To: Yves Thorrez Cc: i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] Update patient count information
Yves,
Sorry for the questions .. but the issue of project_id = null is hard to track down.
When you first start up the workbench there is some messaging that occurs to log-in, set up the views, etc. The very first message you send to PM cell on log in will have project_id = null (because you have not chosen one yet).
This is normal behavior and I am not concerned about this. However, after you choose your project, all messages should have that parameter set.
Specifically I would like you to look at this: Start up the workbench; log in, choose project. On the Utility view, look at the messaging window.
It will have one message pair in the window.
What does the request ("Sent") message look like?
If this message has project_id set to null.... Open up the Navigate Terms views messaging window. What does the first request ("sent") message look like?
Thanks
Lori

From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Thursday, July 21, 2011 3:58 PM To: Phillips, Lori C. Cc: i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] Update patient count information
Lori,
Interestingly, I changed the role of user demo in project Demo2 to ADMIN as well; then logged into the workbench – like before as user demo on project Demo (not Demo2) – and it works.
Even changing the role of user demo in project Demo to USER will allow the updating.
It looks like it's only the role under project Demo2 that is considered for the utility.
On another note: when trying to stop the updating of patient information, when hitting the stop button, the process continues (even though [stop] becomes disabled and [start] enabled) .
The message samples below have no project_id. I also noticed – maybe it's irrelevant – there's a difference in these particular elements:
receiving_application application_nameProject Management Cell/application_name application_version1.0/application_version
/receiving_application
receiving_application application_namePM Cell/application_name application_version1.5/application_version
/receiving_application
Sample messages
message_header i2b2_version_compatible1.1/i2b2_version_compatible hl7_version_compatible2.4/hl7_version_compatible sending_application
application_nameOntology Cell/application_name
application_version1.0/application_version /sending_application sending_facility
facility_namei2b2 Hive/facility_name /sending_facility receiving_application
application_nameProject Management Cell/application_name
application_version1.0/application_version /receiving_application receiving_facility
facility_namei2b2 Hive/facility_name /receiving_facility datetime_of_message2011-07-21T19:34:13.431+02:00/datetime_of_message security
domaini2b2demo/domain usernamedemo/username password token_ms_timeout="1800000" is_token="true"
SessionKey:u4nG5h6ppxAAjEOPQK8M/password /security message_control_id
message_numiNcXaPAJllNaEKLsXjbW/message_num
instance_num0/instance_num /message_control_id processing_id
processing_idP/processing_id
processing_modeI/processing_mode /processing_id accept_acknowledgement_typeAL/accept_acknowledgement_type application_acknowledgement_typeAL/application_acknowledgement_type country_codeUS/country_code project_idDemo/project_id
/message_header request_header
result_waittime_ms120000/result_waittime_ms /request_header message_body
ns9:get_user_configuration / /message_body
message_header i2b2_version_compatible1.0/i2b2_version_compatible hl7_version_compatible2.4/hl7_version_compatible sending_application
application_namei2b2 Project Management/application_name
application_version1.0/application_version /sending_application sending_facility
facility_namei2b2 Hive/facility_name /sending_facility receiving_application
application_nameProject Management Cell/application_name
application_version1.0/application_version /receiving_application receiving_facility
facility_namei2b2 Hive/facility_name /receiving_facility datetime_of_message2011-07-21T00:06:21.591+02:00/datetime_of_message security
domaini2b2demo/domain
44
usernamedemo/username
password is_token="true"SessionKey:cOKnxaJEoItjL9vLO8HA/password /security message_control_id
message_numQEVWcpSwgof8HCRm9S91/message_num
instance_num0/instance_num /message_control_id processing_id
processing_idP/processing_id
processing_modeI/processing_mode /processing_id accept_acknowledgement_typeAL/accept_acknowledgement_type application_acknowledgement_typeAL/application_acknowledgement_type country_codeUS/country_code project_id xmlns:xsi="http://www.w3/2001/XMLSchema-instance" xsi:nil="true" /
/message_header request_header
result_waittime_ms120000/result_waittime_ms /request_header message_body
ns3:get_user_configuration projecti2b2demo/project /ns3:get_user_configuration /message_body
message_header
sending_application application_nameedu.harvard.i2b2.crc/application_name application_version1.6/application_version
/sending_application sending_facility
facility_namesample/facility_name /sending_facility receiving_application
application_nameedu.harvard.i2b2.crc/application_name
application_version1.6/application_version /receiving_application receiving_facility
facility_namesample/facility_name /receiving_facility security
domaini2b2demo/domain usernameOBFSC_SERVICE_ACCOUNT/username passworddemouser/password
/security
project_idDemo/project_id /message_header request_header
result_waittime_ms180000/result_waittime_ms /request_header message_body
ns8:get_all_role project_idDemo/project_id user_nameOBFSC_SERVICE_ACCOUNT/user_name
/ns8:get_all_role /message_body
message_header i2b2_version_compatible1.1/i2b2_version_compatible hl7_version_compatible2.4/hl7_version_compatible sending_application
application_namePM Cell/application_name
application_version1.5/application_version /sending_application sending_facility
facility_namei2b2 Hive/facility_name /sending_facility receiving_application
application_namePM Cell/application_name
application_version1.5/application_version /receiving_application receiving_facility
facility_namei2b2 Hive/facility_name /receiving_facility datetime_of_message2011-07-21T00:06:21.669+02:00/datetime_of_message
message_control_id
message_numQEVWcpSwgof8HCRm9S91/message_num
instance_num1/instance_num /message_control_id processing_id
processing_idP/processing_id
processing_modeI/processing_mode /processing_id accept_acknowledgement_typeAL/accept_acknowledgement_type application_acknowledgement_typeAL/application_acknowledgement_type country_codeUS/country_code project_id xsi:nil="true" xmlns:xsi="http://www.w3/2001/XMLSchema-instance"/
/message_header response_header result_status
status type="DONE"PM processing completed/status
/result_status /response_header message_body
ns4:configure environmentDEVELOPMENT/environment helpURLhttp://www.i2b2/helpURL user
full_namei2b2 User/full_name user_namedemo/user_name password is_token="true"SessionKey:cOKnxaJEoItjL9vLO8HA/password domaini2b2demo/domain
project id="Demo" namei2b2 Demo/name wikihttp://www.i2b2.org/wiki path/Demo/path roleADMIN/role roleDATA_AGG/role roleDATA_DEID/role roleDATA_LDS/role roleDATA_OBFSC/role roleDATA_PROT/role roleEDITOR/role roleMANAGER/role roleUSER/role
/project
project id="Demo2" namei2b2 Demo2/name wikihttp://www.i2b2.org/wiki path/Demo2/path roleDATA_AGG/role roleDATA_DEID/role roleDATA_LDS/role roleDATA_OBFSC/role roleEDITOR/role roleUSER/role /project
/user
domain_namei2b2demo/domain_name domain_idi2b2/domain_id activetrue/active cell_datas
cell_data id="CRC" nameData Repository/name urlhttp://localhost:9090/i2b2/rest/QueryToolService//url project_path//project_path methodREST/method can_overridetrue/can_override
/cell_data
cell_data id="FRC" nameFile Repository /name urlhttp://localhost:9090/i2b2/services/FRService//url project_path//project_path methodSOAP/method can_overridetrue/can_override
/cell_data
cell_data id="ONT" nameOntology Cell/name urlhttp://localhost:9090/i2b2/rest/OntologyService//url project_path//project_path methodREST/method
can_overridetrue/can_override /cell_data cell_data id="WORK"
nameWorkplace Cell/name
50
urlhttp://localhost:9090/i2b2/rest/WorkplaceService//url project_path//project_path methodREST/method can_overridetrue/can_override
/cell_data /cell_datas global_data/
/ns4:configure /message_body /ns2:response

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: donderdag 21 juli 2011 15:22 To: Yves Thorrez Cc: i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] Update patient count information
Yves,
I thought of something else you should look at....
This utility ultimately sends a message to the ONT cell. Does the sent request message have the project_id set?
As a simple comparison, look at one of the request messages sent by the Navigate Terms view; is the project_id set there?
Lori

From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Wednesday, July 20, 2011 4:33 PM To: Phillips, Lori C.; i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] Update patient count information
Aha... Hadn't spotted it. I'll follow that lead - wouldn't mind a suggestion though as to where to start looking for the cause of the missing project_id? I do log in with project Demo...
Thanks
Yves

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: woensdag 20 juli 2011 21:52 To: Yves Thorrez; i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] Update patient count information
This line says other wise:
project_id xmlns:xsi="http://www.w3/2001/XMLSchema-instance" xsi:nil="true" /
What the code does is look at the project list returned in the message body and loops through for the project matching the one listed in the message_header project_id above. Your project_id is empty so it doesnt find it.

