Return-Path: X-Original-To: apmail-ctakes-user-archive@www.apache.org Delivered-To: apmail-ctakes-user-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 6B712177DB for ; Wed, 5 Nov 2014 19:41:55 +0000 (UTC) Received: (qmail 37636 invoked by uid 500); 5 Nov 2014 19:41:55 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 37603 invoked by uid 500); 5 Nov 2014 19:41:55 -0000 Mailing-List: contact user-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: user@ctakes.apache.org Delivered-To: mailing list user@ctakes.apache.org Received: (qmail 37592 invoked by uid 99); 5 Nov 2014 19:41:54 -0000 Received: from nike.apache.org (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Wed, 05 Nov 2014 19:41:54 +0000 X-ASF-Spam-Status: No, hits=1.5 required=5.0 tests=HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (nike.apache.org: domain of vngarla@gmail.com designates 209.85.217.173 as permitted sender) Received: from [209.85.217.173] (HELO mail-lb0-f173.google.com) (209.85.217.173) by apache.org (qpsmtpd/0.29) with ESMTP; Wed, 05 Nov 2014 19:41:27 +0000 Received: by mail-lb0-f173.google.com with SMTP id n15so1298959lbi.18 for ; Wed, 05 Nov 2014 11:40:41 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=Rg3d817IHg7yK8ebmhrPtuaRIw/yt31bvZt7J28gaV0=; b=zyRnUCGtfO03OIftg6fvRRcXmivbs0enugX1w0Du6AujS2eJ+A+L78lSo1LeH694gv 0/l4LU7nH6I6CTsmXpg7PJVY2IQuXJbU2bl0op8LfpaJPSzD0RRo/ueA8rcY3GrDy/p+ DCKIwWKRCv55gij7+2+g0t5OWc4sor/pt4hnc9Vdckug3/7wb9Y3C6DXurLjqTFuUTbT 8vPuckt9RFIjZRMTUPNOwHzyty9KIxnEOPFy7ybpNlUVinht3x/vKvm/DLhAhpzV9ddb 0nSRABuNDqp0i2yOy/DDpyT+J8N1m7ynEvMDTTuaAb3VoPvwivxHVtR0nu030f6oAXKO hiyg== MIME-Version: 1.0 X-Received: by 10.112.87.162 with SMTP id az2mr69581435lbb.15.1415216441721; Wed, 05 Nov 2014 11:40:41 -0800 (PST) Received: by 10.152.9.229 with HTTP; Wed, 5 Nov 2014 11:40:41 -0800 (PST) In-Reply-To: References: Date: Wed, 5 Nov 2014 20:40:41 +0100 Message-ID: Subject: Re: Classpath for conceptGraph in ytex From: vijay garla To: "user@ctakes.apache.org" Content-Type: multipart/alternative; boundary=001a11347e0a4a07df050721c17f X-Virus-Checked: Checked by ClamAV on apache.org --001a11347e0a4a07df050721c17f Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable It looks like there is a trailing space after sct-umls. Check your ytex.properties file and make sure there is no trailing space after the ytex.conceptGraphName property value On Wed, Nov 5, 2014 at 8:35 PM, Natalia Connolly < natalia.v.connolly@gmail.com> wrote: > Well, it't not really an error - ytex runs fine, it's just that the word > sense disambiguation remains disabled without conceptGraph, and I really > need it. Here's the full log of the initialization step, with the releva= nt > parts highlighted in yellow: > > >bin/runctakesCPE.sh > Nov 5 14:27:33 P13-7415 java[15257] : CGContextGetCTM: invalid > context 0x0 > Nov 5 14:27:33 P13-7415 java[15257] : CGContextSetBaseCTM: invali= d > context 0x0 > Nov 5 14:27:33 P13-7415 java[15257] : CGContextGetCTM: invalid > context 0x0 > Nov 5 14:27:33 P13-7415 java[15257] : CGContextSetBaseCTM: invali= d > context 0x0 > log4j: reset attribute=3D "false". > log4j: Threshold =3D"null". > 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} > %5p %c{1} - %m%n]. > log4j: Adding appender named [consoleAppender] to category [root]. > 05 Nov 2014 14:27:34 INFO ClearNLPDependencyParserAE - using Morphy > analysis? true > Loading configuration. > Loading feature templates. > Loading lexica. > Loading model: > > .........................................................................= ............... > 05 Nov 2014 14:27:48 INFO TokenizerAnnotatorPTB - Initializing > org.apache.ctakes.core.ae.TokenizerAnnotatorPTB > 05 Nov 2014 14:27:48 INFO ContextDependentTokenizerAnnotator - Finite > state machines loaded. > 05 Nov 2014 14:27:48 INFO ContextAnnotator - SCOPE ORDER: [1, 3] > 05 Nov 2014 14:27:49 INFO StatusContextAnalyzer - initBoundaryData() > called for ContextInitializer > 05 Nov 2014 14:27:49 INFO ContextAnnotator - SCOPE ORDER: [1, 3] > 05 Nov 2014 14:27:49 INFO NegationContextAnalyzer - initBoundaryData() > called for ContextInitializer > 05 Nov 2014 14:27:49 INFO ApplicationContextHolder - loading > ytex.properties from: > file:/usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/ytex= .properties > 05 Nov 2014 14:27:49 INFO ApplicationContextHolder - > beanRefContext=3Dclasspath*:org/apache/ctakes/ytex/uima/beanRefContext.xm= l > 05 Nov 2014 14:27:49 INFO ClassPathXmlApplicationContext - Refreshing > org.springframework.context.support.ClassPathXmlApplicationContext@3a9d23= c0: > startup date [Wed Nov 05 14:27:49 EST 2014]; root of context hierarchy > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from URL > [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-res-3.2.0.jar!