Return-Path: X-Original-To: archive-asf-public-internal@cust-asf2.ponee.io Delivered-To: archive-asf-public-internal@cust-asf2.ponee.io Received: from cust-asf.ponee.io (cust-asf.ponee.io [163.172.22.183]) by cust-asf2.ponee.io (Postfix) with ESMTP id 0495B200D2E for ; Tue, 31 Oct 2017 12:56:10 +0100 (CET) Received: by cust-asf.ponee.io (Postfix) id 030AC1609EC; Tue, 31 Oct 2017 11:56:10 +0000 (UTC) Delivered-To: archive-asf-public@cust-asf.ponee.io Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by cust-asf.ponee.io (Postfix) with SMTP id 28EE61609EB for ; Tue, 31 Oct 2017 12:56:08 +0100 (CET) Received: (qmail 31879 invoked by uid 500); 31 Oct 2017 11:56:07 -0000 Mailing-List: contact notifications-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@ctakes.apache.org Delivered-To: mailing list notifications@ctakes.apache.org Received: (qmail 31870 invoked by uid 99); 31 Oct 2017 11:56:07 -0000 Received: from pnap-us-west-generic-nat.apache.org (HELO spamd1-us-west.apache.org) (209.188.14.142) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 31 Oct 2017 11:56:07 +0000 Received: from localhost (localhost [127.0.0.1]) by spamd1-us-west.apache.org (ASF Mail Server at spamd1-us-west.apache.org) with ESMTP id 4BFDFD144E for ; Tue, 31 Oct 2017 11:56:06 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd1-us-west.apache.org X-Spam-Flag: NO X-Spam-Score: -100.002 X-Spam-Level: X-Spam-Status: No, score=-100.002 tagged_above=-999 required=6.31 tests=[RP_MATCHES_RCVD=-0.001, SPF_PASS=-0.001, USER_IN_WHITELIST=-100] autolearn=disabled Received: from mx1-lw-us.apache.org ([10.40.0.8]) by localhost (spamd1-us-west.apache.org [10.40.0.7]) (amavisd-new, port 10024) with ESMTP id DvMObf_hIe_D for ; Tue, 31 Oct 2017 11:56:01 +0000 (UTC) Received: from mailrelay1-us-west.apache.org (mailrelay1-us-west.apache.org [209.188.14.139]) by mx1-lw-us.apache.org (ASF Mail Server at mx1-lw-us.apache.org) with ESMTP id 487DA5FBE9 for ; Tue, 31 Oct 2017 11:56:01 +0000 (UTC) Received: from jira-lw-us.apache.org (unknown [207.244.88.139]) by mailrelay1-us-west.apache.org (ASF Mail Server at mailrelay1-us-west.apache.org) with ESMTP id 953E4E06C7 for ; Tue, 31 Oct 2017 11:56:00 +0000 (UTC) Received: from jira-lw-us.apache.org (localhost [127.0.0.1]) by jira-lw-us.apache.org (ASF Mail Server at jira-lw-us.apache.org) with ESMTP id 47C0A212F8 for ; Tue, 31 Oct 2017 11:56:00 +0000 (UTC) Date: Tue, 31 Oct 2017 11:56:00 +0000 (UTC) From: "Alex Zbarcea (JIRA)" To: notifications@ctakes.apache.org Message-ID: In-Reply-To: References: Subject: [jira] [Updated] (CTAKES-469) could not able to run ytex with DBCollection reader MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-JIRA-FingerPrint: 30527f35849b9dde25b450d4833f0394 archived-at: Tue, 31 Oct 2017 11:56:10 -0000 [ https://issues.apache.org/jira/browse/CTAKES-469?page=3Dcom.atlassia= n.jira.plugin.system.issuetabpanels:all-tabpanel ] Alex Zbarcea updated CTAKES-469: -------------------------------- Docs Text:=20 {code} C:\cn\bin>SETLOCAL C:\cn\bin>set CURRENT_DIR=3DC:\cn\bin=20 C:\cn\bin>if not "" =3D=3D "" goto gotHome=20 C:\cn\bin>set CTAKES_HOME=3DC:\cn\bin=20 C:\cn\bin>if exist "C:\cn\bin\bin\runctakesCPE.bat" goto okHome=20 C:\cn\bin>cd ..=20 C:\cn>set CTAKES_HOME=3DC:\cn=20 C:\cn>if exist "C:\cn\bin\runctakesCPE.bat" goto okHome=20 C:\cn>cd C:\cn=20 C:\cn>java -cp "C:\cn/desc/;C:\cn/resources/;C:\cn/lib/*" -Dlog4j.configur= ation=3Dfile:/C:\cn/config/log4j.xml -Xms512M -Xmx3g org.apache.uima.tools.= cpm.CpmFrame=20 Oct 25, 2017 7:37:12 PM java.util.prefs.WindowsPreferences WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at r= oot 0x80000002. Windows RegCreateKeyEx(...) returned error code 5. log4j: reset attribute=3D "false". log4j: Threshold =3D"null". log4j: Retreiving an instance of org.apache.log4j.Logger. log4j: Setting [ProgressAppender] additivity to [false]. log4j: Level value for ProgressAppender is [INFO]. log4j: ProgressAppender level set to INFO log4j: Class name: [org.apache.log4j.ConsoleAppender] log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" log4j: Setting property [conversionPattern] to [%m]. log4j: Adding appender named [noEolAppender] to category [ProgressAppender]= . log4j: Retreiving an instance of org.apache.log4j.Logger. log4j: Setting [ProgressDone] additivity to [false]. log4j: Level value for ProgressDone is [INFO]. log4j: ProgressDone level set to INFO log4j: Class name: [org.apache.log4j.ConsoleAppender] log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" log4j: Setting property [conversionPattern] to [%m%n]. log4j: Adding appender named [eolAppender] to category [ProgressDone]. log4j: Level value for root is [INFO]. log4j: root level set to INFO log4j: Class name: [org.apache.log4j.ConsoleAppender] log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} %5= p %c{1} - %m%n]. log4j: Adding appender named [consoleAppender] to category [root]. 25 Oct 2017 19:37:23 INFO Chunker - Chunker model file: org/apache/ctakes/= chunker/models/chunker-model.zip 25 Oct 2017 19:37:27 INFO TokenizerAnnotatorPTB - Initializing org.apache.= ctakes.core.ae.TokenizerAnnotatorPTB 25 Oct 2017 19:37:27 INFO ContextDependentTokenizerAnnotator - Finite stat= e machines loaded. 25 Oct 2017 19:37:27 INFO ApplicationContextHolder - loading ytex.properti= es from: file:/C:/cn/resources/org/apache/ctakes/ytex/ytex.properties 25 Oct 2017 19:37:27 INFO ApplicationContextHolder - beanRefContext=3Dclas= spath*:org/apache/ctakes/ytex/uima/beanRefContext.xml 25 Oct 2017 19:37:30 INFO InitableJdbcConnectionResourceImpl - Connection = established to: jdbc:sqlserver://localhost;databaseName=3DUMLS;integratedSe= curity=3Dtrue 25 Oct 2017 19:37:30 INFO DictionaryLookupAnnotator - Parsing descriptor: = C:\cn\resources\org\apache\ctakes\ytex\dictionary\lookup\LookupDesc_SNOMED.= xml 25 Oct 2017 19:37:30 INFO FirstTokenPermLookupInitializerImpl - Exclusion = tagset loaded: [pp, pdt, prp$, vbn, vbp, wdt, ls, vbz, dt, pos, md, wp, cc,= cd, in, pp$, wrb, vb, prp, ex, vbd, vbg, to, wps, rp] 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using left , right scope size= s: 10 , 10 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using scope order: LEFT,RIGHT 25 Oct 2017 19:37:31 INFO ContextAnnotator - SCOPE ORDER: [1, 3] 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context analyzer: org.a= pache.ctakes.necontexts.status.StatusContextAnalyzer 25 Oct 2017 19:37:31 INFO StatusContextAnalyzer - initBoundaryData() calle= d for ContextInitializer 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context consumer: org.a= pache.ctakes.necontexts.status.StatusContextHitConsumer 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using lookup window type: org= .apache.ctakes.typesystem.type.textspan.Sentence 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using focus type: org.apache.