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NEXT EMAIL

From:  Heilala, Christopher P [HEILALA.CHRISTOPHER.mcrf.mfldclin]

Sent:   Wednesday, February 29, 2012 2:10 PM

To:       i2b2 AUG Members Subject:        

RE: i2b2 Error Upon Login Attachments:           

Sorry for the spam, but I just realized that the email that I had sent last night didn't go through. The exact error that I am getting is:

Database error in getting environment data

This error appears when I try to log into the i2b2 Admin or Web Client...This is regardless of whether I use the correct credentials or not.

Thanks, Chris

From: Heilala, Christopher P

Sent: Wednesday, February 29, 2012 1:07 PM

To: i2b2 AUG Members

Subject: i2b2 Error Upon Login

Good Afternoon,

In addition to the Database error that I have been receiving, I noticed in the JBOSS Server logs the following:

2012-02-29 13:01:38,663 ERROR [org.jboss.ejb.plugins.jms.JMSContainerInvoker] Reconnect failed: JMS provider failure detected for querytool.QueryExecutorLargeMDB

javax.naming.NameNotFoundException: XAConnectionFactory not bound

at org.jnp.server.NamingServer.getBinding(NamingServer.java:529) at org.jnp.server.NamingServer.getBinding(NamingServer.java:537) at org.jnp.server.NamingServer.getObject(NamingServer.java:543) at org.jnp.server.NamingServer.lookup(NamingServer.java:296)

at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:667) at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:627) at javax.naming.InitialContext.lookup(InitialContext.java:351)

at org.jboss.ejb.plugins.jms.DLQHandler.createService(DLQHandler.java:182)

at org.jboss.system.ServiceMBeanSupport.jbossInternalCreate(ServiceMBeanSupport.java:260)

at org.jboss.system.ServiceMBeanSupport.create(ServiceMBeanSupport.java:188)

at org.jboss.ejb.plugins.jms.JMSContainerInvoker.innerStartDelivery(JMSContainerInvoker.java:510)

at

org.jboss.ejb.plugins.jms.JMSContainerInvoker$ExceptionListenerImpl$ExceptionListenerRunnable.run(JMSContainerInv oker.java:1428)

at java.lang.Thread.run(Thread.java:595)

Does anyone have any ideas on how I can resolve this? Thanks,

Chris Heilala

BioMedical Informatics Research Center

Programmer/Analyst

Ph: 715-221-8169 Fax: 715-221-8638

Email:  heilala.christopher.mcrf.mfldclin



NEXT EMAIL

From:  Chan, Wayne [Wayne.Chan.umassmed]

Sent:   Tuesday, February 28, 2012 4:36 PM

To:       i2b2 AUG Members

Cc:      'Mauro Bucalo'; Sadasivam, Rajani; Houston, Thomas; Ranauro, Paul; Zottola, Ralph

Subject:         the ExportXLS web client plugin from UMass Med School & Universita' di Pavia is now also available for download from MICARD..

Hi, All,

As we stated in our announcement last week, the ExportXLS v2.0 is now also available from the UMass Med School MICARD Downloads page (http://micard.umassmed.edu/downloads.php#ExportXLS), in addition to be also available from Google Codes ([http://code.google.com/p/i2b2-export-xls-plugin/downloads/detail?name=ExportXLS-v2.0-20120217.zip&can=2&q=#makechanges).
]

Again, please don't hesitate to contact us concerning any questions or problems.  Thanks.

On Feb 21, 2012, at 1:35 PM, "Chan, Wayne" <Wayne.Chan.umassmed> wrote:

Hi, all,

As a collaborative effort, we at University of Massachusetts Medical School and Universita' di Pavia are very happy to announce that the v2.0 of the ExportXLS plugin (for webclient).  This release is compatible with i2b2 v.1.3-1.6, as well as compatible with the 4 major web browsers (Firefox, Internet Explorer, Chrome, & safari). New Features in this Release (v2.0) Based on feedbacks and input from other researchers, we have made the following updates, adjustments, enhancements, and fixes that may better serve everyone in the i2b2 community:

1.)   Updated patient_list params to render this plugin compatible with i2b2 v1.3; and fixed a problem in the version for i2b2 v1.6 (it should now work on i2b2 v1.3-v1.6).

2.)   Added table title and caption to the resulting output table.

3.)   Added new 1st column for patient row counts (no column title).

4.)   Renamed the "StateCity" column title to "State/City".

5.)   Removed any leading and trailing redundant "Zip codes" values from each state value string.

6.)   Defaulted to using "concept_cd" for each selected concept entry if neither "tval_char" nor "nval_num" is available.

7.)   Improved efficiencies.

8.)   Facilitated the flexible dropping of any columns (that may contain data too sensitive or personal) from the resulting output table.

9.)   Fixed the Internet Explorer (IE) hang problem.

10.)  Fixed the missing "concept" columns on IE problem.

11.)  Fixed the blank "patient_IDs" (when "Include Patient Date" not selected) on IE problem.

12.)  Fixed table content getting cutoff on IE problem.

13.)  Centered content in each table cell of the resulting output table.

14.)  Added unique time-stamp to name of exported XLS file.

15.)  Updated the description of this plugin displayed (in the available plugin list), to<image003.jpg>

16.)  Added more descriptions in the "Specify Data" and "Plugin Help" tab pages.

17.) Updated plugin category from "text" to "standard".

This new release is packed with installation guide and version supplementary note, and is available now from Google Codes (http://code.google.com/p/i2b2-export-xls-plugin/downloads/detail?name=ExportXLS-v2.0-20120217.zip&can=2&q=#makechanges).&nbsp; It will also be available from the UMass Med School MICARD Downloads page (http://micard.umassmed.edu/downloads.php) by next Tuesday, 2/28.

Please don't hesitate to contact us concerning any questions or problems. Thanks.



NEXT EMAIL

From:  Yves Thorrez [Yves.Thorrez.uzbrussel.be]

Sent:   Tuesday, February 28, 2012 3:02 AM

To:       Murphy, Shawn N.; i2b2 AUG Members

Subject:         RE: SMART i2b2

Hi Shawn,

That is great news. We were impressed by what was shown at the i2b2 AUG last year. Thanks,

Yves


From: Murphy, Shawn N. [SNMURPHY.PARTNERS]

Sent: maandag 27 februari 2012 21:15

To: Yves Thorrez; i2b2 AUG Members

Subject: RE: SMART i2b2

Hi Yves,

In March there will be two cells released to the i2b2 community, a SMART cell and a Mapper Cell that can be joined the core server components of the Hive. There will be a new web client plug-in released to host a view that can be composed of several SMART Apps. This is all leading to full circle method for patients to be selected for clinical trials in i2b2.

Thanks, Shawn.

From: Yves Thorrez [Yves.Thorrez.uzbrussel.be]

Sent: Monday, February 27, 2012 3:32 AM

To: i2b2 AUG Members

Subject: SMART i2b2

Hi,

Will SMART i2b2 remain proof-of-concept? Last update was 7 months ago, and the download link does not work. The links to the SMART apps in the demo are broken too.

Thanks, Yves



NEXT EMAIL

From:  Jack London [jack.london.KimmelCancerCenter]

Sent:   Monday, February 27, 2012 2:22 PM

To:       Chan, Wayne

Cc:      i2b2 AUG Members; 'Mauro Bucalo'; Sadasivam, Rajani; Houston, Thomas

Subject:         Re: Caveat alert concerning the ExportXLS web client plugin from UMass Med School & Universita' di Pavia

We had noticed this issue with the original ExportXLS plugin, and have successfully used the plugin by changing the indicated line below in the SaveToExcel.php file.  I did not realize that we could have also just modified a setting in our php.ini file.  I assumed it was a php version-related artifact.

Jack

On Feb 27, 2012, at 12:28 PM, Chan, Wayne wrote:

Hi, All,

Our special thanks to Gregory Schulte (Children's Hospital Colorado), who has alerted us that if the "short_open_tag"

in the php.ini file of a server (of this web client plugin) is NOT set to* "on*", then the resulting exported Excel spreadsheet may be just a blank file.

He also suggested the following alternatives as workaround options (for those who have encountered this "blank file" problem, else one need not do anything):

either change the "short_open_tag" in the php.ini file to

short_open_tag = On

or change line 15 of the SaveToExcel.php file, from <body><?=$_REQUEST['datatodisplay']?>

to <body><?php echo $_REQUEST['datatodisplay']?>

Of these, we recommend updating the php.ini file.

Incidentally, we determined that this caveat exists for v1.0-2.0 of this web client plugin.

We do hope to have an updated SaveToExcel.php file (that takes care of this caveat without requiring the deployers to update their php.ini files) included in the next release of this web client plugin.

BTW, we have also added this info to the new "Caveats" page of the ExportXLS i2b2 Community wiki (https://community.i2b2.org/wiki/display/ExportXLS/Caveats), as well as updated the corresponding "Features Requested" page with this, for future references.

Thanks.

From: Chan, Wayne

Sent: Friday, February 24, 2012 10:01 AM

To:  i2b2 AUG Members

Cc: Sadasivam, Rajani; Houston, Thomas; 'Mauro Bucalo'; Zottola, Ralph; Ranauro, Paul; English, Thomas

Subject: i2b2 community wiki project page for ExportXLS web client plugin from UMass Med School & Universita' di Pavia

Hi, All,

Per Shawn's invitation, and thanks to Mike's helps, we now have the ExportXLS wiki page set up on the i2b2

Community Dashboard (https://community.i2b2.org/wiki/display/ExportXLS/ExportXLS+Home):

<image001.png>

Alternatively, you can also get there by clicking on the ExportXLS link on the i2b2 Community Dashboard

(https://community.i2b2.org/wiki/dashboard.action) itself:

Thanks.

From: Mike Mendis [mmendis.partners]

Sent: Thursday, February 23, 2012 3:24 PM

To: Chan, Wayne

Subject: Re: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia

All set

From: Chan, Wayne

Sent: Wednesday, February 22, 2012 10:17 AM

To: Murphy, Shawn N.; Mendis, Michael E.

Subject: RE: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia

Shawn & Mike,

Thanks, sure, it'll be our pleasure to do that. Please send me the URL and instructions.

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

From: Murphy, Shawn N. [SNMURPHY.PARTNERS]

Sent: Tuesday, February 21, 2012 5:44 PM

To: Chan, Wayne

Cc: i2b2 AUG Members; Sadasivam, Rajani; Houston, Thomas; Mauro Bucalo; Zottola, Ralph; Ranauro, Paul; English, Thomas; Kinney, Rebecca; Phillips, Barrett D

Subject: Re: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia

Hi Wayne and team,

This is a great resource for our community, and would very much like to have this put up on the community web site. Mike and our team can facilitate this with your own space if you would like.

Thanks,

Shawn Murphy MD

On Feb 21, 2012, at 1:35 PM, "Chan, Wayne" <Wayne.Chan.umassmed> wrote: Hi, all,

As a collaborative effort, we at University of Massachusetts Medical School and Universita' di Pavia are very happy to announce that the v2.0 of the ExportXLS plugin (for webclient).  This release is compatible with i2b2 v.1.3-1.6, as well as compatible with the 4 major web browsers (Firefox, Internet Explorer, Chrome, & safari). New Features in this Release (v2.0) Based on feedbacks and input from other researchers, we have made the following updates, adjustments, enhancements, and fixes that may better serve everyone in the i2b2 community:

1.)   Updated patient_list params to render this plugin compatible with i2b2 v1.3; and fixed a problem in the version for i2b2 v1.6 (it should now work on i2b2 v1.3-v1.6).

2.)   Added table title and caption to the resulting output table.

3.)   Added new 1st column for patient row counts (no column title).

4.)   Renamed the "StateCity" column title to "State/City".

5.)   Removed any leading and trailing redundant "Zip codes" values from each state value string.

6.)   Defaulted to using "concept_cd" for each selected concept entry if neither "tval_char" nor "nval_num" is available.

7.)   Improved efficiencies.

8.)   Facilitated the flexible dropping of any columns (that may contain data too sensitive or personal) from the resulting output table.

9.)   Fixed the Internet Explorer (IE) hang problem.

10.)  Fixed the missing "concept" columns on IE problem.

11.)  Fixed the blank "patient_IDs" (when "Include Patient Date" not selected) on IE problem.

12.)  Fixed table content getting cutoff on IE problem.

13.)  Centered content in each table cell of the resulting output table.

14.)  Added unique time-stamp to name of exported XLS file.

15.)  Updated the description of this plugin displayed (in the available plugin list), to<image003.jpg>

16.)  Added more descriptions in the "Specify Data" and "Plugin Help" tab pages.

17.) Updated plugin category from "text" to "standard".

This new release is packed with installation guide and version supplementary note, and is available now from Google Codes http://code.google.com/p/i2b2-export-xls-plugin/downloads/detail?name=ExportXLS-v2.0-20120217.zip&can=2&q=#makechanges).&nbsp; It will also be available from the UMass Med School MICARD Downloads page (http://micard.umassmed.edu/downloads.php) by next Tuesday, 2/28.

Please don't hesitate to contact us concerning any questions or problems. Thanks.



NEXT EMAIL

From:  Bohne, Jacqueline R [bohne.jacqueline.mcrf.mfldclin]

Sent:   Monday, February 27, 2012 1:00 PM

To:       Luke Vincent Rasmussen; Bickel, Jonathan; i2b2 AUG Members

Cc:      Verhagen, Laurel A; Lin MD, Simon

Subject:         RE: i2b2 + netezza

Jon,

I was the one who made the changes to i2b2 to run against Netezza. Luke is correct by saying the changes that were made were more geared towards a proof of concept than actually changing the logic to utilize Netezza's speed.

If you have any questions about the code changes needed to do this please feel free to send me an email at bohne.jacqueline.mcrf.mfldclin.

