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Posted to user@ctakes.apache.org by "Miller, Timothy" <Ti...@childrens.harvard.edu> on 2020/12/01 15:50:19 UTC
custom dictionary issue
I'm trying to use a custom BSV dictionary as in the examples. I got the
piper file to point to the lookup descriptor, which is based off of
ctakes-dictionary-lookup-fast-
res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/example
/bsv/CustomCuiBsv.xml
but when I run it I get an error (NPE) that sounds like it was looking
for a ConceptFactory:
Caused by: java.lang.NullPointerException
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorPar
ser.parseConceptFactories(DictionaryDescriptorParser.java:218)
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorPar
ser.parseDescriptor(DictionaryDescriptorParser.java:129)
at
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initi
alize(AbstractJCasTermAnnotator.java:138)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initi
alizeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:267)
... 26 more
which that example descriptor doesn't contain. Do I need a concept
factory line in my descriptor? What would that look like for a BSV file
that is just:
ID|Preferred term|Synonyms
Tim
Re: custom dictionary issue [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
OK, got it fixed and finding entities (I forgot to add the
conceptFactoryName field to the dictionaryConceptPair), including both
terms from the standard SNOMED+RxNORM dictionary and my customized
dictionary. One problem I still have is that the custom entities (which
have dummy CUIs and TUIs) are called EntityMention, when they probably
should be EventMentions. I'll poke around a little bit to see if there
is some way to control that, either in the code or with a better
dictionary.
Tim
On Tue, 2020-12-01 at 21:32 +0000, Miller, Timothy wrote:
> * External Email - Caution *
>
>
> FYI I was able to get the dictionary to load by putting in a dummy
> TUI
> in the vocab file and adding a ConceptFactory block to the
> descriptor.
> It's still not finding the terms in my custom dictionary but I'll
> keep
> debugging.
> Tim
>
> On Tue, 2020-12-01 at 15:50 +0000, Miller, Timothy wrote:
> > * External Email - Caution *
> >
> >
> > I'm trying to use a custom BSV dictionary as in the examples. I got
> > the
> > piper file to point to the lookup descriptor, which is based off of
> > ctakes-dictionary-lookup-fast-
> > res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/exa
> > mp
> > le
> > /bsv/CustomCuiBsv.xml
> >
> > but when I run it I get an error (NPE) that sounds like it was
> > looking
> > for a ConceptFactory:
> >
> > Caused by: java.lang.NullPointerException
> > at
> > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescripto
> > rP
> > ar
> > ser.parseConceptFactories(DictionaryDescriptorParser.java:218)
> > at
> > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescripto
> > rP
> > ar
> > ser.parseDescriptor(DictionaryDescriptorParser.java:129)
> > at
> > org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.i
> > ni
> > ti
> > alize(AbstractJCasTermAnnotator.java:138)
> > at
> > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.i
> > ni
> > ti
> > alizeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:267)
> > ... 26 more
> >
> >
> > which that example descriptor doesn't contain. Do I need a concept
> > factory line in my descriptor? What would that look like for a BSV
> > file
> > that is just:
> > ID|Preferred term|Synonyms
> >
> >
> > Tim
> >
> >
Re: custom dictionary issue [EXTERNAL] [SUSPICIOUS]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
FYI I was able to get the dictionary to load by putting in a dummy TUI
in the vocab file and adding a ConceptFactory block to the descriptor.
It's still not finding the terms in my custom dictionary but I'll keep
debugging.
Tim
On Tue, 2020-12-01 at 15:50 +0000, Miller, Timothy wrote:
> * External Email - Caution *
>
>
> I'm trying to use a custom BSV dictionary as in the examples. I got
> the
> piper file to point to the lookup descriptor, which is based off of
> ctakes-dictionary-lookup-fast-
> res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/examp
> le
> /bsv/CustomCuiBsv.xml
>
> but when I run it I get an error (NPE) that sounds like it was
> looking
> for a ConceptFactory:
>
> Caused by: java.lang.NullPointerException
> at
> org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorP
> ar
> ser.parseConceptFactories(DictionaryDescriptorParser.java:218)
> at
> org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorP
> ar
> ser.parseDescriptor(DictionaryDescriptorParser.java:129)
> at
> org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.ini
> ti
> alize(AbstractJCasTermAnnotator.java:138)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
> ti
> alizeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:267)
> ... 26 more
>
>
> which that example descriptor doesn't contain. Do I need a concept
> factory line in my descriptor? What would that look like for a BSV
> file
> that is just:
> ID|Preferred term|Synonyms
>
>
> Tim
>
>