= ctakes.typesystem.type.textsem.IdentifiedAnnotation 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context type: org.apach= e.ctakes.typesystem.type.syntax.BaseToken 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using left , right scope size= s: 7 , 7 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using scope order: LEFT,RIGHT 25 Oct 2017 19:37:31 INFO ContextAnnotator - SCOPE ORDER: [1, 3] 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context analyzer: org.a= pache.ctakes.necontexts.negation.NegationContextAnalyzer 25 Oct 2017 19:37:31 INFO NegationContextAnalyzer - initBoundaryData() cal= led for ContextInitializer 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context consumer: org.a= pache.ctakes.necontexts.negation.NegationContextHitConsumer 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using lookup window type: org= .apache.ctakes.typesystem.type.textspan.Sentence 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using focus type: org.apache.= ctakes.typesystem.type.textsem.IdentifiedAnnotation 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context type: org.apach= e.ctakes.typesystem.type.syntax.BaseToken 25 Oct 2017 19:37:31 INFO SentenceDetector - [SegmentsToSkip, SentenceMode= lFile] 25 Oct 2017 19:37:31 INFO SentenceDetector - Sentence detector model file:= org/apache/ctakes/core/sentdetect/sd-med-model.zip 25 Oct 2017 19:37:31 INFO ClassPathXmlApplicationContext - Refreshing org.= springframework.context.support.ClassPathXmlApplicationContext@1b6e40c5: st= artup date [Wed Oct 25 19:37:31 IST 2017]; root of context hierarchy 25 Oct 2017 19:37:32 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from URL [jar:file:/C:/cn/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/= ctakes/ytex/uima/beanRefContext.xml] 25 Oct 2017 19:37:32 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from URL [jar:file:/C:/cn/lib/ctakes-ytex-web-4.0.0-classes.jar!/org= /apache/ctakes/ytex/uima/beanRefContext.xml] 25 Oct 2017 19:37:32 INFO DefaultListableBeanFactory - Overriding bean def= inition for bean 'ytexApplicationContext': replacing [Generic bean: class [= org.springframework.context.support.ClassPathXmlApplicationContext]; scope= =3D; abstract=3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; dependencyCheck= =3D0; autowireCandidate=3Dtrue; primary=3Dfalse; factoryBeanName=3Dnull; fa= ctoryMethodName=3Dnull; initMethodName=3Dnull; destroyMethodName=3Dnull; de= fined in URL [jar:file:/C:/cn/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/cta= kes/ytex/uima/beanRefContext.xml]] with [Generic bean: class [org.springfra= mework.context.support.ClassPathXmlApplicationContext]; scope=3D; abstract= =3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; dependencyCheck=3D0; autowire= Candidate=3Dtrue; primary=3Dfalse; factoryBeanName=3Dnull; factoryMethodNam= e=3Dnull; initMethodName=3Dnull; destroyMethodName=3Dnull; defined in URL [= jar:file:/C:/cn/lib/ctakes-ytex-web-4.0.0-classes.jar!/org/apache/ctakes/yt= ex/uima/beanRefContext.xml]] 25 Oct 2017 19:37:32 INFO DefaultListableBeanFactory - Pre-instantiating s= ingletons in org.springframework.beans.factory.support.DefaultListableBeanF= actory@7ae65cd2: defining beans [ytexApplicationContext]; root of factory h= ierarchy 25 Oct 2017 19:37:32 INFO ClassPathXmlApplicationContext - Refreshing org.= springframework.context.support.ClassPathXmlApplicationContext@7d3b1153: st= artup date [Wed Oct 25 19:37:32 IST 2017]; root of context hierarchy 25 Oct 2017 19:37:32 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from class path resource [org/apache/ctakes/ytex/beans-datasource.xm= l] 25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml] 25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from class path resource [org/apache/ctakes/ytex/beans-kernel-sim.xm= l] 25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from class path resource [org/apache/ctakes/ytex/uima/beans-uima.hbm= .xml] 25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-dao= .xml] 25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-map= per.xml] 25 Oct 2017 19:37:33 INFO DefaultListableBeanFactory - Overriding bean def= inition for bean 'mapperOperation': replacing [Root bean: class [org.spring= framework.aop.aspectj.AspectJExpressionPointcut]; scope=3Dprototype; abstra= ct=3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; dependencyCheck=3D0; autowi= reCandidate=3Dtrue; primary=3Dfalse; factoryBeanName=3Dnull; factoryMethodN= ame=3Dnull; initMethodName=3Dnull; destroyMethodName=3Dnull] with [Root bea= n: class [org.springframework.aop.aspectj.AspectJExpressionPointcut]; scope= =3Dprototype; abstract=3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; depende= ncyCheck=3D0; autowireCandidate=3Dtrue; primary=3Dfalse; factoryBeanName=3D= null; factoryMethodName=3Dnull; initMethodName=3Dnull; destroyMethodName=3D= null] 25 Oct 2017 19:37:34 INFO PropertyPlaceholderConfigurer - Loading properti= es file from class path resource [org/apache/ctakes/ytex/ytex-default.prope= rties] 25 Oct 2017 19:37:34 INFO PropertyPlaceholderConfigurer - Loading properti= es file from class path resource [org/apache/ctakes/ytex/ytex.properties] 25 Oct 2017 19:37:34 INFO PropertyPlaceholderConfigurer - Loading properti= es file from class path resource [org/apache/ctakes/ytex/ytex-umls.properti= es] 25 Oct 2017 19:37:34 INFO DefaultListableBeanFactory - Pre-instantiating s= ingletons in org.springframework.beans.factory.support.DefaultListableBeanF= actory@202217c7: defining beans [org.springframework.beans.factory.config.P= ropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSourc= e,txAdvice,txTemplate,txTemplateNew,transactionManager,org.springframework.= aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterO= peration,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEva= luatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutA= dvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#= 1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.s= pringframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springfr= amework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework= .aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.su= pport.