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_From: Joe.Terdiman.kp Sent: Wednesday, August 31, 2011 6:36 PM To: I2B2 AUG Members Cc: Michael.C.Ford.nsmtp.kp; Mendis, Michael E. Subject: Multiple i2b2 servers_

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We have a production i2b2 (1.4) server and a test server. Each server can point to the same or different project database. If users on both servers query the SAME i2b2 database simultaneously, will the queries interfere with each other?

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Joe

Joe Terdiman, MD, PhD Division of Research Kaiser Permanente 2000 Broadway Oakland, CA 94612
 
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_From: Brian Ostasiewski \[bostasie.wakehealth\] Sent: Wednesday, August 31, 2011 1:57 PM To: I2B2 AUG Members Subject: C_BASECODE for dimensional queries_

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Looking through the example metadata, I see the ontology has the same c_basecode for both Age (now) and Age At Visit. Are there any consequences to this (both are dimensional queries)?

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_From: Peter Beninato \[beninato.ohsu\] Sent: Tuesday, August 30, 2011 11:34 AM To: Lisa Miao Cc: I2B2 AUG Members Subject: RE: index hint on the observation_fact table_

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Hi,

Ughh. I thought it was a multiple column index that was in the hint which I dropped.

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Maybe the broader discussion, is whether there should be hints at all in the SQL? Maybe in a new version there shouldn't be?

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In the particular when were statistics gathered on the observation fact table? Maybe they are stale?

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 _From: Lisa Miao \[lmiao.regenstrief\] Sent: Tuesday, August 30, 2011 8:26 AM To: Peter Beninato Subject: RE: index hint on the observation_fact table_

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Thanks for getting back to me quickly.

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The index that is in the hint is the primary key for the table. Can I drop that? I wouldn't imagine table without primary key is a good thing, and I would imagine many other queries are using this index also.

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Thanks,

Lisa.

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 _From: Peter Beninato \[beninato.ohsu\] Sent: Tuesday, August 30, 2011 11:23 AM To: Lisa Miao Subject: RE: index hint on the observation_fact table_

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You could drop the index that is in the hint.

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If you feel it is necessary for performance create a new index under a new name, then if the optimizer thinks it is useful it'll use it.
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 _From: Lisa Miao \[lmiao.regenstrief\] Sent: Tuesday, August 30, 2011 7:52 AM To: I2B2 AUG Members members Subject: index hint on the observation_fact table_

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Hello every one,

When we do a query on provider, for instance drag the "Emergency" node under providers from the term tree to the right(Query Tool), following is the query that has been executed:

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select  /*\+ index(observation_fact observation_fact_pk) \*/  patient_num from i2b2demodata.observation_fact where  provider_id IN  (select provider_id from i2b2demodata.provider_dimension
  
  where provider_path LIKE '\i2b2\Providers\Emergency\%Emergency%') group by   patient_num  having count(*y) >= 1;

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In case we have a large number of providers, (which is true in our case), this query never comes back.

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I added an index on provider_id for the observation_fact table, and took out the index hint from the above query and run the query, it came back pretty quickly.

The issue is, the index hint is preventing my new index to be used, and as a result, the query never came back in reasonable time.

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Any idea on how we should address this?

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Thanks,

Lisa.

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_From: Jack London \[jack.london.KimmelCancerCenter\] Sent: Tuesday, August 30, 2011 10:33 AM To: Mendis, Michael E. Cc: Murphy, Shawn N.; I2B2 AUG Members members Subject: Re: cd modifiers with RC4 demo data_

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Mike and Shawn,

RC5 now works fine.  I took Mike's suggestion and just copied the i2b2_config_data.js from the RC4 webclient path to the RC5 path.  (In the process I saw where I was incorrectly setting values in the RC5 file.)

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I now can start trying out cd modifiers with our specimen data, using the demo data set as a guide.

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Thanks for your help ...

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Jack
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_From: Murphy, Shawn N. Sent: Tuesday, August 30, 2011 6:02 AM To: Jack London Cc: I2B2 AUG Members; Mendis, Michael E. Subject: RE: cd modifiers with RC4 demo data_

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Thanks Mike.

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Jack, the change to the web client in RC5 was to fix an issue with setting values in the query panels.  Previously, the setting of a value for an item in a query would result in changes to the exact same item if it were used in other places in the query.

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I think Mike may have sneaked in a bug fix to something with previous queries as well, but that was all.

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Thanks, Shawn.

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_On Aug 29, 2011, at 7:47 PM, Mendis, Michael E. wrote:_

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in your i2b2_config_data.js make sure the domain is set to i2b2demo.  or you can just take the i2b2_config_data.ja from rc4 and use it in the rc5

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mike

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_From: Jack London \[jack.london.KimmelCancerCenter\] Sent: Mon 8/29/2011 5:02 PM To: Murphy, Shawn N. Cc: I2B2 AUG Members members Subject: Re: cd modifiers with RC4 demo data_

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Shawn, Is it also necessary to replace the web client of RC4 with the RC5 web client code? I did this and edited the i2b2_config_data.js file, but I now cannot log in to the web client.  It says "i2b2 not associated with this domain i2b2demo."  I saved the RC4 web client as another path (URL). Using this web client I can log in.  So -- is the code the same from RC4 to RC5?  Will it work ok with the RC5 data set?

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thanks, Jack

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_On Aug 26, 2011, at 11:55 AM, Murphy, Shawn N. wrote:_

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Hi Jack, The demo data of RC5 has the modifier dimension you need.  Everything else in the CRC is the same.

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Thanks, Shawn.

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_From: Jack London \[jack.london.KimmelCancerCenter\] Sent: Friday, August 26, 2011 11:40 AM To: Murphy, Shawn N. Cc: I2B2 AUG Members members Subject: Re: cd modifiers with RC4 demo data_

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Shawn, The RC distribution web page shows for RC5 only a demo data and web client release. Previously, I had used all the v1.6 RC4 installation files to create an RC4 instance. (Note, we only use the web client.) Is it necessary to do a complete re-installation using all the RC4 files along with the new RC5 files, or can I just execute the new RC5 demo data and web client files against our RC4 instance?

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Jack

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_On Aug 26, 2011, at 11:15 AM, Murphy, Shawn N. wrote:_

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Hi Jack, The problem is probably the dimension table.  We had to put together an RC5 release to include it, and it is available at the RC web site. It was optional in the initial implementation, but now it is not.  This allows much more powerful stuff to be used as modifiers, like whole diagnoses hierarchies could be used as a modifier to a concept like "family history".

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Thanks, Shawn.

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_From: Jack London \[jack.london.KimmelCancerCenter\] Sent: Friday, August 26, 2011 11:10 AM To: I2B2 AUG Members members Subject: cd modifiers with RC4 demo data_

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I cannot get queries using the cd modifiers (e.g., Medication Route) to return a non-zero patient count. By looking at the I2B2DEMODATA.OBERSERVATION_FACT table I can see that "MED:ROUTE" modifiers, for example, are used for at least one patient (for Nizatidine 300mg).
 
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Yet using the web client query tool, patient count = 0 is always returned.

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Has anyone been able to obtain patient counts > 0 using the cd modifiers with the v1.6 RC4 demo (or demo2) data?

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Also, the dimension table for MODIFIER_CD in the demo data is empty.  The wiki notes on the "Modifiers in i2b2 Data Model" says this table is "optional" because it is not used by the query tool.
 
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When would it be worthwhile to populate this table?
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thanks ... Jack

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_From: Keith Marsolo \[keith.marsolo.cchmc\] Sent: Tuesday, August 23, 2011 4:40 PM To: Peter Beninato Cc: Lisa Miao; i2b2 AUG Members; q.t.zeng.utah Subject: Re: instance_num in observation_fact table_

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This is where it's good to use modifiers.

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Concept - Diabetes, Modifier - Problem List Concept - HBP, Modifier - Problem List Concept - HBP, Modifier - Family History, Modifier - Father Concept - Diabetes, Modifier - Family History, Modifier - Mother

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We don't use the standard i2b2 modifier scheme, so we'd model this using XML, but it's more or less the same idea.

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_On Aug 23, 2011, at 4:33 PM, Peter Beninato wrote:_

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I think the instance_num may help, but you could have concept_cd:   "FAM_HIST:Diabetes"   "FAM_HIST:HBP"     And then make two observations.
    
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_From: Lisa Miao \[lmiao.regenstrief\]   Sent: Tuesday, August 23, 2011 1:17 PM   To: Peter Beninato; i2b2 AUG Members; q.t.zeng.utah   Subject: RE: instance_num in observation_fact table_
    
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That certainly make sense.     But in our database, we also have data stored as the way I described. I'm trying to figure out a way not to lose those data.
    
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Another example would be our concept_cd is "Family History", under which one patient may have 2 records (diabetes and low blood pressure for instance).

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In this case it's not *you* who are diagnosed as "diabetic" (therefore it cannot be stored as diagnoses for diabetes).
   
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Lisa.
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_From: Peter Beninato \[beninato.ohsu\]   Sent: Tuesday, August 23, 2011 4:06 PM   To: Lisa Miao; i2b2 AUG Members; q.t.zeng.utah   Subject: RE: instance_num in observation_fact table_
    
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Hi,
    
Wouldn't diagnosis for diabetes, and a measure of blood pressure (or an different dx) have different concept_codes?
    
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Peter
        
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_From: Lisa Miao \[lmiao.regenstrief\]   Sent: Tuesday, August 23, 2011 12:40 PM   To: i2b2 AUG Members; q.t.zeng.utah   Subject: instance_num in observation_fact table_
    
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Dear All,
    
In our data model for observation_fact, we have situation where we have the same concept_cd (for instance "patient problem list"), which can have a list of records (for instance, diabete, high blood pressure) that have the same (encounter_num, patient_num, concept_cd, start_time).

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Can we use instance_num (1, 2, 3...) to store the list of records like this?
    
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To make this a real-world example, it would be patient_num 1 has a visit (encounter_num 1), and he has been diagnosed with "patient problem list" (concept_cd), at the same time(start_time), but there're multiple records to store (diabete is 1, high blood pressure is 2, etc).
    
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If we cannot use instance_num (the doc says it's for modifier purpose), it sounds like we are out of luck as far as storing data like the above. ?
    