From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Wednesday, July 20, 2011 3:37 PM To: Phillips, Lori C.; i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] Update patient count information
It's definitely project Demo.
Maybe another (re)installation round then...
I also noticed this error when attempting to save a change in the web Admin console (Manage Cells changing project_path from '/' to '\' – which btw is not necessary).
2011-07-20 20:57:53,259 ERROR [edu.harvard.i2b2.pm.delegate.ServicesHandler] PreparedStatementCallback; uncategorized SQLException for SQL [insert into pm_cell_data (cell_id, project_path, name, url, method_cd, can_override, change_date, entry_date, changeby_char, status_cd) values (?,?,?,?,?,?,?,?,?,?)]; SQL state [null]; error code [0]; Error; - nested throwable: (java.lang.NullPointerException); nested exception is org.jboss.util.NestedSQLException: Error; - nested throwable: (java.lang.NullPointerException)
2011-07-20 20:57:53,259 ERROR [STDERR] org.springframework.jdbc.UncategorizedSQLException: PreparedStatementCallback; uncategorized SQLException for SQL [insert into pm_cell_data (cell_id, project_path, name, url, method_cd, can_override, change_date, entry_date, changeby_char, status_cd) values (?,?,?,?,?,?,?,?,?,?)]; SQL state [null]; error code [0]; Error; - nested throwable: (java.lang.NullPointerException); nested exception is org.jboss.util.NestedSQLException: Error; - nested throwable: (java.lang.NullPointerException)
2011-07-20 20:57:53,259 ERROR [STDERR] org.jboss.util.NestedSQLException: Error; - nested throwable: (java.lang.NullPointerException)
2011-07-20 20:57:53,259 ERROR [STDERR] at org.jboss.resource.adapter.jdbc.WrappedConnection.checkException(WrappedConnection.java:557)
2011-07-20 20:57:53,259 ERROR [STDERR] at org.jboss.resource.adapter.jdbc.WrappedStatement.checkException(WrappedStatement.java:563)
2011-07-20 20:57:53,259 ERROR [STDERR] at org.jboss.resource.adapter.jdbc.WrappedPreparedStatement.setNull(WrappedPreparedStatement.jav a:281)
2011-07-20 20:57:53,259 ERROR [STDERR] at org.springframework.jdbc.core.StatementCreatorUtils.setParameterValue(StatementCreatorUtils.java: 96)
2011-07-20 20:57:53,259 ERROR [STDERR] at org.springframework.jdbc.core.JdbcTemplate $ArgPreparedStatementSetter.setValues(JdbcTemplate.java:1176)
2011-07-20 20:57:53,259 ERROR [STDERR] at org.springframework.jdbc.core.JdbcTemplate $2.doInPreparedStatement(JdbcTemplate.java:697)
2011-07-20 20:57:53,259 ERROR [STDERR] at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:477)
2011-07-20 20:57:53,259 ERROR [STDERR] at org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:693)
2011-07-20 20:57:53,259 ERROR [STDERR] at org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:752)
2011-07-20 20:57:53,259 ERROR [STDERR] at org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:760)
2011-07-20 20:57:53,259 ERROR [STDERR] at org.springframework.jdbc.core.simple.SimpleJdbcTemplate.update(SimpleJdbcTemplate.java:127)
2011-07-20 20:57:53,259 ERROR [STDERR] at edu.harvard.i2b2.pm.dao.PMDbDao.setCell(Unknown Source) 2011-07-20 20:57:53,259 ERROR [STDERR] at edu.harvard.i2b2.pm.delegate.ServicesHandler.runSetCell(Unknown Source)
2011-07-20 20:57:53,259 ERROR [STDERR] at edu.harvard.i2b2.pm.delegate.ServicesHandler.execute(Unknown Source)
2011-07-20 20:57:53,259 ERROR [STDERR] at edu.harvard.i2b2.pm.ws.ExecutorRunnable.run(Unknown Source)
2011-07-20 20:57:53,259 ERROR [STDERR] at java.lang.Thread.run(Thread.java:662)
2011-07-20 20:57:53,259 ERROR [STDERR] Caused by: java.lang.NullPointerException
2011-07-20 20:57:53,259 ERROR [STDERR] at com.microsoft.sqlserver.jdbc.AppDTVImpl $SetValueOp.executeDefault(Unknown Source)
2011-07-20 20:57:53,259 ERROR [STDERR] at com.microsoft.sqlserver.jdbc.DTV.executeOp(Unknown Source)
2011-07-20 20:57:53,259 ERROR [STDERR] at com.microsoft.sqlserver.jdbc.AppDTVImpl.setValue(Unknown Source)
2011-07-20 20:57:53,259 ERROR [STDERR] at com.microsoft.sqlserver.jdbc.DTV.setValue(Unknown Source)
2011-07-20 20:57:53,259 ERROR [STDERR] at com.microsoft.sqlserver.jdbc.Parameter.setValue(Unknown Source)
2011-07-20 20:57:53,259 ERROR [STDERR] at com.microsoft.sqlserver.jdbc.SQLServerPreparedStatement.setObject(Unknown Source) 2011-07-20 20:57:53,259 ERROR [STDERR] at com.microsoft.sqlserver.jdbc.SQLServerPreparedStatement.setNull(Unknown Source)
2011-07-20 20:57:53,259 ERROR [STDERR] at org.jboss.resource.adapter.jdbc.WrappedPreparedStatement.setNull(WrappedPreparedStatement.jav a:277)
2011-07-20 20:57:53,259 ERROR [STDERR] ... 13 more

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: woensdag 20 juli 2011 20:30 To: Yves Thorrez; i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] Update patient count information
So you are running this on project = Demo ?
That should work. .. it has role == ADMIN...
Project = Demo2 does not have role = ADMIN. so it wont run there.

From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Wednesday, July 20, 2011 2:26 PM To: Phillips, Lori C.; i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] Update patient count information
Lori,
Double checked in server.log. Looks ok. Just to be sure, I've included the PM cell's response
I'm using the latest 1.6 RC3 for both the Hive and the clients, and also updated the sqlserver backend for the changes in schema and data. Version numbers in the messages don't match though .
ns2:response xmlns:ns2="http://www.i2b2/xsd/hive/msg/1.1/" xmlns:ns4 ="http://www.i2b2/xsd/cell/pm/1.1/" xmlns:ns3="http://www.i2b2/xsd/hive/msg/version/" message_header i2b2_version_compatible1.1/i2b2_version_compatible hl7_version_compatible2.4/hl7_version_compatible sending_application application_namePM Cell/application_name application_version1.5/application_version /sending_application sending_facility facility_namei2b2 Hive/facility_name /sending_facility receiving_application application_namePM Cell/application_name application_version1.5/application_version /receiving_application receiving_facility facility_namei2b2 Hive/facility_name /receiving_facility datetime_of_message2011-07-20T19:01:29.725+02:00/datetime_of_message message_control_id message_num2g8j0Hcl7JxSBC7arxTo/message_num instance_num1/instance_num /message_control_id processing_id processing_idP/processing_id
57
processing_modeI/processing_mode /processing_id accept_acknowledgement_typeAL/accept_acknowledgement_type application_acknowledgement_typeAL/application_acknowledgement_type country_codeUS/country_code project_id xmlns:xsi="http://www.w3/2001/XMLSchema-instance" xsi:nil="true" /
/message_header response_header result_status
status type="DONE"PM processing completed/status
/result_status /response_header message_body
ns4:configure environmentDEVELOPMENT/environment helpURL http://www.i2b2/helpURL user
full_namei2b2 User/full_name user_namedemo/user_name password token_ms_timeout="1800000" is_token="true"
SessionKey:BITWcfe6r5JoMxxPNssM/password domaini2b2demo/domain project id="Demo" namei2b2 Demo/name wiki http://www.i2b2.org/wiki path/Demo/path roleADMIN/role
roleDATA_AGG/role roleDATA_DEID/role roleDATA_LDS/role roleDATA_OBFSC/role roleDATA_PROT/role roleEDITOR/role roleMANAGER/role roleUSER/role
/project
project id="Demo2" namei2b2 Demo2/name wiki http://www.i2b2.org/wiki path/Demo2/path roleDATA_AGG/role roleDATA_DEID/role roleDATA_LDS/role roleDATA_OBFSC/role roleEDITOR/role roleUSER/role
/project
/user
domain_namei2b2demo/domain_name
domain_idi2b2/domain_id
activetrue/active
cell_datas cell_data id="CRC" nameData Repository/name urlhttp://localhost:9090/i2b2/rest/QueryToolService//url project_path//project_path methodREST/method can_overridetrue/can_override
/cell_data
cell_data id="FRC" nameFile Repository /name urlhttp://localhost:9090/i2b2/services/FRService//url project_path//project_path methodSOAP/method can_overridetrue/can_override
/cell_data
cell_data id="ONT" nameOntology Cell/name urlhttp://localhost:9090/i2b2/rest/OntologyService//url project_path//project_path methodREST/method can_overridetrue/can_override
/cell_data
cell_data id="WORK" nameWorkplace Cell/name urlhttp://localhost:9090/i2b2/rest/WorkplaceService//url project_path//project_path methodREST/method can_overridetrue/can_override
/cell_data /cell_datas
global_data /
/ns4:configure
/message_body
/ns2:response