/o= rg/apache/ctakes/ytex/uima/beanRefContext.xml] > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from URL > [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-web-3.2.0-classe= s.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml] > 05 Nov 2014 14:27:49 INFO DefaultListableBeanFactory - Overriding bean > definition for bean 'ytexApplicationContext': replacing [Generic bean: > class [org.springframework.context.support.ClassPathXmlApplicationContext= ]; > scope=3D; abstract=3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; dependenc= yCheck=3D0; > autowireCandidate=3Dtrue; primary=3Dfalse; factoryBeanName=3Dnull; > factoryMethodName=3Dnull; initMethodName=3Dnull; destroyMethodName=3Dnull= ; > defined in URL > [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-res-3.2.0.jar!/o= rg/apache/ctakes/ytex/uima/beanRefContext.xml]] > with [Generic bean: class > [org.springframework.context.support.ClassPathXmlApplicationContext]; > scope=3D; abstract=3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; dependenc= yCheck=3D0; > autowireCandidate=3Dtrue; primary=3Dfalse; factoryBeanName=3Dnull; > factoryMethodName=3Dnull; initMethodName=3Dnull; destroyMethodName=3Dnull= ; > defined in URL > [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-web-3.2.0-classe= s.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]] > 05 Nov 2014 14:27:49 INFO DefaultListableBeanFactory - Pre-instantiating > singletons in > org.springframework.beans.factory.support.DefaultListableBeanFactory@271d= 5641: > defining beans [ytexApplicationContext]; root of factory hierarchy > 05 Nov 2014 14:27:49 INFO ClassPathXmlApplicationContext - Refreshing > org.springframework.context.support.ClassPathXmlApplicationContext@418342= 2d: > startup date [Wed Nov 05 14:27:49 EST 2014]; root of context hierarchy > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from class path resource > [org/apache/ctakes/ytex/beans-datasource.xml] > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from class path resource > [org/apache/ctakes/ytex/beans-kernel.xml] > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from class path resource > [org/apache/ctakes/ytex/beans-kernel-sim.xml] > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from class path resource > [org/apache/ctakes/ytex/uima/beans-uima.hbm.xml] > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from class path resource > [org/apache/ctakes/ytex/uima/beans-uima-dao.xml] > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from class path resource > [org/apache/ctakes/ytex/uima/beans-uima-mapper.xml] > 05 Nov 2014 14:27:49 INFO DefaultListableBeanFactory - Overriding bean > definition for bean 'mapperOperation': replacing [Root bean: class > [org.springframework.aop.aspectj.AspectJExpressionPointcut]; > scope=3Dprototype; abstract=3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; > dependencyCheck=3D0; autowireCandidate=3Dtrue; primary=3Dfalse; > factoryBeanName=3Dnull; factoryMethodName=3Dnull; initMethodName=3Dnull; > destroyMethodName=3Dnull] with [Root bean: class > [org.springframework.aop.aspectj.AspectJExpressionPointcut]; > scope=3Dprototype; abstract=3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; > dependencyCheck=3D0; autowireCandidate=3Dtrue; primary=3Dfalse; > factoryBeanName=3Dnull; factoryMethodName=3Dnull; initMethodName=3Dnull; > destroyMethodName=3Dnull] > 05 Nov 2014 14:27:49 INFO PropertyPlaceholderConfigurer - Loading > properties file from class path resource > [org/apache/ctakes/ytex/ytex-default.properties] > 05 Nov 2014 14:27:49 INFO PropertyPlaceholderConfigurer - Loading > properties file from class path resource > [org/apache/ctakes/ytex/ytex.properties] > 05 Nov 2014 14:27:49 INFO PropertyPlaceholderConfigurer - Loading > properties file from class path resource > [org/apache/ctakes/ytex/ytex-umls.properties] > 05 Nov 2014 14:27:49 INFO DefaultListableBeanFactory - Pre-instantiating > singletons in > org.springframework.beans.factory.support.DefaultListableBeanFactory@26df= 536f: > defining beans > [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0= ,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTempla= teNew,transactionManager,org.springframework.aop.config.internalAutoProxyCr= eator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOp= eration,treeOperation,utilOperation,corpusEvaluatorOperation,org.springfram= ework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.a= op.