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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 13:07:25 GMT
OK, updated the ytex install page:
https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation


On Tue, Oct 14, 2014 at 2:54 PM, vijay garla <vngarla@gmail.com> wrote:

> 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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