Yves
Yves Thorrez
Medische Informatieverwerking
yves.thorrez.uzbrussel.be
Laarbeeklaan 101 - 1090 Brussel
www.uzbrussel.be

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: woens ag 20 juli 2011 19:44 To: Yves Thorrez; i2b2 AUG Members Subject: RE: [i2b2 1.6 RC3] Update patient count information
Yves,
I am looking at the code for this now...
The ONT cell is expecting role == ADMIN.
Double check in the server.log file that the PM configuation message lists roleADMIN/role for the user/project combination your are running the feature under.
Prior to that you may have needed role == EDITOR.
Since I am not sure which version of the hive you have, you may want to try that.
Lori

From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Wednesday, July 20, 2011 1:04 PM To: Phillips, Lori C.; i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] Update patient count information
Lori,
No, I had changed the role to ADMIN and MANAGER, to no avail (and double-checked with PM_PROJECT_USER_ROLES).
Yves

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: woensdag 20 juli 2011 17:18 To: Yves Thorrez; i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] Update patient count information
Yves,
Are you confusing roles/permissions with data access permissions (DATA_AGG, etc)?
I think this is saying that the role needs to be MANAGER or ADMIN as opposed to USER.
Lori Phillips

From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Wednesday, July 20, 2011 9:45 AM To: i2b2 AUG MembersSubject: [i2b2 1.6 RC3] Update patient count information
When I hit the "Start update term usage" button, I get the message "User does not have correct privileges" in the log box. I set the current user to have all permissions. Am I missing anything?
Thanks,
Yves
Yves Thorrez
Medische Informatieverwerking
yves.thorrez.uzbrussel.be
Laarbeeklaan 101 - 1090 Brussel
www.uzbrussel.be


NEXT EMAIL
From: Peter Beninato [beninato.ohsu] Sent: Monday, July 25, 2011 1:36 PM To: Phillips, Lori C.; i2b2 AUG MembersSubject: RE: Patient Count Update very slow
What database are you using? Can you cull out the select from the sql field in qt_master table, and then run an explain plan. This way you can see if it is using indexes or not.
You might also want to see what the count is like. Indexes are useful, if you are trying to get a subset of data. If the amount of data is over an arbitrary!!! Say 4% then full table scan is useful.
Is this Oracle?
You might want to run dbms_stats on the observation_fact table, if the stats are not current, then you might be getting full table scans were an index might be more efficient.

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: Monday, July 25, 2011 7:44 AM To: i2b2 AUG MembersSubject: FW: Patient Count Update very slow
Forwarding to user group...

From: Anandhi Sowmyan [asowmyan.regenstrief] Sent: Monday, July 25, 2011 10:37 AM To: Phillips, Lori C. Subject: Patient Count Update very slow
Hi Lori
We are trying to run the Patient Count associated with terms and it seems to be very slow. We have around 60,000 terms to update. We have all the indexes created (same as the ones you provide in the oracle express version). Is there something we can do to improve the performance?
Thanks
Anandhi Sowmyan
Regenstrief Institute, Inc.
Medical Informatics
Health Information and Translational Sciences (HITS) Building
410 West 10th Street, Suite 2000
Indianapolis, IN 46202
Email: asowmyan.regenstrief


NEXT EMAIL
From: Jack W. London, Ph.D. [Jack.London.KimmelCancerCenter] Sent: Monday, July 25, 2011 11:34 AM To: Murphy, Shawn N. Cc: i2b2 AUG MembersSubject: RE: v1.6 concept modifier data model
Shawn,
Thanks for your reply.
Yes, each SPEC:T59300 corresponds to actual colon tissue collected for an individual on a specific date (i.e., a surgical pathology case). So your suggestion of adding a modifier indicating the case is excellent, and does complete the loop for allowing an honest broker to actually order the desired specimen. The Surgical Pathology Report (SPR) number is considered PHI, but for those of us using caTissue, the Specimen Collection Group database record identifier would be a de-identified surrogate. Using the "Excel Export" web client plugin, the i2b2 query could generate a spreadsheet with non-PHI information that could be directly used to select specimens with caTissue.
Looking forward to using v1.6.
Jack

Quoting "Murphy, Shawn N." SNMURPHY.PARTNERS:
Hi Jack,
Assuming that each SPEC:T59300 represents a separate piece of actual colon tissue, I think this looks great and a good addition might be the serial number (if it exists) of the specimen, with two caveats: 1 - this assumes the serial number does not represent PHI. If it does, it can be encrypted or mapped. 2 - the serial number is more for finding the specimen when the raw (PDO) data is served rather than for queries (though could be used in queries of course).
The first two entries might look something like:
123|107|1|SPEC:T59300|20100715|.|null|null| 123|107|1|SPEC:T59300|20100715|SPEC:TISTYPE|T|frozen|null| 123|107|1|SPEC:T59300|20100715|SPEC:PATH|T|normal|null| 123|107|1|SPEC:T59300|20100715|SPEC:SERIAL|N|E|234876 123|107|2|SPEC:T59300|20100715|.|null|null| 123|107|2|SPEC:T59300|20100715|SPEC:TISTYPE|T|frozen|null| 123|107|2|SPEC:T59300|20100715|SPEC:PATH|T|malignant|null| 123|107|2|SPEC:T59300|20100715|SPEC:SERIAL|N|E|234877
Thanks,
Shawn.


From: Jack London [jack.london.KimmelCancerCenter] Sent: Friday, July 22, 2011 1:52 PM To: Murphy, Shawn N. Cc: i2b2 AUG Membersmembers Subject: v1.6 concept modifier data model
Shawn,
I want to confirm that I understand the data model for v1.6 concept modifiers. We want to characterize specimens that a patient may have in a biobank. For example, on July 15, 2010, patient #123 at visit #107, has colon tissue banked (SPEC concept), both as frozen tissue and as paraffin-embedded tissue (TISTYPE concept modifier). Furthermore, both normal and malignant tissue sections are banked (PATH concept modifier).
Would the following observation-fact records correctly express this example: (NOTE: T59300 is the SNOMED code for "Colon, NOS")
123|107|1|SPEC:T59300|20100715|.|null|null| 123|107|1|SPEC:T59300|20100715|SPEC:TISTYPE|T|frozen|null| 123|107|1|SPEC:T59300|20100715|SPEC:PATH|T|normal|null| 123|107|2|SPEC:T59300|20100715|.|null|null| 123|107|2|SPEC:T59300|20100715|SPEC:TISTYPE|T|frozen|null| 123|107|2|SPEC:T59300|20100715|SPEC:PATH|T|malignant|null| 123|107|3|SPEC:T59300|20100715|.|null|null| 123|107|3|SPEC:T59300|20100715|SPEC:TISTYPE|T|paraffin|null| 123|107|3|SPEC:T59300|20100715|SPEC:PATH|T|normal|null| 123|107|4|SPEC:T59300|20100715|.|null|null| 123|107|4|SPEC:T59300|20100715|SPEC:TISTYPE|T| paraffin|null| 123|107|4|SPEC:T59300|20100715|SPEC:PATH|T|malignant|null|
In other words, are 4 instance needed to express the four different categories of colon tissue available (frozen normal, frozen malignant, paraffin normal, and paraffin malignant)?
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: Phillips, Lori C. Sent: Monday, July 25, 2011 9:09 AM To: David Choi Cc: i2b2 AUG MembersSubject: RE: i2b2 build error
Yes that is the correct folder/file (BuildAssist) I am attaching the Developer's Guide that shows how to build/run/etc within eclipse. You can also find additional documentation at: https://www.i2b2/software/index.html If you are not running under eclipse, I believe the command is 'ant -f build.xml clean-all build-all'

From: David Choi [choi.david.e.gmail] Sent: Sunday, July 24, 2011 11:08 PM To: Phillips, Lori C. Subject: Re: i2b2 build error
Sorry for the late reply. My BuildAssist folder only has a build.xml
I did a root trunk svn checkout So I have:
Client/
BuildAssist/build.xml --this one?
edu.harvard.i2b2.common
edu.harvard.i2b2.eclipse
edu.harvard.i2b2.eclipse.features.core
edu.harvard.i2b2.eclipse.plugins.analysis edu.harvard.i2b2.eclipse.pluginsmons_apache edu.harvard.i2b2.eclipse.plugins.crcxmljaxb edu.harvard.i2b2.eclipse.plugins.createTables
edu.harvard.i2b2.eclipse.plugins.explorer
edu.harvard.i2b2.eclipse.plugins.jdnc_support
edu.harvard.i2b2.eclipse.plugins.log
edu.harvard.i2b2.eclipse.plugins.ontology
edu.harvard.i2b2.eclipse.plugins.previousQuery
edu.harvard.i2b2.eclipse.plugins.query
edu.harvard.i2b2.eclipse.plugins.webservicesAxis2
edu.harvard.i2b2.eclipse.plugins.workplace
edu.harvard.i2b2.eclipse.plugins.xml_support_jaxb
edu.harvard.i2b2.eclipse.plugins.xml_support_jdom
edu.harvard.i2b2.xml
Common/
Features/
Maven/
build.xml
common crc
fr
i2b2-app
i2b2-war
i2b2.properties
INSTALL.txt
lib
loader
note
ontology pm
pom.xml
README.txt
todo
version
webclient
workplace
xml
Server/
edu.harvard.i2b2.common
edu.harvard.i2b2.crc
edu.harvard.i2b2.crc.loader
edu.harvard.i2b2.fr
edu.harvard.i2b2.ontology
edu.harvard.i2b2.pm
edu.harvard.i2b2.workplace
edu.harvard.i2b2.xml
i2b2 license 2.1-1159.txt
webclient
I'm not too sure if I have the same files as what you see.