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.supp= ort.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.Def= aultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBea= nFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactor= yPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointc= utAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvis= or#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatr= ixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEva= luationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instance= TreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cache= Manager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifi= erEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlin= Parser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterF= actory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFacto= ry,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,w= ekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch= ,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,int= rinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstract= KernelCacheAdvice,pageRankService,conceptSimilarityService,abstractConceptK= ernel,abstractLinKernel,abstractSemanticSimKernel,mainSuiSemanticTypeKernel= ,tuiSemanticTypeKernel,wordSenseDisambiguator,sessionFactory,ytexDaoOperati= on,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#8,docu= mentDao,namedEntityRegexDao,segmentRegexDao,org.springframework.aop.support= .DefaultBeanFactoryPointcutAdvisor#9,ISO8601Converter,documentMapperService= ]; > root of factory hierarchy > 05 Nov 2014 14:27:49 INFO PropertiesFactoryBean - Loading properties fil= e > from class path resource [org/apache/ctakes/ytex/ytex.properties] > 05 Nov 2014 14:27:50 INFO Version - HCANN000001: Hibernate Commons > Annotations {4.0.2.Final} > 05 Nov 2014 14:27:50 INFO Version - HHH000412: Hibernate Core > {4.2.6.Final} > 05 Nov 2014 14:27:50 INFO Environment - HHH000206: hibernate.properties > not found > 05 Nov 2014 14:27:50 INFO Environment - HHH000021: Bytecode provider nam= e > : javassist > 05 Nov 2014 14:27:51 INFO Dialect - HHH000400: Using dialect: > org.hibernate.dialect.MySQLMyISAMDialect > 05 Nov 2014 14:27:51 WARN RootClass - HHH000038: Composite-id class does > not override equals(): > org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink > 05 Nov 2014 14:27:51 WARN RootClass - HHH000039: Composite-id class does > not override hashCode(): > org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink > 05 Nov 2014 14:27:51 INFO TransactionFactoryInitiator - HHH000399: Using > default transaction strategy (direct JDBC transactions) > 05 Nov 2014 14:27:51 INFO ASTQueryTranslatorFactory - HHH000397: Using > ASTQueryTranslatorFactory > 05 Nov 2014 14:27:51 INFO UpdateTimestampsCache - HHH000250: Starting > update timestamps cache at region: > org.hibernate.cache.spi.UpdateTimestampsCache > 05 Nov 2014 14:27:51 INFO StandardQueryCache - HHH000248: Starting query > cache at region: org.hibernate.cache.internal.StandardQueryCache > 05 Nov 2014 14:27:51 INFO TableGenerator - HHH000398: Explicit segment > value for id generator [ytex.hibernate_sequences.sequence_name] suggested= ; > using default [default] > 05 Nov 2014 14:27:51 WARN AbstractEhcacheRegionFactory - HHH020003: Coul= d > not find a specific ehcache configuration for cache named > [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults. > 05 Nov 2014 14:27:51 WARN EhcacheAccessStrategyFactoryImpl - HHH020007: > read-only cache configured for mutable entity > [org.apache.ctakes.ytex.uima.model.UimaType] > 05 Nov 2014 14:27:52 INFO HibernateTransactionManager - Using DataSource > [org.apache.commons.dbcp.BasicDataSource@2fbd46ab] of Hibernate > SessionFactory for HibernateTransactionManager > 05 Nov 2014 14:27:52 INFO EhCacheManagerFactoryBean - Initializing > EHCache CacheManager > 05 Nov 2014 14:27:52 WARN CacheManager - Creating a new instance of > CacheManager using the diskStorePath > "/var/folders/2z/n9b16tpn2f35tk85nx_hjbrhbyn5c4/T/" which is already used > by an existing CacheManager. > The source of the configuration was > net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurat= ionSource@6485a56f. > The diskStore path for this CacheManager will be set to > /var/folders/2z/n9b16tpn2f35tk85nx_hjbrhbyn5c4/T//ehcache_auto_created_14= 15215672746. > To avoid this warning consider using the CacheManager factory methods to > create a singleton CacheManager or specifying a separate ehcache > configuration (ehcache.xml) for each CacheManager instance. > 05 Nov 2014 14:27:53 INFO ConceptSimilarityServiceImpl - begin > initialization for concept graph: sct-umls > 05 Nov 2014 14:27:53 INFO ConceptDaoImpl - could not load conceptGraph > from classpath, attempt to load from: > /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGr= aph/sct-umls > .gz > 05 Nov 2014 14:27:53 INFO ConceptDaoImpl - > /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGr= aph/sct-umls > .gz not found, cannot load concept graph > 05 Nov 2014 14:27:53 INFO ConceptDaoImpl - could not load conceptGraph: > sct-umls > 05 Nov 2014 14:27:53 WARN ConceptSimilarityServiceImpl - concept graph > null, name: sct-umls > 05 Nov 2014 14:27:53 INFO ConceptSimilarityServiceImpl - end > initialization for concept graph: sct-umls > 05 Nov 2014 14:27:53 INFO Dialect - HHH000400: Using dialect: > org.hibernate.dialect.MySQLMyISAMDialect > 05 Nov 2014 14:27:53 INFO DocumentMapperServiceImpl - document table nam= e > =3D ytex.document > 05 Nov 2014 14:27:53 INFO SentenceDetector - [SegmentsToSkip, > SentenceModelFile] > 05 Nov 2014 14:27:53 INFO SentenceDetector - Sentence detector model > file: org/apache/ctakes/core/sentdetect/sd-med-model.zip > 05 Nov 2014 14:27:53 WARN SenseDisambiguatorAnnotator - Concept Graph wa= s > not loaded - word sense disambiguation disabled > 05 Nov 2014 14:27:53 INFO POSTagger - POS tagger model file: > org/apache/ctakes/postagger/models/mayo-pos.zip > Loading configuration. > > > On Wed, Nov 5, 2014 at 2:05 PM, vijay garla wrote: > >> can you send the full stack trace of the error? Please pipe the output >> and stderr to a file >> >> On Wed, Nov 5, 2014 at 8:03 PM, Natalia Connolly < >> natalia.v.connolly@gmail.com> wrote: >> >>> Yes, I did the step and I do see that file in >>> resources/org/apache/ctakes/ytex/conceptGraph. >>> >>> On Wed, Nov 5, 2014 at 1:59 PM, vijay garla wrote: >>> >>>> did you do this part (see below). If so, you should see the file >>>> sct-umls.gz in resources/org/apache/ctakes/ytex/conceptGraph/ >>>> >>>> >>>> 3) Unzip YTEX Resources (Optional - UTS login required) >>>> >>>> Download and unzip ctakes-ytex-resources-3.1.2-SNAPSHOT.zip >>>> 'over' >>>> your installation. This contains: >>>> >>>> - Concept Graphs derived from the UMLS2013AA used to compute >>>> semantic similarity measures >>>> - Dictionary Lookup table derived from UMLS2013AA for named entity >>>> recognition. >>>> >>>> >>>> On Wed, Nov 5, 2014 at 6:01 PM, Natalia Connolly < >>>> natalia.v.connolly@gmail.com> wrote: >>>> >>>>> Hi All, >>>>> >>>>> I'm trying out ytex within cTAKES 3.2. I followed all the >>>>> instructions listed here : >>>>> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation, >>>>> and I verified that the setup was fine (from setup.out). >>>>> >>>>> My ytex.properties file contains the line: >>>>> >>>>> ytex.conceptGraphName=3Dsct-umls >>>>> >>>>> and I do have sct-umls.xml in my >>>>> ${CTAKES_HOME}/resources/org/apache/ctakes/ytex/conceptGraph. >>>>> >>>>> Despite all this I can't seem to get conceptGraph working. The >>>>> error message is the following: >>>>> >>>>> 05 Nov 2014 11:56:31 INFO ConceptSimilarityServiceImpl - begin >>>>> initialization for concept graph: sct-umls >>>>> 05 Nov 2014 11:56:31 INFO ConceptDaoImpl - could not load >>>>> conceptGraph from classpath, attempt to load from: >>>>> /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conce= ptGraph/sct-umls >>>>> .gz >>>>> 05 Nov 2014 11:56:31 INFO ConceptDaoImpl - >>>>> /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conce= ptGraph/sct-umls >>>>> .gz not found, cannot load concept graph >>>>> >>>>> I don't understand what needs to go into CLASSPATH to indicate >>>>> where conceptGraph is, as it already contains ${CTAKES_HOME}/resource= s. My >>>>> class path is set according to the documentation to: >>>>> >>>>> ${CTAKES_HOME}/desc:/${CTAKES_HOME}/resources:${CTAKES_HOME}/lib/* >>>>> >>>>> Any help would be appreciated. >>>>> >>>>> Natalia >>>>> >>>>> >>>>> >>>>> >>>> >>> >> > --001a11347e0a4a07df050721c17f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
It looks like there is a trailing space after sct-umls.=C2= =A0 Check your ytex.properties file and make sure there is no trailing spac= e after the=C2=A0ytex.conceptGraphName prop= erty value

