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