i2b2 Academic Users Group
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NEXT EMAIL
From:Mauro Bucalo <m auro.bucalo.gmail>
Sent:Monday, April 23, 2012 6:14 AM
To:Sebastian Mate
Cc:i2b2 AUG Members
Subject:Re: wizard 1.3.6 problem
Thanks again Sebastian, now it works perfectly!

2012/4/20 Mauro Bucalo <mauro.bucalo.gmail>
Thanks Sebastian! I'll try right now.

2012/4/20 Sebastian Mate <Sebastian.Mate.imi.med.uni-erlangen.de>
Hi Mauro,
you can use your arrow keys to scroll the message window to the right.
If this is a "invalid password" message, the script failed because the Oracle DB's "system" user passwort doesn't match the setting in the "Configure Parameters" menu and the Wizard therefore can't log in with "system" to create a new DB schema. The "system" password is set during the Oracle setup process in i2b2 Wizard (this is when the screen becomes black and asks you to enter stuff). By default, the password should be "i2b2", and this is what a default Wizard installation expects you to have entered during the black screen Oracle setup. If you have used a different password, simply change the password in the "Configure Parameters" menu.
The next version of i2b2 Wizard will implement an automatic check to make sure that the passwords match.

Sebastian
Dipl.?Inf. Sebastian Mate Friedrich?Alexander?University of Erlangen?Nuremberg
Department for Medical Informatics
Krankenhausstrasse 12, 91054 ERLANGEN, GERMANY
Phone +49 9131/85?26785, Fax +49 9131/85?26754
Sebastian.Mate.imi.med.uni?erlangen.dehttp://www.imi.med.uni?erlangen.de

Von: members.i2b2aug [members.i2b2aug] Im Auftrag von Mauro Bucalo Gesendet: Dienstag, 3. April 2012 16:00
An: i2b2 AUG Members members
Betreff: wizard 1.3.6 problem
Hi all, has anyone tried to use the last wizard release(1.3.6)?
I downloaded and installed all the necessary in a fresh 10.04.4 ubuntu.
When i go to the menu "Hive Task" and select "Load I2B2PM and I2B2HIVE" this is what happens:


Thanks in advance.
Mauro.
Ing. Mauro Bucalo, Ext. Collaborator Dipartimento di Informatica e Sistemistica Universita' di Pavia
Via Ferrata 1, 27100 Pavia, Italy tel:++39.0382.985981
e-mail: mauro.bucalo.gmail
web-page: http://it.linkedin.com/in/maurobucalo


NEXT EMAIL
From:Mark Yin <Mark.Yin.einstein.yu>
Sent:Tuesday, April 17, 2012 10:59 AM
To:Murphy, Shawn N.
Cc:Mark Weiner; i2b2 AUG Members; Mark Yin
Subject:RE: i2b2 1.6.03 PM install issue
Dear Shawn:
Yes, I just posted it.
Thank you!
Mark Yin, Ph.D.
System Director, Research Informatics Core (RIC) Einstein?Montefiore Institute for Clinical and Translational Research
(ICTR) Albert Einstein College of Medicine
1300 Morris Park Ave, Mazer Bldg., Rm 530 Bronx, NY 10461 (718) 430?2946 ? mark.yin.einstein.yu

From: Murphy, Shawn N. [SNMURPHY.PARTNERS] Sent: Tuesday, April 17, 2012 10:43 AM
To: Mark Yin
Cc: Mark Weiner; i2b2 AUG Members; Mark Yin
Subject: Re: i2b2 1.6.03 PM install issue
Hi All,
For install issues, can you please use the list http://groups.google.com/group/i2b2?install?help so we can focus on overall postings to the main list.
Thanks,
Shawn Murphy MD Communicating with handheld

On Apr 17, 2012, at 10:29 AM, "Mark Yin" <Mark.Yin.einstein.yu> wrote:
All:
Anyone has successfully installed i2b2 version 1.6.0.3 on Redhat Enterprise Linux 5.8 with 64 bit?
If so, anyone can shed some lights regarding the installation.
We followed
1. to finish the pre?requisites followed by Hive_Installation guide. And
2. performed data installation followed by data installation guide without any problem.
3. finished the PM installation until Page 16 (Administration of the i2b2 Project Management application) followed by Project Management Installation Guide
We followed the exact same version on every step and without error.
However, we went into the issue on the admin login as described below. Any suggestion from anyone? Thank you!
Mark Yin, Ph.D.
System Director, Research Informatics Core (RIC) Einstein?Montefiore
Institute for Clinical and Translational Research (ICTR) Albert
Einstein College of Medicine
1300 Morris Park Ave, Mazer Bldg., Rm 530 Bronx, NY 10461
(718) 430?2946 ? mark.yin.einstein.yu

From: Mark Yin
Sent: Monday, April 16, 2012 2:27 PM
To: 'Mark Weiner'
Subject: RE: i2b2 1.6.03 PM install issue
Mark,
We just checked and here're the results:
C:\Documents and Settings\Mark>sqlplus sys as sysdba
SQL*Plus: Release 10.1.0.2.0 ? Production on Mon Apr 16 14:16:10 2012
Copyright (c) 1982, 2004, Oracle. All rights reserved.
Connected to:
Oracle Database 10g Express Edition Release 10.2.0.1.0 ? Production
SQL> select domain_name from i2b2pm.pm_hive_data;
DOMAIN_NAME
??????????????????????????????????????????????????????????????????????
i2b2demo
SQL>
[root@informatics36 admin]# more i2b2_config_data.js {
urlProxy: "index.php",
urlFramework: "js?i2b2/",
//????????????????????????????????????????????????????????????????????
// THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO
//adminOnly: true,removed from lstDomains below
lstDomains: [
{ name: "localhost",
domain: "i2b2demo",
adminOnly: true,
debug: true,
urlCellPM: "http://informatics36.ric.einstein.yu.edu:9090/i2b2/rest/PMService/"
}
]
//????????????????????????????????????????????????????????????????????
}
[root@informatics36 admin]# pwd
/var/www/html/admin
[root@informatics36 admin]#

The error we are currently getting (in IE; Chrome still gives "Your account does not have access to any i2b2 projects.")
is "Requires ADMIN role, please contact your system administrator"
If we remove
adminOnly: true,
line from i2b2_config_data.js (and restart the browser ? forced reload does not help???), the message is
The PM cell is down or the address in the properties file is incorrect.
Mark Yin, Ph.D.
System Director, Research Informatics Core (RIC) Einstein?Montefiore
Institute for Clinical and Translational Research (ICTR) Albert
Einstein College of Medicine
1300 Morris Park Ave, Mazer Bldg., Rm 530 Bronx, NY 10461
(718) 430?2946 ? mark.yin.einstein.yu

From: Mark Weiner [mweiner.mail.med.upenn]
Sent: Monday, April 16, 2012 1:16 AM
To: Mark Yin
Subject: RE: i2b2 1.6.03 PM install issue
Can you tell from the startup messages if all went well with the jboss startup? Particularly the connection to the database? I presume when you point your browser to http://Jboss_address:jboss_port that you see a generic jboss administrative screen (this has nothing to do with i2b2, but just ensures that jboss is alive and ready to receive connections from the i2b2 code).
I saw you got some advice from Peter Beninato last week. He was helpful in the 1.6.02 version which was missing a key record from the PM_PROJECT_USER_ROLES table. I see he gave you the same advice to insert a record into that table, though that table may have already had that record (the one with an '@' sign in the project_id field and the user_id = i2b2).
AT that time, I see you were getting a different error message ?? one about needing ADMIN privileges. I presume after you took his advice that the error message changed to the current one that says "Your account does not have access to any i2b2 projects"
If your change to the database resulted in a change to the error message, then the good news is that the web service IS likely communicating with the database.
I see you had asked about clarification of the Step2:
domain: have this parameter match the value in i2b2pm.pm_hive_data.domain_name
Did you get that clarification? If not, it is simple, but VERY important!
In your i2b2_config_data.js file in the admin directory, the listing of i2b2 locations includes several parts, one of which is called "domain." The term next to it MUST be "i2b2demo"
If you change that name, then the domain_name field of the pm_hive_data table (in the i2b2pm schema) must also be changed. It is better to leave that alone, at first at least!
Also, make sure the port numbers used in the i2b2_config_data.js file are the same as the port you are running jboss. There was some switching of ports used in older i2b2 versions to newer ones (something to do with the fact that older ones used tomcat for the PM and JBOSS for the "main" i2b2 cells, and now everything uses JBOSS) and sometimes the default ports in the code are NOT correct!
Make sure the above settings are as I describe. If you send me the contents of your i2b2_config_data.js, I may be able to provide additional insight.
Mark