On Wed, Nov 5, 2014 at 8:35 PM, Natalia Connolly &l= t;natalia= .v.connolly@gmail.com> wrote:
Well, it't not really an error - ytex runs fine, it= 's just that the word sense disambiguation remains disabled without con= ceptGraph, and I really need it.=C2=A0 Here's the full log of the initi= alization step, with the relevant parts highlighted in yellow:

>bin/runctakesCPE.sh
Nov =C2=A05 14:27:33 P13-7415= java[15257] <Error>: CGContextGetCTM: invalid context 0x0
= Nov =C2=A05 14:27:33 P13-7415 java[15257] <Error>: CGContextSetBaseCT= M: invalid context 0x0
Nov =C2=A05 14:27:33 P13-7415 java[15257] = <Error>: CGContextGetCTM: invalid context 0x0
Nov =C2=A05 1= 4:27:33 P13-7415 java[15257] <Error>: CGContextSetBaseCTM: invalid co= ntext 0x0
log4j: reset attribute=3D "false".
= log4j: Threshold =3D"null".
log4j: Level value for root= is =C2=A0[INFO].
log4j: root level set to INFO
log4j: = Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing lay= out of class: "org.apache.log4j.PatternLayout"
log4j: S= etting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} %5p %c{1} = - %m%n].
log4j: Adding appender named [consoleAppender] to catego= ry [root].
05 Nov 2014 14:27:34 =C2=A0INFO ClearNLPDependencyPars= erAE - using Morphy analysis? true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading m= odel:
...........................................................= .............................
05 Nov 2014 14:27:48 =C2=A0INFO Tok= enizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnota= torPTB
05 Nov 2014 14:27:48 =C2=A0INFO ContextDependentTokenizerA= nnotator - Finite state machines loaded.
05 Nov 2014 14:27:48 =C2= =A0INFO ContextAnnotator - SCOPE ORDER: [1, 3]
05 Nov 2014 14:27:= 49 =C2=A0INFO StatusContextAnalyzer - initBoundaryData() called for Context= Initializer
05 Nov 2014 14:27:49 =C2=A0INFO ContextAnnotator - SC= OPE ORDER: [1, 3]
05 Nov 2014 14:27:49 =C2=A0INFO NegationContext= Analyzer - initBoundaryData() called for ContextInitializer
05 No= v 2014 14:27:49 =C2=A0INFO ApplicationContextHolder - loading ytex.properti= es from: file:/usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/yt= ex/ytex.properties
05 Nov 2014 14:27:49 =C2=A0INFO ApplicationCon= textHolder - beanRefContext=3Dclasspath*:org/apache/ctakes/ytex/uima/beanRe= fContext.xml
05 Nov 2014 14:27:49 =C2=A0INFO ClassPathXmlApplicat= ionContext - Refreshing org.springframework.context.support.ClassPathXmlApp= licationContext@3a9d23c0: startup date [Wed Nov 05 14:27:49 EST 2014]; root= of context hierarchy
05 Nov 2014 14:27:49 =C2=A0INFO XmlBeanDefi= nitionReader - Loading XML bean definitions from URL [jar:file:/usr/local/a= pache-ctakes-3.2.0/lib/ctakes-ytex-res-3.2.0.jar!/org/apache/ctakes/ytex/ui= ma/beanRefContext.xml]
05 Nov 2014 14:27:49 =C2=A0INFO XmlBeanDef= initionReader - Loading XML bean definitions from URL [jar:file:/usr/local/= apache-ctakes-3.2.0/lib/ctakes-ytex-web-3.2.0-classes.jar!/org/apache/ctake= s/ytex/uima/beanRefContext.xml]
05 Nov 2014 14:27:49 =C2=A0INFO D= efaultListableBeanFactory - Overriding bean definition for bean 'ytexAp= plicationContext': replacing [Generic bean: class [org.springframework.= context.support.ClassPathXmlApplicationContext]; scope=3D; abstract=3Dfalse= ; lazyInit=3Dfalse; autowireMode=3D0; dependencyCheck=3D0; autowireCandidat= e=3Dtrue; primary=3Dfalse; factoryBeanName=3Dnull; factoryMethodName=3Dnull= ; initMethodName=3Dnull; destroyMethodName=3Dnull; defined in URL [jar:file= :/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-res-3.2.0.jar!/org/apache/c= takes/ytex/uima/beanRefContext.xml]] with [Generic bean: class [org.springf= ramework.context.support.ClassPathXmlApplicationContext]; scope=3D; abstrac= t=3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; dependencyCheck=3D0; autowir= eCandidate=3Dtrue; primary=3Dfalse; factoryBeanName=3Dnull; factoryMethodNa= me=3Dnull; initMethodName=3Dnull; destroyMethodName=3Dnull; defined in URL = [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-web-3.2.0-classes.= jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]]
05 Nov 2014= 14:27:49 =C2=A0INFO DefaultListableBeanFactory - Pre-instantiating singlet= ons in org.springframework.beans.factory.support.DefaultListableBeanFactory= @271d5641: defining beans [ytexApplicationContext]; root of factory hierarc= hy
05 Nov 2014 14:27:49 =C2=A0INFO ClassPathXmlApplicationContext= - Refreshing org.springframework.context.support.ClassPathXmlApplicationCo= ntext@4183422d: startup date [Wed Nov 05 14:27:49 EST 2014]; root of contex= t hierarchy
