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From Oranit Dror <ora...@algotec.co.il>
Subject The SegmentRegexAnnotator of Ytex
Date Mon, 13 Jul 2015 07:50:43 GMT
Hello,

I am using ctakes 3.2.2. and recently I have tried to apply the YTEX pipeline. Particularly, I am interested in the SegmentRegexAnnotator of Ytex.

My questions are:

1.       When running the pipeline, an org.apache.uima.resource.ResourceInitializationException is thrown, probably due to a failure in the initialization of org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator. Below is the stack trace.

2.       Where can I find information on how the SegmentRegexAnnotator works, especially where the list of segments is defined.

Thank you,
Oranit.


The stack trace for the Ytex pipeline crash:

12 יול 2015 09:47:52 ERROR RunEngine - Failed to create AE from xml descriptor :E:/Data/Views/oranit_nlp/subprod1/nlp/java/algotec-nlp/desc/desc/algotec-nlp/desc/analysis_engine/AggregateDiseaseYtexUMLSProcessorDescriptor.xml
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed.  (Descriptor: file:/E:/Program Files/apache-ctakes-3.2.2-rc2/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: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 com.algotec.nlp.RunEngine.createCasObjects(RunEngine.java:1399)
       at com.algotec.nlp.RunEngine.ensureCasObjects(RunEngine.java:1373)
       at com.algotec.nlp.RunEngine.analyze(RunEngine.java:954)
       at com.algotec.nlp.servlet.ReportNLPServlet.doPost(ReportNLPServlet.java:128)
       at com.algotec.nlp.servlet.ReportNLPServlet.doPost(ReportNLPServlet.java:103)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
       at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
       at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
       at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
       at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
       at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
       at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
       at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
       at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
       at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
       at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
       at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)
       at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
       at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
       at java.lang.Thread.run(Unknown Source)
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:/E:/Data/Views/oranit_nlp/subprod1/nlp/java/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/wtpwebapps/nlp/WEB-INF/lib/ctakes-ytex-web-3.2.2-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 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       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:65)
       at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
       ... 47 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ytexApplicationContext' defined in URL [jar:file:/E:/Data/Views/oranit_nlp/subprod1/nlp/java/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/wtpwebapps/nlp/WEB-INF/lib/ctakes-ytex-web-3.2.2-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 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       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)
       ... 50 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 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       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)
       ... 63 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
       at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1360)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1118)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
       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(Unknown Source)
       at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
       at java.lang.reflect.Constructor.newInstance(Unknown Source)
       at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
       ... 65 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:997)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:943)
       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.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
       ... 84 more
Caused by: java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       at java.lang.Class.getDeclaredConstructors0(Native Method)
       at java.lang.Class.privateGetDeclaredConstructors(Unknown Source)
       at java.lang.Class.getConstructor0(Unknown Source)
       at java.lang.Class.getDeclaredConstructor(Unknown Source)
       at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:67)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:990)
       ... 92 more
Caused by: java.lang.ClassNotFoundException: org.hibernate.HibernateException
       at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1702)
       at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1547)
       ... 98 more
9684 [http-bio-8080-exec-3] ERROR com.algotec.nlp.RunEngine  - Failed to create AE from xml descriptor :E:/Data/Views/oranit_nlp/subprod1/nlp/java/algotec-nlp/desc/desc/algotec-nlp/desc/analysis_engine/AggregateDiseaseYtexUMLSProcessorDescriptor.xml
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed.  (Descriptor: file:/E:/Program Files/apache-ctakes-3.2.2-rc2/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: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 com.algotec.nlp.RunEngine.createCasObjects(RunEngine.java:1399)
       at com.algotec.nlp.RunEngine.ensureCasObjects(RunEngine.java:1373)
       at com.algotec.nlp.RunEngine.analyze(RunEngine.java:954)
       at com.algotec.nlp.servlet.ReportNLPServlet.doPost(ReportNLPServlet.java:128)
       at com.algotec.nlp.servlet.ReportNLPServlet.doPost(ReportNLPServlet.java:103)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
       at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
       at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
       at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
       at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
       at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
       at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
       at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
       at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
       at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
       at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
       at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)
       at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
       at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
       at java.lang.Thread.run(Unknown Source)
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:/E:/Data/Views/oranit_nlp/subprod1/nlp/java/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/wtpwebapps/nlp/WEB-INF/lib/ctakes-ytex-web-3.2.2-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 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       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:65)
