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 <[email protected]> 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 >