On Sat, Jul 23, 2011 at 9:32 AM, PhillipSs, Lori C. LCPHILLIPS.partners wrote:
sorry , I misunderstood; I did not realize that you did an svn checkout.
I cant tell from your email where you are running the build process from. Start in the project BuildAssist. try ant -f master_build.xml

From: David Choi [davidchoi.i2b2aug] Sent: Fri 7/22/2011 6:56 PM To: members Subject: Fwd: i2b2 build error
Sorry for the duplicate message but I just wanted to make sure that I'm sending this e-mail in the right way.
Forwarded message From: David Choi choi.david.e.gmail Date: Fri, Jul 22, 2011 at 5:54 PM Subject: Fwd: i2b2 build error To: davidchoi.i2b2aug
Forwarded message From: David Choi choi.david.e.gmail Date: Fri, Jul 22, 2011 at 4:07 PM Subject: Re: i2b2 build error To: "Phillips, Lori C." LCPHILLIPS.partners Cc: i2b2 AUG Members
Also I did try it as root as well.

On Fri, Jul 22, 2011 at 4:05 PM, David Choi choi.david.e.gmail wrote:
I did a svn checkout of the current repository and it has this file structure
Client/BuildAssist
Client/edu.harvard.i2b2common
Client/edu.harvard.i2b2.eclipse
Client/edu.harvard.i2b2.eclipse.features.core
Client/edu.harvard.i2b2.eclipse.plugins.analysis
Client/edu.harvard.i2b2.eclipse.pluginsmons_apache ....
So if you meant if I had the package I do have it. I don't exactly what you are referring to when you say the client src location wise. So here is what I understand is going on:
Client/edu.harvard.i2b2.eclipse/buildFiles/build.xml: line 57 calls has line 61: classpath refid="classpath"/ which calls line 13: target name="gensrcInit" path id="classpath" path refid="common-classpath" / /path /target
and this should call on the imported common_build.xml by line 7: import file="../../edu.harvard.i2b2mon/common_build.xml" /
which does have target name="common-classpath" path id="common-classpath" fileset dir="../${i2b2CommonProject}/${lib}" include name="*/.jar" / /fileset fileset dir="${genlib}" include name="*.jar" / /fileset pathelement location="${classes}" / /path /target
so I don't understand why it's not building. I checked permissions on the file system and all of my directories have these permission settings (*nix based OS Ubuntu): drwxr-xr-x
So I feel like it's not even reading in the: import file="../../edu.harvard.i2b2mon/common_build.xml" / for some odd reason.
Yes it does exist on my file system. the command I type in is merely ant.
$~ ant
Do I need to type in ant with some parameters?

On Fri, Jul 22, 2011 at 3:41 PM, Phillips, Lori C. LCPHILLIPS.partners wrote:
David,
The script is looking for the edu.harvard.i2b2.common project.
Is the project edu.harvard.i2b2.common included in the client src package?
If not, download the server src package – it should be there.
You may need the edu.harvard.i2b2.xml project also...
Lori

David Choi [choi.david.e.gmail] Sent: Fri 7/22/2011 4:40 PM To: i2b2 AUG Members Subject: Re: i2b2 build error
Sorry that's a can not

On Fri, Jul 22, 2011 at 3:39 PM, David Choi choi.david.e.gmail wrote:
I was wondering if anyone could help my understand why or how I can successfully build the various i2b2 eclipse plugins. I am running into issues where it outputs
... ... Build Failed: ../Client/edu.harvard.i2b2.eclipse/buildFiles/build.xml:57: Reference common-classpath not found.
I was hoping to get some help on what is wrong. I know that the build.xml is importing a file but at the same time I don't know if it's actually importing the file when I try to run ant.
Here in the edu.harvard.i2b2.eclipse/buildFiles directory where I run ant I see this :
!-- ========== Executable Targets ============== –
import file="../../edu.harvard.i2b2mon/common_build.xml" / property name="gensrc" value="gensrc"/ !- ============= – !-INIT – ! ========== – target name="gensrcInit" path id="classpath" path refid="common-classpath" / /path
And I see that there is a target-name "common-classpath" in ../../edu.harvard.i2b2mon/common_build.xml: line 69 but it's as if the build file is not actually importing in common-classpath, either that or it's something else I'm not familiar with. Please excuse my ignorance but I am not an expert in ant build files.
David Choi


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From: Arnold, Garth [arnold.g.ghc] Sent: Friday, July 22, 2011 7:19 PM To: 'Michael.C.Ford.kp'; i2b2 AUG MembersSubject: RE: JMS Queue question
Hi Michael - there was an i2b2aug post from March 7 that has a bit of information, I'm pasting it in below. One change we've made to handle 30 second queries is in the php.ini file - look for the line max_execution_time=30; (30 is the default) and change to some arbitrarily high value.
Garth
Garth Arnold | MANAGER, TECHNICAL INFRASTRUCTURE
Group Health Research Institute

From: RAJESH KUTTAN [rkuttan.partners] Sent: Monday, March 07, 2011 7:41 PM To: Peter Beninato; i2b2 AUG MembersSubject: Re: i2b2 - v1.4 - crc.properties - timeouts - JBOSS NOT{*}* shutting down
Hi Peter, Please find the details below. Thanks Raj

On 3/7/11 6:37 PM, "Peter Beninato" beninato.ohsu wrote:
Hi,
In crc.properties file there is a line:
Setfinder JMS Queue transaction timeout properties
edu.harvard.i2b2.crc.jms.small.timeoutsec=180
1) Does this correspond with the time that I see in the "Query Status" window?
No, this value just says how long the query can run in the small queue before it can be restarted from the medium queue.. If you want to increase the client wait time for big queries with 4/5 panels, then you can increase the wait timeout using the client's query tool option dialog .
2) Why when I change this to a more reasonable 1200, and redeploy via the ANT target, do I still timeout at 180? Timeout at 180 is set from the client, you can increase it in the client side. If you change the property file, you can simply restart JBoss and no need to redeploy with ANT.

From: Michael.C.Ford.kp [Michael.C.Ford.kp] Sent: Friday, July 22, 2011 3:25 PM To: i2b2 AUG MembersSubject: JMS Queue question
I am trying to understand the CRC parameters, the JMS parameters the install document only states # # # # # # # # # # # # # # # # # # # # # # # # # # Setfinder JMS Queue transaction timeout properties # # # # # # # # # # # # # # # # # # # # # # # # # edu.harvard.i2b2.crc.jms.small.timeoutsecs=180 edu.harvard.i2b2.crc.jms.medium.timeoutsecs=14400 edu.harvard.i2b2.crc.jms.large.timeoutsecs=43200
can I change the values to a higher value and what is the ramifications of doing so ?
we have issues with queries timing out somewhere.
also what is the difference between small medium and large ?


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From: Churchill, Susanne E. Sent: Thursday, July 21, 2011 6:42 PM To: Peter Beninato; i2b2 AUG MembersSubject: RE: Slides - AUG June meeting Boston
they are going up as I receive them - note to all: your page on our website is www.i2b2/work/aug.html; there is also a link from home page: www.i2b2.