05 Nov 2014 14:27:49 =C2=A0INFO XmlBeanDefinitionRead= er - Loading XML bean definitions from class path resource [org/apache/ctak= es/ytex/beans-datasource.xml]
05 Nov 2014 14:27:49 =C2=A0INFO Xml= BeanDefinitionReader - Loading XML bean definitions from class path resourc= e [org/apache/ctakes/ytex/beans-kernel.xml]
05 Nov 2014 14:27:49 = =C2=A0INFO XmlBeanDefinitionReader - Loading XML bean definitions from clas= s path resource [org/apache/ctakes/ytex/beans-kernel-sim.xml]
05 = Nov 2014 14:27:49 =C2=A0INFO XmlBeanDefinitionReader - Loading XML bean def= initions from class path resource [org/apache/ctakes/ytex/uima/beans-uima.h= bm.xml]
05 Nov 2014 14:27:49 =C2=A0INFO XmlBeanDefinitionReader -= Loading XML bean definitions from class path resource [org/apache/ctakes/y= tex/uima/beans-uima-dao.xml]
05 Nov 2014 14:27:49 =C2=A0INFO XmlB= eanDefinitionReader - Loading XML bean definitions from class path resource= [org/apache/ctakes/ytex/uima/beans-uima-mapper.xml]
05 Nov 2014 = 14:27:49 =C2=A0INFO DefaultListableBeanFactory - Overriding bean definition= for bean 'mapperOperation': replacing [Root bean: class [org.sprin= gframework.aop.aspectj.AspectJExpressionPointcut]; scope=3Dprototype; abstr= act=3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; dependencyCheck=3D0; autow= ireCandidate=3Dtrue; primary=3Dfalse; factoryBeanName=3Dnull; factoryMethod= Name=3Dnull; initMethodName=3Dnull; destroyMethodName=3Dnull] with [Root be= an: class [org.springframework.aop.aspectj.AspectJExpressionPointcut]; scop= e=3Dprototype; abstract=3Dfalse; lazyInit=3Dfalse; autowireMode=3D0; depend= encyCheck=3D0; autowireCandidate=3Dtrue; primary=3Dfalse; factoryBeanName= =3Dnull; factoryMethodName=3Dnull; initMethodName=3Dnull; destroyMethodName= =3Dnull]
05 Nov 2014 14:27:49 =C2=A0INFO PropertyPlaceholderConfi= gurer - Loading properties file from class path resource [org/apache/ctakes= /ytex/ytex-default.properties]
05 Nov 2014 14:27:49 =C2=A0INFO Pr= opertyPlaceholderConfigurer - Loading properties file from class path resou= rce [org/apache/ctakes/ytex/ytex.properties]
05 Nov 2014 14:27:49= =C2=A0INFO PropertyPlaceholderConfigurer - Loading properties file from cl= ass path resource [org/apache/ctakes/ytex/ytex-umls.properties]
0= 5 Nov 2014 14:27:49 =C2=A0INFO DefaultListableBeanFactory - Pre-instantiati= ng singletons in org.springframework.beans.factory.support.DefaultListableB= eanFactory@26df536f: defining beans [org.springframework.beans.factory.conf= ig.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataS= ource,txAdvice,txTemplate,txTemplateNew,transactionManager,org.springframew= ork.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,expor= terOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpu= sEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPoint= cutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvi= sor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,o= rg.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.spri= ngframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframe= work.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.ao= p.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.suppo= rt.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsD= ao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter= ,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGram= MatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKe= rnel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,fol= dGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,= libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,spars= eDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFor= matterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormat= terFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,= infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttribute= Evaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeature= Evaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService,concept= SimilarityService,abstractConceptKernel,abstractLinKernel,abstractSemanticS= imKernel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambigu= ator,sessionFactory,ytexDaoOperation,org.springframework.aop.support.Defaul= tBeanFactoryPointcutAdvisor#8,documentDao,namedEntityRegexDao,segmentRegexD= ao,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8= 601Converter,documentMapperService]; root of factory hierarchy