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.D= efaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,w= ekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wek= aResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatr= ixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel= ,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGen= erator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libS= VMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDat= aExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatt= erFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterF= actory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,info= gainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEval= uator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEval= uator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService,conceptSimi= larityService,abstractConceptKernel,abstractLinKernel,abstractSemanticSimKe= rnel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambiguator= ,sessionFactory,ytexDaoOperation,org.springframework.aop.support.DefaultBea= nFactoryPointcutAdvisor#8,documentDao,namedEntityRegexDao,segmentRegexDao,o= rg.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601C= onverter,documentMapperService]; root of factory hierarchy 25 Oct 2017 19:37:34 INFO PropertiesFactoryBean - Loading properties file = from class path resource [org/apache/ctakes/ytex/ytex.properties] 25 Oct 2017 19:37:39 INFO Version - HCANN000001: Hibernate Commons Annotat= ions {4.0.2.Final} 25 Oct 2017 19:37:39 INFO Version - HHH000412: Hibernate Core {4.2.6.Final= } 25 Oct 2017 19:37:39 INFO Environment - HHH000206: hibernate.properties no= t found 25 Oct 2017 19:37:39 INFO Environment - HHH000021: Bytecode provider name = : javassist 25 Oct 2017 19:37:42 INFO Dialect - HHH000400: Using dialect: org.hibernat= e.dialect.SQLServerDialect 25 Oct 2017 19:37:43 WARN RootClass - HHH000038: Composite-id class does n= ot override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainme= ntLink 25 Oct 2017 19:37:43 WARN RootClass - HHH000039: Composite-id class does n= ot override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContain= mentLink 25 Oct 2017 19:37:43 INFO TransactionFactoryInitiator - HHH000399: Using d= efault transaction strategy (direct JDBC transactions) 25 Oct 2017 19:37:43 INFO ASTQueryTranslatorFactory - HHH000397: Using AST= QueryTranslatorFactory 25 Oct 2017 19:37:44 INFO UpdateTimestampsCache - HHH000250: Starting upda= te timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCach= e 25 Oct 2017 19:37:44 INFO StandardQueryCache - HHH000248: Starting query c= ache at region: org.hibernate.cache.internal.StandardQueryCache 25 Oct 2017 19:37:44 INFO TableGenerator - HHH000398: Explicit segment val= ue for id generator [dbo.hibernate_sequences.sequence_name] suggested; usin= g default [default] 25 Oct 2017 19:37:45 WARN AbstractEhcacheRegionFactory - HHH020003: Could = not find a specific ehcache configuration for cache named [org.apache.ctake= s.ytex.uima.model.UimaType]; using defaults. 25 Oct 2017 19:37:45 WARN EhcacheAccessStrategyFactoryImpl - HHH020007: re= ad-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.mo= del.UimaType] 25 Oct 2017 19:37:46 INFO HibernateTransactionManager - Using DataSource [= org.apache.commons.dbcp.BasicDataSource@53ff623b] of Hibernate SessionFacto= ry for HibernateTransactionManager 25 Oct 2017 19:37:47 INFO EhCacheManagerFactoryBean - Initializing EHCache= CacheManager 25 Oct 2017 19:37:47 WARN CacheManager - Creating a new instance of CacheM= anager using the diskStorePath "C:\Users\Sathya\AppData\Local\Temp\" which = is already used by an existing CacheManager. The source of the configuration was net.sf.ehcache.config.generator.Configu= rationSource$InputStreamConfigurationSource@3cdbe5e4. The diskStore path for this CacheManager will be set to C:\Users\Sathya\App= Data\Local\Temp\\ehcache_auto_created_1508940467387. To avoid this warning consider using the CacheManager factory methods to cr= eate a singleton CacheManager or specifying a separate ehcache configuratio= n (ehcache.xml) for each CacheManager instance. 25 Oct 2017 19:37:48 INFO ConceptSimilarityServiceImpl - begin initializat= ion for concept graph: sct-rxnorm 25 Oct 2017 19:37:48 INFO ConceptDaoImpl - loading concept graph from file= :/C:/cn/resources/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.gz 25 Oct 2017 19:37:50 INFO ConceptDaoImpl - concept graph sct-rxnorm, verti= ces: 461241 25 Oct 2017 19:37:50 INFO ConceptSimilarityServiceImpl - initializing simi= larity measures 25 Oct 2017 19:37:50 INFO ConceptSimilarityServiceImpl - loading corpus in= focontent for corpusName=3D, conceptGraphName=3Dsct-rxnorm, conceptSetName= =3D 25 Oct 2017 19:37:51 WARN ConceptSimilarityServiceImpl - IC not found 25 Oct 2017 19:37:51 INFO ConceptSimilarityServiceImpl - end initializatio= n for concept graph: sct-rxnorm 25 Oct 2017 19:37:52 INFO Dialect - HHH000400: Using dialect: org.hibernat= e.dialect.SQLServerDialect 25 Oct 2017 19:37:52 INFO DocumentMapperServiceImpl - document table name = =3D dbo.document 25 Oct 2017 19:37:53 INFO POSTagger - POS tagger model file: org/apache/ct= akes/postagger/models/mayo-pos.zip 25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg= with config file =3D C:\cn\resources\org\apache\ctakes\lvg\data\config\lvg= .properties 25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - config file absolute p= ath =3D C:\cn\resources\org\apache\ctakes\lvg\data\config\lvg.properties 25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - cwd =3D C:\cn 25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - cd C:\cn\resources\org\a= pache\ctakes\lvg\ 25 Oct 2017 19:37:56 INFO ENGINE - open start - state not modified 25 Oct 2017 19:37:56 INFO ENGINE - dataFileCache open start 25 Oct 2017 19:37:56 INFO ENGINE - dataFileCache open end 25 Oct 2017 19:37:58 INFO LvgCmdApiResourceImpl - cd C:\cn 25 Oct 2017 19:37:58 INFO AssertionAnalysisEngine - scope model file: /C:/= cn/resources/org/apache/ctakes/assertion/models/scope.model 25 Oct 2017 19:37:58 INFO AssertionAnalysisEngine - cue model file: /C:/cn= /resources/org/apache/ctakes/assertion/models/cue.model 25 Oct 2017 19:37:58 INFO AssertionAnalysisEngine - pos model file: /C:/cn= /resources/org/apache/ctakes/assertion/models/pos.model 25 Oct 2017 19:37:58 WARN BatchRunner - This class cannot be used until CT= AKES-76 is implemented. 