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 < [email protected]> 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 <[email protected]> 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 < >> [email protected]> 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 <[email protected]> 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 < >>>> [email protected]> 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 <[email protected]> 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 < >>>>>> [email protected]> 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 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
