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*NEXT EMAIL*
_From: Brian Ostasiewski \[bostasie.wakehealth\] Sent: Friday, September 30, 2011 2:28 PM To: Travis Nagler; i2b2 AUG Members Subject: RE: Change title on i2b2 login screen_
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js-i2b2/cells/PM/PM_misc.js: ' <div class="hd">i2b2 Login</div>\n'\+
I'd give you a line number but we've already modified ours from the distributed version.
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_From: Travis Nagler \[travis.nagler.ucdmc.ucdavis\] Sent: Friday, September 30, 2011 2:21 PM To: i2b2 AUG Members Subject: Change title on i2b2 login screen_
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We are running 1.5.2. We're to the point of doing some minor tweaks, one of which being changing the login pop-up box title to something other than "i2b2 Login".
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As near as I can tell, the pop-up is called on the web default.htm page with "i2b2.PM.doLoginDialog();". Does anyone know where this function is maintained so I can make that change? We're using the default everything located in our /opt folder at this point, so if you could point out a complete file address, it would be most appreciated.
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Thank ,
Travis
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Travis H. Nagler
Senior Database Programmer
American Burn Assoc. - Data Coordinating Center
UC Davis Division of Burn Surgery
UC Davis Health System
2921 Stockton Blvd., Suite 1470
Sacramento, CA, 95817
[http://www.ucdmc.ucdavis ]
travis.nagler.ucdmc.ucdavis
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*NEXT EMAIL*
_From: Peter Beninato \[beninato.ohsu\] Sent: Friday, September 30, 2011 1:32 PM To: Brian Ostasiewski; i2b2 AUG Members Subject: RE: i2b2 - v1.4 - Demographics Plugin - Age in Years - ISSUE_
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Thanks Brian.
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Ok, so clearly I have issues reading some code...
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I also... SEE DEAD PEOPLE (reference 6{^}th^ sense).
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What value would you set age_in_years_num for dead people?
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Clearly, \-1 may not be the best choice I made, I think my logic was something like
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I may know they are dead
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I may not know their death date.
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Age is generally a positive number
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Performance problem if left null (I think there was some sort of performance issue with nulls, so I needed a value.)
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I'll set the value to <drum roll> \-1
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Can anyone help me modify the code so \-1 isn't included in the 0-10 bucket?
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Peter
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_From: Brian Ostasiewski \[bostasie.wakehealth\] Sent: Friday, September 30, 2011 10:12 AM To: Peter Beninato; i2b2 AUG Members Subject: RE: i2b2 - v1.4 - Demographics Plugin - Age in Years - ISSUE_
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Looking at the code for the Dem1Set plugin, if age_in_years_num is negative, it is defaulted to zero, which is then put in the zero-to-10 bucket.
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What is the value being returned for age_in_years_num in the XML? It could be your 1921 example is interpreted as 2021, which would result in a negative age when subtracted from today.
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Brian Ostasiewski
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_From: Peter Beninato \[beninato.ohsu\] Sent: Friday, September 30, 2011 12:44 PM To: Peter Beninato; i2b2 AUG Members Subject: RE: i2b2 - v1.4 - Demographics Plugin - Age in Years - ISSUE_
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Hi, Hmmm. So I developed query below to pull patient_num for an i2b2 query from the qt_master_query.query_master_id.
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I grabbed the patient_list and examined patient_dimension birth_date.
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The max is 09/22/1921 -- MM/DD/YYYY (HIPAA 90 y/o at time of ETL run). The min is 06/5/1952.
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So still confused why anyone is in the 0-10 age bucket in the Demographic plugin.
Anyway, I include the SQL for the query to get the patient list out of the data schema to share.
