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