From: Peter Beninato [beninato.ohsu] Sent: Tue 7/19/2011 4:57 PM To: i2b2 AUG MembersSubject: Slides - AUG June meeting Boston
Have the slides from the Boston June AUG meeting been posted to i2b2 website? Probably there and I just can't find link...
Thanks.
Peter Beninato - OCTRI DW Developer
Oregon Health & Science University
beninato.ohsu beninato.ohsu


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From: Phillips, Lori C. Sent: Thursday, July 21, 2011 10:54 AM To: Audrey Hureau; i2b2 AUG MembersSubject: RE: c_metadataxml
see https://community.i2b2/wiki/display/DevForum/Metadata+XML+for+Medication+Modifiers
Although written for modifiers, the Value Metadata content descriptions apply to concepts as well

From: Audrey Hureau [audrey.hureau.gmail] Sent: Thursday, July 21, 2011 10:39 AM To: i2b2 AUG MembersSubject: c_metadataxml
Hi,
I am trying to use the "set values" feature. I would like to know the role played by some flags in the c_metadataxml, which are :
LowofLowValue/ HighofLowValue/ LowofHighValue/ HighofHighValue/
Thank you all.
Audrey Hureau


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From: Audrey Hureau Sent: Thursday, July 21, 2011 2:58 AM To: i2b2 AUG Members Subject: PM Issue
Hi Everyone,
I upgraded the i2b2 version from v1.5.2 to v1.5.4. I rebuilt each cell but now when I try to connect to the workbench, I have the message "The PM Cell is either down or the PM address in the properties file is incorrect. I checked the properties file and the address is correct. Has anyone already face to this problem?
Thank you all.
Audrey Hureau


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From: Marius Petruc Sent: Wednesday, July 20, 2011 4:17 PM To: Dan Connolly; Mendis, Michael E.; i2b2 AUG Members Subject: Re: I2B2 webserver
Mike answered the specific question about threading, but if your question is really "will end users see a speed difference if I give the hive more CPUs/cores?" then I'd say: I doubt it; I suspect the rate-limiting-factor is the database.
We've tried various approaches to improve performance. For many queries, the biggest performance impact comes from giving more RAM to the oracle database server (I think we're giving Oracle 12GB of SGA and 6GB of PGA; we have more RAM on the server, but we're juggling various Oracle instances, so we haven't given any one of them much more than that).
But since the observation_fact table is too big for RAM (even the indexes are too big), we just recently deployed solid state storage (fusion-io cards).

On Wed, 2011-07-20 at 14:46 -0400, Mike Mendis wrote:
Yes it is multithreaded and multiple cores/cpu will increase the performance. Make sure the OS and java is configured to handle it.
mike

On 7/20/11 2:40 PM, "Marius Petruc" petrucm.health.missouri wrote:
Dan, do you know if the i2b2 hive is multithreaded? assuming 10 concurrent users, will a multi core/multi cpu system provide a significant performance increase (i.e. faster response time) than a single CPU system?
thanks a lot
Marius Petruc

On 7/19/2011 10:08 AM, Dan Connolly wrote:
The web client uses very, very little server resources. It mostly - ships a big hunk of javascript for the client to run - routes medium sized hunks of XML from the client to the hive thru a .php script
We run the web client on the same machine as the i2b2 hive. It originally has 2GB but we have since bumped it up to 8GB to give it headroom. (FWIW: http://informatics.kumc/work/wiki/HERON#Architecture )
I can't quite tell from your message if you're talking about running the i2b2 hive (i.e. jboss) on the same machine or a separate machine as the web server for the i2b2 webclient. If you're really running them on separate machines, the server for the i2b2 webclient could be tiny.
Dan Connolly, KUMC Medical Informaticshttp://informatics.kumc/

On Tue, 2011-07-19 at 10:34 -0400, Wei,Xintao wrote:
Hi,
We would like to install I2B2 server and I2B2 webclient on separate machines. A webserver will be used to hold I2B2 webclients only. We would like to know what the minimum requirement of the webserver hardware setup is. For example, how many CPU cores, how many gigs of RAM and how many gigs of local HD do you think we will need to handle I2B2 webclients for our I2B2 servers? 64bit windows server 2008 and I2B2 version 1.5 will be run on the webserver.
Thank you!
Xintao


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From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Wednesday, July 20, 2011 5:34 AM To: i2b2 AUG MembersSubject: [i2b2 1.6 RC3] Same visit vs same patient - bug?
1.6 RC3 / Demo project / web client and workbench:
1) Query: Group 1: Hypertensive disease (Treat Independently) Group 2: Ischemic heart disease (Treat Independently) Nr of patients: 13 (M = 6, F = 7)
2) Query: Group 1: Hypertensive disease (Occurs in Same Encounter) Group 2: Ischemic heart disease (Occurs in Same Encounter) Nr of patients: 6 (M = 1, F = 5)
3) Query: Group 1: Hypertensive disease (Occurs in Same Encounter) Group 2: Ischemic heart disease (Occurs in Same Encounter) Group 3: Female (Occurs in Same Encounter) Nr of patients: 0
So far, so good.
4) Query: Group 1: Hypertensive disease (Occurs in Same Encounter)
Group 2: Ischemic heart disease (Occurs in Same Encounter)
Group 3: Female (Treat Independently) Nr of patients: 0
Should be 5.
Checked it, and the sql generated in 3) and 4) is identical.
It looks like, after selecting the radio button 'Selected groups occur in the same financial encounter', any subsequent changes in an individual group's drop-down list are not considered (so the query is effectively always for 'Occurs in Same Encounter' in any group)?
Thanks,
Yves
Yves Thorrez
Medische Informatieverwerking
yves.thorrez.uzbrussel.be
Laarbeeklaan 101 - 1090 Brussel Tel 02 477 69 45 - Fax 02 477 69 75
www.uzbrussel.be


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From: Phillips, Lori C. Sent: Monday, July 18, 2011 11:09 AM To: Yves Thorrez; i2b2 AUG MembersSubject: RE: [i2b2 1.6 RC3] SQLServer: too many columns in index
Looks like its safe to remove Sourcesystem_cd from the index list.

From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Monday, July 18, 2011 8:14 AM To: i2b2 AUG MembersSubject: [i2b2 1.6 RC3] SQLServer: too many columns in index
Hi,
For SQLServer, running crc_create_datamart_sqlserver.sql gives one error:
The index 'OF_IDX_ALLObservation_Fact' on table 'Observation_Fact' has 17 column names in index key list. The maximum limit for index or statistics key column list is 16.
Adding instance_num to the index from 1.5 to 1.6 exceeds the maximum.
Any hint as to which column to best eliminate from this large index?
Thanks, Yves
CREATE INDEX OF_IDX_ALLObservation_Fact ON Observation_Fact (
Encounter_Num , Patient_Num , Concept_Cd , Start_Date , Provider_Id , Modifier_Cd , instance_num, ValType_Cd , TVal_Char , NVal_Num , ValueFlag_Cd , Quantity_Num , Units_Cd , End_Date , Location_Cd , Confidence_Num , Sourcesystem_Cd ) ;
Yves Thorrez
Medische Informatieverwerking
yves.thorrez.uzbrussel.be
Laarbeeklaan 101 - 1090 Brussel


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From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Monday, July 18, 2011 8:06 AM To: Yves Thorrez; i2b2 AUG MembersSubject: RE: Export Data plugin - missing visits
Resolved. The Visit_Dimension populated from the demodata scripts (1.5.x) had a number of missing records. Thanks to Lori for handing the full data.
Yves


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From: Mendis, Michael E. Sent: Thursday, July 14, 2011 7:50 PM To: Jack London; i2b2 AUG Membersmembers Subject: Re: web client v1.5.4 query-by-value not working
Is both the backend and the webclient 1.5.4? Let me take a look at the 30 and 40 in separate panels. In regards to the second part, we did change the webclient because it was sending the wrong XML to the server, it was adding extra ' .
Can you send the log with the incorrect SQL.
Thanks mike

On 7/14/11 3:35 PM, "Jack London" jack.london.KimmelCancerCenter wrote:
When I query?by?value with web client v1.5.4 it appears that incorrect query xml (and subsequent SQL) is generated. I noticed this problem when querying for paired normal and malignant tissue, but then created a test using a simple age query for patients between 30 and 40, by placing " 30" in panel 1, and "40" in panel 2. THE GENERATED REQUEST XML WRITES WHATEVER IS SPECIFIED IN PANEL 2 FOR BOTH PANEL 1 AND 2 (SEE BELOW).
Also, to get query?by?value to work at all for web client v1.5.4, I had to correct a bug in webclient/jsi2b2/cells/CRC/CRC_ctrlr_QryTool.js, at line 519, where an additional apostrophe was causing incorrect query SQL to be generated:
sEnum = '(\''sEnum'\')'; changed to sEnum = '('sEnum')';
Does anyone have a suggestion for fixing the incorrect generated query xml?
thanks, Jack
?xml version="1.0" encoding="UTF?8" standalone="yes"?
ns2:query_definition xmlns:ns2="http://www.i2b2/xsd/cell/crc/psm/querydefinition/1.1/" query_nameAge?Age.19:15:42/query_name specificity_scale0/specificity_scale panel
panel_number1/panel_number panel_accuracy_scale0/panel_accuracy_scale invert0/invert total_item_occurrences1/total_item_occurrences
item hlevel2/hlevel item_nameAge/item_name item_key\\TJUH_DEMOGRAPHICS\Demographics\Age\/item_key item_iconLA/item_icon tooltip\Demographics\Age\/tooltip classENC/class constrain_by_value
value_operatorLT/value_operator value_constraint40/value_constraint value_unit_of_measureYears/value_unit_of_measure value_typeNUMBER/value_type
/constrain_by_value constrain_by_date/ item_is_synonymfalse/item_is_synonym
/item /panel panel
panel_number2/panel_number panel_accuracy_scale0/panel_accuracy_scale invert0/invert total_item_occurrences1/total_item_occurrences item
hlevel2/hlevel item_nameAge/item_name item_key\\TJUH_DEMOGRAPHICS\Demographics\Age\/item_key item_iconLA/item_icon tooltip\Demographics\Age\/tooltip classENC/class constrain_by_value
value_operatorLT/value_operator value_constraint40/value_constraint value_unit_of_measureYears/value_unit_of_measure value_typeNUMBER/value_type
/constrain_by_value constrain_by_date/ item_is_synonymfalse/item_is_synonym
/item /panel /ns2:query_definition


