Can you share the line in your piper file where you add the DBConsumer? Sean
From: Schenk, Gundolf [mailto:[email protected]] Sent: Monday, March 05, 2018 7:27 PM To: [email protected] Subject: Re: YTEX installation Hi, I was able to solve the errors about missing classes. Somehow, I must have skipped accidentally step 2) in the YTEX installations. Unfortunately, the final error is still there: […] 06 Mar 2018 00:09:05 DEBUG DefaultListableBeanFactory - Retrieved dependent beans for bean 'intrinsicInfoContentEvaluator': [conceptDao] 06 Mar 2018 00:09:05 DEBUG DefaultListableBeanFactory - Retrieved dependent beans for bean 'conceptDao': [intrinsicInfoContentEvaluator] 06 Mar 2018 00:09:05 DEBUG DisposableBeanAdapter - Invoking destroy() on bean with name 'sessionFactory' 06 Mar 2018 00:09:05 DEBUG SessionFactoryImpl - HHH000031: Closing 06 Mar 2018 00:09:05 DEBUG DisposableBeanAdapter - Invoking destroy method 'close' on bean with name 'dataSource' 06 Mar 2018 00:09:05 INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@64c8fcfb<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@64c8fcfb>: defining beans [ytexApplicationContext]; root of factory hierarchy 06 Mar 2018 00:09:05 ERROR PiperFileRunner - Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.DBConsumer" failed. (Descriptor: <unknown>) Unclear to me, what might cause it. Any thoughts welcome! Cheers, Gundolf. From: "Schenk, Gundolf" <[email protected]<mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Date: Monday, March 5, 2018 at 15:12 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: YTEX installation This increased the logging, indeed. Thank you! I am not really sure what to look out for. Here are a few snippets, that might help to shed some light onto it: […] Loading lexica. Loading model: ................................ Loading model: ............................. 05 Mar 2018 22:35:59 DEBUG DataBinder - DataBinder requires binding of required fields [_loggerName] 05 Mar 2018 22:35:59 DEBUG DataBinder - DataBinder requires binding of required fields [] 05 Mar 2018 22:35:59 DEBUG StandardEnvironment - Initializing new StandardEnvironment 05 Mar 2018 22:35:59 DEBUG StandardEnvironment - Adding [systemProperties] PropertySource with lowest search precedence […] 05 Mar 2018 22:35:59 DEBUG StandardEnvironment - Initialized StandardEnvironment with PropertySources [systemProperties,systemEnvironment] 05 Mar 2018 22:35:59 DEBUG BeanUtils - No property editor [org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine$FEATURE_CONFIGEditor] found for type org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine$FEATURE_CONFIG according to 'Editor' suffix convention 05 Mar 2018 22:35:59 DEBUG DataBinder - DataBinder requires binding of required fields [classifierJarPath] 05 Mar 2018 22:35:59 DEBUG DataBinder - DataBinder requires binding of required fields [] 05 Mar 2018 22:35:59 DEBUG StandardEnvironment - Initializing new StandardEnvironment 05 Mar 2018 22:35:59 DEBUG StandardEnvironment - Adding [systemProperties] PropertySource with lowest search precedence […] 05 Mar 2018 22:36:00 DEBUG StandardEnvironment - Initialized StandardEnvironment with PropertySources [systemProperties,systemEnvironment] 05 Mar 2018 22:36:00 INFO XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:/mnt/apache-ctakes-4.0.0/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml] 05 Mar 2018 22:36:00 DEBUG DefaultDocumentLoader - Using JAXP provider [org.apache.xerces.jaxp.DocumentBuilderFactoryImpl] 05 Mar 2018 22:36:00 DEBUG BeansDtdResolver - Found beans DTD [http://www.springframework.org/dtd/spring-beans.dtd] in classpath: spring-beans.dtd 05 Mar 2018 22:36:00 DEBUG DefaultBeanDefinitionDocumentReader - Loading bean definitions 05 Mar 2018 22:36:00 DEBUG BeanDefinitionParserDelegate - No XML 'id' specified - using 'ytexApplicationContext' as bean name and [] as aliases […] 05 Mar 2018 22:36:00 INFO DefaultListableBeanFactory - Overriding bean definition for bean 'ytexApplicationContext': 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:/mnt/apache-ctakes-4.0.0/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.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:/mnt/apache-ctakes-4.0.0/lib/ctakes-ytex-web-4.0.0-classes.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]] 05 Mar 2018 22:36:00 DEBUG XmlBeanDefinitionReader - Loaded 1 bean definitions from location pattern [classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml] 05 Mar 2018 22:36:00 DEBUG ClassPathXmlApplicationContext - Bean factory for org.springframework.context.support.ClassPathXmlApplicationContext@7e18ced7<mailto:org.springframework.context.support.ClassPathXmlApplicationContext@7e18ced7>: org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03>: defining beans [ytexApplicationContext]; root of factory hierarchy 05 Mar 2018 22:36:00 DEBUG ClassPathXmlApplicationContext - Unable to locate MessageSource with name 'messageSource': using default [org.springframework.context.support.DelegatingMessageSource@57e4b86c] 05 Mar 2018 22:36:00 DEBUG ClassPathXmlApplicationContext - Unable to locate ApplicationEventMulticaster with name 'applicationEventMulticaster': using default [org.springframework.context.event.SimpleApplicationEventMulticaster@589dfa6f] 05 Mar 2018 22:36:00 INFO DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03>: defining beans [ytexApplicationContext]; root of factory hierarchy 05 Mar 2018 22:36:00 DEBUG DefaultListableBeanFactory - Creating shared