Thanks, Jacquie Bohne

Research Programmer/Analyst Marshfield Clinic Research Foundation (715) 221-6436

From: Luke Vincent Rasmussen [luke.rasmussen.northwestern] Sent: Wednesday, February 22, 2012 3:44 PM

To: Bickel, Jonathan; i2b2 AUG Members

Cc: Bohne, Jacqueline R; Verhagen, Laurel A; Lin MD, Simon

Subject: Re: i2b2 + netezza

Jon -

Marshfield Clinic has gotten i2b2 running on Netezza. There were code changes required, and we did see some slowness with the queries, however that may be due to our approach of directly porting the code to work and not optimizing it for Netezza's architecture. We had spoken with Netezza, who had pledged support to work on tuning the system to improve performance.

I transitioned to a new position at Northwestern shortly after that work so I (unfortunately) can't provide specific details or code, but I have CC'd folks from Marshfield who were involved with the project and should be able to help with more specific inquiries.

Luke Rasmussen

Systems Analyst/Programmer Senior

Northwestern University Division of Health and Biomedical Informatics

(312) 503-2823

On 2/22/12 3:31 PM, "Bickel, Jonathan" <Jonathan.Bickel.childrens.harvard> wrote:

Hi AUG

Has anyone ever had experience with i2b2 pointing to Netezza?

Good experiences? Bad? Code changes needed? Any thoughts would be

helpful.

Thanks

Jon B.

Jonathan Bickel M.D.

Director of Clinical Research Informatics Children¹s Hospital Boston

Cell: 412.480.1498

Pager: 617.560.9980 (in-house x 2576)

Work: 617.919.3565

Email: Jonathan.Bickel.childrens.harvard

Skype: jonojuno1

On 2/22/12 9:48 AM, "Chan, Wayne" <Wayne.Chan.umassmed> wrote:

We had considered that briefly last year (but put it on the sideline since it does present certain significant challenges) -- we'll see what we can do when our bandwidth opens up again later. Thanks.

Wayne

From: Jack W. London, Ph.D. [Jack.London.KimmelCancerCenter]

Sent: Tuesday, February 21, 2012 8:01 PM

To: Chan, Wayne

Cc: i2b2 AUG Members; Sadasivam, Rajani; Houston, Thomas; 'Mauro Bucalo'; Zottola, Ralph; Ranauro, Paul; English, Thomas; Kinney, Rebecca; Phillips, Barrett D

Subject: Re: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia

Wayne,

Any possibility of a future ExportXLS release that will list all occurrences of a concept for a patient, rather than just the first occurrence that is retrieved?

Jack

Quoting "Chan, Wayne" <Wayne.Chan.umassmed>:

Hi, all,

As a collaborative effort, we at University of Massachusetts Medical School and Universita' di Pavia are very happy to announce that the v2.0 of the ExportXLS plugin (for webclient). This release is compatible with i2b2 v.1.3-1.6, as well as compatible with the 4 major web browsers (Firefox, Internet Explorer, Chrome, & safari).

New Features in this Release (v2.0)

Based on feedbacks and input from other researchers, we have made the  following updates, adjustments, enhancements, and fixes that may better serve everyone in the i2b2 community:

1.)     Updated patient_list params to render this plugin compatible with i2b2 v1.3; and fixed a problem in the version for i2b2 v1.6 (it should now work on i2b2 v1.3-v1.6).

2.)     Added table title and caption to the resulting output table.

3.)     Added new 1st column for patient row counts (no column title).

4.)     Renamed the "StateCity" column title to "State/City".

5.)     Removed any leading and trailing redundant "Zip codes" values from each state value string.

6.)     Defaulted to using "concept_cd" for each selected concept entry if neither "tval_char" nor "nval_num" is available.

7.)     Improved efficiencies.

8.)     Facilitated the flexible dropping of any columns (that may contain data too sensitive or personal) from the resulting output table.

9.)     Fixed the Internet Explorer (IE) hang problem.

10.)   Fixed the missing "concept" columns on IE problem.

11.)   Fixed the blank "patient_IDs" (when "Include Patient Date" not selected) on IE problem.

12.)   Fixed table content getting cutoff on IE problem.

13.)   Centered content in each table cell of the resulting output table.

14.)   Added unique time-stamp to name of exported XLS file.

15.)   Updated the description of this plugin displayed (in the available plugin list), to[Missing image of ExportXLS displayed in the i2b2 web client 'Analysis Tools' list]

16.)   Added more descriptions in the "Specify Data" and "Plugin Help" tab pages.

17.)  Updated plugin category from "text" to "standard".

This new release is packed with installation guide and version supplementary note, and is available now from Google Codes

(http://code.google.com/p/i2b2-export-xls-plugin/downloads/detail?name=ExportXLS-v2.0-20120217.zip&can=2&q=#makechanges). It will also be available from the UMass Med School MICARD Downloads page (http://micard.umassmed.edu/downloads.php) by next Tuesday, 2/28.

Please don't hesitate to contact us concerning any questions or problems. Thanks.



NEXT EMAIL

From:  Chan, Wayne [Wayne.Chan.umassmed]

Sent:   Friday, February 24, 2012 10:01 AM

To:       i2b2 AUG Members

Cc:      Sadasivam, Rajani; Houston, Thomas; 'Mauro Bucalo'; Zottola, Ralph; Ranauro, Paul; English, Thomas

Subject:         i2b2 community wiki project page for ExportXLS web client plugin from UMass Med School & Universita' di Pavia

Hi, All,

Per Shawn's invitation, and thanks to Mike's helps, we now have the ExportXLS wiki page set up on the i2b2 Community Dashboard ([https://community.i2b2.org/wiki/display/ExportXLS/ExportXLS+Home):
]

Alternatively, you can also get there by clicking on the ExportXLS link on the i2b2 Community Dashboard (https://community.i2b2.org/wiki/dashboard.action) itself:

Thanks.

From: Mike Mendis [mmendis.partners]

Sent: Thursday, February 23, 2012 3:24 PM

To: Chan, Wayne

Subject: Re: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia

All set

From: Chan, Wayne

Sent: Wednesday, February 22, 2012 10:17 AM

To: Murphy, Shawn N.; Mendis, Michael E.

Subject: RE: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia

Shawn & Mike,

Thanks, sure, it'll be our pleasure to do that. Please send me the URL and instructions.

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


From: Murphy, Shawn N. [SNMURPHY.PARTNERS]

Sent: Tuesday, February 21, 2012 5:44 PM

To: Chan, Wayne

Cc: i2b2 AUG Members; Sadasivam, Rajani; Houston, Thomas; Mauro Bucalo; Zottola, Ralph; Ranauro, Paul; English, Thomas;

Kinney, Rebecca; Phillips, Barrett D

Subject: Re: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia

Hi Wayne and team,

This is a great resource for our community, and would very much like to have this put up on the community web site. Mike and our team can facilitate this with your own space if you would like.

Thanks,

Shawn Murphy MD

On Feb 21, 2012, at 1:35 PM, "Chan, Wayne" <Wayne.Chan.umassmed> wrote:

Hi, all,

As a collaborative effort, we at University of Massachusetts Medical School and Universita' di Pavia are very happy to announce that the v2.0 of the ExportXLS plugin (for webclient).  This release is compatible with i2b2 v.1.3-1.6, as well as compatible with the 4 major web browsers (Firefox, Internet Explorer, Chrome, & safari). New Features in this Release (v2.0) Based on feedbacks and input from other researchers, we have made the following updates, adjustments, enhancements, and fixes that may better serve everyone in the i2b2 community:

1.)   Updated patient_list params to render this plugin compatible with i2b2 v1.3; and fixed a problem in the version for i2b2 v1.6 (it should now work on i2b2 v1.3-v1.6).

2.)   Added table title and caption to the resulting output table.

3.)   Added new 1st column for patient row counts (no column title).

4.)   Renamed the "StateCity" column title to "State/City".

5.)   Removed any leading and trailing redundant "Zip codes" values from each state value string.

6.)   Defaulted to using "concept_cd" for each selected concept entry if neither "tval_char" nor "nval_num" is available.

7.)   Improved efficiencies.

8.)   Facilitated the flexible dropping of any columns (that may contain data too sensitive or personal) from the resulting output table.

9.)   Fixed the Internet Explorer (IE) hang problem.

10.)  Fixed the missing "concept" columns on IE problem.

11.)  Fixed the blank "patient_IDs" (when "Include Patient Date" not selected) on IE problem.

12.)  Fixed table content getting cutoff on IE problem.

13.)  Centered content in each table cell of the resulting output table.

14.)  Added unique time-stamp to name of exported XLS file.

15.)  Updated the description of this plugin displayed (in the available plugin list), to<image003.jpg>

16.)  Added more descriptions in the "Specify Data" and "Plugin Help" tab pages.

17.) Updated plugin category from "text" to "standard".

This new release is packed with installation guide and version supplementary note, and is available now from Google Codes http://code.google.com/p/i2b2-export-xls-plugin/downloads/detail?name=ExportXLS-v2.0-20120217.zip&can=2&q=#makechanges).&nbsp; It will also be available from the UMass Med School MICARD Downloads page (http://micard.umassmed.edu/downloads.php) by next Tuesday, 2/28.

Please don't hesitate to contact us concerning any questions or problems. Thanks.



NEXT EMAIL

From:  Yves Thorrez [Yves.Thorrez.uzbrussel.be]

Sent:   Friday, February 24, 2012 2:05 AM

To:       'Chan, Wayne'

Cc:      i2b2 AUG Members

Subject:         RE: i2b2 v1.6 Demo1Set webclient plugin (standard) always displays 0 for Patient Count..

Wayne,

Works fine here with i2b2 v1.6.02.

From: Chan, Wayne [Wayne.Chan.umassmed]

Sent: donderdag 23 februari 2012 16:40

To: i2b2 AUG Members

Subject: i2b2 v1.6 Demo1Set webclient plugin (standard) always displays 0 for Patient Count..

I just noticed that the i2b2 v1.6 Demo1Set webclient plugin (standard) always displays 0 for Patient Count:

Whereas, the i2b2 v1.3 Demo1Set webclient plugin (standard) always displays the correct number for Patient Count:

Can someone check it on their v1.6 webclient also (it could be that we picked up an outdated v1.6 webclient)? Thanks.

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:  Chan, Wayne [Wayne.Chan.umassmed]

Sent:   Thursday, February 23, 2012 9:06 AM

To:       Murphy, Shawn N.; Mendis, Michael E.

Cc:      i2b2 AUG Members; 'Mauro Bucalo'

Subject:         RE: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia

Shawn & Mike,

Any updates? Thanks.

Wayne

From: Chan, Wayne

Sent: Wednesday, February 22, 2012 10:17 AM

To: Murphy, Shawn N.; Mendis, Michael E.

Subject: RE: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia

Shawn & Mike,

Thanks, sure, it'll be our pleasure to do that. Please send me the URL and instructions.

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

From: Murphy, Shawn N. [SNMURPHY.PARTNERS]

Sent: Tuesday, February 21, 2012 5:44 PM

To: Chan, Wayne

Cc: i2b2 AUG Members; Sadasivam, Rajani; Houston, Thomas; Mauro Bucalo; Zottola, Ralph; Ranauro, Paul; English, Thomas; Kinney, Rebecca; Phillips, Barrett D

Subject: Re: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia

Hi Wayne and team,

This is a great resource for our community, and would very much like to have this put up on the community web site. Mike and our team can facilitate this with your own space if you would like.

Thanks,

Shawn Murphy MD

On Feb 21, 2012, at 1:35 PM, "Chan, Wayne" <Wayne.Chan.umassmed> wrote: Hi, all,

As a collaborative effort, we at University of Massachusetts Medical School and Universita' di

Pavia are very happy to announce that the v2.0 of the ExportXLS plugin (for webclient).  This

release is compatible with i2b2 v.1.3-1.6, as well as compatible with the 4 major web browsers

(Firefox, Internet Explorer, Chrome, & safari).

New Features in this Release (v2.0)

Based on feedbacks and input from other researchers, we have made the following updates, adjustments, enhancements, and fixes that may better serve everyone in the i2b2 community:

1.)   Updated patient_list params to render this plugin compatible with i2b2 v1.3; and fixed a problem in the version for i2b2 v1.6 (it should now work on i2b2 v1.3-v1.6).

2.)   Added table title and caption to the resulting output table.

3.)   Added new 1st column for patient row counts (no column title).

4.)   Renamed the "StateCity" column title to "State/City".

5.)   Removed any leading and trailing redundant "Zip codes" values from each state value string.

6.)   Defaulted to using "concept_cd" for each selected concept entry if neither "tval_char" nor "nval_num" is available.

7.)   Improved efficiencies.

8.)   Facilitated the flexible dropping of any columns (that may contain data too sensitive or personal) from the resulting output table.

9.)   Fixed the Internet Explorer (IE) hang problem.

10.)  Fixed the missing "concept" columns on IE problem.

11.)  Fixed the blank "patient_IDs" (when "Include Patient Date" not selected) on IE problem.

12.)  Fixed table content getting cutoff on IE problem.

13.)  Centered content in each table cell of the resulting output table.

14.)  Added unique time-stamp to name of exported XLS file.

15.)  Updated the description of this plugin displayed (in the available plugin list), to<image003.jpg>

16.)  Added more descriptions in the "Specify Data" and "Plugin Help" tab pages.

17.) Updated plugin category from "text" to "standard".

This new release is packed with installation guide and version supplementary note, and is available now from Google Codes (http://code.google.com/p/i2b2-export-xls-plugin/downloads/detail?name=ExportXLS-v2.0&#45;

20120217.zip&can=2&q=#makechanges). It will also be available from the UMass Med School MICARD Downloads page (http://micard.umassmed.edu/downloads.php) by next Tuesday, 2/28.

Please don't hesitate to contact us concerning any questions or problems. Thanks.



NEXT EMAIL

From:  Murphy, Shawn N.

Sent:   Wednesday, February 22, 2012 9:04 PM

To:       Henderson, Darren W; Dan Connolly; i2b2 AUG Members

Subject:         RE: experience with Encounter Set queries?

Hi All,

The encounter set will be constrained according to your query timing. If the timing is that that the items should occur within the same encounter, then only the matching encounters will be returned. Otherwise, if the timing is that the items should occur in the same patient, then all the encounters for the matching patients will be returned.

