Last Updated: 12/29/2011
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From: Mendis, Michael E. Sent: Thursday, December 29, 2011 10:51 AM To: Peter Beninato; i2b2 AUG Members Subject: Re: SOLUTION -i2b2 - v1.6_02 - webclient - admin - Requires ADMIN role
Peter,
Glad that it working for you now. We are in the process of updating some the documentation based on your experience to make it easier to understand for other users.
Thanks again
mike
From: Peter Beninato Sent: Wednesday, December 28, 2011 7:20 PM To: Peter Beninato; i2b2 AUG Members Subject: RE: SOLUTION -i2b2 - v1.6_02 - webclient - admin - Requires
ADMIN role
Whoops... if this step is necessary...
Step 3) Edit index.php
//$pmURL = "http://127.0.0.1:8080/i2b2/rest/PMService/getServices";
$pmURL = "http://127.0.0.1:9090/i2b2/rest/PMService/getServices";
Peter
On 12/28/11 6:37 PM, Peter Beninato wrote:
Hi,
Below are the steps to get the ADMIN site available via the thinclient. Please note that some of the
scripting (sql) is geared for Oracle, but easily modified.
Please consider modifying the code for future editions so others won't have to struggle with this.
For instance, the INSERT does not exist in:
i2b2\v1_6_02\i2b2createdb?1602\edu.harvard.i2b2.data\Release_1?6\NewInstall\Pmdata\scripts or i2b2\v1_6_02\i2b2createdb?1602\edu.harvard.i2b2.data\Release_1?6\Upgrade\Pmdata\scripts
Also the project_management_installation_guide.pdf should probably be edited too.
The steps to get the ADMIN site via the thin client is as follows:
1) INSERT INTO I2B2PM.PM_PROJECT_USER_ROLES
2) Edit the file: i2b2\v1_6_02\i2b2core?src?1602\src\admin\i2b2_config_data.js (before deployment or the same file under the apache server after deployment) for the parameters: domain, name, urlCellPM
Step 1(code):
INSERT INTO I2B2PM.PM_PROJECT_USER_ROLES
(
PROJECT_ID,
USER_ID,
USER_ROLE_CD,
CHANGE_DATE,
ENTRY_DATE,
CHANGEBY_CHAR,
STATUS_CD
)
VALUES
(
'@' ,
'i2b2' ,
'ADMIN' ,
sysdate ,
sysdate ,
'i2b2' ,
'A'
);
Commit;
Step2:
domain: have this parameter match the value in i2b2pm.pm_hive_data.domain_name
name: set this to "localhost"
ulrCellPM: http://localhost:9090/i2b2/rest/PMService/
Below is example admin/i2b2_config_data.js:
{
urlProxy: "index.php",
urlFramework: "js?i2b2/",
//??????????????????????????????????????????????????????????????????????????????????????????
// THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO
lstDomains: [
{ domain: "i2b2demo",
name: "localhost",
urlCellPM: "http://localhost:9090/i2b2/rest/PMService/",
allowAnalysis: false,
adminOnly: true,
debug: true
}
]
//??????????????????????????????????????????????????????????????????????????????????????????
}
Peter Beninato - OCTRI DW Developer Oregon Health & Science University
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From: Peter Beninato [beninato.ohsu] Sent: Wednesday, December 28, 2011 2:50 PM To: Mendis, Michael E.; Michael.C.Ford.kp Cc: i2b2 AUG Members Subject: RE: i2b2 - v1.6_02 - webclient - admin - Requires ADMIN role
Webclient update... Not sure this was valid test?
When I look at the webclient i2b2_config_data.js, it seems that the urlCellPM is pointing to i2b2.org, and not a localhost.
I just copied over the webclient folder, let me troll through the documentation to see what I might need to edit.
urlCellPM: "http://webservices.i2b2.org/i2b2/rest/PMService/",
From: Mike Mendis [mmendis.partners] Sent: Wednesday, December 28, 2011 11:01 AM To: Peter Beninato; Michael.C.Ford.kp Cc: i2b2 AUG Members Subject: Re: i2b2 - v1.6_02 - webclient - admin - Requires ADMIN role
The entries all look correct.
A few things, is this a new install or upgrade? Can you log into the regular webclient without issues? If not, try install curl. Also is php installed on the linux machine
mike
On 12/28/11 1:55 PM, "Peter Beninato" <beninato.ohsu> wrote:
Hi,
I'm wondering if the "@" entry in PM_PROJECT_USER_ROLES for "i2b2" needs anything else like "USER" too? And/or if I should DELETE other entries for "i2b2" from that table?
Below is my i2b2_config_data.js. I changed domain to "i2b2" since that was the domain_id in pm_hive_data. I can change it back. The domain_name is "i2b2demo"
I have also edited the index.php for $pmURL, and added this line, "http://localhost:9090/i2b2/rest/",
to the $WHITELIST.
index.php
//$pmURL = "http://127.0.0.1:8080/i2b2/rest/PMService/getServices"; $pmURL = "http://127.0.0.1:9090/i2b2/rest/PMService/getServices";
i2b2_config_data.js
{
urlProxy: "index.php",
urlFramework: "js-i2b2/",
//------------------------------------------------------------------------------------------
// THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO
lstDomains: [
{ //domain: "i2b2demo",
domain: "i2b2",
name: "i2b2demo",
urlCellPM: "http://localhost:9090/i2b2/rest/PMService/",
allowAnalysis: false,
adminOnly: true,
debug: false
}
]
//------------------------------------------------------------------------------------------}
From: Mike Mendis [mmendis.partners] Sent: Wednesday, December 28, 2011 10:47 AM To: Peter Beninato; Michael.C.Ford.kp Cc: i2b2 AUG Members Subject: Re: i2b2 - v1.6_02 - webclient - admin - Requires ADMIN role
What does your i2b2_config_data.js look like. It does looks like port 9090 is the correct based on that response you got back from the jboss
On 12/28/11 1:28 PM, "Peter Beninato" <beninato.ohsu> wrote:
Hi,
Might there need to be some edits to index.php too?
Like the $pmURL? Should I change the port to 9090. Also, I don't see an entry in the $WHITELIST for something like http://localhost:9090/i2b2/rest
-
-
-
- FROM index.php ************************************* $pmURL = "http://127.0.0.1:8080/i2b2/rest/PMService/getServices"; $pmCheckAllRequests = false;
$WHITELIST = array( "http://", "http://127.0.0.1:9090/axis2/rest/", "http://localhost:9090/axis2/rest/", "http://127.0.0.1:7070/i2b2/rest/", "http://localhost:7070/i2b2/rest/", "http://webservices.i2b2.org", "https://webservices.i2b2.org"
);
From: Peter Beninato [beninato.ohsu] Sent: Wednesday, December 28, 2011 10:10 AM To: Mike Mendis; Michael.C.Ford.kp Cc: i2b2 AUG Members Subject: RE: i2b2 - v1.6_02 - webclient - admin - Requires ADMIN role
Hi,
After restarts still error.
When I go to http://localhost:9090/i2b2/services/listServices, I see the PM service:
Service EPR : http://localhost:9090/i2b2/services/PMService Service REST epr : http://localhost:9090/i2b2/services/PMService : http://localhost:9090/i2b2/rest/PMService
Service Description : PMService
Service Status : Active Available Operations
getVersion
getServices
However, if I enter URL from js config file: http://localhost:9090/i2b2/rest/PMService/
<soapenv:Fault><faultcode/><faultstring>I can not find a service for this request to be serviced. Check the WSDL and the request URI; nested exception is:
org.apache.axis2.AxisFault: I can not find a service for this request to be serviced. Check the WSDL and the request URI</faultstring><detail/></soapenv:Fault>
If I go to the Service EPR from the listServices: http://localhost:9090/i2b2/services/PMService
And below is what I see in JBOSS log?
09:50:31,141 INFO [Server] JBoss (MX MicroKernel) [4.2.2.GA (build: SVNTag=JBoss_4_2_2_GA date=200710221139)] Started n 26s:475ms 09:59:42,740 ERROR [AxisRESTServlet] org.apache.axis2.AxisFault: I can not find a service for this request to be servic
d. Check the WSDL and the request URI; nested exception is:
org.apache.axis2.AxisFault: I can not find a service for this request to be serviced. Check the WSDL and the re uest URI
From: Mike Mendis [mmendis.partners] Sent: Wednesday, December 28, 2011 9:49 AM To: Peter Beninato; Michael.C.Ford.kp Cc: i2b2 AUG Members Subject: Re: i2b2 - v1.6_02 - webclient - admin - Requires ADMIN role
Yes that could
Try poer 9090 for jboss
On 12/28/11 12:46 PM, "Peter Beninato" <beninato.ohsu> wrote:
Hi
In the file i2b2_config_data.js, there is the following line: urlCellPM: http://localhost:8080/i2b2/rest/PMService/
Port 8080 is mapped to OracleXE. I need to check JBOSS port/services... Could this be problem?
Peter
From: Peter Beninato [beninato.ohsu] Sent: Wednesday, December 28, 2011 9:39 AM To: Mike Mendis; Michael.C.Ford.kp Cc: i2b2 AUG Members Subject: RE: i2b2 - v1.6_02 - webclient - admin - Requires ADMIN role
Hi,
I did an insert for that entry. Restarted JBOSS/Apache. Even tried a different browser, in case there was cacheing.
Still get that error, about ADMIN role?
Peter
From: Mike Mendis [mmendis.partners] Sent: Wednesday, December 28, 2011 9:15 AM To: Peter Beninato; Michael.C.Ford.kp Cc: i2b2 AUG Members Subject: Re: i2b2 - v1.6_02 - webclient - admin - Requires ADMIN role
Yes it needs a project_id of '@'
On 12/28/11 12:11 PM, "Peter Beninato" <beninato.ohsu> wrote:
Hi,
Thanks. I'm installing/upgrading locally. I have user i2b2.
The user i2b2, had entries on two Project_ids: Demo and Demo2, where it has user_role_cd of ADMIN, and status_cd A.
Does there need to be an entry for a Project_ID of "@"?
Peter
From: Mike Mendis [mmendis.partners] Sent: Wednesday, December 28, 2011 9:07 AM To: Peter Beninato; Michael.C.Ford.kp Cc: i2b2 AUG Members Subject: Re: i2b2 - v1.6_02 - webclient - admin - Requires ADMIN role
Are you using the vm image or installing locally. Because the i2b2 account is the admin account and the password is demouser.
In order for a user to be a admin, they need to have the following in the pm_project_user_role table:
Project_ID @
user_id {the user in this case i2b2}
user_role_cd ADMIN
status_cd A
The only variable that would change is the user_id.
mike
On 12/28/11 11:55 AM, "Peter Beninato" <beninato.ohsu> wrote:
Hi,
I don't see a user "admin" in the table pm_user_data, but hey I'll try anything... ahhh, doesn't work.
Curiously, if I logon with "admin" or as i2b2 (which may have admin privledges) and a bad password (other than demouser), I get the same error regardless.
Several standard users have the same encrypted password, presumably "demouser".
Not sure.
Peter
From: Michael.C.Ford.kp [Michael.C.Ford.kp] Sent: Wednesday, December 28, 2011 8:39 AM To: Peter Beninato Cc: Peter Beninato; i2b2 AUG Members Subject: RE: i2b2 - v1.6_02 - webclient - admin - Requires ADMIN role
You may want to try user admin with the same password
Michael C. Ford
Application Development Project Manager
Kaiser Permanente
Division of Research 2000 Broadway Oakland, CA 94612
kp.org/thrive <http://kp.org/thrive>
Peter Beninato <beninato.ohsu> 12/28/2011 08:29 AM ToPeter Beninato <beninato.ohsu>, i2b2 AUG Members cc SubjectRE: i2b2 - v1.6_02 - webclient - admin - Requires ADMIN role
Hi,
I saw there were some emails about this: Rob Schuff 10/21/2011 Anandhi Sowmyan on 10/21/2011 Askar Ibragimov 11/29/2011
I reach the URL: http://localhost/admin <http://localhost/admin>
But I can't logon due to error: "Requires ADMIN role, please contact your system administrator."
Stuck/Stopped/Halted on installation of v1.6.02 until this can be resolved.
Have not found solution on WIKI.
Has anyone found a solution?
Peter
From: Peter Beninato Sent: Wednesday, December 21, 2011 1:04 PM To: i2b2 AUG Members Subject: i2b2 - v1.6_02 - webclient - admin - Requires ADMIN role
Hi,
Working through the local install. As part of the Project_Management_Installation_Guide, Step 4, I can reach the URL: http://localhost/admin <http://localhost/admin>
But when I logon as i2b2, I seem to get an error. In a pop-up it says:
"Requires ADMIN role, please contact your system administrator"
I thought I saw some email in regards to this error. Is there a column missing like "is_admin"?
Thanks for assistance in resolving.
Peter Beninato - OCTRI DW Developer Oregon Health & Science University 503-494-9985 beninato.ohsu <beninato.ohsu>
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From: Murphy, Shawn N. Sent: Wednesday, December 28, 2011 11:55 AM To: Peter Beninato; Mendis, Michael E.; Russ Waitman Cc: i2b2 AUG Members Subject: RESOLVED: i2b2 1.6 doesn't seem to run queires maide with i2b2 1.4
Hi Peter,
This issue was resolved and indeed was on that exact track, there were old queries that were unavailable in Russ' new instance whose master_id's were thus not present (just like the deleted queries). The error message is coming back correctly from the server, so to change the hanging behavior needs some web client programming.
Thanks, Shawn.
From: Peter Beninato [beninato.ohsu] Sent: Wednesday, December 28, 2011 11:36 AM To: Mendis, Michael E.; Russ Waitman; Murphy, Shawn N. Cc: i2b2 AUG Members Subject: RE: i2b2 1.6 doesn't seem to run queires maide with i2b2 1.4
Hi,
I saw a "known issue" regarding using old queries. Perhaps this issue is related?
Query: Using old "deleted" previous queries will cause web client to crash
https://community.i2b2.org/wiki/display/releases/1.6.02+Known+Issues
From: Dan Connolly [dconnolly.kumc] Sent: Thursday, December 22, 2011 9:24 AM To: Russ Waitman Cc: i2b2 AUG Members; Murphy, Shawn N. Subject: Re: i2b2 1.6 doesn't seem to run queires maide with i2b2 1.4
I think I found the problem, and it's on our end. It looks like we migrated our workplace data but not our QT tables from our 1.4 installation.
The log shows:
2011-12-22 08:06:17,553 ERROR [edu.harvard.i2b2.crc.dao.CRCDAO] Querydoesn't exists for masterId :[2103]
So I looked in the QT tables, and sure enough, the QT_QUERY_MASTER table doesn't have data corresponding to the queries that fail to run.
Mike, I'm attaching the XML message, just for reference.
From: Mendis, Michael E. [MMENDIS.PARTNERS] Sent: Thursday, December 22, 2011 5:22 AM To: Russ Waitman; Murphy, Shawn N. Cc: i2b2 AUG Members Subject: RE: i2b2 1.6 doesn't seem to run queires maide with i2b2 1.4
If you can provide a screenshot that would be great. Also if you post the XML messages.
thanks
mike
From: Russ Waitman [rwaitman.kumc] Sent: Thu 12/22/2011 3:06 AM To: Mendis, Michael E.; Murphy, Shawn N. Cc: i2b2 AUG Members Subject: RE: i2b2 1.6 doesn't seem to run queires maide with i2b2 1.4
It's all done with the webclient both when they were created in 1.4 and now being played back in 1.6. We'll try to get a screenshot but when you drag it over it goes into a single panel instead of rehydrating into the proper multipanel query.
Russ
"Mendis, Michael E." 12/21/11 9:41 PM
Russ,
When you created the queries in 1.4, where they done using the webclient or the eclipse workbench?
mike
From: Murphy, Shawn N. Sent: Tuesday, December 27, 2011 12:32 PM To: Russ Waitman Cc: Mendis, Michael E.; i2b2 AUG Members Subject: RE: i2b2 1.6 doesn't seem to run queries made with i2b2 1.4
Hi Russ,
We aren't able to reproduce 591, is it all the time or sporadic? If sporadic, any ideas about when it happens?
Thanks,
Shawn.
From: Russ Waitman [rwaitman.kumc] Sent: Wednesday, December 21, 2011 5:39 PM To: Russ Waitman; Murphy, Shawn N. Cc: i2b2 AUG Members Subject: Re: i2b2 1.6 doesn't seem to run queries made with i2b2 1.4
The only other bug that we've verified is still there is
Ticket 591 i2b2 hangs when you modify the "occurs" criteria http://informatics.kumc.edu/work/ticket/591
We have another bug we want to check but we can't because we can't reuse our test scenario.
Ticket 497 When you "reuse" queries, you get a different resultthe second time http://informatics.kumc.edu/work/ticket/497
We'll let people know if we get these resolved. We also had an enhancement below to 1.4 which we plan to fix in 1.6. We'll update the group when that code fix is committed on our site.
Ticket 243 Make the timeline hover show the name of the concept instead of just concept_cd http://informatics.kumc.edu/work/ticket/243
Russ
On Wed, 2011-12-21 at 16:25 -0600, Russ Waitman wrote:
Thanks Shawn. We may have done something wrong and can share details. Otherwise, we're going over noted 1.4 bugs and happy to see them fixed in 1.6.
Russ
"Murphy, Shawn N." 12/21/11 4:22 PM
We'll look into this Russ, would not want that.
Shawn Murphy MD
On Dec 21, 2011, at 4:55 PM, "Russ Waitman" wrote:
Hi,
Dan and Arvinder are closing down on migrating us from 1.4 to 1.6. We're getting excited except when we drag over a query created on 1.4 it causes the client to lock up in 1.6 (http://informatics.kumc.edu/work/ticket/775) . It says locked and stays that way.
Any ideas? We may not have done the database migration quite right?
We'd hate to tell people "write down the queries you want to keep and rebuild them after our downtime".
Russ Waitman
Director of Medical Informatics Associate Professor, Department of Biostatistics University of Kansas Medical Center rwaitman.kumc
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From: Henderson, Darren W [darren.henderson.uky] Sent: Friday, December 23, 2011 6:23 PM To: i2b2 AUG Members Subject: Query optimization for large datasets
Greetings all. I am a database analyst working at the University of Kentucky for our CTSA/BMI group. For the better part of the past 9 months or so I've been tasked with bringing i2b2 up for our clinicians and researchers on campus. We are currently on i2b2 v 1.6 with a SQL server 2008 instance backing it with 8 cores and 32gb of RAM attached to a SAN. I have worked here as one of our research database gurus (read data mining monkey) for several years now.
