This gets not only all facts from the query but all facts period for these
patients, no?
--- 8< ---
cur.execute("""select * from observation_fact where patient_num in (
select DISTINCT( PATIENT_NUM ) from QT_PATIENT_SET_COLLECTION WHERE
RESULT_INSTANCE_ID = :qtresultInstanceId
) """, qtresultInstanceId = qtresultInstanceId )
--- 8< ---
https://github.com/MCW-BMI/i2b2Exporter/blob/master/i2b2Exporter.py
2fe5373
--
Dan
________________________________________
From: Kowalski, George [gkowal...@mcw.edu]
Sent: Friday, July 08, 2016 10:39 AM
To: Dan Connolly; Phillip Reeder; French, Tony; GPC-DEV@LISTSERV.KUMC.EDU
Subject: Re: DataBuilder installation instructions
MCW is in. I’d prefer a docker instance.
In the mean time I’ve developed a separate tool to extract all the data for a
query into a sqlite file.
https://github.com/MCW-BMI/i2b2Exporter
It does not just take the concepts requested in the query as databuilder does
, but all associated concepts for the query.
G
George Kowalski
Biomedical Informatics Software Engineer
Clinical & Translational Science Institute
Medical College of Wisconsin
9200 West Wisconsin Avenue, Suite L722A
Milwaukee, Wisconsin USA 53226
414.805.7318 (office) / gkowal...@mcw.edu<mailto:gkowal...@mcw.edu>
From: <gpc-dev-boun...@listserv.kumc.edu> on behalf of Dan Connolly
<dconno...@kumc.edu>
Date: Thursday, July 7, 2016 at 2:54 PM
To: Phillip Reeder <phillip.ree...@utsouthwestern.edu>, "French, Tony"
<adfre...@regenstrief.org>, "GPC-DEV@LISTSERV.KUMC.EDU"
<gpc-dev@listserv.kumc.edu>
Subject: RE: DataBuilder installation instructions
Yes, I'd like that. Interested sites, please do chime in.
I'll try to figure out details.
I tend to use the normal Tuesday call slot for such things; perhaps it could
start at 11:30 or something. We'll see.
--
Dan
________________________________
From: Phillip Reeder [phillip.ree...@utsouthwestern.edu]
Sent: Thursday, July 07, 2016 12:53 PM
To: Dan Connolly; French, Tony; GPC-DEV@LISTSERV.KUMC.EDU
Subject: Re: DataBuilder installation instructions
Dan,
Any chance someone from your site could go through the install of the current
version so that other sites could be on the most recent version? I know we,
at UTSW, would like to get to a more recent version as well. I know you have
made numerous changes and enhancements in the past year that we would like to
have. Maybe we could schedule an installathon and get a bunch of people up to
the latest version? Would other sites be interested?
Phillip
From:
<gpc-dev-boun...@listserv.kumc.edu<redir.aspx?REF=-TuGCYglDB3qOBv4gp8MAZB2QepWxTb78D9rgtdx2YEETABEoKbTCAFtYWlsdG86Z3BjLWRldi1ib3VuY2VzQGxpc3RzZXJ2Lmt1bWMuZWR1>>
on behalf of Dan Connolly
<dconno...@kumc.edu<redir.aspx?REF=Q1HPM7XGpVog9uReo0Fi62hTciKe6gZrDzYtwzGs1qQETABEoKbTCAFtYWlsdG86ZGNvbm5vbGx5QGt1bWMuZWR1>>
Date: Thursday, July 7, 2016 at 11:10 AM
To: "French, Tony"
<adfre...@regenstrief.org<redir.aspx?REF=Qj1yzHStiwpKhM0Nfa84xQflx-JkcYQMYMEy0hQd_6IETABEoKbTCAFtYWlsdG86YWRmcmVuY2hAcmVnZW5zdHJpZWYub3Jn>>,
"GPC-DEV@LISTSERV.KUMC.EDU<redir.aspx?REF=pNh1vDjJti-nD9aNPMpgnVIvXOKsAs399Z_-3bk3iEoETABEoKbTCAFtYWlsdG86R1BDLURFVkBMSVNUU0VSVi5LVU1DLkVEVQ..>"
<GPC-DEV@LISTSERV.KUMC.EDU<redir.aspx?REF=pNh1vDjJti-nD9aNPMpgnVIvXOKsAs399Z_-3bk3iEoETABEoKbTCAFtYWlsdG86R1BDLURFVkBMSVNUU0VSVi5LVU1DLkVEVQ..>>
Subject: RE: DataBuilder installation instructions
That's pretty much the main installation documentation, still. And that it is
out of date is a known problem:
* #335: problem: DataBuilder VM deployment outdated by migration of middle
tier to jboss
<redir.aspx?REF=l02ArUG3YbclGkb9YkfVT16GJ9tWpKyq6Cu_b5DnFNoETABEoKbTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvMzM1>
I suggest you report details of the errors you're getting; perhaps there are
easy fixes to the documentation that will get you going.