Thanks, Shawn.

From: Henderson, Darren W [darren.henderson.uky]

Sent: Tuesday, February 21, 2012 10:06 AM

To: Dan Connolly; i2b2 AUG Members

Subject: RE: experience with Encounter Set queries?

Remember that "Encounter Sets" are not the encounters that matched your query constraints. Instead, it is a set of all encounters (ever) for the patients that matched your query constraints. For your 7597 patients, that's likely many many encounters.

From: Dan Connolly [dconnolly.kumc]

Sent: Monday, February 20, 2012 6:01 PM

To:  i2b2 AUG Members

Subject: experience with Encounter Set queries?

Has anybody had much luck with Encounter Set queries in i2b2 1.602?

I'm having trouble using them, and I wonder if I'm beyond the supported state-of-the-art or if I have an installation/config problem.

We're developing an analysis tool where they would be helpful.

They're documented in the help pages, but they didn't show up in our web client "Run Query" dialog. I couldn't find any reason why not in in the javascript code, but then I saw 'LH' in

QT_QUERY_RESULT_TYPE.

I changed LH to LA, and presto, the choice appears in the "Run Query" dialog. When I ran the query, it took quite a while (62 seconds where a patient set takes 4.8 seconds). Are patient set queries indexed or optimized in some way that encounter set queries are not?

I got an Encounter Set that had "patient_count: 7597"

I clicked on it in in the "Previous Queries" area; probably not a good idea; it spun forever.

I suppose analog to the "that patient set is really big; you don't really want to display it" check for patient sets isn't there yet?

Dan Connolly, KUMC Medical Informatics

913-945-6741



NEXT EMAIL

From:  Peter Beninato [beninato.ohsu]

Sent:   Wednesday, February 22, 2012 7:59 PM

To:       Lakshminarayanan, Prakash; i2b2 AUG Members

Subject:         RE: i2b2 - v1.6.x - QueryTool - Run Query - hiding Set options

Awesome! Thanks.

From: Lakshminarayanan, Prakash [Prakash.Lakshminarayanan.ucsf] Sent: Wednesday, February 22, 2012 4:56 PM

To: Peter Beninato; i2b2 AUG Members

Subject: RE: i2b2 - v1.6.x - QueryTool - Run Query - hiding Set options

Peter

The Run Query dialog options are controlled by display attributes stored in QT_QUERY_RESULT_TYPE table in i2b2demodata schema. The column VISUAL_ATTRIBUTE_TYPE_ID could be set to 'LH' for options that need to be hidden or unwanted records could be erased from the table. The first option is preferable since this allows to revert back easily if needed..

Prakash

From: Peter Beninato [beninato.ohsu]

Sent: Wednesday, February 22, 2012 4:05 PM To: i2b2 AUG Members

Subject: i2b2 - v1.6.x - QueryTool - Run Query - hiding Set options

Hi,

How can the options that appear under Run Query dialog be prevented from being displayed? I see a section in default.htm

### <Query Run Dialog> ####

But that only includes three options for Patient Count, Patient Set, Encounter Set.

And does not include options like: Timeline, Gender patient breakdown, Vital Status patient breakdown, Race patient breakdown, Age patient breakdown.

So, I'm not sure that section is truly the source for the dialog?

Any insight on the source for this dialog and how to hide items like?: Encounter Set

Timeline

Gender patient breakdown

Vital Status patient breakdown

Race patient breakdown

Age patient breakdown

Thanks.

Peter Beninato – OCTRI DW Developer

Oregon Health & Science University

503-494-9985

beninato.ohsu<beninato.ohsu >



NEXT EMAIL

From:  Chan, Wayne [Wayne.Chan.umassmed]

Sent:   Wednesday, February 22, 2012 9:49 AM

To:       'Jack W. London, Ph.D.'

Cc:      i2b2 AUG Members; Sadasivam, Rajani; Houston, Thomas; 'Mauro Bucalo'

Subject:         RE: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia

We had considered that briefly last year (but put it on the sideline since it does present certain significant challenges) -- we'll see what we can do when our bandwidth opens up again later. Thanks.

 Wayne

From: Jack W. London, Ph.D. [Jack.London.KimmelCancerCenter] Sent: Tuesday, February 21, 2012 8:01 PM

To: Chan, Wayne

Cc: i2b2 AUG Members; Sadasivam, Rajani; Houston, Thomas; 'Mauro Bucalo'; Zottola, Ralph; Ranauro, Paul; English, Thomas; Kinney, Rebecca; Phillips, Barrett D

Subject: Re: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia

Wayne,

Any possibility of a future ExportXLS release that will list all occurrences of a concept for a patient, rather than just the first occurrence that is retrieved?

Jack

Quoting "Chan, Wayne" <Wayne.Chan.umassmed>:

Hi, all,

As a collaborative effort, we at University of Massachusetts Medical School and Universita' di Pavia are very happy to announce that the v2.0 of the ExportXLS plugin (for webclient). This release is compatible with i2b2 v.1.3-1.6, as well as compatible with the 4 major web browsers (Firefox, Internet Explorer, Chrome, & safari).

New Features in this Release (v2.0)

Based on feedbacks and input from other researchers, we have made the following updates, adjustments, enhancements, and fixes that may better serve everyone in the i2b2 community:

1.)   Updated patient_list params to render this plugin compatible with i2b2 v1.3; and fixed a problem in the version for i2b2 v1.6 (it should now work on i2b2 v1.3-v1.6).

2.)   Added table title and caption to the resulting output table.

3.)   Added new 1st column for patient row counts (no column title).

4.)   Renamed the "StateCity" column title to "State/City".

5.)   Removed any leading and trailing redundant "Zip codes" values from each state value string.

6.)   Defaulted to using "concept_cd" for each selected concept entry if neither "tval_char" nor "nval_num" is available.

7.)   Improved efficiencies.

8.)   Facilitated the flexible dropping of any columns (that may contain data too sensitive or personal) from the resulting output table.

9.)   Fixed the Internet Explorer (IE) hang problem.

10.)  Fixed the missing "concept" columns on IE problem.

11.)  Fixed the blank "patient_IDs" (when "Include Patient Date" not selected) on IE problem.

12.)  Fixed table content getting cutoff on IE problem.

13.)  Centered content in each table cell of the resulting output table.

14.)  Added unique time-stamp to name of exported XLS file.

15.)  Updated the description of this plugin displayed (in the available plugin list), to[Missing image of ExportXLS displayed in the i2b2 web client 'Analysis Tools' list]

16.)  Added more descriptions in the "Specify Data" and "Plugin Help" tab pages.

17.) Updated plugin category from "text" to "standard".

 This new release is packed with installation guide and version supplementary note, and is available now from Google Codes (http://code.google.com/p/i2b2-export-xls-plugin/downloads/detail?name=ExportXLS-v2.0-20120217.zip&can=2&q=#makechanges). It will also be available from the UMass Med School MICARD Downloads page (http://micard.umassmed.edu/downloads.php) by next Tuesday, 2/28.

Please don't hesitate to contact us concerning any questions or problems. Thanks.



NEXT EMAIL

From:  Henderson, Darren W [darren.henderson.uky]

Sent:   Wednesday, February 22, 2012 9:17 AM

To:       Jeremy.Nix.cchmc

Cc:      i2b2 AUG Members

Subject:         RE: experience with Encounter Set queries?

Wow, this looks great Jeremy. I'll try it out and play with it. There are cases where the #DX table doesn't get created in the stock install of i2b2. I force it to always be made for some of our other breakdowns that rely on it. Thanks for putting the time into this! I'll let you know how it goes.

From: Jeremy Nix [Jeremy.Nix.cchmc]

Sent: Tuesday, February 21, 2012 4:28 PM

To: Henderson, Darren W

Cc: i2b2 AUG Members

Subject: Re: experience with Encounter Set queries?

You make an excellent point.  I think the approach you suggest makes sense.  I couldn't tell you why the current approach was taken.  I tested out the approach and it seems to work pretty well.  I'm attaching the classes for reference. I haven't tested extensively, so use at your own risk.

Jeremy Nix

Senior Application Developer

Cincinnati Children's Hospital Medical Center

On 02/21/2012 01:52 PM, Henderson, Darren W wrote:

Hmmm, I guess I'm more confused on why this approach of buffering them into memory is used? It seems that it would've been much simpler to just select distinct patient_num from #DX after you create the table directly into the QT_PATIENT_SET_COLLECTION table. The method you describe sounds very strange. Moving the data from the database, only to insert it right back to the database? Instead of just a table to table move? Maybe I'm misunderstanding the process as you describe it.

From: Jeremy Nix [Jeremy.Nix.cchmc]

Sent: Tuesday, February 21, 2012 1:36 PM

To: Henderson, Darren W

Cc:  i2b2 AUG Members

Subject: Re: experience with Encounter Set queries?

Not exactly. The way things are coded, the patients (or patient/encounters) are buffered in memory until there are 1000 of them.  Then, a prepared statement is created to insert those buffered records into the qt_patient_set_collection or qt_patient_enc_collection table. The JDBC default batch size will affect how many times a batch update is performed when the 1000 patient/encounters are being inserted.  By default, the batch size is 10, so exactly 100 flushes would be performed per 1000 batch.  By increasing that number to 100, you cut the amount of flushes down to 10.  >From what I've read, they recommend to keep the batch size 100 or under.  I would recommend trying out a few values and see how well the queries perform.  Make sure to keep an eye on CPU and memory utilization on the server as you may find values that are optimal for 1 user but make things unusable for 5 users.

Jeremy Nix

Senior Application Developer

Cincinnati Children's Hospital Medical Center

On 02/21/2012 01:06 PM, Henderson, Darren W wrote:

Ah interesting. So if I edit the datasources, can I exceed the 1000 batch size that is in the Set Collection DAOs?

From: Jeremy Nix [Jeremy.Nix.cchmc]

Sent: Tuesday, February 21, 2012 1:00 PM

To: Henderson, Darren W

Cc: Dan Connolly; i2b2 AUG Members

Subject: Re: experience with Encounter Set queries?

What you are seeing in the logfiles is actually just a debug statement and does not represent the actual batch statement (see QueryResultPatientSetGenerator or QueyrResultEncounterSetGenerator):

\if ((i % 500) == 0)
{ log.debug("Loading [" + loadCount + "] patients" + " for query instance = " + queryInstanceId); }


The actual batch size is 1000 (see PatientSetCollectionSpringDao and EncounterSetCollectionSpringDao).  You can always tweak the JDBC settings without having to make code changes.  I've configured our jboss datasources to look like this:

Example crc-ds.xml:

<local-tx-datasource>

<jndi-name>QueryToolDemoDS</jndi-name>

<connection-url>jdbc:oracle:thin:@127.0.0.1:1521:XE</connection-url>

<driver-class>oracle.jdbc.driver.OracleDriver</driver-class>

<user-name>i2b2demodata</user-name>

<password>demouser</password>

<min-pool-size>0</min-pool-size>

<max-pool-size>20</max-pool-size>

<idle-timeout-minutes>1</idle-timeout-minutes>

<new-connection-sql>SELECT 1 FROM dual</new-connection-sql>

<check-valid-connection-sql>SELECT 1 FROM dual</check-valid-connection-sql>

<exception-sorter-class- name>org.jboss.resource.adapter.jdbc.vendor.OracleExceptionSorter</exception-sorter- class-name>

<metadata>

<type-mapping>Oracle9i</type-mapping>

</metadata>

<connection-property>100</connection-property><!--

default is 10 -->

<connection-property>100</connection-property><!- default is 10 ->

</local-tx-datasource>

Similarly for the Spring datasources in JBOSS_HOME/server/default/conf/app/*ApplicationContext.xml you can do this:

Example CRCApplicationContext.xml:

<bean destroy-method="close">

<property value="oracle.jdbc.driver.OracleDriver" />

<property value="jdbc:oracle:thin:@127.0.0.1:1521:XE" />

<property value="i2b2hive" />

<property value="demouser" />

<property value="0" />

<property value="20" />

<property value="60000" /><!-60 seconds->

<property value="true"/>

<property value="SELECT 1 FROM dual" />

<property>

<props>

<prop key="defaultRowPrefetch">100</prop>

<prop key="defaultBatchValue">100</prop>

</props>

</property>

</bean>

Jeremy Nix

Senior Application Developer

Cincinnati Children's Hospital Medical Center

On 02/21/2012 12:39 PM, Henderson, Darren W wrote:

Your question this morning reminded me that I had looked into this back in January and had also asked another question regarding Encounter Sets to the devs:

On a side-note, when a user chooses an encounter set result type, in the server log I'm seeing batch size commits of only 500 rows to the qt_patient_enc_collection table. Is there a server control variable somewhere in the configuration files to increase this batch size to reduce the number of transactions required to store the encounter set?

I'm not sure if this had anything to do with your issues Dan, but I had begun my inspection of the encounter set issue when I began using i2b2 as a tool for our State Medicaid dataset that is nearly 150M visits. Encounter sets as they were designed was just simply unsupportable in terms of time and storage when it's everything that ever happened to the resulting patients. We decided to disable them as a result type.

From: Dan Connolly [dconnolly.kumc]

Sent: Tuesday, February 21, 2012 10:45 AM

To: Henderson, Darren W

Cc:  i2b2 AUG Members

Subject: RE: experience with Encounter Set queries?

On Tue, 2012-02-21 at 10:06 -0500, Henderson, Darren W wrote:

Remember that "Encounter Sets" are not the encounters that matched your query constraints. Instead, it is a set of all encounters (ever) for the patients that matched your query constraints.

Oh. Sigh. Then it's not useful for the analytics tool that we're building after all. I didn't see that in any documentation. Any pointers would be appreciated.

Or did you pick it up from the code? Or just by inspection of results?

For your 7597 patients, that's likely many many encounters.

From: Dan Connolly [dconnolly.kumc]

Sent: Monday, February 20, 2012 6:01 PM

To: i2b2 AUG Members

Subject: experience with Encounter Set queries?