Our current desires are to use i2b2 to provide access to clinical data from the University Medcenter, as well as access to two large datasets that we currently maintain. We maintain a snapshot of all Medicaid claims for the state of Kentucky for the years 2000-2009, and will soon have 2010 – current available as well. We also have 3 years of the commercial insurance I3 database, 2007-2009. In my work to prepare the Medicaid data and I3 data for use in i2b2 I have come across a couple issues that I would like to discuss, in hopes of learning how others are approaching large scale databases in i2b2. My colleague Daniel Harris participated in a webinar recently led by Shawn Murphy in which I believe the comment was made in passing that Partners currently has an instance of i2b2 with ~1.5 Billion rows. The i3 data is nearing 3B without prescription or lab data in the model. The Medicaid data is ~220M rows in Observation, ~148M in Visit_dimension, for ~2M rows in patient dimension.
The main issue that I have come across that prompted me to begin participating in the AUG is query behavior I noticed when an exclusion panel is added to a query. Our instance may be lacking some setting in the files to prompt a more efficient query generation, but what I'm seeing with this kind of query is a dump of the entire visit_dimension into a temporary table where it is then processed one panel concept at a time as a large series of update statements. The SQL server that we are maintaining the data on has a lot of horsepower, but the query ran for 3 hours before failing due to a lack of tempdb space, or transaction log space (the error message was not captured at failure).
I've been working at an experimental fix so that my first message to the AUG would not simply be a complaint. I wanted to be able to offer something for the developers to consider. I've developed a hack that I kind of shoehorned into the SQL server side of things, so that I would not need to edit as many java files in order to deploy the change. The change is applied to the QT_QUERY_MASTER table. First, the REQUEST_XML field must be altered to varchar(max) instead of the deprecated TEXT datatype. Then the functions that I have attached take the REQUEST_XML that is stored, and with a trigger on the QT_QUERY_MASTER table, generates a field that I added to the table called generated_sql_v2. Then the only change I really had to make in the java files was to add that field as a member of the class that pulls from the qt_query_master. As it turns out, there was already a check in place that says if generated sql is null go generate it, else run it. So by shoehorning my column in its way, your generation never fires (my apologies).
The function that I developed creates SQL that uses a feature of SQL server known as Common-table expressions. Similar syntax is available in Oracle, but I have not developed anything for an Oracle solution since we are SQL server for our i2b2 purposes. Each common table that is built refers to the one above it as the starting point for the joins that take place. I chose to use LEFT OUTER JOIN within each common-table for every concept that is placed in the panel. The reason behind this is that this makes dealing with an exclusion panel much easier and elegant. The predicate at the bottom of the common table is either: WHERE not (or1.patient_num is null AND or2.patient_num is null) for a normal panel or WHERE (or1.patient_num is null AND or2.patient_num is null). So for the normal panel you want all those from the LEFT member of the join where at least one of the right members returned something. For the invert, you want only those where none of the members returned something. The or1, or2, orX aliases are tracked programmatically as I iterate through panel items that exist in the request for the current panel. The document that I attached will show an example of some of the queries that are generated programmatically along with their generation and a timestamp.
The benefit that I've noticed is that queries that contain exclusions or several concepts are returned much more rapidly. The function does attempt to order the panels using the TOTALNUM field in the metadata, so the first CTE is usually small. The left joins simply make each successive CTE a smaller set.
I am not suggesting that anyone should attempt to shove my hack into their active systems. This was more an experiment or proof-of-concept so that I could suggest to the development team a cleaner way of accomplishing the exclusion (invert) logic. The current version of the code that I have attached does not provide functionality for occurs constraints yet. I simply did not finish it before I left for the holiday break. I was also unsure about the intent of the occurs modifier. IF it supposed to apply to each concept in a panel independently e.g. this happens 2 times OR this happens 2 times, then it would be fairly easy to program this functionality into the left join by replacing the dimension table joined with an inline view using a group by having.
I apologize that my first message to the user group is such a mouthful, but I look forward to your feedback, and/or adoption of some or all of the query approach so that i2b2 performs as fast as possible for data sets of all sizes. Or should you already have a fix for query times inflating during exclusions I look forward to it.
Thank you all for your work and time put into i2b2. We have many people excited here at UK about the prospect of our data being useable for simple things in a much more approachable medium.
Darren W. Henderson
Institute for Pharmaceutical Outcomes and Policy
College of Pharmacy
University of Kentucky
789 S. Limestone Rm. 182
Lexington, KY 40536
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From: Mendis, Michael E. Sent: Friday, December 23, 2011 9:18 AM To: Patibandla, Nandan Cc: i2b2 AUG Members Subject: RE: ERROR while running the query
Was this is a new install or a upgrade? If you where upgrading verify that the new paramaters are in crc.properties. the one the error was referring to was: edu.harvard.i2b2.crc.setfinderquery.obfuscation.count.sigma
From: Patibandla, Nandan [Nandan.Patibandla.childrens.harvard] Sent: Fri 12/23/2011 9:01 AM To: Mendis, Michael E. Cc: i2b2 AUG Members Subject: ERROR while running the query
Hi Mike, I just deployed the new version 1.6.02 of i2b2 and was able to successfully able to deploy it, but when I run the query on the webclient(on;y selected the patient count) , I am getting the following error, please let me know why this is occurring.
Thank you
Nandan
2011-12-23 08:53:37,983 ERROR [edu.harvard.i2b2.crc.dao.CRCDAO] Error executing Application property file(crc.properties) missing edu.harvard.i2b2.crc.setfinderquery.obfuscation.count.sigma entry edu.harvard.i2b2.common.exception.I2B2Exception: Application property file(crc.properties) missing edu.harvard.i2b2.crc.setfinderquery.obfuscation.count.sigma entry
at edu.harvard.i2b2.crc.util.QueryProcessorUtil.getPropertyValue(Unknown Source)
at edu.harvard.i2b2.crc.util.QueryProcessorUtil.getCRCPropertyValue(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.GaussianBoxMuller.getCountSigma(Unknown Source)
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.jav a: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(MessageDrivenCo ntainer.java:495)
at org.jboss.resource.connectionmanager.CachedConnectionInterceptor.invoke(CachedCo nnectionInterceptor.java:158)
at org.jboss.ejb.plugins.CallValidationInterceptor.invoke(CallValidationInterceptor .java:63)
at org.jboss.ejb.plugins.AbstractTxInterceptor.invokeNext(AbstractTxInterceptor.jav a:121)
at org.jboss.ejb.plugins.AbstractTxInterceptorBMT.invokeNext(AbstractTxInterceptorB MT.java:173)
at org.jboss.ejb.plugins.MessageDrivenTxInterceptorBMT.invoke(MessageDrivenTxInterc eptorBMT.java:47)
at org.jboss.ejb.plugins.MessageDrivenInstanceInterceptor.invoke(MessageDrivenInsta nceInterceptor.java:116)
at org.jboss.ejb.plugins.RunAsSecurityInterceptor.invoke(RunAsSecurityInterceptor.j ava:109)
at org.jboss.ejb.plugins.LogInterceptor.invoke(LogInterceptor.java:205)
at org.jboss.ejb.plugins.ProxyFactoryFinderInterceptor.invoke(ProxyFactoryFinderInt erceptor.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:98 7)
at org.jboss.ejb.plugins.jms.JMSContainerInvoker$MessageListenerImpl.onMessage(JMSC ontainerInvoker.java:1287)
at org.jboss.jms.asf.StdServerSession.onMessage(StdServerSession.java:266)
at org.jboss.mq.SpyMessageConsumer.sessionConsumerProcessMessage(SpyMessageConsumer .java:891)
at
org.jboss.mq.SpyMessageConsumer.addMessage(SpyMessageConsumer.java:170) at org.jboss.mq.SpySession.run(SpySession.java:323) at
org.jboss.jms.asf.StdServerSession.run(StdServerSession.java:194)
at EDU.oswego.cs.dl.util.concurrent.PooledExecutor$Worker.run(PooledExecutor.java:7 56)
at java.lang.Thread.run(Thread.java:662) 2011-12-23 08:53:37,983 ERROR [STDERR] java.lang.IllegalStateException: BaseTransaction.rollback [com.arjuna.ats.internal.jta.transaction.arjunacore.notx] [com.arjuna.ats.internal.jta.transaction.arjunacore.notx] no transaction!
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From: Phillips, Lori C. Sent: Thursday, December 22, 2011 1:28 PM To: Dan Connolly; i2b2 AUG Members Subject: RE: documentation on age concepts in i2b2 1.6?
Dan,
Where did you get the oracle script from? This should contain sysdate, not getdate(), in the c_dimcode. (getdate is used in sqlserver).
In 1.6 we demonstrated the use of metadata that is computed dynamically .. meaning if you want run a query for all 10 year olds, the age is computed from the patient_dim as you see below. In 1.4 this was done by placing a static 'fact' into the obs_fact table. In this case it doesnt matter when you run the query, the patient is always listed as a 10 year old (unless the record is modified and updated).
If you want to run age facts the same way you did in 1.4, use the 1.4 age related metadata that refers to concept_dimension based facts.
Lori
From: Dan Connolly [dconnolly.kumc] Sent: Thursday, December 22, 2011 10:33 AM To: i2b2 AUG Members Subject: documentation on age concepts in i2b2 1.6?
We're loading age facts just like we used to with 1.4, but i2b2 1.6 seems to ignore them.
It seems to go by birthdate:
C_FACTTABLECOLUMN C_TABLENAME C_COLUMNNAME C_COLUMNDATATYPE
C_OPERATOR C_DIMCODE patient_num patient_dimension birth_date N BETWEEN getdate() - (365.25 * 2) +1 AND getdate() - 365.25 + 1
When I run an age query, I get: java.sql.SQLException: ORA-00904: "GETDATE": invalid identifier (full request/response XML attached)
I suspect I missed some documentation on this, though I remember something about it from a presentation at an AUG meeting a while back.
I read the 1.602 release notes, but they only seemed to discuss the differences between 1.601 and
1.602. Is there something about the differences between 1.4 and 1.6 (or at least: between 1.5 and 1.6) that I can read? I just skimmed some of the CRC and Metadata docs, and I don't see anything about this.
for reference: this is #780 in our trac.
Dan Connolly, KUMC Medical Informatics 913-945-6741
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From: Peter Beninato [beninato.ohsu] Sent: Wednesday, December 21, 2011 1:55 PM To: Mendis, Michael E.; i2b2 AUG Members Subject: RE: i2b2 - v1.6_02 - UPDATE_QUERYINSTANCE_MESSAGE.sql
The comment sounds like a good idea, especially for someone like me!
From: Mike Mendis [mmendis.partners] Sent: Wednesday, December 21, 2011 10:53 AM To: Peter Beninato; i2b2 AUG Members Subject: Re: i2b2 - v1.6_02 - UPDATE_QUERYINSTANCE_MESSAGE.sql
Yes it is a placeholder, which is needed by the ant script. Because the buid.xml is used by both oracle and sqlserver, if we did not have the file, the oracle would break looking for that file.
I can add the file as a comment something like "/* This file was left intentionally blank */'
Thanks
mike
On 12/21/11 1:50 PM, "Peter Beninato" <beninato.ohsu> wrote:
Hi,
Not sure, in that this might just be a placeholder file.
But when comparing the script to the procedures created there was mismatch.
There was no procedure, UPDATE_QUERYINSTANCE_MESSAGE.
When looking at the file it appears to be empty:
i2b2\v1_6_02\i2b2createdb-1602\edu.harvard.i2b2.data\Release_1-6\NewInstall\Crcdata\scripts \procedures\oracle\UPDATE_QUERYINSTANCE_MESSAGE.sql
FYI.
Peter Beninato - OCTRI DW Developer Oregon Health & Science University 503-494-9985 beninato.ohsu <beninato.ohsu>
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From: Mendis, Michael E. Sent: Wednesday, December 21, 2011 8:54 AM To: Peter Beninato; i2b2 AUG Members Subject: Re: v1.6_02 - Modifier Dimension - Upgrade -
crc_create_datamart_oracle.sql
Peter,
You are correct, they are in fact missing, I looked at the upgrade scripts for 1.6 and they don't have the modifier_dimensions scripts in them. I have added them now, and will be incorporated into the next release.
Thanks for finding it.
Mike
On 12/20/11 7:59 PM, "Peter Beninato" <beninato.ohsu> wrote:
Hi,
I'm working on Upgrading a local install to v1.6. I'm comparing the NewInstall scripts to the Upgrade scripts, and hand running data scripts etc. since, I have a production system, and need to be careful to maintain existing data.
While I'm on v1.4, I took some time to extract v1.5 upgrade scripts and incorporate any changes there into my scripts.
It seems to me that the script for the MODIFIER_DIMENSION might be missing from the Upgrade script ( I don't think this dim was in v1.5).
I see the CTAS statement for Modifier_Dimension in \i2b2\v1_6_02\i2b2createdb?1602 \edu.harvard.i2b2.data\Release_1?6\NewInstall\Crcdata\scripts\crc_create_datamart_oracle.sql
But I don't see it in
i2b2\v1_6_02\i2b2createdb?1602\edu.harvard.i2b2.data\Release_1?6\Upgrade\Crcdata\scripts \crc_create_datamart_oracle.sql
FYI.
Peter Beninato - OCTRI DW Developer Oregon Health & Science University
beninato.ohsu <beninato.ohsu>
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From: Brian Ostasiewski [bostasie.wakehealth] Sent: Wednesday, December 21, 2011 8:38 AM To: i2b2 AUG Members Subject: RE: bug with Dates contraint on dimensional queries?
I never got a response to this original email, and I've hit a similar situation with another dimensional query when specifying "same financial encounter". The SQL that is generated contains this:
update i2b2data.QUERY_GLOBAL_TEMP set panel_count =2 where exists ( select 1 as panel_count from ( select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ provider_id, start_date, concept_cd, instance_num, encounter_num, patient_num from i2b2data.visit_dimension where encounter_num IN (select encounter_num from i2b2data.visit_dimension where dsch_phyn_id = '00745') group by encounter_num ,instance_num, concept_cd,start_date,provider_id, patient_num ) t where i2b2data.QUERY_GLOBAL_TEMP.panel_count = 1 and i2b2data.QUERY_GLOBAL_TEMP.patient_num = t.patient_num and i2b2data.QUERY_GLOBAL_TEMP.encounter_num = t.encounter_num )
which is trying to select observation_fact columns from visit_dimension.
Brian
From: Brian Ostasiewski Sent: Monday, November 14, 2011 10:49 AM To: i2b2 AUG Members Subject: bug with Dates contraint on dimensional queries?
In 1.6.01, we had a user attempt to filter the Dates on a query of Age now, which is a dimensional query against the patient_dimension. The resulting query underneath appears to assume it is going against the observation_fact table.
Can someone verify this is an issue?
Also, is there a way to disable use of the Dates filter for specific concepts via c_metadataxml?
Brian Ostasiewski
The sql from qt_query_master:
select count(distinct patient_num) as patient_num_count from (
(select patient_num ,1 as panel_count from ( select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num from i2b2data.patient_dimension where patient_num IN (select patient_num from i2b2data.patient_dimension where birth_date <= sysdate - (365.25*65) ) AND ( start_date >= to_date('31-Dec-2010 19:00:00','DD-MON-YYYY HH24:MI:SS') ) group by patient_num ) t
)
INTERSECT
(select patient_num ,1 as panel_count from ( select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num from i2b2data.observation_fact where CONCEPT_CD IN (select CONCEPT_CD from i2b2data.CONCEPT_DIMENSION where CONCEPT_PATH LIKE '\WFUBMC\Diagnoses\ICD9\Circulatory system (390-459)\Hypertensive disease (401-405)(401) Essential hypertension(401-1) Benign essential hyperten~%') group by patient_num ) t UNION ALL
select patient_num ,1 as panel_count from ( select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num from i2b2data.observation_fact where CONCEPT_CD IN (select CONCEPT_CD from i2b2data.CONCEPT_DIMENSION where CONCEPT_PATH LIKE '\WFUBMC\Diagnoses\ICD9\Circulatory system (390-459)\Hypertensive disease (401-405)(401) Essential hypertension(401-9) Unspecified essential hyp~%') group by patient_num ) t
UNION ALL
select patient_num ,1 as panel_count from ( select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num from i2b2data.observation_fact where CONCEPT_CD IN (select CONCEPT_CD from i2b2data.CONCEPT_DIMENSION where CONCEPT_PATH LIKE '\WFUBMC\Diagnoses\ICD9\Endocrine disorders (240-259)\Other endocrine gland diseases (250-259)(250) Diabetes mellitus(250-0) Diabetes mellitus without~%') group by patient_num ) t
)
) allitem
Results in logged exception:
2011-11-14 10:34:50,763 ERROR [edu.harvard.i2b2.crc.dao.CRCDAO] Error while executing sql java.sql.SQLException: ORA-00904: "START_DATE": invalid identifier
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.executeForDescribe(T4CStatement.java:790)
at oracle.jdbc.driver.OracleStatement.executeMaybeDescribe(OracleStatement.java:1037)
at oracle.jdbc.driver.T4CStatement.executeMaybeDescribe(T4CStatement.java:830)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1124)
at oracle.jdbc.driver.OracleStatement.executeQuery(OracleStatement.java:1272)
at
org.jboss.resource.adapter.jdbc.WrappedStatement.executeQuery(WrappedStatement.java:226) 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(CachedConnectionInter
ceptor.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.ja
va: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:1092) at org.jboss.ejb.plugins.jms.JMSContainerInvoker
$MessageListenerImpl.onMessage(JMSContainerInvoker.java:1392) at org.jboss.jms.asf.StdServerSession.onMessage(StdServerSession.java:266) at
org.jboss.mq.SpyMessageConsumer.sessionConsumerProcessMessage(SpyMessageConsumer.jav a:906) at org.jboss.mq.SpyMessageConsumer.addMessage(SpyMessageConsumer.java:170) at org.jboss.mq.SpySession.run(SpySession.java:323) at org.jboss.jms.asf.StdServerSession.run(StdServerSession.java:194) at EDU.oswego.cs.dl.util.concurrent.PooledExecutor$Worker.run(PooledExecutor.java:761) at java.lang.Thread.run(Thread.java:619)
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From: Bhargav Adagarla [badagarla.kumc] Sent: Tuesday, December 20, 2011 12:37 PM To: i2b2 AUG Members Subject: RE: any "R Engine Cell" for i2b2 users?
Hello,
I am Bhargav Adagarla, (from University of Kansas Medical Center) trying to install the R-Engine plugin that Daniele and team developed (http://code.google.com/p/i2b2-r-engine-project/).