       at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
       ... 47 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ytexApplicationContext' defined in URL [jar:file:/E:/Data/Views/oranit_nlp/subprod1/nlp/java/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/wtpwebapps/nlp/WEB-INF/lib/ctakes-ytex-web-3.2.2-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 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       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)
       ... 50 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 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       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)
       ... 63 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
       at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1360)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1118)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
       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(Unknown Source)
       at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
       at java.lang.reflect.Constructor.newInstance(Unknown Source)
       at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
       ... 65 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:997)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:943)
       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.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
       ... 84 more
Caused by: java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       at java.lang.Class.getDeclaredConstructors0(Native Method)
       at java.lang.Class.privateGetDeclaredConstructors(Unknown Source)
       at java.lang.Class.getConstructor0(Unknown Source)
       at java.lang.Class.getDeclaredConstructor(Unknown Source)
       at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:67)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:990)
       ... 92 more
Caused by: java.lang.ClassNotFoundException: org.hibernate.HibernateException
       at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1702)
       at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1547)
       ... 98 more
12 יול 2015 09:47:52  INFO RunEngine - Unknown error
9690 [http-bio-8080-exec-3] INFO com.algotec.nlp.RunEngine  - Unknown error
java.lang.RuntimeException: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed.  (Descriptor: file:/E:/Program Files/apache-ctakes-3.2.2-rc2/desc/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml)
       at com.algotec.nlp.RunEngine.createCasObjects(RunEngine.java:1413)
       at com.algotec.nlp.RunEngine.ensureCasObjects(RunEngine.java:1373)
       at com.algotec.nlp.RunEngine.analyze(RunEngine.java:954)
       at com.algotec.nlp.servlet.ReportNLPServlet.doPost(ReportNLPServlet.java:128)
       at com.algotec.nlp.servlet.ReportNLPServlet.doPost(ReportNLPServlet.java:103)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
       at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
       at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
       at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
       at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
       at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
       at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
       at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
       at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
       at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
       at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
       at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)
       at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
       at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
       at java.lang.Thread.run(Unknown Source)
Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed.  (Descriptor: file:/E:/Program Files/apache-ctakes-3.2.2-rc2/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: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 com.algotec.nlp.RunEngine.createCasObjects(RunEngine.java:1399)
       ... 25 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:/E:/Data/Views/oranit_nlp/subprod1/nlp/java/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/wtpwebapps/nlp/WEB-INF/lib/ctakes-ytex-web-3.2.2-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 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       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:65)
       at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
       ... 47 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ytexApplicationContext' defined in URL [jar:file:/E:/Data/Views/oranit_nlp/subprod1/nlp/java/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/wtpwebapps/nlp/WEB-INF/lib/ctakes-ytex-web-3.2.2-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 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       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)
       ... 50 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 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       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)
       ... 63 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAdvice' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Cannot resolve reference to bean 'transactionManager' while setting bean property 'transactionManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
       at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1360)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1118)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
       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(Unknown Source)
       at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
       at java.lang.reflect.Constructor.newInstance(Unknown Source)
       at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
       ... 65 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'transactionManager' defined in class path resource [org/apache/ctakes/ytex/beans-datasource.xml]: Instantiation of bean failed; nested exception is java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:997)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:943)
       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.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
       ... 84 more
Caused by: java.lang.NoClassDefFoundError: org/hibernate/HibernateException
       at java.lang.Class.getDeclaredConstructors0(Native Method)
       at java.lang.Class.privateGetDeclaredConstructors(Unknown Source)
       at java.lang.Class.getConstructor0(Unknown Source)
       at java.lang.Class.getDeclaredConstructor(Unknown Source)
       at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:67)
       at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:990)
       ... 92 more
Caused by: java.lang.ClassNotFoundException: org.hibernate.HibernateException
       at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1702)
       at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1547)
       ... 98 more



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