Alan,
Have you had any luck getting past this issue? I am getting similar errors
trying to install YTEX on Windows 7. I tried downgrading to jdk1.7.0_71 but am
still getting a NoClassDefFoundException when running the ant script
setup-build.xml. The error message I get in setup.out is:
[java] 22 Nov 2016 13:56:05 INFO PropertiesFactoryBean - Loading
properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
[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:/C:/Users/spm9r/ctakes/apache-ctakes-3.2.2/lib/ctakes-ytex-web-3.2.2-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.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
[java] at
org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
[java] at
org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:28)
[java] ... 2 more
[java] Caused by: org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'kernelApplicationContext' defined in URL
[jar:file:/C:/Users/spm9r/ctakes/apache-ctakes-3.2.2/lib/ctakes-ytex-web-3.2.2-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.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
[java] at
org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:288)
[java] at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1035)
[java] at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:939)
[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:294)
[java] at
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
[java] at
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
[java] at
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
[java] at
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
[java] at
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
[java] at
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
[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.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
[java] 22 Nov 2016 13:56:05 INFO DefaultListableBeanFactory - Destroying
singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@1a3d8b15:
defining beans
[org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService];
root of factory hierarchy
[java] at
org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:162)22 Nov
2016 13:56:05 INFO DefaultListableBeanFactory - Destroying singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@a78f12e:
defining beans [kernelApplicationContext]; root of factory hierarchy
[java]
[java] at
org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:110)
[java] at
org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:280)
[java] ... 16 more
[java] 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
[java] at
org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
[java] at
org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
[java] at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1360)
[java] at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1118)
[java] at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
[java] at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
[java] at
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
[java] at
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
[java] at
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
[java] at
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
[java] at
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
[java] at
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
[java] at
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
[java] at
org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
[java] at
org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
[java] at
sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[java] at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
[java] at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[java] at
java.lang.reflect.Constructor.newInstance(Constructor.java:526)
[java] at
org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
[java] ... 18 more
[java] 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
[java] at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:997)
[java] at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:943)
[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:294)
[java] at
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
[java] at
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
[java] at
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
[java] at
org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
[java] ... 37 more
[java] Caused by: java.lang.NoClassDefFoundError:
org/hibernate/HibernateException
[java] at java.lang.Class.getDeclaredConstructors0(Native Method)
[java] at
java.lang.Class.privateGetDeclaredConstructors(Class.java:2585)
[java] at java.lang.Class.getConstructor0(Class.java:2885)
[java] at java.lang.Class.getDeclaredConstructor(Class.java:2058)
[java] at
org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:67)
[java] at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:990)
[java] ... 45 more
[java] Caused by: java.lang.ClassNotFoundException:
org.hibernate.HibernateException
[java] at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
[java] at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
[java] at java.security.AccessController.doPrivileged(Native
Method)
[java] at
java.net.URLClassLoader.findClass(URLClassLoader.java:354)
[java] at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
[java] at
sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
[java] at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
[java] ... 51 more
From: Alan Simmons [mailto:[email protected]]
Sent: Tuesday, November 15, 2016 12:56 PM
To: [email protected]
Subject: Re: ytex
I'm currently struggling with similar issues.
I think that the problem has something to do with the fact that there was a
change between Java 1.7 and 1.8. Java 1.8 requires that the get and set methods
of classes be the same type, unlike 1.7 (apparently).
I was able to get CVD to run by downgrading my JDK to 1.7. I did this using
jenv (http://www.jenv.be/) on my OSX machine. Once I switched my JDK between
1.8 and 1.7, CVD stopped throwing the exceptions. Yay!
Unfortunately, I am still encountering problems when trying to install YTEX so
that it creates lookups with the UMLS database that I installed locally,
instead of just using the toy dictionary (i.e., creating the umls_aui_fword
tables). I get the introspection errors that I thought that I had eliminated by
going down to JDK 1.7.
My exceptions occur when the build script tries to build a bean for
org.apache.ctakes.ytex.weka.GramMatrixExporterImpl. Based on the documentation
that I found, this class is deprecated, so I'm not sure why I'm getting this
error. I don't even know that I need weka. However, I do need WSD, which is why
I'm installing YTEX at all.
Alan
On Tue, Nov 15, 2016 at 10:56 AM, lewis john mcgibbney
<[email protected]<mailto:[email protected]>> wrote:
Hi Taylor,
This seems to be some issue with JDK1.8.X
https://issues.apache.org/jira/browse/CTAKES-334
On Mon, Nov 7, 2016 at 2:11 PM,
<[email protected]<mailto:[email protected]>>
wrote:
From: Taylor Cassidy
<[email protected]<mailto:[email protected]>>
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Cc:
Date: Mon, 07 Nov 2016 22:11:12 +0000
Subject: ytex
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
--
J. Alan Simmons
Solution Architect
(c) +1.773.220.5018<tel:%2B1.773.220.5018>
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