[
https://issues.apache.org/jira/browse/CTAKES-469?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Alex Zbarcea updated CTAKES-469:
--------------------------------
Docs Text:
<pre>
C:\cn\bin>SETLOCAL
C:\cn\bin>set CURRENT_DIR=C:\cn\bin
C:\cn\bin>if not "" == "" goto gotHome
C:\cn\bin>set CTAKES_HOME=C:\cn\bin
C:\cn\bin>if exist "C:\cn\bin\bin\runctakesCPE.bat" goto okHome
C:\cn\bin>cd ..
C:\cn>set CTAKES_HOME=C:\cn
C:\cn>if exist "C:\cn\bin\runctakesCPE.bat" goto okHome
C:\cn>cd C:\cn
C:\cn>java -cp "C:\cn/desc/;C:\cn/resources/;C:\cn/lib/*"
-Dlog4j.configuration=file:/C:\cn/config/log4j.xml -Xms512M -Xmx3g
org.apache.uima.tools.cpm.CpmFrame
Oct 25, 2017 7:37:12 PM java.util.prefs.WindowsPreferences <init>
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root
0x80000002. Windows RegCreateKeyEx(...) returned error code 5.
log4j: reset attribute= "false".
log4j: Threshold ="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} %5p
%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 state
machines loaded.
25 Oct 2017 19:37:27 INFO ApplicationContextHolder - loading ytex.properties
from: file:/C:/cn/resources/org/apache/ctakes/ytex/ytex.properties
25 Oct 2017 19:37:27 INFO ApplicationContextHolder -
beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml
25 Oct 2017 19:37:30 INFO InitableJdbcConnectionResourceImpl - Connection
established to:
jdbc:sqlserver://localhost;databaseName=UMLS;integratedSecurity=true
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 sizes:
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.apache.ctakes.necontexts.status.StatusContextAnalyzer
25 Oct 2017 19:37:31 INFO StatusContextAnalyzer - initBoundaryData() called
for ContextInitializer
25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context consumer:
org.apache.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.apache.ctakes.typesystem.type.syntax.BaseToken
25 Oct 2017 19:37:31 INFO ContextAnnotator - Using left , right scope sizes: 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.apache.ctakes.necontexts.negation.NegationContextAnalyzer
25 Oct 2017 19:37:31 INFO NegationContextAnalyzer - initBoundaryData() called
for ContextInitializer
25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context consumer:
org.apache.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.apache.ctakes.typesystem.type.syntax.BaseToken
25 Oct 2017 19:37:31 INFO SentenceDetector - [SegmentsToSkip,
SentenceModelFile]
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:
startup date [Wed Oct 25 19:37:31 IST 2017]; root of context hierarchy
25 Oct 2017 19:37:32 INFO XmlBeanDefinitionReader - Loading XML bean
definitions 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
definitions 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
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:/C:/cn/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]]
with [Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[jar:file:/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 - Pre-instantiating
singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@7ae65cd2:
defining beans [ytexApplicationContext]; root of factory hierarchy
25 Oct 2017 19:37:32 INFO ClassPathXmlApplicationContext - Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@7d3b1153:
startup date [Wed Oct 25 19:37:32 IST 2017]; root of context hierarchy
25 Oct 2017 19:37:32 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/beans-datasource.xml]
25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel-sim.xml]
25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/uima/beans-uima.hbm.xml]
25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/uima/beans-uima-dao.xml]
25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/uima/beans-uima-mapper.xml]
25 Oct 2017 19:37:33 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]
25 Oct 2017 19:37:34 INFO PropertyPlaceholderConfigurer - Loading properties
file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
25 Oct 2017 19:37:34 INFO PropertyPlaceholderConfigurer - Loading properties
file from class path resource [org/apache/ctakes/ytex/ytex.properties]
25 Oct 2017 19:37:34 INFO PropertyPlaceholderConfigurer - Loading properties
file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
25 Oct 2017 19:37:34 INFO DefaultListableBeanFactory - Pre-instantiating
singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@202217c7:
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
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 Annotations
{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 not