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_/\*_
_NAME: query_for_i2b2_pat_ids_from_i2b2_patient_set_query.sql_
_AUTHOR: Peter Beninato_
_DATE: 29-Sept-2011_
_Purpose: To get the list of pat_ids from an_
_i2b2 query. *_
_Ususge: *_
_2) Query the qt_query_master table for the_
_query_master_id of interest._
_3) Edit the SELECT of query_master_id table in the WITH_
_clause for the query_master_id number_
_4) Run query_
_5) Export pat_id list or plug it into another query. * *_
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_\**********************************************************************\*_
_Change the query_master_id for the particular query_
_This ID is found in the octrii2b2data.qt_query_master table * \**********************************************************************\* \*/_
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with query_master_id as (
_CHANGE THE NUMBER BELOW FOR THE ID\!\!\!\!\!_
select <replace with master_query_id> as query_master_id
from dual
),
query_id as
(
select query_master_id.query_master_id, q_inst.query_instance_id
from query_master_id
join octrii2b2data.qt_query_instance q_inst
on query_master_id.query_master_id = q_inst.query_master_id
where status_type_id = 6
) select qry_reslt.query_master_id
,qry_reslt.query_instance_id
,qry_reslt.result_instance_id
,i2b2_pat_set.patient_num
from
(
select query_id.query_master_id
,query_id.query_instance_id
,qry_reslt_inst.result_instance_id
from query_id
join octrii2b2data.qt_query_result_instance qry_reslt_inst
on query_id.query_instance_id = qry_reslt_inst.query_instance_id
and result_type_id = 1
) qry_reslt
join octrii2b2data.qt_patient_set_collection i2b2_pat_set
on qry_reslt.result_instance_id = i2b2_pat_set.result_instance_id
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_From: Peter Beninato Sent: Thursday, September 29, 2011 9:35 AM To: i2b2 AUG Members Subject: i2b2 - v1.4 - Demographics Plugin - Age in Years - ISSUE_
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Hi,
I think we stumbled on an issue with the Demographics (1 Patient Set) - Simple Counts plugin.
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The query was something like: Patient Age >= 60
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DX: hypertensive ( 2 years ago).
MEDS: who are prescribed some drugs in the following year ( 1 year ago).
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I2b2 returns a patient set. What was very curious is that when the patient set is viewed via the plugin...
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THERE ARE PATIENTS in the 0-10 bucket\!
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It seems to me the logic in the snippet below may not be correct.
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In our patient dimension no AGE_IN_YEARS_NUM is greater than 90 per HIPAA. Also, I peg the birth_date to no greater than 90 years ago.
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In our data set we had dead people, but I can't see how a birth_date in the year 1921 ( 90 years ago when ETL was run), could put someone in the 0-10 bucket.
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If this PLUGIN code is the same in v1.6 it probably needs to be reviewed.
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Also, since there already is an age_in_years_num in the patient dimension why not just use that? (Or could someone maybe help me figure out how to implement that?)
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I see the parsing of "T" which makes me think that some of this code might be particular to Microsoft, which sometimes pegs a date to 01/01/1900.
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Anyway not sure of the solution. But I hope someone else can run a patient set through the plugin, confirm the issue, so that some work can be done to correct.
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Thanks.
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// get all the patient records var pData = i2b2.h.XPath(results.refXML,
'descendant::patient/param\[.name\]/text()/..');
var hData = new Hash();
for (var i1=0; i1<pData.length; i1++) \{
var n = pData\[i1\].getAttribute('name');
var t1 = hData.get(n) ;
if (\!t1) \{ t1 = new Hash(); \}
var v = pData\[i1\].firstChild.nodeValue;
if (n=="birth_date") \{
v = v.substring(0, v.indexOf("T"));
\}
if (n=="age_in_years_num") \{
v = Math.floor(v/10);
if (v<0) \{v=0;\}
if (v>9) \{v=9;\}
if (v==0) \{v='0-10';\} else \{v=v+'0-'+(v+1)+'0';\}
\}
var t2 = t1.get(v);
if (\!t2) \{ t2 = 1; \} else \{
t2++; \} t1.set(v, t2); hData.set(n, t1);
\}
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Peter Beninato - OCTRI DW Developer Oregon Health & Science University
beninato.ohsu
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*NEXT EMAIL*
_From: Murphy, Shawn N. Sent: Thursday, September 29, 2011 9:02 AM To: Mauro; Michael Horvath Cc: i2b2 AUG Members Subject: RE: Current roadmap_
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Hi Mauro,
We are targeting the 1.6 release for next Friday pending any unforeseen issues.
Thanks, Shawn.
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_From: Mauro \[mauro.bucalo.gmail\] Sent: Thursday, September 29, 2011 5:17 AM To: Michael Horvath Cc: i2b2 AUG Members Subject: Re: Current roadmap_
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Any news about the final 1.6 release?
Thanks.
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2011/9/15 Michael Horvath <mhorvath.wakehealth>
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Is there a new estimate on when the final release will be available?
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_From: Murphy, Shawn N. \[SNMURPHY.PARTNERS\] Sent: Friday, August 12, 2011 3:11 PM To: Michael.C.Ford.kp; i2b2 AUG Members Subject: RE: Current roadmap_
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Hi Michael,
We are hoping to release it in early September. The plan for version 1.7 is on the front page of the i2b2 site towards the bottom.
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Thanks, Shawn.
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_From: Michael.C.Ford.kp \[Michael.C.Ford.kp\] Sent: Friday, August 12, 2011 2:07 PM To: i2b2 AUG Members Subject: Re: Current roadmap_
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Anyone ?
