Thanks you for your help, Sean! When commenting out the grammatrixexporterimpl
bean, I'm getting the error below.
Did you face this error too?
[java] 03 Mar 2017 19:03:37 INFO DefaultListableBeanFactory - Overriding bean
definition for bean 'kernelApplicationContext': replacing [Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-res-3.2.3-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]
with [Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]
[java] 03 Mar 2017 19:03:37 INFO DefaultListableBeanFactory -
Pre-instantiating singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@3427b02d:
defining beans [kernelApplicationContext]; root of factory hierarchy
[java] 03 Mar 2017 19:03:37 INFO ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@4d5d943d:
startup date [Fri Mar 03 19:03:37 CET 2017]; root of context hierarchy
[java] 03 Mar 2017 19:03:37 INFO XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-datasource.xml]
[java] 03 Mar 2017 19:03:38 INFO XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.hbm.xml]
[java] Exception in thread "main" java.lang.ExceptionInInitializerError
[java] at
org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
[java] at
org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
[java] Caused by:
org.springframework.beans.factory.access.BootstrapException: Unable to
initialize group definition. Group resource name
[classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml], factory key
[kernelApplicationContext]; nested exception is
org.springframework.beans.factory.BeanCreationException: Error creating bean
with name 'kernelApplicationContext' defined in URL
[jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.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.xml.XmlBeanDefinitionStoreException: Line 80
in XML document from class path resource
[org/apache/ctakes/ytex/beans-kernel.xml] is invalid; nested exception is
org.xml.sax.SAXParseException; lineNumber: 80; columnNumber: 4; The element
type "beans" must be terminated by the matching end-tag "</beans>".
[java] at
org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
[java] at
org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:29)
[java] ... 2 more
[java] Caused by: org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'kernelApplicationContext' defined in URL
[jar:file:/Users/leandermelms/coding/ctakes-3.2.3-spring/lib/ctakes-ytex-web-3.2.3-SNAPSHOT-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.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.xml.XmlBeanDefinitionStoreException: Line 80
in XML document from class path resource
[org/apache/ctakes/ytex/beans-kernel.xml] is invalid; nested exception is
org.xml.sax.SAXParseException; lineNumber: 80; columnNumber: 4; The element
type "beans" must be terminated by the matching end-tag "</beans>".
[java] at
org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:285)
[java] at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1077)
[java] at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:981)
[java] at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
[java] at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
[java] at
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
[java] at
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
[java] at
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
[java] at
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
[java] at
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:638)
[java] at
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:942)
[java] at
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
[java] at
org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
[java] at
org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
[java] ... 3 more
[java] 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.xml.XmlBeanDefinitionStoreException: Line 80
in XML document from class path resource
[org/apache/ctakes/ytex/beans-kernel.xml] is invalid; nested exception is
org.xml.sax.SAXParseException; lineNumber: 80; columnNumber: 4; The element
type "beans" must be terminated by the matching end-tag "</beans>".
> On 3 Mar 2017, at 18:23, Mullane, Sean *HS <[email protected]>
> wrote:
>
> I think Joyce solved the GramMatrixExporterImpl issue differently than I did,
> but the way I got past that was to comment out the bean for
> grammatrixexporterimpl in these two files before I ran Maven:
> ctakes-ytex-res/src/main/resources/org/apache/ctakes/beans-kernel.xml
> ctakes-ytex-res/target/classes/org/apache/ctakes/beans-kernel.xml
>
> Sean
>
> -----Original Message-----
> From: Leander Melms [mailto:[email protected]]
> Sent: Friday, March 03, 2017 11:43 AM
> To: [email protected]
> Subject: Re: [EXTERNAL] Re: YTEX User Inferace Users?
>
> I'm running 3.2.3 and tried to get it running. However, it fails with the
> output below.
>
> Did you face this as well? Is the line:
> 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 the issue here?
>
> Could you share what your team did to make ytex running? I'm working at the
> Phillips University in Marburg, Germany, Department for rare and orphan
> diseases. We're a small team of students, physicians and developers commited
> to make use of supporting systems for differential diagnosis.
>
>
>
> 03 Mar 2017 17:33:20 INFO DefaultListableBeanFactory - Destroying singletons
> in
> org.springframework.beans.factory.support.DefaultListableBeanFactory@2f162cc0:
> defining beans [ytexApplicationContext]; root of factory hierarchy Exception
> in thread "main" org.apache.uima.resource.ResourceInitializationException:
> Initialization of annotator class
> "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" failed.