Has anybody had much luck with Encounter Set queries in i2b2 1.602?

I'm having trouble using them, and I wonder if I'm beyond the supported state-of-the-art or if I have an installation/config problem.

We're developing an analysis tool where they would be helpful.

They're documented in the help pages, but they didn't show up in our web client "Run Query" dialog.

I couldn't find any reason why not in in the javascript code, but then I saw 'LH' in

QT_QUERY_RESULT_TYPE.

I changed LH to LA, and presto, the choice appears in the "Run Query" dialog. When I ran the query,

it took quite a while (62 seconds where a patient set takes 4.8 seconds). Are patient set queries indexed or optimized in some way that encounter set queries are not?

I got an Encounter Set that had "patient_count: 7597"

I clicked on it in in the "Previous Queries" area; probably not a good idea; it spun forever.

I suppose analog to the "that patient set is really big; you don't really want to display it" check for patient sets isn't there yet?

Dan Connolly, KUMC Medical Informatics

913-945-6741



NEXT EMAIL

From:  Henderson, Darren W [darren.henderson.uky]

Sent:   Tuesday, February 21, 2012 11:01 AM

To:       Dan Connolly

Cc:      i2b2 AUG Members

Subject:         RE: experience with Encounter Set queries?

I remember seeing that in the documentation somewhere, and also from inspection of the set returned itself. You could easily alter the generator class, or make your own result generator to pull the encounters that did match your query. If the same encounter timing is chosen the encounters are already sitting in the #DX table waiting to be used for something.  We created a couple different breakdowns for calendar year and fiscal year breakdown by abusing this table before it disappears after the query completes.

From: Dan Connolly [dconnolly.kumc]

Sent: Tuesday, February 21, 2012 10:45 AM

To: Henderson, Darren W

Cc: i2b2 AUG Members

Subject: RE: experience with Encounter Set queries?

On Tue, 2012-02-21 at 10:06 -0500, Henderson, Darren W wrote:

Remember that "Encounter Sets" are not the encounters that matched your query constraints. Instead, it is a set of all encounters (ever) for the patients that matched your query constraints.

Oh. Sigh. Then it's not useful for the analytics tool that we're building after all. I didn't see that in any documentation. Any pointers would be appreciated.

Or did you pick it up from the code? Or just by inspection of results? For your 7597 patients, that's likely many many encounters.

From: Dan Connolly [dconnolly.kumc]

Sent: Monday, February 20, 2012 6:01 PM

To:  i2b2 AUG Members

Subject: experience with Encounter Set queries?

Has anybody had much luck with Encounter Set queries in i2b2 1.602?

I'm having trouble using them, and I wonder if I'm beyond the supported state-of-the-art or if I have an installation/config problem.

We're developing an analysis tool where they would be helpful.

They're documented in the help pages, but they didn't show up in our web client "Run Query" dialog.

I couldn't find any reason why not in in the javascript code, but then I saw 'LH' in QT_QUERY_RESULT_TYPE.

I changed LH to LA, and presto, the choice appears in the "Run Query" dialog. When I ran the query, it took quite a while (62 seconds where a patient set takes 4.8 seconds). Are patient set queries indexed or optimized in some way that encounter set queries are not?

I got an Encounter Set that had "patient_count: 7597"

I clicked on it in in the "Previous Queries" area; probably not a good idea; it spun forever.

I suppose analog to the "that patient set is really big; you don't really want to display it" check for patient sets isn't there yet?

Dan Connolly, KUMC Medical Informatics

913-945-6741



NEXT EMAIL

From:  Jack London [jack.london.KimmelCancerCenter]

Sent:   Tuesday, February 21, 2012 9:25 AM

To:       Wilson, Brian

Cc:      i2b2 AUG Members members

Subject:         Re: constrain by instance in v1.6?

Brian,

Thank you! Just did as you suggest, and it works fine. Jack

On Feb 20, 2012, at 10:18 PM, Wilson, Brian wrote:

Jack

If you drag and drop a concept modifier into a panel an extra option should appear in the temporal constraint pulldown.

B

From: Jack W. London, Ph.D. [Jack.London.KimmelCancerCenter]

Sent: Mon 2/20/2012 5:29 PM

To: i2b2 AUG Members

Subject: constrain by instance in v1.6?

According to the "help" window in the v1.6.02 web client, a query panel can be temporally constrained to have the same instance number. But the temporal constraint pulldown only offers "independent" or "same financial encounter." Is the instance number constraint available with any of the v1.6 releases?

Jack



NEXT EMAIL

From:  Schulte, Gregory [Gregory.Schulte.childrenscolorado]

Sent:   Friday, February 17, 2012 4:38 PM

To:       i2b2 AUG Members members

Subject:         RE: Query running over 30 secs never returns result to panel

Think I got it...

Noticed this error in my apache log:

[Fri Feb 17 14:19:43 2012] [error] [client 10.34.36.52] PHP Fatal error: Maximum execution time of 30 seconds exceeded in G:\\opt
web
webclient
index.php on line 181, referer: [http://tchi2b202/i2b2/
]

In the php.ini file there is a "resource limits" section.

By default its set to 30 seconds, increasing the time corrected the problem.

Resource Limits

Maximum execution time of each script, in seconds

http://php.net/max-execution-time

Note: This directive is hardcoded to 0 for the CLI SAPI max_execution_time = 30

Greg

From: Schulte, Gregory [Gregory.Schulte.childrenscolorado]

Sent: Friday, February 17, 2012 1:34 PM

To: i2b2 AUG Members

Subject: Query running over 30 secs never returns result to panel

All,

We are using version 1.6.0.2, and have an "issue" every time a query runs over 30 secs per the "query status" panel. When the timer gets past the 30 sec mark, it just continues to increment and never returns results even if query completed in say 34 seconds.

After some time we just end up canceling the query that isn't returning, then grab that query from the "previous queries" panel and place it in the query tool and low and behold the output is presented in the query status panel.

I can watch the server.log update with the result but as we've experienced, the result won't display if the query runs over 30 secs.

Here's an example ... the query ran for 34 secs but it never shows up in the "query status" panel unless I cancel it and put it back in the query tool.

<query_result_instance>

<result_instance_id>236</result_instance_id>

<query_instance_id>184</query_instance_id>

<description>Number of patients for "Tobra-(277.- Visi@13:09:57"</description>

<query_result_type>

<result_type_id>4</result_type_id>

<name>PATIENT_COUNT_XML</name>

<display_type>CATNUM</display_type>

<visual_attribute_type>LA</visual_attribute_type>

<description>Number of patients</description>

</query_result_type>

<set_size>216</set_size>

<obfuscate_method></obfuscate_method>

<start_date>2012-02-17T13:10:03.043-07:00</start_date>

<end_date>2012-02-17T13:10:37.117-07:00</end_date>

<message/>

<query_status_type>

<status_type_id>3</status_type_id>

<name>FINISHED</name>

<description>FINISHED</description>

</query_status_type>

</query_result_instance>

Anyone experience this? Any query that runs under 30 seconds seems to return just fine.

Thanks,

Greg Schulte | Clinical Research Data Warehouse Database Analyst

13123 East 16th Avenue, Box 485 | Aurora, CO 80045

Phone: 720.777.5740 |  Gregory.Schulte.childrenscolorado



NEXT EMAIL

From:  Churchill, Susanne E.

Sent:   Wednesday, February 15, 2012 3:15 PM

To:       i2b2 AUG Members

Subject:         i2b2 Workshop March 20

Dear Colleagues,

The date for the workshop in conjunction with the March AMIA Translational IT Meeting in San Francisco (Parc 55 Hotel) has been set for the evening of Tuesday, March 20 at 6:30 pm, location to be announced. Per your feedback, we'll video the session and post it to your page on our website (www.i2b2.org/work/aug.html).

Could I get a show of hands from anyone who did not respond to my earlier message so we can size the room (and reception) appropriately?

Thanks,

Susanne

Susanne E. Churchill, Ph.D. Executive Director

i2b2/Nat'l Center for Biomedical Computing

77 Avenue Louis Pasteur, Room 255

Boston, MA 02115 tel: (617) 525-4465 fax: (617 525-4491



NEXT EMAIL

From:  Henderson, Darren W [darren.henderson.uky]

Sent:   Wednesday, February 15, 2012 10:31 AM

To:       i2b2 AUG Members

Subject:         May be useful to someone out there.

We recently needed to update our ICD9 and CPT ontologies in i2b2 when we found some missing codes that were fairly new. We were missing codes for MRSA and some other random things. So I tossed this together to pull the i2b2 ontology out of the UMLS tables mrhier and mrconso that you can download out of the umls and then import into a database to work with. I figured I'd toss this out into the members list wind so no one has to waste time reinventing the wheel if you happen to need an update to your ontology. Cheers.

Darren W. Henderson

Institute for Pharmaceutical Outcomes and Policy

Center for Clinical and Translational Science Division for Biomedical Informatics University of Kentucky

789 S. Limestone Rm. 182

Lexington, KY 40536

(859) 323-7146

(859) 967-4914



NEXT EMAIL

From:  Jeremy Nix [Jeremy.Nix.cchmc]

Sent:   Wednesday, February 15, 2012 9:27 AM

To:       i2b2 AUG Members

Subject:         Updating Axis Version

I'm curious if there is any desire to upgrade the version of Axis that is currently being used within i2b2 from 2-1.1 to 2-1.2 or to the most recent version 2-1.6.1.  The specific reason that I bring this is up is that there is bug in Axis2-1.1 that causes request coming from newer Axis2 clients (any clients not sending content-type of "application/x-www-form-urlencoded") to fail. The specific bug report is here (https://issues.apache.org/jira/browse/AXIS2-1788).&nbsp; I found that (although not documented with the bug report) it was fixed in the 2-1.2 release.

We've successfully updated our i2b2 codebase to use Axis2-1.6.1, and all functionality has been preserved.  In fact, the ?wsdl functionality has even started to work (although we have performed some tweaks in the services.xml files).  In reading the release notes, there have been many bug fixes and enhancements (new functionality, increased performance, etc...) that have occurred within the last 5 years that I think would make it worth the upgrade.

I was going to file an enhancement request in the i2b2.org/jira site, but it appears that site is currently unavailable.

Jeremy Nix

Senior Application Developer

Cincinnati Children's Hospital Medical Center



NEXT EMAIL

From:  Peter Beninato [beninato.ohsu]

Sent:   Tuesday, February 14, 2012 7:27 PM

To:       i2b2-install-help.googlegroups; i2b2 AUG Members

Subject:         RE: SQL queries / logging

Hi,

This was probably on the other list server "members".

There was a posting related to version 1.6.02. Could be same problem with "occur" See 1st email from Lisa Miao (two emails down)

Peter


Peter,

That is a really good point.

I was NOT linking anything related to encounter.

And I agreed with you also, I don't see why encounter_num should be part of the concatenation. Perhaps anyone from i2b2 team could explain?

Thanks, Lisa.

From: Peter Beninato [beninato.ohsu]

Sent: Thursday, February 09, 2012 11:04 AM

To: Lisa Miao; i2b2 AUG Members

Subject: RE: occurrence > 1 bug --> encounter_num in concatenation

Hi Lisa,

In regards to your example below, I see that encounter_num is included in the concatenation. Were you linking "financial encounters" together amongst the panels?

If so, then I can see the reasoning of including the encounter_num in the concatenation.

If you weren't linking panels by encounter, then this might warrant additional investigation, in that it might be of interest that the concept recurs for the patient, but not necessarily on the same encounter(or for that matter instance_num?).

In which case, encounter_num(instance_num) should not be part of concatenation?

Peter

From: Lisa Miao [lmiao.regenstrief]

Sent: Thursday, February 09, 2012 6:47 AM

To:  i2b2 AUG Members

Subject: occurrence > 1 bug

Dear i2b2 team,

When we run an "occur > 1" query (in the constrain panel), the following SQL was executed:

select  patient_num ,1 as panel_count from (

select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num from observation_fact

where concept_cd IN (select concept_cd

from concept_dimension

where concept_path like '\i2b2\VITALS\VITALS CLINIC\BP Dias Sitting%')

group by   patient_num having count( distinct patient_num || encounter_num ||

instance_num || concept_cd || cast(start_date varchar(50) ) ) >= 2 ) t;

The above SQL is an invalid SQL statement, Oracle will say "missing keyword".

The offender is cast(start_date varchar(50) ). We are missing the word "as". It should be: cast(start_date as

varchar(50) ).

At first I thought it was an Oracle version issue (we are running 11g), but by issuing the same command to an

10g server, I got the same error.

Please validate whether or not what I'm saying is the situation for everyone else, and if so, I can submit a bug report.

Thanks, Lisa.

From: i2b2-install-help.googlegroups [i2b2-install-help.googlegroups] On Behalf Of George Kowalski

Sent: Tuesday, February 14, 2012 2:17 PM To: i2b2-install-help.googlegroups Subject: Re: SQL queries / logging

The error I'm trying to track down is when a user selects within the wbeclient :   "Event(s) within the group occur more than 1 time"  on a given field. This is on a 1.6.01 system . Any Ideas as I ran the query just before the failure and it works .  My UID is now my windows account ID domain\userid . We've modified the login to take our windows userid / password, but not touched any backend code.  But I log in with the admin account and the error is the same : "ORA-00905: missing keyword" error.  The search works great if one does not select the "Occurs more than once drop down ".  Any Ideas on how to debug this ?

