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From vijay garla <vnga...@gmail.com>
Subject Re: Classpath for conceptGraph in ytex
Date Wed, 05 Nov 2014 19:40:41 GMT
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 relevant
> parts highlighted in yellow:
>
> >bin/runctakesCPE.sh
> Nov  5 14:27:33 P13-7415 java[15257] <Error>: CGContextGetCTM: invalid
> context 0x0
> Nov  5 14:27:33 P13-7415 java[15257] <Error>: CGContextSetBaseCTM: invalid
> context 0x0
> Nov  5 14:27:33 P13-7415 java[15257] <Error>: CGContextGetCTM: invalid
> context 0x0
> Nov  5 14:27:33 P13-7415 java[15257] <Error>: CGContextSetBaseCTM: invalid
> context 0x0
> log4j: reset attribute= "false".
> log4j: Threshold ="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=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml
> 05 Nov 2014 14:27:49  INFO ClassPathXmlApplicationContext - Refreshing
> org.springframework.context.support.ClassPathXmlApplicationContext@3a9d23c0:
> 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!/org/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-classes.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=; 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:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-res-3.2.0.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:/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  INFO DefaultListableBeanFactory - Pre-instantiating
> singletons in
> org.springframework.beans.factory.support.DefaultListableBeanFactory@271d5641:
> defining beans [ytexApplicationContext]; root of factory hierarchy
> 05 Nov 2014 14:27:49  INFO ClassPathXmlApplicationContext - Refreshing
> org.springframework.context.support.ClassPathXmlApplicationContext@4183422d:
> 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=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 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@26df536f:
> 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 Nov 2014 14:27:49  INFO PropertiesFactoryBean - Loading properties file
> 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 name
> : 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: Could
> 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$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
> 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/conceptGraph/sct-umls
> .gz
> 05 Nov 2014 14:27:53  INFO ConceptDaoImpl -
> /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGraph/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 name
> = 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 was
> 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 <vngarla@gmail.com> 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 <vngarla@gmail.com> 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
>>>> <http://www.ytex-nlp.org/umls.download/secure/3.1/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=sct-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/conceptGraph/sct-umls
>>>>> .gz
>>>>> 05 Nov 2014 11:56:31  INFO ConceptDaoImpl -
>>>>> /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGraph/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}/resources.
 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>

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