instance of singleton bean 'ytexApplicationContext' 05 Mar 2018 22:36:00 DEBUG DefaultListableBeanFactory - Creating instance of bean 'ytexApplicationContext' 05 Mar 2018 22:36:00 DEBUG StandardEnvironment - Initializing new StandardEnvironment […] 05 Mar 2018 22:36:00 DEBUG StandardEnvironment - Initialized StandardEnvironment with PropertySources [systemProperties,systemEnvironment] 05 Mar 2018 22:36:00 DEBUG BeanUtils - No property editor [org.springframework.context.ApplicationContextEditor] found for type org.springframework.context.ApplicationContext according to 'Editor' suffix convention 05 Mar 2018 22:36:00 DEBUG StandardEnvironment - Initializing new StandardEnvironment […] 05 Mar 2018 22:36:00 DEBUG PluggableSchemaResolver - Found XML schema [http://www.springframework.org/schema/beans/spring-beans-2.5.xsd] in classpath: org/springframework/beans/factory/xml/spring-beans-2.5.xsd 05 Mar 2018 22:36:00 DEBUG DefaultBeanDefinitionDocumentReader - Loading bean definitions 05 Mar 2018 22:36:00 DEBUG BeanDefinitionParserDelegate - Neither XML 'id' nor 'name' specified - using generated bean name [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0] 05 Mar 2018 22:36:00 DEBUG XmlBeanDefinitionReader - Loaded 8 bean definitions from location pattern [org/apache/ctakes/ytex/beans-datasource.xml] 05 Mar 2018 22:36:00 INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml] 05 Mar 2018 22:36:00 DEBUG DefaultDocumentLoader - Using JAXP provider [org.apache.xerces.jaxp.DocumentBuilderFactoryImpl] […] 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Ignoring bean class loading failure for bean 'infogainAttributeEval' org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [weka.attributeSelection.InfoGainAttributeEval] for bean with name 'infogainAttributeEval' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: weka.attributeSelection.InfoGainAttributeEval at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1262) […] at org.apache.ctakes.core.pipeline.PiperFileRunner.main(PiperFileRunner.java:81) Caused by: java.lang.ClassNotFoundException: weka.attributeSelection.InfoGainAttributeEval at java.net.URLClassLoader.findClass(URLClassLoader.java:381) […] ... 57 more 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Ignoring bean class loading failure for bean 'rankerSearch' org.springframework.beans.factory.CannotLoadBeanClassException: Cannot find class [weka.attributeSelection.Ranker] for bean with name 'rankerSearch' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]; nested exception is java.lang.ClassNotFoundException: weka.attributeSelection.Ranker at org.springframework.beans.factory.support.AbstractBeanFactory.resolveBeanClass(AbstractBeanFactory.java:1262) […] 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Finished creating instance of bean 'hibernateProperties' 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Creating shared instance of singleton bean 'dataSource' 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Creating instance of bean 'dataSource' 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Returning cached instance of singleton bean 'org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0' […] 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Returning cached instance of singleton bean 'org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9' 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Eagerly caching bean 'dataSource' to allow for resolving potential circular references 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Returning cached instance of singleton bean 'org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0' […] 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Returning cached instance of singleton bean 'org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9' 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Finished creating instance of bean 'dataSource' 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Creating shared instance of singleton bean 'txAdvice' 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Creating instance of bean 'txAdvice' 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Eagerly caching bean 'txAdvice' to allow for resolving potential circular references 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Creating shared instance of singleton bean 'transactionManager' 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Creating instance of bean 'transactionManager' 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Returning cached instance of singleton bean 'org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0' […] 05 Mar 2018 22:36:01 DEBUG DefaultListableBeanFactory - Returning cached instance of singleton bean 'org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9' 05 Mar 2018 22:36:01 INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@26a45089<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@26a45089>: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,[…],org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601Converter,documentMapperService]; root of factory hierarchy 05 Mar 2018 22:36:01 DEBUG DisposableBeanAdapter - Invoking destroy method 'close' on bean with name 'dataSource' 05 Mar 2018 22:36:01 INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@7606bd03>: defining beans [ytexApplicationContext]; root of factory hierarchy 05 Mar 2018 22:36:01 ERROR PiperFileRunner - Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.DBConsumer" failed. (Descriptor: <unknown>) Seems to me that some classes were not found? Is my $CLASSPATH correct? > echo $CLASSPATH /mnt/apache-ctakes-4.0.0/desc/:/mnt/apache-ctakes-4.0.0/resources/:/mnt/apache-ctakes-4.0.0/lib/* Cheers, Gundolf. From: "Mullane, Sean *HS" <[email protected]<mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Date: Monday, March 5, 2018 at 14:32 To: "Schenk, Gundolf" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: YTEX installation I’m assuming you’re using a file called ‘log4j.xml’ in the directory %CTAKES_HOME%\config – let me know if this is not the case. In my log4j.xml file, I would make that change by replacing INFO with DEBUG in these lines: <root> <level value="INFO"/> <appender-ref ref="consoleAppender" /> </root> If you are using the consoleAppender appender, you should just see logs in the CLI. You would only see file-based logs if you use a fileAppender appender. These are also set within the log4j.xml file. Sean From: Schenk, Gundolf [mailto:[email protected]] Sent: Monday, March 05, 2018 5:25 PM To: Mullane, Sean *HS; [email protected]<mailto:[email protected]> Subject: Re: YTEX installation Hi Sean, Do you mean that I should set debug=true in config.log4j.xml ? This is what I already have. I do not see any log-files (only logging I can see is in the CLI). Is there a place where I might find log-files? Do I have to set a command-line parameter? Many thanks for helping, Gundolf. From: "Mullane, Sean *HS" <[email protected]<mailto:[email protected]>> Date: Monday, March 5, 2018 at 12:36 To: "Schenk, Gundolf" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: YTEX installation You could try setting the log level to DEBUG in log4j.xml if you haven’t already, then re-run the pipeline. You should get more detailed feedback in the logs that way. Sean From: Schenk, Gundolf [mailto:[email protected]] Sent: Monday, March 05, 2018 2:03 PM To: [email protected]<mailto:[email protected]> Subject: Re: YTEX installation Yes, step 7) of the YTEX install instructions worked successfully. Which environment variables need to be set? I have (manually) sourced ~/ctakes.profile, which sets $CTAKES_HOME and $CLASSPATH. What else should I check? Cheers, Gundolf. From: "Mullane, Sean *HS" <[email protected]<mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Date: Monday, March 5, 2018 at 10:43 To: "Schenk, Gundolf" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: YTEX installation Have you done step 7 listed here? ( https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation ) If so, maybe check that your environment variables are set correctly. From: Schenk, Gundolf [mailto:[email protected]] Sent: Monday, March 05, 2018 1:38 PM To: Mullane, Sean *HS; [email protected]<mailto:[email protected]> Subject: Re: YTEX installation Hi Sean, Thanks for your reply. I think, I did set the DB access parameters correctly. This was already done for the DB creation and has worked there. Any other thoughts? Cheers, Gundolf. From: "Mullane, Sean *HS" <[email protected]<mailto:[email protected]>> Date: Monday, March 5, 2018 at 10:21 To: "Schenk, Gundolf" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: YTEX installation Have you set the references to your database in the ytex.properties file? This is necessary so that ctakes knows how to connect to the database. Sean From: Schenk, Gundolf [mailto:[email protected]] Sent: Monday, March 05, 2018 12:57 PM To: [email protected]<mailto:[email protected]> Subject: Re: YTEX installation Hi Gandhi, Many thanks for your reply! It looks like cTAKES can find the DBConsumer module now. However, I am getting an initialization error when I run the pipeline. Here is the output: apache-ctakes-4.0.0> bin/runClinicalPipelineWithYtex.sh -i input/ --xmiOut output/ --user xxx –pass xxx […] Loading model: ............................. 05 Mar 2018 17:13:51 INFO ApplicationContextHolder - loading ytex.properties from: file:/mnt/apache-ctakes-4.0.0/resources/org/apache/ctakes/ytex/ytex.properties 05 Mar 2018 17:13:51 INFO ApplicationContextHolder - beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml 05 Mar 2018 17:13:51 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@7e18ced7<mailto:org.springframework.context.support.ClassPathXmlApplicationContext@7e18ced7>: startup date [Mon Mar 05 17:13:51 UTC 2018]; root of context hierarchy 05 Mar 2018 17:13:51 INFO XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:/mnt/apache-ctakes-4.0.0/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml] 05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean definitions from URL [jar:file:/mnt/apache-ctakes-4.0.0/lib/ctakes-ytex-web-4.0.0-classes.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml] 05 Mar 2018 17:13:52 INFO DefaultListableBeanFactory - Overriding bean definition for bean 'ytexApplicationContext': 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:/mnt/apache-ctakes-4.0.0/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.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:/mnt/apache-ctakes-4.0.0/lib/ctakes-ytex-web-4.0.0-classes.