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_From: Michael.C.Ford.kp \[Michael.C.Ford.kp\] Sent: Friday, August 11, 2011 8:51 AM To: i2b2 AUG Members Subject: Re: Current roadmap_
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Looking for the road map of the product and I can't seem to find it. I was wondering when 1.6 would become GA vs the current 1.5.4
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*NEXT EMAIL*
_From: Yves Thorrez \[Yves.Thorrez.uzbrussel.be\] Sent: Friday, September 23, 2011 3:09 AM To: i2b2 AUG Members Subject: metadataxml: flags and reference values_
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Hi,
In the context of reference values for our lab results, in C_METADATAXML there are following elements:
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<Flagstouse></Flagstouse>
<LowofLowValue></LowofLowValue> <HighofLowValue></HighofLowValue> <LowofHighValue></LowofHighValue> <HighofHighValue></HighofHighValue> <LowofToxicValue></LowofToxicValue> <HighofToxicValue></HighofToxicValue> 1)
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The documentation states the acceptable values for 'flagstouse' as 'L' (low), 'N' (normal), 'H' (high), 'A' (abnormal) and 'X' (toxic). Is it possible to define additional flags and how they are displayed in the i2b2 client? The Demo data contains codes A, P, X, L, M in OBSERVATION_FACT::VALUEFLAG_CD
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How are the remaining elements <Lowof...> and <Highof...> used when values are filled in? If we set the valueflag_cd at load time, can these elements play an additional role?
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Thanks,
Yves
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*Yves Thorrez*
Medische Informatieverwerking
yves.thorrez.uzbrussel.be
Laarbeeklaan 101 - 1090 Brussel
www.uzbrussel.be
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*NEXT EMAIL*
_From: Michael.C.Ford.kp Sent: Monday, September 19, 2011 2:13 PM To: i2b2 AUG Members Subject: Eclipse Deployment_
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Good morning
I was wondering if anyone had a complete Eclipse based I2B2 build and deployment setup that was documented ?
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Thanks in advance Michael C Ford Application Development Project Manager Division of Research 2000 Broadway Oakland Ca 041W09
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*NEXT EMAIL*
_From: Michael.C.Ford.kp Sent: Monday, September 19, 2011 1:40 PM To: i2b2 AUG Members Subject: Illegal characters in the concept dimension path_
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We are finding some problems with some special characters in the concept dimension path. ~ being one of these characters. I expect it's all the characters not allowed in the URL ~ # ? / \ % :
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anyone know the rules on this ?
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*NEXT EMAIL*
_From: Walter Knesel \[Walter.Knesel.cchmc\] Sent: Thursday, September 15, 2011 5:00 PM To: i2b2 AUG Members Subject: PM 1.6 RC4 miscellaneous table_
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Hi,
I am looking at the 1.6 RC4 PM_Design_1-6 document and I see that it mentions a PM_CODE_LOOKUP table. So I wanted to see what data was in it, etc. When I go to the RC download page, I can only find an RC5 i2b2demodata zip file. That zip file in the PM folder does not create that table or load that data.
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So is this table still a future item or just missing?
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Thanks, Walter Knesel
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*NEXT EMAIL*
_From: Chan, Wayne \[Wayne.Chan.umassmed\] Sent: Friday, September 09, 2011 9:43 AM To: I2B2 AUG Members Subject: FW: i2b2 - v1.4 - Edit login Form - Where?_
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That file is in <webclient>/js-i2b2/cells/PM (where <webclient> is, for instance, on my v1.3 install, it'll be /var/www/html/webclient)
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Also the background picture for that login dialog is <webclient>/js-i2b2/cells/PM/assets/login_bg.jpg -- one can replace that with another with the same name if so desired.
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Wayne
_Wayne Chan_
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Biomedical Research Informatics Development Group (BRIDG) and Biomedical Research Informatics Consultation & Knowledge Service (BRICKS),
Division of Health Informatics & Implementation Science (HIIS),
Department of Quantitaive Health Sciences (QHS),
University of Massachusetts Medical School (UMMS) at Worcester, MA 01655
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_From: Peter Beninato \[beninato.ohsu\] Sent: Thursday, September 08, 2011 6:48 PM To: Rasmussen, Luke V; I2B2 AUG Members Subject: RE: i2b2 - v1.4 - Edit login Form - Where?_
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Applause\!
Thanks.