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.hibernate.dialect.SQLServerDialect
25 Oct 2017 19:37:43 WARN RootClass - HHH000038: Composite-id class does not
override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
25 Oct 2017 19:37:43 WARN RootClass - HHH000039: Composite-id class does not
override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
25 Oct 2017 19:37:43 INFO TransactionFactoryInitiator - HHH000399: Using
default transaction strategy (direct JDBC transactions)
25 Oct 2017 19:37:43 INFO ASTQueryTranslatorFactory - HHH000397: Using
ASTQueryTranslatorFactory
25 Oct 2017 19:37:44 INFO UpdateTimestampsCache - HHH000250: Starting update
timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
25 Oct 2017 19:37:44 INFO StandardQueryCache - HHH000248: Starting query cache
at region: org.hibernate.cache.internal.StandardQueryCache
25 Oct 2017 19:37:44 INFO TableGenerator - HHH000398: Explicit segment value
for id generator [dbo.hibernate_sequences.sequence_name] suggested; using
default [default]
25 Oct 2017 19:37:45 WARN AbstractEhcacheRegionFactory - HHH020003: Could not
find a specific ehcache configuration for cache named
[org.apache.ctakes.ytex.uima.model.UimaType]; using defaults.
25 Oct 2017 19:37:45 WARN EhcacheAccessStrategyFactoryImpl - HHH020007:
read-only cache configured for mutable entity
[org.apache.ctakes.ytex.uima.model.UimaType]
25 Oct 2017 19:37:46 INFO HibernateTransactionManager - Using DataSource
[org.apache.commons.dbcp.BasicDataSource@53ff623b] of Hibernate SessionFactory
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
CacheManager 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.ConfigurationSource$InputStreamConfigurationSource@3cdbe5e4.
The diskStore path for this CacheManager will be set to
C:\Users\Sathya\AppData\Local\Temp\\ehcache_auto_created_1508940467387.
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.
25 Oct 2017 19:37:48 INFO ConceptSimilarityServiceImpl - begin initialization
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, vertices:
461241
25 Oct 2017 19:37:50 INFO ConceptSimilarityServiceImpl - initializing
similarity measures
25 Oct 2017 19:37:50 INFO ConceptSimilarityServiceImpl - loading corpus
infocontent for corpusName=, conceptGraphName=sct-rxnorm, conceptSetName=
25 Oct 2017 19:37:51 WARN ConceptSimilarityServiceImpl - IC not found
25 Oct 2017 19:37:51 INFO ConceptSimilarityServiceImpl - end initialization
for concept graph: sct-rxnorm
25 Oct 2017 19:37:52 INFO Dialect - HHH000400: Using dialect:
org.hibernate.dialect.SQLServerDialect
25 Oct 2017 19:37:52 INFO DocumentMapperServiceImpl - document table name =
dbo.document
25 Oct 2017 19:37:53 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
C:\cn\resources\org\apache\ctakes\lvg\data\config\lvg.properties
25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - config file absolute path
= C:\cn\resources\org\apache\ctakes\lvg\data\config\lvg.properties
25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - cwd = C:\cn
25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - cd
C:\cn\resources\org\apache\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
CTAKES-76 is implemented.
25 Oct 2017 19:37:58 WARN JarafeMEDecoder - This class cannot be used until
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
declared multiple times with different definitions. The definition of the
resource in component
/AggregatePlaintextUMLSProcessor/AssertionAnnotator/assertionAnalysisEngine/
will be used. The definition in component
/AggregatePlaintextUMLSProcessor/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 scopeModelResourceImpl has been declared
multiple times with different definitions. The definition of the resource in
component
/AggregatePlaintextUMLSProcessor/AssertionAnnotator/assertionAnalysisEngine/
will be used. The definition in component
/AggregatePlaintextUMLSProcessor/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 cueModelResourceImpl has been declared
multiple times with different definitions. The definition of the resource in
component
/AggregatePlaintextUMLSProcessor/AssertionAnnotator/assertionAnalysisEngine/
will be used. The definition in component
/AggregatePlaintextUMLSProcessor/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
declared multiple times with different definitions. The definition of the
resource in component
/AggregatePlaintextUMLSProcessor/AssertionAnnotator/assertionAnalysisEngine/
will be used. The definition in component
/AggregatePlaintextUMLSProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/
will be ignored.
