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Posted to dev@ctakes.apache.org by Oranit Dror <or...@algotec.co.il> on 2015/07/13 09:50:43 UTC
The SegmentRegexAnnotator of Ytex
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
RE: The SegmentRegexAnnotator of Ytex
Posted by Oranit Dror <or...@algotec.co.il>.
Hello Matt,
Unfortunately, I have not managed to solve the problem that causes the Ytex pipeline to crash when using the SegmentRegexAnnotator class.
The exception that I get is:
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201507.mbox/%3C798E66FF532D5A44AE06D6D87F64AD94BD75C873@RAVEN.algotec.co.il%3E
To overcome the problem, I simply implemented my own segment annotator.
Sorry for not being able to help,
Oranit.
-----Original Message-----
From: Matt Bouchard [mailto:matt.bouchard@medisapien.com]
Sent: Thursday, July 30, 2015 6:27 PM
To: dev@ctakes.apache.org
Subject: Re: The SegmentRegexAnnotator of Ytex
Hello Oranit,
Did you have any success solving this issue? If so, could you share how you resolved it?
I am running into the same issue using cTAKES 3.2.2, and have carefully followed the instructions in https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
numerous time as well to no avail.
Thanks,
Matt
Re: The SegmentRegexAnnotator of Ytex
Posted by Matt Bouchard <ma...@medisapien.com>.
Hello Oranit,
Did you have any success solving this issue? If so, could you share how you
resolved it?
I am running into the same issue using cTAKES 3.2.2, and have carefully
followed the instructions in
https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
numerous time as well to no avail.
Thanks,
Matt
Re: The SegmentRegexAnnotator of Ytex
Posted by vijay garla <vn...@gmail.com>.
Can you make sure you did everything documented here:
https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
I can see from the stack trace that hibernate is not in the classpath (see
section 'Unzip YTEX Libraries')
Best,
VJ
On Tue, Jul 14, 2015 at 2:41 AM, Oranit Dror <or...@algotec.co.il> wrote:
> Thank you, Vijay.
> However, I am still encountering with the crash.
>
> Best,
> Oranit.
>
> -----Original Message-----
> From: vijay garla [mailto:vngarla@gmail.com]
> Sent: Monday, July 13, 2015 5:53 PM
> To: dev@ctakes.apache.org
> Subject: Re: The SegmentRegexAnnotator of Ytex
>
> see https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide
>
> best,
>
> vj
>
> On Mon, Jul 13, 2015 at 2:50 AM, Oranit Dror <or...@algotec.co.il> wrote:
>
> > 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
> >
> >
> >
>
RE: The SegmentRegexAnnotator of Ytex
Posted by Oranit Dror <or...@algotec.co.il>.
Thank you, Vijay.
However, I am still encountering with the crash.
Best,
Oranit.
-----Original Message-----
From: vijay garla [mailto:vngarla@gmail.com]
Sent: Monday, July 13, 2015 5:53 PM
To: dev@ctakes.apache.org
Subject: Re: The SegmentRegexAnnotator of Ytex
see https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide
best,
vj
On Mon, Jul 13, 2015 at 2:50 AM, Oranit Dror <or...@algotec.co.il> wrote:
> 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
>
>
>
Re: The SegmentRegexAnnotator of Ytex
Posted by vijay garla <vn...@gmail.com>.
see https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide
best,
vj
On Mon, Jul 13, 2015 at 2:50 AM, Oranit Dror <or...@algotec.co.il> wrote:
> 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
>
>
>