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Thanks,
    
Lisa.
          
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_From: Dan Connolly \[dconnolly.kumc\] Sent: Tuesday, August 23, 2011 11:08 AM To: jack.london.KimmelCancerCenter Cc: i2b2 AUG Members; John.P.Reber.KimmelCancerCenter; Phillips, Lori C._ _Subject: Re: adding project causes demo queries to fail_

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Yeah... the data dependencies are pretty tricky. When deviating from the documented installation instructions, remember:

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"A shortcut is the longest distance between two points" \--Murphy

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_On Tue, 2011-08-23 at 10:51 \-0400, Jack London wrote:_

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Lori,

Problem solved and perhaps a valuable lesson learned:

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Our system administrator looked at the jboss log and quickly saw an error, which wasrather global in nature. When I reviewed what I had done -- edited the ds.xml files in the working directories and made database entries -- he immediately pointed out the flaw in my process: I did not edit the source files in the distribution path and thenexecute the ant clean and rebuild commands. So while I had modified the working ds.xmlfiles, there were a whole host of other activities (compiles etc.) that were not doneto incorporate the additions to the domain environment.

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So the lesson learned is not to shortcut the install process, even when you are making"a small addition." The two demos work fine again, and I have an additional project which points to our specific Jefferson Kimmel Cancer Center deployment. I can now work on enhancing our instance with the new capabilities of v1.6 RC4.
 
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Jack

Jack London, Ph.D.Research Professor Cancer BiologyThomas Jefferson UniversityDirector, Informatics Shared ResourceKimmel Cancer Center 808 BLSB, 233 S. 10th St.Philadelphia, PA 19107215-503-4599

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_On Aug 23, 2011, at 9:05 AM, Phillips, Lori C. wrote:_

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Hi Jack,
   
You will have to send us the actual error(s) from the server.log file...
 
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Your new project is ORACLE, is the same true for the demo and demo2 projects?
   
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Lori
        
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_From: Jack London \[jack.london.KimmelCancerCenter\]  Sent: Monday, August 22, 2011 5:32 PM  To: Phillips, Lori C.  Cc:  i2b2 AUG Members    Subject: Re: adding project causes demo queries to fail_
   
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Yes. I left the demo/demo2 rows intact, and added a row for the new data source,  using the same domain id (first column) as demo/demo2.
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_On Aug 22, 2011, at 4:35 PM, "Phillips, Lori C."  LCPHILLIPS.PARTNERS wrote:_
        
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Did you modify the CRC_DB_LOOKUP table correctly when you added the new   project?   Are the Demo and Demo2 entries still intact?
      
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_From: Jack London \[jack.london.KimmelCancerCenter\]   Sent: Monday, August 22, 2011 4:30 PM   To: i2b2 AUG Members members    Subject: adding project causes demo queries to fail_
    
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I can get the demo and demo2 projects to run fine with v1.6 RC4. But after I add a new set of metadata, data, and work ORACLE users, edit the ont, crc, and   work ds.xml files to include the new data sources, and use the admin interface   to add a new project to the i2b2demo domain, all demo and demo2 queries stop working. The correct ontologies are displayed when I select each project, but any query issued never completes ("ERROR" displayed in query XML message).
     
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Any suggestions of how incorrectly adding a project can mess up working   demo/demo2 queries?
     
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Jack
              
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_From: Phillips, Lori C._ _Sent: Monday, August 22, 2011 4:02 PM To: Davis, Michael (Oncology); i2b2 AUG Members Subject: RE: Unlock the ontology_

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For terms to appear unlocked they have to have a visualAttribute ending in 'E' (meaning editable) So active folders are FAE; leaves LAE , etc.

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Lori
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_From: Davis, Michael (Oncology) \[davismk.upmc\] Sent: Monday, August 22, 2011 4:00 PM To: i2b2 AUG Members Subject: Unlock the ontology_

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I created a custom ontology (different from 'Custom Metadata') with new table etc., It appears within the concept tree, but how do I get this to appear unlocked when I'm in the Edit Terms tool? I've tried setting the TABLE_ACCESS.C_PROTECTED_ACCESS to 'N' but my ontology is still locked. I'm currently using 1.6rc4.

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Thanks

Mike

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_From: Michael.C.Ford.kp Sent: Monday, August 22, 2011 3:00 PM To: i2b2 AUG Members Subject: Configuration tables._

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I have an i2b2 instance I am setting up.

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the performance is poor and I was wondering if I may have missed a configuration file.

all I am doing at this point is changing the configuration to point at another database. I have the following files changed.

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conf\crcapp\CRCApplicationContext.xml conf\crcloaderapp\CRCLoaderApplicationContext.xml conf\i2b2\CRCApplicationContext.xml conf\i2b2\CRCLoaderApplicationContext.xml conf\i2b2\OntologyApplicationContext.xml conf\ontologyapp\OntologyApplicationContext.xml deploy\crc-ds.xml deploy\crc-jms-ds.xml deploy\ont-ds.xml deploy\pm-ds.xml deploy\work-ds.xml

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did I get all the database configuration files ?

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_From: Chanumolu, Vijayalakshmi \[vijayalakshmi.chanumolu.uky\] Sent: Thursday, August 18, 2011 5:00 PM To: Phillips, Lori C.; i2b2 AUG Members Subject: RE: Regarding NLP cell_

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HI Lori,

I have a small problem.When I want to highlight a nlp term in text analyzer I am not unable to do it.I am attaching a screen shot with this mail.

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DO I need to install nlp cell for this(I am little bit confused).I have drag and dropped medications , procedure etc.But I cannot see any of the term highlighted in the text.Can you please look over this issue.

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Thanks, Vijaya

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_From: Phillips, Lori C. \[LCPHILLIPS.PARTNERS\] Sent: Thursday, August 18, 2011 4:32 PM To: Chanumolu, Vijayalakshmi Subject: RE: Regarding NLP cell_
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You have to run a query that corresponds to notes or reports.  In the Demo data this is "Reports" folder.
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Drag the appropriate 'Report' concept to the query tool.
  
Run the query.
  
Double click on the tick mark in the timeline that corresponds to the note.
  
It may ask for an encryption key.
 
Enter the key from the document.
  
Note will appear in the viewer.

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Lori

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 _From: Chanumolu, Vijayalakshmi \[vijayalakshmi.chanumolu.uky\] Sent: Thursday, August 18, 2011 4:15 PM To: Phillips, Lori C.; i2b2 AUG Members Subject: RE:_ _Regarding NLP cell_

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HI lori,

Thanks for the help..But In the documentation it is given that you need to double click on the note viewer in the time line plug in.But I cannot find any note viewer in the time line plug in.Can you help me on where can I find it.

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Thanks, Vijaya

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_From: Phillips, Lori C. \[LCPHILLIPS.PARTNERS\] Sent: Thursday, August 18, 2011 3:59 PM To: Chanumolu, Vijayalakshmi; i2b2 AUG Members Subject: RE: Regarding NLP cell_

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This can be found on the documentation page: [https://www.i2b2/software/#documents]

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Hover over the text analyzer plugin node and choose the Help Guide.

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The introduction explains what parameters have to be set in the obs_fact table for this tool to recognize a text document.

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Lori

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 _From: Chanumolu, Vijayalakshmi \[vijayalakshmi.chanumolu.uky\] Sent: Thursday, August 18, 2011 2:40 PM To: i2b2 AUG Members Subject: FW: Regarding NLP cell_

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HI Murphy,

Is there any documentation for that set up of nlp-friendly fashion environment .I am really confused of what to do because When I open text analyzer and want to run a sample text I cannot see anything in it.I am attaching a screen shot of

it ..

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Thanks, Vijaya

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_From: Murphy, Shawn N. \[SNMURPHY.PARTNERS\] Sent: Thursday, August 18, 2011 12:39 PM To: Chanumolu, Vijayalakshmi; i2b2 AUG Members Subject: RE: Regarding NLP cell_

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No, the text analyzer runs independently of the NLP cell.  It does require the metadata to be set up in a NLP-friendly fashion however.

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Thanks, Shawn.

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 _From: Chanumolu, Vijayalakshmi \[vijayalakshmi.chanumolu.uky\] Sent: Thursday, August 18, 2011 12:22 PM To: Murphy, Shawn N.; i2b2 AUG Members Subject: RE: Regarding NLP cell_

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HI Murphy,

I have a small doubt.For utilizing text analyzer in workbench do we need to install nlp cell??

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Thanks, Vijaya

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_From: Murphy, Shawn N. \[SNMURPHY.PARTNERS\] Sent: Thursday, August 18, 2011 9:08 AM To: Chanumolu, Vijayalakshmi Subject: RE: Regarding NLP cell_

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Hi Vijaya,

Qing Zeng "owns" the GATE processing code (the internals of the NLP).  She is at q.t.zeng.utah

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Thanks, Shawn.

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 _From: Chanumolu, Vijayalakshmi \[vijayalakshmi.chanumolu.uky\] Sent: Tuesday, August 16, 2011 5:19 PM To: i2b2 AUG Members Subject: Regarding NLP cell_

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HI everyone,

I am interested in NLP cell of i2b2.But I can see that only the installation of nlp in windows is given.I have installed i2b2 1.5.4 in linux ubuntu.How can I use the nlp cell for processing?
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Thanks in advance...

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Thanks all, vijaya
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*NEXT EMAIL*

_From: Dan Connolly \[dconnolly.kumc\] Sent: Thursday, August 18, 2011 11:50 AM To: Dana.Ludwig.kp Cc: i2b2 AUG Members Subject: Re: concurrency, Oracle and QUERY_GLOBAL_TEMP_

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_On Wed, 2011-08-17 at 10:52 \-0700, Dana.Ludwig.kp wrote:_

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Since we don't see a session id column on that table, we were wondering how multiple users can execute their queries at the same time, and keep their interim results separated from the results of other users in QUERY_GLOBAL_TEMP.

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Our best guess is that the rows are never commited, and this is the way each session sees a different set of rows.  Is this the case?

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ANSWER: Yes, that's my understanding. And indeed, Oracle docs say:

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In addition to permanent tables, Oracle can create temporary tables to hold session-private data that exists only for the duration of a transaction or session.