Be sure to include the exact revision hash of the code you're trying to use; if
you checked out the current code from the heron_extract<UrlBlockedError.aspx>
repository, you might have better luck with an older version (such as rev
1b8a53f78be0 from Nov 2014, available in
heron_extract.zip<redir.aspx?REF=MQLAqihRp1HMw4GwABGrrORljLijDE8LTVk97voAqBQETABEoKbTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC9hdHRhY2htZW50L3dpa2kvQnVpbGRlclNhZ2EvaGVyb25fZXh0cmFjdC56aXA.>).
--
Dan
________________________________
From:
gpc-dev-boun...@listserv.kumc.edu<redir.aspx?REF=-TuGCYglDB3qOBv4gp8MAZB2QepWxTb78D9rgtdx2YEETABEoKbTCAFtYWlsdG86Z3BjLWRldi1ib3VuY2VzQGxpc3RzZXJ2Lmt1bWMuZWR1>
[gpc-dev-boun...@listserv.kumc.edu<redir.aspx?REF=-TuGCYglDB3qOBv4gp8MAZB2QepWxTb78D9rgtdx2YEETABEoKbTCAFtYWlsdG86Z3BjLWRldi1ib3VuY2VzQGxpc3RzZXJ2Lmt1bWMuZWR1>]
on behalf of French, Tony
[adfre...@regenstrief.org<redir.aspx?REF=Qj1yzHStiwpKhM0Nfa84xQflx-JkcYQMYMEy0hQd_6IETABEoKbTCAFtYWlsdG86YWRmcmVuY2hAcmVnZW5zdHJpZWYub3Jn>]
Sent: Thursday, July 07, 2016 10:56 AM
To:
GPC-DEV@LISTSERV.KUMC.EDU<redir.aspx?REF=pNh1vDjJti-nD9aNPMpgnVIvXOKsAs399Z_-3bk3iEoETABEoKbTCAFtYWlsdG86R1BDLURFVkBMSVNUU0VSVi5LVU1DLkVEVQ..>
Subject: DataBuilder installation instructions
We are working on getting DataBuilder installed in our environment. I found
the BuilderSaga<UrlBlockedError.aspx> article for installing it into an i2b2
demo VM. Is that the best guide to reference for installing it into an actual
working environment or are there step by step manual instructions available
anywhere?
I have tried following the screencast to install using the latest i2b2 demo VM
but have already ran into several errors. Does anyone have a historical link to
i2b2vmware-1703a.zip ?
Thanks,
Tony
Tony French | Software Development Manager
Tools and Shared Resources
Center for Biomedical Informatics
[cid:image001.png@01D1D904.F4DD3790]
1101 West Tenth Street
Indianapolis, IN, 46202
Tel 317-274-9087 | Fax: 317-274-9305
Twitter: @Regenstrief |
Facebook.com/regenstriefinstitute<UrlBlockedError.aspx>
www.regenstrief.org<UrlBlockedError.aspx>
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