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:gundolf.sch...@ucsf.edu] Sent: Monday, March 05, 2018 5:25 PM To: Mullane, Sean *HS; user@ctakes.apache.org 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" <sp...@hscmail.mcc.virginia.edu<mailto:sp...@hscmail.mcc.virginia.edu>> Date: Monday, March 5, 2018 at 12:36 To: "Schenk, Gundolf" <gundolf.sch...@ucsf.edu<mailto:gundolf.sch...@ucsf.edu>>, "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> 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:gundolf.sch...@ucsf.edu] Sent: Monday, March 05, 2018 2:03 PM To: user@ctakes.apache.org<mailto:user@ctakes.apache.org> 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" <sp...@hscmail.mcc.virginia.edu<mailto:sp...@hscmail.mcc.virginia.edu>> Reply-To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> Date: Monday, March 5, 2018 at 10:43 To: "Schenk, Gundolf" <gundolf.sch...@ucsf.edu<mailto:gundolf.sch...@ucsf.edu>>, "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> 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:gundolf.sch...@ucsf.edu] Sent: Monday, March 05, 2018 1:38 PM To: Mullane, Sean *HS; user@ctakes.apache.org<mailto:user@ctakes.apache.org> 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" <sp...@hscmail.mcc.virginia.edu<mailto:sp...@hscmail.mcc.virginia.edu>> Date: Monday, March 5, 2018 at 10:21 To: "Schenk, Gundolf" <gundolf.sch...@ucsf.edu<mailto:gundolf.sch...@ucsf.edu>>, "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> 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:gundolf.sch...@ucsf.edu] Sent: Monday, March 05, 2018 12:57 PM To: user@ctakes.apache.org<mailto:user@ctakes.apache.org> 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 <gandhi.natara...@arisglobal.com<mailto:gandhi.natara...@arisglobal.com>> Reply-To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> Date: Saturday, March 3, 2018 at 02:15 To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto: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<mailto: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. 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