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From vijay garla <vnga...@gmail.com>
Subject Re: Classpath for conceptGraph in ytex
Date Wed, 05 Nov 2014 20:23:53 GMT
The only concept graphs shipped are:
umls.gz
sct-rxnorm.gz
sct-msh-csp-aod.gz

If you really want sct-umls.gz, you will have to create a concept graph,
discussed here:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2.0+-+Semantic+Similarity

You will need UMLS installed in your database to do so.

-vj

On Wed, Nov 5, 2014 at 9:03 PM, Natalia Connolly <
natalia.v.connolly@gmail.com> wrote:

> I am afraid that while your point about the space is valid, it still did
> not fix the issue, because for some reason the code expects the .gz
> extension for the concept graph file, while what I have is a .xml file
> (sct-umls.xml, not sct-umls.gz).
>
> I tried to manually gzip the xml file and specify
> ytex.conceptGraphName=sct-umls.xml
> so it would find conceptGraph/sct-umls.xml.gz.  It found the file all
> right and then crashed:
>
>
> 05 Nov 2014 14:55:23  INFO ConceptSimilarityServiceImpl - begin
> initialization for concept graph: sct-umls.xml
> 05 Nov 2014 14:55:23  INFO ConceptDaoImpl - loading concept graph from
> file:/usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls.xml.
> *gz*
> 05 Nov 2014 14:55:23  INFO DefaultListableBeanFactory - Destroying
> singletons in
> org.springframework.beans.factory.support.DefaultListableBeanFactory@ce67fe:
> defining beans
> [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService,conceptSimilarityService,abstractConceptKernel,abstractLinKernel,abstractSemanticSimKernel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambiguator,sessionFactory,ytexDaoOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#8,documentDao,namedEntityRegexDao,segmentRegexDao,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601Converter,documentMapperService];
> root of factory hierarchy
> 05 Nov 2014 14:55:23  INFO EhCacheManagerFactoryBean - Shutting down
> EHCache CacheManager
> 05 Nov 2014 14:55:23  INFO DefaultListableBeanFactory - Destroying
> singletons in
> org.springframework.beans.factory.support.DefaultListableBeanFactory@212b52d3:
> defining beans [ytexApplicationContext]; root of factory hierarchy
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of CAS Processor with name "AggregatePlaintextUMLSProcessor" failed.
> at
> org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:83)
> at
> org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingEngine(UIMAFramework_impl.java:420)
> at
> org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAFramework.java:864)
> at org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:573)
> at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105)
> at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713)
> Caused by: org.apache.uima.resource.ResourceConfigurationException:
> Initialization of CAS Processor with name "AggregatePlaintextUMLSProcessor"
> failed.
> at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1104)
> at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProcessors(CPEFactory.java:550)
> at
> org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java:253)
> at
> org.apache.uima.collection.impl.cpm.BaseCPMImpl.<init>(BaseCPMImpl.java:127)
> at
> org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:75)
> ... 5 more
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> Initialization of annotator class
> "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed.