25 Oct 2017 19:37:58 WARN JarafeMEDecoder - This class cannot be used unti= l CTAKES-76 is implemented. Oct 25, 2017 7:37:58 PM org.apache.uima.resource.impl.ResourceManager_impl = initializeExternalResources WARNING: The external resource named assertionModelResourceImpl has been de= clared multiple times with different definitions. The definition of the res= ource in component /AggregatePlaintextUMLSProcessor/AssertionAnnotator/asse= rtionAnalysisEngine/ will be used. The definition in component /AggregateP= laintextUMLSProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ wi= ll be ignored. Oct 25, 2017 7:37:58 PM org.apache.uima.resource.impl.ResourceManager_impl = initializeExternalResources WARNING: The external resource named scopeModelResourceImpl has been declar= ed multiple times with different definitions. The definition of the resourc= e in component /AggregatePlaintextUMLSProcessor/AssertionAnnotator/assertio= nAnalysisEngine/ will be used. The definition in component /AggregatePlain= textUMLSProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ will b= e ignored. Oct 25, 2017 7:37:58 PM org.apache.uima.resource.impl.ResourceManager_impl = initializeExternalResources WARNING: The external resource named cueModelResourceImpl has been declared= multiple times with different definitions. The definition of the resource = in component /AggregatePlaintextUMLSProcessor/AssertionAnnotator/assertionA= nalysisEngine/ will be used. The definition in component /AggregatePlainte= xtUMLSProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ will be = ignored. Oct 25, 2017 7:37:58 PM org.apache.uima.resource.impl.ResourceManager_impl = initializeExternalResources WARNING: The external resource named enabledFeaturesResourceImpl has been d= eclared multiple times with different definitions. The definition of the re= source in component /AggregatePlaintextUMLSProcessor/AssertionAnnotator/ass= ertionAnalysisEngine/ will be used. The definition in component /Aggregate= PlaintextUMLSProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ w= ill be ignored. 25 Oct 2017 19:37:58 INFO ClearNLPDependencyParserAE - using Morphy analys= is? true Loading configuration. Loading feature templates. Loading lexica. Loading model: ...........................................................................= ............. Loading configuration. Loading feature templates. Loading model: . Loading configuration. Loading feature templates. Loading lexica. Loading model: ... Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: ....... Loading model: . Loading model: . Loading model: . Loading model: . Loading model: .......... 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Loading model: ............................. org.apache.uima.resource.ResourceInitializationException: Initialization of= CAS Processor with name "DBCollectionReader.xml" failed. =20 =09at org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initi= alize(CollectionProcessingEngine_impl.java:81) =09at org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingE= ngine(UIMAFramework_impl.java:420) =09at org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAF= ramework.java:918) =09at org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:573) =09at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105) =09at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713) Caused by: org.apache.uima.resource.ResourceConfigurationException: Initial= ization of CAS Processor with name "DBCollectionReader.xml" failed. =20 =09at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceInteg= ratedCasProcessor(CPEFactory.java:1101) =09at org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProces= sors(CPEFactory.java:547) =09at org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java= :253) =09at org.apache.uima.collection.impl.cpm.BaseCPMImpl.(BaseCPMImpl.ja= va:127) =09at org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initi= alize(CollectionProcessingEngine_impl.java:73) =09... 5 more Caused by: org.apache.uima.resource.ResourceInitializationException: Initia= lization of annotator class "org.apache.ctakes.ytex.uima.DBCollectionReader= " failed. (Descriptor: file:/c:/cn/desc/ctakes-ytex-uima/desc/collection_r= eader/DBCollectionReader.xml) =09at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini= tializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271) =09at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini= tialize(PrimitiveAnalysisEngine_impl.java:170) =09at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy= sisEngineFactory_impl.java:94) =09at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co= mpositeResourceFactory_impl.java:62) =09at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279) =09at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:331) =09at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav= a:448) =09at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceInteg= ratedCasProcessor(CPEFactory.java:1085) =09... 9 more Caused by: java.lang.IllegalArgumentException: SQL must not be null =09at org.springframework.util.Assert.notNull(Assert.java:112) =09at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:43= 2) =09at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:46= 4) =09at org.springframework.jdbc.core.JdbcTemplate.queryForList(JdbcTemplate.= java:495) =09at org.springframework.jdbc.core.simple.SimpleJdbcTemplate.queryForList(= SimpleJdbcTemplate.java:238) =09at org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCo= llectionReader.java:179) =09at org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCo= llectionReader.java:1) =09at org.springframework.transaction.support.TransactionTemplate.execute(T= ransactionTemplate.java:130) =09at org.apache.ctakes.ytex.uima.DBCollectionReader.loadDocumentIds(DBColl= ectionReader.java:173) =09at org.apache.ctakes.ytex.uima.DBCollectionReader.initialize(DBCollectio= nReader.java:116) =09at org.apache.uima.collection.CollectionReader_ImplBase.initialize(Colle= ctionReader_ImplBase.java:70) =09at org.apache.uima.analysis_engine.impl.compatibility.CollectionReaderAd= apter.initialize(CollectionReaderAdapter.java:87) =09at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini= tializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266) =09... 16 more {code} was: C:\cn\bin>SETLOCAL C:\cn\bin>set CURRENT_DIR=3DC:\cn\bin=20 C:\cn\bin>if not "" =3D=3D "" goto gotHome=20 C:\cn\bin>set CTAKES_HOME=3DC:\cn\bin=20 C:\cn\bin>if exist "C:\cn\bin\bin\runctakesCPE.bat" goto okHome=20 C:\cn\bin>cd ..=20 C:\cn>set CTAKES_HOME=3DC:\cn=20 C:\cn>if exist "C:\cn\bin\runctakesCPE.bat" goto okHome=20 C:\cn>cd C:\cn=20 C:\cn>java -cp "C:\cn/desc/;C:\cn/resources/;C:\cn/lib/*" -Dlog4j.configur= ation=3Dfile:/C:\cn/config/log4j.xml -Xms512M -Xmx3g org.apache.uima.tools.