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Dan Connolly, KUMC Medical Informatics

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_From: Mendis, Michael E._ _Sent: Thursday, August 18, 2011 9:27 AM To: Chanumolu, Vijayalakshmi; Phillips, Lori C.; i2b2 AUG Members Subject: Re: Problem in installation_

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What verison of the client are you running?

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_On 8/17/11 7:27 PM, "Chanumolu, Vijayalakshmi"  vijayalakshmi.chanumolu.uky  wrote:_

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HI ,
    
Thanks for the help..I again reconfigured the crc cell .Now it works fine and I can see the crc cell.
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Thank you so much for the help
    
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But after login into workbench when I try to add new features to it.It is giving me an error that

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Network connection problems encountered during search Unable to access "https://www.i2b2/updateSites".   Unable to access site: "https://www.i2b2/updateSites" \[Server returned   HTTP response code: "404 Not Found" for URL:   [https://www.i2b2/updateSites.\]\]   Server returned HTTP response code: "404 Not Found" for URL:   [https://www.i2b2/updateSites].   Unable to access site: "https://www.i2b2/updateSites" \[Server returned   HTTP response code: "404 Not Found" for URL:   [https://www.i2b2/updateSites.\]\]   Server returned HTTP response code: "404 Not Found" for URL:   [https://www.i2b2/updateSites].
    
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I dont know whats wrong with the update sites..
    
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Thanks,   Vijaya
    
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_From: Phillips, Lori C. \[LCPHILLIPS.PARTNERS\]   Sent: Wednesday, August 17, 2011 2:15 PM   To: Chanumolu, Vijayalakshmi; i2b2 AUG Members   Subject: RE: Problem in installation_
    
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Your CRC cell is trying to resolve the QueryToolDemoDS data source.     1. Your hive's CRC_DB_LOOKUP table has an entry for QueryToolDemoDS   (datasource to your obs_fact table, dimension tables etc)     2. The data source is not configured in one of the   jboss/server/default/deploy/crc*-ds.xml files
    
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You did something similar when you configured the ontology cell; only then   you   modified   the ONT_DB_LOOKUP table and the ont-ds.xml file.
     
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Lori Phillips
          
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_From: Chanumolu, Vijayalakshmi \[vijayalakshmi.chanumolu.uky\]   Sent: Wednesday, August 17, 2011 1:54 PM   To: i2b2 AUG Members   Subject: RE: Problem in installation_
    
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HI Everyone,
    
I am repeating my problem which I have mentioned above by attaching the log file of jboss (the log file containing the error messages which are occurred when I run a query using web client)     I have installed all the cells in i2b2.I can see them active in   [http://localhost:9090/i2b2/services/listServices]. But when I try to connect through workbench I can see the ontologies loaded. But I can see the error message that data repository cell unavailable.
    
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I am attaching a snapshot of workbench. And also I am attaching the screen shot of cells how they are configured in PM cell. And also attaching the jboss log file.

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Can anyone please help me regarding this problem?
    
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Thanks,   Vijaya
          
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_From: Chanumolu, Vijayalakshmi \[vijayalakshmi.chanumolu.uky\]   Sent: Wednesday, August 17, 2011 12:57 PM   To: i2b2 AUG Members   Subject: RE: Problem in installation_
    
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HI Michael,
    
The problem which I have mentioned above is solved.There is a full stop beside   admin only=true. where there should be a comma.
    
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I am again stuck with another problem: I have installed all the cells in   i2b2.I   can see them active in [http://localhost:9090/i2b2/services/listServices.But] when I try to connect through workbench I can see the ontologies loaded.
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But I can see the error message that data repository cell unavailable.
    
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I am attaching a snapshot of workbench.

and also I am attaching the screen shot of cells how they are configured in PM cell.
    
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Thanks,   Vijaya
  
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_From: Michael.C.Ford.kp \[Michael.C.Ford.kp\]   Sent: Wednesday, August 17, 2011 12:06 PM   To: Chanumolu, Vijayalakshmi   Subject: Re: Problem in installation_
    
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is your jboss running ?
    
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_From: "Chanumolu, Vijayalakshmi"  vijayalakshmi.chanumolu.uky  Sent: 08/16/2011 12:58 PM  To: i2b2 AUG Members cc:  Subject: Problem in installation_

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HI Everyone,
    
I am trying to install i2b2 1.54 version in Ubuntu.
   
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I have completed the installation of pm cell. But when I am trying to login into   localhost/admin.     I am getting an error box specifying that "The user-defined I2B2 Hive   Configuration message is invalid (try looking for an extra comma)"..
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I dont   know   why I am getting the error.
    
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My i2b2_config_data.js file look like this :
    
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\{     urlProxy: "index.php",     urlFramework: "js-i2b2/",       //-------------\-  -  \-----------\-    // THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO     lstDomains: \[     \{ name: "localhost",     domain: "i2b2demo",     debug: true,     adminOnly: true.     urlCellPM:   "http://localhost:9090/i2b2/rest/PMService/"     \},     \{ name: "i2b2",     domain: "HarvardDemo",     debug: true,     urlCellPM:   "http://webservices.i2b2/i2b2/rest/PMService/"     \}     \]       //------------------------------\-  -  \-----------\-    \}
   
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Can Anyone please help me on this issue.
    
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Thanks,   Vijaya
      
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*NEXT EMAIL*

_From: Dana.Ludwig.kp Sent: Wednesday, August 17, 2011 1:52 PM To: i2b2 AUG Members Subject: concurrency, Oracle and QUERY_GLOBAL_TEMP_

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Here at Kaiser Permanente, Division of Research, we are in the middle of implementing i2b2 on 14 years of EMR facts, covering around 1.3 billion facts. We are looking at the generated code of our queries in i2b2demodata.qt_query_master.

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We are starting with version 1.4, and our database is Oracle 10g.

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We noticed that as each panel is processed, the results are inserted or updated into QUERY_GLOBAL_TEMP.

\\
Since we don't see a session id column on that table, we were wondering how multiple users can execute their queries at the same time, and keep their interim results separated from the results of other users in QUERY_GLOBAL_TEMP.

\\
Our best guess is that the rows are never commited, and this is the way each session sees a different set of rows.  Is this the case? Is there another mechanism that we aren't seeing?

\\
We want to know so that we can avoid mistakes in our performance optimization attempts.

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Dana Ludwig Division of Research

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*NEXT EMAIL*

_From: Russ Waitman \[rwaitman.kumc\] Sent: Tuesday, August 16, 2011 3:55 PM To: Dustin Key; i2b2 AUG Members Subject: RE: Loading Tumor Registries into i2b2_

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Dustin, That would be really wonderful. We'd definitely benefit from your file,

Russ

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_"Key, Dustin"  key.d.ghc  8/16/2011 1:48 PM_
    
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Russ,

We've been building a version 12 NAACCR ontology here at GHRI with the help of the vendor, Recombinant. It's about 95% complete, with a few of the summary staging variables not yet finished (to be done soon.) All of the site specific factors are part of the ontology and are categorized by cancer schema.

\\
I'd be happy to share our metadata.i2b2 file where sourcesystem_cd='NAACCR'.  Just let me know\!

\\
Dustin Key Programmer Analyst Group Health Research Institute

\\
\\
_From: Russ Waitman \[rwaitman.kumc\] Sent: Friday, August 12, 2011 6:01 AM To: i2b2 AUG Members Subject: Loading Tumor Registries into i2b2_

\\
Hi all, Has anyone attempted to load hospital or state tumor registries into i2b2?  We are looking at this to integrate with our EMR and biospecimen data.
 
\\
If anyone has already done this and based it on the NAACR file extract (version 12.1), we'd love to build on/borrow/beg for your approach.

\\
The vendor of our hospital's registry is ERS.

\\
[http://www.ers-can.com/]

A related question would be has anyone built an i2b2 ontology for ICD-O (international classification of diseases for oncology)?

\\
Sincerely,

Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center

rwaitman.kumc [http://informatics.kumc]
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*NEXT EMAIL*

From: Yves Thorrez \[Yves.Thorrez.uzbrussel.be\] Sent: Tuesday, August 16, 2011 11:54 AM To: Phillip Reeder; i2b2 AUG Members Subject: RE: Navigating terms is slow

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Thank you, Phillip.

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We are using MS SQL Server 2008, but clearly we'll need to use a similar approach.

\\
Yves

Yves Thorrez

Medische Informatieverwerking

yves.thorrez.uzbrussel.be

Laarbeeklaan 101 - 1090 Brussel

www.uzbrussel.be
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_From: Phillip Reeder \[Phillip.Reeder.uth.tmc\] Sent: maandag 15 augustus 2011 23:25 To: Yves Thorrez; i2b2 AUG Members Subject: RE: Navigating terms is slow_

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We had the same issue. Our DBA ran Oracle Enterprise Manager and monitored the queries coming from the client while we browsed through the terminology.  Here are the recommended indexes it gave us. You'll need to change the tablespace to your local value, or remove it to send the index to the default table space. On our configuration, it made a big difference in the performance of the terminology through the webclient.

\\
CREATE INDEX "DEMODATA"."I2B2_IDX$$_71280000" ON "DEMODATA"."I2B2" ("M_APPLIED_PATH","C_HLEVEL","M_EXCLUSION_CD","C_FULLNAME")
COMPUTE STATISTICS TABLESPACE "DEMODATA_INDX";

CREATE INDEX "DEMODATA"."I2B2_IDX$$_71280001" ON "DEMODATA"."I2B2" ("C_HLEVEL","M_EXCLUSION_CD","C_FULLNAME")
COMPUTE STATISTICS TABLESPACE "DEMODATA_INDX";

CREATE BITMAP INDEX "DEMODATA"."I2B2_IDX$$_71280002" ON "DEMODATA"."I2B2" ("M_EXCLUSION_CD")
COMPUTE STATISTICS TABLESPACE "DEMODATA_INDX";

CREATE INDEX "DEMODATA"."I2B2_IDX$$_71280003" ON "DEMODATA"."I2B2" ("C_FULLNAME")
COMPUTE STATISTICS TABLESPACE "DEMODATA_INDX";

CREATE BITMAP INDEX "DEMODATA"."I2B2_IDX$$_71280004" ON "DEMODATA"."I2B2" ("C_SYNONYM_CD")
COMPUTE STATISTICS TABLESPACE "DEMODATA_INDX";

CREATE INDEX "DEMODATA"."I2B2_IDX$$_71280005" ON "DEMODATA"."I2B2" ("C_HLEVEL","C_FULLNAME","M_APPLIED_PATH")
COMPUTE STATISTICS TABLESPACE "DEMODATA_INDX";

CREATE INDEX "DEMODATA"."I2B2_IDX$$_71280007" ON "DEMODATA"."I2B2" ("M_EXCLUSION_CD","C_FULLNAME")
COMPUTE STATISTICS TABLESPACE "DEMODATA_INDX";

\\
\\
_From: Yves Thorrez \[Yves.Thorrez.uzbrussel.be\] Sent: Wednesday, August 10, 2011 6:34 AM To: i2b2 AUG Members Subject: Navigating terms is slow_

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Hi,

I was wondering, does anyone else using 1.6 RC4 experience slow opening of folders/containers while navigating terms (10-20 seconds and even longer)? With modifiers disabled, navigating is a lot smoother.

