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: 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: defining beans [ytexApplicationContext]; root of factory hierarchy 05 Mar 2018 17:13:52 INFO ClassPathXmlApplicationContext - Refreshing 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: 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: 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: 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 <gandhi.natara...@arisglobal.com> Reply-To: "user@ctakes.apache.org" <user@ctakes.apache.org> Date: Saturday, March 3, 2018 at 02:15 To: "user@ctakes.apache.org" <user@ctakes.apache.org> 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:gundolf.sch...@ucsf.edu] Sent: Saturday, March 03, 2018 4:11 AM To: user@ctakes.apache.org 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 <brianwil...@hsl.harvard.edu<mailto:brianwil...@hsl.harvard.edu>> Reply-To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> Date: Friday, February 23, 2018 at 15:13 To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> 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: brianwil...@hsl.harvard.edu<mailto:brianwil...@hsl.harvard.edu> ________________________________ 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.