From: Mark Yin [Mark.Yin.einstein.yu]
Sent: Sunday, April 15, 2012 11:14 PM
To: 'mweiner.mail.med.upenn'
Subject: Re: i2b2 1.6.03 PM install issue
Mark:
Yes.
Mark

From: Mark Weiner [mweiner.mail.med.upenn]
Sent: Sunday, April 15, 2012 11:04 PM
To: Mark Yin
Subject: RE: i2b2 1.6.03 PM install issue
Are you sure that jboss is running??
Mark

From: Mark Yin [Mark.Yin.einstein.yu]
Sent: Sunday, April 15, 2012 11:01 PM
To: 'mweiner.mail.med.upenn'
Subject: Re: i2b2 1.6.03 PM install issue
Mark:
I used apache server comes from linux box.
Service.com/admin/default.htm
Login I'd i2b2, or i2b2demo, etc.
Password: demouser.
None of these is working.
I was frustrated... Any hint?
Thanks.
Mark

From: Mark Weiner [mweiner.mail.med.upenn]
Sent: Sunday, April 15, 2012 09:55 PM
To: Mark Yin
Subject: RE: i2b2 1.6.03 PM install issue
There are so many little things that can go wrong, it is hard to know! I What URL are you using for the admin tool? What login credentials are you using?
Mark

From: Mark Yin [Mark.Yin.einstein.yu]
Sent: Friday, April 13, 2012 11:59 PM
To: Mark Weiner
Cc: Mark Yin
Subject: RE: i2b2 1.6.03 PM install issue
Mark:
We installed i2b2 (V1.6.03) and webserver (Linux Apache) for the webclient on he same machine (Redhat Linux 64 bit).
I copied admin directory from the source code.
I tried to access the web browser from my local computer and it did not work.
Regardless what user name and password I used, it returned the same message, It did not even talk to database.
"Your account does not have access to any i2b2 projects"
Any suggestions?
Mark Yin, Ph.D.
System Director, Research Informatics Core (RIC) Einstein?Montefiore
Institute for Clinical and Translational Research (ICTR) Albert
Einstein Cancer Center Albert Einstein College of Medicine
1300 Morris Park Ave, Mazer Bldg., Rm 530 Bronx, NY 10461
(718) 430?2946 ? mark.yin.einstein.yu

From: Mark Weiner [mweiner.mail.med.upenn]
Sent: Friday, April 13, 2012 6:11 PM
To: Mark Yin; i2b2 AUG Members
Subject: RE: i2b2 1.6.03 PM install issue
I'm not sure if our problem is similar, but for us, it made a huge difference if we logged into the admin tool using a Web browser that was physically running on the same machine as the I2B2 components and the webserver, versus a web Browser on a different machine that connected to the admin website. The connection to the admin tool did not work from the browser running directly on the webserver, but worked fine when I connected from another machine. To this day, I cannot explain it ?? its not a port problem, nor a firewall problem nor anything else I can identify.
So try connecting to the admin tool from machines different from the web/i2b2 server and see if it works for you!
Mark

From: Mark Yin [Mark.Yin.einstein.yu]
Sent: Friday, April 13, 2012 5:29 PM
To: 'i2b2 AUG Members'
Cc: Mark Yin
Subject: Re: i2b2 1.6.03 PM install issue
All:
We tried to install the i2b2 from the source. In the PM install, we copied admin directory to apache /var/www/html directory and modified .js file.
But the login does not work. The login appears that it does not talk to jboss webserver.
Anyone has any suggestion?
Thank you!
Mark


NEXT EMAIL
From:Mendis, Michael E.
Sent:Friday, April 13, 2012 5:57 PM
To:Mark Yin
Cc:i2b2 AUG Members
Subject:Re: i2b2 1.6.03 PM install issue
Install all the cells first, than try again. also did you install the database section? What errors do you see on the jboss log.
Also there is a google group: google groups (http://groups.google.com/group/i2b2?install?help) that is good for i2b2 install issues
thanks mike

On Apr 13, 2012, at 5:28 PM, Mark Yin wrote:
All:
We tried to install the i2b2 from the source. In the PM install, we copied admin directory to apache /var/www/html directory and modified .js file.
But the login does not work. The login appears that it does not talk to jboss webserver.
Anyone has any suggestion?
Thank you!
Mark


NEXT EMAIL
From: Phillips, Lori C.
Sent:Thursday, April 12, 2012 1:10 PM
To:Peter Beninato; i2b2 AUG Members
Subject:RE: i2b2 - v1.6.03 - workbench - developer guide - eclipse
Keep going in the document; Step 2.2.2 performs the actual build where the gensrc and genlib items get built. Lori

From: Peter Beninato [beninato.ohsu]
Sent: Thursday, April 12, 2012 12:35 PM
To: i2b2 AUG Members
Subject: i2b2 - v1.6.03 - workbench - developer guide - eclipse
Hi,
Following the i2b2 Workbench Developers Guide.
Get to step 2.1.2.12, basically importing the project, and get the following 8 Java Build path problems: DescriptionResource PathLocationType
Project 'edu.harvard.i2b2.common' is missing required source folder:
'gensrc' edu.harvard.i2b2.commonBuild pathBuild Path Problem
Project 'edu.harvard.i2b2.eclipse.plugins.analysis' is missing required library: 'genlib/i2b2Common?
core.jar' edu.harvard.i2b2.eclipse.plugins.analysisBuild path Build Path Problem
Project 'edu.harvard.i2b2.eclipse.plugins.explorer' is missing required library: 'genlib/i2b2Common?
core.jar' edu.harvard.i2b2.eclipse.plugins.explorerBuild pathBuild Path Problem
Project 'edu.harvard.i2b2.eclipse.plugins.ontology' is missing required library: 'genlib/i2b2Common?
core.jar' edu.harvard.i2b2.eclipse.plugins.ontologyBuild path Build Path Problem
Project 'edu.harvard.i2b2.eclipse.plugins.previousQuery' is missing required library: 'genlib/i2b2Common?
core.jar' edu.harvard.i2b2.eclipse.plugins.previousQueryBuild pathBuild Path Problem
Project 'edu.harvard.i2b2.eclipse.plugins.query' is missing required library: 'genlib/i2b2Common? core.jar' edu.harvard.i2b2.eclipse.plugins.queryBuild pathBuild Path Problem Project 'edu.harvard.i2b2.eclipse.plugins.workplace' is missing required library: 'genlib/i2b2Common?
core.jar' edu.harvard.i2b2.eclipse.plugins.workplaceBuild path Build Path Problem
Project 'edu.harvard.i2b2.eclipse' is missing required library: 'genlib/i2b2Common?
core.jar'edu.harvard.i2b2.eclipseBuild pathBuild Path Problem
Any advice? Thanks.
Peter Beninato – OCTRI DW Developer
Oregon Health & Science University


NEXT EMAIL
From: Phillips, Lori C.
Sent: Thursday, April 12, 2012 9:11 AM
To: Jennifer Cai; Mendis, Michael E.; i2b2 AUG Members
Subject: RE: AxisRESTServlet error on i2b2 1.6.0.3
Jennifer,
What you are witnessing is the webclient trying to access one of the cells you have not installed yet (e.g CRC or WORK). The problem should disappear once all the cells are installed.
Lori

From: Jennifer Cai [Jennifer.Cai.UTSouthwestern] Sent: Wednesday, April 11, 2012 6:10 PM
To: Mendis, Michael E.; i2b2 AUG Members
Subject: AxisRESTServlet error on i2b2 1.6.0.3
Hi,
We are installing 1.6.0.3. So far we installed PM and Ontology cells (we have NOT installed CRC, workplace and FR yet). Admin (PM) tool works fine. We tried to launch webclient now, but we got following error in the Jboss log. Do we need to install all the rest cells to be able to make the error disappear?
15:22:51,389 ERROR [AxisRESTServlet] org.apache.axis2.AxisFault: Service not found operation terminated !!; nested exception is:
org.apache.axis2.AxisFault: Service not found operation terminated !!
Thanks, Jennifer


