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From Natalia Connolly <natalia.v.conno...@gmail.com>
Subject Re: Classpath for conceptGraph in ytex
Date Wed, 05 Nov 2014 20:03:44 GMT
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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