When I was trying to build it, according to the instructions: (http://code.google.com/p/i2b2-r-engineproject/wiki/HowTo) the code fails at ant -f master_build.xml build-all with the following error message:
jaxb_gen: [java] Exception in thread "main" java.lang.NullPointerException [java] at com.sun.tools.xjc.reader.internalizer.Internalizer.buildTargetNodeMap(Internalizer.java:18 7) [java] at com.sun.tools.xjc.reader.internalizer.Internalizer.buildTargetNodeMap(Internalizer.java:27 1) [java] at com.sun.tools.xjc.reader.internalizer.Internalizer.transform(Internalizer.java:118) [java] at com.sun.tools.xjc.reader.internalizer.Internalizer.transform(Internalizer.java:80) [java] at com.sun.tools.xjc.reader.internalizer.DOMForest.transform(DOMForest.java:432) [java] at com.sun.tools.xjc.ModelLoader.buildDOMForest(ModelLoader.java:326) [java] at com.sun.tools.xjc.ModelLoader.loadXMLSchema(ModelLoader.java:358) [java] at com.sun.tools.xjc.ModelLoader.load(ModelLoader.java:151) [java] at com.sun.tools.xjc.ModelLoader.load(ModelLoader.java:97) [java] at com.sun.tools.xjc.Driver.run(Driver.java:293) [java] at com.sun.tools.xjc.Driver.run(Driver.java:174) [java] at com.sun.tools.xjc.Driver. _main(Driver.java:99) [java] at com.sun.tools.xjc.Driver.access$000(Driver.java:57) [java] at com.sun.tools.xjc.Driver$1.run(Driver.java:79) BUILD FAILED /home/badagarla/REngine/it.fsm.i2b2.recell/it.fsm.i2b2.rengine/master_build.xml:8: The following error occurred while executing this line: /home/badagarla/REngine/it.fsm.i2b2.recell/it.fsm.i2b2.common/build.xml:55: Java returned: 1
I was wondering if this was an error you had encountered or an error that you would expect and have pointers as to how I can resolve it. Any help would be appreciated.
I have also attached a more detailed log from ant. Thanks.
Regards, Adagarla, Bhargav Srinivas Clinical Application Administrator University of Kansas - Medical Center
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From: McMurry, Andrew J. [Andrew_McMurry.hms.harvard] Sent: Friday, December 16, 2011 5:16 PM To: Lisa Miao Cc: i2b2 AUG Members Subject: Re: standard race code
In SHRINE, a project that networks many i2b2 hospitals together, we have found common agreement on the following Demographic standards https://open.med.harvard.edu/display/SHRINE/Core+Ontology
Race and Ethnicity - CDC Race & Ethnicity Code Sets
On Dec 16, 2011, at 2:50 PM, Lisa Miao wrote:
Dear i2b2 team and everyone else,
I'm wondering what race codes everyone (and i2b2 demo project) is using, and in particular if anyone is using standard(rather than proprietary) race code.
Thanks,
Lisa.
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From: Michael Horvath [mhorvath.wakehealth] Sent: Friday, December 16, 2011 3:40 PM To: i2b2 AUG Members members Subject: RE: restarting jboss on i2b2 server VM boot
I've noticed in some of the VM's that the third field of the entry /etc/oratab function is set to 'N'. Switching this to 'Y' will tell the dbstart utility to bring it up at boot. I haven't noticed any problems with jboss starting, however.
From: Jack London [jack.london.KimmelCancerCenter] Sent: Friday, December 16, 2011 2:38 PM To: i2b2 AUG Members members Subject: restarting jboss on i2b2 server VM boot
We have noticed that it is almost always necessary to restart jboss upon rebooting our i2b2 VM server. If we just reboot and then start the web client, queries fail. If we then stop and restart jboss, everything works fine.
We suspect that Oracle is not COMPLETELY "up" when jboss initially starts. Stopping and restarting jboss always works.
Anyone have this experience?
Jack
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From: Jack London [jack.london.KimmelCancerCenter] Sent: Friday, December 16, 2011 1:53 PM To: i2b2 AUG Members members Subject: web client v1.6 multiple query status lines
Have others seen multiple query status lines appear, as shown below:
Finished Query: "Breast, NOS@13:47:06" Compute Time: 10 secs Number of patients for "Breast, NOS@13:47:06" patient_count: 744 Number of patients for "Breast, NOS@13:47:06" patient_count: 744
Any idea why?
thanks Jack
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From: Mendis, Michael E. Sent: Friday, December 16, 2011 1:51 PM To: Jack London Cc: Murphy, Shawn N.; i2b2 AUG Members Subject: RE: width of web client query tool panels
The left panels (ontology, previous queries) are set to a specific size. The right size will max to the width of the window. But you cant realize the way you are thinking.
mike
From: Jack London [jack.london.KimmelCancerCenter] Sent: Fri 12/16/2011 1:49 PM To: Mendis, Michael E. Cc: Murphy, Shawn N.; i2b2 AUG Members members Subject: width of web client query tool panels
is there any way to make them wider?
Jack
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From: Murphy, Shawn N. Sent: Friday, December 16, 2011 10:55 AM To: i2b2 AUG Members Subject: I2b2 1.6.02 is released
Hi All,
The next set of fixes and enhancements is available, new stuff is outlined below and in the release notes.
Thanks, Shawn.
String Constraint
In the 1.6.02 release there is now an option to constrain a query by a string of text. Similar to other text and numeric constraints, a user can narrow down their search criteria when setting up the query in the query tool view. The main difference between this new constraint and the existing ones is the string constraint allows users to enter a string of text as opposed to an enumerated or numerical value.
Lockout / Obfuscation Parameters
In the 1.6.02 new parameters were added to the crc.properties file to support the lockout process for obfuscated users as well as the obfuscation process itself.
Data
In release 1.6.02, no changes were made to the structure of the database. The only change was to add examples to the metadata, concept_dimension, modifier_dimension, and observation_fact tables to support the new string constraint.
Fixes:
The following fixes were added to this release:
Memory error: not able to load PDO
Not able to search for terms with an '&' in the name
Demo Database Scripts: Passwords inconsistent
PM: ProjectUser parameters are not saved with the project
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From: Russ Waitman [rwaitman.kumc] Sent: Friday, December 16, 2011 9:56 AM To: Joe.Terdiman.kp; beninato.ohsu Cc: Andrew_McMurry.hms.harvard; i2b2 AUG Members Subject: RE: i2b2/Shrine - ontology - Smoking Status
Joe, Thanks for that pointer. Hadn't looked at that table. We'll see if we can pull that in at a subsequent point and see how it overlaps or exchanges with flowsheet and notes information,
Russ
<Joe.Terdiman.kp> 12/15/2011 7:14 PM
Although we do not yet included smoking hx in our i2b2 database or SHRINE, we have looked in our EPIC system at the percentage of patients with smoking hx in the social_hx table vs. free text progress notes. Using NLP on progress notes and an SQL query on the social_hx table in a sample of 1000 patients, we found 20% of patients had a positive hx of smoking from progress notes, but the social_hx table indicated they were either non-smokers or were blank. This ad hoc study clearly demonstrates the ability of NLP to extract significant clinical information from free text reports in the EHR, and the potential for large discrepancies in estimating the prevalence of clinical conditions (smoking in this case) without
it.
Joe
Joe Terdiman, MD, PhD Division of Research Kaiser Permanente 2000 Broadway Oakland, CA 94612
From: Peter Beninato <beninato.ohsu> Sent: 12/15/2011 04:37 PM To: "McMurry, Andrew J." <Andrew_McMurry.hms.harvard>, Russ Waitman <rwaitman.kumc>, i2b2 AUG Members Subject RE: i2b2/Shrine - ontology - Smoking Status
Hi Andy,
Was smoking status included in any of the SHRINE implementations you've worked on?
Our research data warehouse source for smoking status currently comes from EPIC -> CLARITY -> SOCIAL_HX table, but in our data warehouse, if there are other flowsheet sources of interest to our investigators we may include them too.
Peter
From: Russ Waitman [rwaitman.kumc] Sent: Friday, December 16, 2011 9:07 AM To: Andrew J. McMurry Cc: i2b2 AUG Members; Peter Beninato Subject: Re: i2b2/Shrine - ontology - Smoking Status
It's coded value in the flowsheet measures. We don't process any text notes at KUMC yet. We'll probably extract "smart data" from Epic first.
Russ
From: McMurry, Andrew J. [Andrew_McMurry.hms.harvard] Sent: Thursday, December 15, 2011 4:23 PM To: Russ Waitman Cc: Peter Beninato; i2b2 AUG Members Subject: Re: i2b2/Shrine - ontology - Smoking Status
Curious how you are obtaining "smoking status" – as a coded value or by processing of the text note?
andy
On Dec 15, 2011, at 6:30 PM, Russ Waitman wrote:
It's in several places but pretty much a peer at the top of the tree with things like vital signs. We derive the local ontology out of the Epic tables.
At a some point Judy Warren in nursing here would like to build a top down approach but until that's done, we're going with a bottom up approach: using the local view of reality as opposed to imposing our world view. We did some clustering of concepts as described in the paper but we need to figure out a naming scheme for the clustered concepts before we make that our normal solution.
http://informatics.kumc.edu/work/attachment/wiki/KUBMIPresentations/HERONNursingOntologyTalkAMIAOctober262011 v6.pdf
Here's a common spot though and a picture:
\Flowsheets\KU\KU Inpatient\Tobacco Use\
Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center
rwaitman.kumc http://informatics.kumc.edu
Peter Beninato <beninato.ohsu> 12/15/2011 5:19 PM
What does the tree/path look like for where you locate smoking status in your ontology?
I was thinking of a top-level folder called something like Social History, but would like to know where others are putting it.
Thanks.
From: Russ Waitman [rwaitman.kumc] Sent: Thursday, December 15, 2011 3:15 PM To: i2b2 AUG Members; Peter Beninato Subject: Re: i2b2/Shrine - ontology - Smoking Status
Hi Peter, It's part of the hierarchy we suck out of our Epic flowsheet build. For the most part these ontologies are highly localized though sharable. We described the project to incorporate that data at AMIA this year if you're interested.
Waitman LR, Warren JJ, Manos L, Connolly DW. Expressing Observations from Electronic Medical Record Flowsheets in an i2b2 based Clinical Data Repository to Support Research and Quality Improvement. (presented at AMIA Annual Symposium 2011)
Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center
rwaitman.kumc http://informatics.kumc.edu
Peter Beninato <beninato.ohsu> 12/15/2011 5:10 PM
Hi,
Beginning the process of adding Smoking Status to our OHSU Cohort Discovery ontology.
Has/was Smoking Status added to any Shrine ontology?
If so please reply with c_fullname/c_dimcode (aka) path. If possible would like standardize.
If your organization's ontology includes Smoking Status (but not part of a Shrine network), where did you include it in your ontology?
Thanks.
Peter Beninato - OCTRI DW Developer Oregon Health & Science University
beninato.ohsu
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From: Natter, Marc [Marc.Natter.childrens.harvard] Sent: Friday, December 16, 2011 9:53 PM To: i2b2 AUG Members Subject: Re: questions to the actual i2b2 users
And a little more follow-up inline regarding how we do it with i2b2-SSR (i2b2 self-scaling registry platform), used for the CARRAnet and the Harvard-wide Inflammatory Bowel Disease registries - which use a modified SHRINE client to federate results across i2b2 sites and over i2b2 projects:
From: Keith Marsolo [keith.marsolo.cchmc] Sent: Wednesday, December 14, 2011 9:29 AM To: Kohane, Isaac Samuel Cc: Askar Ibragimov; i2b2 AUG Members Subject: Re: questions to the actual i2b2 users
To follow up on Zak's comments.
On Dec 14, 2011, at 8:37 AM, Kohane, Isaac Samuel wrote:
One questions answered below:
On Dec 14, 2011, at 5:02 AM, Askar Ibragimov wrote:
Dear colleagues, we at FIMM evaluating i2b2 as a platform to publish the data collected jointly from one or several databases and appreciate if you share your practical experience on the following topics. In your opinion:
1. Is i2b2 able to store and display all kind of your data in a convenient manner?
ANSWER: In the experience of Cincinnati Children's, yes to storing the data and "it depends" on display. It depends on your definition of convenient. CCHMC has built its own version of a workbench (freely available) that adds functionality for displaying reports. Creating those reports are still not as straightforward as we'd like, but we're creating a Report Builder to facilitate this.
2. Have anyone used the system with epidemiological / questionnaire based data?
ANSWER: Yes, the CARRAnet (60 sites using i2b2 linked by SHRINE) uses a lot of questionnaire based data (https://carranetwork.org/projects/carranet-registry)
In addition to the CARRANet project (in which CCHMC has played a part), we've also built a Forms cell that allows for the display/completion of web forms. It's built on CDISC ODM, which is a standard that allows for the modeling of questionnaire data and metadata. There's a mapping from this forms cell to the CRC.
3. Are existing abilities of Workbench matches your needs and did you ever need something that Workbench does not offer? What kind new functionalities people like to have, is something crucial missing related to queries, web services, data integration etc on basic operations. When we started working with i2b2, the web-based workbench did not exist, so we ended up building our own.
ANSWER: We've tried to target our i2b2 installations to the general clinical research user. The eclipse-based workbench is too advanced for this type of user (in my opinion), so we've targeted our tools for use cases like cohort identification, chart review, on-demand reporting, and the request of biosamples. We've also made a few extra changes to allow the handling of observation-related metadata which is similar to the concept of modifiers in version 1.6.
4. Did somebody tried to replace standard data providing cells with someting custom, that takes information from completely other database (for example, a replacement Ontology cell)? How difficult was such a task?
5. Can somebody comment on how easy it s to extend the system for newcomers, especially adding / creating new cells
ANSWER: If someone understands Java programming and takes the time to look through the i2b2 documentation and the source code, then it's not horrendously difficult to create new cells. But I don't know if most newcomers would have that experience. It also depends on the complexity of the cell itself. We've made modifications to existing cells and created new ones. So it's possible, but you do need to know what you're doing. Adding new cells that make calls to existing cells is definitely easier than trying to go in a hack away at the existing code.
6 . Our users ask, would it be possible to query several projects at once? Is there a possibility to do queries also based on free text or range of values? How we can create a new query based on an old one?
ANSWER: Depending on what you mean by "querying several projects at once", you could hook up the various i2b2 CRCs using SHRINE. We do this in our multi-center registries, where every center in the network has their own i2b2 CRC and they communicate via SHRINE. We've follow the Harvard/Partners model, where only one project is stored in a CRC. We've also made changes to allow us to get by with one PM cell, one ontology cell, etc., but then use multiple CRCs.
And I believe that version 1.6 allows you to use previous queries as criteria in new queries. You can take a query, drag it into the cohort tool and add new criteria, filtering down the list.
Cheers, Askar
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From: Peter Beninato [beninato.ohsu] Sent: Wednesday, December 14, 2011 7:07 PM To: i2b2 AUG Members Subject: i2b2 - v1.6.x - data - PM - is_admin - add_user
Hi,
I downloaded the source code on Dec. 6, 2011. I am reviewing the data upgrade scripts and incorporating changes into some custom scripts.
Below are some copy/pastes from some emails that went by concerning problems with adding users via the webclient, and some corrective action for v1.6.01.
I think these changes were incorporated in v1.6.01, so maybe I'm missing it, but I don't see the column, is_admin, in either the data install or upgrade scripts.
So...
1) In the i2b2pm schema, which table should have a column IS_ADMIN?
2) What value does the column, IS_ADMIN, need to be set to? (Y or Yes?)
3) Is this ALTER TABLE statement in the codebase? If so where?
Thanks.
Peter Beninato - OCTRI DW Developer
Oregon Health & Science University
beninato.ohsu
From: Peter Beninato Sent: Wednesday, December 14, 2011 3:53 PM To: Peter Beninato Subject: RE: Add user not working correcting in 1.6.00
Are you using 1.6 or 1.6.01? Also correct me, but you are copying the current vm install to a new one correct? Which is fine and should work. On the database side, did you create a user in the pm_projct_user_role table with the following
Project_id @
user_id snmtest
user_role ADMIN
status_cd A
mike
From: Peter Beninato Sent: Wednesday, December 14, 2011 3:52 PM To: Peter Beninato Subject: FW: Add user not working correcting in 1.6.00
From: Mike Mendis [mmendis.partners] Sent: Thursday, October 27, 2011 12:56 PM To: i2b2 AUG Members Subject: Add user not working correcting in 1.6.00
When using the webclient add to add a new user, it returns a database error. We are going to be releasing a new 1.6.01 that corrects this and other issues.
As a temporary fix, alter that PM_USER_TABLE and add the column IS_ADMIN as a varchar2(50)
mike
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From: Peter Beninato [beninato.ohsu] Sent: Wednesday, December 14, 2011 6:20 PM To: i2b2 AUG Members Subject: i2b2 - v1.6.x - data - upgrade
Hi,
I am reviewing the DB upgrade to incorporate changes into some custom scripts.
In the script:
i2b2\v1_6_01\i2b2createdb-1601\edu.harvard.i2b2.data\Release_1-6\Upgrade\Metadata\scripts \upgrade_oracle_i2b2metadata_tables.sql
I think the indexes in the following two statements should be on the "BIRN" table. (There are indexes for these two fields on the i2b2 table created earlier in the script.
Please note and create a JIRA issue as needed.
CREATE INDEX META_FULLNAME_BIRN_IDX ON I2B2(C_FULLNAME) ;
CREATE INDEX META_APPLIED_PATH_BIRN_IDX ON I2B2(M_APPLIED_PATH) ;
FYI
Peter Beninato - OCTRI DW Developer Oregon Health & Science University
beninato.ohsu
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From: Dat Q. Phan [Dat.Q.Phan.uth.tmc] Sent: Wednesday, December 14, 2011 3:25 PM To: Lusted, Jeff; i2b2 AUG Members Subject: RE: I2b2 using SSL
Jeff, Take a look at i2b2 - Security Baseline from here:
https://community.i2b2.org/wiki/display/community/Supplemental+Documentation+for+Installing+and+Configuring+i2b2+v1.6
Hope that helps.
Johnny
From: Lusted, Jeff [jl99.leicester.ac.uk] Sent: Wednesday, December 14, 2011 12:23 PM To: i2b2 AUG Members Subject: I2b2 using SSL
Hi Colleagues!
At Leicester we have recently deployed test i2b2 servers with successful access to them from web client and workbench. We have even written a small command line utility which can upload patient data using a PDO. The servers are deployed in two environments: university and hospital.
As you can imagine, the hospital environment is locked down, secure and closed. No outside access!
The university environment is by its nature somewhat more open. Although we can limit access only to within the university environment, keeping a more open policy would be advantageous. To that end I would like to ask members whether they have experience of securing i2b2 using SSL? Was it straightforward? And what problems were encountered, if any?
Looking forward to your replies.