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]] 05 Mar 2018 17:13:52 INFO DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@21be14c2<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy 05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93<mailto:org.springframework.context.support.ClassPathXmlApplicationContext@1fcaea93>: startup date [Mon Mar 05 17:13:52 UTC 2018]; root of context hierarchy 05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml] 05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml] 05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel-sim.xml] 05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima.hbm.xml] 05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-dao.xml] 05 Mar 2018 17:13:52 INFO XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-mapper.xml] 05 Mar 2018 17:13:52 INFO DefaultListableBeanFactory - Overriding bean definition for bean 'mapperOperation': replacing [Root bean: class [org.springframework.aop.aspectj.AspectJExpressionPointcut]; scope=prototype; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null] with [Root bean: class [org.springframework.aop.aspectj.AspectJExpressionPointcut]; scope=prototype; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null] 05 Mar 2018 17:13:52 INFO PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties] 05 Mar 2018 17:13:52 INFO PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 05 Mar 2018 17:13:52 INFO PropertyPlaceholderConfigurer - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties] 05 Mar 2018 17:13:52 INFO DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@5b665a30<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@5b665a30>: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,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,conceptSimilarityService,abstractConceptKernel,abstractLinKernel,abstractSemanticSimKernel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambiguator,sessionFactory,ytexDaoOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#8,documentDao,namedEntityRegexDao,segmentRegexDao,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601Converter,documentMapperService]; root of factory hierarchy 05 Mar 2018 17:13:52 INFO PropertiesFactoryBean - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties] 05 Mar 2018 17:13:52 INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@5b665a30<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@5b665a30>: defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,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,conceptSimilarityService,abstractConceptKernel,abstractLinKernel,abstractSemanticSimKernel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambiguator,sessionFactory,ytexDaoOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#8,documentDao,namedEntityRegexDao,segmentRegexDao,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601Converter,documentMapperService]; root of factory hierarchy 05 Mar 2018 17:13:52 INFO DefaultListableBeanFactory - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@21be14c2<mailto:org.springframework.beans.factory.support.DefaultListableBeanFactory@21be14c2>: defining beans [ytexApplicationContext]; root of factory hierarchy 05 Mar 2018 17:13:52 ERROR PiperFileRunner - Initialization of annotator class "org.apache.ctakes.ytex.uima.annotators.DBConsumer" failed. (Descriptor: <unknown>) I am not sure where to look next. Any clues of what it could be? Cheers, Gundolf. From: Gandhi Rajan Natarajan <[email protected]<mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Date: Saturday, March 3, 2018 at 02:15 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: YTEX installation HI Gundolf, Try using – “add org.apache.ctakes.ytex.uima.annotators.DBConsumer” Also “documentMapperService” bean should be available in your application context. Regards, Gandhi From: Schenk, Gundolf [mailto:[email protected]] Sent: Saturday, March 03, 2018 4:11 AM To: [email protected]<mailto:[email protected]> Subject: Re: YTEX installation Hi Brian, The link helped indeed. Thanks! I had to change also the db engine to innodb on mysql. So now that I am through with the DB creation, I am unsure how to include (add) the DBConsumer annotator. A simple: add DBConsumer at the end of the DefaultClinicalPipeline.piper results in an error: 02 Mar 2018 22:09:01 ERROR PiperFileRunner - MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for DBConsumer How can I tell the system where to look at? Thanks, Gundolf. From: Brian Wilson <[email protected]<mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Date: Friday, February 23, 2018 at 15:13 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: YTEX installation might help... https://code.google.com/archive/p/ytex/downloads On 02/23/2018 05:45 PM, Schenk, Gundolf wrote: Hi, Does anyone know how to export the resulting XMI files to a sql database efficiently? I found the YTEX DBConsumer module but I am not able to install YTEX properly as the links the the zip files seem to be outdated/broken at: https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation Are there updated instructions anywhere? Many thanks, Gundolf. -- Brian Wilson Data Warehouse Architect Hebrew SeniorLife 1200 Centre Street Boston, MA 02131 Tel: (617) 971-5742 email: [email protected]<mailto:[email protected]> ________________________________ CONFIDENTIAL NOTICE: This electronic mail transmission contains confidential information including Protected Health Information (PHI) that is legally privileged. If you are not the intended recipient, or designee, you are hereby notified that any disclosure, copying, distribution or use of any and all attachments to this transmission is STRICTLY PROHIBITED. If you have received this transmission in error, please notify the sender immediately to arrange for return or destruction of these documents. This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