25 Oct 2017 19:37:58 INFO ClearNLPDependencyParserAE - using Morphy analysis?
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:
..........
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:
...
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:
.
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:
.
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:
.......
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:
.
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:
.
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:
.
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:
.......
Loading model:
.
Loading model:
.
Loading model:
.
Loading model:
...
Loading model:
.
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
................................
Loading model:
.............................
org.apache.uima.resource.ResourceInitializationException: Initialization of CAS
Processor with name "DBCollectionReader.xml" failed.
at
org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:81)
at
org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingEngine(UIMAFramework_impl.java:420)
at
org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAFramework.java:918)
at org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:573)
at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105)
at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713)
Caused by: org.apache.uima.resource.ResourceConfigurationException:
Initialization of CAS Processor with name "DBCollectionReader.xml" failed.
at
org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1101)
at
org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProcessors(CPEFactory.java:547)
at
org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java:253)
at
org.apache.uima.collection.impl.cpm.BaseCPMImpl.<init>(BaseCPMImpl.java:127)
at
org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:73)
... 5 more
Caused by: org.apache.uima.resource.ResourceInitializationException:
Initialization of annotator class
"org.apache.ctakes.ytex.uima.DBCollectionReader" failed. (Descriptor:
file:/c:/cn/desc/ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:331)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:448)
at
org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1085)
... 9 more
Caused by: java.lang.IllegalArgumentException: SQL must not be null
at org.springframework.util.Assert.notNull(Assert.java:112)
at
org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:432)
at
org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:464)
at
org.springframework.jdbc.core.JdbcTemplate.queryForList(JdbcTemplate.java:495)
at
org.springframework.jdbc.core.simple.SimpleJdbcTemplate.queryForList(SimpleJdbcTemplate.java:238)
at
org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCollectionReader.java:179)
at
org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCollectionReader.java:1)
at
org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:130)
at
org.apache.ctakes.ytex.uima.DBCollectionReader.loadDocumentIds(DBCollectionReader.java:173)
at
org.apache.ctakes.ytex.uima.DBCollectionReader.initialize(DBCollectionReader.java:116)
at
org.apache.uima.collection.CollectionReader_ImplBase.initialize(CollectionReader_ImplBase.java:70)
at
org.apache.uima.analysis_engine.impl.compatibility.CollectionReaderAdapter.initialize(CollectionReaderAdapter.java:87)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266)
... 16 more
</pre>
was:
{code}
C:\cn\bin>SETLOCAL
C:\cn\bin>set CURRENT_DIR=C:\cn\bin
C:\cn\bin>if not "" == "" goto gotHome
C:\cn\bin>set CTAKES_HOME=C:\cn\bin
C:\cn\bin>if exist "C:\cn\bin\bin\runctakesCPE.bat" goto okHome
C:\cn\bin>cd ..
C:\cn>set CTAKES_HOME=C:\cn
C:\cn>if exist "C:\cn\bin\runctakesCPE.bat" goto okHome
C:\cn>cd C:\cn
C:\cn>java -cp "C:\cn/desc/;C:\cn/resources/;C:\cn/lib/*"
-Dlog4j.configuration=file:/C:\cn/config/log4j.xml -Xms512M -Xmx3g
org.apache.uima.tools.cpm.CpmFrame
Oct 25, 2017 7:37:12 PM java.util.prefs.WindowsPreferences <init>
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root
0x80000002. Windows RegCreateKeyEx(...) returned error code 5.
log4j: reset attribute= "false".
log4j: Threshold ="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} %5p
%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 state
machines loaded.
