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 [[email protected]]
Sent: Friday, July 08, 2016 10:39 AM
To: Dan Connolly; Phillip Reeder; French, Tony; [email protected]
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) / [email protected]<mailto:[email protected]>
From: <[email protected]> on behalf of Dan Connolly
<[email protected]>
Date: Thursday, July 7, 2016 at 2:54 PM
To: Phillip Reeder <[email protected]>, "French, Tony"
<[email protected]>, "[email protected]"
<[email protected]>
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 [[email protected]]
Sent: Thursday, July 07, 2016 12:53 PM
To: Dan Connolly; French, Tony; [email protected]
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:
<[email protected]<redir.aspx?REF=-TuGCYglDB3qOBv4gp8MAZB2QepWxTb78D9rgtdx2YEETABEoKbTCAFtYWlsdG86Z3BjLWRldi1ib3VuY2VzQGxpc3RzZXJ2Lmt1bWMuZWR1>>
on behalf of Dan Connolly
<[email protected]<redir.aspx?REF=Q1HPM7XGpVog9uReo0Fi62hTciKe6gZrDzYtwzGs1qQETABEoKbTCAFtYWlsdG86ZGNvbm5vbGx5QGt1bWMuZWR1>>
Date: Thursday, July 7, 2016 at 11:10 AM
To: "French, Tony"
<[email protected]<redir.aspx?REF=Qj1yzHStiwpKhM0Nfa84xQflx-JkcYQMYMEy0hQd_6IETABEoKbTCAFtYWlsdG86YWRmcmVuY2hAcmVnZW5zdHJpZWYub3Jn>>,
"[email protected]<redir.aspx?REF=pNh1vDjJti-nD9aNPMpgnVIvXOKsAs399Z_-3bk3iEoETABEoKbTCAFtYWlsdG86R1BDLURFVkBMSVNUU0VSVi5LVU1DLkVEVQ..>"
<[email protected]<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:
[email protected]<redir.aspx?REF=-TuGCYglDB3qOBv4gp8MAZB2QepWxTb78D9rgtdx2YEETABEoKbTCAFtYWlsdG86Z3BjLWRldi1ib3VuY2VzQGxpc3RzZXJ2Lmt1bWMuZWR1>
[[email protected]<redir.aspx?REF=-TuGCYglDB3qOBv4gp8MAZB2QepWxTb78D9rgtdx2YEETABEoKbTCAFtYWlsdG86Z3BjLWRldi1ib3VuY2VzQGxpc3RzZXJ2Lmt1bWMuZWR1>]
on behalf of French, Tony
[[email protected]<redir.aspx?REF=Qj1yzHStiwpKhM0Nfa84xQflx-JkcYQMYMEy0hQd_6IETABEoKbTCAFtYWlsdG86YWRmcmVuY2hAcmVnZW5zdHJpZWYub3Jn>]
Sent: Thursday, July 07, 2016 10:56 AM
To:
[email protected]<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:[email protected]]
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>
Confidentiality Notice: The contents of this message and any files transmitted
with it may contain confidential and/or privileged information and are intended
solely for the use of the named addressee(s). Additionally, the information
contained herein may have been disclosed to you from medical records with
confidentiality protected by federal and state laws. Federal regulations and
State laws prohibit you from making further disclosure of such information
without the specific written consent of the person to whom the information
pertains or as otherwise permitted by such regulations. A general authorization
for the release of medical or other information is not sufficient for this
purpose.
If you have received this message in error, please notify the sender by return
e-mail and delete the original message. Any retention, disclosure, copying,
distribution or use of this information by anyone other than the intended
recipient is strictly prohibited.
________________________________
UT Southwestern
Medical Center
The future of medicine, today.
_______________________________________________
Gpc-dev mailing list
[email protected]
http://listserv.kumc.edu/mailman/listinfo/gpc-dev
