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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 14:09:38 GMT
can you drop the -Dlog4j.conf=xxx param?

On Tue, Oct 14, 2014 at 3:59 PM, David Kincaid <kincaid.dave@gmail.com>
wrote:

> Yes. I did do that. I just redid that step again to be sure and am still
> getting the same error.
>
> On Tue, Oct 14, 2014 at 8:50 AM, vijay garla <vngarla@gmail.com> wrote:
>
>> Hi Dave,
>>
>> I uploaded scripts to the wiki page (step 1.5) - that issue should be
>> ironed out with the updated scripts - did you unpack them?
>>
>> -vj
>>
>> On Tue, Oct 14, 2014 at 3:43 PM, David Kincaid <kincaid.dave@gmail.com>
>> wrote:
>>
>>> 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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