\\
Thanks,

Yves

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*NEXT EMAIL*

_From: Murphy, Shawn N. Sent: Saturday, August 13, 2011 11:03 PM To: Jack London; i2b2 AUG Members Subject: RE: C_SYMBOL and C_PATH_

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Hi Jack,

We will fill them in the final release.  They are simply the splitting of c_fullname into two strings, but it helps with the explicit creation of c_symbol in many of Lori's programs that work with the NCBO web services.

\\
Thanks, Shawn.

\\
\\
 _From: Jack London \[jack.london.KimmelCancerCenter\] Sent: Tuesday, August 09, 2011 1:20 PM To: i2b2 AUG Members members Subject: C_SYMBOL and C_PATH_

\\
These two columns are in the v1.6 RC4 metadata table.  They are described briefly in the documentation.  However, in the demo and demo2 metadata tables these columns seem to be all null.
 \\
Are these columns used in v1.6?

\\
Jack

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*NEXT EMAIL*

_From: Jack London \[jack.london.KimmelCancerCenter\] Sent: Saturday, August 13, 2011 12:04 AM To: Alma Novakovic Cc:  rwaitman.kumc ;  i2b2 AUG Members  Subject: Re: Loading Tumor Registries into i2b2_

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We have integrated data in our i2b2 data mart from our caTissue biospecimen database with our tumor registry data, along with the clinical data from our hospital's clinical data warehouse (EMR).

\\
Jack

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_From: Russ Waitman \[rwaitman.kumc\] Sent: Friday, August 12, 2011 12:08 PM To: Alma Novakovic; jack.london.KimmelCancerCenter Cc: i2b2 AUG Members Subject: Re: Loading Tumor Registries into i2b2_

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Alma,

Here at KUMC they use a homegrown system. We're just getting a very simple extract from it and we're writing the ETL scripts right now to bring it into i2b2.  We will refine it over time especially if/when we move to different biospecimen repository software.

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Russ

\\
\\
_On Aug 12, 2011, at 9:48 AM, "Alma Novakovic"  ANOVAKOV.georgiahealth  wrote:_

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Do you use any software for biospecimen inventory and have it integrated with the tumor registry and/or the synoptic reports applications? We have just implemented i2b2 and have started to watch this listserv more closely. We would be very interested to know if anyone has tried to load data from the tumor registry and biospecimen inventory (specifically the tissue bank) systems.
    
\\
Thank you,
    
Alma Novakovic
  
Georgia Health Sciences University   Augusta, GA
       
\\
\\
_From: "Russ Waitman"  rwaitman.kumc   Cc:  i2b2 AUG Members_ _To: London, Jack  jack.london.KimmelCancerCenter   Sent: 8/12/2011 10:06:21 AM  Subject: Re: Loading Tumor Registries into i2b2_
    
\\
Jack,
  
That would be wonderful.
 
\\
Thank you so much,
    
Russ
         
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_Jack London  jack.london.KimmelCancerCenter  8/12/2011 9:00 AM_
     
\\
We have our Tumor Registry data in i2b2.  Our hospital has Impac as its registry vendor. I will send you the metadata when I am back in the office next Thursday.
  
\\
Jack
    
\\
\\
_On Aug 12, 2011, at 9:01 AM, "Russ Waitman"  rwaitman.kumc  wrote:_
        
\\
Hi all,   Has anyone attempted to load hospital or state tumor registries into i2b2?  We are looking at this to integrate with our EMR and biospecimen data.
     
\\
If anyone has already done this and based it on the NAACR file extract (version 12.1), we'd love to build on/borrow/beg for your approach.
    
\\
The vendor of our hospital's registry is ERS.
   
 [http://www.ers-can.com/]
    
\\
A related question would be has anyone built an i2b2 ontology for ICD-O (international classification of diseases for oncology)?
    
\\
Sincerely,
          
Russ Waitman
  
Associate Professor   Director of Medical Informatics   Department of Biostatistics   University of Kansas Medical Center   rwaitman.kumc   [http://informatics.kumc         
]
\\
On February 1st, MCG became Georgia Health Sciences University.  My email address has also changed to the format ".georgiahealth".  Please update your address book to reflect this change.
  
\\
\\
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*NEXT EMAIL*

_From: Lisa Miao \[lmiao.regenstrief\] Sent: Thursday, August 11, 2011 4:18 PM To: Phillips, Lori C.; i2b2 AUG Members Subject: RE: documentation on how to create new project_

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Lori,

Thanks so much for your quick response\! Yes, that did solve my issue. It wasn't very clear that project_path need to match with project_id. Now my project is up and running\!

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Thanks so much\!

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Lisa.
 \\
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_From:_ _Phillips, Lori C. \[LCPHILLIPS.PARTNERS\] Sent: Thursday, August 11, 2011 3:33 PM To: Lisa Miao; i2b2 AUG Members Subject: RE: documentation on how to create new project_

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I believe one of your db_lookup tables \[CRC_DB_LOOKUP, ONT_DB_LOOKUP... etc\] is generating that message.

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In these tables: domain_id = hive_id; project_path = project_id

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So its looking for an entry of domain_id = i2b2demo; and project_id = =\[/regenstrief1/\]

from there it finds the associated data sources, etc.
\\
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_From: Lisa Miao \[lmiao.regenstrief\] Sent: Thursday, August 11, 2011 3:11 PM To: i2b2 AUG Members Subject: RE: documentation on how to create new project_

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Hi all,

I created a new project and assigned a user (let's call it user1) to it, and also created 3 data sources, QueryToolDemo3DS OntologyDemo3DS WorkplaceDemo3DS

\\
And also setup table entries in i2b2hive and i2b2pm.

\\
When I logged in as user1, I could see my new project, when I choose the new project, I got an error: "An error has occurred in the Cell's AJAX library".

\\
Looking through the log, it was complaining: (one complaint was "Could not match Project id=\[/regenstrief1/\] Trying with hive =i2b2demo")

\\
How do I associate project_id with the hive?

\\
Thanks,

Lisa.

\\
2011-08-11 14:30:21,910 DEBUG \[edu.harvard.i2b2.ontology.delegate.RequestHandler\] Matching PM response's project name \[i2b2 Demo\] with the request  project name \[regenstrief1\]

2011-08-11 14:30:21,910 DEBUG \[edu.harvard.i2b2.ontology.delegate.RequestHandler\] Matching PM response's project name \[Wishard\] with the request  project name \[regenstrief1\]

2011-08-11 14:30:21,911 DEBUG \[org.springframework.jdbc.core.JdbcTemplate\] Executing SQL query \[select * from i2b2hive.ont_db_lookup where LOWER(c_domain_id) = ? and LOWER(c_project_path) like ? and (LOWER(c_owner_id) =? or c_owner_id = '.') order by c_project_path\]

2011-08-11 14:30:21,916 DEBUG \[org.springframework.jdbc.datasource.DataSourceUtils\] Fetching JDBC Connection from DataSource

2011-08-11 14:30:21,924 DEBUG \[org.springframework.jdbc.core.StatementCreatorUtils\] Setting SQL statement parameter value: column index 1, parameter value \[i2b2demo\], value class \[java.lang.String\], SQL type unknown

2011-08-11 14:30:21,924 DEBUG \[org.springframework.jdbc.core.StatementCreatorUtils\] Setting SQL statement parameter value: column index 2, parameter value \[regenstrief1/%\], value class \[java.lang.String\], SQL type unknown

2011-08-11 14:30:21,924 DEBUG \[org.springframework.jdbc.core.StatementCreatorUtils\] Setting SQL statement parameter value: column index 3, parameter value \[lmiao\], value class \[java.lang.String\], SQL type unknown

2011-08-11 14:30:21,935 DEBUG \[org.springframework.jdbc.datasource.DataSourceUtils\] Returning JDBC Connection to DataSource

2011-08-11 14:30:21,935 DEBUG \[edu.harvard.i2b2.ontology.dao.DataSourceLookupHelper\] Could not match Project id=\[/regenstrief1/\] Trying with hive =i2b2demo

2011-08-11 14:30:21,935 DEBUG \[org.springframework.jdbc.core.JdbcTemplate\] Executing SQL query \[select * from i2b2hive.ont_db_lookup where LOWER(c_domain_id) = ? and c_project_path = ? and (LOWER(c_owner_id) = ? or c_owner_id ='.') order by c_project_path\]

2011-08-11 14:30:21,935 DEBUG \[org.springframework.jdbc.datasource.DataSourceUtils\] Fetching JDBC Connection from DataSource

2011-08-11 14:30:21,936 DEBUG \[org.springframework.jdbc.core.StatementCreatorUtils\] Setting SQL statement parameter value: column index 1, parameter value \[i2b2demo\], value class \[java.lang.String\], SQL type unknown

2011-08-11 14:30:21,936 DEBUG \[org.springframework.jdbc.core.StatementCreatorUtils\] Setting SQL statement parameter value: column index 2, parameter value \[.\], value class \[java.lang.String\], SQL type unknown

2011-08-11 14:30:21,939 DEBUG \[org.springframework.jdbc.core.StatementCreatorUtils\] Setting SQL statement parameter value: column index 3, parameter value \[lmiao\], value class \[java.lang.String\], SQL type unknown

2011-08-11 14:30:21,953 DEBUG \[org.springframework.jdbc.datasource.DataSourceUtils\] Returning JDBC Connection to DataSource

2011-08-11 14:30:21,957 ERROR \[org.apache.axis2.transport.http.AxisRESTServlet\] org.apache.axis2.AxisFault: Could not locate hive= i2b2demo; nested exception is:

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_From:_ _Mike Mendis \[mmendis.partners\] Sent: Thursday, August 11, 2011 9:40 AM To: Lisa Miao; i2b2 AUG Members Subject: Re: documentation on how to create new project_

\\
Check out the PM install doc [http://www.i2b2.org/software]

\\
\\
_On 8/11/11 9:38 AM, "Lisa Miao"  lisamiao.i2b2aug  wrote:_

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Could someone point out where we have documentation for  how to create a new project in I2B2?