>  (Descriptor:
> file:/usr/local/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: org.springframework.beans.factory.access.BootstrapException:
> Unable to initialize group definition. Group resource name
> [classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml], factory key
> [ytexApplicationContext]; nested exception is
> org.springframework.beans.factory.BeanCreationException: Error creating
> bean with name 'ytexApplicationContext' defined in URL
> [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-web-3.2.0-classes.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]:
> Instantiation of bean failed; nested exception is
> org.springframework.beans.BeanInstantiationException: Could not instantiate
> bean class
> [org.springframework.context.support.ClassPathXmlApplicationContext]:
> Constructor threw exception; nested exception is
> org.springframework.beans.factory.BeanCreationException: Error creating
> bean with name 'conceptSimilarityService' defined in class path resource
> [org/apache/ctakes/ytex/beans-kernel-sim.xml]: Invocation of init method
> failed; nested exception is java.lang.RuntimeException:
> java.io.StreamCorruptedException: invalid stream header: 3C3F786D
> at
> org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
> 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
> Caused by: org.springframework.beans.factory.BeanCreationException: Error
> creating bean with name 'ytexApplicationContext' defined in URL
> [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-web-3.2.0-classes.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]:
> Instantiation of bean failed; nested exception is
> org.springframework.beans.BeanInstantiationException: Could not instantiate
> bean class
> [org.springframework.context.support.ClassPathXmlApplicationContext]:
> Constructor threw exception; nested exception is
> org.springframework.beans.factory.BeanCreationException: Error creating
> bean with name 'conceptSimilarityService' defined in class path resource
> [org/apache/ctakes/ytex/beans-kernel-sim.xml]: Invocation of init method
> failed; nested exception is java.lang.RuntimeException:
> java.io.StreamCorruptedException: invalid stream header: 3C3F786D
> at
> org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:288)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1035)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:939)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
> at
> org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
> at
> org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
> at
> org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
> at
> org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
> at
> org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
> at
> org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
> at
> org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
> at
> org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
> at
> org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
> ... 27 more
> Caused by: org.springframework.beans.BeanInstantiationException: Could not
> instantiate bean class
> [org.springframework.context.support.ClassPathXmlApplicationContext]:
> Constructor threw exception; nested exception is
> org.springframework.beans.factory.BeanCreationException: Error creating
> bean with name 'conceptSimilarityService' defined in class path resource
> [org/apache/ctakes/ytex/beans-kernel-sim.xml]: Invocation of init method
> failed; nested exception is java.lang.RuntimeException:
> java.io.StreamCorruptedException: invalid stream header: 3C3F786D
> at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:162)
> at
> org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:110)
> at
> org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:280)
> ... 40 more
> Caused by: org.springframework.beans.factory.BeanCreationException: Error
> creating bean with name 'conceptSimilarityService' defined in class path
> resource [org/apache/ctakes/ytex/beans-kernel-sim.xml]: Invocation of init
> method failed; nested exception is java.lang.RuntimeException:
> java.io.StreamCorruptedException: invalid stream header: 3C3F786D
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1455)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
> at
> org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
> at
> org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
> at
> org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
> at
> org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
> at
> org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
> at
> org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
> at
> org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
> at
> org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
> at
> org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
> at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
> at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
> ... 42 more
> Caused by: java.lang.RuntimeException: java.io.StreamCorruptedException:
> invalid stream header: 3C3F786D
> at
> org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl.readConceptGraph(ConceptDaoImpl.java:519)
> at
> org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl.getConceptGraph(ConceptDaoImpl.java:358)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at
> org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:319)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
> at
> org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at
> org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:90)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at
> org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
> at com.sun.proxy.$Proxy7.getConceptGraph(Unknown Source)
> at
> org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl.init(ConceptSimilarityServiceImpl.java:705)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1581)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1522)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
> ... 58 more
> Caused by: java.io.StreamCorruptedException: invalid stream header:
> 3C3F786D
> at java.io.ObjectInputStream.readStreamHeader(ObjectInputStream.java:802)
> at java.io.ObjectInputStream.<init>(ObjectInputStream.java:299)
> at
> org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl.readConceptGraph(ConceptDaoImpl.java:511)
> ... 80 more
>
>
> On Wed, Nov 5, 2014 at 2:40 PM, vijay garla <vngarla@gmail.com> wrote:
>
>> It looks like there is a trailing space after sct-umls.  Check your
>> ytex.properties file and make sure there is no trailing space after the ytex.conceptGraphName
>> property value
>>
>> On Wed, Nov 5, 2014 at 8:35 PM, Natalia Connolly <
>> natalia.v.connolly@gmail.com> wrote:
>>
>>> Well, it't not really an error - ytex runs fine, it's just that the word
>>> sense disambiguation remains disabled without conceptGraph, and I really
>>> need it.  Here's the full log of the initialization step, with the relevant
>>> parts highlighted in yellow:
>>>
>>> >bin/runctakesCPE.sh
>>> Nov  5 14:27:33 P13-7415 java[15257] <Error>: CGContextGetCTM: invalid
>>> context 0x0
>>> Nov  5 14:27:33 P13-7415 java[15257] <Error>: CGContextSetBaseCTM:
>>> invalid context 0x0
>>> Nov  5 14:27:33 P13-7415 java[15257] <Error>: CGContextGetCTM: invalid
>>> context 0x0
>>> Nov  5 14:27:33 P13-7415 java[15257] <Error>: CGContextSetBaseCTM:
>>> invalid context 0x0
>>> log4j: reset attribute= "false".