05= Nov 2014 14:27:49 =C2=A0INFO PropertiesFactoryBean - Loading properties fi= le from class path resource [org/apache/ctakes/ytex/ytex.properties]
<= div>05 Nov 2014 14:27:50 =C2=A0INFO Version - HCANN000001: Hibernate Common= s Annotations {4.0.2.Final}
05 Nov 2014 14:27:50 =C2=A0INFO Versi= on - HHH000412: Hibernate Core {4.2.6.Final}
05 Nov 2014 14:27:50= =C2=A0INFO Environment - HHH000206: hibernate.properties not found
05 Nov 2014 14:27:50 =C2=A0INFO Environment - HHH000021: Bytecode provid= er name : javassist
05 Nov 2014 14:27:51 =C2=A0INFO Dialect - HHH= 000400: Using dialect: org.hibernate.dialect.MySQLMyISAMDialect
0= 5 Nov 2014 14:27:51 =C2=A0WARN RootClass - HHH000038: Composite-id class do= es not override equals(): org.apache.ctakes.ytex.uima.model.AnnotationConta= inmentLink
05 Nov 2014 14:27:51 =C2=A0WARN RootClass - HHH000039:= Composite-id class does not override hashCode(): org.apache.ctakes.ytex.ui= ma.model.AnnotationContainmentLink
05 Nov 2014 14:27:51 =C2=A0INF= O TransactionFactoryInitiator - HHH000399: Using default transaction strate= gy (direct JDBC transactions)
05 Nov 2014 14:27:51 =C2=A0INFO AST= QueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
05 Nov 2014 14:27:51 =C2=A0INFO UpdateTimestampsCache - HHH000250: Start= ing update timestamps cache at region: org.hibernate.cache.spi.UpdateTimest= ampsCache
05 Nov 2014 14:27:51 =C2=A0INFO StandardQueryCache - HH= H000248: Starting query cache at region: org.hibernate.cache.internal.Stand= ardQueryCache
05 Nov 2014 14:27:51 =C2=A0INFO TableGenerator - HH= H000398: Explicit segment value for id generator [ytex.hibernate_sequences.= sequence_name] suggested; using default [default]
05 Nov 2014 14:= 27:51 =C2=A0WARN AbstractEhcacheRegionFactory - HHH020003: Could not find a= specific ehcache configuration for cache named [org.apache.ctakes.ytex.uim= a.model.UimaType]; using defaults.
05 Nov 2014 14:27:51 =C2=A0WAR= N EhcacheAccessStrategyFactoryImpl - HHH020007: read-only cache configured = for mutable entity [org.apache.ctakes.ytex.uima.model.UimaType]
0= 5 Nov 2014 14:27:52 =C2=A0INFO HibernateTransactionManager - Using DataSour= ce [org.apache.commons.dbcp.BasicDataSource@2fbd46ab] of Hibernate SessionF= actory for HibernateTransactionManager
05 Nov 2014 14:27:52 =C2= =A0INFO EhCacheManagerFactoryBean - Initializing EHCache CacheManager
=
05 Nov 2014 14:27:52 =C2=A0WARN CacheManager - Creating a new instance= of CacheManager using the diskStorePath "/var/folders/2z/n9b16tpn2f35= tk85nx_hjbrhbyn5c4/T/" which is already used by an existing CacheManag= er.
The source of the configuration was net.sf.ehcache.config.gen= erator.ConfigurationSource$InputStreamConfigurationSource@6485a56f.
The diskStore path for this CacheManager will be set to /var/folders/2z/= n9b16tpn2f35tk85nx_hjbrhbyn5c4/T//ehcache_auto_created_1415215672746.
=
To avoid this warning consider using the CacheManager factory methods = to create a singleton CacheManager or specifying a separate ehcache configu= ration (ehcache.xml) for each CacheManager instance.
05 Nov 2014 14:27:53 =C2=A0INFO Concep= tSimilarityServiceImpl - begin initialization for concept graph: sct-umls= =C2=A0
05 = Nov 2014 14:27:53 =C2=A0INFO ConceptDaoImpl - could not load conceptGraph f= rom classpath, attempt to load from: /usr/local/apache-ctakes-3.2.0/resourc= es/org/apache/ctakes/ytex/conceptGraph/sct-umls .gz
05 Nov 2014 14:27:53 =C2=A0INFO C= onceptDaoImpl - /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/= ytex/conceptGraph/sct-umls .gz not found, cannot load concept graph<= /div>
05 Nov 2014 14:27= :53 =C2=A0INFO ConceptDaoImpl - could not load conceptGraph: sct-umls=C2=A0=
05 Nov 20= 14 14:27:53 =C2=A0WARN ConceptSimilarityServiceImpl - concept graph null, n= ame: sct-umls=C2=A0
05 Nov 2014 14:27:53 =C2=A0INFO ConceptSimilarityServiceImpl - en= d initialization for concept graph: sct-umls=C2=A0
05 Nov = 2014 14:27:53 =C2=A0INFO Dialect - HHH000400: Using dialect: org.hibernate.= dialect.MySQLMyISAMDialect
05 Nov 2014 14:27:53 =C2=A0INFO Docume= ntMapperServiceImpl - document table name =3D ytex.document
05 No= v 2014 14:27:53 =C2=A0INFO SentenceDetector - [SegmentsToSkip, SentenceMode= lFile]
05 Nov 2014 14:27:53 =C2=A0INFO SentenceDetector - Sentenc= e detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
05 Nov 2014 14:27:= 53 =C2=A0WARN SenseDisambiguatorAnnotator - Concept Graph was not loaded - = word sense disambiguation disabled
05 Nov 2014 14:27:53 = =C2=A0INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/m= odels/mayo-pos.zip
Loading configuration.


