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From vijay garla <vnga...@gmail.com>
Subject Re: NPE with ytex in ctakes 3.2.0
Date Tue, 14 Oct 2014 08:25:06 GMT
The error is caused by not finding the required properties files/xml config
files.
There are some issues with the ytex setup scripts for the 3.2 release; I
have fixed that in trunk.  I am updating the 3.2 installation guide with
the patched setup scripts.

It's not clear to me if you're running from a dev environment/eclipse, or
running from the ctakes distro.
If running from a development environment, see
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-ytex/README
If running from the ctakes distro, make sure you follow the ytex setup:
https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation

For the dev environment, the xml config file is in the ctakes-ytex-res (
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml
)
For the binary distro, the xml config files are in
lib\ctakes-ytex-res-3.2.0.jar


-vj


On Fri, Oct 10, 2014 at 10:56 PM, David Kincaid <kincaid.dave@gmail.com>
wrote:

> I don't have that file anywhere either. Where do I get it from?
>
> On Fri, Oct 10, 2014 at 3:53 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu
> >
> wrote:
>
> > I think it’s in ctakes-ytex-res.jar (is that in your classpath)?
> > This is just a guess… vj may have a better idea if it still doesn’t work
> > for you.
> >
> > From: David Kincaid [mailto:kincaid.dave@gmail.com]
> > Sent: Friday, October 10, 2014 4:51 PM
> > To: user@ctakes.apache.org
> > Subject: Re: NPE with ytex in ctakes 3.2.0
> >
> > No. I have no file named beanRefContext.xml anywhere on my hard drive.
> >
> >
> >
> > On Fri, Oct 10, 2014 at 3:45 PM, Chen, Pei <
> Pei.Chen@childrens.harvard.edu
> > <mailto:Pei.Chen@childrens.harvard.edu>> wrote:
> > I’m not too familiar with the ytex component,
> > but my guess is that the ytexApplicationContext bean is null?
> > It seems that it would be expected to be in the
> > classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml?  Do those
> exists?
> >
> > From: David Kincaid [mailto:kincaid.dave@gmail.com<mailto:
> > kincaid.dave@gmail.com>]
> > Sent: Friday, October 10, 2014 4:23 PM
> > To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
> > Subject: NPE with ytex in ctakes 3.2.0
> >
> > I'm trying to experiment the ytex in 3.2.0. Trying to run
> > AggregatePlaintextUMLSProcessor with the FilesInDirectoryCollectionReader
> > and FileWriterCASConsumer. When I try to run it against some text files
> it
> > blows up with a null pointer exception during initialization. Here's the
> > relevant part of the stack trace. Anyone have any ideas what I might have
> > wrong?:
> >
> > Caused by: org.apache.uima.resource.ResourceInitializationException:
> > Initialization of annotator class
> > "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed.
> > (Descriptor:
> >
> file:/home/davek/apps/apache-ctakes-3.2.0/desc/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml)
> >           at
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> >           at
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
> >           at
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> >           at
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> >           at
> > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> >           at
> >
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> >           at
> >
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> >           at
> >
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> >           at
> >
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> >           at
> >
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> >           at
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> >           at
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> >           at
> > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> >           at
> > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
> >           at
> >
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
> >           at
> >
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
> >           ... 9 more
> > Caused by: java.lang.NullPointerException
> >           at
> >
> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
> >           at
> >
> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
> >           at
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> >           ... 24 more
> >
> >
> >
>

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