>>> log4j: Threshold ="null".
>>> log4j: Level value for root is  [INFO].
>>> log4j: root level set to INFO
>>> log4j: Class name: [org.apache.log4j.ConsoleAppender]
>>> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
>>> log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss}
>>> %5p %c{1} - %m%n].
>>> log4j: Adding appender named [consoleAppender] to category [root].
>>> 05 Nov 2014 14:27:34  INFO ClearNLPDependencyParserAE - using Morphy
>>> analysis? true
>>> Loading configuration.
>>> Loading feature templates.
>>> Loading lexica.
>>> Loading model:
>>>
>>> ........................................................................................
>>> 05 Nov 2014 14:27:48  INFO TokenizerAnnotatorPTB - Initializing
>>> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
>>> 05 Nov 2014 14:27:48  INFO ContextDependentTokenizerAnnotator - Finite
>>> state machines loaded.
>>> 05 Nov 2014 14:27:48  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
>>> 05 Nov 2014 14:27:49  INFO StatusContextAnalyzer - initBoundaryData()
>>> called for ContextInitializer
>>> 05 Nov 2014 14:27:49  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
>>> 05 Nov 2014 14:27:49  INFO NegationContextAnalyzer - initBoundaryData()
>>> called for ContextInitializer
>>> 05 Nov 2014 14:27:49  INFO ApplicationContextHolder - loading
>>> ytex.properties from:
>>> file:/usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/ytex.properties
>>> 05 Nov 2014 14:27:49  INFO ApplicationContextHolder -
>>> beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml
>>> 05 Nov 2014 14:27:49  INFO ClassPathXmlApplicationContext - Refreshing
>>> org.springframework.context.support.ClassPathXmlApplicationContext@3a9d23c0:
>>> startup date [Wed Nov 05 14:27:49 EST 2014]; root of context hierarchy
>>> 05 Nov 2014 14:27:49  INFO XmlBeanDefinitionReader - Loading XML bean
>>> definitions from URL
>>> [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-res-3.2.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]
>>> 05 Nov 2014 14:27:49  INFO XmlBeanDefinitionReader - Loading XML bean
>>> definitions from URL
>>> [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-web-3.2.0-classes.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]
>>> 05 Nov 2014 14:27:49  INFO DefaultListableBeanFactory - Overriding bean
>>> definition for bean 'ytexApplicationContext': replacing [Generic bean:
>>> class [org.springframework.context.support.ClassPathXmlApplicationContext];
>>> scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
>>> autowireCandidate=true; primary=false; factoryBeanName=null;
>>> factoryMethodName=null; initMethodName=null; destroyMethodName=null;
>>> defined in URL
>>> [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-res-3.2.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]]
>>> with [Generic bean: class
>>> [org.springframework.context.support.ClassPathXmlApplicationContext];
>>> scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
>>> autowireCandidate=true; primary=false; factoryBeanName=null;
>>> factoryMethodName=null; initMethodName=null; destroyMethodName=null;
>>> defined in URL
>>> [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-web-3.2.0-classes.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]]
>>> 05 Nov 2014 14:27:49  INFO DefaultListableBeanFactory -
>>> Pre-instantiating singletons in
>>> org.springframework.beans.factory.support.DefaultListableBeanFactory@271d5641:
>>> defining beans [ytexApplicationContext]; root of factory hierarchy
>>> 05 Nov 2014 14:27:49  INFO ClassPathXmlApplicationContext - Refreshing
>>> org.springframework.context.support.ClassPathXmlApplicationContext@4183422d:
>>> startup date [Wed Nov 05 14:27:49 EST 2014]; root of context hierarchy