\\
Thanks,

lisa.

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*NEXT EMAIL*

_From: Sebastian Mate \[Sebastian.Mate.imi.med.uni-erlangen.de\] Sent: Thursday, August 11, 2011 3:43 PM To: Lisa Miao Cc: i2b2 AUG Members Subject: Re: documentation on how to create new project_

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Hi Lisa,

actually, with a working i2b2 wizard creating a new i2b2 project is VERY easy:

Assuming that you have a fresh Linux machine and have started the wizard script for the first time (without having installed anything related to i2b2), you can directly head to the "New i2b2 Project" menu. The i2b2 wizard automatically detects which software components are missing and installs them. It detects that there is no i2b2 yet, downloads and installs JBoss, compiles the i2b2 webservices, detects that the schemata I2B2PM and I2B2HIVE are not existing, etc. In short: it automatically and recursively solves installation dependencies.

\\
After that, it automatically creates the project schema (in contrast to the i2b2 installation, all schemata (ONT, CRC, WORK) are inside one schema for simplicity), registers the datasources (*-ds.xml files) and redeploys the webservices. Furthermore, it creates a simple SQL file which populates the project with some sample data. It also automatically handles starting and stopping of JBoss.

\\
If everything went OK, this procedure takes only seconds (for the new project). The full i2b2 installation can be done in maybe 10 minutes (from scratch\!), if the Ubuntu VM is set up.

\\
One issue with i2b2 wizard is that its communication (e. g. with the Oracle DB) is one-way. The tool only writes, but does not read. If, for example, if Oracle is not properly working, the installation might fail and you don't know why. The next version, however, will have an improved error handler, so that you can see what's going on. Also, this is the reason why you can't run the program on an exiting i2b2 installation. It is unable to read/import the current i2b2 configuration (users, projects). i2b2 wizard keeps track of this information in the "conf" subdirectory when you use i2b2 wizard. Maybe I will address this in a future version.

\\
The i2b2 wizard comes with a comprehensive (20 pages) documentation to get started.
\\
Also, to reply to your other e-mail (Could not match Project id=\[/regenstrief1/\] Trying with hive =i2b2demo"): The Hive ID is not properly set up in your configuration and database. I can't remember, where. In i2b2 wizard, there is menu to change this parameter automatically.

\\
A suggestion: if you don't want to use i2b2 wizard, you could use the script to get guidance on how to do it manually. I know that people do this. But I'm a friend of automation and think that I have spent too much time fuzzing around in the i2b2 config files -- for me, i2b2 wizard does the job (should I say dirty work?) ... ;-)

\\
Sebastian

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_Am 11.08.2011 um 21:12 schrieb Lisa Miao:_

\\
Sebastian, would you mind sharing your steps on how to create a new project in i2b2?
    
\\
Thanks,
    
Lisa.
        
\\
\\
_From: Sebastian Mate \[Sebastian.Mate.imi.med.uni-erlangen.de\]   Sent: Thursday, August 11, 2011 10:35 AM   To: Lisa Miao   Cc: i2b2 AUG Members   Subject: Re: documentation on how to create new project_
    
\\
It's located here: [http://www.imi.med.uni-erlangen.de/~matesn/i2b2wizard/]
    
\\
Currently, it only supports 1.5.1 on Ubuntu 10.04 32 Bit with Oracle. Since these packages are no longer available on the i2b2 site

(1.5.4 is the latest), I have uploaded the old versions here: [http://www.imi.med.uni-erlangen.de/~matesn/i2b2wizard/packages/] .

\\
Simply copy all files (especially the i2b2 packages) into the packages subdirectory of the i2b2 wizard. Before running the wizard, make sure to install Oracle XE by hand (see TXT file on server), or provide a database connection a dedicated Oracle server (see doc).
    
\\
Maybe it works with 1.6 RC4 out of the box if you change the filenames and MD5 sums of the i2b2 source code packages in the script wizard.sh. I will update the wizard to 1.5.4 soon, and to 1.6 as soon as the final version is out. Currently, I'm working on a full SHRINE integration.
\\
 Sebastian
      
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_Am 11.08.2011 um 16:07 schrieb Lisa Miao:_
     
\\
Thanks Sebastian\!
      
Sounds very powerful.

Where do we get "i2b2 wizard" and can it install RC4?
      
\\
Thanks,
      
Lisa.
      
\\
\\
_From: Sebastian Mate \[Sebastian.Mate.imi.med.uni-erlangen.de\]    Sent: Thursday, August 11, 2011 9:58 AM    To: 'Lisa Miao'; i2b2 AUG Members    Subject: AW: documentation on how to create new project_
      
\\
Hi Lisa,

and just to advertise our "i2b2 wizard" (in the hope that this helps, see i2b2 Wiki):       Run i2b2 wizard and select "Project Management" =  "Create i2b2 Project" and fill out three parameters:
       
\\
Hit "OK" and you're done within 10 seconds. The wizard even populates the new datatabse schema with a working minimal "demo" dataset. J
     
\\
Does not work with an existing (manually configured) i2b2 installation, though. I2b2 has to be installed with "i2b2 wizard" from the beginning on.

\\
 Sebastian
        
Dipl.-Inf. Univ. Sebastian Mate    Chair of Medical Informatics, Friedrich-Alexander-University Erlangen-Nuremberg, Germany    Krankenhausstrasse 12, 91054 Erlangen
   
\\
\\
_From: Mendis, Michael E._ _Sent: Thursday, August 11, 2011 9:40 AM To: Lisa Miao; i2b2 AUG Members Subject: Re: documentation on how to create new project_

\\
Check out the PM install doc [http://www.i2b2.org/software]

\\
\\
_On 8/11/11 9:38 AM, Lisa Miao wrote:_

\\
Could someone point out where we have documentation for how to create a new project in I2B2?

\\
Thanks,

lisa.

\\
\\
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*NEXT EMAIL*
_From: Nigam Shah \[nigam.stanford\] Sent: Wednesday, August 10, 2011 9:25 PM To: i2b2 AUG Members Subject: Invitation to participate in the 2012 Joint Summits -- 10 days to paper deadline_

\\
Dear Colleagues,

On behalf of AMIA, we invite your submission to the 2012 Joint Summits, March 19-23, 2012, in San Francisco. The Translational Bioinformatics (TBI) Summit opens the AMIA Joint Summits on Translational Science and will be followed by the Summit on Clinical Research Informatics (CRI) from March 21-- 23, 2012, at the same venue.

For TBI, we look forward to submissions that include innovative data--centric approaches that compute on large amounts of data to discover patterns and to make clinically relevant predictions that are the forte of Translational Bioinformatics. The changes in public policy, the availability of large datasets from multiple molecular level measurements, and increasing electronic heath record (EHR) adoption, coupled with recent advances in natural language processing, access to vast computing infrastructure, sophisticated ontologies, data-mining and machine learning tools that have all converged to enable Big Data mining in Translational Bioinformatics.  This year, four tracks will cover research that takes the field from base pairs to bedside, with an emphasis on clinical implications of mining massive data-sets, and on bridging the latest multimodal measurement technologies with large amounts of healthcare data.

\\
Concepts, Tools and Techniques for Translational Bioinformatics

Integrative Analysis of multi modal measurements

Base pairs to Bedside

Informatics with Big Data

\\
Track details at: www.amia.org/jointsummits2012/tbi-submission

For CRI, we look forward to submissions that showcase leading-edge innovative methods and technologies that focus on accelerating all phases of translational science -- including study of conceptual design and simulation, patient identification and recruitment, data collection, integration and visualization, and data analysis, dissemination and knowledge transfer. We highlight four specific areas for special emphasis. But we invite submissions from across the CRI community to present the broad range of activities that are addressing translational research informatics needs.

\\
Research and Resource Discovery, Collaboration and Sharing

Bedside to Base Pairs -- From Clinical Observations to Genetic Discovery

Clinical Care and Clinical Research Work Flow Integration

Emerging Informatics Platforms for Integrated Translational Research

\\
Track details at: <span style="color: #0000ff"><span style="text-decoration: underline; ">www.amia.org/jointsummits2012/cri-submission</span></span>

Key dates: Paper Proposals: due August 19, 2011 Panels, Posters, Podium Abstract Proposals: due October 21, 2011

Details on submission types: <span style="color: #0000ff"><span style="text-decoration: underline; ">www.amia.org/jointsummits2012/types-proposals</span></span>

We look forward to your submissions and hope that you will join us in San Francisco in March of 2012.

Nigam H. Shah, Stanford University Chair, 2012 Scientific Program Committee TBI Summit

Michael Kahn, University of Colorado Chair, 2012 Scientific Program Committee CRI Summit
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*NEXT EMAIL*

_From: Debbie Yoshihara \[yoshi.biostat.wisc\] Sent: Wednesday, August 10, 2011 9:09 AM To: Wynden, Rob Cc: i2b2 AUG Members Subject: Re: Loading a Protege ontology into I2b2_

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Thanks Rob, I'm just getting HOM installed on our I2B2 instance now and may take you up on the call if I have more specifc questions.

\\
Debbie

\\
\\
_Wynden, Rob wrote:_

\\
Hello, We do this all the time now on the HOM project (Health Ontology Mapper). Would you be able to join is on our regular Tuesday concall?  The contact details are listed on our wiki on the i2b2 Community site...