25 Oct 2017 19:37:27 INFO ApplicationContextHolder - loading ytex.properties
from: file:/C:/cn/resources/org/apache/ctakes/ytex/ytex.properties
25 Oct 2017 19:37:27 INFO ApplicationContextHolder -
beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml
25 Oct 2017 19:37:30 INFO InitableJdbcConnectionResourceImpl - Connection
established to:
jdbc:sqlserver://localhost;databaseName=UMLS;integratedSecurity=true
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 sizes:
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.apache.ctakes.necontexts.status.StatusContextAnalyzer
25 Oct 2017 19:37:31 INFO StatusContextAnalyzer - initBoundaryData() called
for ContextInitializer
25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context consumer:
org.apache.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.apache.ctakes.typesystem.type.syntax.BaseToken
25 Oct 2017 19:37:31 INFO ContextAnnotator - Using left , right scope sizes: 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.apache.ctakes.necontexts.negation.NegationContextAnalyzer
25 Oct 2017 19:37:31 INFO NegationContextAnalyzer - initBoundaryData() called
for ContextInitializer
25 Oct 2017 19:37:31 INFO ContextAnnotator - Using context consumer:
org.apache.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.apache.ctakes.typesystem.type.syntax.BaseToken
25 Oct 2017 19:37:31 INFO SentenceDetector - [SegmentsToSkip,
SentenceModelFile]
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:
startup date [Wed Oct 25 19:37:31 IST 2017]; root of context hierarchy
25 Oct 2017 19:37:32 INFO XmlBeanDefinitionReader - Loading XML bean
definitions 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
definitions 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
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:/C:/cn/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]]
with [Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[jar:file:/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 - Pre-instantiating
singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@7ae65cd2:
defining beans [ytexApplicationContext]; root of factory hierarchy
25 Oct 2017 19:37:32 INFO ClassPathXmlApplicationContext - Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@7d3b1153:
startup date [Wed Oct 25 19:37:32 IST 2017]; root of context hierarchy
25 Oct 2017 19:37:32 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/beans-datasource.xml]
25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel-sim.xml]
25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/uima/beans-uima.hbm.xml]
25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/uima/beans-uima-dao.xml]
25 Oct 2017 19:37:33 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/uima/beans-uima-mapper.xml]
25 Oct 2017 19:37:33 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]
25 Oct 2017 19:37:34 INFO PropertyPlaceholderConfigurer - Loading properties
file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
25 Oct 2017 19:37:34 INFO PropertyPlaceholderConfigurer - Loading properties
file from class path resource [org/apache/ctakes/ytex/ytex.properties]
25 Oct 2017 19:37:34 INFO PropertyPlaceholderConfigurer - Loading properties
file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
25 Oct 2017 19:37:34 INFO DefaultListableBeanFactory - Pre-instantiating
singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@202217c7:
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
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 Annotations
{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 not
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.hibernate.dialect.SQLServerDialect
25 Oct 2017 19:37:43 WARN RootClass - HHH000038: Composite-id class does not
override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
25 Oct 2017 19:37:43 WARN RootClass - HHH000039: Composite-id class does not
override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
25 Oct 2017 19:37:43 INFO TransactionFactoryInitiator - HHH000399: Using
default transaction strategy (direct JDBC transactions)
25 Oct 2017 19:37:43 INFO ASTQueryTranslatorFactory - HHH000397: Using
ASTQueryTranslatorFactory
25 Oct 2017 19:37:44 INFO UpdateTimestampsCache - HHH000250: Starting update
timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
25 Oct 2017 19:37:44 INFO StandardQueryCache - HHH000248: Starting query cache
at region: org.hibernate.cache.internal.StandardQueryCache
25 Oct 2017 19:37:44 INFO TableGenerator - HHH000398: Explicit segment value
for id generator [dbo.hibernate_sequences.sequence_name] suggested; using
default [default]
25 Oct 2017 19:37:45 WARN AbstractEhcacheRegionFactory - HHH020003: Could not
find a specific ehcache configuration for cache named
[org.apache.ctakes.ytex.uima.model.UimaType]; using defaults.