= cpm.CpmFrame=20 Oct 25, 2017 7:37:12 PM java.util.prefs.WindowsPreferences WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at r= oot 0x80000002. Windows RegCreateKeyEx(...) returned error code 5. log4j: reset attribute=3D "false". log4j: Threshold =3D"null". log4j: Retreiving an instance of org.apache.log4j.Logger. log4j: Setting [ProgressAppender] additivity to [false]. log4j: Level value for ProgressAppender is [INFO]. log4j: ProgressAppender level set to INFO log4j: Class name: [org.apache.log4j.ConsoleAppender] log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" log4j: Setting property [conversionPattern] to [%m]. log4j: Adding appender named [noEolAppender] to category [ProgressAppender]= . log4j: Retreiving an instance of org.apache.log4j.Logger. log4j: Setting [ProgressDone] additivity to [false]. log4j: Level value for ProgressDone is [INFO]. log4j: ProgressDone level set to INFO log4j: Class name: [org.apache.log4j.ConsoleAppender] log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" log4j: Setting property [conversionPattern] to [%m%n]. log4j: Adding appender named [eolAppender] to category [ProgressDone]. log4j: Level value for root is [INFO]. log4j: root level set to INFO log4j: Class name: [org.apache.log4j.ConsoleAppender] log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} %5= p %c{1} - %m%n]. log4j: Adding appender named [consoleAppender] to category [root]. 25 Oct 2017 19:37:23 INFO Chunker - Chunker model file: org/apache/ctakes/= chunker/models/chunker-model.zip 25 Oct 2017 19:37:27 INFO TokenizerAnnotatorPTB - Initializing org.apache.= ctakes.core.ae.TokenizerAnnotatorPTB 25 Oct 2017 19:37:27 INFO ContextDependentTokenizerAnnotator - Finite stat= e machines loaded. 25 Oct 2017 19:37:27 INFO ApplicationContextHolder - loading ytex.properti= es from: file:/C:/cn/resources/org/apache/ctakes/ytex/ytex.properties 25 Oct 2017 19:37:27 INFO ApplicationContextHolder - beanRefContext=3Dclas= spath*:org/apache/ctakes/ytex/uima/beanRefContext.xml 25 Oct 2017 19:37:30 INFO InitableJdbcConnectionResourceImpl - Connection = established to: jdbc:sqlserver://localhost;databaseName=3DUMLS;integratedSe= curity=3Dtrue 25 Oct 2017 19:37:30 INFO DictionaryLookupAnnotator - Parsing descriptor: = C:\cn\resources\org\apache\ctakes\ytex\dictionary\lookup\LookupDesc_SNOMED.= xml 25 Oct 2017 19:37:30 INFO FirstTokenPermLookupInitializerImpl - Exclusion = tagset loaded: [pp, pdt, prp$, vbn, vbp, wdt, ls, vbz, dt, pos, md, wp, cc,= cd, in, pp$, wrb, vb, prp, ex, vbd, vbg, to, wps, rp] 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using left , right scope size= s: 10 , 10 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using scope order: LEFT,RIGHT 25 Oct 2017 19:37:31 INFO ContextAnnotator - SCOPE ORDER: [1, 3] 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context analyzer: org.a= pache.ctakes.necontexts.status.StatusContextAnalyzer 25 Oct 2017 19:37:31 INFO StatusContextAnalyzer - initBoundaryData() calle= d for ContextInitializer 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context consumer: org.a= pache.ctakes.necontexts.status.StatusContextHitConsumer 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using lookup window type: org= .apache.ctakes.typesystem.type.textspan.Sentence 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using focus type: org.apache.= ctakes.typesystem.type.textsem.IdentifiedAnnotation 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context type: org.apach= e.ctakes.typesystem.type.syntax.BaseToken 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using left , right scope size= s: 7 , 7 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using scope order: LEFT,RIGHT 25 Oct 2017 19:37:31 INFO ContextAnnotator - SCOPE ORDER: [1, 3] 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context analyzer: org.a= pache.ctakes.necontexts.negation.NegationContextAnalyzer 25 Oct 2017 19:37:31 INFO NegationContextAnalyzer - initBoundaryData() cal= led for ContextInitializer 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context consumer: org.a= pache.ctakes.necontexts.negation.NegationContextHitConsumer 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using lookup window type: org= .apache.ctakes.typesystem.type.textspan.Sentence 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using focus type: org.apache.= ctakes.typesystem.type.textsem.IdentifiedAnnotation 25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context type: org.apach= e.ctakes.typesystem.type.syntax.BaseToken 25 Oct 2017 19:37:31 INFO SentenceDetector - [SegmentsToSkip, SentenceMode= lFile] 25 Oct 2017 19:37:31 INFO SentenceDetector - Sentence detector model file:= org/apache/ctakes/core/sentdetect/sd-med-model.zip 25 Oct 2017 19:37:31 INFO ClassPathXmlApplicationContext - Refreshing org.= springframework.context.support.ClassPathXmlApplicationContext@1b6e40c5: st= artup date [Wed Oct 25 19:37:31 IST 2017]; root of context hierarchy 25 Oct 2017 19:37:32 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from URL [jar:file:/C:/cn/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/= ctakes/ytex/uima/beanRefContext.xml] 25 Oct 2017 19:37:32 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from URL [jar:file:/C:/cn/lib/ctakes-ytex-web-4.0.0-classes.jar!/org= /apache/ctakes/ytex/uima/beanRefContext.xml] 25 Oct 2017 19:37:32 INFO DefaultListableBeanFactory - Overriding bean def= inition for bean 'ytexApplicationContext': replacing [Generic bean: class [= org.springframework.context.support.ClassPathXmlApplicationContext]; scope= =3D; abstract=3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; dependencyCheck= =3D0; autowireCandidate=3Dtrue; primary=3Dfalse; factoryBeanName=3Dnull; fa= ctoryMethodName=3Dnull; initMethodName=3Dnull; destroyMethodName=3Dnull; de= fined in URL [jar:file:/C:/cn/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/cta= kes/ytex/uima/beanRefContext.xml]] with [Generic bean: class [org.springfra= mework.context.support.ClassPathXmlApplicationContext]; scope=3D; abstract= =3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; dependencyCheck=3D0; autowire= Candidate=3Dtrue; primary=3Dfalse; factoryBeanName=3Dnull; factoryMethodNam= e=3Dnull; initMethodName=3Dnull; destroyMethodName=3Dnull; defined in URL [= jar:file:/C:/cn/lib/ctakes-ytex-web-4.0.0-classes.jar!/org/apache/ctakes/yt= ex/uima/beanRefContext.xml]] 25 Oct 2017 19:37:32 INFO DefaultListableBeanFactory - Pre-instantiating s= ingletons in org.springframework.beans.factory.support.DefaultListableBeanF= actory@7ae65cd2: defining beans [ytexApplicationContext]; root of factory h= ierarchy 25 Oct 2017 19:37:32 INFO ClassPathXmlApplicationContext - Refreshing org.