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From David Kincaid <kincaid.d...@gmail.com>
Subject Re: NPE with ytex in ctakes 3.2.0
Date Tue, 14 Oct 2014 12:46:23 GMT
Thanks, Vijay. I'm running from the ctakes distro. I'll run through the
steps in the link you included.

- Dave

On Tue, Oct 14, 2014 at 3:25 AM, vijay garla <vngarla@gmail.com> wrote:

> 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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