NEXT EMAIL
From:Schulte, Gregory <Gregory.Schulte.childrenscolorado>
Sent:Wednesday, April 11, 2012 11:08 PM
To:Jennifer Cai
Cc:Mendis, Michael E.; i2b2 AUG Members
Subject:Re: AxisRESTServlet error on i2b2 1.6.0.3
Jennifer,
Are there any error messages in the apache server.log or error.log
Many of the webclient errors will be located on the apache side.
Greg

On Apr 11, 2012, at 4:10 PM, Jennifer Cai wrote:
Hi,
We are installing 1.6.0.3. So far we installed PM and Ontology cells (we have NOT installed CRC, workplace and FR yet). Admin (PM) tool works fine. We tried to launch webclient now, but we got following error in the Jboss log. Do we need to install all the rest cells to be able to make the error disappear?
15:22:51,389 ERROR [AxisRESTServlet] org.apache.axis2.AxisFault: Service not found operation terminated !!; nested exception is:
org.apache.axis2.AxisFault: Service not found operation terminated !!
Thanks,
Jennifer
UT Southwestern Medical Center
The future of medicine, today.


NEXT EMAIL
From:Mendis, Michael E.
Sent:Monday, April 09, 2012 4:25 PM
To:i2b2 AUG Members
Subject:ASP proxy file for windows webclient
Does anyone have a ASP proxy file that they use instead of the PHP one that is included in the webclient distribution. That they would not mind donating to the future webclients.
Thanks
Mike


NEXT EMAIL
From: Chan, Wayne <Wayne.Chan.umassmed>
Sent:Friday, April 06, 2012 4:03 PM
To:'i2b2 AUG Members'
Cc:Sadasivam, Rajani; Houston, Thomas; English, Thomas; Zottola, Ralph; Ranauro, Paul; Guilarte-Murphy, Yurima; Kinney, Rebecca; Phillips, Barrett D
Subject:v1.1 of the 2 Workplace Items Sharing Enhancement plugins (for webclient) from
UMass Med School
Hi, everyone,
We, at University of Massachusetts Medical School, like to announce the new release (v1.1) of our 2 Workplace Items Sharing Enhancement (WISE) plugins (for webclient). They are available for download from our website: http://micard.umassmed.edu/downloads.php
The new features of the latest release of these 2 plugins are:
Workplace Items Sharing Enhancement - Tagger / Annotator
This plugin facilitates the annotation (with tags or notes) of a Workplace item (folder, query, patient set, etc.) within the web client framework.


1.1


Added support for Internet Explorer;

 

 


fixed the unscrollable panel problem, on IE, against i2b2 webclient v1.6.0.2;
compatible browsers: Firefox, Chrome, Internet

Explorer, & Safari.

Compatible i2b2 webclients: v1.3 - v1.6.0.2.

 




Workplace Items Sharing Enhancement - Searcher
This plugin facilitates searching for similar Workplace items (folder, query, patient set, etc.) within the web client framework.


1.1

 


Added supports for 'ignoring case', 'exclusion terms &

 

 

 

 


options', & 'CSV export', etc.;

 

 

 


updated both XLS & CSV exports to be independent of server php setting; &
fixed the unscrollable panel problem, on IE, against i2b2 webclient v1.6.0.2.
Compatible browsers: Firefox, Chrome, Internet

Explorer, & Safari.

Compatible i2b2 webclients: v1.3 - v1.6.0.2.

 

 

 





Note that each downloadable kit contains its own "installation document", for easy reference.
Please don't hesitate to contact us regarding any questions, problems, feedbacks, or suggestions for improvements.
Wayne
S. Wayne Chan, MSEE, MSME Biomedical Research Informatics Development Group (BRIDG) and Biomedical Research Informatics Consultation & Knowledge Service (BRICKS), Division of Health Informatics & Implementation Science (HIIS),
Department of Quantitaive Health Sciences (QHS), University of Massachusetts Medical School (UMMS) at Worcester, MA 01655 (508) 856?8947


NEXT EMAIL
From:Mark Yin <Mark.Yin.einstein.yu>
Sent:Friday, April 06, 2012 11:19 AM
To:Peter Beninato; Darren W Henderson; i2b2 AUG Members
Cc:Mark Yin
Subject:RE: i2b2 PM install issue
Peter:
I still can't get it working.
Could you clarify this step for me:
Step2:
domain: have this parameter match the value in i2b2pm.pm_hive_data.domain_name

Thank you! Mark Yin, Ph.D.
System Director, Research Informatics Core (RIC)
Einstein?Montefiore Institute for Clinical and Translational Research (ICTR)
Albert Einstein College of Medicine
1300 Morris Park Ave, Mazer Bldg., Rm 530
Bronx, NY 10461
(718) 430?2946 – mark.yin.einstein.yu

From: Peter Beninato [beninato.ohsu]
Sent: Thursday, April 05, 2012 4:48 PM
To: Mark Yin; Darren W Henderson; i2b2 AUG Members
Subject: RE: i2b2 PM install issue
Hi,
Below are the steps to get the ADMIN site available via the thinclient. Please note that some of the scripting (sql) is geared for Oracle, but easily modified.
Please consider modifying the code for future editions so others won't have to struggle with this. For instance, the INSERT does not exist in:
i2b2\v1_6_02\i2b2createdb-1602\edu.harvard.i2b2.data\Release_1-6\NewInstall\Pmdata\scripts or
i2b2\v1_6_02\i2b2createdb-1602\edu.harvard.i2b2.data\Release_1-6\Upgrade\Pmdata\scripts
Also the project_management_installation_guide.pdf should probably be edited too.
The steps to get the ADMIN site via the thinclient is as follows:
1) INSERT INTO I2B2PM.PM_PROJECT_USER_ROLES
2) Edit the file: i2b2\v1_6_02\i2b2core-src-1602\src\admin\i2b2_config_data.js (before deployment or the same file under the apache server after deployment) for the parameters: domain, name, urlCellPM
Step 1(code):
INSERT INTO I2B2PM.PM_PROJECT_USER_ROLES (
PROJECT_ID, USER_ID, USER_ROLE_CD, CHANGE_DATE, ENTRY_DATE, CHANGEBY_CHAR, STATUS_CD
)
VALUES (
'@'
,'i2b2'
,'ADMIN'
,sysdate
,sysdate
,'i2b2'
,'A'
); Commit;
Step2:
domain: have this parameter match the value in i2b2pm.pm_hive_data.domain_name name: set this to "localhost"
ulrCellPM: http://localhost:9090/i2b2/rest/PMService/
Below is example admin/i2b2_config_data.js:
{
urlProxy: "index.php", urlFramework: "js-i2b2/",
//-------------------------------------------------------------------------------------------
// THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO
lstDomains: [
{ domain: "i2b2demo", name: "localhost",
urlCellPM: "http://localhost:9090/i2b2/rest/PMService/", allowAnalysis: false,
adminOnly: true, debug: true
}
]
//-------------------------------------------------------------------------------------------
}

Peter Beninato – OCTRI DW Developer

From: Mark Yin [Mark.Yin.einstein.yu]
Sent: Thursday, April 05, 2012 1:44 PM
To: Peter Beninato; Darren W Henderson; i2b2 AUG Members
Cc: Mark Yin
Subject: i2b2 PM install issue
Hello:
While I followed the documentation to install PM, I was asked to get on PM admin page, i.e., http://server1.com/admin/default.htm
The default user i2b2 and default password demouser. The loin gives me that "Requires ADMIN role, please contact system administrator."
I did not see the documentation on where the password was set up. Anyone can help? Thank you!
Mark Yin, Ph.D.
System Director, Research Informatics Core (RIC)
Einstein?Montefiore Institute for Clinical and Translational Research (ICTR) Albert Einstein College of Medicine
1300 Morris Park Ave, Mazer Bldg., Rm 530
Bronx, NY 10461
(718) 430?2946 – mark.yin.einstein.yu


NEXT EMAIL
From:Peter Beninato <beninato.ohsu>
Sent:Wednesday, April 04, 2012 11:04 AM
To:Darren W Henderson; i2b2 AUG Members
Subject:RE: Can anyone else replicate this error?
Hi,
I could duplicate behavior.