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From: Chan, Wayne [Wayne.Chan.umassmed] Sent: Tuesday, July 12, 2011 1:52 PM To: Donahoe, Janice M; Phillips, Lori C. Cc: i2b2 AUG MembersSubject: RE: question on "observation_set" in a getPDO response..
Lori,
Thanks for getting to the bottom of this.
I guess I should stay away from the 'i2b2 Demo 2' project to avoid similar confusions in the future.
Wayne

From: Donahoe, Janice M [JDONAHOE.PARTNERS] Sent: Tuesday, July 12, 2011 12:37 PM To: Chan, Wayne; Phillips, Lori C. Cc: i2b2 AUG MembersSubject: RE: question on "observation_set" in a getPDO response.
Hi Wayne,
After some digging I think I figured out what is going on.
The VM image is setup with two projects and each one points to a different schema in the oracle database.
Project "i2b2 Demo" uses "i2b2demodata"
Project "i2b2 Demo 2" uses "i2b2demodata2"
All the tables in i2b2demodata have been updated; in particular the encounter numbers have been changed to support the new visit queries. In i2b2demodata2, the visit_dimension table was updated but the observation_fact table has not been updated with the data changes made in 1.6.
My guess is you were logged into the i2b2 Demo 2 project which would explain why you were seeing the old encounter numbers that happen to be the same as the patient numbers. When you ran your query in the Oracle database you may have logged into i2b2demodata instead of i2b2demodata2. Since i2b2demodata has the updated encounter numbers it looked like the PDO was sending the wrong number in the event_id.
If you log into i2b2 Demo and follow your same steps I believe you will see the correct event_id in the observation_set.
There was also one other question you had regarding the number of records returned in the PDO not matching your SQL query. In the PDO you received 3 observations but when you queried the database directly you only received two. In your select statement you restricted it to patient_num= 1000000001 and concept_cd='ICD9:427.9' and when I looked at the third observation in your PDO I noticed the concept_cd is different (ICD9:427.9) which is why it wouldn't be returned when you queried the database directly.
I hope this answers all of your questions.
Thanks.
Janice

From: Chan, Wayne [Wayne.Chan.umassmed] Sent: Tuesday, July 05, 2011 12:39 PM To: Phillips, Lori C. Cc: 'members.i2b2aug'; Donahoe, Janice M Subject: RE: question on "observation_set" in a getPDO response..
Lori,
My 1.6RC2 was installed on a brand new CentOS 5.6 x64 VM, so there is no previously installed
1.5 DB to speak of.
I simply ran the Plugins "Example #3 – PD Request" using the resulting patient set of a query of "Ontology / Diagnoses / Circulatory system", and the Concept of "Ontology / Diagnoses / Circulatory system". If you meant the result_waittime_ms when you asked about "Query Timing choice" , then it was 180000. Any way, I've attached the corresponding PDO_request & PDO_response files for your reference / further examinations.
Thanks.
Wayne

From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: Tuesday, July 05, 2011 11:45 AM To: Chan, Wayne; Donahoe, Janice M Cc: i2b2 AUG MembersSubject: RE: question on "observation_set" in a getPDO response..
Wayne,
Is there any chance your configuration is pointing to a previously installed 1.5 database?
In other words, were the ONT_DB_LOOKUP, CRC_DB_LOOKUP, etc and ds.xml files reconfigured to point to the new 1.6 db?
Also what Query Timing choice did you select when you ran the query?
Lori

From: Chan, Wayne [Wayne.Chan.umassmed] Sent: Tuesday, July 05, 2011 11:23 AM To: Donahoe, Janice M Cc: i2b2 AUG Membersmembers Subject: RE: question on "observation_set" in a getPDO response.
Hi Janice,
Thanks for the response. I didn't upgrade from 1.5 – i.e. my 1.6RC2 is a fresh install. That said, the encounter_num in all the tables you mentioned are indeed different from the patient_num – and that was one of my concerns – that why are the event_id's in the returned observation_set being the same as the patient_num (I kind of expect them to correlate to the encounter_num, but wasn't sure if that should have been the case).
I guess I may not have been too clear in my original post – my other concern was that the observation_set contained at least 3 entries for the patient_num=1000000001 while I only got the following 2 entries when I did a direct DB query:
May be I have wrong assumptions somewhere?

From: Donahoe, Janice M [JDONAHOE.PARTNERS] Sent: Tuesday, July 05, 2011 10:27 AM To: Chan, Wayne; i2b2 AUG Members Subject: RE: question on "observation_set" in a getPDO response.
Hi Wayne,
By any chance did you upgrade your demo data from 1.5 to 1.6-RC2? In 1.6 we have been working on making the demo data more robust, one of the areas we have been concentrating on is encounters. In 1.6 we have built up the visit_dimension and encounter_mapping tables and cleaned up the encounter_num in other tables such as the observation_fact. In the 1.5 demo data a lot of the encounter_num were the same as the patient_num which might explain why you are seeing the same value in the event_id and patient_id.
As far as the data returned... I am not sure I am following your concern / question. Are you expecting more results to be returned in the PDO for patient_num='1000000001' and concept_cd='ICD9:427.9'?
Thanks
Janice

From: Chan, Wayne [Wayne.Chan.umassmed] Sent: Friday, July 01, 2011 4:14 PM To: i2b2 AUG Membersmembers Subject: question on "observation_set" in a getPDO response..
On my v1.6RC2, I notice that each "event_id" of the "observation_set" coming back in a"request_typegetPDO_fromInputList/request_type" appear to be the same as each"patient_id"; and the number of entries for a given "patient_id" is more than the apparententries (2) in the observation_fact table when I used the following SQL statement (select

• from observation_fact where patient_num=1000000001 and concept_cd='ICD9:458.9' toquery it directly.
  The excerpt of my "observation_set" is as following:
  ns2:observation_set panel_name="\\i2b2\i2b2\Diagnoses\Circulatory system (390-459)\"
  observation event_id1000000001/event_id patient_id1000000001/patient_id concept_cdICD9:458.9/concept_cd observer_cd./observer_cd start_date1999-08-11T00:00:00.000-04:00/start_date modifier_cd1/modifier_cd instance_num1/instance_num tval_char / nval_num / valueflag_cd / units_cd./units_cd end_date1999-08-11T00:00:00.000-04:00/end_date location_cd./location_cd
  /observation
  observation event_id1000000001/event_id patient_id1000000001/patient_id concept_cdICD9:458.9/concept_cd observer_cd./observer_cd start_date1999-08-12T00:00:00.000-04:00/start_date modifier_cd2/modifier_cd instance_num1/instance_num tval_char / nval_num / valueflag_cd / units_cd./units_cd end_date1999-08-12T00:00:00.000-04:00/end_date location_cd./location_cd
  /observation
  observation event_id1000000001/event_id patient_id1000000001/patient_id concept_cdICD9:427.9/concept_cd observer_cd./observer_cd start_date2005-07-29T00:00:00.000-04:00/start_date modifier_cd2/modifier_cd instance_num1/instance_num tval_char / nval_num / valueflag_cd /
  units_cd./units_cd
  end_date2005-07-29T00:00:00.000-04:00/end_date
  location_cd./location_cd
  /observation
  Thanks in advance for any help anyone can offer.
  Wayne
  
  
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  From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Tuesday, July 12, 2011 3:50 AM To: Yves Thorrez; i2b2 AUG MembersSubject: RE: Analysis types
  Please ignore my question. The Analysis View is obviously where the analysis types are being used.
  Thanks,
  Yves
  Yves Thorrez
  Medische Informatieverwerking
  Laarbeeklaan 101 - 1090 Brussel
  
  From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: maandag 11 juli 2011 22:38 To: i2b2 AUG MembersSubject: Analysis types
  Hi,
  In the i2b2 workbench (v1.5.2), I'm wondering why the breakdown according to gender, vital status, race, age which can be checked in the Analysis Types section does not work. When I check one or more, I can see the corresponding nodes in the results (Previous Queries) but with no further information, they seem useless. No problem drilling down in the patient set though. Changing the roles does not seem to help...
  Thanks, Yves
  
  
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  From: Phillips, Lori C. Sent: Monday, July 11, 2011 2:02 PM To: Peter Beninato; Keith Marsolo Cc: i2b2 AUG MembersSubject: RE: i2b2 - Project - Use Case/Implementation
  What Keith outlines is exactly how we intended for this to work. In fact the intention Demo/Demo2 projects within the supplied i2b2 demo data was to demonstrate how two projects are set up.
  None of you mentioned this so I thought I'd add that the Export Data plugin was designed to permit export of a project subset. So, if you wanted to extract all the woman in the demo data set and create a new project with that data, you could set up the Export Data plugin to do just that.
  Lori
  
  From: Peter Beninato [beninato.ohsu] Sent: Monday, July 11, 2011 1:05 PM To: Keith Marsolo Cc: i2b2 AUG MembersSubject: RE: i2b2 - Project - Use Case/Implementation
  Hi Keith,
  I have my Dev and QA running on the same instance, and that involved creating separate "projects" and modfifying the spring/jboss config files, kinda like the Demo/Demo2 approach in out-of-the-box i2b2 and similar to what you outline ( I think).
  And I don't recall in newer version when using ADMIN, if there are properties for indicating different schemas, so I think the exercise of re-deploying via ANT will still be required.
  Does that sound right to you?
  