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_From: Rasmussen, Luke V \[rasmussen.luke.mcrf.mfldclin\] Sent: Thursday, September 08, 2011 3:22 PM To: Peter Beninato; I2B2 AUG Members_
_Subject: RE: i2b2 - v1.4 - Edit login Form - Where?_
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I'm looking at 1.5 code, but I believe you just need to go to the webclient code and modify PM_misc.js.
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Luke Rasmussen Senior Programmer/Analyst Marshfield Clinic Research Foundation Biomedical Informatics Research Center
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_From: Peter Beninato \[beninato.ohsu\] Sent: Thursday, September 08, 2011 5:16 PM To: I2B2 AUG Members Subject: i2b2 - v1.4 - Edit login Form - Where?_
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Hi,
Where can one go and edit the title bar on the login form?
I want to edit the "i2b2 Login".
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This is v1.4, I'm not compiling and deploying the application via Eclipse. Using the webclient, and would like to edit the title of the login box. But, I seem to lose the trail in PM_view.js (i2b2.PM.doLoginDialog).
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Does this web form exist in the "source" so could edit it (somewhere) and redeploy via ant target?
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Thanks.
Peter Beninato - OCTRI DW Developer
Oregon Health & Science University
beninato.ohsu
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*NEXT EMAIL*
_From: Murphy, Shawn N. Sent: Thursday, September 08, 2011 3:53 PM To: Davis, Michael (Oncology); I2B2 AUG Members Subject: RE: 1.6 new feature - temporal constraint_
Hi Mike,
Yes, that is right, a query done with the "same financial encounter" timing constraint will insist that all the elements in the query happened in the same encounter (encounter_num for techies). This constraint can be overridden in each panel though, so that if you have "male" for example that does not need to be recorded in the same encounter but you want to use it in the query, you can do that too.
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Thanks, Shawn.
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_From: Davis, Michael (Oncology) \[davismk.upmc\] Sent: Thursday, September 08, 2011 2:59 PM To: Murphy, Shawn N.; I2B2 AUG Members Subject: RE: 1.6 new feature - temporal constraint_
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Shawn,
Good question\! J I'm looking at the workbench and really referring to the Query Timing (labeled as Temporal Constraints in web client) options (i.e, Selected groups occur in the same financial encounter, etc). I'm not sure how these are working on the data. Does this option use the ENCOUNTER_NUM for grouping 'liked' transactions? Not sure.
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Thanks
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_From: Murphy, Shawn N. \[SNMURPHY.PARTNERS\] Sent: Thursday, September 08, 2011 1:56 PM To: Davis, Michael (Oncology); I2B2 AUG Members Subject: RE: 1.6 new feature - temporal constraint_
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Hi Mike,
Which temporal constraints are you referring to, the ones controlled by SQL in the patient and visit metadata tables?
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Thanks,
Shawn.
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_From: Davis, Michael (Oncology) \[davismk.upmc\] Sent: Thursday, September 08, 2011 1:50 PM To: I2B2 AUG Members Subject: RE: 1.6 new feature - temporal constraint_
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Is there a document that explains the usage of the Temporal Constraints features which appears on the query tool? I'm trying to figure out what this means in terms of how the fact and dimension data should be loaded to take advantage of these features.
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Mike
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_From: Murphy, Shawn N. \[SNMURPHY.PARTNERS\] Sent: Saturday, July 30, 2011 8:49 PM To: I2B2 AUG Members Subject: 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: Michael.C.Ford.kp Sent: Tuesday, September 06, 2011 6:00 PM Cc: I2B2 AUG Members Subject: RE: install of the Workbench client_
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Thanks this issue seems to be associated with the current 1.5 release. once I installed a 1.4 release it worked fine.
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From: Phillips, Lori C. Sent: 09/06/2011 11:19 AM To: Michael C Ford, I2B2 AUG Members Subject RE: install of the Workbench client
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try
JAVA_HOME = C:\Program Files\Java\jdk1.6.0_16\bin
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Also your classpath looks suspect I am guessing that C:\Program Files\Java\jre6\lib\ext\QTJava.zip does not exist.
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perhaps try
CLASSPATH = .;C:\Program Files\Java\jdk1.6.0_16\bin
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_From: Michael.C.Ford.kp \[Michael.C.Ford.kp\] Sent: Tuesday, September 06, 2011 1:52 PM To: I2B2 AUG Members Subject: install of the Workbench client_
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Hello I am hoping someone can give me a pointer on install of the workbench client.
I followed the install document, but I think it's a bit light. I unpacked the windows zip file into a folder C:\i2b2Client so I have C:\i2b2Client\Windows.
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Modified the I2b2Workbench.ini ( I have XP, 3 gigs 2.66GHZ )
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