= springframework.context.support.ClassPathXmlApplicationContext@7d3b1153: st= artup date [Wed Oct 25 19:37:32 IST 2017]; root of context hierarchy 25 Oct 2017 19:37:32 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from class path resource [org/apache/ctakes/ytex/beans-datasource.xm= l] 25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml] 25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from class path resource [org/apache/ctakes/ytex/beans-kernel-sim.xm= l] 25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from class path resource [org/apache/ctakes/ytex/uima/beans-uima.hbm= .xml] 25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-dao= .xml] 25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean defin= itions from class path resource [org/apache/ctakes/ytex/uima/beans-uima-map= per.xml] 25 Oct 2017 19:37:33 INFO DefaultListableBeanFactory - Overriding bean def= inition for bean 'mapperOperation': replacing [Root bean: class [org.spring= framework.aop.aspectj.AspectJExpressionPointcut]; scope=3Dprototype; abstra= ct=3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; dependencyCheck=3D0; autowi= reCandidate=3Dtrue; primary=3Dfalse; factoryBeanName=3Dnull; factoryMethodN= ame=3Dnull; initMethodName=3Dnull; destroyMethodName=3Dnull] with [Root bea= n: class [org.springframework.aop.aspectj.AspectJExpressionPointcut]; scope= =3Dprototype; abstract=3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; depende= ncyCheck=3D0; autowireCandidate=3Dtrue; primary=3Dfalse; factoryBeanName=3D= null; factoryMethodName=3Dnull; initMethodName=3Dnull; destroyMethodName=3D= null] 25 Oct 2017 19:37:34 INFO PropertyPlaceholderConfigurer - Loading properti= es file from class path resource [org/apache/ctakes/ytex/ytex-default.prope= rties] 25 Oct 2017 19:37:34 INFO PropertyPlaceholderConfigurer - Loading properti= es file from class path resource [org/apache/ctakes/ytex/ytex.properties] 25 Oct 2017 19:37:34 INFO PropertyPlaceholderConfigurer - Loading properti= es file from class path resource [org/apache/ctakes/ytex/ytex-umls.properti= es] 25 Oct 2017 19:37:34 INFO DefaultListableBeanFactory - Pre-instantiating s= ingletons in org.springframework.beans.factory.support.DefaultListableBeanF= actory@202217c7: defining beans [org.springframework.beans.factory.config.P= ropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSourc= e,txAdvice,txTemplate,txTemplateNew,transactionManager,org.springframework.= aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterO= peration,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEva= luatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutA= dvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#= 1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.s= pringframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springfr= amework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework= .aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.su= pport.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.D= efaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,w= ekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wek= aResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatr= ixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel= ,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGen= erator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libS= VMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDat= aExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatt= erFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterF= actory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,info= gainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEval= uator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEval= uator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService,conceptSimi= larityService,abstractConceptKernel,abstractLinKernel,abstractSemanticSimKe= rnel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambiguator= ,sessionFactory,ytexDaoOperation,org.springframework.aop.support.DefaultBea= nFactoryPointcutAdvisor#8,documentDao,namedEntityRegexDao,segmentRegexDao,o= rg.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601C= onverter,documentMapperService]; root of factory hierarchy 25 Oct 2017 19:37:34 INFO PropertiesFactoryBean - Loading properties file = from class path resource [org/apache/ctakes/ytex/ytex.properties] 25 Oct 2017 19:37:39 INFO Version - HCANN000001: Hibernate Commons Annotat= ions {4.0.2.Final} 25 Oct 2017 19:37:39 INFO Version - HHH000412: Hibernate Core {4.2.6.Final= } 25 Oct 2017 19:37:39 INFO Environment - HHH000206: hibernate.properties no= t found 25 Oct 2017 19:37:39 INFO Environment - HHH000021: Bytecode provider name = : javassist 25 Oct 2017 19:37:42 INFO Dialect - HHH000400: Using dialect: org.hibernat= e.dialect.SQLServerDialect 25 Oct 2017 19:37:43 WARN RootClass - HHH000038: Composite-id class does n= ot override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainme= ntLink 25 Oct 2017 19:37:43 WARN RootClass - HHH000039: Composite-id class does n= ot override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContain= mentLink 25 Oct 2017 19:37:43 INFO TransactionFactoryInitiator - HHH000399: Using d= efault transaction strategy (direct JDBC transactions) 25 Oct 2017 19:37:43 INFO ASTQueryTranslatorFactory - HHH000397: Using AST= QueryTranslatorFactory 25 Oct 2017 19:37:44 INFO UpdateTimestampsCache - HHH000250: Starting upda= te timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCach= e 25 Oct 2017 19:37:44 INFO StandardQueryCache - HHH000248: Starting query c= ache at region: org.hibernate.cache.internal.StandardQueryCache 25 Oct 2017 19:37:44 INFO TableGenerator - HHH000398: Explicit segment val= ue for id generator [dbo.hibernate_sequences.sequence_name] suggested; usin= g default [default] 25 Oct 2017 19:37:45 WARN AbstractEhcacheRegionFactory - HHH020003: Could = not find a specific ehcache configuration for cache named [org.apache.ctake= s.ytex.uima.model.UimaType]; using defaults. 25 Oct 2017 19:37:45 WARN EhcacheAccessStrategyFactoryImpl - HHH020007: re= ad-only cache configured for mutable entity [org.apache.ctakes.ytex.uima.mo= del.UimaType] 25 Oct 2017 19:37:46 INFO HibernateTransactionManager - Using DataSource [= org.apache.commons.dbcp.BasicDataSource@53ff623b] of Hibernate SessionFacto= ry for HibernateTransactionManager 25 Oct 2017 19:37:47 INFO EhCacheManagerFactoryBean - Initializing EHCache= CacheManager 25 Oct 2017 19:37:47 WARN CacheManager - Creating a new instance of CacheM= anager using the diskStorePath "C:\Users\Sathya\AppData\Local\Temp\" which = is already used by an existing CacheManager. The source of the configuration was net.sf.ehcache.config.generator.Configu= rationSource$InputStreamConfigurationSource@3cdbe5e4. The diskStore path for this CacheManager will be set to C:\Users\Sathya\App= Data\Local\Temp\\ehcache_auto_created_1508940467387. To avoid this warning consider using the CacheManager factory methods to cr= eate a singleton CacheManager or specifying a separate ehcache configuratio= n (ehcache.xml) for each CacheManager instance. 