  From: Lakshminarayanan, Prakash [Prakash.Lakshminarayanan.ucsf] Sent: Monday, July 11, 2011 1:16 PM To: Wynden, Rob; Peter Beninato; Keith Marsolo Cc: i2b2 AUG Members Subject: RE: i2b2 - Project - Use Case/Implementation
  Peter
  The views are named as follows pertaining to respective i2b2 tables:
  query_name_Patient
  query_name_Concept
  query_name_ObsFact
  query_name_Visit,
  query_name_AllVisit
  Prakash
  
  From: Wynden, Rob [Rob.Wynden.ucsf] Sent: Monday, July 11, 2011 10:09 AM To: Peter Beninato; Keith Marsolo Cc: i2b2 AUG MembersSubject: Re: i2b2 - Project - Use Case/Implementation
  Hi,
  There are 5 view types available. One of them allows you to get access to the obs fact data as EAV. There are also ViewCreator views that have all of the data for a patient organized in rows where each row is a patient encounter.
  Rob
  
  On 7/11/11 10:06 AM, "Peter Beninato" beninato.ohsu wrote:
  Hi, ViewCreator is an alternative. Do the views created follow the i2b2 naming convention of patient_dimension, observation_fact etc.?
  Peter
  
  From: Wynden, Rob [Rob.Wynden.ucsf] Sent: Monday, July 11, 2011 10:03 AM To: Keith Marsolo; Peter Beninato Cc: i2b2 AUG MembersSubject: Re: i2b2 - Project - Use Case/Implementation
  Peter,
  Could you use ViewCreator for that? Since the ViewCreator views are permissioned within the database it seems like you would be able to.
  Regards,
  Rob Wynden UCSF
  
  
  From: Keith Marsolo [keith.marsolo.cchmc] Sent: Monday, July 11, 2011 9:57 AM To: Peter Beninato Cc: i2b2 AUG MembersSubject: Re: i2b2 - Project - Use Case/Implementation
  Peter,
  I may be mistaken, but the last time we checked, there was no easy way to do what you're proposing, aside from manually creating a second schema, or duplicating fact records and creating a second ontology viewable only by the users in the second project (and I'm not even sure if this is possible in "stock" i2b2 - it may have been something that we did custom in an earlier version).
  We have the same use case, and are looking at different ways of tackling this. Not to speak for Partners, but I believe they stick with one project per warehouse/schema, and simply copy the data over for every new request.
  Keith
  Keith Marsolo, PhD
  Assistant Professor
  Division of Biomedical Informatics Cincinnati Children's Hospital Medical Center 3333 Burnet Ave MLC 7024 Cincinnati, OH 45229
  keith.marsolo.cchmc
  
  On Jul 11, 2011, at 12:28 PM, Peter Beninato wrote:
  Hi,
  Was wondering about the Use Case for setting up additional Projects in i2b2 and what steps might be involved.
  One example I think would be to change an investigator's access privileges. So in the standard project they are an obfuscated user, and now you want to give them broader privileges.
  This seems straightforward. Create another project, add the user and grant them different privileges.
  But what happens if you only want to allow those broader privileges on the subset of data of interest?
  The investigator runs a query that returns a count of say 10,000 patients. What are the steps to create another i2b2 universe for this project?
  So, Do you have to create a 2^nd data schema and populate the patient dimension, and observation fact with the subset of data?
  How would this be achieved?
  Also...
  Are any institutions creating projects for investigator data subsets?
  Thanks.
  Peter Beninato - OCTRI DW Developer Oregon Health & Science University
  beninato.ohsu
  
  
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  From: Russ Waitman [rwaitman.kumc] Sent: Friday, July 08, 2011 2:55 PM To: members.i2b2aug; Paul AVILLACH Subject: Re: i2b2: Letter of information, Consent form for reusing data, IRB Form and list of 'High Risk' variables
  Paul,
  Our wiki has some relevant info but not the consent letter (1 and 2) http://informatics.kumc/work/wiki/HERON
  For #3 specifically, our IRB protocol is below (though we may revise it as we provide more functionality this year).
  http://informatics.kumc/work/attachment/wiki/HERON/HERON_Repository_HSC_IRB_Protocolv1 _1.docx
  Didn't have to make any explicit "high risk" data elements though we discussed it with the hospitals and clinics contributing data.
  Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center
  
  From: Paul AVILLACH avillach.mac Sent: 7/8/2011 11:51 AM
  Dear i2b2 community,
  In Paris, we would be very interested to read, if possible, the documents from other institutions on: 1) the information letter you give to patients for reusing their data for research 2) the consent form, if you have one, for reusing their data for research 3) the form to get an IRB approval for an i2b2 project
  Our IRB would also like to have a list of variables at "Hight Risk" (HIV virology tests, abortion status, etc...) The IRB would like to always have all those "Hight Risk" variables discarded for the construction of i2b2 projects. It's only if the purpose of a particular research needs some of them that the PI would have to justify to have access to it.
  Did any other institution had to create this very difficult list ?? If so, can you share it?
  Thanks for any answers!
  Best R
  Paul Avillach
  MD, PhD Student - Assistant Hospitalo-Universitaire - Informatique médicale
  DIH-HEGP - APHP - 20 rue Leblanc - Paris 15 INSERM UMRS 872, eq. 20 - SPIM -Université Paris Descartes - 83 http://ics.upmc.fr/ http://www.spim.jussieu.fr/
  
  
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  From: McMurry, Andrew J. [Andrew_McMurry.hms.harvard] Sent: Wednesday, July 06, 2011 10:14 AM To: Key, Dustin Cc: i2b2 AUG MembersSubject: Re: SAS code for i2b2 and shrine
  Thank you Dustin !
  HMO sites evaluating i2b2 may leverage this code to get i2b2 online quickly.
  We have been following this with interest.
  Andrew McMurry, MS http://open.med.harvard.edu/display/SHRINE
  
  On Jul 5, 2011, at 4:50 PM, Key, Dustin wrote:
  I'm writing in order to share some SAS code that builds the i2b2 query interfaces. You can toggle whether you want Rx, Px (CPT-4, HCPCs), Dx (ICD-09), Demographic, or Enrollment. Also, I set up modules for building the corresponding concept_dimension, and filling c_totalnum. Also, we customized the fields a little bit so that the procedure/diagnosis code ranges are part of the c_name. That way, if you are looking for code '450' you can follow the tree to that point.
  Full Disclosures:
  The c_totalnum module needs some work (I'm running an inner join where I should probably be running some sort of 'like' join.) ICD-09 PX needs to be built (will have that done very soon.) Also, the concept_dimension module is untested. (Should work, but first to use will probably find a bug. Also, keep in mind that your fact naming scheme needs to mesh with what I've chosen for the concept dimension.)
  The Details:
  Andrew McMurry set up a subversion code sharing repository for us at the following. The main program is called Ontology_Deploy_V1.sas. http://scm.open.med.harvard/svn/repos/shrine-hmorn/releases/1.0/Deploy
  The main idea of the programs is to leverage the hierarchies already in the UMLS "MRHIER" tables. These hierarchies get expressed in the c_fullpath field such as
  \i2b2\rx\A17892768\A17926163\A17918467\
  Someone during the meeting mentioned the benefits of storing the path information in this way---it can make for a more narrow field. On the minus side, it is more difficult to debug these strings by eyeball.
  One thing I want to point out about this method is that we can somewhat rapidly include any UMLS taxonomy that has a hierarchy. For instance, if you take one of these modules, and modify it a little bit, you should be able to incorporate something completely different like the NCI Methathesaurus (250K concepts!) very quickly. On a rainy day here in Seattle, I plan to try loading some other ontologies to see if they will be useful to investigators. For instance, CCS looks interesting and since it has a hierarchy I ought to be able to load it and see how it works with our data, very quickly.
  Over time we will switch over to the NCBO method for our main taxonomies. So, I think what I have here will be mainly useful for those using SAS and need to run something in the short term. This SAS program doesn't address versioning, modifiers, the patient or visit dimension, etc.. At Group Health, we've been on version 1.4, so we've been working via the concept_dimension only, and not patient or visit dimensions.
  I invite anyone to make changes or add modules via subversion.
  Thanks and it was nice meeting lots of you last week!
  Dustin Key Programmer/Analyst Group Health Research Institute
  