> (Descriptor:
> file:/Users/leandermelms/coding/ctakes-server/desc/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
> at de.dfki.lt.ctakes.Server$.main(Server.scala:35)
> at de.dfki.lt.ctakes.Server.main(Server.scala)
> Caused by: org.springframework.beans.factory.access.BootstrapException:
> Unable to initialize group definition. Group resource name
> [classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml], factory key
> [ytexApplicationContext]; nested exception is
> org.springframework.beans.factory.BeanCreationException: Error creating bean
> with name 'ytexApplicationContext' defined in URL
> [jar:file:/Users/leandermelms/coding/ctakes-server/target/ctakes-server-0.1.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]:
> Instantiation of bean failed; nested exception is
> org.springframework.beans.BeanInstantiationException: Could not instantiate
> bean class
> [org.springframework.context.support.ClassPathXmlApplicationContext]:
> Constructor threw exception; nested exception is
> org.springframework.beans.factory.BeanCreationException: Error creating bean
> with name 'gramMatrixExporter' defined in class path resource
> [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed;
> nested exception is org.springframework.beans.FatalBeanException: Failed to
> obtain BeanInfo for class
> [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is
> java.beans.IntrospectionException: type mismatch between read and write
> methods
> at
> org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
> at
> org.apache.ctakes.ytex.uima.ApplicationContextHolder.getApplicationContext(ApplicationContextHolder.java:79)
> at
> org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator.initialize(SegmentRegexAnnotator.java:65)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> ... 15 more
> Caused by: org.springframework.beans.factory.BeanCreationException: Error
> creating bean with name 'ytexApplicationContext' defined in URL
> [jar:file:/Users/leandermelms/coding/ctakes-server/target/ctakes-server-0.1.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]:
> Instantiation of bean failed; nested exception is
> org.springframework.beans.BeanInstantiationException: Could not instantiate
> bean class
> [org.springframework.context.support.ClassPathXmlApplicationContext]:
> Constructor threw exception; nested exception is
> org.springframework.beans.factory.BeanCreationException: Error creating bean
> with name 'gramMatrixExporter' defined in class path resource
> [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed;
> nested exception is org.springframework.beans.FatalBeanException: Failed to
> obtain BeanInfo for class
> [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is
> java.beans.IntrospectionException: type mismatch between read and write
> methods
> at
> org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:288)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1035)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:939)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
> at
> org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
> at
> org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
> at
> org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
> at
> org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
> at
> org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
> at
> org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
> at
> org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
> at
> org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
> at
> org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
> ... 18 more
> Caused by: org.springframework.beans.BeanInstantiationException: Could not
> instantiate bean class
> [org.springframework.context.support.ClassPathXmlApplicationContext]:
> Constructor threw exception; nested exception is
> org.springframework.beans.factory.BeanCreationException: Error creating bean
> with name 'gramMatrixExporter' defined in class path resource
> [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed;
> nested exception is org.springframework.beans.FatalBeanException: Failed to
> obtain BeanInfo for class
> [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is
> java.beans.IntrospectionException: type mismatch between read and write
> methods
> at
> org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:162)
> at
> org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:110)
> at
> org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:280)
> ... 31 more
> Caused by: org.springframework.beans.factory.BeanCreationException: Error
> creating bean with name 'gramMatrixExporter' defined in class path resource
> [org/apache/ctakes/ytex/beans-kernel.xml]: Initialization of bean failed;
> nested exception is org.springframework.beans.FatalBeanException: Failed to
> obtain BeanInfo for class
> [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception is
> java.beans.IntrospectionException: type mismatch between read and write
> methods
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:527)
> at
> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
> at
> org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
> at
> org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
> at
> org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
> at
> org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
> at
> org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
> at
> org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
> at
> org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
> at
> org.springframework.context.support.ClassPathXmlApplicationContext.<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)
> ... 33 more
> Caused by: org.springframework.beans.FatalBeanException: Failed to obtain
> BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl];
> nested exception is java.beans.IntrospectionException: type mismatch between
> read and write methods
> at
> org.springframework.beans.CachedIntrospectionResults.<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)
> ... 48 more
> Caused by: java.beans.IntrospectionException: type mismatch between read and
> write methods
> at
> java.beans.PropertyDescriptor.findPropertyType(PropertyDescriptor.java:661)
> at
> java.beans.PropertyDescriptor.setReadMethod(PropertyDescriptor.java:257)
> at
> org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:282)
> at
> org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:180)
> at
> org.springframework.beans.ExtendedBeanInfo.<init>(ExtendedBeanInfo.java:100)
> at
> org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:224)
> ... 54 more
>
>
> Leander
>> On 3 Mar 2017, at 17:25, Dunlop, Joyce (HP) <[email protected]> wrote:
>>
>> ed to work with Java 8 so manual intervention is not needed. It would be
>> nice if the instructions mentioned the bin.xml and the pom to include the
>> database resources you may need. I am sure, some database(s) jars cannot be
>> included because of licensing concerns.
>>
>> We are working with 3.2.2 version of cTAKES and the group is working to
>> release 3.2.3, so I don't know what has already been included.
>>
>> We were able to get YTEX started but it is still not fully functional.
>
>
>
