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From Natalia Connolly <natalia.v.conno...@gmail.com>
Subject Re: Classpath for conceptGraph in ytex
Date Wed, 05 Nov 2014 19:35:57 GMT
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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