\\
\\
_Rob Wynden On 8/9/11 1:03 PM, "Debbie Yoshihara" <yoshi.biostat.wiscwrote:_

\\
Hi, I've searched the literature about putting an ontology into i2b2 and I've found references to BioPortal.   Are there any notes or other tools on how to do this?
\\
Thanks, Debbie Yoshihara

Dept of Biostatistics and Medical Informatics University of Wisconsin - Madison

\\
\\
_From: Debbie Yoshihara \[yoshi.biostat.wisc\] Sent: Wednesday, August 10, 2011 9:08 AM To: Mobed, Ketty Cc: i2b2 AUG Members Subject: Re: Loading a Protégé ontology_ _into I2b2_

\\
Thanks Kathy - I'll have more specific questions soon.

\\
\\
_Mobed, Ketty wrote:_

\\
Hi Debbie, I have been developing our clinical ontologies and uploaded them to BioPortal. Let me know if you have a specific question on how I can help you.

\\
Cheers, Ketty Ketty Mobed,

PhD MSPH Research Analyst / Terminologist ITS - Academic Research Systems UCSF - Campus Box 0707

\\
\\
_From: Debbie Yoshihara \[yoshi.biostat.wisc\] Sent: Tuesday, August 09, 2011 1:04 PM To: i2b2 AUG Members Subject: Loading a Protege ontology into I2b2_

\\
Hi, I've searched the literature about putting an ontology into i2b2 and I've found references to BioPortal.   Are there any notes or other tools on how to do this?

\\
Thanks, Debbie Yoshihara

Dept of Biostatistics and Medical Informatics University of Wisconsin - Madison

\\
\\
_From: Debbie Yoshihara \[yoshi.biostat.wisc\] Sent: Wednesday, August 10, 2011 9:04 AM To: Mate, Sebastian Cc: i2b2 AUG Members Subject: Re: AW: Loading a Protege ontology into I2b2_

\\
Thank you for this information. This is exactly the kind of thing I'm looking for. Don't worry about about it being in it's infancy stage - for fall back I was going to do it brute force hand-made SQL statements.

\\
Debbie

\\
\\
_Mate, Sebastian wrote:_

\\
Dear Debbie, we're working on the same thing. I think that building i2b2 Ontologies at the database level is the wrong approach. I have created a tool (OntoEdit, see screenshot) that allows the editing of i2b2 ontologies in OWL format, which can also be opened with Protégé. OntoEdit is designed to allow the fast editing of i2b2-compatible OWL ontologies (which is cumbersome to do with Protégé ...). It should be easy to import other OWL ontologies, as long as their concepts are modeled in a hierarchy. With another tool (OntoExport), the ontologies can be translated into the i2b2 database format. Basically it translates the OWL file into SQL statements. The whole thing supports the largest parts of the i2b2 semantics, including the creation of the C_METADATAXML column. What is not (yet) supported is the handling of units and synonyms. I think this is information can be automatically integrated by using other ontologies (like UCUM), but I haven't done any deeper research on that. The whole toolset, which I call "i2b2 OntoImport Suite", is actually designed to integrate heterogeneous data (form data from CRFs, the EMR, etc.) for i2b2. Data elements can be mapped and transformed to the concepts inside the i2b2 ontology (created with OntoEdit). It's completely based on OWL ontologies (even facts data transformations are modeled in OWL\!), which are then translated into SQL statements to perform data export to i2b2.

\\
You can find the tools, along with lots of additional information, right here:

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[http://www.imi.med.uni-erlangen.de/~matesn/i2b2%20OntoImport%20Suite/] <http<[http://www.imi.med.uni-erlangen.de/%7Ematesn/i2b2%20OntoImport%20Suite/]

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Please note that this is still VERY prototypical, though. I keep working on that ... J

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Sebastian /-----------------------------------------------------\--/ /Dipl.-Inf. Univ. Sebastian Mate/ /Chair of Medical Informatics, Friedrich-Alexander-University Erlangen-Nuremberg, Germany/ /Krankenhausstrasse 12, 91054 Erlangen/ / / \-----Ursprüngliche Nachricht-\--\-

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_Von: i2b2 AUG Members Im Auftrag von Debbie Yoshihara Gesendet: Dienstag, 9. August 2011 22:04 An: i2b2 AUG Members Betreff: Loading a Protege ontology into I2b2_

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Hi, I've searched the literature about putting an ontology into i2b2 and I've found references to BioPortal. Are there any notes or other tools on how to do this?

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Thanks, Debbie Yoshihara

Dept of Biostatistics and Medical Informatics University of Wisconsin - Madison

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_From: Yves Thorrez \[Yves.Thorrez.uzbrussel.be\] Sent: Wednesday, August 10, 2011 7:34 AM To: i2b2 AUG Members Subject: Navigating terms is slow_

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Hi,

I was wondering, does anyone else using 1.6 RC4 experience slow opening of folders/containers while navigating terms (10-20 seconds and even longer)? With modifiers disabled, navigating is a lot smoother.

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Thanks,

Yves
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_From: Peter Beninato \[beninato.ohsu\] Sent: Tuesday, August 09, 2011 2:42 PM To: Peter Kenah; i2b2 AUG Members Subject: RE: An i2b2 Style concept/ontology tree_

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Just a guess, but maybe your bulk importer is substituting Unicode 0 for nulls?

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_From: Peter Kenah \[peter.kenah.duke\] Sent: Tuesday, August 09, 2011 11:38 AM To: Peter Beninato; i2b2 AUG Members Subject: RE: An i2b2 Style concept/ontology tree_
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27 more Caused by: java.net.SocketException: Broken pipe
        at java.net.SocketOutputStream.socketWrite0(Native Method)
        at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:92)
        at java.net.SocketOutputStream.write(SocketOutputStream.java:136)
        at org.apache.coyote.http11.InternalOutputBuffer.realWriteBytes(InternalOutputBuffer.java:737)
        at org.apache.tomcat.util.buf.ByteChunk.flushBuffer(ByteChunk.java:434)
        at org.apache.coyote.http11.InternalOutputBuffer.flush(InternalOutputBuffer.java:299)
        at org.apache.coyote.http11.Http11Processor.action(Http11Processor.java:963)
 at org.apache.coyote.Response.action(Response.java:183)
        at org.apache.catalina.connector.OutputBuffer.doFlush(OutputBuffer.java:314)
35 more 14:31:05,786 INFO \[DataSourceLookupHelper\] Located DataSource for hiveId=\[i2b2Demo\] projectId=\[/DukeDev/\]

14:31:05,788 INFO \[OracleDAOFactory\] Using datasource java:QueryToolDev_DS 14:31:07,880 ERROR \[AxisRESTServlet\] org.apache.axis2.AxisFault: com.ctc.wstx.exc.WstxUnexpectedCharException: Illegal character (NULL, unicode 0) encounte red: not valid in any content at \[row,col \{unknown-source\}\]: \[51,35\]; nested exception is:
        org.apache.axiom.om.OMException: com.ctc.wstx.exc.WstxUnexpectedCharException: Illegal character (NULL, unicode 0) encountered: not valid in any co ntent

at \[row,col \{unknown-source\}\]: \[51,35\]; nested exception is:
        org.apache.axis2.AxisFault: com.ctc.wstx.exc.WstxUnexpectedCharException: Illegal character (NULL, unicode 0) encountered: not valid in any content

at \[row,col \{unknown-source\}\]: \[51,35\]; nested exception is:
        org.apache.axiom.om.OMException: com.ctc.wstx.exc.WstxUnexpectedCharException: Illegal character (NULL, unicode 0) encountered: not valid in any co ntent

at \[row,col \{unknown-source\}\]: \[51,35\]

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_From: Peter Beninato \[beninato.ohsu\] Sent: Tuesday, August 09, 2011 1:49 PM To: Peter Kenah; i2b2 AUG Members Subject: RE: An i2b2 Style concept/ontology tree_

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What's the error?

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_From: Peter Kenah \[peter.kenah.duke\] Sent: Tuesday, August 09, 2011 10:42 AM To: i2b2 AUG Members Subject: An i2b2 Style concept/ontology tree_

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We are having some issues when we bulk load the ontology tree into the i2b2 table.
 
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When records are loaded using out bulk load utility and we try to traverse the tree in the workbench we get an error message. However when we manually insert the records using the oracle insert statement, it works.

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We created 2 trees, 1 using a bulk load utility and the other using the insert statement with the same data. Visually the records look the same but when the  tree bulk loaded is traversed we get an error.

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Peter Kenah

Duke University

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_From: Jack London \[jack.london.KimmelCancerCenter\] Sent: Monday, August 08, 2011 11:32 AM To: i2b2 AUG Members members Subject: web client v1.6 RC4 query results_

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If I perform a simple query, such as "find patient count for patients with medication observation-facts of 'Aspirin' " the query status window at the bottom right repeats 6 times the result statement, "Number of patients etc. patient_count: 2"

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Why the repeated result statement?

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Jack

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_From: Jack London \[jack.london.KimmelCancerCenter\] Sent: Monday, August 08, 2011 11:04 AM To: Mendis, Michael E._ _Cc: i2b2 AUG Members members Subject: Re: v1.6 RC4 web client display xml icon_

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mike,

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Yep\! that fixed it.

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Thanks ...

jack

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_On Aug 8, 2011, at 10:59 AM, Mike Mendis wrote:_

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Oh sorry, my mistake.

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There is a user config param: In the i2b2_config_data.js Set debug = true like: domain: "HarvardDemo", name: "HarvardDemo", urlCellPM: "http://services.i2b2.org/PM/rest/PMService/", allowAnalysis: false, debug: true

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mike

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_On 8/8/11 10:56 AM, "Jack London" <jack.london.KimmelCancerCenter> wrote:_

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using Safari browser ...

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_On Aug 8, 2011, at 10:45 AM, Mike Mendis wrote:_

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No they are not a user config parameter.  Can you send a screenshot.

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Thanks

Mike

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_On 8/8/11 10:42 AM, "Jack London" <jack.london.KimmelCancerCenter> wrote:_

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The icon to show the xml message stack does not appear in our installation of the v1.6 RC4 web client. Is the display of icon dependent on a user configuration parameter?

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Jack

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_From: Jack London \[jack.london.KimmelCancerCenter\] Sent: Thursday, August 04, 2011 5:02 PM To: i2b2 AUG Members members Subject: v1.6 RC4 project demo2 queries fail_

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Any idea what may be causing the following behavior with the v1.6 RC4 web client:

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1) Works fine with Project i2b2 Demo.

