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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 13:43:13 GMT
Thanks. I'm getting an error on step 7 (Execute the setup script). When I
try to run it using the command line given I get the following:

[~/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts]> nohup ../../ant -f
build-setup.xml -Dlog4j.conf=CTAKES_HOME/config/log4j.xml all > setup.out
2>&1 &
[1] 8129
[~/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts]> tail -f setup.out
nohup: ignoring input
Error: Could not find or load main class org.apache.tools.ant.Main

So, I tried to run it using my already installed version of ant and get
this different error:

[~/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts]> nohup ant -f
build-setup.xml -Dlog4j.conf=CTAKES_HOME/config/log4j.xml all > setup.out
2>&1 &
[1] 8178
[~/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts]> tail -f setup.out
nohup: ignoring input
Buildfile:
/home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-setup.xml

BUILD FAILED
/home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-setup.xml:44:
The following error occurred while executing this line:
/home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/build-classpath.xml:109:
A source file is missing:
/home/davek/apps/apache-ctakes-3.2.0/bin/ctakes-ytex/scripts/CTAKES_HOME/config/log4j.xml

that second one looks like a typo in the build.xml, but since I'm not too
familiar with ant scripts I can't spot where it is.

On Tue, Oct 14, 2014 at 8:07 AM, vijay garla <vngarla@gmail.com> wrote:

> 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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