  
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  From: Brian Ostasiewski [bostasie.wfubmc] Sent: Tuesday, July 05, 2011 1:40 PM To: i2b2 AUG MembersSubject: Reports Evaluation Cell
  I have uploaded the Wake Forest Baptist Health cell/plugin for searching observation_blob text. The poster we presented at last week's meeting is in PDF form on the downloads page. Instructions for install are on the wiki page.
  http://code.google.com/p/i2b2-reports-evaluation-cell/
  Brian Ostasiewski
  
  
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  From: Jack London [jack.london.KimmelCancerCenter] Sent: Tuesday, July 05, 2011 12:04 PM To: i2b2 AUG Membersmembers Cc: Mauro Subject: additional comments about ExportXLS plugin
  Some additional notes about our experiences with the ExportXLS plugin:
  1) We use PHP version 5.3.2, and needed to change the php code in the body of export-files/SaveToExcel.php to read:
  ?php echo $_REQUEST['datatodisplay']; ?
  2) We found the drag-and-drop of the patient set not to work on a PC running IE8. The drag-and-drop worked fine on this machine with Firefox v4.01.1.
  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
  
  
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  From: Jack London [jack.london.KimmelCancerCenter] Sent: Tuesday, July 05, 2011 9:57 AM To: Mauro Cc: i2b2 AUG Membersmembers Subject: Export XLS plugin works fine!
  Mauro,
  I was able to get your ExportXLS to work with our i2b2 deployment. (I went back and overwrote a library file I had messed up with your distribution copy.) We will now move the plugin to our production server deployment.
  Once again, thank you for your contribution.
  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
  
  
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  From: Mendis, Michael E. Sent: Saturday, July 02, 2011 7:33 AM To: i2b2 AUG MembersSubject: unzip on mac issues
  On some instances of Snow Leopard it appears that uaers can not unzip using the internal unzipper for RC3 of the VM image, to resolve this download and install p7zip for the Mac.
  I will look into this a little more and see why.
  mike
  
  
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  From: Jack W. London, Ph.D. [Jack.London.KimmelCancerCenter] Sent: Friday, July 01, 2011 5:10 PM To: Mauro Cc: i2b2 AUG Membersmembers Subject: Re: Export Plugin
  I have successfully incorporated the plugin in my v1.5 i2b2 web client, but when I run it, it hangs with "Creating the table" displayed in the "View Results" panel. When I look at the Message Log, the last entry is "getPDO_fromInputList called by Plugin:ExportXLS." The generated XML message looks fine, with appropriate entries for the Patients and Observations.
  Any ideas what my problem is?
  thanks,
  Jack
  
  Quoting Mauro mauro.bucalo.gmail:
  Hi everyone, here in Pavia, we finished a new general-purpose Export Plugin. Basically the plugin allows to dinamically create and download in excel format a data table with patients' observations by merging a Patient Set and multiple Concepts (Ontology Terms). Source and documentation can be found at http://code.google/p/i2b2-export-xls-plugin/downloads/listhttp://code.google/p/i2b2-export-xls-plugin/ .
  We welcome comments and suggestions to improve the plugin.
  Best regards.
  Mauro Bucalo
  Ext. Collaborator Dipartimento di Informatica e Sistemistica Universita' di Pavia Via Ferrata 1, 27100 Pavia, Italy e-mail: mauro.bucalo.gmail web-page: http://it.linkedin/in/maurobucalo
  
  
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  From: Chan, Wayne [Wayne.Chan.umassmed] Sent: Friday, July 01, 2011 4:41 PM To: 'Jack W. London, Ph.D.' Cc: Mauro; i2b2 AUG Membersmembers Subject: RE: Export Plugin
  Jack,
  Thanks for the update. That sounded like a similar experience I had (didn't remember that one before) – these difference VM snapshot instances are valuable but keeping track of them could be tricky. The query I had success with is \diagnosis\circulatory system (using the data shipped with v1.6RC2), if you like to try it.
  Wayne
  
  From: Jack W. London, Ph.D. [Jack.London.KimmelCancerCenter] Sent: Friday, July 01, 2011 3:54 PM To: Chan, Wayne Cc: Mauro; i2b2 AUG Membersmembers Subject: RE: Export Plugin
  Wayne,
  Problem solved!!!
  I was using the wrong path for the i2b2 instance I am using. So all the modifications were being made to another i2b2 instance, not the one I was accessing from my browser.
  The plugin now appears on the list and can be executed. However rather than successfully run, it "hangs." I am looking at the Message Log for an indication as to why it never completes. I have seen this behavior before, and it usually results from a null in a patient dimension column that should not be null.
  thanks for your help.
  Jack Jack W. London, Ph.D. Thomas Jefferson University Research Professor, Cancer Biology Kimmel Cancer Center Director, KCC Informatics Core Facility 808 Bluemle Life Science Bldg. 233 S. 10th Street Philadelphia, PA 19107
  
  Quoting "Chan, Wayne" Wayne.Chan.umassmed:
  Jack, Based on previous problems I had with other web client plugins, other possibilities for double-checks are: 1) make sure that the location of the ExportXLS folder matches that stated in the /webclient/js-i2b2/i2b2loader.js file; 2) make sure to scroll through the list of available plugins to make sure that it doesn't get tuck near the end (in correspondence to placement of the inserted code segment)
  I usually would click on the "listZoomView" icon to have the full plugin list displayed when I tried to look for a hiding plugin I think Mauro stated that his plugin was developed on webclient 1.5 on his google URL.
  Again, hope these help & good luck. Any way, Mauro should be coming online pretty soon - he responded to my other questions to him in the mid afternoon EDT yesterday.
  Wayne
  
  From: Jack London [jack.london.KimmelCancerCenter] Sent: Friday, July 01, 2011 12:08 PM To: Chan, Wayne Cc: Mauro; i2b2 AUG Members Subject: Re: Export Plugin
  Wayne, I also "copied-and-pasted" the file edits, to avoid typo's. So they are accurate. I'm wondering whether it's a web client v1.5 vs. v1.6 issue. My browsers are Mac Firefox 4.0 and Safari 5.0.4.
  thanks for your response.
  Jack
  
  On Jul 1, 2011, at 12:01 PM, Chan, Wayne wrote:
  Jack, I also downloaded & installed Mauro's ExportXLS plugin on my v.1.6RC2 i2b2 dev VM, and have been able to run it (there were some problems with IE 8, but OK on Firefox 4.0.1 & Chrome 12.0.742.112) since yesterday. I copied & pasted from his "installation guide" when updating the /webclient/jsi2b2/i2b2loader.js file to avoid possible typo's - may be that's a good place to start debugging it.
  Good luck.
  Wayne
  
  From: Jack London [jack.london.KimmelCancerCenter] Sent: Friday, July 01, 2011 11:32 AM To: Mauro Cc: i2b2 AUG Members Subject: Re: Export Plugin
  Mauro,
  Thank you very much for distributing this i2b2 plugin. It is something we need very much. I installed the plugin on a development deployment of v1.5 i2b2 web client. (Your instructions were excellent!) I made sure all file ownerships and permissions were correct. I emptied the browser cache and restarted jboss. Unfortunately, the ExportXLS plugin does not appear in the plugin list when the "Analysis Tools" tab is clicked. I re-checked everything I did, and could not find an error. I did notice that the library file you distributed, jquery-1.6.1.min.js, did not have "new lines" in the code section, so it appeared to editors as having only 3 lines. I replaced all semicolons ( with semi-colon-new-line. This made the code readable (I'm not sure if it really made any difference to its execution). Anyway, the plugin still did not appear in the list. Any help you can provide would be very appreciated as we really can use this plugin.
  Thank you again for your contribution.
  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
  
  On Jun 30, 2011, at 9:35 AM, Mauro wrote:
  Hi everyone, here in Pavia, we finished a new general-purpose Export Plugin. Basically the plugin allows to dinamically create and download in excel format a data table with patients' observations by merging a Patient Set and multiple Concepts (Ontology Terms). Source and documentation can be found at http://code.google/p/i2b2-export-xls-plugin/downloads/listhttp://code.google/p/i2b2-export-xls-plugin/.
  We welcome comments and suggestions to improve the plugin.
  Best regards.
  Ing. Mauro Bucalo, Ext. Collaborator Dipartimento di Informatica e Sistemistica Universita' di Pavia Via Ferrata 1, 27100 Pavia, Italy e-mail: mauro.bucalo.gmailmauro.bucalo.gmail web-page: http://it.linkedin/in/maurobucalo