>>> 05 Nov 2014 14:27:49  INFO XmlBeanDefinitionReader - Loading XML bean
>>> definitions from class path resource
>>> [org/apache/ctakes/ytex/beans-datasource.xml]
>>> 05 Nov 2014 14:27:49  INFO XmlBeanDefinitionReader - Loading XML bean
>>> definitions from class path resource
>>> [org/apache/ctakes/ytex/beans-kernel.xml]
>>> 05 Nov 2014 14:27:49  INFO XmlBeanDefinitionReader - Loading XML bean
>>> definitions from class path resource
>>> [org/apache/ctakes/ytex/beans-kernel-sim.xml]
>>> 05 Nov 2014 14:27:49  INFO XmlBeanDefinitionReader - Loading XML bean
>>> definitions from class path resource
>>> [org/apache/ctakes/ytex/uima/beans-uima.hbm.xml]
>>> 05 Nov 2014 14:27:49  INFO XmlBeanDefinitionReader - Loading XML bean
>>> definitions from class path resource
>>> [org/apache/ctakes/ytex/uima/beans-uima-dao.xml]
>>> 05 Nov 2014 14:27:49  INFO XmlBeanDefinitionReader - Loading XML bean
>>> definitions from class path resource
>>> [org/apache/ctakes/ytex/uima/beans-uima-mapper.xml]
>>> 05 Nov 2014 14:27:49  INFO DefaultListableBeanFactory - Overriding bean
>>> definition for bean 'mapperOperation': replacing [Root bean: class
>>> [org.springframework.aop.aspectj.AspectJExpressionPointcut];
>>> scope=prototype; abstract=false; lazyInit=false; autowireMode=0;
>>> dependencyCheck=0; autowireCandidate=true; primary=false;
>>> factoryBeanName=null; factoryMethodName=null; initMethodName=null;
>>> destroyMethodName=null] with [Root bean: class
>>> [org.springframework.aop.aspectj.AspectJExpressionPointcut];
>>> scope=prototype; abstract=false; lazyInit=false; autowireMode=0;
>>> dependencyCheck=0; autowireCandidate=true; primary=false;
>>> factoryBeanName=null; factoryMethodName=null; initMethodName=null;
>>> destroyMethodName=null]
>>> 05 Nov 2014 14:27:49  INFO PropertyPlaceholderConfigurer - Loading
>>> properties file from class path resource
>>> [org/apache/ctakes/ytex/ytex-default.properties]
>>> 05 Nov 2014 14:27:49  INFO PropertyPlaceholderConfigurer - Loading
>>> properties file from class path resource
>>> [org/apache/ctakes/ytex/ytex.properties]
>>> 05 Nov 2014 14:27:49  INFO PropertyPlaceholderConfigurer - Loading
>>> properties file from class path resource
>>> [org/apache/ctakes/ytex/ytex-umls.properties]
>>> 05 Nov 2014 14:27:49  INFO DefaultListableBeanFactory -
>>> Pre-instantiating singletons in
>>> org.springframework.beans.factory.support.DefaultListableBeanFactory@26df536f:
>>> defining beans
>>> [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService,conceptSimilarityService,abstractConceptKernel,abstractLinKernel,abstractSemanticSimKernel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambiguator,sessionFactory,ytexDaoOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#8,documentDao,namedEntityRegexDao,segmentRegexDao,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601Converter,documentMapperService];
>>> root of factory hierarchy
>>> 05 Nov 2014 14:27:49  INFO PropertiesFactoryBean - Loading properties
>>> file from class path resource [org/apache/ctakes/ytex/ytex.properties]
>>> 05 Nov 2014 14:27:50  INFO Version - HCANN000001: Hibernate Commons
>>> Annotations {4.0.2.Final}
>>> 05 Nov 2014 14:27:50  INFO Version - HHH000412: Hibernate Core
>>> {4.2.6.Final}
>>> 05 Nov 2014 14:27:50  INFO Environment - HHH000206: hibernate.properties
>>> not found
>>> 05 Nov 2014 14:27:50  INFO Environment - HHH000021: Bytecode provider
>>> name : javassist
>>> 05 Nov 2014 14:27:51  INFO Dialect - HHH000400: Using dialect:
>>> org.hibernate.dialect.MySQLMyISAMDialect
>>> 05 Nov 2014 14:27:51  WARN RootClass - HHH000038: Composite-id class
>>> does not override equals():
>>> org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
