Hi Alan, I have figured out why I was getting this additional error (it turned out it was a malformed ytex.properties file) and run the build script successfully. I never ran into a Weka error. Did you encounter that error when running Step 7 from https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation? I can give you some information about my system configuration so you can compare and perhaps figure out what caused the Weka issue.
The only weka jar file that shows up in the log file is C:\Users\xxxxxx\ctakes\apache-ctakes-3.2.2\lib\weka-stable-3.6.10.jar. Also I see that GramMatrixExporterImpl isn't mentioned in my log file, but GramMatrixExporter is. Not sure why the difference. I'm using Java jdk1.7.0_71 on Windows 7 if that helps. Sean -----Original Message----- From: Mullane, Sean *HS [mailto:sp...@hscmail.mcc.virginia.edu] Sent: Tuesday, November 22, 2016 6:34 PM To: Alan Simmons Cc: user@ctakes.apache.org Subject: Re: ytex Alan, I didn't think I needed to do that step for cTAKES 3.2.2. But it looks like it worked to resolve those errors. I'm getting a new error now ( com.microsoft.sqlserver.jdbc.SQLServerException). I suspect has to do with the fact that I'm using SQL Server 2012 but it's hard to tell. I'm curious what your alternative is to using YTEX. Are you still planning to use cTAKES or are you going a different route for NLP? I'm very interested in being able to run annotation pipelines in the database; as far as I can tell vanilla cTAKES can't do that. It may be worth the effort for us to work through the Weka issue if we don't have any good alternatives. Thanks, Sean ________________________________ From: Alan Simmons <alan.simm...@tempus.com> Sent: Tuesday, November 22, 2016 2:43 PM To: Mullane, Sean *HS Cc: user@ctakes.apache.org Subject: Re: ytex Sean, Your exception mentions problems with hibernate objects. When I encountered these kinds of problems, I was able to resolve them by finding the right versions of various dependency jars--in particular, those related to Hibernate and jboss. The instructions for YTEX install (Step 2) mention that you need to install "non-APACHE 2.0 license compliant libraries", including Hibernate and Weka. The link to the ZIP that you need is no longer current; however, you can find it on the same site (https://code.google.com/archive/p/ytex/downloads). That ZIP contains a number of the jars that you need. You may need to install additional dependencies. I found this link (https://mvnrepository.com/artifact/org.apache.ctakes/ctakes-ytex/3.2.2) helpful. Also helpful is just to paste excerpts from exception messages messages into Google (which almost always led me to Stack Overflow articles). Once you make sure that all of the necessary jars are in the CTAKES_HOME/lib folder, errors related to Hibernate should go away. I think that you'll still get an error related to Weka. This error actually does not appear to be related to the Java JDK, but seems to have something to do with a deprecated cTAKES wrapper around a Weka class. (This one, to be exact: http://ctakes.apache.org/apidocs/3.2.2/org/apache/ctakes/ytex/weka/GramMatrixExporterImpl.html) I was prepared to start doing wacky things like editing bean-related XMLs in jars to comment out references to Weka, but my team agreed that I was on the edge of falling down a rabbit hole and that the effort might not be worth the result. If you can get past the Weka error, please let me know what you did. Alan On Tue, Nov 22, 2016 at 1:09 PM, Mullane, Sean *HS <sp...@hscmail.mcc.virginia.edu<mailto:sp...@hscmail.mcc.virginia.edu>> wrote: 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:alan.simm...@tempus.com<mailto:alan.simm...@tempus.com>] Sent: Tuesday, November 15, 2016 12:56 PM To: user@ctakes.apache.org<mailto:user@ctakes.apache.org> 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 <lewi...@apache.org<mailto:lewi...@apache.org>> 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, <user-digest-h...@ctakes.apache.org<mailto:user-digest-h...@ctakes.apache.org>> wrote: From: Taylor Cassidy <taylorcassid...@gmail.com<mailto:taylorcassid...@gmail.com>> To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> 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> [Image removed by sender.] This email and any attachments may contain privileged and confidential information and/or protected health information (PHI) that is protected by federal and state privacy laws. It is intended solely for the use of Tempus Labs and the recipient(s) named above. Nothing contained in this communication and any attachments thereto is intended to waive any privileges or rights of confidentiality. If you are not the recipient, or the employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any review, dissemination, distribution, printing or copying of this email message and/or any attachments is strictly prohibited. If you have received this transmission in error, please notify us immediately at (877)-654-5544<tel:%28877%29-654-5544> and permanently delete this email and any attachments. -- J. Alan Simmons Solution Architect (c) +1.773.220.5018<tel:%2B1.773.220.5018> [https://docs.google.com/uc?export=download&id=0B_ZiIlRgT_0DRHBNQ20zYkNvYjg&revid=0B_ZiIlRgT_0DUDFod1hqNWFCbjdCcGRNZ2Q4d3RhaFF6bHZJPQ] This email and any attachments may contain privileged and confidential information and/or protected health information (PHI) that is protected by federal and state privacy laws. It is intended solely for the use of Tempus Labs and the recipient(s) named above. Nothing contained in this communication and any attachments thereto is intended to waive any privileges or rights of confidentiality. If you are not the recipient, or the employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any review, dissemination, distribution, printing or copying of this email message and/or any attachments is strictly prohibited. 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