2012-02-14 15:38:49,873 DEBUG [edu.harvard.i2b2.common.util.jaxb.JAXBUtil]

object.toString()edu.harvard.i2b2.crc.datavo.i2b2message.RequestMessageType

2012-02-14 15:38:49,874 DEBUG [org.springframework.beans.factory.support.DefaultListableBeanFactory] Returning cached instance of singleton bean 'appType'

2012-02-14 15:38:49,875 DEBUG [edu.harvard.i2b2.common.util.jaxb.JAXBUtil]

object.toString()edu.harvard.i2b2.crc.datavo.i2b2message.RequestMessageType

2012-02-14 15:38:49,875 DEBUG [edu.harvard.i2b2.common.util.jaxb.JAXBUtil]

object.toString()edu.harvard.i2b2.crc.datavo.i2b2message.RequestMessageType

2012-02-14 15:38:49,876 DEBUG [edu.harvard.i2b2.crc.dao.OracleDataSourceLookupDAO] Executing SQL query [select * from i2b2hive.crc_db_lookup where c_domain_id = ? and c_project_path like ? and (c_owner_id =? or c_owner_id = '@') order by c_project_path]

2012-02-14 15:38:49,876 DEBUG [org.springframework.jdbc.datasource.DataSourceUtils] Fetching JDBC Connection from DataSource

2012-02-14 15:38:49,876 DEBUG [org.springframework.jdbc.core.StatementCreatorUtils] Setting SQL statement parameter value: column index 1, parameter value [i2b2demo], value class [java.lang.String], SQL type 12

2012-02-14 15:38:49,876 DEBUG [org.springframework.jdbc.core.StatementCreatorUtils] Setting SQL statement parameter value: column index 2, parameter value [/CDW/%], value class [java.lang.String], SQL type 12

2012-02-14 15:38:49,876 DEBUG [org.springframework.jdbc.core.StatementCreatorUtils] Setting SQL statement parameter value: column index 3, parameter value [mcw_hmgc\windowsid], value class [java.lang.String], SQL type 12

2012-02-14 15:38:49,876 DEBUG [edu.harvard.i2b2.crc.axis2.QueryService] Response in service<?xml version="1.0" encoding="UTF-8" standalone="yes"?> <ns5:response xmlns:ns2="http://www.i2b2.org/xsd/hive/pdo/1.1/" xmlns:ns4="http://www.i2b2.org/xsd/cell/crc/psm/1.1/" xmlns:ns3="http://www.i2b2.org/xsd/cell/crc/pdo/1.1/" xmlns:ns9="http://www.i2b2.org/xsd/cell/ont/1.1/" xmlns:ns5="http://www.i2b2.org/xsd/hive/msg/1.1/" xmlns:ns6="http://www.i2b2.org/xsd/cell/crc/psm/querydefinition/1.1/" xmlns:ns10="http://www.i2b2.org/xsd/hive/msg/result/1.1/" xmlns:ns7="http://www.i2b2.org/xsd/cell/crc/psm/analysisdefinition/1.1/" xmlns:ns8="http://www.i2b2.org/xsd/cell/pm/1.1/">

<message_header>

<i2b2_version_compatible>1.1</i2b2_version_compatible>

<hl7_version_compatible>2.4</hl7_version_compatible>

<sending_application>

<application_name>CRC Cell</application_name>

<application_version>1.601</application_version>

</sending_application>

<sending_facility>

<facility_name>i2b2 Hive</facility_name>

</sending_facility>

<receiving_application>

<application_name>i2b2_QueryTool</application_name>

<application_version>1.6</application_version>

</receiving_application>

<receiving_facility>

<facility_name>i2b2 Hive</facility_name>

</receiving_facility>

<message_control_id>

<instance_num>1</instance_num>

</message_control_id>

<project_id>CDW</project_id>

</message_header>

<response_header>

<info>Log information</info>

<result_status>

<status>DONE</status>

<polling_url interval_ms="100"/>

</result_status>

</response_header>

<message_body>

<ns4:response xsi:type="ns4:instance_responseType" xmlns:xsi="http://www.w3.org/2001/XMLSchema- instance">

<status>

<condition>DONE</condition>

</status>

<query_instance>

<query_instance_id>1959</query_instance_id>

<query_master_id>2019</query_master_id>

<user_id>mcw_hmgc\windowsid</user_id>

<group_id>CDW</group_id>

<start_date>2012-02-14T15:38:47.000-06:00</start_date>

<end_date>2012-02-14T15:38:48.000-06:00</end_date>

<message>java.sql.SQLException: ORA-00905: missing keyword

at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:112)

at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:331) at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:288) at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:743)

at oracle.jdbc.driver.T4CStatement.doOall8(T4CStatement.java:207)

at oracle.jdbc.driver.T4CStatement.executeForRows(T4CStatement.java:946)

at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1168) at oracle.jdbc.driver.OracleStatement.executeUpdateInternal(OracleStatement.java:1614) at oracle.jdbc.driver.OracleStatement.executeUpdate(OracleStatement.java:1579)

at org.jboss.resource.adapter.jdbc.WrappedStatement.executeUpdate(WrappedStatement.java:249)

at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorHelperDao.executeQuery(Unknown Source)

at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorDao.executeSQL(Unknown Source)

at edu.harvard.i2b2.crc.ejb.ExecRunnable.processQueryRequest(Unknown Source)

at edu.harvard.i2b2.crc.ejb.ExecRunnable.execute(Unknown Source)

at edu.harvard.i2b2.crc.ejb.QueryExecutorMDB.onMessage(Unknown Source)

at edu.harvard.i2b2.crc.ejb.QuerySmallExecutorMDB.onMessage(Unknown Source)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.jboss.invocation.Invocation.performCall(Invocation.java:359)

at org.jboss.ejb.MessageDrivenContainer$ContainerInterceptor.invoke(MessageDrivenContainer.java:495)

at org.jboss.resource.connectionmanager.CachedConnectionInterceptor.invoke(CachedConnectionInterceptor.java

:158)

at org.jboss.ejb.plugins.CallValidationInterceptor.invoke(CallValidationInterceptor.java:63)

at org.jboss.ejb.plugins.AbstractTxInterceptor.invoedu.harvard.i2b2.common.exception.I2B2DAOException: Error while executing sql

at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorHelperDao.executeQuery(Unknown Source)

at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorDao.executeSQL(Unknown Source)

at edu.harvard.i2b2.crc.ejb.ExecRunnable.processQueryRequest(Unknown Source)

at edu.harvard.i2b2.crc.ejb.ExecRunnable.execute(Unknown Source)

at edu.harvard.i2b2.crc.ejb.QueryExecutorMDB.onMessage(Unknown Source)

at edu.harvard.i2b2.crc.ejb.QuerySmallExecutorMDB.onMessage(Unknown Source)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.jboss.invocation.Invocation.performCall(Invocation.java:359)

at org.jboss.ejb.MessageDrivenContainer$ContainerInterceptor.invoke(MessageDrivenContainer.java:495)

at org.jboss.resource.connectionmanager.CachedConnectionInterceptor.invoke(CachedConnectionInterceptor.java

:158)

at org.jboss.ejb.plugins.CallValidationInterceptor.invoke(CallValidationInterceptor.java:63)

at org.jboss.ejb.plugins.AbstractTxInterceptor.invokeNext(AbstractTxInterceptor.java:121)

at org.jboss.ejb.plugins.AbstractTxInterceptorBMT.invokeNext(AbstractTxInterceptorBMT.java:173)

at org.jboss.ejb.plugins.MessageDrivenTxInterceptorBMT.invoke(MessageDrivenTxInterceptorBMT.java:47)

at org.jboss.ejb.plugins.MessageDrivenInstanceInterceptor.invoke(MessageDrivenInstanceInterceptor.java:116)

at org.jboss.ejb.plugins.RunAsSecurityInterceptor.invoke(RunAsSecurityInterceptor.java:109)

at org.jboss.ejb.plugins.LogInterceptor.invoke(LogInterceptor.java:205)

at org.jboss.ejb.plugins.ProxyFactoryFinderInterceptor.invoke(ProxyFactoryFinderInterceptor.java:138)

at org.jboss.ejb.MessageDrivenContainer.internalInvoke(MessageDrivenContainer.java:402)

at org.jboss.ejb.Container.</message>

<query_status_type>

<status_type_id>4</status_type_id>

<name>ERROR</name>

<description>ERROR</description>

</query_status_type>

</query_instance>

</ns4:response>

</message_body>

</ns5:response>

2012-02-14 15:38:49,879 DEBUG [org.springframework.jdbc.datasource.DataSourceUtils] Returning JDBC Connection to DataSource



NEXT EMAIL

From:   Peter Beninato [beninato.ohsu]

Sent:   Tuesday, February 14, 2012 7:24 PM

To:     Travis Nagler

Cc:      i2b2 AUG Members

Subject:         RE: i2b2 1.6 and Users under"Manage Projects"

What is the amount of memory you have configured for JBOSS JVM? I think I put that max at 4 gig.

It is just a hunch, but to display the result probably has to parse the result sets/XML.

If not enough memory thrown at the JVM, then a lot of crunching and that would explain why small results set show.

From: Travis Nagler [travis.nagler.ucdmc.ucdavis]

Sent: Tuesday, February 14, 2012 2:15 PM

To: Peter Beninato

Cc: i2b2 AUG Members

Subject: RE: i2b2 1.6 and Users under"Manage Projects"

Peter,

I just sent out an email yesterday with the same kind of error, only mine was in the "Previous Queries" section and it was just "working" on opening the items to see the previous query patient counts, but never completed.

It doesn't work whether I click the plus sign or click the text. It does, however open the count for queries with <10 patients. I included a screenshot in my email yesterday. We're in v1.5.5. You have any suggestions as to what might  be the problem?

Thanks,

Travis

Travis H. Nagler

Senior Database Programmer

American Burn Assoc. - Data Coordinating Center

UC Davis Division of Burn Surgery

UC Davis Health System

2921 Stockton Blvd., Suite 1470

Sacramento, CA, 95817 tel: (916) 703-9215

fax: (916) 703-9124 http://www.ucdmc.ucdavis.edu travis.nagler.ucdmc.ucdavis.edu

From:  Peter Beninato <beninato.ohsu>

To:       Jennifer Cai <Jennifer.Cai.UTSouthwestern>, "i2b2 AUG Members" <i2b2 AUG Members> Date:                        02/14/2012 02:00 PM

Subject:         RE: i2b2 1.6 and Users under"Manage Projects"

Hi,

One of the mechanism to look at the user fails, I think just clicking on the plus sign... I think you need to click on "Users", and then click the plus sign.

I think the clicking identifies the user folder as what you want to expand.

Peter

From: Jennifer Cai [Jennifer.Cai.UTSouthwestern]

Sent: Tuesday, February 14, 2012 1:52 PM

To:  i2b2 AUG Members

Subject: i2b2 1.6 and Users under"Manage Projects"

Hi,

We tried to associate the newly created user account to a project. When we clicked the "Users" under the "Manage Projects" in the

PM admin tool,  the timer kept running forever, but  the "User" could not be expanded. In JBOSS log, there is no error. We re-deployed the PM, but it did not fix the problem. Does anyone have the similar experience on it?

Thanks,

Jennifer

UT Southwestern Medical Center

The future of medicine, today.



NEXT EMAIL

From:  Jennifer Cai [Jennifer.Cai.UTSouthwestern]

Sent:   Tuesday, February 14, 2012 5:05 PM

To:       Peter Beninato; i2b2 AUG Members

Subject:         RE: i2b2 1.6 and Users under"Manage Projects"

Peter,

Exactly. It works now by clicking the "Users" Thanks,

Jennifer

From: Peter Beninato [beninato.ohsu]

Sent: Tuesday, February 14, 2012 4:00 PM

To: Jennifer Cai; i2b2 AUG Members

Subject: RE: i2b2 1.6 and Users under"Manage Projects"

Hi,

One of the mechanism to look at the user fails, I think just clicking on the plus sign... I think you need to click on "Users", and then click the plus sign.

I think the clicking identifies the user folder as what you want to expand.

Peter

From: Jennifer Cai [Jennifer.Cai.UTSouthwestern]

Sent: Tuesday, February 14, 2012 1:52 PM

To:  i2b2 AUG Members

Subject: i2b2 1.6 and Users under"Manage Projects"

Hi,

We tried to associate the newly created user account to a project. When we clicked the "Users" under the "Manage Projects" in the PM admin tool, the timer kept running forever, but the "User" could not be expanded. In JBOSS log, there is no error.

We re-deployed the PM, but it did not fix the problem. Does anyone have the similar experience on it? Thanks,

Jennifer

UT Southwestern Medical Center

The future of medicine, today.



NEXT EMAIL

From:  Davis, Michael (Oncology) [davismk.upmc]

Sent:   Tuesday, February 14, 2012 4:44 PM

To:       i2b2 AUG Members

Subject:         CronStartService error

All,

I'm trying to build and deploy v1.6.02, everything looks as though it compiles error free, however, when I try to start JBoss I receive the following error which states that the CronStartService will not start. Has anyone encounter this problem before or have any clues to how to fix?