Kindest regards Jeff
Jeff Lusted, Senior Programmer (RCS, IT Services) University of Leicester Email: jl99.le.ac.uk
Elite Without Being Elitist Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011 Follow us on Twitter http://twitter.com/uniofleicsnews
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From: Kohane, Isaac Samuel [Isaac_Kohane.hms.harvard] Sent: Wednesday, December 14, 2011 10:26 AM To: Steward, Duane Cc: i2b2 AUG Members; Murphy, Shawn N.; Churchill, Susanne E. Subject: Re: IRB submission artifacts <-- Re: questions about dataschema
Are any of you at liberty to share your successful IRB submission artifacts or portions thereof?
I think we can do that and I encourage others to do the same. I wonder if we could keep a set of these documents on our community site?
Zak
On Dec 14, 2011, at 9:59 AM, Steward, Duane wrote:
Zak, et al,
The response to one question this morning prompts action on a tangent need we have---i.e., due diligence with IRB submission for a newly deployed hive.
Rather than reinvent that wheel from a blank page, it sure makes sense to humbly ask---especially
in view of the fact that it entails submitting a protocol for unspecified research use---just one example of unprecedented aspects we're asking an IRB to consider. I for one greatly appreciate the pavement laid in Boston on this path and hope to take lessons learned and shared to heart.
In terms of the answer to this morning's question, is there some place where I can "access" IRB protocols of Brian Wilson, Boston entities or elsewhere? We are eager to learn from any willing to share or advise. I am happy to share with others as we wordsmith an IRB submission for our hive in the next several weeks.
Duane
Duane Steward, DVM, MSIE, PhD Chief Computer Scientist for Health Informatics Nemours
From: Kohane, Isaac Samuel [Isaac_Kohane.hms.harvard] Sent: Wednesday, December 14, 2011 8:43 AM To: Laukkanen Markku Cc: i2b2 AUG Members Subject: Re: questions about dataschema
[...]
3. With regard to specimens: I would look at the new cells that Brian Wilson has developed that speaks to better integration with biorepositories and the IRB protocols for access.
[...]
Zak
Isaac S. Kohane, MD, PhD Professor of Pediatrics and Health Sciences and Technology Children's Hospital and Harvard Medical School Director, Countway Library of Medicine Director, i2b2 National Center for Biomedical Computing Co-Director, HMS Center for Biomedical Informatics 10 Shattuck Street Boston, MA 02115 617-432-2144
isaac_kohane.harvard http://www.chip/~zak/
From: Phillips, Lori C. Sent: Wednesday, December 14, 2011 9:35 AM To: Askar Ibragimov; i2b2 AUG Members Subject: RE: questions about dataschema
Askar,
The sample data in the demo package is purely an example that we expected most people would find useful. It demonstrates several properties of our Ontology design: 1. Ontologies may be organized in several tables.
The TABLE_ACCESS table specifies the root level nodes of the navigation tree and may be used to display ontologies from more than one table.
A single table (I2B2 in this case) may be used to specify more than one root level node.
You ask where a new term , BMI, should be placed. Your first question should be: where do I want it to appear in the tree? If the answer is "I would like a root level node to display this concept" then the easiest solution is to create a new table for that concept and add an entry to TABLE_ACCESS for that table. If the answer is "Place it in the Custom metadata table" then the easiest solution is to either use the Edit Terms feature of the workbench to create the BMI nodes in the Custom metadata tree or create the appropriate entries in the Custom_meta table.
The attached document should help explain how the ontology and concept_dimension entries are related.
Lori
From: Askar Ibragimov [askar.ibragimov.gmail] Sent: Wednesday, December 14, 2011 9:17 AM To: i2b2 AUG Members Subject: Fwd: questions about dataschema
Dear Lori,
thanks for the explanations. I found these tables. TABLE_ACCESS got in particular the following info:
| C_TABLE_CD | C_TABLE_NAME | C_PROTETED_ACCESS | C_HLEVEL | C_FULLNAME |BIRN
BIRN
N
0
\BIRN|
CUST
CUSTOM_META
N
0
\Custom Metadaa|
i2b2_DEMO
I2B2
N
1
\i2b2\Demographics|
i2b2_DIAG
I2B2
N
1
\i2b2\Diagnoses|
i2b2_EXPR
I2B2
N
1
\i2b2\Expression Profiles Data|
i2b2_LABS
I2B2
N
1
\i2b2\Labtests|
i2b2_MEDS
I2B2
N
1
\i2b2\Medications|
i2b2_PROC
I2B2
N
1
\i2b2\Procedures|
i2b2_PROV
I2B2
N
1
\i2b2\Providers|
i2b2_REP
I2B2
N
1
\i2b2\Reports|
i2b2_VISIT
I2B2
N
1
\i2b2\Visit Details|
Basically I would like to have more insight on which basis it was divided, and what steps are needed if I need to add, for example, a phenotype such as BMI (assuming it's not in the tree). In which ontology table I shall put it? How it is related to concept_dimension table - I am quite confused about parallel entries in concept and ontology tables and I appreciate if someone help me to understand their purpose/connection.
All the best, Askar
From: Kohane, Isaac Samuel [Isaac_Kohane.hms.harvard] Sent: Wednesday, December 14, 2011 8:43 AM To: Laukkanen Markku Cc: i2b2 AUG Members Subject: Re: questions about dataschema
Hi Markku,
these are great questions and you have an impressive set of cohorts to study. I'll answer a few of the questions and pose others and let others in the community respond too:
1. You say: "From the i2b2 point of view, it seems that only patient data points are supported ? " Are you asking if there are time points represented that are NOT patient-linked or are you asking if intervals are represented?
2. If you have multiple locally curated ontology trees (as opposed to standard ones such as those hosted at NCBO) then any i2b2 instance will have a set of fixed ontologies. Youday "define, that ontology items are similar, opposite, nearly similar etc etc. For me it seems, that i2b2 ontology tree only defines exact match?" I may be misunderstanding the question but if you are referring to selecting patient cohorts based on these ontologies then a variety of boolean combinations can be specified.
With regard to specimens: I would look at the new cells that Brian Wilson has developed that speaks to better integration with biorepositories and the IRB protocols for access.
I am unaware of i2b2 implementations that include family structure (but I would be interested to hear if others have implemented such). Technically, I do not believe it is particularly challenging but it would be enormously useful for those sites that have that kind of data (few EHR's have those relationships explicitly modeled but several cohort studies, such as yours, of course do. If no one else has done it, this would be a major contribution to the i2b2 community if you took it on.
Zak
Isaac S. Kohane, MD, PhD Professor of Pediatrics and Health Sciences and Technology Children's Hospital and Harvard Medical School Director, Countway Library of Medicine Director, i2b2 National Center for Biomedical Computing Co-Director, HMS Center for Biomedical Informatics 10 Shattuck Street Boston, MA 02115 617-432-2144
isaac_kohane.harvard http://www.chip.org/~zak/
On Dec 14, 2011, at 12:04 AM, Laukkanen Markku wrote:
Hi all AUG members,
I am part of team evaluating i2b2 to our purposes.
First some background info:
Currently we have about 120 projects/cohorts (~ 250000 subjects with about million samples).
We are in phase of importing phenotypes into our in house LIMS (some of the cohorts already have those in db)
Our phenotype structure is build using trees, e.q. compared into i2b2 ontology tree, our trees doesn't specify the full parent hierarchy, only nearest parent. So the leaf node is simply node with no children
Phenotypes (leaf nodes) can be specified very strictly, namely by type, by allowed values, by minmax values, by enumerated questionnaire values (1 means sick, 2 means maybe sick etc etc). This is for that, that it is automatically possible to do checks for values when importing information for samples/subjects. Also missing values are taken into account, and the "certainty of information", some of the cohorts date back into 70s
Each cohort will have it's own ontology tree, and similarities between ontology leafs are defined in other table. This makes it possible to define, that ontology items are similar, opposite, nearly similar etc etc. For me it seems, that i2b2 ontology tree only defines exact match ?
The measurement(s)/data points for items in cohorts come both for individuals, and for specific samples (e.q. gender check for samples to look for contamination).
So basically data items for subject can contain measured phenotypes, and data times for samples
contain measured items from that particular sample (sampling date, individual's medicine at the time of sampling etc etc)
From the i2b2 point of view, it seems that only patient data points are supported ?
Our samples also create sample tree, in style blood->dna->aliquote->aliquote->aliquote
Our individuals also create family structures parent-child-grand child etc etc
Our question is, is it feasible to try to use i2b2 framework for this, when our researches has a need to
a) query subjects from one/several different project(s) at the time b) query availability of samples for subjects c) do queries based on family structures d) exclude from queries subjects without any sample's to use left e) access to projects are restricted by end user privileges
Regards, Hi
From: Sebastian Mate [Sebastian.Mate.imi.med.uni-erlangen.de] Sent: Wednesday, December 14, 2011 4:12 AM To: 'Askar Ibragimov'; i2b2 AUG Members Subject: AW: questions about dataschema
Hi Askar,
we're basically having the same issue with the access rights. Some time ago, I have implemented a proof-of-concept, based on "access vectors" for each data record in OBSERVATION_FACT. The idea behind this is explained in the power point file.
The user rights were defined as i2b2 "user variable". The changes in the CRC cell and were minimal. All that was required was source code to read the user variables and to add another JOIN clause to the SQL statement which fetches the observation facts.
However, I have never tested this with real data and can't comment on the performance.
Cheers, Sebastian
From: Phillips, Lori C. [LCPHILLIPS.PARTNERS] Sent: Tuesday, December 13, 2011 6:28 PM To: Askar Ibragimov; i2b2 AUG Members Subject: RE: questions about dataschema
Askar,
I can help with your Ontology table questions.
The Ontology table described in Section 2.2 is equivalent to the I2B2 table identified in the metadata database. This table governs the display of terms in the Navigate Terms view.
Relation to concept_dimension table Each concept in the metadata table is uniquely defined by its c_fullname. Each unique c_fullname, in turn, has a record in the concept_dimension table where metadata.c_fullname = concept_dimension.concept_path.
Configuring metadata across two tables. A prime example of this is provided in the demo package metadata database tables. Three tables are provided: I2B2, CUSTOM_META and BIRN (the structure off all three of these tables is identical to the Ontology table shown in section 2.2) A separate table, TABLE_ACCESS, identifies the tables used to create a project's metadata or ontology. In our demo package this table contains entries that assign these three tables to a root level entry in the Navigate Terms view.
I hope this helps you.
Lori Phillips
From: Askar Ibragimov [askar.ibragimov.gmail] Sent: Tuesday, December 13, 2011 11:03 AM To: i2b2 AUG Members Subject: questions about dataschema
Dear AUG members,
I went across data format for i2b2 and hope that I could resolve few of my questions and verify that I have understood everything right. I am still in understanding process, so some querstions might be a little silly
In our production, we will need a rather complex data access rights. Is it right that for each project we would need to create separate set of datatables? I could not see project-related info in data mart tables (observation_fact etc). Or if not, how users
Can we query somehow two or more projects at once, or we're limited to one project at a time?
Is it correct, that for any "enumerated types" (when you have a "lab test" resulting in some choice out of fixed amount), you define all enumerations in CODE_LOOKUP?
Could somebody explain what is the Ontology table defined in Ontology Design, sect.2.2 document? It's not a table in the database. Where this entity exists, how it is related to concepts table?
It is said that ontology can be splitted across few tables, how would you configure that in practice?
Does concepts table allow for some additional columns?
If I have addtional colimns in visit and patient data, are they automatically shown in query results?
and few more from our users who tried workbench:
How do you define variables?
How do you define individuals, samples, family relations, etc.?
Thank you in advance,
Askar
NEXT EMAIL
From: Jack London [jack.london.KimmelCancerCenter] Sent: Tuesday, December 13, 2011 1:53 PM To: Juha Muilu Cc: Justin Prosser; i2b2 AUG MembersSubject: Re: i2b2 on mac
we only use the i2b2 web client, and everything occurs with Linux under VM Fusion.
Now using VM Fusion 4.1.1.
I would not assume Windows 7 behavior is transferrable to Linux under VM Fusion.
From: Justin Prosser [jprosser.uw] Sent: Tuesday, December 13, 2011 1:44 PM To: Juha Muilu Cc: Jack London; i2b2 AUG MembersSubject: Re: i2b2 on mac
I do all my dev work on the Mac and run Linux and Windows with VMware. Also, I stuck with Fusion 3 until 4.1 (currently running 4.1.1). I don't often go for .0 releases if I can help it I'm also one of those old school types opting for vi generally (http://code.google.com/p/macvim/) but go with Netbeans when an IDE makes sense (involved debug cycles come to mind here).
Justin
On Dec 13, 2011, at 1:26 PM, Juha Muilu wrote:
Fusion used to be ok but when I upgraded to 4.0 it became very slow for some reason, at least when running windows7. Have not yet tried Linux yet.
Do you still keeping your development environments on Mac or are you using Linux for coding as well?
By any chance, does there exist preconfigured eclipse project, with the latest i2b2 tools and things, somewhere as there use to be for the version 1.3. It was really nice.
Best, Juha
From: Askar Ibragimov [askar.ibragimov.gmail] Sent: Tuesday, December 13, 2011 1:00 PM To: Juha Muilu Cc: Steward, Duane; i2b2 AUG Members Subject: Re: i2b2 on mac
P.S. under Fusion
2011/12/13 Askar Ibragimov <askar.ibragimov.gmail>:
Moi Juha, the mac I got with your kind help is pretty fast actually — I have both i2b2 image and Ubuntu for Erlangen running just fine.
Cheers,
Askar
On 13 Dec 2011, at 20:14, Justin Prosser wrote:
FWIW, Fusion has always been the best choice for me (running on various MacBook Pros over the years, intel). I haven't checked Virtual Box or Parallels recently, but I'd have to guess you won't find better performance with the others. Keep in mind you are running an entire OS here so RAM is probably you're most important data point.
Justin
On Tue, Dec 13, 2011 at 10:10 AM, Jack London <jack.london.kimmelcancercenter> wrote:
I have found slow performance under VM fusion on the Mac to have two possible explanations:
1) VM fusion settings for the VM.
2) your Mac hardware capabilities.
I was using a Macbook laptop for i2b2 development, but eventually my obs-fact data sets got too large for reasonable performance. I switched to VM Fusion on my beefier iMac desktop, but I know that the performance will never be as good as our i2b2 production server. Initially, an older Macbook I had proved inadequate for running i2b2 under VM Fusion at all.
jack
On Dec 13, 2011, at 12:56 PM, Juha Muilu wrote:
Great thanks to all for the feedback!
I found the latest vmware Fusion bit slow for some reason, but perhaps I should try the VirtualBox thing. The wizard looks promising.
Best, Juha
From: Matvey Palchuk [MPalchuk.recomdata] Sent: Tuesday, December 13, 2011 12:36 PM To: Jack London; Juha Muilu Cc: i2b2 AUG Members Subject: Re: i2b2 on mac
If you just need to run the VM, I use free VirtualBox from Oracle. One trick to get it to work is - set Network preference to "Host-only Adapter" and your Mac browser will "see" the server running on the VM.
Matvey
Matvey B. Palchuk, MD, MS Director of Medical Informatics Recombinant Data Corp.
.matveyp
On 12/13/11 12:16 PM, "Jack London" <jack.london.KimmelCancerCenter> wrote:
It might be worth the $49 license cost for VMware Fusion for the Mac, and using a Centos VM. We have used this platform a number of times for development, and is a handy way to have multiple versions of i2b2 for development.
Jack
On 13 Dec 2011, at 19:32, Steward, Duane wrote:
I have succeeded with the VMware image (CentOS) on VMware Fusion on the Mac. This is by far the easiest way to get a working instance in less than 30 minutes effort. It also serves as a gold standard when trying to figure out the finer points of building from source.
Another thing we've employed to shed light has been the i2b2wizard from
Sebastian Mate (1.3.1 for i2b2 1.6.01 announced on 12/5 http://www.imi.med.uni-erlangen.de/~matesn/i2b2wizard/). This comes with some very helpful documentation for using VirtualBox as a free VM server. Off the shelf, this leads to a Ubuntu hosted I2B2 hive. I had no problem using this on my Mac. In fact, building a Linux version on a VM server on the Mac was the easiest way for me to get an instance of Oracle that I could point other instances of i2b2 toward as I mastered the build process layer by layer with the Mac.
Duane Steward, DVM, MSIE, PhD
Chief Computer Scientist for Health Informatics Nemours
From: Juha Muilu [juha.muilu.helsinki.fi] Sent: Tuesday, December 13, 2011 11:24 AM To: i2b2 AUG Members Subject: i2b2 on mac
Hi
Wondering is anyone developing and running the i2b2 server (except the db) on Mac?
Best, Juha
Justin Prosser Software Engineer ITHS Biomedical Informatics University of Washington http://www.iths.org/BMI
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From: Jennifer Cai [Jennifer.Cai.UTSouthwestern] Sent: Tuesday, December 13, 2011 1:09 PM To: Mendis, Michael E.; Donahoe, Janice M; Askar Ibragimov; i2b2 AUG Members Subject: RE: Installing import and export Cells
Mike,
We are installing 1.6. Our institute has the proxy server. I think that we missed the proxy setting in our 1.6 workbench, but I could not find any document mention proxy settings. Do you know how to set up proxy in the workbench?
We could not see the screen shot in your email.
Thanks,
Jennifer
From: Mike Mendis [mmendis.partners] Sent: Tuesday, December 13, 2011 10:17 AM To: Jennifer Cai; Donahoe, Janice M; Askar Ibragimov; i2b2 AUG Members Subject: Re: Installing import and export Cells
I am not sure if you need a proxy setup, so you are not seeing the screenshot I attached. Which workbench are you using?
On 12/12/11 4:31 PM, "Jennifer Cai" <Jennifer.Cai.UTSouthwestern> wrote:
Hi,
We are trying to install the plug-ins from i2b2 workbench by "HelpàAdd New Features". But we got a pop window with following message:
"Network connection problems encountered during search". After we click "Details" in the pop window, we got the following message:
Unable to access "https://www.i2b2.org/updateSite Error parsing site stream [Premature end of file.] Premature end of files. Error parsing site stream. [Premature end of file.] Premature end of file.
We already set the proxy in our web browser. Did anyone encounter the same problem?
Thanks, Jennifer
From: Donahoe, Janice M [JDONAHOE.PARTNERS] Sent: Monday, December 12, 2011 10:27 AM To: Askar Ibragimov; i2b2 AUG Members Subject: RE: Installing import and export Cells
Hi Askar,
The import data and export data plug-ins are what we refer to as optional plug-ins. Although the import and export data plug-ins will work with the 1.6 software it is important to note that they do not currently support the new modifier tables and columns added to the 1.6 version of the i2b2 database.
This is because both plug-ins are still at version 1.4/1.5. All the other tables will import and export correctly.