From: dwhend0.gmail [dwhend0.gmail] On Behalf Of Darren W Henderson
Sent: Wednesday, April 04, 2012 7:19 AM
To: i2b2 AUG Members
Subject: Can anyone else replicate this error?
We think we discovered an error. We have also tried this on the web demo at i2b2.org and also see an error result.
To replicate can anyone try their respective clients with a query that has:
Multiple panels
Same Encounter Timing
One panel is an exclude that also has an occurs constraint > 1 (or any number > 0 really)
We get an error, and the generated SQL appears to lack its group by clause prior to the having <concatenated fields> predicate:
insert into stock_i2b2data.dbo.#global_temp_table ( encounter_num, patient_num , panel_count) select encounter_num, patient_num ,1 as panel_count from ( select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ encounter_num, patient_num from stock_i2b2data.dbo.observation_fact
where concept_cd IN (select concept_cd from stock_i2b2data.dbo.concept_dimension where concept_path LIKE '\i2b2\Diagnoses\DISEASES AND INJURIES\INFECTIOUS AND PARASITIC DISEASES\OTHER BACTERIAL DISEASES\Diphtheria\Faucial diphtheria%') group by encounter_num , patient_num ) t
update stock_i2b2data.dbo.#global_temp_table set panel_count = 2 where
stock_i2b2data.dbo.#global_temp_table.panel_count = 1
update stock_i2b2data.dbo.#global_temp_table set panel_count = -1 where stock_i2b2data.dbo.#global_temp_table.panel_count = 2
and exists ( select 1 as panel_count
from ( select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ encounter_num, patient_num from stock_i2b2data.dbo.observation_fact
where concept_cd IN /<CONCEPT SUBQUERY>/
<SHOULD HAVE A GROUP BY ENCOUNTER_NUM, PATIENT_NUM HERE>
having count( distinct cast(patient_num as varchar) + '|' + cast(encounter_num as varchar) + '|' + provider_id +
'|' + cast(start_date as varchar) + '|' + cast(instance_num as varchar) + '|' +concept_cd) >= 2 ) t
where stock_i2b2data.dbo.#global_temp_table.patient_num = t.patient_num and stock_i2b2data.dbo.#global_temp_table.encounter_num = t.encounter_num
group by encounter_num , patient_num )
insert into stock_i2b2data.dbo.#dx ( patient_num , encounter_num ) select * from ( select distinct patient_num , encounter_num from stock_i2b2data.dbo.#global_temp_table where panel_count = 2 ) q
Darren W. Henderson
University of Kentucky
Division for Biomedical Informatics
Bio-Pharmacy Complex Rm182
789 S Limestone Lexington, KY 40511 (859) 323-7146
(859) 967-4914


NEXT EMAIL
From:Russ Waitman <rwaitman.kumc>
Sent:Tuesday, April 03, 2012 6:52 PM
To:i2b2 AUG Members; Brian Ostasiewski
Cc:BKelly.fusionio; <George Harrison; <Joel Grace
Subject:RE: I2B2 webserver
Brian,
Glad to hear the fusionio cards are working for you too. Always nice to move a software problem to a hardware solution.
We've still go our staging database on old drives so our main improvement has been in queries. Some times things take longer than I think they should but I want to probably approach this methodically as opposed to randomly investigate individual queries.
Russ Waitman
Director of Medical Informatics
Associate Professor, Department of Biostatistics Assistant Vice Chancellor for Enterprise Analytics University of Kansas Medical Center
913-945-7087 rwaitman.kumc

Brian Ostasiewski <bostasie.wakehealth.edu> 4/3/2012 8:32 AM
Just wanted to reply to this chain of emails – we recently finished an upgrade of our main i2b2 database and staging database to the Fusion IO SSD drives and saw a 20x increase in our ETL processing speed (when you're talking about something that took days, this is huge). We also saw a similarly large improvement in i2b2 query speed, particularly with very complex queries – ones that involved dimensional queries and date constraints. Some of these went from taking hours to complete to taking under an hour; most routine queries are seconds. We're on 1.6 and have 730 million facts in our database.
Brian

From: Chanchai McDonald [cmcdon12.uthsc]
Sent: Friday, November 18, 2011 10:08 AM
To: Russ Waitman
Cc: Parth Divekar; Dan Connolly; petrucm.health.missouri.edu; i2b2 AUG Members; mmendis.partners
Subject: Re: I2B2 webserver
Russ,
I will running into the same issue as yours since the team plan to operates to having our researchers
using i2b2 for their research questions and explore the hypothesis.
Thank you. I am interested to talk to you more about this issue.
Chanchai

On Nov 18, 2011, at 8:56 AM, Russ Waitman wrote:
Chanchai and all,
I suppose it all depends on your definition of "acceptable", how big your audience of simultaneous users will be, and knowing if 1.6 really boosts performance.
We have ~ half a billion facts on 250,000 to 500,000 people depending on what you're looking for. We're running 1.4.
Prior to the fusionio cards, we'd have queries which would never return data. I'd set a lab threshold like potassium < 3.5 and loop diuretic medicaiton exposure: not even sophisticated queries. It was embarrassing. I had to do puppet shows on projector when I was demoing things. We also noticed that on local SAS storage, we were completely disk bound such that one user was consuming all disk utilization.
Now one user typically runs less than 10% disk utilization which means we can support simultaneous queries. That's important because when we hold classes we've had 6-8 people hitting "run query" at the same time. Simple queries resolve in less than 20 seconds. Still, we hit spots where queries can take
over 40 seconds but I am hoping improved performance with 1.6 will help.
For me, I think you want the system to be pretty responsive so that people can really do hypothesis exploration and not get frustrated. Based on my experience running CPOE, clinicians and researchers (and I) are inherently impatient so anything over 15 or 20 seconds is not great. But when they realize what the computer is doing for them, I suppose you can take a sip of coffee during the delay. If it gets over 60 seconds or hangs up on a simple query, they will think it's broken.
We're now getting to the point where people are beginning to use i2b2 for real research questions (4-10 groups, labs, diagnoses, flowsheet data, demographics multiple occurrence thresholds, over 20 exclusion criteria). Those larger queries are running over 20 seconds and in some cases still take a long time to resolve. one example I just did has 3 groups: first with 25 items, second with 45 exclusion concepts, and third with over 100: query takes 154 seconds. But, I am fairly sure these may have taken forever without the memory cards or we'd spend a ton of hours learning how to configure Oracle. Actually, it often takes longer for them to reload in the web client from the shared folder than it takes to actually run the query.
I've always worried that a conventional relational database like Oracle or SqlServer would choke on big data compared to other
DBs like column stores but that was just based on academic reading. But I think the cards allowed us to use off the shelf oracle and move on to the fun stuff instead of spending our time loading interesting data.
Russ Waitman
Associate Professor
Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center
913-945-7087 rwaitman.kumc http://informatics.kumc

"Parth Divekar" <Parth.Divekar.cchmc> 11/18/2011 7:02 AM
Chanchai,
Whether you need SSD or not will depend upon amount of data and number of users accessing data. We have SSD for ETL but not for application database.
We are currently porting in excess of 50 mill rows in fact table and the performance is acceptable.
We have tuned our database for memory and have made some changes in the query that gets executed when you hit "run query from application.
FYI: we are using Oracle 11gR2.
Regards
Parth
Parth Divekar
Database Administrator II
Cincinnati Children's Hospital Medical Center
Ph: - 513-636-1004 (O)

Chanchai McDonald <cmcdon12.uthsc> 11/17/2011 6:25 PM
We concern if the Database storage really requires using Solid state Storage (Fusion-io Cards). We do not currently use/have this type of storage. Will it impact performance adversely if we won't use it?
Chanchai
Chanchai Singhanayok McDonald, Ph.D. Director Biomedical Informatics
The Office of Research, UTHSC
910 Madison Building Suite 620
Telephone: (901) 448-2088