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2) With Project i2b2 Demo2, when the "Run Query" button is pressed, the "Run Query" dialogue appears with the default query name, but the "query result type(s)" selection box is empty. It behaves as if the I2B2DEMODATA2.QT_QUERY_RESULT_TYPE table entries were not accessible. Since the metadata is properly displayed, I2B2METADATA2 tables seem to be accessible, but it acts as if I2B2DEMODATA2 tables are not.

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Any suggestions on where to look?

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thanks,

Jack

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_From: Mendis, Michael E._ _Sent: Thursday, August 04, 2011 3:54 PM To: i2b2 AUG Members Subject:_ _Re: 1.6 RC4 is Available (UPDATE)_

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The Sql Server Modifiers Dimension Table data was missing from the data release file.

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We have added it as a extra download in the RC section.

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Once you download the file, place it in the Release_1?6/NewInstall/metadata/demo/sqlserver and Release\_ 1?6/NewInstall/metadata/demo2/sqlserver directory

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Thanks

Mike

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_From: John Hook \[jhook.regenstrief\] Sent: Wednesday, August 03, 2011 1:56 PM To: Russ Waitman; i2b2 AUG MembersSubject: RE: Is there additional documentation on DATA_OBFSC and DATA_AGG_

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Professor Waitman,

Thank you very much for your prompt reply. This information looks very helpful and I will certainly pass it along.

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Thanks again,

John Hook

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_From: Russ Waitman \[rwaitman.kumc\] Sent: Wednesday, August 03, 2011 12:19 PM To: members.i2b2aug; John Hook Subject: Re: Is there additional documentation on DATA_OBFSC and DATA_AGG_

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Hi John,

Shawn Murphy gave a great talk at the SHRINE conference on levels of security that provide some explanation as well as future directions. It's available here.

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[https://cbmi.med.harvard/shrine2011/agenda]

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specifically:

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[https://cbmi.med.harvard/shrine2011/sites/cbmi.med.harvard.shrine2011/files/Strategies%] 20for%20maintaining%20privacy%20levels%20in%20i2b2_Shawn%20Murphy.pdf

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I needed to explain these things further to our Data Request Oversight Committee.  Since we build our i2b2 off of a completely de-identified repository, I made a graph that shows people how one might perceive relative risk versus the type of access you grant to the different types of databases you might be creating. It's available here:

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[http://informatics.kumc/work/attachment/wiki/DROCMeetingMinutes/HERON_i2b2] \_ReidentificationandSensitivityRiskGraph.pdf

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The agenda item for our committee meeting was was:

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_Line-item view and plug in access_

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I'd like to explore adding an additional capability for our investigators and users: viewing line-item data and the ability to use analysis plug-ins.

I am attaching a document from the i2b2 architect, Dr. Shawn Murphy,

I've created a graph which helps explain where we are with system access and how this new capability would fit in.

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We need to think of the appropriate level of oversight required to provide this additional functionality

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Hope that helps though Shawn and Mike probably have some good info in the new help they are preparing for i2b2 1.6.

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Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center

rwaitman.kumc

[http://informatics.kumc|http://informatics.kumc]

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_John Hook jhook.regenstrief 8/3/2011 9:47 AM_
 
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Hi all,

Out management and legal staff is asking for details about data obfuscation and aggregation in i2b2. I've provided them with the documentation from the CRC_Design document but they are looking for more. Is there any additional documentation that gives an in-depth explanation of the DATA_OBSFC and DATA_AGG roles?

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Thanks,

John Hook

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_From: Jack W. London, Ph.D. \[Jack.London.KimmelCancerCenter\] Sent: Wednesday, August 03, 2011 1:15 PM To: Mendis, Michael E. Cc: Michael.C.Ford.kp; Dat.Q.Phan.uth.tmc; i2b2 AUG Members_ _Subject: Re: v1.6 RC4 installation question_

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yes, extension=php_curl.dll is uncommented in php.ini

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Jack

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_Quoting Mike Mendis mmendis.partners:_

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 If this is a linux, than make sure the curl is installed
   
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_On 8/3/11 1:04 PM, "Jack W. London, Ph.D."  Jack.London.KimmelCancerCenter wrote:_
  
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Mike,
  
When I try connecting to  [http://services.i2b2/PM/rest/PMService/]  I get the message
 
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"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"
  
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Jack

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_Quoting Mike Mendis mmendis.partners:_
  
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Try connecting to the harvard demo to see if it is a server or client:  "http://services.i2b2/PM/rest/PMService/²
  
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mike
   
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_From: Jack W. London, Ph.D. \[Jack.London.KimmelCancerCenter\] Sent: Wednesday, August 03, 2011 12:55 PM To: Dat Q. Phan Cc: i2b2 AUG MembersSubject: RE: v1.6 RC4 installation question_

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Ontology cell installed -- still cannot access PM.

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Jack

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_On 8/3/11 12:50 PM, "Michael.C.Ford.kp" Michael.C.Ford.kp wrote:_
   
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I am no expert but if i2b2_config_data.js  shows urlCellPM: "http://localhost:8080/i2b2/rest/PMService/"   this is then going to the browser and at the browser it's making an  AJAX call  to localhost:8080.
   
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_From: Dat Q. Phan \[Dat.Q.Phan.uth.tmc\] Sent: Wednesday, August 03, 2011 12:47 PM To: Jack W. London, Ph.D. Cc: i2b2 AUG MembersSubject: RE: v1.6 RC4 installation question_

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Oh and if you're using Linux then make sure SELinux is disabled.  That's more likely the culprit.

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Johnny

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 _From: Jack W. London, Ph.D. \[Jack.London.KimmelCancerCenter\] Sent: Wednesday, August 03, 2011 11:34 AM To: Dat Q. Phan Cc: i2b2 AUG MembersSubject: RE: v1.6 RC4 installation question_

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Dat,

Yes, I tried that url and it shows the PMService is active.  I'll continue on, and install the Ontology cell.

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Thanks for your help.

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Jack

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_From: "Dat Q. Phan" Dat.Q.Phan.uth.tmc Sent: 08/03/2011 09:26 AM  To:"Jack W. London, Ph.D." Jack.London.KimmelCancerCenter  cc: "members.i2b2aug" members.i2b2aug  Subject: RE: v1.6 RC4 installation question_

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From your i2b2 server, if you can access  [http://localhost:8080/i2b2/services/listServices] and see that the  PMService is  active then you should be OK.   I usually get that error message after I've installed the PM cell.  Once I  install the Ontology cell then I'm able to access the admin web  page. That's  from my experience with v1.6 RC2 and RC3.  I have yet to try RC4.
  
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Regards,
  
Johnny Phan
 
Programmer Analyst II  UTHealth  School of Biomedical Informatics  Dat.Q.Phan.uth.tmc
 
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_From: Jack W. London, Ph.D. \[Jack.London.KimmelCancerCenter\]  Sent: Wednesday, August 03, 2011 10:58 AM  To: Mike Mendis  Cc: i2b2 AUG Members Subject: Re: v1.6 RC4 installation question_
  
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Mike,
  
Trying to log-in to the web client also returns the message:  "Your account does not have access to any i2b2 projects."
  
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Jack
   
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_Quoting Mike Mendis mmendis.partners:_
  
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Does the regular webclient work fine?
   
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_On 8/3/11 10:03 AM, "Jack W. London, Ph.D." wrote:_
  
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When I try to log-in at  [http://172.16.44.129/admin/]  I get the message  Your account does not have access to any i2b2 projects.   i2b2_config_data.js has:  // THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO  lstDomains: \[  \{ name: "KCC i2b2 Admin",  domain: "i2b2demo",  debug: true,  adminOnly: true,  urlCellPM: "http://localhost:8080/i2b2/rest/PMService/"  \}    extension=php_curl.dll is uncommented in php.ini    when I go to  [http://172.16.44.129:8080/i2b2/rest/PMService]  I get the message:  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
   
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Suggestions for fixing the admin log-in problem?
 
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thanks,
 
Jack

Jack W. London, Ph.D.

Thomas Jefferson University Research Professor, Cancer Biology Kimmel Cancer Center Director, KCC Informatics Core Facility 808 Bluemle Life Science Bldg. 233 S. 10th Street Philadelphia, PA 19107

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*NEXT EMAIL*
_From: Peter Beninato \[beninato.ohsu\] Sent: Tuesday, August 02, 2011 4:36 PM To: Arvinder Choudhary; Michael.C.Ford.kp Cc: i2b2 AUG MembersSubject: RE: Jboss Log Error_

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The part about estimated size, still makes me think about the max_count in the i2b2 table.

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Try logging on as the owner of the observation_fact table, and selecting from the i2b2 table.

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_From: Arvinder Choudhary \[achoudhary.kumc\] Sent: Tuesday, August 02, 2011 1:32 PM To: Michael.C.Ford.kp; Peter Beninato Cc: i2b2 AUG MembersSubject: RE: Jboss Log Error_

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Another interesting thing I noted was that number of below statement

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   ERROR \[edu.harvard.i2b2.crc.dao.CRCDAO\] Unable to get Estimated Size: ORA-00942: table or view does not exist

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is based on the parameters I pass. Say if I have 2 groups (Group1 and Group2) for a query  in the i2b2 Query & Analysis Tool , I see 2 entries of the above statement in the jboss log file and if 3 Groups then 3 and so on....

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Something has to do how we parse the query in the database using the application code....

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Arvinder

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_Arvinder Choudhary 8/1/2011 12:18 PM_
 
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We are on 1.4 . I did stop/start jboss but the same log error issue

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_Peter Beninato beninato.ohsu 8/1/2011 11:55 AM_
 
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After the grant, presumably you stop/start jboss?

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I saw that error, and the GRANT on the i2b2 to the data schema appeared to fix it for me?

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Maybe something else. Which version?

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_From: Arvinder Choudhary \[achoudhary.kumc\] Sent: Monday, August 01, 2011 9:50 AM To: Michael.C.Ford.kp; Peter Beninato Cc: i2b2 AUG MembersSubject: RE: Jboss Log Error_

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Peter:
 I have set select any table on i2b2 database for all the schemas but still the same error shows up in the log after I run a query. (Query does produce a result)

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Arvinder

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_Peter Beninato beninato.ohsu 8/1/2011 11:32 AM_
 
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GRANT SELECT on i2b2 table to the "data schema".

