Unable to create bean?

[jtgreen]

Hi Dirk - Any clues here? I had this working awhile ago. Circling back to the project and went to set it up on a VM to run it as a server and got this:

java -Dctakes.umlsuser=jtgreen -Dctakes.umlspw= -Xmx5g -cp target/ctakes-server-0.1.jar:resources/ de.dfki.lt.ctakes.Server localhost 9999 desc/ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml log4j: reset attribute= "false". log4j: Threshold ="null". log4j: Retreiving an instance of org.apache.log4j.Logger. log4j: Setting [ProgressAppender] additivity to [false]. log4j: Level value for ProgressAppender is [INFO]. log4j: ProgressAppender 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 [%m]. log4j: Adding appender named [noEolAppender] to category [ProgressAppender]. log4j: Retreiving an instance of org.apache.log4j.Logger. log4j: Setting [ProgressDone] additivity to [false]. log4j: Level value for ProgressDone is [INFO]. log4j: ProgressDone 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 [%m%n]. log4j: Adding appender named [eolAppender] to category [ProgressDone]. 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]. 01 Mar 2017 17:11:56 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg with config file = /home/ctakes/ctakes/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties 01 Mar 2017 17:11:56 INFO LvgCmdApiResourceImpl - config file absolute path = /home/ctakes/ctakes/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties 01 Mar 2017 17:11:56 INFO LvgCmdApiResourceImpl - cwd = /home/ctakes/ctakes/ctakes-server-master 01 Mar 2017 17:11:56 INFO LvgCmdApiResourceImpl - cd /home/ctakes/ctakes/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/ 01 Mar 2017 17:11:57 INFO LvgCmdApiResourceImpl - cd /home/ctakes/ctakes/ctakes-server-master 01 Mar 2017 17:11:57 INFO ClearNLPDependencyParserAE - using Morphy analysis? true Loading configuration. Loading feature templates. Loading lexica. Loading model: ........................................................................................ 01 Mar 2017 17:12:11 INFO Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip 01 Mar 2017 17:12:13 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded. 01 Mar 2017 17:12:13 INFO ApplicationContextHolder - loading ytex.properties from: file:/home/ctakes/ctakes/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/ytex.properties 01 Mar 2017 17:12:13 INFO ApplicationContextHolder - beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml 01 Mar 2017 17:12:13 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@58bf8650: startup date [Wed Mar 01 17:12:13 EST 2017]; root of context hierarchy 01 Mar 2017 17:12:13 INFO XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:/home/ctakes/ctakes/ctakes-server-master/target/ctakes-server-0.1.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml] 01 Mar 2017 17:12:13 INFO DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@5d5d9e5: defining beans [ytexApplicationContext]; root of factory hierarchy 01 Mar 2017 17:12:13 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@724f138e: startup date [Wed Mar 01 17:12:13 EST 2017]; root of context hierarchy 01 Mar 2017 17:12:13 INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml] 01 Mar 2017 17:12:14 INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml] 01 Mar 2017 17:12:14 INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel-sim.xml] 01 Mar 2017 17:12:14 INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima.hbm.xml] 01 Mar 2017 17:12:14 INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-dao.xml] 01 Mar 2017 17:12:14 INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-mapper.xml] 01 Mar 2017 17:12:14 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] 01 Mar 2017 17:12:15 INFO PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties] 01 Mar 2017 17:12:15 INFO PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 01 Mar 2017 17:12:15 INFO PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties] 01 Mar 2017 17:12:15 INFO DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7561db12: 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 01 Mar 2017 17:12:15 INFO PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 01 Mar 2017 17:12:16 INFO Version - HCANN000001: Hibernate Commons Annotations {4.0.2.Final} 01 Mar 2017 17:12:16 INFO Version - HHH000412: Hibernate Core {4.2.6.Final} 01 Mar 2017 17:12:16 INFO Environment - HHH000206: hibernate.properties not found 01 Mar 2017 17:12:16 INFO Environment - HHH000021: Bytecode provider name : javassist 01 Mar 2017 17:12:17 