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From vijay garla <vnga...@gmail.com>
Subject Re: cTAKES 3.2 Analysis Batch Issue
Date Wed, 09 Jul 2014 17:25:09 GMT
I don't see any initialization errors, and I also don't see the DBConsumer
being called.  Can you please try the following - set up a new CPE
configuration with just the DBCollectionReader and only the DBConsumer as
the analysis engine?  This will have very few annotations obviously, but
we'll see if anything happens

TIA!

VJ


On Tue, Jul 8, 2014 at 9:36 PM, Clayton Turner <caturner3@g.cofc.edu> wrote:

> Alright.
>
> Here is my logfile:
>
>
>
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT\bin>SETLOCAL
>
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT\bin>set
> CURRENT_DIR=C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT\bin
>
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT\bin>if
> not "C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT" ==
> "" goto gotHome
>
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT\bin>if
> exist
> "C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT\bin\runctakesCPE.bat"
> goto okHome
>
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT\bin>cd
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT
>
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT>java
> -Dctakes.umlsuser=pharre -Dctakes.umlspw=learn*1031 -cp
> "C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT/lib/*;C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT/desc/;C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT/resources/"
> -Dlog4j.configuration=file:/C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT/config/log4j.xml
> -Xms512M -Xmx2g org.apache.uima.tools.cpm.CpmFrame
> Jul 08, 2014 3:27:34 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: 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].
> 08 Jul 2014 15:27:40  INFO ClearNLPDependencyParserAE - using Morphy
> analysis? true
> Loading configuration.
> Loading feature templates.
> Loading lexica.
> Loading model:
>
> ........................................................................................
> 08 Jul 2014 15:27:52  INFO TokenizerAnnotatorPTB - Initializing
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:27:52  INFO ContextDependentTokenizerAnnotator - Finite
> state machines loaded.
> 08 Jul 2014 15:27:52  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
> 08 Jul 2014 15:27:52  INFO StatusContextAnalyzer - initBoundaryData()
> called for ContextInitializer
> 08 Jul 2014 15:27:52  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
> 08 Jul 2014 15:27:52  INFO NegationContextAnalyzer - initBoundaryData()
> called for ContextInitializer
> 08 Jul 2014 15:27:52  INFO ApplicationContextHolder - loading
> ytex.properties from:
> file:/C:/ctakes/ctakes-distribution/target/apache-ctakes-3.1.2-SNAPSHOT/resources/org/apache/ctakes/ytex/ytex.properties
> 08 Jul 2014 15:27:52  INFO ApplicationContextHolder -
> beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml
> 08 Jul 2014 15:27:52  INFO ClassPathXmlApplicationContext - Refreshing
> org.springframework.context.support.ClassPathXmlApplicationContext@6a383173:
> startup date [Tue Jul 08 15:27:52 EDT 2014]; root of context hierarchy
> 08 Jul 2014 15:27:52  INFO XmlBeanDefinitionReader - Loading XML bean
> definitions from URL
> [file:/C:/ctakes/ctakes-distribution/target/apache-ctakes-3.1.2-SNAPSHOT/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml]
> 08 Jul 2014 15:27:52  INFO DefaultListableBeanFactory - Pre-instantiating
> singletons in
> org.springframework.beans.factory.support.DefaultListableBeanFactory@32627731:
> defining beans [ytexApplicationContext]; root of factory hierarchy
> 08 Jul 2014 15:27:53  INFO ClassPathXmlApplicationContext - Refreshing
> org.springframework.context.support.ClassPathXmlApplicationContext@2e5e45b0:
> startup date [Tue Jul 08 15:27:53 EDT 2014]; root of context hierarchy
> 08 Jul 2014 15:27:53  INFO XmlBeanDefinitionReader - Loading XML bean
> definitions from class path resource
> [org/apache/ctakes/ytex/beans-datasource.xml]
> 08 Jul 2014 15:27:53  INFO XmlBeanDefinitionReader - Loading XML bean
> definitions from class path resource
> [org/apache/ctakes/ytex/beans-kernel.xml]
> 08 Jul 2014 15:27:53  INFO XmlBeanDefinitionReader - Loading XML bean
> definitions from class path resource
> [org/apache/ctakes/ytex/beans-kernel-sim.xml]
> 08 Jul 2014 15:27:53  INFO XmlBeanDefinitionReader - Loading XML bean
> definitions from class path resource
> [org/apache/ctakes/ytex/uima/beans-uima.hbm.xml]
> 08 Jul 2014 15:27:53  INFO XmlBeanDefinitionReader - Loading XML bean
> definitions from class path resource
> [org/apache/ctakes/ytex/uima/beans-uima-dao.xml]