25 Oct 2017 19:37:45 WARN EhcacheAccessStrategyFactoryImpl - HHH020007:
read-only cache configured for mutable entity
[org.apache.ctakes.ytex.uima.model.UimaType]
25 Oct 2017 19:37:46 INFO HibernateTransactionManager - Using DataSource
[org.apache.commons.dbcp.BasicDataSource@53ff623b] of Hibernate SessionFactory
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
CacheManager 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.ConfigurationSource$InputStreamConfigurationSource@3cdbe5e4.
The diskStore path for this CacheManager will be set to
C:\Users\Sathya\AppData\Local\Temp\\ehcache_auto_created_1508940467387.
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.
25 Oct 2017 19:37:48 INFO ConceptSimilarityServiceImpl - begin initialization
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, vertices:
461241
25 Oct 2017 19:37:50 INFO ConceptSimilarityServiceImpl - initializing
similarity measures
25 Oct 2017 19:37:50 INFO ConceptSimilarityServiceImpl - loading corpus
infocontent for corpusName=, conceptGraphName=sct-rxnorm, conceptSetName=
25 Oct 2017 19:37:51 WARN ConceptSimilarityServiceImpl - IC not found
25 Oct 2017 19:37:51 INFO ConceptSimilarityServiceImpl - end initialization
for concept graph: sct-rxnorm
25 Oct 2017 19:37:52 INFO Dialect - HHH000400: Using dialect:
org.hibernate.dialect.SQLServerDialect
25 Oct 2017 19:37:52 INFO DocumentMapperServiceImpl - document table name =
dbo.document
25 Oct 2017 19:37:53 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
C:\cn\resources\org\apache\ctakes\lvg\data\config\lvg.properties
25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - config file absolute path
= C:\cn\resources\org\apache\ctakes\lvg\data\config\lvg.properties
25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - cwd = C:\cn
25 Oct 2017 19:37:54 INFO LvgCmdApiResourceImpl - cd
C:\cn\resources\org\apache\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
CTAKES-76 is implemented.
25 Oct 2017 19:37:58 WARN JarafeMEDecoder - This class cannot be used until
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
declared multiple times with different definitions. The definition of the
resource in component
/AggregatePlaintextUMLSProcessor/AssertionAnnotator/assertionAnalysisEngine/
will be used. The definition in component
/AggregatePlaintextUMLSProcessor/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 scopeModelResourceImpl has been declared
multiple times with different definitions. The definition of the resource in
component
/AggregatePlaintextUMLSProcessor/AssertionAnnotator/assertionAnalysisEngine/
will be used. The definition in component
/AggregatePlaintextUMLSProcessor/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 cueModelResourceImpl has been declared
multiple times with different definitions. The definition of the resource in
component
/AggregatePlaintextUMLSProcessor/AssertionAnnotator/assertionAnalysisEngine/
will be used. The definition in component
/AggregatePlaintextUMLSProcessor/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
declared multiple times with different definitions. The definition of the
resource in component
/AggregatePlaintextUMLSProcessor/AssertionAnnotator/assertionAnalysisEngine/
will be used. The definition in component
/AggregatePlaintextUMLSProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/
will be ignored.
25 Oct 2017 19:37:58 INFO ClearNLPDependencyParserAE - using Morphy analysis?
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:
..........
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:
...
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:
.
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:
.
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:
.......
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:
.
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:
.
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:
.
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:
.......
Loading model:
.
Loading model:
.
Loading model:
.
Loading model:
...
Loading model:
.
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
................................