INFO Dialect - HHH000400: Using dialect: org.hibernate.dialect.MySQLMyISAMDialect 01 Mar 2017 17:12:17 WARN RootClass - HHH000038: Composite-id class does not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 01 Mar 2017 17:12:17 WARN RootClass - HHH000039: Composite-id class does not override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink 01 Mar 2017 17:12:17 INFO TransactionFactoryInitiator - HHH000399: Using default transaction strategy (direct JDBC transactions) 01 Mar 2017 17:12:17 INFO ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory 01 Mar 2017 17:12:18 INFO UpdateTimestampsCache - HHH000250: Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache 01 Mar 2017 17:12:18 INFO StandardQueryCache - HHH000248: Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache 01 Mar 2017 17:12:18 INFO TableGenerator - HHH000398: Explicit segment value for id generator [ytex.hibernate_sequences.sequence_name] suggested; using default [default] 01 Mar 2017 17:12:19 WARN AbstractEhcacheRegionFactory - HHH020003: Could not find a specific ehcache configuration for cache named [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults. 01 Mar 2017 17:12:19 WARN EhcacheAccessStrategyFactoryImpl - HHH020007: read-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType] 01 Mar 2017 17:12:19 INFO HibernateTransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSource@444f44c5] of Hibernate SessionFactory for HibernateTransactionManager 01 Mar 2017 17:12:20 INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7561db12: 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 01 Mar 2017 17:12:20 INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@5d5d9e5: defining beans [ytexApplicationContext]; root of factory hierarchy Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed. (Descriptor: file:/home/ctakes/ctakes/ctakes-server-master/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.produceAnalysisEngine(UIMAFramework.java:354) at de.dfki.lt.ctakes.Server$.main(Server.scala:35) at de.dfki.lt.ctakes.Server.main(Server.scala) 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:/home/ctakes/ctakes/ctakes-server-master/target/ctakes-server-0.1.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 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods 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) ... 15 more Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ytexApplicationContext' defined in URL [jar:file:/home/ctakes/ctakes/ctakes-server-master/target/ctakes-server-0.1.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 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods 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) ... 18 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 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods 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) ... 31 more Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:527) 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.(ClassPathXmlApplicationContext.java:139) at org.springframework.context.support.ClassPathXmlApplicationContext.(ClassPathXmlApplicationContext.java:93) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147) ... 33 more Caused by: org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is java.beans.IntrospectionException: type mismatch between read and write methods at org.springframework.beans.CachedIntrospectionResults.(CachedIntrospectionResults.java:262) at org.springframework.beans.CachedIntrospectionResults.forClass(CachedIntrospectionResults.java:149) at org.springframework.beans.BeanWrapperImpl.getCachedIntrospectionResults(BeanWrapperImpl.java:324) at org.springframework.beans.BeanWrapperImpl.getPropertyDescriptors(BeanWrapperImpl.java:331) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.filterPropertyDescriptorsForDependencyCheck(AbstractAutowireCapableBeanFactory.java:1242) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1101) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517) ... 48 more Caused by: java.beans.IntrospectionException: type mismatch between read and write methods at java.beans.PropertyDescriptor.findPropertyType(PropertyDescriptor.java:661) at java.beans.PropertyDescriptor.setReadMethod(PropertyDescriptor.java:257) at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:282) at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:180) at org.springframework.beans.ExtendedBeanInfo.(ExtendedBeanInfo.java:100) at org.springframework.beans.CachedIntrospectionResults.(CachedIntrospectionResults.java:224) ... 54 more

