can you drop the -Dlog4j.conf=xxx param? On Tue, Oct 14, 2014 at 3:59 PM, David Kincaid <[email protected]> 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 <[email protected]> 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 <[email protected]> >> 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 <[email protected]> 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 <[email protected]> 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 <[email protected] >>>>> > 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 <[email protected]> >>>>>> 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 < >>>>>>> [email protected]> 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 < >>>>>>>> [email protected]> >>>>>>>> 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:[email protected]] >>>>>>>> > Sent: Friday, October 10, 2014 4:51 PM >>>>>>>> > To: [email protected] >>>>>>>> > 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 < >>>>>>>> [email protected] >>>>>>>> > <mailto:[email protected]>> 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:[email protected]<mailto: >>>>>>>> > [email protected]>] >>>>>>>> > Sent: Friday, October 10, 2014 4:23 PM >>>>>>>> > To: [email protected]<mailto:[email protected]> >>>>>>>> > 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 >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