On Jul 20, 2011, at 3:17 PM, Dan Connolly wrote:
Marius,
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


NEXT EMAIL
From:Mark Yin <Mark.Yin.einstein.yu>
Sent:Tuesday, April 03, 2012 12:50 PM
To:i2b2 AUG Members
Cc:Mark Yin
Subject:i2b2 question
Hello:
Anyone can provide any suggestions? Thank you!
We are in the process of deployment of i2b2. Here are technical some questions need to have help from you. Who should we contact? Thank you!
The question is that we installed PM without any problem, but when we launch the website for the service link, we get http://informatics36.aecom.yu.edu:9090/i2b2/services/listServices


looks ok, but when we click any link, we got error, i.e.,
http:// informatics36.aecom.yu.edu:9090/i2b2/services/PMService
<soapenv:Fault xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/">
<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>

Mark Yin, Ph.D.
System Director, Research Informatics Core (RIC)
Einstein?Montefiore Institute for Clinical and Translational Research (ICTR) Albert Einstein College of Medicine
1300 Morris Park Ave, Mazer Bldg., Rm 530
Bronx, NY 10461
(718) 430?2946 – mark.yin.einstein.yu


NEXT EMAIL
From:Peter Beninato <beninato.ohsu>
Sent:Tuesday, April 03, 2012 12:32 PM
To:Peter Beninato; Mendis, Michael E. Cc:i2b2 AUG Members
Subject:RE: i2b2 - v1.6.03 - Webclient - occurs
Hi,
This is curious. So problem is not related to default.htm.
The problem is related to .../weclient/js?i2b2/i2b2_loader.js
Our plugin strategy is fluctuating, before we allowed Demographics( Dem1set).
My approach this version is at this time to comment out all the plugins, but I left the PLUGINMGR. The edits to i2b2_loader.js is what is preventing the Occurs pop?up...
I wratched it up a level, and commented out PLUGINMGR, but still no occurs pop?up. So, then I reverted to v1.4 approach, include only one plug?in, but still no pop?up.
To recap, no Occurs pop?up happens when:
1) Comment out all plugins, but leave Pluginmgr
2) Comment out all plugins, and comment out Pluginmgr
3) Comment out *some* plugins, leaving Dem1Set and Pluginmgr
I have reverted to original i2b2_loader.js.
It is unclear to me why when this file is edited, it breaks the occurs pop?up. FYI.
Peter

From: Peter Beninato [beninato.ohsu] Sent: Tuesday, April 03, 2012 8:01 AM
To: Mendis, Michael E.
Cc: i2b2 AUG Members
Subject: RE: i2b2 ? v1.6.03 ? Webclient ? occurs
Hi,
Thanks for the suggestion.
I did a full replace of the webclient and occurs functionality works.
So far, I have restored my "Less than 10" edits, and still get the Occurs window, so that was not the problem.
I have a few more mods to reintroduce, several on default.htm, which if I fat?fingered a comment clause or something, though I did not see anything when I checked, may have introduced the issue.
I hope to identify the mod that is causing the problem and correct.
Peter

From: Mendis, Michael E. [MMENDIS.PARTNERS]
Sent: Tuesday, April 03, 2012 7:15 AM
To: Peter Beninato
Cc: i2b2 AUG Members
Subject: Re: i2b2 ? v1.6.03 ? Webclient ? occurs
Peter,
Can we try a clean webclient 1.6.03 and see if the occurs popup does not occur on your environment
mike

On Apr 2, 2012, at 5:30 PM, Peter Beninato wrote:
Ok... took my own advice, and compared what is on demo site, and the query panel controller matches.
Ugh.

From: Peter Beninato
Sent: Monday, April 02, 2012 2:11 PM
To: Peter Beninato; 'Mendis, Michael E.'
Cc: 'i2b2 AUG Members'
Subject: RE: i2b2 ? v1.6.03 ? Webclient ? occurs
Hi,
I tried to send email with the CRC_ctrlr_QryPanel.js attached, but I think it may not have gotten beyond the Great Firewall.
To recap:
1) I could hit the demo site, and the occurs window pops up.
2) I'm on version 11.0 of Firefox.
3) Below is version of showOccurs() that is in Query Panel controller. Can someone check to see if it matches what they are running?
Thanks.
Peter
//
==================================================================
//
this.showOccurs = function(iMinCount) {
if (i2b2.CRC.model.queryCurrent.panels.length==0) { return;}
var dm = i2b2.CRC.model.queryCurrent.panels[this.panelCurrentIndex];
if (undefined!==dm) {
if (i2b2.CRC.ctrlr.QT.queryTiming == "ENCOUNTER")
{
$('constraintEncounterBased').show();
$('constraintTextBased').hide();
} else {
$('constraintEncounterBased').hide();
$('constraintTextBased').hide();
}
// load value
$('constraintOccursInput').value = dm.occurs;
// prep variables for JS closure
var qpi = this.panelCurrentIndex;
var cpc = this;
// show occurs window
if (!Object.isUndefined(this.modalOccurs)) { delete this.modalOccurs; }
if (!this.modalOccurs) {
if (!Object.isUndefined(handleSubmit)) { delete handleSubmit; }
//init slider
var slider,
bg="slider?bg", thumb="slider?thumb",
valuearea="slider?value", textfield="slider?converted?value";
// The slider can move 0 pixels up
var topConstraint = 0;
// The slider can move 200 pixels down
var bottomConstraint = 200;
// Custom scale factor for converting the pixel offset into a real value
var scaleFactor = 2;
// The amount the slider moves when the value is changed with the arrow
// keys
var keyIncrement = 10;
var tickSize = 10;
Event.onDOMReady(function() {
slider = YAHOO.widget.Slider.getHorizSlider(bg,
thumb, topConstraint, bottomConstraint);
// Sliders with ticks can be animated without YAHOO.util.Anim
slider.animate = true;
slider.setValue(dm.relevance * 2);
slider.getRealValue = function() {
return Math.round(this.getValue() / scaleFactor);
}
slider.subscribe("change", function(offsetFromStart) {
var valnode = Dom.get(valuearea);
// Display the pixel value of the control
valnode.innerHTML = slider.getRealValue()// offsetFromStart ;
// slider.getRealValue();
//var fld = Dom.get(textfield);
});
Event.on(textfield, "keydown", function(e) {
// set the value when the 'return' key is detected
if (Event.getCharCode(e) === 13) {
var v = parseFloat(this.value, 10);
v = (lang.isNumber(v)) ? v : 0;
// convert the real value into a pixel offset
slider.setValue(Math.round(v/scaleFactor));
}
});
// Use setValue to reset the value to white:
Event.on("putval", "click", function(e) {
slider.setValue(100, false); //false here means to animate if possible
});
});
var handleSubmit = function(){
var closure_qpi = qpi;
var closure_cpc = cpc;
// submit value(s)
if (this.submit()) {
var pd = i2b2.CRC.model.queryCurrent.panels[closure_qpi];
pd.occurs = parseInt($('constraintOccursInput').value, 10);
pd.relevance = slider.getRealValue();
slider.setValue(0);
delete(slider);
closure_cpc._redrawButtons(pd);
i2b2.CRC.ctrlr.QT.doSetQueryName.call(this, '');
}
}
var handleCancel = function(){
this.cancel();
}
var handleHelp = function(){
alert("Help soon");
}
this.modalOccurs = new YAHOO.widget.SimpleDialog("constraintOccurs", {
width: "400px",
fixedcenter: true,
constraintoviewport: true,
modal: true,
zindex: 700,
buttons: [{
text: "OK",
handler: handleSubmit,
isDefault: true
}, {
text: "Cancel",
handler: handleCancel
}]
});
$('constraintOccurs').show();
this.modalOccurs.validate = function(){
// now process the form data
var t = parseInt($('constraintOccursInput').value, 10);
if (isNaN(t)) {
alert('The number you entered could not be understood.\nPlease make sure that you entered a valid number.');
return false;
}
if (t > 19) {
alert('The number you entered was too large.\nThe maximum number you can enter is 19.');
return false;
}
if (t < 0) {
alert('The number you entered was too small.\nThe minimum number you can enter is 0.');
return false;
}
return true;
};
this.modalOccurs.render(document.body);
}
//$('constraintOccurs_c').show();
this.modalOccurs.show();
//this.modalOccurs.visible = true;
}
}