[leanderme]

Having the same issue here. Did you manage to solve this?

[dirkweissenborn]

Did you use Java 7? 8 doesn't work for that reason...

On Fri, Mar 3, 2017, 11:45 Leander Melms notifications@github.com wrote:

Having the same issue here. Did you manage to solve this?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/dirkweissenborn/ctakes-server/issues/3#issuecomment-284005456, or mute the thread https://github.com/notifications/unsubscribe-auth/ABU6GxvU7ZJCenAylJLvDjErly5w5Js0ks5riEOpgaJpZM4MQSDw .

[leanderme]

Used Java 8. Sorry, should have read the instructions more carefully. Everything works now 👍

[dirkweissenborn]

I never used it with Java 8 because of a bean exception. So no idea. We recently got it running again though without ytex. It was very odd, also for us. Ctakes with maven is a real pain, because their poms seem to be broken.

On Mar 3, 2017 11:51, "Leander Melms" notifications@github.com wrote:

No, I've had success with java 8 and ctakes 3.2.3. I had to update spring to 3.2.18.RELEASE along with some other modifications.

Could you briefly explain how you got it running? Any help / hints are greatly appreciated!

Thanks Leander

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[leanderme]

I've actually packaged ctakes 3.2.3 with java 8. There is a thread in the mailing list describing how to do this. But switching to java 7 did it for me.

Unfortunately, ctakes doesn't acually recognize any concept. I think that this is related to my ytex install. Did you face this as well following the guide at confluence? my output for "Pain in the left leg":

[  
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode",
      "annotation":{  
         "begin":0,
         "cpostag":null,
         "pdeprel":null,
         "lemma":null,
         "head":null,
         "postag":null,
         "id":0,
         "sofa":null,
         "end":21,
         "deprel":null,
         "feats":null,
         "form":null,
         "phead":null
      }
   },
   {  
      "typ":"uima.tcas.DocumentAnnotation",
      "annotation":{  
         "sofa":null,
         "begin":0,
         "end":21,
         "language":"x-unspecified"
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.textspan.Segment",
      "annotation":{  
         "begin":0,
         "preferredText":null,
         "id":"DEFAULT",
         "sofa":null,
         "end":21
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.textspan.Sentence",
      "annotation":{  
         "begin":0,
         "segmentId":null,
         "sentenceNumber":0,
         "sofa":null,
         "end":21
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation",
      "annotation":{  
         "sofa":null,
         "begin":0,
         "end":20
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.NP",
      "annotation":{  
         "sofa":null,
         "begin":0,
         "chunkType":"NP",
         "end":20
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode",
      "annotation":{  
         "begin":0,
         "cpostag":"NN",
         "pdeprel":"_",
         "lemma":"pain",
         "head":null,
         "postag":"NN",
         "id":1,
         "sofa":null,
         "end":4,
         "deprel":"root",
         "feats":"_",
         "form":"Pain",
         "phead":null
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.WordToken",
      "annotation":{  
         "begin":0,
         "capitalization":1,
         "tokenNumber":0,
         "lemmaEntries":null,
         "canonicalForm":"pain",
         "sofa":null,
         "numPosition":0,
         "end":4,
         "suggestion":null,
         "normalizedForm":"pain",
         "partOfSpeech":"NN"
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode",
      "annotation":{  
         "begin":5,
         "cpostag":"IN",
         "pdeprel":"_",
         "lemma":"in",
         "head":null,
         "postag":"IN",
         "id":2,
         "sofa":null,
         "end":7,
         "deprel":"prep",
         "feats":"_",
         "form":"in",
         "phead":null
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.PP",
      "annotation":{  
         "sofa":null,
         "begin":5,
         "chunkType":"PP",
         "end":7
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.WordToken",
      "annotation":{  
         "begin":5,
         "capitalization":0,
         "tokenNumber":1,
         "lemmaEntries":null,
         "canonicalForm":null,
         "sofa":null,
         "numPosition":0,
         "end":7,
         "suggestion":null,
         "normalizedForm":"in",
         "partOfSpeech":"IN"
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.NP",
      "annotation":{  
         "sofa":null,
         "begin":8,
         "chunkType":"NP",
         "end":20
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode",
      "annotation":{  
         "begin":8,
         "cpostag":"DT",
         "pdeprel":"_",
         "lemma":"the",
         "head":null,
         "postag":"DT",
         "id":3,
         "sofa":null,
         "end":11,
         "deprel":"det",
         "feats":"_",
         "form":"the",
         "phead":null
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.WordToken",
      "annotation":{  
         "begin":8,
         "capitalization":0,
         "tokenNumber":2,
         "lemmaEntries":null,
         "canonicalForm":null,
         "sofa":null,
         "numPosition":0,
         "end":11,
         "suggestion":null,
         "normalizedForm":"the",
         "partOfSpeech":"DT"
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode",
      "annotation":{  
         "begin":12,
         "cpostag":"JJ",
         "pdeprel":"_",
         "lemma":"left",
         "head":null,
         "postag":"JJ",
         "id":4,
         "sofa":null,
         "end":16,
         "deprel":"amod",
         "feats":"_",
         "form":"left",
         "phead":null
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.WordToken",
      "annotation":{  
         "begin":12,
         "capitalization":0,
         "tokenNumber":3,
         "lemmaEntries":null,
         "canonicalForm":"left",
         "sofa":null,
         "numPosition":0,
         "end":16,
         "suggestion":null,
         "normalizedForm":"left",
         "partOfSpeech":"JJ"
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode",
      "annotation":{  
         "begin":17,
         "cpostag":"NN",
         "pdeprel":"_",
         "lemma":"leg",
         "head":null,
         "postag":"NN",
         "id":5,
         "sofa":null,
         "end":20,
         "deprel":"pobj",
         "feats":"_",
         "form":"leg",
         "phead":null
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.WordToken",
      "annotation":{  
         "begin":17,
         "capitalization":0,
         "tokenNumber":4,
         "lemmaEntries":null,
         "canonicalForm":"leg",
         "sofa":null,
         "numPosition":0,
         "end":20,
         "suggestion":null,
         "normalizedForm":"leg",
         "partOfSpeech":"NN"
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode",
      "annotation":{  
         "begin":20,
         "cpostag":".",
         "pdeprel":"_",
         "lemma":".",
         "head":null,
         "postag":".",
         "id":6,
         "sofa":null,
         "end":21,
         "deprel":"punct",
         "feats":"_",
         "form":".",
         "phead":null
      }
   },
   {  
      "typ":"org.apache.ctakes.typesystem.type.syntax.PunctuationToken",
      "annotation":{  
         "begin":20,
         "tokenNumber":5,
         "lemmaEntries":null,
         "sofa":null,
         "end":21,
         "normalizedForm":".",
         "partOfSpeech":"."
      }
   }
]

