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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: v_document_cui_sent not being populated
Date Wed, 10 Sep 2014 15:32:12 GMT
Applied fix in trunk r.1624031
https://issues.apache.org/jira/browse/CTAKES-311
VJ- I'm not sure if there is test coverage for this, but let us know if you have any idea/sconcerns.
--Pei

> -----Original Message-----
> From: Tim O'Connell [mailto:tim.oconnell@gmail.com]
> Sent: Monday, September 08, 2014 7:05 PM
> To: dev@ctakes.apache.org
> Subject: Re: v_document_cui_sent not being populated
> 
> Hi Pei,
> 
> Happy to do so.  Just created the issue in JIRA.  Traveling at present.
>  Will do the patch over the next few days.
> 
> Best,
> Tim
> 
> On Mon, Sep 8, 2014 at 1:55 PM, Pei Chen <chenpei@apache.org> wrote:
> 
> > Hi Tim,
> > Thanks for catching that- yes, would you mind creating a jira for that?
> > Even better if you can attach a patch for it (perhaps a good idea to
> > search/replace on the entire project) and we can include in the next
> > 3.2.1 patch...
> > --Pei
> >
> > On Mon, Sep 8, 2014 at 4:50 PM, Tim O'Connell <tim.oconnell@gmail.com>
> > wrote:
> > > Hi Clayton,
> > >
> > > (One of) problems here is that the source for the creation of the
> > > v_document_cui_sent view contains an error (I think).
> > >
> > > You can see the view source (in MySQL anyway) by using 'show create
> > > view v_document_cui_sent'.
> > >
> > > You'll then see '....where (`ref_uima_type`.`uima_type_name` =
> > > 'edu.mayo.bmi.uima.core.type.textspan.Sentence'))))) join `document`
> > > `d` on((`da`.`document_id` = `d`.`document_id...' in the view definition.
> > >
> > > The 'edu.mayo.bmi.uima...' is the old notation for the
> > > uima_type_name
> > that
> > > this view depends on. It should be '
> > > org.apache.ctakes.typesystem.type.textspan.Sentence'.
> > >
> > > You can drop the view and re-create it with the correction using the
> > > correct syntax for your SQL DB.  The bug lives in the ytex setup
> > > script
> > in
> > > CTAKES_HOME\bin\ctakes-
> ytex\scripts\data\SQL_TYPE\uima\create_view.s
> > > ql
> > >
> > > Pei - let me know if you want me to create an issue for this in Jira.
> > >
> > > Best,
> > > Tim
> > >
> > > On Mon, Sep 8, 2014 at 11:09 AM, Clayton Turner
> > > <caturner3@g.cofc.edu>
> > > wrote:
> > >
> > >> Hey everyone:
> > >>
> > >> I'm using the ytex branch of ctakes and am trying to pull down
> > polarities
> > >> of concepts and other related information after running the ytex
> > pipeline
> > >> AE on my data.
> > >>
> > >> the v_document_cui_sent table contains 0 rows of data, but
> > >> v_document
> > and
> > >> v_document_ontoanno both contain data.
> > >>
> > >> I would be able to get by with the latter 2, but I'm hitting some
> > oddities
> > >> in my data. I'm sure there's a simple way to do this, but I'm not
> > >> able
> > to
> > >> come up with a solution right now.
> > >>
> > >> I run:
> > >> select d.instance_id,v.polarity from document d join
> > v_document_ontoanno v
> > >> on d.document_id=v.document_id where d.analysis_batch="sle1" and
> > >> v.code="C0277942"; in order to look at which of my noteid's
> > >> expressed
> > the
> > >> concept matching C0277942. A lot of these noteid's contain
> > >> differing polarities, so running an update on an external table to
> > >> grab the polarities differs on which update is run first (-1
> > >> polarities or 1 polarities). Is there a way to dynamically add
> > >> these or just have some formal resolution that isn't dependent on
> which command runs first?
> > >>
> > >> Thanks,
> > >> Clayton
> > >>
> >
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