From: Peter Beninato
Sent: Monday, April 02, 2012 12:22 PM
To: 'Mendis, Michael E.'
Cc: members.i2b2aug
Subject: RE: i2b2 ? v1.6.03 ? Webclient ? occurs
Hi,
I hit the demo site, and occurs worked. I'm on Firefox 11.0.
Attached find my local version of the QryPanel controller.
I can revert to original .js files (w/o Less than 10 mods), if that seems like a worthwhile experiment.
Peter

From: Mendis, Michael E. [MMENDIS.PARTNERS]
Sent: Monday, April 02, 2012 11:59 AM
To: Peter Beninato
Cc: members.i2b2aug
Subject: Re: i2b2 ? v1.6.03 ? Webclient ? occurs
can you try it against the i2b2 demo site: http://webservices.i2b2.org/webclient/ and see if has the same results. Also which firefox version are you using?
Mike

On Apr 2, 2012, at 2:33 PM, Peter Beninato wrote:
Hi,
I'm on Firefox. When I turn on web developer it complains the onDOMReady is not a function. I see that code in showOccurs(), but not sure how to correct...
[11:04:48.896] Event.onDOMReady is not a function .https://localhost:9000/webclient/js?i2b2/cells/CRC/CRC_ctrlr_QryPanel
.js:225

From: Mendis, Michael E. [MMENDIS.PARTNERS]
Sent: Monday, April 02, 2012 11:24 AM
To: Peter Beninato
Cc: members.i2b2aug
Subject: Re: i2b2 ? v1.6.03 ? Webclient ? occurs
Peter,
I tried with firefox and ie on the i2b2 demosite and they both had a dialog appear for the occurances.
What browser are you using?
thanks
mike

On Apr 2, 2012, at 12:41 PM, Peter Beninato wrote:
Hi,
The occurs functionality does not appear to work in v1.6.03.
When clicking on "Occurs", no other window pops up, In the lower left corner of the browser it says
"javascript:i2b2.CRC.ctrlr.QT.panelcontrollers[1].showOccurs().
Is anyone else experiencing this problem?
Has anyone developed a work?around?

Peter Beninato ? OCTRI DW Developer
Oregon Health & Science University
503?494?9985
beninato.ohsu<beninato.ohsu>


NEXT EMAIL
From:Bickel, Jonathan <Jonathan.Bickel.childrens.harvard>
Sent:Tuesday, April 03, 2012 11:59 AM
To:i2b2 AUG Members
Subject:ODM to i2b2
Dear i2b2 community. Children's Boston is proud to announce the publishing of an ODM? to i2b2 importer as an i2b2 related project.
The source files and instructions are located on the community wiki [https://community.i2b2.org/wiki/display/ODM2i2b2/Home ] .
With these files you are able to take an ODM XML document and process it into staging tables for loading into i2b2's ontology and CRC cells.
We have gone further to build a REDCAp to ODM loader which can help sites which are using REDcap as one of their EDC system.
Please don't hesitate to contact us with questions.
Jon Bickel
Jonathan Bickel M.D.
Director of Clinical Research Informatics Children¹s Hospital Boston
Work: 617.919.3565
Email: Jonathan.Bickel.childrens.harvard


NEXT EMAIL
From:Peter Beninato <beninato.ohsu>
Sent:Tuesday, April 03, 2012 11:01 AM
To:Mendis, Michael E.
Cc:i2b2 AUG Members
Subject:RE: i2b2 - v1.6.03 - Webclient - occurs
Hi,
Thanks for the suggestion.
I did a full replace of the webclient and occurs functionality works.
So far, I have restored my "Less than 10" edits, and still get the Occurs window, so that was not the problem.
I have a few more mods to reintroduce, several on default.htm, which if I fat?fingered a comment clause or something, though I did not see anything when I checked, may have introduced the issue.
I hope to identify the mod that is causing the problem and correct.
Peter

From: Mendis, Michael E. [MMENDIS.PARTNERS] Sent: Tuesday, April 03, 2012 7:15 AM
To: Peter Beninato
Cc: i2b2 AUG Members
Subject: Re: i2b2 ? v1.6.03 ? Webclient ? occurs
Peter,
Can we try a clean webclient 1.6.03 and see if the occurs popup does not occur on your environment
mike


On Apr 2, 2012, at 5:30 PM, Peter Beninato wrote:
Ok... took my own advice, and compared what is on demo site, and the query panel controller matches.
Ugh.

From: Peter Beninato
Sent: Monday, April 02, 2012 2:11 PM
To: Peter Beninato; 'Mendis, Michael E.'
Cc: 'i2b2 AUG Members'
Subject: RE: i2b2 ? v1.6.03 ? Webclient ? occurs
Hi,
I tried to send email with the CRC_ctrlr_QryPanel.js attached, but I think it may not have gotten beyond the Great Firewall.
To recap:
1) I could hit the demo site, and the occurs window pops up.
2) I'm on version 11.0 of Firefox.
3) Below is version of showOccurs() that is in Query Panel controller. Can someone check to see if it matches what they are running?
Thanks.
Peter


//
==================================================================
//
this.showOccurs = function(iMinCount) {
if (i2b2.CRC.model.queryCurrent.panels.length==0) { return;}
var dm = i2b2.CRC.model.queryCurrent.panels[this.panelCurrentIndex];
if (undefined!==dm) {
if (i2b2.CRC.ctrlr.QT.queryTiming == "ENCOUNTER")
{
$('constraintEncounterBased').show();
$('constraintTextBased').hide();
} else {
$('constraintEncounterBased').hide();
$('constraintTextBased').hide();
}
// load value
$('constraintOccursInput').value = dm.occurs;
// prep variables for JS closure
var qpi = this.panelCurrentIndex;
var cpc = this;
// show occurs window
if (!Object.isUndefined(this.modalOccurs)) { delete this.modalOccurs; }
if (!this.modalOccurs) {
if (!Object.isUndefined(handleSubmit)) { delete handleSubmit; }
//init slider
var slider,
bg="slider?bg", thumb="slider?thumb",
valuearea="slider?value", textfield="slider?converted?value";
// The slider can move 0 pixels up
var topConstraint = 0;
// The slider can move 200 pixels down
var bottomConstraint = 200;
// Custom scale factor for converting the pixel offset into a real value
var scaleFactor = 2;
// The amount the slider moves when the value is changed with the arrow
// keys
var keyIncrement = 10;
var tickSize = 10;
Event.onDOMReady(function() {
slider = YAHOO.widget.Slider.getHorizSlider(bg,
thumb, topConstraint, bottomConstraint);
// Sliders with ticks can be animated without YAHOO.util.Anim
slider.animate = true;
slider.setValue(dm.relevance * 2);
slider.getRealValue = function() {
return Math.round(this.getValue() / scaleFactor);
}
slider.subscribe("change", function(offsetFromStart) {
var valnode = Dom.get(valuearea);

// Display the pixel value of the control
valnode.innerHTML = slider.getRealValue()// offsetFromStart ;
// slider.getRealValue();
//var fld = Dom.get(textfield);
});
Event.on(textfield, "keydown", function(e) {
// set the value when the 'return' key is detected
if (Event.getCharCode(e) === 13) {
var v = parseFloat(this.value, 10);
v = (lang.i2Number(v)) ? v : 0;
// convert the real value into a pixel offset
Slider.setValue(Math.round(v/scaleFactor));
}
});
// Use setValue to reset the value to white:
Event.on("putval", "click", function(e){
slider.setValue(100,false); //false here meant to animate if
});
});
var handleSubmit = function(){
var closure_qpi = qpi;
var closure_cpc = cpc;
// submit value(s)
if (this.submit()) {
var pd = i2b2.CRC.model.queryCurrent.panels[closure_qpi];
pd.occurs = parseInt($('constraintOccursInput').value, 10);
pd.relevance = slider.getRealValue();
slider.setValue(0);
delete(slider);
closure_cpc._redrawButtons(pd);
i2b2.CRC.ctrlr.QT.doSetQueryName.call(this, '');
}
}
var handleCancel = function(){
this.cancel();
}
var handleHelp = function(){
alert("Help soon");
}
this.modalOccurs = new YAHOO.widget.SimpleDialog("constraintOccurs", {
width: "400px",
fixedcenter: true,
constraintoviewport: true,
modal: true,
zindex: 700,
buttons: [{
text: "OK",
handler: handleSubmit,
isDefault: true
}, {
text: "Cancel",
handler: handleCancel
}]
});
$('constraintOccurs').show();
this.modalOccurs.validate = function(){
// now process the form data
var t = parseInt($('constraintOccursInput').value, 10);
if (isNaN(t)) {
alert('The number you entered could not be understood.\nPlease make sure that you entered a valid number.');
return false;
}
if (t > 19) {
alert('The number you entered was too large.\nThe maximum number you can enter is 19.');
return false;
}
if (t < 0) {
alert('The number you entered was too small.\nThe minimum number you can enter is 0.');
return false;
}
return true;
};
this.modalOccurs.render(document.body);
}
//$('constraintOccurs_c').show();
this.modalOccurs.show();
//this.modalOccurs.visible = true;
}
}

