Re: I think I found a bug. [EXTERNAL]

["Miller, Timothy" <Ti...@childrens.harvard.edu>]

Peter,
I think the email server doesn't let images through. Can you post an
imgur link maybe?
Tim

On Sun, 2020-08-30 at 14:35 -0700, Peter Abramowitsch wrote:
> * External Email - Caution *
> 
> Hi,
> I was getting a StringIndexOutOfBoundsException in
> DependencyUtil.doesSubsume(annot1, annot2)  with exactly this
> situation:
> 
> negex annotator
> the text begins  "negative for <anything>"
> 
> If the chunk negative for xyz is preceded by anything else, even a
> space, the problem goes away.  It also goes away when you choose
> another style of negation.   "no headache", for instance
> 
> I've traced the problem back to some illegal entries in the jCAS  You
> can see from the image below that the ContextAnnotation's begin
> offset is illegal.  
> 
> Clearly there's an off-by-one error and this triggered the exception
> because in my example, the Annotation is created right from the 0th
> char of my note text.  But it occurred to me that in every other
> case, where the annotation doesn't begin on the first character and
> it doesn't throw an exception, it might cause  downstream methods
> like doesSubsume to give the wrong result because the begin/end
> offsets are wrong.
> 
> I'm not sure how to follow this up.  But if anyone wants to tackle
> it....?
> 
> This is from HistoryAttributeClassifier beginning at line 274
> 
> 
> 
> 
> 

Re: I think I found a bug. [EXTERNAL]

[Peter Abramowitsch <pa...@gmail.com>]

Thanks Jeff,  I don't think the image is needed.  here's what it showed.

With the negex annotator in the pipeline

With "Negative for headache"  as the text starting at position 0
In HistoryAttributeClassifier beginning near line 274
the first IdentifiedAnnotation in the

*List<IdentifiedAnnotation> lsmentions*

contains a ContextAnnotation where the offset range is   -1, 13.
Looking at the text, it should probably have been 0, 11.

Add any text ahead of the "Negative for" and it works brilliantly.
Probably one of those  off-by-one errors  that comes from staying up too
late.

Peter



Peter

Peter


On Mon, Aug 31, 2020 at 3:48 AM Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:

> Peter,
> I think the email server doesn't let images through. Can you post an
> imgur link maybe?
> Tim
>
> On Sun, 2020-08-30 at 14:35 -0700, Peter Abramowitsch wrote:
> > * External Email - Caution *
> >
> > Hi,
> > I was getting a StringIndexOutOfBoundsException in
> > DependencyUtil.doesSubsume(annot1, annot2)  with exactly this
> > situation:
> >
> > negex annotator
> > the text begins  "negative for <anything>"
> >
> > If the chunk negative for xyz is preceded by anything else, even a
> > space, the problem goes away.  It also goes away when you choose
> > another style of negation.   "no headache", for instance
> >
> > I've traced the problem back to some illegal entries in the jCAS  You
> > can see from the image below that the ContextAnnotation's begin
> > offset is illegal.
> >
> > Clearly there's an off-by-one error and this triggered the exception
> > because in my example, the Annotation is created right from the 0th
> > char of my note text.  But it occurred to me that in every other
> > case, where the annotation doesn't begin on the first character and
> > it doesn't throw an exception, it might cause  downstream methods
> > like doesSubsume to give the wrong result because the begin/end
> > offsets are wrong.
> >
> > I'm not sure how to follow this up.  But if anyone wants to tackle
> > it....?
> >
> > This is from HistoryAttributeClassifier beginning at line 274
> >
> >
> >
> >
> >
>