Loading model:
.............................
org.apache.uima.resource.ResourceInitializationException: Initialization of CAS
Processor with name "DBCollectionReader.xml" failed.
at
org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:81)
at
org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingEngine(UIMAFramework_impl.java:420)
at
org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAFramework.java:918)
at org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:573)
at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105)
at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713)
Caused by: org.apache.uima.resource.ResourceConfigurationException:
Initialization of CAS Processor with name "DBCollectionReader.xml" failed.
at
org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1101)
at
org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProcessors(CPEFactory.java:547)
at
org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java:253)
at
org.apache.uima.collection.impl.cpm.BaseCPMImpl.<init>(BaseCPMImpl.java:127)
at
org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:73)
... 5 more
Caused by: org.apache.uima.resource.ResourceInitializationException:
Initialization of annotator class
"org.apache.ctakes.ytex.uima.DBCollectionReader" failed. (Descriptor:
file:/c:/cn/desc/ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:331)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:448)
at
org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1085)
... 9 more
Caused by: java.lang.IllegalArgumentException: SQL must not be null
at org.springframework.util.Assert.notNull(Assert.java:112)
at
org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:432)
at
org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:464)
at
org.springframework.jdbc.core.JdbcTemplate.queryForList(JdbcTemplate.java:495)
at
org.springframework.jdbc.core.simple.SimpleJdbcTemplate.queryForList(SimpleJdbcTemplate.java:238)
at
org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCollectionReader.java:179)
at
org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCollectionReader.java:1)
at
org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:130)
at
org.apache.ctakes.ytex.uima.DBCollectionReader.loadDocumentIds(DBCollectionReader.java:173)
at
org.apache.ctakes.ytex.uima.DBCollectionReader.initialize(DBCollectionReader.java:116)
at
org.apache.uima.collection.CollectionReader_ImplBase.initialize(CollectionReader_ImplBase.java:70)
at
org.apache.uima.analysis_engine.impl.compatibility.CollectionReaderAdapter.initialize(CollectionReaderAdapter.java:87)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266)
... 16 more
{code}
> could not able to run ytex with DBCollection reader
> ----------------------------------------------------
>
> 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-SetupAuiFirstWord.CTAKES-334.svn-01.patch
> Reporter: athyanarayana
> Assignee: Alex Zbarcea
> 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 the
> error i am getting
> {code:java}
> Loading model:
> ................................
> Loading model:
> .............................
> org.apache.uima.resource.ResourceInitializationException: Initialization of
> CAS Processor with name "DBCollectionReader.xml" failed.
> at
> org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:81)
> at
> org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingEngine(UIMAFramework_impl.java:420)
> at
> org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAFramework.java:918)
> at org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:573)
> at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105)
> at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713)
> Caused by: org.apache.uima.resource.ResourceConfigurationException:
> Initialization of CAS Processor with name "DBCollectionReader.xml" failed.
> at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1101)
> at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProcessors(CPEFactory.java:547)
> at
> org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java:253)
> at
> org.apache.uima.collection.impl.cpm.BaseCPMImpl.<init>(BaseCPMImpl.java:127)
> at
> org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:73)
> ... 5 more
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> Initialization of annotator class
> "org.apache.ctakes.ytex.uima.DBCollectionReader" failed. (Descriptor:
> file:/c:/cn/desc/ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:331)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:448)
> at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1085)
> ... 9 more
> Caused by: java.lang.IllegalArgumentException: SQL must not be null
> at org.springframework.util.Assert.notNull(Assert.java:112)
> at
> org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:432)
> at
> org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:464)
> at
> org.springframework.jdbc.core.JdbcTemplate.queryForList(JdbcTemplate.java:495)
> at
> org.springframework.jdbc.core.simple.SimpleJdbcTemplate.queryForList(SimpleJdbcTemplate.java:238)
> at
> org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCollectionReader.java:179)
> at
> org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCollectionReader.java:1)
> at
> org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:130)
> at
> org.apache.ctakes.ytex.uima.DBCollectionReader.loadDocumentIds(DBCollectionReader.java:173)
> at
> org.apache.ctakes.ytex.uima.DBCollectionReader.initialize(DBCollectionReader.java:116)
> at
> org.apache.uima.collection.CollectionReader_ImplBase.initialize(CollectionReader_ImplBase.java:70)
> at
> org.apache.uima.analysis_engine.impl.compatibility.CollectionReaderAdapter.initialize(CollectionReaderAdapter.java:87)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266)
> ... 16 more
> {code}
--
This message was sent by Atlassian JIRA
(v7.6.3#76005)