As far as documentation, I am assuming you have already installed the File Repository (FR) cell. If not, the FR_Installation_Guide_1-6.pdf will help you in this process. The import data plug-in uses the FR cell so it is important that this is installed in order for importing to work correctly.
The process of installing / adding the import data plug-ins into the i2b2 Workbench is defined in the i2b2Workbench_Install_Guide_1-6.pdf. It can be found in section 1.4 called Features.
Both the FR and i2b2 Workbench install guides can be found on the i2b2 website but to make it easier for you I have attached both of them to this email.
Please let me know if you have any other questions.
Thanks.
Janice
From: Askar Ibragimov [askar.ibragimov.gmail] Sent: Thursday, December 08, 2011 11:04 AM To: i2b2 AUG Members Subject: Installing import and export Cells
Hello,
we're interested in evaluating i2b2 for our instiutute and for that purpose we are ultimately need to use import and export of data, so does anybody know:
are these importData\exportData cells, and relevant workbench functionality, work ok with 1.6.01?
HOW I can install the cells? There is no installation guide and my humble attempts in running 'ant' did not result in anything good.
I appreciate all the input.
Cheers, Askar
UT Southwestern Medical Center The future of medicine, today.
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From: Mendis, Michael E. Sent: Tuesday, December 13, 2011 11:13 AM To: Pablo, Ray; Travis Nagler Cc: i2b2 AUG Members Subject: Re: Data coming up non-obfuscated
Are you running the 1.5.5 sever?
It can be found at. https://www.i2b2.org/software/archive.html
On 12/12/11 4:50 PM, "Pablo, Ray" <pablorp.uci> wrote:
We are also experiencing the same issue as Travis. We are on 1.5.4 webclient. I tested on a user with DATA_OBFSC and USER. Also, we are staying with this version and have no plans to upgrade to 1.6. Any info would be greatly appreciated. Thanks.
Ray Pabl | Business Intelligence Developer | University of California, Irvine | 200 S. Manchester Avenue, Suite 508 | Orange, CA 92868 | pablorp.uci <taylorla.uci>
From: Travis Nagler [travis.nagler.ucdmc.ucdavis] Sent: Monday, November 21, 2011 2:48 PM To: Mike Mendis Cc: i2b2 AUG Members Subject: Re: Data coming up non?obfuscated
Mike/All,
I removed my user name from Demo2, and it still gives a number when below 10 (even if only approximate). I also tried looking up the queries on the Workbench, but it is having the same error. So it's not just on the webclient, it seems.
Anyway, I went online to the i2b2 website to try and find an archived version of 1.5.5 webclient. The only archive I can find is 1.5 (presumably ".0" because it's older than my 1.5.2 files). Is there a special place that you know of that has a list of ALL the various versions for download? A search didn't bring up anything for "1.5.5" from the website.
Thanks,
Travis
Travis H. Nagler
Senior Database Programmer American Burn Assoc. ?Data Coordinating Center UC Davis Division of Burn Surgery UC Davis Health System 2921 Stockton Blvd., Suite 1470 Sacramento, CA, 95817 http://www.ucdmc.ucdavis.edu <http://www.ucdmc.ucdavis.edu/> travis.nagler.ucdmc.ucdavis
From: Mike Mendis <mmendis.partners> To: Travis Nagler <travis.nagler.ucdmc.ucdavis> Cc: Date: 11/21/2011 12:21 PM Subject: Re: Data coming up non?obfuscated
Can you try using the latest 1.5.5 webclient. I think there was a bug in the client in that it would not parse the roles correctly. If it found a non?obfscucated role from a different project it would say this project was also non?obfuc. This was only a issue on the client.
mike
On 11/21/11 2:45 PM, "Travis Nagler" <travis.nagler.ucdmc.ucdavis> wrote:
P.S. I am logged in through AD and using Demo, not Demo2.
Travis
From: Travis Nagler/SOM/HS/UCD To: Mike Mendis <mmendis.partners <mmendis.partners> > Cc: i2b2 AUG Members Date: 11/21/2011 11:43 AM Subject: Re: Data coming up non?obfuscated
I have attached a text file with the PM cell response.
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
From: Mike Mendis To: Travis Nagler, i2b2 AUG Members Date: 11/21/2011 10:31 AM Subject: Re: Data coming up non?obfuscated
In the webclient what is the reppoonse from the pm server. If you click on Message Log on the top right, and than on the popup GetUserAuth, which should be the first one in the list.
mike
On 11/21/11 1:26 PM, "Travis Nagler" <travis.nagler.ucdmc.ucdavis> wrote:
I sent this question out on Friday afternoon last week, and I think I missed a lot of people heading out for the weekend. Does anyone have an idea on this problem (below)?
Thanks,
Travis
Forwarded by Travis Nagler/SOM/HS/UCD on 11/21/2011 10:25 AM
From: Travis Nagler/SOM/HS/UCD To: i2b2 AUG Members Date: 11/18/2011 01:40 PM Subject: Data coming up non?obfuscated
I was running a few queries, just checking things out on my dev install of v1.5.2, when I ran one that ended up with 1 record. It told me that at the bottom of the screen (screenshot below). I thought the answers were automatically obfuscated?
I was logged in as me through my AD account, and my user role on this project are USER, DATA_OBFSC, and DATA_AGG. I got the answer shown to me, as well, when I was just USER and DATA_OBFSC. The USER and DATA_OBFSC are what the Project Management installation PDF showed as it's example, so that's what I did.
The problem is not the obfuscation, which sometimes it showed 0 and sometimes it showed 1. It's that it showed anything at all. My understanding was that if the result set was less than 10, it just returns an answer of "<10" instead of the obfuscated result.
Is there something I need to turn on within the v1.5.2 code to get it obfuscated for less than 10 results?
Thanks,
Travis
P.S. Don't mind the 29.8 seconds. I was running some other scripts on the db at the same time. It usually only takes 3?5 seconds.
Travis H. Nagler
Senior Database Programmer American Burn Assoc. ?Data Coordinating Center UC Davis Division of Burn Surgery UC Davis Health System 2921 Stockton Blvd., Suite 1470 Sacramento, CA, 95817 http://www.ucdmc.ucdavis.edu
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From: Cowall, Jeff [jcowall.med.umich] Sent: Monday, December 12, 2011 3:59 PM To: Cowall, Jeff; 'Dan Connolly' Cc: Marc.Natter.childrens.harvard; askar.ibragimov.gmail; i2b2 AUG MembersSubject: RE: minimal clinical data loading into i2b2 [was: incremental...]
Make that logical key.
In the cancer registry version, we overloaded the encounter dimension to represent individual tumors, since each tumor is, in essence, a separate long-lived encounter, or a sub-patient, and we needed to keep separate records for each tumor. Works well. We plan on revisiting all of this, and the use of modifers, and possibly partitioned obs_fact tables when we move to 1.6+.
Jeff Cowall Sr. Data Architect – Clinical Research University of Michigan Medical Center IT 734 763-8141 desk 734 355-0330 cell
jcowall.med.umich
From: Cowall, Jeff [jcowall.med.umich] Sent: Monday, December 12, 2011 3:50 PM To: 'Dan Connolly' Cc: Marc.Natter.childrens.harvard; askar.ibragimov.gmail; i2b2 AUG MembersSubject: RE: minimal clinical data loading into i2b2 [was: incremental...]
"1" works. The only restriction we've found that the encounter_num in the observation fact can't be null, and is one component of the composite key of obs_fact. (This is all in v1.5)
For most observations, we load the source database name as the SOURCESYSTEM_CD, the table in the DB as the PROVIDER_ID, and the physical key of the row in the table that contains the observation as the ENCOUNTER_NUM. If users give us their successful query, we can give them a result table back that will join precisely with the source systems' data.
Makes life easier for us as a service provider.
Jeff Cowall
Sr. Data Architect – Clinical Research
University of Michigan Medical Center IT
734 763-8141 desk
734 355-0330 cell
jcowall.med.umich
From: Dan Connolly [dconnolly.kumc] Sent: Monday, December 12, 2011 11:59 AM To: Cowall, Jeff Cc: Marc.Natter.childrens.harvard; askar.ibragimov.gmail; i2b2 AUG MembersSubject: RE: minimal clinical data loading into i2b2 [was: incremental...]
We also do not currently load the provider or encounter dimensions,
Dan Connolly, KUMC Medical Informatics
On Mon, 2011-12-12 at 16:24 +0000, Cowall, Jeff wrote:
No encounter dimension? I didn't realize that was possible. How did you handle the encounter_num column in observation_fact? Just set it to something trivial? (e.g. 1)
From: Cowall, Jeff [jcowall.med.umich] Sent: Monday, December 12, 2011 11:25 AM To: 'Dan Connolly'; askar.ibragimov.gmail Cc: Marc.Natter.childrens.harvard; i2b2 AUG MembersSubject: RE: minimal clinical data loading into i2b2 [was: incremental...]
We currently do a "complete" reload monthly, mostly from our operational Health System Data Warehouse (source, finance oriented), our homegrown Clinical Data Repository (EMR).
We create a Limited Data Set version, de-identified Cohort version, and a NAACCR-based Cancer Registry version.
It's 99% Oracle pl/sql code and it takes about a day to load approximately a billion observation_fact rows across the three versions.
Cohort relies on PATIENT_MAPPING, and we're using MODIFIER_DIMENSION for the Cancer Registry. We haven't bothered with CODE_LOOKUP yet.
We also do not currently load the provider or encounter dimensions, but our result sets are joinable back into the HSDW and CDR if need be.
We're just starting to get experience with Informatica, and intend to move more towards that as we go on.
My advice is stay simple, play to your available skill sets, and to the level of access to the source data you have. The more direct, the better.
All best,
Jeff Cowall Sr. Data Architect - Clinical Research University of Michigan Medical Center IT jcowall.med.umich
From: Askar Ibragimov [askar.ibragimov.gmail] Sent: Monday, December 12, 2011 9:42 AM To: Natter, Marc Cc: i2b2 AUG Members Subject: Re: Incremental clinical data loading into i2b2
Hello, I am stydying i2b2 data schema and have following questions to the comuunity:- am I right that for a "complete" data import I need to fill (only) data tables:
ENCOUNTER_MAPPING
PATIENT_MAPPING
CODE_LOOKUP
CONCEPT_DIMENSION
OBSERVATION_FACT
PATIENT_DIMENSION
PROVIDER_DIMENSION
MODIFIER_DIMENSION
are there any sample, easy examples of someone's else import? Perhaps, a description document?
user i2b2demodata in the demo instance got many other tables in use, not described in the docs. These are:
QT_QUERY_RESULT_TYPE
QT_QUERY_STATUS_TYPE
QT_QUERY_INSTANCE
QT_QUERY_RESULT_INSTANCE
QT_PATIENT_SET_COLLECTION
QT_PATIENT_ENC_COLLECTION
QT_XML_RESULT
QT_ANALYSIS_PLUGIN
QT_ANALYSIS_PLUGIN_RESULT_TYPE
QT_PDO_QUERY_MASTER
QT_PRIVILEGE
QT_BREAKDOWN_PATH
ARCHIVE_OBSERVATION_FACT
DATAMART_REPORT
UPLOAD_STATUS
QT_QUERY_MASTER
SET_TYPE SOURCE_MASTER
SET_UPLOAD_STATUS
in import of clinical data, do I care about anything there?
Cheers, Askar
2011/12/8 Natter, Marc <Marc.Natter.childrens.harvard>:
Hi Nick,
To elaborate on Dave's comments, we use a two-step process, designed by Griffin Weber whose group consulted on the design and implementation of the project.
We pull transactional data via web services from another system (InForm electronic data capture platform) that handles all of the overhead involved with assuring ACID transaction validity. Our pipeline puts the incoming XML through an initial XSLT transform and maps CDISC ODM concepts to i2b2 ontology concepts (we have additional XML mapping tables), then generates a set of SQL commands which result in a validation report. If no errors are thrown, then a second set of SQL is generated for the inserts/updates/deletes.
Right now seems to work fine for our relatively modest needs (<1 GB) and our bottleneck is the webservice feeding our pipeline rather than the pipeline itself.
We're happy to share our code with others - only reason we haven't fully open-sourced already is that we have not documented this adequately for public release just yet and we don't have the bandwidth to support others' use at the moment.
Marc
From: Natter, Marc [Marc.Natter.childrens.harvard] Sent: Thursday, December 08, 2011 12:46 PM To: i2b2 AUG Members Subject: Re: Incremental clinical data loading into i2b2
Hi Nick,
To elaborate on Dave's comments, we use a two-step process, designed by Griffin Weber whose group consulted on the design and implementation of the project.
We pull transactional data via web services from another system (InForm electronic data capture platform) that handles all of the overhead involved with assuring ACID transaction validity. Our pipeline puts the incoming XML through an initial XSLT transform and maps CDISC ODM concepts to i2b2 ontology concepts (we have additional XML mapping tables), then generates a set of SQL commands which result in a validation report. If no errors are thrown, then a second set of SQL is generated for the inserts/updates/deletes.
Right now seems to work fine for our relatively modest needs (<1 GB) and our bottleneck is the webservice feeding our pipeline rather than the pipeline itself.
We're happy to share our code with others - only reason we haven't fully open-sourced already is that we have not documented this adequately for public release just yet and we don't have the bandwidth to support others' use at the moment.
Marc
From: Jack London [jack.london.KimmelCancerCenter] Sent: Thursday, December 08, 2011 12:40 PM To: nrh11.le.ac.uk Cc: i2b2 AUG Members Subject: Re: Incremental clinical data loading into i2b2
Nick,
We also do a complete refresh monthly. Recombinant Data has worked with our hospital to send us Oracle dump files of all clinical data. We add the specimen and registry data, and do whatever transformations are necessary to present the data in whatever version of i2b2 we are currently using (currently 1.6.01).
Jack
Jack London, Ph.D. Research Professor Cancer Biology Thomas Jefferson University Director, Informatics Shared Resource Kimmel Cancer Center 808 BLSB, 233 S. 10th St. Philadelphia, PA 19107
From: Peter Beninato [beninato.ohsu] Sent: Thursday, December 08, 2011 12:00 PM To: nrh11.le.ac.uk; i2b2 AUG Members Subject: RE: Incremental clinical data loading into i2b2
Hi,
The OHSU Cohort Discovery ETL process runs against Oracle and uses PL/SQL.
We maintain patient and visit map tables, they include data that allows tying back to the source system.
These are loaded/updated (MERGEd) incrementally.
They contain other fields related to patient and encounter. Initially, we were going to do a hash, but subsequently settled on a date comparison between the last "completed" run of the i2b2 system, and an etl_date on the source system tables.
The ontology, and observations are a full reload.
Peter
On 12/8/11 11:43 AM, "Ortiz, David" <David.Ortiz.childrens.harvard> wrote:
Nick,
Over on the Carranet project we're using home built ETL pipeline to take data from Phase Forward Inform and push it into a number of i2b2 systems via SQL inserts/updates. The pipeline as far as I know runs at least daily. We've been running that pipeline for a few months now and haven't any major issues to speak of.
I can't speak to the usefulness of the data import facilities in i2b2. They seem to be geared towards a single user interactively editing the data in i2b2 however, I could be mistaken. I'm really interested to know if anyone is using the built in web services for pushing large amounts of data into i2b2.
Dave Ortiz
CHIP
From: Russ Waitman [rwaitman.kumc] Sent: Thursday, December 08, 2011 11:58 AM To: Deborah Batson; 'nrh11.le.ac.uk' Cc: 'i2b2 AUG Members' Subject: RE: Incremental clinical data loading into i2b2
Hi Nick,
We don't do incremental either. We get source files from our contributing sources (such as the whole Epic Clarity backup file) at the beginning of a month. We bake a new copy of our repository every month (build identified star schema and then transform it to our de-id server which i2b2 hits) and then switch over to the new release (target mid month). This also lets us roll back if we screwed something up.
Pretty much all done with PL/SQL wrapped by python by Dan and Arvinder. http://informatics.kumc.edu/work/wiki/HERON
It's described on our site and the source code is mostly here: http://informatics.kumc.edu/work/browser/heron_load
Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center 913-945-7087
rwaitman.kumc.edu http://informatics.kumc.edu
Batson, Deborah <Deborah.Batson.childrenscolorado> 12/8/2011 10:37 AM
ETL Tools: We've used PL/SQL scripts and Talend against our Oracle data for i2b2 1.3, and currently we use SSIS against SQL Server for i2b2 1.6.RC1 and 1.6.Final. We load the pertinent Clarity (EPIC) tables into a staging area and generate the i2b2 data from there.
Strategy: We do not currently load data incrementally. We generate a Research Master Patient Index on the fly during data loading, originally because our first patient data set contained MRNs from two institutions and we needed a merge map, and now because "That's Just The Way We Do It". It's a one-time map of real MRN to rMPI, and we recreate that map for each load.
Incremental ETL is in our future, and I'm curious to see how others do this as well.
Please note – our website and email addresses have changed!
Deborah H Batson | Clinical Research Data Warehouse Architect | Department of Clinical Informatics
Anschutz Medical Campus | 13123 East 16th Avenue, Box B400 | Aurora, CO 80045
deborah.batson.childrenscolorado
From: Zapletal Eric [eric.zapletal.egp.aphp.fr] Sent: Thursday, December 08, 2011 9:30 AM To: nrh11.le.ac.uk Cc: i2b2 AUG Members Subject: Re: Incremental clinical data loading into i2b2
Dear All,
at AP-HP (Paris, France) we are using Talend Open Studio ( http://www.talend.com/index.php ) to load clinical data into I2B2 database.
Best regards,
Eric
On Dec 8, 2011, at 11:14 AM, Nick Holden wrote:
Dear AUG colleagues,
Could I ask you to describe the strategies and technologies you are each using to load clinical data into your i2b2 deployments?
We have made an initial effort loading some clinical data into our i2b2 datamart by converting data from our Onyx data capture / questionnaire tool into SQL inserts and running those inserts. We are also loading some pathology result data by making direct SQL inserts from our hospital's SQL data warehouse.
But we recognise some limitations with this reliance on SQL inserts, not least when the data we wish to load will be incrementally updated modifying existing Patient Data Objects is presumably accomplished more effectively using i2b2's web services, such as the data import cell?
We've identified three broad options for loading data - one at the database layer using SQL to SQL or similar, one using i2b2's data import functionality, and one using some messaging middleware such as an implementation of IHE's XDS.
We'd like to learn from other people's experiences, so can existing i2b2 users comment on the processes they use to load data into i2b2, and whether their approach delivers automated incremental updates to their i2b2 datamart?
