ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Tim O'Connell" <tim.oconn...@gmail.com>
Subject Re: v_document_cui_sent not being populated
Date Mon, 08 Sep 2014 20:50:10 GMT
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.sql

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
>

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message