>>> 05 Nov 2014 14:27:51  WARN RootClass - HHH000039: Composite-id class
>>> does not override hashCode():
>>> org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
>>> 05 Nov 2014 14:27:51  INFO TransactionFactoryInitiator - HHH000399:
>>> Using default transaction strategy (direct JDBC transactions)
>>> 05 Nov 2014 14:27:51  INFO ASTQueryTranslatorFactory - HHH000397: Using
>>> ASTQueryTranslatorFactory
>>> 05 Nov 2014 14:27:51  INFO UpdateTimestampsCache - HHH000250: Starting
>>> update timestamps cache at region:
>>> org.hibernate.cache.spi.UpdateTimestampsCache
>>> 05 Nov 2014 14:27:51  INFO StandardQueryCache - HHH000248: Starting
>>> query cache at region: org.hibernate.cache.internal.StandardQueryCache
>>> 05 Nov 2014 14:27:51  INFO TableGenerator - HHH000398: Explicit segment
>>> value for id generator [ytex.hibernate_sequences.sequence_name] suggested;
>>> using default [default]
>>> 05 Nov 2014 14:27:51  WARN AbstractEhcacheRegionFactory - HHH020003:
>>> Could not find a specific ehcache configuration for cache named
>>> [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults.
>>> 05 Nov 2014 14:27:51  WARN EhcacheAccessStrategyFactoryImpl - HHH020007:
>>> read-only cache configured for mutable entity
>>> [org.apache.ctakes.ytex.uima.model.UimaType]
>>> 05 Nov 2014 14:27:52  INFO HibernateTransactionManager - Using
>>> DataSource [org.apache.commons.dbcp.BasicDataSource@2fbd46ab] of
>>> Hibernate SessionFactory for HibernateTransactionManager
>>> 05 Nov 2014 14:27:52  INFO EhCacheManagerFactoryBean - Initializing
>>> EHCache CacheManager
>>> 05 Nov 2014 14:27:52  WARN CacheManager - Creating a new instance of
>>> CacheManager using the diskStorePath
>>> "/var/folders/2z/n9b16tpn2f35tk85nx_hjbrhbyn5c4/T/" which is already used
>>> by an existing CacheManager.
>>> The source of the configuration was
>>> net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurationSource@6485a56f.
>>> The diskStore path for this CacheManager will be set to
>>> /var/folders/2z/n9b16tpn2f35tk85nx_hjbrhbyn5c4/T//ehcache_auto_created_1415215672746.
>>> To avoid this warning consider using the CacheManager factory methods to
>>> create a singleton CacheManager or specifying a separate ehcache
>>> configuration (ehcache.xml) for each CacheManager instance.
>>> 05 Nov 2014 14:27:53  INFO ConceptSimilarityServiceImpl - begin
>>> initialization for concept graph: sct-umls
>>> 05 Nov 2014 14:27:53  INFO ConceptDaoImpl - could not load conceptGraph
>>> from classpath, attempt to load from:
>>> /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls
>>> .gz
>>> 05 Nov 2014 14:27:53  INFO ConceptDaoImpl -
>>> /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls
>>> .gz not found, cannot load concept graph
>>> 05 Nov 2014 14:27:53  INFO ConceptDaoImpl - could not load conceptGraph:
>>> sct-umls
>>> 05 Nov 2014 14:27:53  WARN ConceptSimilarityServiceImpl - concept graph
>>> null, name: sct-umls
>>> 05 Nov 2014 14:27:53  INFO ConceptSimilarityServiceImpl - end
>>> initialization for concept graph: sct-umls
>>> 05 Nov 2014 14:27:53  INFO Dialect - HHH000400: Using dialect:
>>> org.hibernate.dialect.MySQLMyISAMDialect
>>> 05 Nov 2014 14:27:53  INFO DocumentMapperServiceImpl - document table
>>> name = ytex.document
>>> 05 Nov 2014 14:27:53  INFO SentenceDetector - [SegmentsToSkip,
>>> SentenceModelFile]
>>> 05 Nov 2014 14:27:53  INFO SentenceDetector - Sentence detector model
>>> file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
>>> 05 Nov 2014 14:27:53  WARN SenseDisambiguatorAnnotator - Concept Graph
>>> was not loaded - word sense disambiguation disabled
>>> 05 Nov 2014 14:27:53  INFO POSTagger - POS tagger model file:
>>> org/apache/ctakes/postagger/models/mayo-pos.zip
>>> Loading configuration.