On Wed, Nov 5, 2014 at 2:05 PM, vijay garla= <vngarla@gmail.com> wrote:
can you send the full stack trace of the error?=C2=A0 Pl= ease pipe the output and stderr to a file

On Wed, Nov 5, 2014 at 8:03 PM, Nat= alia Connolly <natalia.v.connolly@gmail.com> wrot= e:
Yes, I did the step a= nd I do see that file in resources/org/apache/ctakes/ytex/conceptGraph. =C2= =A0

On Wed, Nov 5, 2014 at 1:59 PM, vijay garla <vngarla@gmail.com> wrote:
did you do = this part (see below).=C2=A0 If so, you should see the file sct-umls.gz in= =C2=A0resources/org/apache/ctakes/ytex/conceptGraph/


3) Unzip= YTEX Resources (Optional - UTS login required)

Download and unzip=C2=A0ctakes-ytex-resources-3.1.2-SNAPSHOT.zip=C2=A0'over' your = installation. This contains:

    Concept Graphs derived from the UMLS2013AA used to compute semantic simila= rity measures
  • Dictionary Lookup table derived from UMLS2013AA for n= amed entity recognition.

On Wed, Nov 5, 2014 at 6:01 PM, Nata= lia Connolly <natalia.v.connolly@gmail.com> wrote= :
Hi All,

=
=C2=A0 =C2=A0I'm trying out ytex within cTAKES 3.2. =C2=A0 I follo= wed all the instructions listed here : https://cwik= i.apache.org/confluence/display/CTAKES/YTEX+Installation, and I verifie= d that the setup was fine (from setup.out).

=C2=A0= =C2=A0My ytex.properties file contains the line:

=
ytex.conceptGraphName=3Dsct-umls=C2=A0

= =C2=A0 =C2=A0and I do have sct-umls.xml in my ${CTAKES_HOME}/resources/org/= apache/ctakes/ytex/conceptGraph.

=C2=A0 =C2=A0Desp= ite all this I can't seem to get conceptGraph working.=C2=A0 The error = message is the following:

05 Nov 2014 11:56:3= 1 =C2=A0INFO ConceptSimilarityServiceImpl - begin initialization for concep= t graph: sct-umls=C2=A0
05 Nov 2014 11:56:31 =C2=A0INFO ConceptDa= oImpl - could not load conceptGraph from classpath, attempt to load from: /= usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGraph= /sct-umls .gz
05 Nov 2014 11:56:31 =C2=A0INFO ConceptDaoImpl - /u= sr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGraph/= sct-umls .gz not found, cannot load concept graph

=C2=A0 =C2=A0I don't understand what needs to go into CLASSPATH t= o indicate where conceptGraph is, as it already contains ${CTAKES_HOME}/res= ources.=C2=A0 My class path is set according to the documentation to:
=

${CTAKES_HOME}/desc:/${CTAKES_HOME}/resources:${CTAKES_= HOME}/lib/*

=C2=A0 =C2=A0 =C2=A0Any help would be = appreciated.

=C2=A0 = =C2=A0 =C2=A0Natalia








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