Many thanks
Nick
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From: Daniele Segagni [daniele.segagni.fsm.it] Sent: Monday, December 12, 2011 3:30 AM To: Russ Waitman Cc: daniele.segagni.gmail; i2b2 AUG Members; riccardo.bellazzi.unipv.it; Dustin Key;
Jack London; Bhargav Adagarla; Dan Connolly; John Keighley; Matthew Mayo Subject: Re: any "R Engine Cell" for i2b2 users?
Dear Mr. Waitman,
thank you for your interest in our work. The paper you found describes the efforts made to integrate the r engine in the i2b2 infrastructure through a dedicated cell. As we mentioned in the paper and in the website where we posted the plug-in source code, we first concentrated our efforts on making Kaplan Meier analyses available within the cardiology desease area.
This work was one of our first attempts related to expanding and customizing the i2b2 system: it was done over a year and a half ago without using the i2b2 Virtual Machine with installed the development environment for creating new cell. For these reasons the R Engine Cell code posted here works fine on the i2b2 1.3 version. Actually out team is working in order to make the Kaplan Meier survival analysis plug-in compliant with the newer versions of i2b2.
Are you doing cancer survival analysis?
Actually we made only survival analysis with cardiological data, using events like syncopes, cardiac arrests or number of ICD (implantable cardioverter defibrillator) discharges
Longer term we may want to let people select their categorical stratifications dynamically, or, let them compare two sets dynamically created in i2b2 against one another.
Actually the statification is made only by gender, but one of the future implementation of the plug-in will let people to dynamically select their categorical stratifications using onology's concepts.
Since the cancer is also one of our area of interest, we could work together in an effort to expand and improve the integration of R within i2b2, initially making some changes to the plug-in for survival analysis.
Regards
Ing. Daniele SegagniLaboratorio di Informatica e Sistemistica per la Ricerca ClinicaIRCCS Fondazione S.Maugeri, Pavia, Italy
Russ Waitman ha scritto:
Dear Dr. Bellazzi, Daniele Segagni, and i2b2 community,
We've been working on loading our hospital tumor registry into i2b2 to integrate with the rest of
our data (based on the trail blazed by Jack London and Dustin Key).
We've got our first draft in i2b2 and would also like to see if we could begin to do basic survival analysis via an i2b2 plugin. We were excited to see the paper by Daniele Segagni et al
J Am Med Inform Assoc. 2011 May 1;18(3):314-7. Epub 2011 Jan 24. R engine cell: integrating R into the i2b2 software infrastructure. Segagni D, Ferrazzi F, Larizza C, Tibollo V, Napolitano C, Priori SG, Bellazzi R.
and then find their code was posted:
http://orbit.nlm.nih.gov/resource/r-engine-cell-integrating-r-i2b2-software-infrastructure http://code.google.com/p/i2b2-r-engine-project/downloads/list
Who else is using this approach to linking R to i2b2?
Any issues getting it to work?
What version of i2b2 were/are you running?
Are you doing cancer survival analysis?
We're thinking of first pass generating Kaplan Meier curves with stage (TNM from the NAACCR file, then possibly collaborative) and gender.
We'll use Vital Status from the NAACCR file as our initial event – Longer term we may want to let people select their categorical stratifications dynamically, or, let them compare two sets dynamically created in i2b2 against one another.
Any other high value statistical analysis you're doing?
We are currently on 1.4 but actively moving to 1.6 and will target getting this to work under 1.6.
Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center
rwaitman.kumc http://informatics.kumc.edu
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From: Sebastian Mate [Sebastian.Mate.imi.med.uni-erlangen.de] Sent: Thursday, December 08, 2011 10:39 AM To: 'Askar Ibragimov' Cc: i2b2 AUG Members Subject: AW: getting Workbench to work - pm cells connects but no other cells
Hi Askar,
just in the case that you are using the "i2b2 Wizard i2b2 hive": it uses port 9090 by default. Therefore, the entry in your i2b2workbench.properties should look this:
I2b2.1=i2b2demo,REST,http://192.168.56.101:9090/i2b2/rest/PMService/
For the standard VM, simply remove the ":9090" portion.
Another source of the problem could be a wrong registration of the hive cells. The URLs are stored somewhere inside the I2B2PM or I2B2HIVE schema. If you are using i2b2 Wizard, simply select "System Setup" => "Hive Tasks" => "Update Hive-IP". There, make sure to select the right network interface.
Sebastian
Von: i2b2 AUG Members Im Auftrag von Askar Ibragimov Gesendet: Donnerstag, 8. Dezember 2011 14:48 An: i2b2 AUG Members Betreff: getting Workbench to work - pm cells connects but no other cells
Hello,
I am experiencing an impossiblity to connect to my brand new i2b2 instance using Workbench. I have
edited its properties file to point to my IP and relevant PM cell. I can see that authorization interaction happens ok and JBoss log shows some interchange. However, nothing else happens and the workbench reports that it can not connect to other cells. Despite that web interface works fine, shows ontology etc etc., that is, i2b2 server is functional. However, harvard demo and VMWare image work fine, workbench can connect.
Note that I use different PCs for server and Workbench, and workbench for windows (precompiled) is downloaded from i2b2 server.
I appreciate some insights into subject
Sincerely yours, Askar
NEXT EMAIL
From: Sebastian Mate [Sebastian.Mate.imi.med.uni-erlangen.de] Sent: Thursday, December 08, 2011 10:33 AM To: 'Askar Ibragimov' Cc: i2b2 AUG EmailSubject: AW: i2b2 Wizard 1.3.1 for i2b2 1.6.01 released
Hi Askar,
thank you so much for providing this comprehensive feedback!
I know that the menu structure is rather mixed. This is because it's a grown system and changing everything would probably cause confusion among "long term" users. Maybe I will regroup everything in version 2.0.0 ...
Regarding APEX: it should work, but can only be accessed from localhost (from inside your VM) by default. There are some solutions and I will integrate them in the next version. Also, I will address the issues with the ADMIN interface. Until then keep in mind that the i2b2 Wizard duplicates almost all functions of the ADMIN interface ...
Cheers, Sebastian
Von: i2b2 AUG Email Im Auftrag von Askar Ibragimov Gesendet: Donnerstag, 8. Dezember 2011 13:46 An: Sebastian Mate Cc: i2b2 AUG EmailBetreff: Re: i2b2 Wizard 1.3.1 for i2b2 1.6.01 released
Hi again,
in database supplied by (demo project) there is no user i2b2 specified in the relevant datatable, though user roles table do contain some info for it. User demo did not had ADMIN role and changing role from USER to ADMIN in user roles datatable did not effect in access to /admin. The installed stuff differs from contents of VMWare image datatable where i2b2 user does exist.
Creating of i2b2 user manually in the relevant table I2B2PM.PM_USER_DATA solved the issue - now I can login to admin.
All the best, Askar
2011/12/8 Askar Ibragimov <askar.ibragimov.gmail>
Hi Sebastian,
thanks for reply!
Indeed it went better in 10.04.x TLS. But what is your login/pass for admin user? I can login with i2b2:demouser in VMWare image, but not in yours. Authorization in webclient works for demo:demouser.
Some other notes: Perhaps you would include information about needed version of Ubuntu in your download page? Also, aptitude is also not default there too, so you might check for it in the script. Also, I have noticed that order of menu items is rather mixed. Perhaps you would put download installation, jboss in order, then demodata. APEX service is not running somehow, so I can not access DB from web client.
Cheers, Askar
2011/12/7 Sebastian Mate <Sebastian.Mate.imi.med.uni-erlangen.de>:
Hi Askar,
thanks a lot for trying it!!!
If you're really using the very latest Ubuntu, this could be the issue. Please note that the only version that has been tested is 10.04.x LTS (with five years of "Long Term Support"). Later versions could use a different Java version and require a different installation procedure. Also, always make sure to pick the 32 bit version and always use US-English as your system's language (other languages could affect the initialization of date formats inside the Oracle DB). If everything is OK, it should install Java and Oracle automatically ... Anyway, I will check the Oracle installer again, maybe it can be improved.
It's also correct that it doesn't download the i2b2 source code. The reason is an licensing issue: obviously the i2b2 website asks you to accept the i2b2 license before you can download i2b2. I can't override this. Admittedly, there is a hidden directory on the Erlangen server, but this is for Erlangen-internal use only ...
Cheers, Sebastian
PS: One of my colleagues (a true i2b2 greenhorn) is currently trying to install it, I'm very curious about his progress ... :-D
Von: i2b2 AUG Members Im Auftrag von Askar Ibragimov Gesendet: Mittwoch, 7. Dezember 2011 15:09 An: Sebastian Mate; i2b2 AUG EmailBetreff: Re: i2b2 Wizard 1.3.1 for i2b2 1.6.01 released
Hi Sebastian,
I have tested your script and have the following comments. I am performing a fresh install on very last ubuntu taken from its website.
it does not download i2b2 out of the box and it attempts to do so from some place in Erlangen server. This I had to do manually.
it fails to get java. After manually installing java (according to https://help.ubuntu.com/community/Java#Sun_Java) your script still complains that java is not installable. You perhaps need to debug autoAptInstall. In fact, your script does not check for aptitude package which is NOT installed by default and causes false negatives.
upon installation, I tried again to log in. No luck. Then I noticed that ORACLE is not running (no apex). Running checks on daemon show:
root@autoinst:/etc/init.d# ./oracle-xe status Oracle Database 10g Express Edition is not configured. You must run '/etc/init.d/oracle-xe configure' as the root user to configure the database.
apparently it should be done automatically after install?
cheers Askar
2011/12/6 Mauro <mauro.bucalo.gmail>:
Many many thanks!!
2011/12/5 Askar Ibragimov <askar.ibragimov.gmail>:
Thank you! Will be tried out firth thing after I back to office.
From: Kohane, Isaac Samuel [Isaac_Kohane.hms.harvard] Sent: Monday, December 05, 2011 5:22 PM To: Sebastian Mate Cc: i2b2 AUG EmailSubject: Re: i2b2 Wizard 1.3.1 for i2b2 1.6.01 released
Thank you Sebastian!
On Dec 5, 2011, at 12:43 PM, Sebastian Mate wrote:
Hi all,
I'm very happy to present a new version of i2b2 Wizard with full support for i2b2 1.6 this evening.
From the change log:
Major upgrade to support i2b2 1.6.01
Added auto-update function for i2b2 Wizard
Dramatically improved error handler, which operates much finer-grained now
Improved program structure to simplify the integration of future i2b2 versions
Changed/Improved Oracle XE installation
Added a 'repair my i2b2 installation' function
Added 'awareness' of project names 'Demo' and user names 'i2b2' and 'demo' (reserved by the Boston Demodata)
Improved/fixed progress-bars (thanks to Eric Zapletal)
Updated PDF documentation
SHRINE is not working in this version, however, installation procedure is still included
Changed version naming to Unix style (1.3.0 instead of 1.30)
Please note that it cannot be used to upgrade an existing i2b2 installation. You have to start from scratch with i2b2 wizard.
The program, as well as some screenshots and videos, can be found here: http://www.imi.med.uni-erlangen.de/~matesn/i2b2wizard/
Please make sure to pick version 1.3.1!
The tool seems to work fine, but it still needs heavy, very heavy testing. Any feedback is highly appreciated!
Thanks, Sebastian
Dipl.-Inf. Univ. Sebastian Mate Chair of Medical Informatics, Friedrich-Alexander-University Erlangen-Nuremberg, Germany Krankenhausstrasse 12, 91054 Erlangen
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From: Keith Marsolo [keith.marsolo.cchmc] Sent: Tuesday, December 06, 2011 8:56 AM To: Bickel, Jonathan Cc: i2b2 AUG Members Subject: Re: Age at first time fact appears
Jon,
Jeremy's described our approach to age at event, but after reading your message a couple of times, I think you're asking for a fact that would denote the patient's age at the first occurrence? I think the most straightforward approach would just to treat "age_when_concept_appears" as any other derived attribute and compute the value as part of the ETL process. It's probably most logical to add it as a modifier, and then only calculate the value if the fact is indeed the first occurrence. In the end, though, it's probably simpler to just compute age at fact for every observation, and for each concept, select the minimum age and create the "age_when_concept_appears" variable.
I'm not sure if it's possible to use the dynamic calculation features of 1.6 (or whatever they're called) to do this. Calculating the age part is easy (same as you'd do "age at event"), but you need a way to select the minimum value. I don't know enough about 1.6 to know if this is possible without modifying the code. I'm usually in favor of actually instantiating the derived variables instead of just calculating them on the fly, simply because if someone is going to want to query on something in i2b2, they're probably going to end up wanting to query it in SAS. Having it already computed saves a step.
That's my two cents, anyway.
Keith
On Dec 6, 2011, at 8:29 AM, Jeremy Nix wrote: Jon,
We choose to create an additional column in the observation_fact column named "age_at_event" which identifies the patients age when the observation was recorded (fact start date - birth date). This did require us to modify the CRC cell code to add in support for querying of this column. We then could then constrain by concept and by age at event. Our code is not currently 1.6 compatible, so I can't help you out completely. I can refer you to our public SVN site (https://bmi.cchmc.org/svn/i2b2/i2b2/public)where you can see what we did and incorporate those changes yourself. Or, you could wait until we have implemented the 1.6 changes into our codebase (unknown timeframe). I also believe other institutions have implemented similar changes.
Another potential option would be for you to create a modifier for every concept (@AgeAtEvent). I'm less familiar with modifiers as they currently exist, so I wouldn't know how to guide you with this option. Some other users on this list should be able to fill in the gaps though.
Jeremy Nix Senior Application Developer Cincinnati Children's Hospital Medical Center
On 12/05/2011 04:11 PM, Bickel, Jonathan wrote:
Has anyone ever tried to establish a concept in the ontology table of "age at firsttime concept appears"?Looking for advice of how to use the new features of i2b2 1.6 to do such a thing.
Thanks
Jon
Jonathan Bickel M.D. Director of Clinical Research Informatics Children's Hospital Boston
Email: Jonathan.Bickel.childrens.harvard Skype: jonojuno1
From: Jennifer Cai Date: Mon, 5 Dec 2011 19:58:55 To: i2b2 AUG Members Subject: Group Variable (optional) in File Repository installation
Hi,
On the page 7 of the installation guide of 1.6 file repository cell, there is anoptional step to set up the Group Variable FRMethod. (optional) To allow adminusers to transfer files directly via SFTP, create aGroup Variable called FRMethod with the value of SFTP and FRHost with the name ofthe machine.
In which application/system should we set up the Group Variable?
Thanks, Jennifer
UT Southwestern Medical Center The future of medicine, today.
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From: Mendis, Michael E. Sent: Monday, December 05, 2011 6:02 PM To: Jennifer Cai; i2b2 AUG Members Subject: RE: Import data view in workbench 1.6
It is an optional plugin, if you goto Help -> Add new software, it will connect to the i2b2 website and download the plugin
mike
From: Jennifer Cai [Jennifer.Cai.UTSouthwestern] Sent: Mon 12/5/2011 5:46 PM To: i2b2 AUG Members Subject: Import data view in workbench 1.6
Hello,
We installed the File repository cell without any errors on the window server. FR service is on. But in workbench application, we can't find the Import data view tab.
Do we miss anything?
Thanks, Jennifer
Back Home<http://localhost:9090/i2b2/axis2-web/index.jsp> | Refresh<http://localhost:9090/i2b2/>
Available services FRService<http://localhost:9090/i2b2/services/FRService?wsdl>
Service EPR : http://localhost:9090/i2b2/services/FRService Service REST epr : http://localhost:9090/i2b2/services/FRService : http://localhost:9090/i2b2/rest/FRService Service Description : FRService Service Status : Active Available Operations
recvfileRequest
sendfileRequest
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From: Michael.C.Ford.kp Sent: Monday, December 05, 2011 5:22 PM To: i2b2 AUG Members Subject: Re: VMware i2b2
I received no response but I have upgraded my VM image so that it is functional for my needs.
The VMImage is a Centos 5.7 release ( open source red hat )
So I brought up the VM and tested that it was working, then logged in as root.
Update to Gome
yum groupinstall "X Window System" "GNOME Desktop Environment"
Reset my run level to 5
vi /etc/inittab
id:5:initdefault:
reboot found the HTTP server had stopped so I restarted System->Administration->Server settings->services->https
System works with desktop access.
Install of VMtools to allow file shares and created file share to my PC.
Note: drag and drop functionality seems to be unavailable with VMPlayer, but that's a minor inconvenace.
firefox not avaliable : yum install firefox
All working but at this point I have hit a snag the image is set with a fixed size of 8 gig the root folder is 96% filled, leaving no room for tools. I wanted to install eclipse with the subversion to allow for a nice development environment.
I might suggest in your next vm build to create with variable space this will allow for new tool to be added to the image.
http://www.centos.org/modules/smartfaq/faq.php?faqid=50 http://www.cyberciti.biz/tips/linux-changing-run-levels.html
Thank you.
Michael C Ford/CA/KAIPERM
12/01/2011 12:00 PM To: i2b2 AUG Members cc Subject VMware i2b2 Link
I have been looking at the VMware i2b2 and I had a few questions.
possible to get access to the linux desktop?
I would like to reconfigure to access an external database as a preliminary test this would be the ontology, work and CRC .
I can ping to the database server from the VM so this seems very feasible to me.
Michael C Ford
Application Development Project Manager Division of Research 2000 Broadway Oakland Ca 041W09 Michael.C.Ford.kp
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From: Jennifer Cai [Jennifer.Cai.UTSouthwestern] Sent: Monday, December 05, 2011 2:59 PM To: i2b2 AUG Members Subject: Group Variable (optional) in File Repository installation
Hi,
On the page 7 of the installation guide of 1.6 file repository cell, there is an optional step to set up the Group Variable FRMethod_. (optional) To allow admin users to transfer files directly via SFTP, create a_
Group Variable called FRMethod with the value of SFTP and FRHost with the name of
the machine.
In which application/system should we set up the Group Variable?
Thanks,
Jennifer
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From: Askar Ibragimov [askar.ibragimov.gmail] Sent: Monday, December 05, 2011 12:15 PM To: Mendis, Michael E. Cc: Peter Beninato; Luke Vincent Rasmussen; i2b2 AUG Members Subject: Re: can not login to /admin !
Hi,
nope, I run on 9090 because 8080 is used by Oracle.
In fact these files are the sam on your VMWare yet both admin and client work there, regardless of what is said in these files. These files are located inder /admin and /webclinet folders and there
are some ontehr similar files in upstream directory. But I repeat,everything in /var/www/html was copied directly as in your image.
Something else should cause problem.
Also I wonder why your image doesnt care about wrong URL for webclient PM.
Cheers, ASkar
2011/12/5 Mike Mendis <mmendis.partners>:
On the VM jboss is running on port 9090, if your new jboss is not on that port, than change 9090 to 8080 (default)
mike
On 12/5/11 11:55 AM, "Askar Ibragimov" <askar.ibragimov.gmail> wrote:
Hi!
these files were actually directly copied from VM. However, Java stuff and Data were installed manually - so what I have copied are only the online web files.
