[CTAKES-469] could not able to run ytex with DBCollection reader

• Type: Bug
• Status: Open
• Priority: Critical
• Resolution: Unresolved
• Affects Version/s: 4.0.0, 4.0.1
• Fix Version/s: 4.0.0, 4.0.1
• Component/s: ctakes-ytex, ctakes-ytex-uima
• Labels: error
• Environment: windows 10, java 8, catkes-4 , MS SQL SERVER fix-SetupAuiFirstWord.CTAKES-334.svn-01.patch

Docs Text

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
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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

• Assignee: Alex Zbarcea
• Reporter: athyanarayana
• Created: 25/Oct/17 14:12
• Updated: 23/Jul/18 00:43

Description

i cant abel to run ctakes CPE with ytex db collection reder , below is the error i am getting

 
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

Issue Links

• is broken by: CTAKES-334 GramMatrixExporterImpl initialization failed
• is caused by: CTAKES-446 Piper file parameter value ignored when it contains quoted equals