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 >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> >