CLIENT
[root@centos_vm webclient]# cat i2b2_config_data.js
{
urlProxy: "index.php",
urlFramework: "js-i2b2/",
//-----------------------------------------------------------------------------------------
// THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO
lstDomains: [
{ domain: "i2b2demo",
name: "i2b2demo",
urlCellPM: "http://127.0.0.1/i2b2/rest/PMService/",
allowAnalysis: true,
debug: true
}
]
//-----------------------------------------------------------------------------------------
}
ADMIN
[root@centos_vm admin]# cat i2b2_config_data.js
{
urlProxy: "index.php",
urlFramework: "js-i2b2/",
//-----------------------------------------------------------------------------------------
// THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO
lstDomains: [
{ name: "localhost",
domain: "i2b2demo",
debug: true,
adminOnly: true,
urlCellPM: http://localhost:9090/i2b2/rest/PMService/
}
]
//-----------------------------------------------------------------------------------------
}
Cheers Askar
2011/12/5 Mike Mendis <mmendis.partners>:
Adding
@i2b2ADMIN---A
Would allow the user i2b2 to login as a admin. In regards to the possible database or login, can you login to the webclient to the i2b2 server without any issues? Also can you email the i2b2_config_data.js for both the webclient and the admin.
Thanks
mike
On 12/5/11 11:17 AM, "Askar Ibragimov" <askar.ibragimov.gmail> wrote:
Hello Mike,
many thanks for the answer. I hope to figure out the cause together with the developers.
here's content of my pm_project_user_role (created by "Data installation procedure" that was performed according to docs)
PROJECT_ID USER_ID USER_ROLE_CD CHANGE_DATE ENTRY_DATE CHANGEBY_CHAR
STATUS_CD
@ i2b2 ADMIN - - - A
Demo OBFSC_SERVICE_ACCOUNT USER - - - A
Demo OBFSC_SERVICE_ACCOUNT MANAGER - - - A
Demo OBFSC_SERVICE_ACCOUNT DATA_OBFSC - - - A
Demo AGG_SERVICE_ACCOUNT USER - - - A
Demo AGG_SERVICE_ACCOUNT DATA_OBFSC - - - A
Demo AGG_SERVICE_ACCOUNT DATA_AGG - - - A
Demo i2b2 MANAGER - - - A
Demo i2b2 USER - - - A
Demo i2b2 DATA_OBFSC - - - A
Demo demo USER - - - A
Demo demo DATA_DEID - - - A
Demo demo DATA_OBFSC - - - A
Demo demo DATA_AGG - - - A
Demo demo DATA_LDS - - - A
Demo demo EDITOR - - - A
Here's what you got in VMWare demo
PROJECT_ID USER_ID USER_ROLE_CD CHANGE_DATE ENTRY_DATE CHANGEBY_CHAR
STATUS_CD
@ i2b2 ADMIN - - - A
Demo OBFSC_SERVICE_ACCOUNT USER - - - A
Demo OBFSC_SERVICE_ACCOUNT MANAGER - - - A
Demo OBFSC_SERVICE_ACCOUNT DATA_OBFSC - - - A
Demo AGG_SERVICE_ACCOUNT USER - - - A
Demo AGG_SERVICE_ACCOUNT DATA_OBFSC - - - A
Demo AGG_SERVICE_ACCOUNT DATA_AGG - - - A
Demo i2b2 MANAGER 24.11.11 - i2b2 A
Demo i2b2 USER 24.11.11 - i2b2 A
Demo i2b2 DATA_OBFSC 24.11.11 - i2b2 A
Demo demo USER 24.11.11 - i2b2 A
Demo demo DATA_DEID 24.11.11 - i2b2 A
Demo demo DATA_OBFSC 24.11.11 - i2b2 A
Demo demo DATA_AGG 24.11.11 - i2b2 A
Demo demo DATA_LDS 24.11.11 - i2b2 A
Demo demo EDITOR 24.11.11 - i2b2 A
@ miketest ADMIN 02.11.11 02.11.11 i2b2 A <-- including \ below this line data is NOT in my table.
Demo demo MANAGER 24.11.11 24.11.11 i2b2 A
Demo demo DATA_PROT 24.11.11 24.11.11 i2b2 A
Demo i2b2 DATA_PROT 24.11.11 24.11.11 i2b2 A
Demo i2b2 DATA_AGG 24.11.11 24.11.11 i2b2 A
Demo i2b2 DATA_LDS 24.11.11 24.11.11 i2b2 A
Demo i2b2 DATA_DEID 24.11.11 24.11.11 i2b2 A
Demo i2b2 EDITOR 24.11.11 24.11.11 i2b2 A
none of these contain the line you suggested.
Inserting the line you specified (snmtest) – I wonder how I could figure out what is needed to be inserted – did not changed the situation.
I also proceed to add the lines that I have seen in VMWare image. This also changed nothing.
I therefore conclude that it is likely problem with database connection problem, java and interface stuff seem not to be able to reach actual information. Or, some other tables shall be altered.
I apprecitate if you let me know where to look in order to ensure that connection between application body and database is ok?
Cheers, Askar
2011/12/2 Mike Mendis <mmendis.partners>:
Are you using 1.6 or 1.6.01? Also correct me, but you are copying the current vm install to a new one correct? Which is fine and should work. On the database side, did you create a user in the pm_projct_user_role table with the following
Project_id user_id user_role status_cd
@ snmtest ADMIN A
mike
On 12/2/11 11:55 AM, "Peter Beninato" <beninato.ohsu> wrote:
Haven't there been other posts about a missing column?
And w/o that column there is an error like you are receiving?
From: Askar Ibragimov [askar.ibragimov.gmail] Sent: Friday, December 02, 2011 8:13 AM To: Mike Mendis Cc: Luke Vincent Rasmussen; i2b2 AUG Members Subject: Re: can not login to /admin !
Hello,
the VMWare image indeed allows access, but despite I double checked configuration of my own installation, this does not work. I am continue to getting answers about "Requires ADMIN role". Could you please point me towards some checks that might locate the source of a problem?
It has to be noted, that on my own installation in Admin login I got
"i2b2 Host" = "i2b2demo", snd on VMWare image, the windows says that I am logging in to "localhost". My own istallation contains files directly copied from VMWare image! Could it possibly suggest something?
here's how config file for admin looks like:
[root@centos_vm admin]# cat i2b2_config_data.js
{
urlProxy: "index.php",
urlFramework: "js-i2b2/",
//---------------------------------------------------------------------------------------
// THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO
lstDomains: [
{ name: "localhost",
domain: "i2b2demo",
debug: true,
adminOnly: true,
urlCellPM: "http://localhost:9090/i2b2/rest/PMService/"
}
]
//---------------------------------------------------------------------------------------
}
Sincerely yours, Askar
2011/11/29 Mike Mendis <mmendis.partners>:
For the admin user try:
user: i2b2
pass: demouser
mike
On 11/29/11 9:25 AM, "Luke Vincent Rasmussen" <luke.rasmussen.northwestern> wrote:
Askar - I just got the VM downloaded and was able to give this a shot. When I go to the admin page, if I login with the default credentials that appear (demo:demouser), I get the same error that you do about requiring the ADMIN role. If I login as i2b2:demouser I don't have any issues.
Could you double-check that you put in the login and password in correctly, and if it still doesn't work then you may need to start digging into the Jboss log at /opt/jboss/server/default/log
Luke
On 11/29/11 4:28 AM, "Askar Ibragimov" <askar.ibragimov.gmail> wrote:
Hello,
I am installing i2b2 for first time and have further questions.
Documentation for PM cell says that I may login with user i2b2:demouser to the admin section of i2b2. It does not happen and I see "Requies ADMIN role" dialogie box. Your current VMWare image on the website has the same problem. How do I fix it?
In ontology, file etc/spring/ontology.properties, file contains
ontology.ws.pm.bypass.role=MANAGER while doc suggests
ontology.ws.pm.bypass.role=ADMIN.
Which one is correct?
Cheers, Askar
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From: Askar Ibragimov [askar.ibragimov.gmail] Sent: Friday, December 02, 2011 6:28 AM To: i2b2 AUG Members Subject: changing hostname makes JBoss not working in VMWare image
Hello,
apparently in my case changing hostname in supplied VMWare image (via system-config-network) from localhost.localdomain to something else (I tried name i2b2) will result in failure of starting JBoss and non-functioning i2b2. I appreciate a suggestion how to stop it to happen
error log:
12:33:43,669 INFO [Server] Starting JBoss (MX MicroKernel)... 12:33:43,670 INFO [Server] Release ID: JBoss [Trinity] 4.2.2.GA (build: SVNTag=JBoss_4_2_2_GA date=200710221139) 12:33:43,671 INFO [Server] Home Dir: /opt/jboss-4.2.2.GA 12:33:43,671 INFO [Server] Home URL: file:/opt/jboss-4.2.2.GA/ 12:33:43,671 INFO [Server] Patch URL: null 12:33:43,671 INFO [Server] Server Name: default 12:33:43,671 INFO [Server] Server Home Dir: /opt/jboss-4.2.2.GA/server/default 12:33:43,671 INFO [Server] Server Home URL: file:/opt/jboss-4.2.2.GA/server/default/ 12:33:43,671 INFO [Server] Server Log Dir: /opt/jboss-4.2.2.GA/server/default/log 12:33:43,672 INFO [Server] Server Temp Dir: /opt/jboss-4.2.2.GA/server/default/tmp 12:33:43,672 INFO [Server] Root Deployment Filename: jboss-service.xml 12:33:43,853 INFO [ServerInfo] Java version: 1.6.0_16,Sun Microsystems Inc. 12:33:43,853 INFO [ServerInfo] Java VM: Java HotSpot(TM) Server VM 14.2-b01,Sun Microsystems Inc. 12:33:43,853 INFO [ServerInfo] OS-System: Linux 2.6.18-274.3.1.el5,i386 12:33:44,201 INFO [Server] Core system initialized 12:33:46,416 WARN [BasicMBeanRegistry] javax.management.MBeanRegistrationException: preRegister() failed: [ObjectName='jboss.remoting:service=NetworkRegistry', Class=org.jboss.remoting.network.NetworkRegistry (org.jboss.remoting.network.NetworkRegistry@b7b3f9)] 12:33:46,429 ERROR [MainDeployer] Could not create deployment: file:/opt/jboss-4.2.2.GA/server/default/conf/jboss-service.xml org.jboss.deployment.DeploymentException: - nested throwable: (java.lang.reflect.InvocationTargetException)
To add to the list of things missing in the docs, for some reason there is user "tomcat" exists in image, JBoss is running from this user; /opt/jboss is the symlink to jboss install dir and there is /etc/init.d/jboss startup script used in the image. Installing also requires avoiding GNU java that is installed by default in CentOS.
Documentation do not describe installing jboss as a service, unfortunately, neither any of these issues.
Cheers, Askar
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From: Russ Waitman [rwaitman.kumc] Sent: Thursday, December 01, 2011 3:27 PM To: Mendis, Michael E.; Nagler, Travis Cc: Connolly, Dan; Murphy, Shawn N.; Qiu, Haijun; i2b2 AUG Members Subject: Re: CAS/Kerberos login?
Hi Travis,
Dan C's on vacation but can probably comment when he gets back on Tuesday. Dan, Phillip Reeder and I did meet with Mike at the June conference about some changes Mike made to better support integration of different authentication mechanisms. We are finally now at a point where Dan and Arvinder are going to dig into refactoring our project into 1.6 so that might also be the time Dan would re-evaluate that code,
Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center
rwaitman.kumc http://informatics.kumc.edu
"Travis Nagler" <travis.nagler.ucdmc.ucdavis> 12/1/2011 12:57 PM
Did a solution for a CAS sign-on ever come around? We are using an AD login now and it works great, very easy to setup in the Params area. But we're looking at changing over to CAS/Kerberos.
Are there parameter names available? Documentation would be nice but I'll take whatever I can get.
I read through the KUMC CAS ticket page but it ended up leading to ticket #115 which essentially had this email thread below as the last entry.
We're on v1.5.5.
Thanks,
Travis
Travis H. Nagler
Senior Database Programmer American Burn Assoc. - Data Coordinating Center UC Davis Division of Burn Surgery UC Davis Health System 2921 Stockton Blvd., Suite 1470 Sacramento, CA, 95817 http://www.ucdmc.ucdavis.edu
travis.nagler.ucdmc.ucdavis
From: Mike Mendis <mmendis.partners> To: "Murphy, Shawn N." <SNMURPHY.PARTNERS>, Russ Waitman <rwaitman.kumc>, Haijun Qiu <QIUH.email.chop>,
Date: 06/29/2011 10:10 AM Subject: Re: openldap user authentication
I have refactored the code for rc4, that it now contains a interface called SecurityAuthentication I created a class called SecurityAuthenticationNTLM and extended the interface to deal with NTLM calls. Any parameters that are needed such as domain for NTLM, would be in a param similar to the screenshot below. We can easy create a another class for CAS. I looked at the ticket but did not see any code, if you have some code I can transform to the class and we can try it out.
mike
On 6/21/11 9:37 AM, "Murphy, Shawn N." <SNMURPHY.PARTNERS> wrote:
I think Mike put either Dan's or Phillips's implementation into the 1.6 upcoming RC4 release as well, accessible through the PM Navigation...
Thanks, Shawn.
From: Russ Waitman [rwaitman.kumc] Sent: Monday, June 06, 2011 4:43 PM To: Haijun Qiu; i2b2 AUG Members Subject: Re: openldap user authentication
Hiajun,
Dan Connolly here did CAS integration as that was KUMC's single sign on solution. I think he's put our code hooks between i2b2 and CAS up on our TRAC website. The ticket that discusses the work is at: http://informatics.kumc.edu/work/ticket/8
Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center
rwaitman.kumc http://informatics.kumc.edu <http://informatics.kumc.edu/>
"Qiu, Haijun" <QIUH.email.chop> 6/6/2011 1:09 PM
Hello,
Does anybody know what it takes to support openldap user authentication in i2b2. Which source and configuration files to modify? Link to some detailed documentation? We are looking into letting users use their openldap credentials to login into i2b2. We are currently running i2b2 1.5.
If openldap is still not supported, some documentation on Windows Active Directory sign?on will also help us to understand how much efforts may require to eventually support single sign?on.
Thanks,
Haijun Qiu
Bioinformatics Scientist Center for Applied Genomics The Children's Hospital of Philadelphia Phone:
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From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Thursday, December 01, 2011 2:45 PM To: i2b2 AUG Members Subject: Encounter set info in web client
When the Encounter Set is part of the query results, new in 1.6, the information that is visualized in the Previous Queries plugin is rather cryptic, like 'PR CRC_ID-XX'. Maybe for the sake of the user this could be changed to include encounter_num, patient_num, start_date...?
Thanks,
Yves
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From: Patibandla, Nandan [Nandan.Patibandla.childrens.harvard] Sent: Thursday, December 01, 2011 2:05 PM To: Jeremy Nix; Mendis, Michael E. Cc: i2b2 AUG Members Subject: RE: Not generating the Patient sets
HI Mike
I created a new crc database with same database setting/permission imported a small subset of 100 patients in to the new database all the other databases are same and I was able to get the results but if I do it with database which has all the records (Observation_fact table has 200000000 records), I am having this issue.
We did not have the issue when we used 1.5
Nix,
I was not able to figure anything the Ontology table. I am using the modifiers, but I am only using the modifiers on one set of ontology which I am using on the new database I created.
Thank you
Nandan
From: Jeremy Nix [Jeremy.Nix.cchmc] Sent: Thursday, December 01, 2011 12:28 PM To: Patibandla, Nandan; Mike Mendis Cc: i2b2 AUG Members Subject: RE: Not generating the Patient sets
Looking at the original stacktrace/error log, it looks like the out of memory error is occuring in MetadataDao.getMetadataForOptionalField. That seems like an odd place to run out of memory off hand. You may want to look at how your ontology is structured. Are you utilizing 1.6 modifiers? Is there any cyclical paths being created. I do not have the source code for MetadataDao on hand, but I would review that method to see what exactly is going on that could generate a large need for memory.
Jeremy Nix
"Patibandla, Nandan" <Nandan.Patibandla.childrens.harvard> 12/1/2011 12:14 PM
HI Mike, I increased the heap size, but still having the same issue. The machine has 8Gb memory
Error, when I open the tree to look at the patnums
12:11:19,861 INFO [OracleDAOFactory] Using datasource java:QueryToolDSv15 12:11:19,877 INFO [DataSourceLookupHelper] Located DataSource for hiveId=[i2b2d ev] projectId=[/i2b2_v15/] 12:11:19,877 INFO [OracleDAOFactory] Using datasource java:QueryToolDSv15 12:11:19,877 INFO [STDOUT] ->INSERT INTO i2b2_v16_crc.dbo.QT_PDO_QUERY_MASTER ( USER_ID, GROUP_ID,CREATE_DATE,REQUEST_XML,I2B2_REQUEST_XML) VALUES
(?,?,?,?,?) 12:11:19,939 INFO [DataSourceLookupHelper] Located DataSource for hiveId=[i2b2d ev] projectId=[/i2b2_v15/] 12:11:19,955 INFO [OracleDAOFactory] Using datasource java:QueryToolDSv15 12:11:27,068 INFO [STDOUT] dateTime
12:11:27,068 INFO [DataSourceLookupHelper] Located DataSource for hiveId=[i2b2d
ev] projectId=[/i2b2_v15/] 12:11:27,068 INFO [OracleDAOFactory] Using datasource java:QueryToolDSv15 12:12:02,901 ERROR [ContainerBase] Exception invoking periodic operation: java.lang.OutOfMemoryError: GC overhead limit exceeded 12:12:11,703 WARN [LocalManagedConnectionFactory] Error notifying of connection error for listener: org.jboss.resource.connectionmanager.TxConnectionManager$Tx ConnectionEventListener@14e1cc5[state=NORMAL mc=org.jboss.resource.adapter.jdbc. local.LocalManagedConnection@ebef3b handles=1 lastUse=1322759479861 permit=true trackByTx=true mcp=org.jboss.resource.connectionmanager.JBossManagedConnectionPo ol$OnePool@1a70f10 context=org.jboss.resource.connectionmanager.InternalManagedC onnectionPool@ce0102 xaResource=org.jboss.resource.connectionmanager.TxConnectio nManager$LocalXAResource@9301eb txSync=null] java.lang.OutOfMemoryError: GC overhead limit exceeded
Thank you Nandan
From: Mike Mendis [mmendis.partners] Sent: Thursday, December 01, 2011 10:51 AM To: Patibandla, Nandan Cc: i2b2 AUG Members Subject: Re: Not generating the Patient sets
Looks like a memory heap error. Ran out of memory. Try increasing the heap size:
set JAVA_OPTS=%JAVA_OPTS% -Xms1024m -Xmx2048m
How much memory is on the machine?