16:39:47,391 INFO [EARDeployer] Started J2EE application: [file:/C:/jboss-4.2.2.GA/server/default/deploy/QP1.ear]

16:39:47,422 WARN [ServiceController] Problem starting service crc.startCron:service=CronStartService javax.ejb.EJBException: java.lang.NullPointerException

at org.jboss.ejb3.tx.Ejb3TxPolicy.handleExceptionInOurTx(Ejb3TxPolicy.java:63)

at org.jboss.aspects.tx.TxPolicy.invokeInOurTx(TxPolicy.java:83)

at org.jboss.aspects.tx.TxInterceptor$Required.invoke(TxInterceptor.java:191)

at org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:101)

at org.jboss.aspects.tx.TxPropagationInterceptor.invoke(TxPropagationInterceptor.java:95)

at org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:101)

at org.jboss.ejb3.stateless.StatelessInstanceInterceptor.invoke(StatelessInstanceInterceptor.java:62)

at org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:101)

at org.jboss.aspects.security.AuthenticationInterceptor.invoke(AuthenticationInterceptor.java:77)

at org.jboss.ejb3.security.Ejb3AuthenticationInterceptor.invoke(Ejb3AuthenticationInterceptor.java:110)

at org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:101)

at org.jboss.ejb3.ENCPropagationInterceptor.invoke(ENCPropagationInterceptor.java:46)

at org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:101)

at org.jboss.ejb3.asynchronous.AsynchronousInterceptor.invoke(AsynchronousInterceptor.java:106)

at org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:101) at org.jboss.ejb3.stateless.StatelessContainer.localInvoke(StatelessContainer.java:240) at org.jboss.ejb3.stateless.StatelessContainer.localInvoke(StatelessContainer.java:210) at org.jboss.ejb3.stateless.StatelessLocalProxy.invoke(StatelessLocalProxy.java:84)

at $Proxy145.start(Unknown Source)

at edu.harvard.i2b2.crc.mbean.CronStartService.startService(Unknown Source)

at org.jboss.system.ServiceMBeanSupport.jbossInternalStart(ServiceMBeanSupport.java:289)

at org.jboss.system.ServiceMBeanSupport.jbossInternalLifecycle(ServiceMBeanSupport.java:245)

at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)

at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)

at org.jboss.mx.server.Invocation.invoke(Invocation.java:86)

at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)

at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)

at org.jboss.system.ServiceController$ServiceProxy.invoke(ServiceController.java:978)

at $Proxy0.start(Unknown Source)

at org.jboss.system.ServiceController.start(ServiceController.java:417)

at sun.reflect.GeneratedMethodAccessor9.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)

at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)

at org.jboss.mx.server.Invocation.invoke(Invocation.java:86)

at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)

at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)

at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)

at $Proxy4.start(Unknown Source)

at org.jboss.deployment.SARDeployer.start(SARDeployer.java:302)

at org.jboss.deployment.MainDeployer.start(MainDeployer.java:1025) at org.jboss.deployment.MainDeployer.start(MainDeployer.java:1015) at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:819) at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:782) at sun.reflect.GeneratedMethodAccessor27.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)

at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)

at org.jboss.mx.interceptor.AbstractInterceptor.invoke(AbstractInterceptor.java:133)

at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)

at org.jboss.mx.interceptor.ModelMBeanOperationInterceptor.invoke(ModelMBeanOperationInterceptor.java:142)

at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)

at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)

at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)

at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)

at $Proxy9.deploy(Unknown Source)

at org.jboss.deployment.scanner.URLDeploymentScanner.deploy(URLDeploymentScanner.java:421)

at org.jboss.deployment.scanner.URLDeploymentScanner.scan(URLDeploymentScanner.java:634)

at org.jboss.deployment.scanner.AbstractDeploymentScanner$ScannerThread.doScan(AbstractDeploymentScanner.java:2

63)

at org.jboss.deployment.scanner.AbstractDeploymentScanner.startService(AbstractDeploymentScanner.java:336)

at org.jboss.system.ServiceMBeanSupport.jbossInternalStart(ServiceMBeanSupport.java:289)

at org.jboss.system.ServiceMBeanSupport.jbossInternalLifecycle(ServiceMBeanSupport.java:245)

at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)

at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)

at org.jboss.mx.server.Invocation.invoke(Invocation.java:86)

at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)

at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)

at org.jboss.system.ServiceController$ServiceProxy.invoke(ServiceController.java:978)

at $Proxy0.start(Unknown Source)

at org.jboss.system.ServiceController.start(ServiceController.java:417)

at sun.reflect.GeneratedMethodAccessor9.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)

at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)

at org.jboss.mx.server.Invocation.invoke(Invocation.java:86)

at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)

at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)

at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)

at $Proxy4.start(Unknown Source)

at org.jboss.deployment.SARDeployer.start(SARDeployer.java:302)

at org.jboss.deployment.MainDeployer.start(MainDeployer.java:1025) at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:819) at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:782) at org.jboss.deployment.MainDeployer.deploy(MainDeployer.java:766) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.jboss.mx.interceptor.ReflectedDispatcher.invoke(ReflectedDispatcher.java:155)

at org.jboss.mx.server.Invocation.dispatch(Invocation.java:94)

at org.jboss.mx.interceptor.AbstractInterceptor.invoke(AbstractInterceptor.java:133)

at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)

at org.jboss.mx.interceptor.ModelMBeanOperationInterceptor.invoke(ModelMBeanOperationInterceptor.java:142)

at org.jboss.mx.server.Invocation.invoke(Invocation.java:88)

at org.jboss.mx.server.AbstractMBeanInvoker.invoke(AbstractMBeanInvoker.java:264)

at org.jboss.mx.server.MBeanServerImpl.invoke(MBeanServerImpl.java:659)

at org.jboss.mx.util.MBeanProxyExt.invoke(MBeanProxyExt.java:210)

at $Proxy5.deploy(Unknown Source)

at org.jboss.system.server.ServerImpl.doStart(ServerImpl.java:482)

at org.jboss.system.server.ServerImpl.start(ServerImpl.java:362)

at org.jboss.Main.boot(Main.java:200) at org.jboss.Main$1.run(Main.java:508) at java.lang.Thread.run(Thread.java:662)

Caused by: java.lang.NullPointerException

at edu.harvard.i2b2.crc.ejb.analysis.CronEjb.start(Unknown Source)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:112)

at org.jboss.ejb3.interceptor.InvocationContextImpl.proceed(InvocationContextImpl.java:166)

at org.jboss.ejb3.interceptor.EJB3InterceptorsInterceptor.invoke(EJB3InterceptorsInterceptor.java:63)

at org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:101)

at

org.jboss.ejb3.entity.TransactionScopedEntityManagerInterceptor.invoke(TransactionScopedEntityManagerInterceptor.j ava

at org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:101)

at org.jboss.ejb3.AllowedOperationsInterceptor.invoke(AllowedOperationsInterceptor.java:47)

at org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:101)

at org.jboss.aspects.tx.TxPolicy.invokeInOurTx(TxPolicy.java:79)

... 110 more

16:39:47,579 ERROR [URLDeploymentScanner] Incomplete Deployment listing:

 MBeans waiting for other MBeans --- ObjectName: crc.startCron:service=CronStartService State: FAILED

Reason: javax.ejb.EJBException: java.lang.NullPointerException

I Depend On:

jboss :service=Naming

 MBEANS THAT ARE THE ROOT CAUSE OF THE PROBLEM--­ ObjectName: crc.startCron:service=CronStartService

State: FAILED

Reason: javax.ejb.EJBException: java.lang.Null PointerException

I Depend On:

jboss :service=Naming



NEXT EMAIL

From:  Travis Nagler [travis.nagler.ucdmc.ucdavis]

Sent:   Monday, February 13, 2012 7:01 PM

To:       i2b2 AUG Members

Subject:         Previous Queries quirk in v1.5.5

In the Previous Queries section, when I click on the "plus" sign to drop-down the patient count in already-run queries, I only get shown those items with Patient Counts of less than 10. In queries where there is a larger number to return, the results are not shown and I just get the [working] circles (see picture below).

I can drag the queries back into the Query Tool and re-run them, no problem, but I just can't make the previous counts show up.

Anyone see this before? Any ideas to fix it? Thanks,

Travis

Travis H. Nagler

Senior Database Programmer

American Burn Assoc. - Data Coordinating Center

UC Davis Division of Burn Surgery

UC Davis Health System

2921 Stockton Blvd., Suite 1470

Sacramento, CA, 95817 tel: (916) 703-9215

fax: (916) 703-9124 http://www.ucdmc.ucdavis

travis.nagler.ucdmc.ucdavis



NEXT EMAIL

From:  Arvinder Choudhary [achoudhary.kumc]

Sent:   Friday, February 10, 2012 5:07 PM

To:       i2b2 AUG Members; Phillips, Lori C.; Mendis, Michael E.; Murphy, Shawn N.

Subject:         RE: Navigating the concept hierarchy seems slow in i2b2 1.6

Yes thank you so much Philips and Mike ...It worked

Phillips, Lori C. <LCPHILLIPS.PARTNERS.ORG> 2/10/2012 3:34 PM 

Correction:

the indexes are on c_fullname and m_applied_path

CREATE INDEX META_FULLNAME_I2B2_IDX ON I2B2(C_FULLNAME);

CREATE INDEX META_APPLIED_PATH_I2B2_IDX ON I2B2(M_APPLIED_PATH)

From: Phillips, Lori C.

Sent: Friday, February 10, 2012 4:32 PM

To: Arvinder Choudhary; i2b2 AUG Members; Mendis, Michael E.; Murphy, Shawn N.

Subject: RE: Navigating the concept hierarchy seems slow in i2b2 1.6

There should be two; one on the c_basecode ; the other on m_applied_path

Another thing to try is to disable the display of modifiers if you are not using them

See the options Button on the right that looks like a gear in the workbench.

From: Arvinder Choudhary [achoudhary.kumc]

Sent: Friday, February 10, 2012 4:28 PM

To: i2b2 AUG Members; Mendis, Michael E.; Murphy, Shawn N.

Subject: Re: Navigating the concept hierarchy seems slow in i2b2 1.6

Mike

It is fresh install. What is the name of the index. We have index

            i2b2_pk  (on Term_id) for the i2b2 table.

Are we missing any index.

Regards

Arvinder

Mike Mendis <mmendis.partners> 2/10/2012 3:21 PM

Is this a upgrade or fresh install? If upgrade verify that the index on the metadata table exists.

mike

On 2/10/12 4:14 PM, "Arvinder Choudhary" <achoudhary.kumc> wrote:

Dear Team:

We went live with 1.6 and have already run over 500 queries on this version. One thing we have noticed is slowness while navigating the concept hierarchy. Specially under general Chemistry that has 90 concepts.

Laboratory Tests -> Chemistry -> General chemistry

The reason we have issue is that

1.) we have fast Fusion-IO cards (solid state storage) ,

2.) Oracle stats are run on all the tables under metadata schema.

3.) Most of hierarchial concepts that have less than 5 concept return within few seconds but this

General Chemistry takes over 30 seconds...

Below log shows the navigation started at 2012-02-10 10:26:20,733  and finished at 2012-02-10

10:26:59,271 49 seconds

information from debug.log

{{

Unknown macro: {\ 2012-02-10 10}

}}

Please Advice

Regards

Arvinder Choudhary, BE MS PMP

Medical informatics Project Director

University of Kansas Medical Center

3901 Rainbow Blvd, KS 66160

(913) 945-6922 Tel

(913) 588-0252 Fax



NEXT EMAIL

From:  Bhargav Adagarla [badagarla.kumc]

Sent:   Friday, February 10, 2012 4:56 PM

To:       i2b2 AUG Members

Subject:         Index OBFACT_PATCON_SDED_NVTV_IDX: Missing?

Dear Members,

We are trying to tune performance, after upgrading to I2B2 1.602. For example, we have noticed slower performance when using an analysis tool like the timeline for a large number of patients. The following is a query generated in such a case. We isolated it from the application logs. Please note the hint at the very beginning that mentions the index, OBFACT_PATCON_SDED_NVTV_IDX. We do not see any such index, including in the I2B2 database scripts!!

Does any one else have this issue?

SELECT a.* FROM i2b2datab.observation_FACT obs , (SELECT a.*

FROM (SELECT

/+ index (obs OBFACT_PATCON_SDED_NVTV_IDX)/

obs.encounter_num obs_encounter_num, obs.patient_num obs_patient_num,

obs.concept_cd obs_concept_cd, obs.provider_id obs_provider_id, obs.start_date obs_start_date , obs.modifier_cd obs_modifier_cd, obs.instance_num obs_instance_num , obs.valtype_cd obs_valtype_cd,

obs.tval_char obs_tval_char, obs.nval_num obs_nval_num, obs.valueflag_cd obs_valueflag_cd, obs.quantity_num obs_quantity_num, obs.units_cd obs_units_cd, obs.end_date obs_end_date,

obs.location_cd obs_location_cd, obs.confidence_num obs_confidence_num , concept_lookup.name_char concept_name, provider_lookup.name_char provider_name, modifier_lookup.name_char modifier_name ,

location_lookup.name_char location_name ,

'\\TR_GHC\i2b2\naaccr\S:1 Cancer Identification\0390 Date of Diagnosis\' panel_name FROM

( SELECT concept_cd FROM i2b2datab.concept_dimension WHERE concept_path like '\i2b2\naaccr\S:1 Cancer

Identification\0390 Date of Diagnosis%' group by concept_cd          ) dimension

, i2b2datab.observation_FACT obs

left JOIN i2b2datab.code_lookup modifier_lookup

ON (obs.modifier_cd = modifier_lookup.code_Cd AND modifier_lookup.column_cd = 'MODIFIER_CD')

left JOIN i2b2datab.concept_dimension concept_lookup

ON (obs.concept_cd = concept_lookup.concept_Cd)

left JOIN i2b2datab.provider_dimension provider_lookup

ON (obs.provider_id = provider_lookup.provider_id)

left JOIN i2b2datab.code_lookup location_lookup

ON (obs.location_Cd = location_lookup.code_Cd AND location_lookup.column_cd = 'LOCATION_CD') WHERE

obs.patient_num IN  ( select pset.patient_num from i2b2datab.qt_patient_set_collection pset where pset.result_instance_id = :patient_set and pset.set_index between 1 and 1000 )

AND obs.concept_cd = dimension.concept_cd

ORDER BY 2,5,3,7,6) a

) a where obs.encounter_num = a.obs_encounter_num and obs.patient_num = a.obs_patient_num and obs.concept_cd = a.obs_concept_cd and obs.provider_id = a.obs_provider_id and obs.start_date = a.obs_start_date

and obs.modifier_cd = a.obs_modifier_cd and obs.instance_num = a.obs_instance_num

Thanks.

Regards,

Adagarla, Bhargav Srinivas

Clinical Application Administrator

University of Kansas-Medical Center



NEXT EMAIL

From:  Peter Beninato [beninato.ohsu]

Sent:   Friday, February 10, 2012 10:02 AM

To:       Murphy, Shawn N.; Mendis, Michael E.; Lisa Miao; i2b2 AUG Members

Subject:         RE: occurrence > 1 bug

Whew! Thanks for the clarification! ;-)

From: Murphy, Shawn N. [SNMURPHY.PARTNERS]

Sent: Friday, February 10, 2012 5:56 AM

To: Peter Beninato; Mendis, Michael E.; Lisa Miao; i2b2 AUG Members

Subject: RE: occurrence > 1 bug

(that's the TBI-CRI AMIA, not the fall one)

Shawn.