From: Peter Beninato
Sent: Monday, April 02, 2012 12:22 PM
To: 'Mendis, Michael E.'
Cc: members.i2b2aug
Subject: RE: i2b2 ? v1.6.03 ? Webclient ? occurs
Hi,
I hit the demo site, and occurs worked. I'm on Firefox 11.0.
Attached find my local version of the QryPanel controller.
I can revert to original .js files (w/o Less than 10 mods), if that seems like a worthwhile experiment.
Peter

From: Mendis, Michael E. [MMENDIS.PARTNERS]
Sent: Monday, April 02, 2012 11:59 AM
To: Peter Beninato
Cc: members.i2b2aug
Subject: Re: i2b2 ? v1.6.03 ? Webclient ? occurs
can you try it against the i2b2 demo site: http://webservices.i2b2.org/webclient/ and see if has the same results. Also which firefox version are you using?
mike

On Apr 2, 2012, at 2:33 PM, Peter Beninato wrote:
Hi,
I'm on Firefox. When I turn on web developer it complains the onDOMReady is not a function. I see that code in showOccurs(), but not sure how to correct...
[11:04:48.896] Event.onDOMReady is not a function @ https://localhost:9000/webclient/js?i2b2/cells/CRC/CRC_ctrlr_QryPanel
.js:225

From: Mendis, Michael E. [MMENDIS.PARTNERS]
Sent: Monday, April 02, 2012 11:24 AM
To: Peter Beninato
Cc: members.i2b2aug
Subject: Re: i2b2 ? v1.6.03 ? Webclient ? occurs
Peter,
I tried with firefox and ie on the i2b2 demosite and they both had a dialog appear for the occurances.
What browser are you using?
thanks
mike

On Apr 2, 2012, at 12:41 PM, Peter Beninato wrote:
Hi,
The occurs functionality does not appear to work in v1.6.03.
When clicking on "Occurs", no other window pops up, In the lower left corner of the browser it says
"javascript:i2b2.CRC.ctrlr.QT.panelcontrollers[1].showOccurs().
Is anyone else experiencing this problem?
Has anyone developed a work?around?
Peter Beninato ? OCTRI DW Developer
Oregon Health & Science University
503?494?9985
beninato.ohsu<beninato.ohsu>

NEXT EMAIL
From:Mauro Bucalo <mauro.bucalo.gmail>
Sent: Tuesday, April 03, 2012 10:00 AM
To: i2b2 AUG Members members
Subject: wizard 1.3.6 problem
Hi all, has anyone tried to use the last wizard release(1.3.6)?
I downloaded and installed all the necessary in a fresh 10.04.4 ubuntu.
When i go to the menu "Hive Task" and select "Load I2B2PM and I2B2HIVE" this is what happens:

Thanks in advance. Mauro.
Ing. Mauro Bucalo, Ext. Collaborator Dipartimento di Informatica e Sistemistica Universita' di Pavia
Via Ferrata 1, 27100 Pavia, Italy tel:++39.0382.985981
e-mail: mauro.bucalo.gmail
web-page: http://it.linkedin.com/in/maurobucalo



NEXT EMAIL
From: McDonald, Chanchai Singhanayok <cmcdon12.uthsc>
Sent: Tuesday, April 03, 2012 9:56 AM
To: Brian Ostasiewski
Cc: i2b2 AUG Members
Subject: Re: I2B2 webserver
Brian,
This is a good news for us. We are in the middle of the project to have EHR migrate to the system soon. I will keep all up to date of how it works.
Chanchai

On Apr 3, 2012, at 8:32 AM, Brian Ostasiewski wrote:
Just wanted to reply to this chain of emails – we recently finished an upgrade of our main i2b2 database and staging database to the Fusion IO SSD drives and saw a 20x increase in our ETL processing speed (when you're talking about something that took days, this is huge). We also saw a similarly large improvement in i2b2 query speed, particularly with very complex queries – ones that involved dimensional queries and date constraints. Some of these went from taking hours to complete to taking under an hour; most routine queries are seconds. We're on 1.6 and have 730 million facts in our database.
Brian

From: Chanchai McDonald [cmcdon12.uthsc]
Sent: Friday, November 18, 2011 10:08 AM
To: Russ Waitman
Cc: Parth Divekar; Dan Connolly; petrucm.health.missouri; i2b2 AUG Members; mmendis.partners
Subject: Re: I2B2 webserver
Russ,
I will running into the same issue as yours since the team plan to operates to having our researchers using i2b2 for their research questions and explore the hypothesis.
Thank you. I am interested to talk to you more about this issue. Chanchai


On Nov 18, 2011, at 8:56 AM, Russ Waitman wrote:
Chanchai and all,
I suppose it all depends on your definition of "acceptable", how big your audience of simultaneous users will be, and knowing if 1.6 really boosts performance.
We have ~ half a billion facts on 250,000 to 500,000 people depending on what you're looking for. We're running 1.4. Prior to the fusionio cards, we'd have queries which would never return data. I'd set a lab threshold like potassium <3.5 and loop diuretic medicaiton exposure: not even sophisticated queries. It was embarrassing. I had to do puppet shows on projector when I was demoing things. We also noticed that on local SAS storage, we were completely disk bound such that one user was consuming all disk utilization.
Now one user typically runs less than 10% disk utilization which means we can support simultaneous queries. That's important because when we hold classes we've had 6-8 people hitting "run query" at the same time. Simple queries resolve in less than 20 seconds. Still, we hit spots where queries can take over 40 seconds but I am hoping improved performance with 1.6 will help.
For me, I think you want the system to be pretty responsive so that people can really do hypothesis exploration and not get frustrated. Based on my experience running CPOE, clinicians and researchers (and I) are inherently impatient so anything over 15 or 20 seconds is not great. But when they realize what the computer is doing for them, I suppose you can take a sip of coffee during the delay. If it gets over 60 seconds or hangs up on a simple query, they will think it's broken.
We're now getting to the point where people are beginning to use i2b2 for real research questions (4-10 groups, labs, diagnoses, flowsheet data, demographics multiple occurrence thresholds, over 20 exclusion criteria). Those larger queries are running over 20 seconds and in some cases still take a long time to resolve. one example I just did has 3 groups: first with 25 items, second with 45 exclusion concepts, and third with over 100: query takes 154 seconds. But, I am fairly sure these may have taken forever without the memory cards or we'd spend a ton of hours learning how to configure Oracle. Actually, it often takes longer for them to reload in the web client from the shared folder than it takes to actually run the query.
I've always worried that a conventional relational database like Oracle or SqlServer would choke on big data compared to other DBs like column stores but that was just based on academic reading. But I think the cards allowed us to use off the shelf oracle and move on to the fun stuff instead of spending our time loading interesting data.
Russ Waitman
Associate Professor
Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center
913-945-7087
rwaitman.kumc http://informatics.kumc
"Parth Divekar" <Parth.Divekar.cchmc> 11/18/2011 7:02 AM
Chanchai,
Whether you need SSD or not will depend upon amount of data and number of users accessing data. We have SSD for ETL but not for application database.
We are currently porting in excess of 50 mill rows in fact table and the performance is acceptable.
We have tuned our database for memory and have made some changes in the query that gets executed when you hit "run query from application.
FYI: we are using Oracle 11gR2.
Regards
Parth
Parth Divekar
Database Administrator II
Cincinnati Children's Hospital Medical Center
Ph: - 513-636-1004 (O)

