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.