>>>
>>>
>>> On Wed, Nov 5, 2014 at 2:05 PM, vijay garla <vngarla@gmail.com> wrote:
>>>
>>>> can you send the full stack trace of the error?  Please pipe the output
>>>> and stderr to a file
>>>>
>>>> On Wed, Nov 5, 2014 at 8:03 PM, Natalia Connolly <
>>>> natalia.v.connolly@gmail.com> wrote:
>>>>
>>>>> Yes, I did the step and I do see that file in
>>>>> resources/org/apache/ctakes/ytex/conceptGraph.
>>>>>
>>>>> On Wed, Nov 5, 2014 at 1:59 PM, vijay garla <vngarla@gmail.com>
wrote:
>>>>>
>>>>>> did you do this part (see below).  If so, you should see the file
>>>>>> sct-umls.gz in resources/org/apache/ctakes/ytex/conceptGraph/
>>>>>>
>>>>>>
>>>>>> 3) Unzip YTEX Resources (Optional - UTS login required)
>>>>>>
>>>>>> Download and unzip ctakes-ytex-resources-3.1.2-SNAPSHOT.zip
>>>>>> <http://www.ytex-nlp.org/umls.download/secure/3.1/ctakes-ytex-resources-3.1.2-SNAPSHOT.zip>
'over'
>>>>>> your installation. This contains:
>>>>>>
>>>>>>    - Concept Graphs derived from the UMLS2013AA used to compute
>>>>>>    semantic similarity measures
>>>>>>    - Dictionary Lookup table derived from UMLS2013AA for named
>>>>>>    entity recognition.
>>>>>>
>>>>>>
>>>>>> On Wed, Nov 5, 2014 at 6:01 PM, Natalia Connolly <
>>>>>> natalia.v.connolly@gmail.com> wrote:
>>>>>>
>>>>>>> Hi All,
>>>>>>>
>>>>>>>    I'm trying out ytex within cTAKES 3.2.   I followed all the
>>>>>>> instructions listed here :
>>>>>>> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation,
>>>>>>> and I verified that the setup was fine (from setup.out).
>>>>>>>
>>>>>>>    My ytex.properties file contains the line:
>>>>>>>
>>>>>>> ytex.conceptGraphName=sct-umls
>>>>>>>
>>>>>>>    and I do have sct-umls.xml in my
>>>>>>> ${CTAKES_HOME}/resources/org/apache/ctakes/ytex/conceptGraph.
>>>>>>>
>>>>>>>    Despite all this I can't seem to get conceptGraph working.
 The
>>>>>>> error message is the following:
>>>>>>>
>>>>>>> 05 Nov 2014 11:56:31  INFO ConceptSimilarityServiceImpl - begin
>>>>>>> initialization for concept graph: sct-umls
>>>>>>> 05 Nov 2014 11:56:31  INFO ConceptDaoImpl - could not load
>>>>>>> conceptGraph from classpath, attempt to load from:
>>>>>>> /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls
>>>>>>> .gz
>>>>>>> 05 Nov 2014 11:56:31  INFO ConceptDaoImpl -
>>>>>>> /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls
>>>>>>> .gz not found, cannot load concept graph
>>>>>>>
>>>>>>>    I don't understand what needs to go into CLASSPATH to indicate
>>>>>>> where conceptGraph is, as it already contains ${CTAKES_HOME}/resources.
 My
>>>>>>> class path is set according to the documentation to:
>>>>>>>
>>>>>>> ${CTAKES_HOME}/desc:/${CTAKES_HOME}/resources:${CTAKES_HOME}/lib/*
>>>>>>>
>>>>>>>      Any help would be appreciated.
>>>>>>>
>>>>>>>      Natalia
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

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