Chanchai McDonald <cmcdon12.uthsc> 11/17/2011 6:25 PM
We concern if the Database storage really requires using Solid state Storage (Fusion-io Cards). We do not currently use/have this type of storage. Will it impact performance adversely if we won't use it?
Chanchai
Chanchai Singhanayok McDonald, Ph.D. Director Biomedical Informatics
The Office of Research, UTHSC
910 Madison Building Suite 620
Telephone: (901) 448-2088

On Jul 20, 2011, at 3:17 PM, Dan Connolly wrote:
Marius,
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

NEXT EMAIL
From:Peter Beninato <beninato.ohsu>
Sent:Monday, April 02, 2012 4:14 PM
To:Peter Beninato; Mendis, Michael E. Cc:i2b2 AUG Members
Subject:RE: i2b2 - v1.6.03 - Webclient - occurs
I reverted to original .js for
CRC_ctrlr_QryPanel.js CRC_ctrlr_QryStatus.js CRC_ctrlr_QryTool.js CRC_sdx_QI.js
But still get error regarding onDOMReady is not a function. Fyi.
Peter

From: Peter Beninato
Sent: Monday, April 02, 2012 12:22 PM
To: 'Mendis, Michael E.'
Cc: i2b2 AUG Members
Subject: RE: i2b2 ? v1.6.03 ? Webclient ? occurs
Hi,
I hit the demo site, and occurs worked. I'm on Firefox 11.0. Attached find my local version of the QryPanel controller.
I can revert to original .js files (w/o Less than 10 mods), if that seems like a worthwhile experiment.
Peter

From: Mendis, Michael E. [MMENDIS.PARTNERS]
Sent: Monday, April 02, 2012 11:59 AM
To: Peter Beninato
Cc: i2b2 AUG Members
Subject: Re: i2b2 ? v1.6.03 ? Webclient ? occurs
can you try it against the i2b2 demo site: http://webservices.i2b2.org/webclient/ and see if has the same results. Also which firefox version are you using?
mike

On Apr 2, 2012, at 2:33 PM, Peter Beninato wrote:
Hi,
I'm on Firefox. When I turn on web developer it complains the onDOMReady is not a function. I see that code in showOccurs(), but not sure how to correct...
[11:04:48.896] Event.onDOMReady is not a function @https://localhost:9000/webclient/js?i2b2/cells/CRC/CRC_ctrlr_QryPanel.
js:225

From: Mendis, Michael E. [MMENDIS.PARTNERS]
Sent: Monday, April 02, 2012 11:24 AM
To: Peter Beninato
Cc: members.i2b2aug
Subject: Re: i2b2 ? v1.6.03 ? Webclient ? occurs
Peter,
I tried with firefox and ie on the i2b2 demosite and they both had a dialog appear for the occurances.
What browser are you using?
thanks
mike

On Apr 2, 2012, at 12:41 PM, Peter Beninato wrote:
Hi,
The occurs functionality does not appear to work in v1.6.03.
When clicking on "Occurs", no other window pops up, In the lower left corner of the browser it says
"javascript:i2b2.CRC.ctrlr.QT.panelcontrollers[1].showOccurs().
Is anyone else experiencing this problem?
Has anyone developed a work?around?
Peter Beninato ? OCTRI DW Developer
Oregon Health & Science University
503?494?9985
beninato.ohsu<beninato.ohsu>


NEXT EMAIL
From:Peter Beninato <beninato.ohsu>
Sent:Monday, April 02, 2012 2:40 PM
To:Darren W Henderson
Cc:Mendis, Michael E.; i2b2 AUG Members
Subject:RE: i2b2 - v1.6.03 - Webclient - occurs
Hi,
The QueryPanel controller was untouched as part of "Less than 10" work, that work involved the following: CRC_ctrlr_QryStatus.js
CRC_ctrlr_QryTool.js
CRC_sdx_QI.js
Not sure, how that would impact this?
Peter

From: dwhend0.gmail.com [dwhend0.gmail] On Behalf Of Darren W Henderson
Sent: Monday, April 02, 2012 11:37 AM
To: Peter Beninato
Cc: Mendis, Michael E.; members.i2b2aug
Subject: Re: i2b2 - v1.6.03 - Webclient - occurs
Hmmm. Did you consider that you modified that javascript file in your work related to the <10 issue you posted to the group last week? Have you confirmed that you have not inadvertently commented out or deleted the function required for the occurs feature, or at the least introduced a syntax error?

On Mon, Apr 2, 2012 at 2:33 PM, Peter Beninato <beninato.ohsu> wrote:
Hi,
I'm on Firefox. When I turn on web developer it complains the onDOMReady is not a function. I see that code in showOccurs(), but not sure how to correct...
[11:04:48.896] Event.onDOMReady is not a function @ https://localhost:9000/webclient/js- i2b2/cells/CRC/CRC_ctrlr_QryPanel.js:225

From: Mendis, Michael E. [MMENDIS.PARTNERS.ORG] Sent: Monday, April 02, 2012 11:24 AM
To: Peter Beninato
Cc: members.i2b2aug
Subject: Re: i2b2 - v1.6.03 - Webclient - occurs
Peter,
I tried with firefox and ie on the i2b2 demosite and they both had a dialog appear for the occurances. What browser are you using?
thanks mike

On Apr 2, 2012, at 12:41 PM, Peter Beninato wrote:
Hi,
The occurs functionality does not appear to work in v1.6.03.
When clicking on "Occurs", no other window pops up, In the lower left corner of the browser it says "javascript:i2b2.CRC.ctrlr.QT.panelcontrollers[1].showOccurs(). Is anyone else experiencing this problem?
Has anyone developed a work-around?
Peter Beninato = OCTRI DW Developer
Oregon Health & Science University
503-494-9985 beninato.ohsu<beninato.ohsu>


NEXT EMAIL
From:dwhend0.gmail on behalf of Darren W Henderson <darren.henderson.uky>
Sent:Monday, April 02, 2012 2:26 PM
To:Mendis, Michael E.
Cc:Peter Beninato; i2b2 AUG Members
Subject:Re: i2b2 - v1.6.03 - Webclient - occurs
I just attempted this in Chrome and it works fine as long as a concept has been added to the panel. On Mon, Apr 2, 2012 at 2:23 PM, Mendis, Michael E. <MMENDIS.partners> wrote:
Peter,
I tried with firefox and ie on the i2b2 demosite and they both had a dialog appear for the occurances. What browser are you using?
thanks mike

On Apr 2, 2012, at 12:41 PM, Peter Beninato wrote: Hi,
The occurs functionality does not appear to work in v1.6.03.
When clicking on "Occurs", no other window pops up, In the lower left corner of the browser it says "javascript:i2b2.CRC.ctrlr.QT.panelcontrollers[1].showOccurs(). Is anyone else experiencing this problem?
Has anyone developed a work-around?
Peter Beninato = OCTRI DW Developer
Oregon Health & Science University
503-494-9985 beninato.ohsu<beninato.ohsu>



NEXT EMAIL
From:Daniele Segagni <daniele.segagni.fsm.it>
Sent:Monday, April 02, 2012 9:29 AM
To:i2b2 members
Subject:same instance num question
Hi all,
we have a question related to the possibility of making query using the same intance num constraint in version 1.6.03. Is this feature possible only using modifiers of the same concept or it is possible to use different concepts (even without modifiers)?
This question is linked to a behavior of the query tool published on the i2b2 live demo: we noted that if a query is made using concepts with no modifiers the same instance constraint in the temporal constraint level is not selectable, but you can only select this feature on each single concept you have dropped in the query tool panel. The query performed in this way always returns ERROR.
Any idea? Thank you all
Daniele
Ing. Daniele Segagni
Laboratorio di Informatica e Sistemistica per la Ricerca Clinica
IRCCS Fondazione S.Maugeri, Pavia, Italy tel: +39 0382 592038



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