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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 12:54:01 GMT
Hi Dave,

Let me update the instructions first - I'll tell you when I'm done.

-vj

On Tue, Oct 14, 2014 at 2:46 PM, David Kincaid <kincaid.dave@gmail.com>
wrote:

> 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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