The CRC uses the max_count to try to determine which panel is most selective.

That's my guess.

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_From: Michael.C.Ford.kp \[Michael.C.Ford.kp\] Sent: Monday, August 01, 2011 9:29 AM To: achoudhary.kumc Cc: i2b2 AUG MembersSubject: Re: Jboss Log Error_

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I have seen this for some time also, would love to find an answer.

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_From: "Arvinder Choudhary" achoudhary.kumc  Sent: 07/29/2011 07:29 AM  To: members.i2b2aug Subject: Jboss Log Error_

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Team:
  
I see this error in the log files on and off ; am I missing something in the setup..

ERROR \[edu.harvard.i2b2.crc.dao.CRCDAO\] Unable to get Estimated Size: ORA-00942: table or view does not exist

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Regards

Arvinder Choudhary

BE MS PMP Medical informatics Project Director University of Kansas Medical Center 3901 Rainbow Blvd, KS 66160

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*NEXT EMAIL*
_From: Brian Ostasiewski \[bostasie.wfubmc\] Sent: Monday, August 01, 2011 2:56 PM To: i2b2 AUG MembersSubject: RE: 1.6 RC4 is Available_

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FYI, I'm going through the demo data load for 1.6 RC4 and I noticed the DB usernames are hardcoded in:

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edu.harvard.i2b2.data/Release_1-6/NewInstall/Metadata/demo/scripts/oracle/i2b2 \_metadata_demographics_insert_data.sql

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edu.harvard.i2b2.data/Release\_ 1-6/NewInstall/Demodata/scripts/oracle/observation_fact_demo_insert_data.sql

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If your users aren't named I2B2METADATA or I2B2DEMODATA you will have to global replace in those files before doing the ant loads.

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_From: Murphy, Shawn N. \[SNMURPHY.PARTNERS\] Sent: Saturday, July 30, 2011 8:49 PM To: i2b2 AUG MembersSubject: 1.6 RC4 is Available_

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Please see at: 
[https://www.i2b2.org/RC/]

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Thanks,

Shawn.

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*NEXT EMAIL*
_From: Peter Kenah \[peter.kenah.duke\] Sent: Monday, August 01, 2011 2:01 PM To: i2b2 AUG Members_ _Subject: Jboss won't start_

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I copied my jboss directory to a new location and edited all the "-ds.xml" files.  I changed all usernames and passwords to point to a new sets of i2b2 schemas containing a fresh install of i2b2 data.

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The problem I have is that, when I tried to start jboss,  it will starts but is seems that some of the installation still points to the original directory where jboss was initially install.  I know this because if I rename my initial jboss directory,  jboss doen not start.

Does anyone know all the list of files that reference the jboss installation directory and the i2b2 schema references.

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Sample jboss log:

13:32:47,016 INFO \[EjbModule\] Deploying ejb.crc.loader.frbean

13:32:47,176 INFO \[BaseLocalProxyFactory\] Bound EJB LocalHome 'ejb.crc.loader.frbean' to jndi 'ejb.crc.loader.FRBeanLocal'

13:32:47,191 INFO \[ProxyFactory\] Bound EJB Home 'ejb.crc.loader.frbean' to jndi 'ejb.crc.loader.FRBean'

13:32:47,195 INFO \[EJBDeployer\] Deployed: [file:/opt/jboss-4.2.2.GA_dev1/server/default/deploy/CRCLoaderFR-EJB.jar]

13:32:47,409 INFO \[TomcatDeployer\] deploy, ctxPath=/i2b2, warUrl=.../deploy/i2b2.war/ 13:32:47,989 INFO \[DeploymentEngine\] Deploying module : soapmonitor-1.1 13:32:48,016 INFO \[DeploymentEngine\] Deploying module : addressing-1.1 13:32:48,269 INFO \[DeploymentEngine\] Deploying Web service  FRC.aar 13:32:48,348 INFO \[DeploymentEngine\] Deploying Web service  Workplace.aar 13:32:48,405 INFO \[DeploymentEngine\] Deploying Web service  ProjectManagement.aar 13:32:48,545 INFO \[DeploymentEngine\] Deploying Web service  Ontology.aar 13:32:48,622 INFO \[DeploymentEngine\] Deploying Web service  QueryProcessor.aar 13:32:48,639 INFO \[DeploymentEngine\] Deploying Web service  version.aar 13:32:48,777 INFO \[TomcatDeployer\] deploy, ctxPath=/jmx-console, warUrl=.../deploy/jmx

console.war/

13:32:48,933 INFO \[EARDeployer\] Init J2EE application: [file:/opt/jboss-4.2.2.GA_dev1/server/default/deploy/QP1.ear] 13:32:50,291 INFO \[EjbModule\] Deploying querytool.PdoQuery 13:32:50,305 INFO \[EjbModule\] Deploying querytool.QueryInfo 13:32:50,313 INFO \[EjbModule\] Deploying querytool.QueryManager 13:32:50,320 INFO \[EjbModule\] Deploying querytool.QueryResult 13:32:50,327 INFO \[EjbModule\] Deploying querytool.QueryRun 13:32:50,334 INFO \[EjbModule\] Deploying querytool.QueryExecutorMDB 13:32:50,359 INFO \[EjbModule\] Deploying querytool.QueryExecutorLargeMDB 13:32:50,367 INFO \[EjbModule\] Deploying querytool.QueryExecutorMediumMDB 13:32:50,375 INFO \[EjbModule\] Deploying querytool.QueryExecutorSmallMDB 13:32:50,592 INFO \[JmxKernelAbstraction\] creating wrapper delegate for:

org.jboss.ejb3.stateless.StatelessContainer

13:32:50,592 INFO \[JmxKernelAbstraction\] installing MBean: jboss.j2ee:ear=QP1.ear,jar=QP-AnEJB.jar,name=AnalysisPluginInfo,service=EJB3 with dependencies: 13:32:50,604 INFO \[EJBContainer\] STARTED EJB:

edu.harvard.i2b2.crc.ejb.analysis.AnalysisPluginInfo ejbName: AnalysisPluginInfo 13:32:50,626 INFO \[JmxKernelAbstraction\] creating wrapper delegate for: org.jboss.ejb3.stateless.StatelessContainer

13:32:50,627 INFO \[JmxKernelAbstraction\] installing MBean: jboss.j2ee:ear=QP1.ear,jar=QP-AnEJB.jar,name=CronEjb,service=EJB3 with dependencies:

13:32:50,638 INFO \[EJBContainer\] STARTED EJB: edu.harvard.i2b2.crc.ejb.analysis.CronEjb ejbName: CronEjb

13:32:50,684 INFO \[JmxKernelAbstraction\] creating wrapper delegate for: org.jboss.ejb3.stateless.StatelessContainer

13:32:50,690 INFO \[JmxKernelAbstraction\] installing MBean: jboss.j2ee:ear=QP1.ear,jar=QP-AnEJB.jar,name=LargeCronEjb,service=EJB3 with dependencies:

13:32:50,731 INFO \[EJBContainer\] STARTED EJB: edu.harvard.i2b2.crc.ejb.analysis.LargeCronEjb ejbName: LargeCronEjb

13:32:50,777 INFO \[JmxKernelAbstraction\] creating wrapper delegate for: org.jboss.ejb3.stateless.StatelessContainer

13:32:50,778 INFO \[JmxKernelAbstraction\] installing MBean: jboss.j2ee:ear=QP1.ear,jar=QP-AnEJB.jar,name=StartAnalysis,service=EJB3 with dependencies:

13:32:50,806 INFO \[EJBContainer\] STARTED EJB: edu.harvard.i2b2.crc.ejb.analysis.StartAnalysis ejbName: StartAnalysis

13:32:50,815 INFO \[PropertiesFactoryBean\] Loading properties file from class path resource \[crc_application_directory.properties\]

13:32:50,815 INFO \[PropertiesFactoryBean\] Loading properties file from class path resource \[crc_application_directory.properties\]

13:32:50,837 INFO \[JmxKernelAbstraction\] creating wrapper delegate for: org.jboss.ejb3.stateless.StatelessContainer

13:32:50,837 INFO \[JmxKernelAbstraction\] installing MBean: jboss.j2ee:ear=QP1.ear,jar=QP-AnEJB.jar,name=PriviledgeBean,service=EJB3 with dependencies:

13:32:50,838 INFO \[PropertiesFactoryBean\] Loading properties file from file \[/opt/jboss-4.2.2.GA/server/default/conf/crcapp/crc.properties\]

13:32:50,838 INFO \[PropertiesFactoryBean\] Loading properties file from file \[/opt/jboss-4.2.2.GA/server/default/conf/crcapp/crc.properties\]

13:32:50,840 ERROR \[STDERR\] edu.harvard.i2b2mon.exception.I2B2Exception: Application property file(/opt/jboss-4.2.2.GA/server/default/conf/crcapp/crc.properties) missing entries or not loaded properly

13:32:50,840 ERROR \[STDERR\] at edu.harvard.i2b2.crc.util.QueryProcessorUtil.getPropertyValue(Unknown Source)

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*NEXT EMAIL*
_From: Wei,Xintao \[XWEI.uchc\] Sent: Monday, August 01, 2011 1:52 PM To: i2b2 AUG Membersmembers Subject: error when starting Jboss_

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Hi,

An I2B2 1.5.2 server has been installed on Windows server 2008. However, one error reported when I start the Jboss:

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13:45:27,659 INFO \[ProxyFactory\] Bound EJB Home 'querytool.QueryInfo' to jndi 'ejb.querytool.QueryInfo'

13:45:27,669 ERROR \[TimerImpl\] Error invoking ejbTimeout: javax.ejb.EJBException: java.lang.IllegalArgumentException: dataSource is required

13:45:27,679 INFO \[BaseLocalProxyFactory\] Bound EJB LocalHome 'querytool.QueryManager' to jndi 'ejb.querytool.QueryManagerLocal'

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I have no idea what it is about and how to solve the problem. Any suggestions about this?
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Thank you\!

Xintao

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