From: Peter Beninato [beninato.ohsu]

Sent: Thursday, February 09, 2012 10:56 AM

To: Mendis, Michael E.; Lisa Miao; i2b2 AUG Members

Subject: RE: occurrence > 1 bug

Hi Mike,

Is there an estimated delivery date when v1.6.03 will be released? Thanks.

Peter

From: Mike Mendis [mmendis.partners]

Sent: Thursday, February 09, 2012 7:00 AM To: Lisa Miao; i2b2 AUG Members Subject: Re: occurrence > 1 bug

Lisa,

Sorry about the bug, in our current testing we recently also discovered this. The fix will be part of 1.6.03. Thanks again

mike

On 2/9/12 9:46 AM, "Lisa Miao" <lmiao.regenstrief> wrote:

Dear i2b2 team,

When we run an "occur > 1" query (in the constrain panel), the following SQL was executed:

select   patient_num ,1 as panel_count from (

select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num from observation_fact

where concept_cd IN (select concept_cd from concept_dimension

where concept_path like '\i2b2\VITALS\VITALS CLINIC\BP Dias Sitting%')

group by  patient_num having count( distinct patient_num || encounter_num || instance_num ||

concept_cd || cast(start_date  varchar(50) ) ) >= 2 ) t;

The above SQL is an invalid SQL statement, Oracle will say "missing keyword".

The offender is cast(start_date varchar(50) ). We are missing the word "as". It should be: cast(start_date as varchar(50) ).

At first I thought it was an Oracle version issue (we are running 11g), but by issuing the same command to an 10g server, I got the same error.

Please validate whether or not what I'm saying is the situation for everyone else, and if so, I can submit a bug report. Thanks,

Lisa.



NEXT EMAIL

From:  Murphy, Shawn N.

Sent:   Friday, February 10, 2012 8:54 AM

To:       Peter Beninato; Mendis, Michael E.; Lisa Miao; i2b2 AUG Members

Subject:         RE: occurrence > 1 bug

Hi Peter,

We are looking a the beginning of March, definitely before AMIA. Thanks,

Shawn.

From: Peter Beninato [beninato.ohsu]

Sent: Thursday, February 09, 2012 10:56 AM

To: Mendis, Michael E.; Lisa Miao; i2b2 AUG Members

Subject: RE: occurrence > 1 bug

Hi Mike,

Is there an estimated delivery date when v1.6.03 will be released? Thanks.

Peter

From: Mike Mendis [mmendis.partners]

Sent: Thursday, February 09, 2012 7:00 AM To: Lisa Miao; i2b2 AUG Members Subject: Re: occurrence > 1 bug

Lisa,

Sorry about the bug, in our current testing we recently also discovered this. The fix will be part of 1.6.03. Thanks again

Mike

On 2/9/12 9:46 AM, "Lisa Miao" <lmiao.regenstrief> wrote:

Dear i2b2 team,

When we run an "occur > 1" query (in the constrain panel), the following SQL was executed:

select   patient_num ,1 as panel_count from (

select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num

from observation_fact

where  concept_cd IN (select concept_cd

from concept_dimension

where concept_path like '\i2b2\VITALS\VITALS CLINIC\BP Dias Sitting%')

group by  patient_num having count( distinct patient_num || encounter_num || instance_num ||

concept_cd || cast(start_date  varchar(50) ) ) >= 2 ) t;

The above SQL is an invalid SQL statement, Oracle will say "missing keyword".

The offender is cast(start_date varchar(50) ). We are missing the word "as". It should be: cast(start_date as varchar(50) ).

At first I thought it was an Oracle version issue (we are running 11g), but by issuing the same command to an 10g server, I got the same error.

Please validate whether or not what I'm saying is the situation for everyone else, and if so, I can submit a bug report. Thanks,

Lisa.



NEXT EMAIL

From:  Murphy, Shawn N.

Sent:   Thursday, February 09, 2012 9:17 PM

To:       Steward, Duane; i2b2 AUG Members

Subject:         RE: What is the difference between Note-enabled LDS access and PHI-enabled access?

Hi Duane,

I think the demo set up to show some of the decryption of the notes with the Workbench, but the true demo with resolution of names (and the 16 other HIPAA PHI non-LDS elements) will not come until version 1.7 with the identity management cell.

Thanks, Shawn.

From: Steward, Duane [dsteward.NEMOURS]

Sent: Thursday, February 09, 2012 6:58 PM

To: i2b2 AUG Members

Subject: What is the difference between Note-enabled LDS access and PHI-enabled access?

When I compare data exported from the i2b2 demo data with Note-enabled access to the same with PHI-enabled access I don't see any difference, particularly with respect to the patient number. What is the difference between these two levels supposed to be? Does the demo data set in any way illustrate replaced PHI at some level of access compared to PHI-enabled access?

Duane Steward, DVM, MSIE, PhD Chief Computer Scientist for Health Informatics Nemours

Office: (407) 650-7675

Cell: (407) 230-6081

Fax: (407) 650-7722

From: Lisa Miao [lmiao.regenstrief]

Sent: Monday, January 30, 2012 2:37 PM

To:  i2b2 AUG Members

Subject: which role will allow user to see patient set

Does anyone know which role will allow a user to be able to bring back patient set? I have a user that has "DATA_AGG" role, but can NOT see patient set.

Looking through the document, it seems like the next level is admin. Is it true only ADMIN can see patient set? Is there something in between?

Thanks, Lisa.



NEXT EMAIL

From:  Wei,Xintao [XWEI.uchc]

Sent:   Thursday, February 09, 2012 12:00 PM

To:       i2b2 AUG Members

Subject:         limit a query when few patients returned

Hi,

How can I limit the query on I2B2 when the number of patients are less than 10? We don't want to run the query and report results to users when a query gets less than 10 patients.

For example, a query will return 5 patients. When a user send the query on I2B2, I2B2 can popup a message, something like "Query is denied because too small number of patients will be returned".

How can we setup I2B2 to limit those queries? Or any suggestions? Thank you, Xintao



NEXT EMAIL

From:  Lisa Miao [lmiao.regenstrief]

Sent:   Thursday, February 09, 2012 11:27 AM

To:       'Peter Beninato'; i2b2 AUG Members

Subject:         RE: occurrence > 1 bug --> encounter_num in concatenation

Peter,

That is a really good point.

I was NOT linking anything related to encounter.

And I agreed with you also, I don't see why encounter_num should be part of the concatenation. Perhaps anyone from i2b2 team could explain?

Thanks, Lisa.

From: Peter Beninato [beninato.ohsu]

Sent: Thursday, February 09, 2012 11:04 AM

To: Lisa Miao; i2b2 AUG Members

Subject: RE: occurrence > 1 bug --> encounter_num in concatenation

Hi Lisa,

In regards to your example below, I see that encounter_num is included in the concatenation. Were you linking "financial encounters" together amongst the panels?

If so, then I can see the reasoning of including the encounter_num in the concatenation.

If you weren't linking panels by encounter, then this might warrant additional investigation, in that it might be of interest that the concept recurs for the patient, but not necessarily on the same encounter(or for that matter instance_num?).

In which case, encounter_num(instance_num) should not be part of concatenation?

Peter

From: Lisa Miao [lmiao.regenstrief]

Sent: Thursday, February 09, 2012 6:47 AM

To:  i2b2 AUG Members

Subject: occurrence > 1 bug

Dear i2b2 team,

When we run an "occur > 1" query (in the constrain panel), the following SQL was executed:

select  patient_num ,1 as panel_count from (

select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num from observation_fact

where concept_cd IN (select concept_cd

from concept_dimension

where concept_path like '\i2b2\VITALS\VITALS CLINIC\BP Dias Sitting%')

group by   patient_num having count( distinct patient_num || encounter_num ||

instance_num || concept_cd || cast(start_date varchar(50) ) ) >= 2 ) t;

The above SQL is an invalid SQL statement, Oracle will say "missing keyword".

The offender is cast(start_date varchar(50) ). We are missing the word "as". It should be: cast(start_date as

varchar(50) ).

At first I thought it was an Oracle version issue (we are running 11g), but by issuing the same command to an 10g server, I got the same error.

Please validate whether or not what I'm saying is the situation for everyone else, and if so, I can submit a bug report. Thanks,

Lisa.



NEXT EMAIL

From:  Henderson, Darren W [darren.henderson.uky]

Sent:   Tuesday, February 07, 2012 10:38 AM

To:       McMurry, Andrew J.; i2b2 AUG Members

Subject:         RE: Preferred Rx Hiearchy

Ah, thank you for the rapid response. We were just beginning to investigate SHRINE ourselves.

From: McMurry, Andrew J. [Andrew_McMurry.hms.harvard]

Sent: Tuesday, February 07, 2012 10:23 AM

To: Henderson, Darren W

Cc: i2b2 AUG Members

Subject: Re: Preferred Rx Hiearchy

In SHRINE, we used RxNorm with the NDF-RT hierarchy. [https://open.med.harvard.edu/display/SHRINE/Core+Ontology
]

hope this helps,

andy

On Feb 7, 2012, at 10:16 AM, Henderson, Darren W wrote:

Good morning AUG. I would like to get some feedback on what drug hierarchy is typically preferred in the community. We're working on medications now and need a good ontology for looking up medications.

Darren W. Henderson

Institute for Pharmaceutical Outcomes and Policy Center for Clinical and Translational Science Division for Biomedical Informatics

University of Kentucky

789 S. Limestone Rm. 182

Lexington, KY 40536 (859) 323-7146

(859) 967-4914



NEXT EMAIL

From:  Schulte, Gregory [Gregory.Schulte.childrenscolorado]

Sent:   Monday, February 06, 2012 5:59 PM

To:       i2b2 AUG Members members Subject:   Principal vs Principle Diagnosis

We are testing some of our modifier queries in version 1.6.02 and we weren't getting any count back for "Principal

Diagnosis".

From this we noticed a little issue with the modifier insert script.

Looking at the SQL in the query master table that was produced from our principal diagnose query, it was trying to pull the modifier_cd for "Principal Diagnosis" and nothing was returning.

select MODIFIER_CD from i2b2demodata.MODIFIER_DIMENSION

where MODIFIER_PATH LIKE '\Principal Diagnosis%' )

The modifier_dimension table is populated with "Principle" instead of "Principal" in the SQL Server script :

modifier_dimension_insert_data.sql

INSERT INTO MODIFIER_DIMENSION(MODIFIER_PATH, MODIFIER_CD, NAME_CHAR, MODIFIER_BLOB, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, UPLOAD_ID)

VALUES('\Principle Diagnosis\', '1', 'Principle Diagnosis', '', '20110414

00:55:00.0', NULL, '20110414 00:55:00.0', 'DEMO', NULL);

Editing the entry to "Principal" in the table solved our issue, but thought I'd send an email to the group in case anyone else runs into the issue.

Thanks,

Greg Schulte | Clinical Research Data Warehouse Database Analyst

13123 East 16th Avenue, Box 485 | Aurora, CO 80045

Phone: 720.777.5740 |  Gregory.Schulte.childrenscolorado



NEXT EMAIL

From:  John Reber [John.P.Reber.KimmelCancerCenter]

Sent:   Monday, February 06, 2012 12:52 PM

To:       Steward, Duane

Cc:      i2b2 AUG Members; Schulte, Gregory; Jack London

Subject:         Re: jboss startup warning

With pointers from Greg, we are now error free by adding these two tables to our i2b2hive (This is an Oracle

Database)

Tow tables that I added:

1:

create table i2b2hive.HILOSEQUENCES (SEQUENCENAME varchar(50) not null, HIGHVALUES

integer not null, constraint hilo_pk primary key (SEQUENCENAME))

2: ( I had to change BIGINT to NUMBER and VARBINARY to BLOB from Greg's examples) CREATE  TABLE i2b2hive.TIMERS(TIMERID VARCHAR(80) NOT NULL,TARGETID VARCHAR(250) NOT NULL,INITIALDATE TIMESTAMP NOT NULL,TIMERINTERVAL NUMBER,INSTANCEPK BLOB,INFO BLOB,CONSTRAINT TIMERS_PK PRIMARY KEY(TIMERID,TARGETID))

John Reber

On Feb 6, 2012, at 12:48 PM, Steward, Duane wrote:

I am very interested in the results of this quandary. We too are getting the same thing Jack London is whenever we startup JBoss running on Red Hat 6.1 hosting a version 1.602 i2b2 instance.

My additional observations:

         i2b2 seems work despite the logged exceptions

       A cascade of WARNings ensue all having in common the "Unable to get timer handles for containerId:" of various named beans

        This cascade follows a failure to create the timer table

12:16:29,381 ERROR [GeneralPurposeDatabasePersistencePlugin] Cannot create timer table

java.lang.IllegalStateException: Cannot obtain type mapping from:

jboss.jdbc:datasource=DefaultDS,service=metadata

at org.jboss.ejb.txtimer.GeneralPurposeDatabasePersistencePlugin.creat eTableIfNotExists(GeneralPurposeDatabasePersistencePlugin.java:13

7)

[. . . ]

Duane Steward, DVM, MSIE, PhD Chief Computer Scientist for Health Informatics Nemours

Office: (407) 650-7675

Cell: (407) 230-6081

Fax: (407) 650-7722

From: Schulte, Gregory [Gregory.Schulte.childrenscolorado] Sent: Monday, February 06, 2012 12:10 PM

To: 'Jack London'

Cc: i2b2 AUG Members members; John Reber

Subject: RE: jboss startup warning

From the ejb-deployer.xml

<mbean code="org.jboss.ejb.txtimer.DatabasePersistencePolicy">

<!- DataSourceBinding ObjectName ->

<depends optional-attribute-

name="DataSource">jboss.jca:service=DataSourceBinding,name=DefaultDS</depends>

<!- The plugin that handles database persistence ->

<attribute>org.jboss.ejb.txtimer.GeneralPurposeDatabasePers istencePlugin</attribute>

<!- The timers table name ->

<attribute>TIMERS</attribute>

</mbean>

Take a look for the TIMERS table under DefaultDS datasource (same place as the hilosequences table)

Not sure where the create DDL statement is for that table though.