25 Oct 2017 19:37:48 INFO ConceptSimilarityServiceImpl - begin initializat= ion for concept graph: sct-rxnorm 25 Oct 2017 19:37:48 INFO ConceptDaoImpl - loading concept graph from file= :/C:/cn/resources/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.gz 25 Oct 2017 19:37:50 INFO ConceptDaoImpl - concept graph sct-rxnorm, verti= ces: 461241 25 Oct 2017 19:37:50 INFO ConceptSimilarityServiceImpl - initializing simi= larity measures 25 Oct 2017 19:37:50 INFO ConceptSimilarityServiceImpl - loading corpus in= focontent for corpusName=3D, conceptGraphName=3Dsct-rxnorm, conceptSetName= =3D 25 Oct 2017 19:37:51 WARN ConceptSimilarityServiceImpl - IC not found 25 Oct 2017 19:37:51 INFO ConceptSimilarityServiceImpl - end initializatio= n for concept graph: sct-rxnorm 25 Oct 2017 19:37:52 INFO Dialect - HHH000400: Using dialect: org.hibernat= e.dialect.SQLServerDialect 25 Oct 2017 19:37:52 INFO DocumentMapperServiceImpl - document table name = =3D dbo.document 25 Oct 2017 19:37:53 INFO POSTagger - POS tagger model file: org/apache/ct= akes/postagger/models/mayo-pos.zip 25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg= with config file =3D C:\cn\resources\org\apache\ctakes\lvg\data\config\lvg= .properties 25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - config file absolute p= ath =3D C:\cn\resources\org\apache\ctakes\lvg\data\config\lvg.properties 25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - cwd =3D C:\cn 25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - cd C:\cn\resources\org\a= pache\ctakes\lvg\ 25 Oct 2017 19:37:56 INFO ENGINE - open start - state not modified 25 Oct 2017 19:37:56 INFO ENGINE - dataFileCache open start 25 Oct 2017 19:37:56 INFO ENGINE - dataFileCache open end 25 Oct 2017 19:37:58 INFO LvgCmdApiResourceImpl - cd C:\cn 25 Oct 2017 19:37:58 INFO AssertionAnalysisEngine - scope model file: /C:/= cn/resources/org/apache/ctakes/assertion/models/scope.model 25 Oct 2017 19:37:58 INFO AssertionAnalysisEngine - cue model file: /C:/cn= /resources/org/apache/ctakes/assertion/models/cue.model 25 Oct 2017 19:37:58 INFO AssertionAnalysisEngine - pos model file: /C:/cn= /resources/org/apache/ctakes/assertion/models/pos.model 25 Oct 2017 19:37:58 WARN BatchRunner - This class cannot be used until CT= AKES-76 is implemented. 25 Oct 2017 19:37:58 WARN JarafeMEDecoder - This class cannot be used unti= l CTAKES-76 is implemented. Oct 25, 2017 7:37:58 PM org.apache.uima.resource.impl.ResourceManager_impl = initializeExternalResources WARNING: The external resource named assertionModelResourceImpl has been de= clared multiple times with different definitions. The definition of the res= ource in component /AggregatePlaintextUMLSProcessor/AssertionAnnotator/asse= rtionAnalysisEngine/ will be used. The definition in component /AggregateP= laintextUMLSProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ wi= ll be ignored. Oct 25, 2017 7:37:58 PM org.apache.uima.resource.impl.ResourceManager_impl = initializeExternalResources WARNING: The external resource named scopeModelResourceImpl has been declar= ed multiple times with different definitions. The definition of the resourc= e in component /AggregatePlaintextUMLSProcessor/AssertionAnnotator/assertio= nAnalysisEngine/ will be used. The definition in component /AggregatePlain= textUMLSProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ will b= e ignored. Oct 25, 2017 7:37:58 PM org.apache.uima.resource.impl.ResourceManager_impl = initializeExternalResources WARNING: The external resource named cueModelResourceImpl has been declared= multiple times with different definitions. The definition of the resource = in component /AggregatePlaintextUMLSProcessor/AssertionAnnotator/assertionA= nalysisEngine/ will be used. The definition in component /AggregatePlainte= xtUMLSProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ will be = ignored. Oct 25, 2017 7:37:58 PM org.apache.uima.resource.impl.ResourceManager_impl = initializeExternalResources WARNING: The external resource named enabledFeaturesResourceImpl has been d= eclared multiple times with different definitions. The definition of the re= source in component /AggregatePlaintextUMLSProcessor/AssertionAnnotator/ass= ertionAnalysisEngine/ will be used. The definition in component /Aggregate= PlaintextUMLSProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ w= ill be ignored. 25 Oct 2017 19:37:58 INFO ClearNLPDependencyParserAE - using Morphy analys= is? true Loading configuration. Loading feature templates. Loading lexica. Loading model: ...........................................................................= ............. Loading configuration. Loading feature templates. Loading model: . Loading configuration. Loading feature templates. Loading lexica. Loading model: ... Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: . Loading model: ....... Loading model: . Loading model: . Loading model: . Loading model: . Loading model: .......... 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Loading model: ............................. org.apache.uima.resource.ResourceInitializationException: Initialization of= CAS Processor with name "DBCollectionReader.xml" failed. =20 =09at org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initi= alize(CollectionProcessingEngine_impl.java:81) =09at org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingE= ngine(UIMAFramework_impl.java:420) =09at org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAF= ramework.java:918) =09at org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:573) =09at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105) =09at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713) Caused by: org.apache.uima.resource.ResourceConfigurationException: Initial= ization of CAS Processor with name "DBCollectionReader.xml" failed. =20 =09at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceInteg= ratedCasProcessor(CPEFactory.java:1101) =09at org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProces= sors(CPEFactory.java:547) =09at org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java= :253) =09at org.apache.uima.collection.impl.cpm.BaseCPMImpl.(BaseCPMImpl.ja= va:127) =09at org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initi= alize(CollectionProcessingEngine_impl.java:73) =09... 