[leanderme]

In my case, when changing the DictionaryLookupAnnotatorDB to

<delegateAnalysisEngine key="DictionaryLookupAnnotatorDB"> 
    <!--import location="./DictionaryLookupAnnotator.xml" /--> 
    <import location="../../../ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml"/> 
</delegateAnalysisEngine>

it fails with Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed

Running the CVD / CPE from command line works fine; I've been trying for hours to debug this. All resources files are present and in place. Though this might not be related to this repo, does anyone know what's going on here?

03 Mar 2017 18:17:11 INFO AbstractJCasTermAnnotator - Using minimum term text span: 3 Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: file:/Users/leandermelms/coding/ctakes-server/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.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.produceAnalysisEngine(UIMAFramework.java:354) at de.dfki.lt.ctakes.Server$.main(Server.scala:35) at de.dfki.lt.ctakes.Server.main(Server.scala) Caused by: java.lang.NullPointerException

[ajayramakrishnan]

Facing the same issues as mentioned above, did anyone find a fix?

[PrithivirajDamodaran]

Facing the same issues as mentioned above

[LeninChristopher]

@leandermelms - is the below command line is correct java -Dctakes.umlsuser="leninchris7" -Dctakes.umlspw="mypwd" -Xmx5g -cp D:/cTakes/ctakes-server-master/target/ctakes-server-0.1.jar:resources/ de.dfki.lt.ctakes.Server localhost 9999 D:/cTakes/ctakes-server-master/desc/ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml

Getting the below error : Error: Could not find or load main class de.dfki.lt.ctakes.Server

[raghavbali]

@LeninChristopher Just replace : to ; . Thanks to the solution https://github.com/dirkweissenborn/ctakes-server/issues/6