Greg

From: Jack London [jack.london.KimmelCancerCenter] Sent: Monday, February 06, 2012 9:54 AM

To: Schulte, Gregory

Cc: i2b2 AUG Members members; John Reber

Subject: Re: jboss startup warning

Greg,

Thanks for your help.

We created the HILOSEQUENCES table in I2B2HIVE and that error did not recur. However, we now get another notice of a missing table/view:

10:14:54,174 INFO  [DLQ] Bound to JNDI name: queue/DLQ

10:14:54,297 INFO  [ConnectionFactoryBindingService] Bound ConnectionManager

'jboss.jca:service=ConnectionFactoryBinding,name=JmsXA' to JNDI name 'java:JmsXA'

10:14:54,465 INFO  [ConnectionFactoryBindingService] Bound ConnectionManager

'jboss.jca:service=DataSourceBinding,name=OntologyBootStrapDS' to JNDI name

'java:OntologyBootStrapDS'

10:14:54,477 INFO  [ConnectionFactoryBindingService] Bound ConnectionManager

'jboss.jca:service=DataSourceBinding,name=OntologyDemoDS' to JNDI name

'java:OntologyDemoDS'

10:14:54,489 INFO  [ConnectionFactoryBindingService] Bound ConnectionManager

'jboss.jca:service=DataSourceBinding,name=OntologyKCCDS' to JNDI name

'java:OntologyKCCDS'

10:14:54,570 INFO  [ConnectionFactoryBindingService] Bound ConnectionManager

'jboss.jca:service=DataSourceBinding,name=PMBootStrapDS' to JNDI name

'java:PMBootStrapDS'

10:14:54,707 INFO  [ConnectionFactoryBindingService] Bound ConnectionManager

'jboss.jca:service=DataSourceBinding,name=WorkplaceBootStrapDS' to JNDI name

'java:WorkplaceBootStrapDS'

10:14:54,716 INFO  [ConnectionFactoryBindingService] Bound ConnectionManager

'jboss.jca:service=DataSourceBinding,name=WorkplaceDemoDS' to JNDI name

'java:WorkplaceDemoDS'

10:14:54,719 INFO  [ConnectionFactoryBindingService] Bound ConnectionManager

'jboss.jca:service=DataSourceBinding,name=WorkplaceKCCDS' to JNDI name

'java:WorkplaceKCCDS'

10:14:56,846 INFO  [JmxKernelAbstraction] creating wrapper delegate for:

org.jboss.ejb3.stateless.StatelessContainer

10:14:56,851 INFO  [JmxKernelAbstraction] installing MBean: jboss.j2ee:jar=CRCLoader-EJB.jar,name=DataMartLoader,service=EJB3 with dependencies:

10:14:56,927 INFO  [EJBContainer] STARTED EJB:

edu.harvard.i2b2.crc.loader.ejb.DataMartLoader ejbName: DataMartLoader

10:14:56,944 WARN           [DatabasePersistencePolicy] Unable to get timer handles for containerId: jboss.j2ee:service=EJB3,jar=CRCLoader-EJB.jar,name=DataMartLoader

java.sql.SQLException: ORA-00942: table or view does not exist

Any suggestions? Jack

On Feb 6, 2012, at 9:21 AM, Schulte, Gregory wrote:

I think it's looking for the HILOSEQUENCES table that is created under your

DefaultDS data source.

The create statement for the table is in the jboss-service.xml file located under $JBOSS_HOME/all/deploy/uuid-key-generator.sar/META-INF/

Greg

From: Jack London [jack.london.KimmelCancerCenter]

Sent: Friday, February 03, 2012 2:48 PM

To: i2b2 AUG Members members

Subject: jboss startup warning

Does anyone know the cause of this warning that appears in the jboss log upon starting up i2b2:

WARN            [ServiceController]   Problem starting service jboss:service=KeyGeneratorFactory,type=HiLo

java.sql.SQLException: ORA-00942: table or view does not exist

John Reber

John.P.Reber.KimmelCancerCenter



NEXT EMAIL

From:  Mendis, Michael E.

Sent:   Monday, February 06, 2012 11:07 AM

To:       Lisa Miao; i2b2 AUG Members

Subject:         Re: VM-image

Lisa,

The VM instructions that are provided are for windows VM Server, but the actual vm image can be used with VM Fusion (Mac) or VM Server for Linux. If using VM Server (Linux), the instructions are very similar.

mike

On 2/6/12 11:01 AM, "Lisa Miao" <lmiao.regenstrief> wrote: Dear I2b2 team,

When I look at the VM image provided for release 1.6.02, it looks like it is only for Window platform. Do we have an image for linux? We used to have linux VM image, didn't we?

Thanks,

Lisa.



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From:  Lisa Miao [lmiao.regenstrief]

Sent:   Friday, February 03, 2012 9:55 AM

To:       i2b2 AUG Members

Subject:         occurrence query in constrain panel

Dear all,

Has anyone successfully executed a query which specifies the occurrence (for instance occurrence > 1) in the constraining panel (the one under "Group 1", "Group 2" etc in the query tool window)?

I am getting the following error which eventually seems to boil down to the SQL error of "missing keyword". Thanks,

Lisa.

09:47:47,167 INFO [CRCDAO] Trying to update error status to query instance[57420]

09:47:47,224 INFO [CRCDAO] Updated error status to query instance[57420]

09:47:47,224 ERROR [ExecRunnable] Error while executing sql

edu.harvard.i2b2.common.exception.I2B2DAOException: Error while executing sql

at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorHelperDao.executeQuery(Unknown Source)

at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorDao.executeSQL(Unknown Source)

at edu.harvard.i2b2.crc.ejb.ExecRunnable.processQueryRequest(Unknown Source)

at edu.harvard.i2b2.crc.ejb.ExecRunnable.execute(Unknown Source)

at edu.harvard.i2b2.crc.ejb.QueryExecutorMDB.onMessage(Unknown Source)

at edu.harvard.i2b2.crc.ejb.QuerySmallExecutorMDB.onMessage(Unknown Source)

at sun.reflect.GeneratedMethodAccessor163.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:597)

at org.jboss.invocation.Invocation.performCall(Invocation.java:359)

at org.jboss.ejb.MessageDrivenContainer$ContainerInterceptor.invoke(MessageDrivenContainer.java:495)

at org.jboss.resource.connectionmanager.CachedConnectionInterceptor.invoke(CachedConnectionInterceptor.java:158)

at org.jboss.ejb.plugins.CallValidationInterceptor.invoke(CallValidationInterceptor.java:63)

at org.jboss.ejb.plugins.AbstractTxInterceptor.invokeNext(AbstractTxInterceptor.java:121)

at org.jboss.ejb.plugins.AbstractTxInterceptorBMT.invokeNext(AbstractTxInterceptorBMT.java:173)

at org.jboss.ejb.plugins.MessageDrivenTxInterceptorBMT.invoke(MessageDrivenTxInterceptorBMT.java:47)

at org.jboss.ejb.plugins.MessageDrivenInstanceInterceptor.invoke(MessageDrivenInstanceInterceptor.java:116)

at org.jboss.ejb.plugins.RunAsSecurityInterceptor.invoke(RunAsSecurityInterceptor.java:109)

at org.jboss.ejb.plugins.LogInterceptor.invoke(LogInterceptor.java:205)

at org.jboss.ejb.plugins.ProxyFactoryFinderInterceptor.invoke(ProxyFactoryFinderInterceptor.java:138)

at org.jboss.ejb.MessageDrivenContainer.internalInvoke(MessageDrivenContainer.java:402)

at org.jboss.ejb.Container.invoke(Container.java:960)

at org.jboss.ejb.plugins.jms.JMSContainerInvoker.invoke(JMSContainerInvoker.java:987)

at org.jboss.ejb.plugins.jms.JMSContainerInvoker$MessageListenerImpl.onMessage(JMSContainerInvoker.java:1287)

at org.jboss.jms.asf.StdServerSession.onMessage(StdServerSession.java:266)

at org.jboss.mq.SpyMessageConsumer.sessionConsumerProcessMessage(SpyMessageConsumer.java:891)

at org.jboss.mq.SpyMessageConsumer.addMessage(SpyMessageConsumer.java:170)

at org.jboss.mq.SpySession.run(SpySession.java:323)

at org.jboss.jms.asf.StdServerSession.run(StdServerSession.java:194)

at EDU.oswego.cs.dl.util.concurrent.PooledExecutor$Worker.run(PooledExecutor.java:761)

at java.lang.Thread.run(Thread.java:619)

Caused by: java.sql.SQLException: ORA-00905: missing keyword



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From:  Lusted, Jeff [jl99.leicester.ac.uk]

Sent:   Thursday, February 02, 2012 6:37 AM

To:       i2b2 AUG Members

Subject:         RE: Web service based upload of data...

Hi Colleagues!

Regarding the failure of the crc_loader to deal with loading data into the patient_dimension. I've been code reading the loader (v1.5.4 and v1.6)...

There appears to be at least two problems with the code.

The CRCLoaderDAO uses the attribute Name rather than Column as a source of keys to establish a map of params (see method buildNVParam(List<ParamType> paramTypeList) ). When this map is used within the PatientDAO it uses constants which reflect the column names, so nothing is found within the map. When the CRCLoaderDAO is changed, things start to appear. But...

The PatientDAO has not been adjusted to use dates correctly. It tries to load plain string data as an SQL timestamp, and then fails.

I've attached code changes to the CRCLoaderDAO and PatientDAO (based upon v1.5.4). After making these changes the patient_dimension loads correctly, as far as I can see. Patient_dimension OK, but I still have no rows inserted within the visit_dimension.

I'll raise these on the bug tracker too. Regards

Jeff

Jeff Lusted,

Senior Programmer (RCS, IT Services)

University of Leicester

Mob: 07941599062

Glenfield contact: 0116-2583792

Email: jl99.le.ac.uk

Elite Without Being Elitist

Times Higher Awards Winner 2007, 2008, 2009, 2010

Follow us on Twitter [http://twitter.com/uniofleicsnews
]

From: Lusted, Jeff

Sent: 01 February 2012 12:37

To: i2b2 AUG Members

Subject: Web service based upload of data...

Hi Colleagues! Help!

I've been working on producing a command line upload facility which uses the inbuilt web services route to import PDO data into i2b2. This looks an attractive route as we have a need to make small, regular imports of data based around a questionnaire. The questionnaire gains patient consent (required in the UK) as well as providing a fair amount of further information. For us this is what kicks off entry of a patient into i2b2. The plan is to augment this with further data from clinical systems once consent (and basic data) has been loaded.

Having the facility as a command line utility enables us to script the upload so that it can be automated.

I've studied the workbench import plugin to gain knowledge of how to do this. And so far we have a utility which can logon to the PM cell, upload a PDO file to the File Repository cell, and trigger the CRC loader to process the file. I'm particularly taken with the idea of the hive allocating it's own internal identifiers for new patients, although indeed we have tried two forms of PDO: one with i2b2 identifiers explicitly set (patient_num and encounter_num with HIVE as a source), and one where we are leaving the CRC loader to do the allocating and the sources within the PDO are only external.

We are encountering problems whichever form of PDO we try. Both have the same failures for the same tables: (a) Patient_Mapping is perfect as far as I can see.

(b) Encounter_Mapping could be OK. Each row seems to lack the patient-id and its source. But the encounter-id and its source are there.

(c) Patient_Dimension. All the optional columns are null when they shouldn't be (eg: Birth_Date, Sex_Cd,

Age_In_Years_Num etc).

(d) Visit_Dimension is empty when it shouldn't be.

(e) Observation_Fact is perfect as far as I can see. Everything recorded as it should be.

This is annoying, because the two tables which look the most difficult to get correct, are correct as far as I can see. Looking at the relevant temporary tables:

(1) The temporary eid mapping (corresponding to point b above) has the same data in it.

(2) The temporary patient (point c above) has the same data in it: all the optional columns are null, and is clearly wrong. (3) The temporary visit (point d above) is not empty and maybe as it should be (although it is missing the internally allocated encounter_num)

I've re-read the documentation. I've looked at the example PDO's.

I've examined the programme that sends the PDO with it's processing options. This is the relevant section of code:

LoadOptionType loType = new LoadOptionType() ; loType.setEncryptBlob( false ) ; loType.setIgnoreBadData( true ) ;

FactLoadOptionType floType = new FactLoadOptionType() ;

 appendFlag is supplied by the command line args... floType.setAppendFlag( this.appendFlag ) ;

 NOTES:

 (1) Need to consider the possible differences here.

 (2) ObserverSet is not requested. loadType.setLoadPidSet( loType ) ;

loadType.setLoadObservationSet( floType ) ; loadType.setLoadEidSet( loType ) ; loadType.setLoadEventSet( loType ) ; loadType.setLoadPatientSet( loType ) ;

I cannot see many clues of where we are going wrong at the moment. Given the order of processing, it could be the encounter mapping or the patient dimension that is letting us down.

As an alternative to using the web service upload, we have another scripted route that uses an XSLT transform of the PDO to generate SQL insert commands. This is our fall-back position. When we try this alternative route we get usable data within i2b2, so this somewhat validates our PDO formatting procedure.

I've attached

(1) an example PDO (one where we expect the hive to do the allocating of internal ids) with most of the observation facts removed for brevity.

(2) a printout showing the relevant CRC tables that result from the web service process.

(3) a printout showing three of the temporary tables.

Any pointers of where I'm going wrong, or even where to look, would be welcome. We are on version i2b2 v1.5.2, and are using schema v1.1 of the PDO.

Kindest regards

Jeff

Jeff Lusted,

Senior Programmer (RCS, IT Services) University of Leicester

Mob: 07941599062

Glenfield contact: 0116-2583792

Email: jl99.le.ac.uk

Elite Without Being Elitist

Times Higher Awards Winner 2007, 2008, 2009, 2010

Follow us on Twitter [http://twitter.com/uniofleicsnews
]

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