5 more Caused by: org.apache.uima.resource.ResourceInitializationException: Initia= lization of annotator class "org.apache.ctakes.ytex.uima.DBCollectionReader= " failed. (Descriptor: file:/c:/cn/desc/ctakes-ytex-uima/desc/collection_r= eader/DBCollectionReader.xml) =09at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini= tializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271) =09at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini= tialize(PrimitiveAnalysisEngine_impl.java:170) =09at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy= sisEngineFactory_impl.java:94) =09at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co= mpositeResourceFactory_impl.java:62) =09at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279) =09at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:331) =09at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav= a:448) =09at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceInteg= ratedCasProcessor(CPEFactory.java:1085) =09... 9 more Caused by: java.lang.IllegalArgumentException: SQL must not be null =09at org.springframework.util.Assert.notNull(Assert.java:112) =09at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:43= 2) =09at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:46= 4) =09at org.springframework.jdbc.core.JdbcTemplate.queryForList(JdbcTemplate.= java:495) =09at org.springframework.jdbc.core.simple.SimpleJdbcTemplate.queryForList(= SimpleJdbcTemplate.java:238) =09at org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCo= llectionReader.java:179) =09at org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCo= llectionReader.java:1) =09at org.springframework.transaction.support.TransactionTemplate.execute(T= ransactionTemplate.java:130) =09at org.apache.ctakes.ytex.uima.DBCollectionReader.loadDocumentIds(DBColl= ectionReader.java:173) =09at org.apache.ctakes.ytex.uima.DBCollectionReader.initialize(DBCollectio= nReader.java:116) =09at org.apache.uima.collection.CollectionReader_ImplBase.initialize(Colle= ctionReader_ImplBase.java:70) =09at org.apache.uima.analysis_engine.impl.compatibility.CollectionReaderAd= apter.initialize(CollectionReaderAdapter.java:87) =09at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini= tializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266) =09... 16 more > could not able to run ytex with DBCollection reader=20 > ---------------------------------------------------- > > Key: CTAKES-469 > URL: https://issues.apache.org/jira/browse/CTAKES-469 > Project: cTAKES > Issue Type: Bug > Components: ctakes-ytex, ctakes-ytex-uima > Affects Versions: 4.0.0, 4.0.1 > Environment: windows 10, java 8, catkes-4 , MS SQL SERVER fix-Set= upAuiFirstWord.CTAKES-334.svn-01.patch > Reporter: athyanarayana > Priority: Critical > Labels: error > Fix For: 4.0.0, 4.0.1 > > Attachments: out1.txt, ytexerror.png > > Original Estimate: 168h > Remaining Estimate: 168h > > i cant abel to run ctakes CPE with ytex db collection reder , below is th= e error i am getting=20 > Loading model: > ................................ > Loading model: > ............................. > org.apache.uima.resource.ResourceInitializationException: Initialization = of CAS Processor with name "DBCollectionReader.xml" failed. =20 > =09at org.apache.uima.collection.impl.CollectionProcessingEngine_impl.ini= tialize(CollectionProcessingEngine_impl.java:81) > =09at org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessin= gEngine(UIMAFramework_impl.java:420) > =09at org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIM= AFramework.java:918) > =09at org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:57= 3) > =09at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105) > =09at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713) > Caused by: org.apache.uima.resource.ResourceConfigurationException: Initi= alization of CAS Processor with name "DBCollectionReader.xml" failed. =20 > =09at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceInt= egratedCasProcessor(CPEFactory.java:1101) > =09at org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProc= essors(CPEFactory.java:547) > =09at org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.ja= va:253) > =09at org.apache.uima.collection.impl.cpm.BaseCPMImpl.(BaseCPMImpl.= java:127) > =09at org.apache.uima.collection.impl.CollectionProcessingEngine_impl.ini= tialize(CollectionProcessingEngine_impl.java:73) > =09... 5 more > Caused by: org.apache.uima.resource.ResourceInitializationException: Init= ialization of annotator class "org.apache.ctakes.ytex.uima.DBCollectionRead= er" failed. (Descriptor: file:/c:/cn/desc/ctakes-ytex-uima/desc/collection= _reader/DBCollectionReader.xml) > =09at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.i= nitializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271) > =09at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.i= nitialize(PrimitiveAnalysisEngine_impl.java:170) > =09at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Ana= lysisEngineFactory_impl.java:94) > =09at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(= CompositeResourceFactory_impl.java:62) > =09at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:27= 9) > =09at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:33= 1) > =09at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.j= ava:448) > =09at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceInt= egratedCasProcessor(CPEFactory.java:1085) > =09... 9 more > Caused by: java.lang.IllegalArgumentException: SQL must not be null > =09at org.springframework.util.Assert.notNull(Assert.java:112) > =09at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:= 432) > =09at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:= 464) > =09at org.springframework.jdbc.core.JdbcTemplate.queryForList(JdbcTemplat= e.java:495) > =09at org.springframework.jdbc.core.simple.SimpleJdbcTemplate.queryForLis= t(SimpleJdbcTemplate.java:238) > =09at org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DB= CollectionReader.java:179) > =09at org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DB= CollectionReader.java:1) > =09at org.springframework.transaction.support.TransactionTemplate.execute= (TransactionTemplate.java:130) > =09at org.apache.ctakes.ytex.uima.DBCollectionReader.loadDocumentIds(DBCo= llectionReader.java:173) > =09at org.apache.ctakes.ytex.uima.DBCollectionReader.initialize(DBCollect= ionReader.java:116) > =09at org.apache.uima.collection.CollectionReader_ImplBase.initialize(Col= lectionReader_ImplBase.java:70) > =09at org.apache.uima.analysis_engine.impl.compatibility.CollectionReader= Adapter.initialize(CollectionReaderAdapter.java:87) > =09at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.i= nitializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266) > =09... 16 more -- This message was sent by Atlassian JIRA (v6.4.14#64029)