On 12/1/11 10:44 AM, "Patibandla, Nandan" <Nandan.Patibandla.childrens.harvard> wrote:
Hi Mike,
I am having this problem again, I created a new database and imported all the data from 1.5 version to 1.6 version of the database.
When I run the query, it gives the patient count but do not produce the patient_set. I looked in to the QT_PATIENT_SET_COLLECTION to check whether the data was loaded in to the table and I see that the patients numbers are inserted in to the table but when I expand the patient_set tree in the webclient, it just doesn't show anything instead I see the wait symbol.
Below is the error message I received after 5 -10 minutes of waiting.
No record was inserted in to the [QT_PDO_QUERY_MASTER] table.
Also I used the old 1.5 webclient and ran the same query and in the message logs I found that the getPDO_fromInputlist is giving the error (attached is the error message)
Thank you
Nandan
16:55:10,515 INFO [OracleDAOFactory] Using datasource java:QueryToolDSv15 16:55:10,531 INFO [DataSourceLookupHelper] Located DataSource for hiveId=[i2b2d ev] projectId=[/i2b2_v15/] 16:55:10,531 INFO [OracleDAOFactory] Using datasource java:QueryToolDSv15 16:55:10,750 INFO [STDOUT] ->INSERT INTO i2b2_v16_crc.dbo.QT_PDO_QUERY_MASTER ( USER_ID, GROUP_ID,CREATE_DATE,REQUEST_XML,I2B2_REQUEST_XML) VALUES (?,?,?,?,?) 16:55:10,797 INFO [DataSourceLookupHelper] Located DataSource for hiveId=[i2b2d ev] projectId=[/i2b2_v15/] 16:55:10,797 INFO [OracleDAOFactory] Using datasource java:QueryToolDSv15 16:55:18,723 INFO [STDOUT] dateTime 16:55:18,739 INFO [DataSourceLookupHelper] Located DataSource for hiveId=[i2b2d ev] projectId=[/i2b2_v15/] 16:55:18,739 INFO [OracleDAOFactory] Using datasource java:QueryToolDSv15 16:56:02,561 ERROR [STDERR] Exception in thread "ContainerBackgroundProcessor[St andardEngine[jboss.web]]" 16:56:02,561 WARN [LocalManagedConnectionFactory] Error notifying of connection error for listener: org.jboss.resource.connectionmanager.TxConnectionManager$Tx ConnectionEventListener@4102f2[state=NORMAL mc=org.jboss.resource.adapter.jdbc.l ocal.LocalManagedConnection@e1bc04 handles=1 lastUse=1322517310531 permit=true t rackByTx=true mcp=org.jboss.resource.connectionmanager.JBossManagedConnectionPoo l$OnePool@1fedd53 context=org.jboss.resource.connectionmanager.InternalManagedCo nnectionPool@1749e33 xaResource=org.jboss.resource.connectionmanager.TxConnectio nManager$LocalXAResource@286948 txSync=null] java.lang.OutOfMemoryError: GC overhead limit exceeded 16:59:16,749 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceed ed 16:59:21,080 ERROR [STDERR] Exception in thread "Thread-5" 16:59:21,080 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceed ed 16:59:22,643 ERROR [STDERR] org.jboss.util.NestedSQLException: Error; - nested t hrowable: (java.lang.OutOfMemoryError: Java heap space) 16:59:22,643 ERROR [STDERR] at org.jboss.resource.adapter.jdbc.WrappedConnec tion.checkException(WrappedConnection.java:557) 16:59:22,643 ERROR [STDERR] at org.jboss.resource.adapter.jdbc.WrappedStatem ent.checkException(WrappedStatement.java:563)
16:59:22,643 ERROR [STDERR] at org.jboss.resource.adapter.jdbc.WrappedStatem ent.executeQuery(WrappedStatement.java:176) 16:59:22,643 ERROR [STDERR] at edu.harvard.i2b2.crc.dao.pdo.MetadataDao.getM etadataForOptionalField(Unknown Source) 16:59:22,643 ERROR [STDERR] at edu.harvard.i2b2.crc.ejb.PdoQueryBean.getPDOT emplate(Unknown Source) 16:59:22,643 ERROR [STDERR] at edu.harvard.i2b2.crc.ejb.PdoQueryBean.getPlai nPatientData(Unknown Source) 16:59:22,643 ERROR [STDERR] at sun.reflect.NativeMethodAccessorImpl.invoke0( Native Method) 16:59:22,643 ERROR [STDERR] at sun.reflect.NativeMethodAccessorImpl.invoke(N ativeMethodAccessorImpl.java:39) 16:59:22,643 ERROR [STDERR] at sun.reflect.DelegatingMethodAccessorImpl.invo ke(DelegatingMethodAccessorImpl.java:25) 16:59:22,643 ERROR [STDERR] at java.lang.reflect.Method.invoke(Method.java:5 97) 16:59:22,643 ERROR [STDERR] at org.jboss.invocation.Invocation.performCall(I nvocation.java:359) 16:59:22,643 ERROR [STDERR] at org.jboss.ejb.StatelessSessionContainer$Conta inerInterceptor.invoke(StatelessSessionContainer.java:237) 16:59:22,643 ERROR [STDERR] at org.jboss.resource.connectionmanager.CachedCo nnectionInterceptor.invoke(CachedConnectionInterceptor.java:158) 16:59:22,643 ERROR [STDERR] at org.jboss.ejb.plugins.StatelessSessionInstanc eInterceptor.invoke(StatelessSessionInstanceInterceptor.java:169) 16:59:22,643 ERROR [STDERR] at org.jboss.ejb.plugins.CallValidationIntercept or.invoke(CallValidationInterceptor.java:63) 16:59:22,643 ERROR [STDERR] at org.jboss.ejb.plugins.AbstractTxInterceptor.i nvokeNext(AbstractTxInterceptor.java:121) 16:59:22,643 ERROR [STDERR] at org.jboss.ejb.plugins.TxInterceptorCMT.runWit hTransactions(TxInterceptorCMT.java:350) 16:59:22,643 ERROR [STDERR] at org.jboss.ejb.plugins.TxInterceptorCMT.invoke (TxInterceptorCMT.java:181) 16:59:25,098 WARN [WrappedConnection] Exception trying to close statement: java.lang.OutOfMemoryError: GC overhead limit exceeded 16:59:37,558 ERROR [LogInterceptor] Unexpected Error in method: public abstract edu.harvard.i2b2.crc.datavo.pdo.query.PatientDataResponseType edu.harvard.i2b2.c rc.ejb.PdoQueryLocal.getPlainPatientData(edu.harvard.i2b2.crc.datavo.db.DataSour ceLookup,edu.harvard.i2b2.crc.datavo.pdo.query.GetPDOFromInputListRequestType,ja va.lang.String) throws edu.harvard.i2b2.common.exception.I2B2Exception java.lang.OutOfMemoryError: Java heap space 16:59:37,558 ERROR [PdoQueryRequestDelegate] Throwable javax.ejb.EJBException: Unexpected Error java.lang.OutOfMemoryError: Java heap space
at org.jboss.ejb.plugins.LogInterceptor.handleException(LogInterceptor.j
ava:430) at org.jboss.ejb.plugins.LogInterceptor.invoke(LogInterceptor.java:209) at org.jboss.ejb.plugins.ProxyFactoryFinderInterceptor.invoke(ProxyFacto
ryFinderInterceptor.java:138) at org.jboss.ejb.SessionContainer.internalInvoke(SessionContainer.java:6
48) at org.jboss.ejb.Container.invoke(Container.java:960) at org.jboss.ejb.plugins.local.BaseLocalProxyFactory.invoke(BaseLocalPro
xyFactory.java:430)
at org.jboss.ejb.plugins.local.StatelessSessionProxy.invoke(StatelessSes sionProxy.java:103)
at $Proxy161.getPlainPatientData(Unknown Source)
at edu.harvard.i2b2.crc.delegate.pdo.GetPDOFromInputListHandler.execute( Unknown Source)
at edu.harvard.i2b2.crc.delegate.pdo.PdoQueryRequestDelegate.handleReque st(Unknown Source)
at edu.harvard.i2b2.crc.axis2.QueryService.handleRequest(Unknown Source)
at edu.harvard.i2b2.crc.axis2.QueryService.pdorequest(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl. java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces sorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.axis2.receivers.RawXMLINOutMessageReceiver.invokeBusinessL ogic(RawXMLINOutMessageReceiver.java:88)
at org.apache.axis2.receivers.AbstractInOutSyncMessageReceiver.receive(A bstractInOutSyncMessageReceiver.java:39)
at org.apache.axis2.engine.AxisEngine.receive(AxisEngine.java:493)
at org.apache.axis2.transport.http.util.RESTUtil.invokeAxisEngine(RESTUt il.java:153)
at org.apache.axis2.transport.http.util.RESTUtil.processPostRequest(REST Util.java:102)
at org.apache.axis2.transport.http.AxisRESTServlet.doPost(AxisRESTServle t.java:66)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:710)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Appl icationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationF ilterChain.java:206)
at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFi lter.java:96)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Appl icationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationF ilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperV alve.java:230)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextV alve.java:175)
at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(Securit yAssociationValve.java:179)
at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValv e.java:84)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.j ava:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.j ava:102)
at org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedC
onnectionValve.java:157)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineVal ve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.jav a:262)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java :844)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.proce ss(Http11Protocol.java:583)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:44 6)
at java.lang.Thread.run(Thread.java:662) 16:59:49,299 ERROR [QueryService] Throwable java.lang.OutOfMemoryError: GC overhead limit exceeded 17:00:14,470 ERROR [AxisRESTServlet] java.lang.NullPointerException
From: Patibandla, Nandan Sent: Monday, November 28, 2011 3:53 PM To: 'Mike Mendis' Subject: RE: Not generating the Patient sets
Hi Mike,
I am having this problem again, I created a new database and imported all the data from 1.5 version to 1.6 version of the database.
When I run the query, it gives the patient count but do not produce the patient_set. I looked in to the QT_PATIENT_SET_COLLECTION to check whether the data was loaded in to the table and I see that the patients numbers are inserted in to the table but when I expand the patient_set tree in the webcleint, it just doesn't show anything instead I see the wait symbol.
I don't see anything in the log, please help.
Thank you
Nandan
From: Mike Mendis [mmendis.partners] Sent: Monday, November 21, 2011 4:16 PM To: Patibandla, Nandan Subject: Re: Not generating the Patient sets
thanks
On 11/21/11 4:06 PM, "Patibandla, Nandan" <Nandan.Patibandla.childrens.harvard> wrote:
Hi Mike,
The problem was fixed. CRC upgrade issue.
Thank you
Nandan
From: Mike Mendis [mmendis.partners] Sent: Monday, November 21, 2011 4:04 PM To: Patibandla, Nandan; i2b2 AUG Members Subject: Re: Not generating the Patient sets
That is fine, in the log.
Are you still getting this bug? Also is this on the 133 patient set?
mike
On 11/11/11 5:09 PM, "Patibandla, Nandan" <Nandan.Patibandla.childrens.harvard> wrote:
HI,
With respect to the same issue as below, I found this in the error log, Is there a fix around for this issue:
2011-11-11 16:45:48,536 DEBUG [org.jboss.mq.il.uil2.ServerSocketManagerHandler] Exiting on IOE java.net.SocketException: socket closed
at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:129) at java.io.BufferedInputStream.fill(BufferedInputStream.java:218) at java.io.BufferedInputStream.read(BufferedInputStream.java:237) at
org.jboss.util.stream.NotifyingBufferedInputStream.read(NotifyingBufferedInputStream.java:79) at java.io.ObjectInputStream$PeekInputStream.peek(ObjectInputStream.java:2248) at java.io.ObjectInputStream
$BlockDataInputStream.readBlockHeader(ObjectInputStream.java:2428) at java.io.ObjectInputStream$BlockDataInputStream.refill(ObjectInputStream.java:2498) at java.io.ObjectInputStream$BlockDataInputStream.read(ObjectInputStream.java:2570) at java.io.ObjectInputStream
$BlockDataInputStream.readByte(ObjectInputStream.java:2719) at java.io.ObjectInputStream.readByte(ObjectInputStream.java:894) at org.jboss.mq.il.uil2.SocketManager$ReadTask.run(SocketManager.java:340) at java.lang.Thread.run(Thread.java:662)
Thank you
Nandan
From: Patibandla, Nandan Sent: Friday, November 11, 2011 12:38 PM To: i2b2 AUG Members Cc: 'Mike Mendis' Subject: Not generating the Patient sets
Hi,
I am able to deploy the i2b2 v 1.6 successfully but not able to get the patient set after running the query, and if I click on the sub tree of the patient set in the previous queries, the wait symbol is there forever. By seeing the error log, I am see the below message and might be the possible cause for not generating the patient sets. Can you guys please let me know fix for this issue.
Thank you
Nandan
ERROR
2011-11-11 12:29:39,851 DEBUG [org.springframework.core.CollectionFactory] Creating [java.util.LinkedHashMap] 2011-11-11 12:29:39,851 DEBUG [org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory $ConstructorResolverAdapter] Ignoring constructor [public java.lang.String(byte[],int,int,int)] of bean 'defaultSetfinderResultType': Error creating bean with name 'defaultSetfinderResultType' defined in URL [file:C:/prod/jboss-4.2.2.GA/server/default/conf/crcapp/CRCApplicationContext.xml <file:///C: \prod\jboss-4.2.2.GA\server\default\conf\crcapp\CRCApplicationContext.xml> <file:///C:\prod \jboss-4.2.2.GA\server\default\conf\crcapp\CRCApplicationContext.xml> ]: Unsatisfied dependency expressed through constructor argument with index 0 of type [byte[]]: Ambiguous constructor argument types - did you specify the correct bean references as constructor arguments? 2011-11-11 12:29:39,851 DEBUG [org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory $ConstructorResolverAdapter] Ignoring constructor [public java.lang.String(byte[],int,int,int)] of bean 'defaultSetfinderResultType': Error creating bean with name 'defaultSetfinderResultType' defined in URL [file:C:/prod/jboss-4.2.2.GA/server/default/conf/crcapp/CRCApplicationContext.xml <file:///C: \prod\jboss-4.2.2.GA\server\default\conf\crcapp\CRCApplicationContext.xml> <file:///C:\prod \jboss-4.2.2.GA\server\default\conf\crcapp\CRCApplicationContext.xml> ]: Unsatisfied dependency expressed through constructor argument with index 0 of type [byte[]]: Ambiguous constructor argument types - did you specify the correct bean references as constructor arguments? 2011-11-11 12:29:39,851 DEBUG [org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory $ConstructorResolverAdapter] Ignoring constructor [public java.lang.String(byte[],int,int,java.lang.String) throws java.io.UnsupportedEncodingException] of bean 'defaultSetfinderResultType': Error creating bean with name 'defaultSetfinderResultType' defined in URL [file:C:/prod/jboss-4.2.2.GA/server/default/conf/crcapp/CRCApplicationContext.xml <file:///C: \prod\jboss-4.2.2.GA\server\default\conf\crcapp\CRCApplicationContext.xml> <file:///C:\prod \jboss-4.2.2.GA\server\default\conf\crcapp\CRCApplicationContext.xml> ]: Unsatisfied dependency expressed through constructor argument with index 0 of type [byte[]]: Ambiguous constructor argument types - did you specify the correct bean references as constructor arguments? 2011-11-11 12:29:39,851 DEBUG [org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory $ConstructorResolverAdapter] Ignoring constructor [public java.lang.String(byte[],int,int,java.lang.String) throws java.io.UnsupportedEncodingException] of bean 'defaultSetfinderResultType': Error creating bean with name 'defaultSetfinderResultType' defined in URL [file:C:/prod/jboss-4.2.2.GA/server/default/conf/crcapp/CRCApplicationContext.xml <file:///C: \prod\jboss-4.2.2.GA\server\default\conf\crcapp\CRCApplicationContext.xml> <file:///C:\prod \jboss-4.2.2.GA\server\default\conf\crcapp\CRCApplicationContext.xml> ]: Unsatisfied dependency expressed through constructor argument with index 0 of type [byte[]]: Ambiguous constructor argument types - did you specify the correct bean references as constructor arguments?
NEXT EMAIL
From: Murphy, Shawn N. Sent: Thursday, December 01, 2011 11:04 AM To: Yves Thorrez; Mendis, Michael E.; i2b2 AUG Members Subject: RE: Temporal constraint missing in 1.6 web client
Hi Yves,
There are three temporal constraints:
1 - The items in the groups/panels occur at any time in the patient's life
2 - The items in the groups/panels must occur in the same encounter (unless you specify the panel can be "any time")
3 - The items in the groups/panels must occur in the same fact/instance
1 and 2 are always available, but 3 only really makes sense if one is working with modifiers, otherwise it is implicit that the items can occur between facts and occurring within the same fact isn't really possible. We choose to show that constraint only when a modifier is present because if one picks this / leaves it by mistake, the performance is much worse for the query but it has no real effect on the outcome of the query.
Thanks,
Shawn.
From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Thursday, December 01, 2011 10:47 AM To: Mendis, Michael E.; i2b2 AUG Members Subject: RE: Temporal constraint missing in 1.6 web client
However, it was {}always{} available in the release candidates, which allowed one to state that the concepts (regardless of whether they are modifiers) should appear in the same visit cluster. Now you can only do such a thing when you make a concept a modifier of another concept?
Yves
Yves Thorrez
Medische Informatieverwerking
yves.thorrez.uzbrussel.be
Laarbeeklaan 101 - 1090 Brussel
www.uzbrussel.be
From: Mike Mendis [mmendis.PARTNERS] Sent: donderdag 1 december 2011 16:27 To: Yves Thorrez; i2b2 AUG Members Subject: Re: Temporal constraint missing in 1.6 web client
If you drag over a concept that is a modifer it will appear in the dropdown
mike
On 12/1/11 10:19 AM, "Yves Thorrez" <Yves.Thorrez.uzbrussel.be> wrote:
I just noticed the third temporal constraint 'Items instance will be the same' for queries is missing in the final 1.6 release of the web client. It was still there in the latest release candidate. Is it forgotten in the final release? We actually have some use cases in which the instance_num attribute is used to cluster observations within the same visit (other than its use for modifiers).
Thanks,
Yves
- FROM index.php ************************************* $pmURL = "http://127.0.0.1:8080/i2b2/rest/PMService/getServices"; $pmCheckAllRequests = false;
-
-
