Hi,
After installing ctakes 3.2.2, installing UMLS on a mysql server, and
running ytex build scripts, I ran CVD and tried to load the ytex AE called
AggregatePlaintextUMLSProcessor.xml. I cannot load it and have pasted my
log file below. Could anyone please explain what is causing this problem?
Thank you.
-Taylor
11/7/16 5:07:22 PM - 14:
org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
Initialization of annotator class
"org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed.
(Descriptor:
file:/home/tc/projects/Indegene/ctakes/apache-ctakes-3.2.2/desc/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class
"org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed.
(Descriptor:
file:/home/tc/projects/Indegene/ctakes/apache-ctakes-3.2.2/desc/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
at
org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)
at
org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
at java.awt.Component.processMouseEvent(Component.java:6533)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6298)
at java.awt.Container.processEvent(Container.java:2236)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4711)
at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: org.springframework.beans.factory.access.BootstrapException:
Unable to initialize group definition. Group resource name
[classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml], factory key
[ytexApplicationContext]; nested exception is
org.springframework.beans.factory.BeanCreationException: Error creating
bean with name 'ytexApplicationContext' defined in URL
[jar:file:/home/tc/projects/Indegene/ctakes/apache-ctakes-3.2.2/lib/ctakes-ytex-res-3.2.2.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]:
Instantiation of bean failed; nested exception is
org.springframework.beans.BeanInstantiationException: Could not instantiate
bean class
[org.springframework.context.support.ClassPathXmlApplicationContext]:
Constructor threw exception; nested exception is
org.springframework.beans.factory.BeanCreationException: Error creating
bean with name 'gramMatrixExporter' defined in class path resource
[org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed;
nested exception is org.springframework.beans.FatalBeanException: Failed to
obtain BeanInfo for class
[org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is
java.beans.IntrospectionException: type mismatch between read and write
methods
at
org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
at
org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
at
org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:64)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 54 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'ytexApplicationContext' defined in URL
[jar:file:/home/tc/projects/Indegene/ctakes/apache-ctakes-3.2.2/lib/ctakes-ytex-res-3.2.2.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]:
Instantiation of bean failed; nested exception is
org.springframework.beans.BeanInstantiationException: Could not instantiate
bean class
[org.springframework.context.support.ClassPathXmlApplicationContext]:
Constructor threw exception; nested exception is
org.springframework.beans.factory.BeanCreationException: Error creating
bean with name 'gramMatrixExporter' defined in class path resource
[org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed;
nested exception is org.springframework.beans.FatalBeanException: Failed to
obtain BeanInfo for class
[org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is
java.beans.IntrospectionException: type mismatch between read and write
methods
at
org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:288)
at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1035)
at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:939)
at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
at
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
at
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
at
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
at
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
at
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
at
org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
at
org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
... 57 more
Caused by: org.springframework.beans.BeanInstantiationException: Could not
instantiate bean class
[org.springframework.context.support.ClassPathXmlApplicationContext]:
Constructor threw exception; nested exception is
org.springframework.beans.factory.BeanCreationException: Error creating
bean with name 'gramMatrixExporter' defined in class path resource
[org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed;
nested exception is org.springframework.beans.FatalBeanException: Failed to
obtain BeanInfo for class
[org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is
java.beans.IntrospectionException: type mismatch between read and write
methods
at
org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:162)
at
org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:110)
at
org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:280)
... 70 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'gramMatrixExporter' defined in class path resource
[org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed;
nested exception is org.springframework.beans.FatalBeanException: Failed to
obtain BeanInfo for class
[org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is
java.beans.IntrospectionException: type mismatch between read and write
methods
at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:527)
at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
at
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
at
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
at
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
at
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
at
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
at
org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
at
org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at
org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
... 72 more
Caused by: org.springframework.beans.FatalBeanException: Failed to obtain
BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl];
nested exception is java.beans.IntrospectionException: type mismatch
between read and write methods
at
org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:262)
at
org.springframework.beans.CachedIntrospectionResults.forClass(CachedIntrospectionResults.java:149)
at
org.springframework.beans.BeanWrapperImpl.getCachedIntrospectionResults(BeanWrapperImpl.java:324)
at
org.springframework.beans.BeanWrapperImpl.getPropertyDescriptors(BeanWrapperImpl.java:331)
at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.filterPropertyDescriptorsForDependencyCheck(AbstractAutowireCapableBeanFactory.java:1242)
at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1101)
at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
... 87 more
Caused by: java.beans.IntrospectionException: type mismatch between read
and write methods
at
java.beans.PropertyDescriptor.findPropertyType(PropertyDescriptor.java:661)
at
java.beans.PropertyDescriptor.setReadMethod(PropertyDescriptor.java:257)
at
org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:282)
at
org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:180)
at
org.springframework.beans.ExtendedBeanInfo.<init>(ExtendedBeanInfo.java:100)
at
org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:224)
... 93 more