> 08 Jul 2014 15:27:53  INFO XmlBeanDefinitionReader - Loading XML bean
> definitions from class path resource
> [org/apache/ctakes/ytex/uima/beans-uima-mapper.xml]
> 08 Jul 2014 15:27:53  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]
> 08 Jul 2014 15:27:53  INFO PropertyPlaceholderConfigurer - Loading
> properties file from class path resource
> [org/apache/ctakes/ytex/ytex-default.properties]
> 08 Jul 2014 15:27:53  INFO PropertyPlaceholderConfigurer - Loading
> properties file from class path resource
> [org/apache/ctakes/ytex/ytex.properties]
> 08 Jul 2014 15:27:53  INFO PropertyPlaceholderConfigurer - Loading
> properties file from class path resource
> [org/apache/ctakes/ytex/ytex-umls.properties]
> 08 Jul 2014 15:27:53  INFO DefaultListableBeanFactory - Pre-instantiating
> singletons in
> org.springframework.beans.factory.support.DefaultListableBeanFactory@49ad9f73:
> 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
> 08 Jul 2014 15:27:53  INFO PropertiesFactoryBean - Loading properties file
> from class path resource [org/apache/ctakes/ytex/ytex.properties]
> 08 Jul 2014 15:27:54  INFO Version - HCANN000001: Hibernate Commons
> Annotations {4.0.2.Final}
> 08 Jul 2014 15:27:54  INFO Version - HHH000412: Hibernate Core
> {4.2.6.Final}
> 08 Jul 2014 15:27:54  INFO Environment - HHH000206: hibernate.properties
> not found
> 08 Jul 2014 15:27:54  INFO Environment - HHH000021: Bytecode provider name
> : javassist
> 08 Jul 2014 15:27:55  INFO Dialect - HHH000400: Using dialect:
> org.hibernate.dialect.MySQLMyISAMDialect
> 08 Jul 2014 15:27:55  WARN RootClass - HHH000038: Composite-id class does
> not override equals():
> org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
> 08 Jul 2014 15:27:55  WARN RootClass - HHH000039: Composite-id class does
> not override hashCode():
> org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
> 08 Jul 2014 15:27:55  INFO TransactionFactoryInitiator - HHH000399: Using
> default transaction strategy (direct JDBC transactions)
> 08 Jul 2014 15:27:55  INFO ASTQueryTranslatorFactory - HHH000397: Using
> ASTQueryTranslatorFactory
> 08 Jul 2014 15:27:55  INFO UpdateTimestampsCache - HHH000250: Starting
> update timestamps cache at region:
> org.hibernate.cache.spi.UpdateTimestampsCache
> 08 Jul 2014 15:27:55  INFO StandardQueryCache - HHH000248: Starting query
> cache at region: org.hibernate.cache.internal.StandardQueryCache
> 08 Jul 2014 15:27:55  INFO TableGenerator - HHH000398: Explicit segment
> value for id generator [ytex.hibernate_sequences.sequence_name] suggested;
> using default [default]
> 08 Jul 2014 15:27:55  WARN AbstractEhcacheRegionFactory - HHH020003: Could
> not find a specific ehcache configuration for cache named
> [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults.
> 08 Jul 2014 15:27:55  WARN EhcacheAccessStrategyFactoryImpl - HHH020007:
> read-only cache configured for mutable entity
> [org.apache.ctakes.ytex.uima.model.UimaType]
> 08 Jul 2014 15:27:56  INFO HibernateTransactionManager - Using DataSource
> [org.apache.commons.dbcp.BasicDataSource@5c2c7585] of Hibernate
> SessionFactory for HibernateTransactionManager
> 08 Jul 2014 15:27:57  INFO EhCacheManagerFactoryBean - Initializing
> EHCache CacheManager
> 08 Jul 2014 15:27:57  WARN CacheManager - Creating a new instance of
> CacheManager using the diskStorePath "C:\Users\clayton\AppData\Local\Temp\"
> which is already used by an existing CacheManager.
> The source of the configuration was
> net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurationSource@1057b7b6.
> The diskStore path for this CacheManager will be set to
> C:\Users\clayton\AppData\Local\Temp\\ehcache_auto_created_1404847677285.
> 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.
> 08 Jul 2014 15:27:57  INFO ConceptSimilarityServiceImpl - begin
> initialization for concept graph: sct-msh-csp-aod
> 08 Jul 2014 15:27:58  INFO ConceptDaoImpl - loading concept graph from
> file:/C:/ctakes/ctakes-distribution/target/apache-ctakes-3.1.2-SNAPSHOT/resources/org/apache/ctakes/ytex/conceptGraph/sct-msh-csp-aod.gz
> 08 Jul 2014 15:28:00  INFO ConceptDaoImpl - concept graph sct-msh-csp-aod,
> vertices: 606041
> 08 Jul 2014 15:28:00  INFO ConceptSimilarityServiceImpl - initializing
> similarity measures
> 08 Jul 2014 15:28:00  INFO ConceptSimilarityServiceImpl - loading corpus
> infocontent for corpusName=, conceptGraphName=sct-msh-csp-aod,
> conceptSetName=
> 08 Jul 2014 15:28:00  WARN ConceptSimilarityServiceImpl - IC not found
> 08 Jul 2014 15:28:00  WARN SqlExceptionHelper - SQL Error: 1146, SQLState:
> 42S02
> 08 Jul 2014 15:28:00 ERROR SqlExceptionHelper - Table 'ytex.mrsty' doesn't
> exist
> 08 Jul 2014 15:28:00  INFO ConceptSimilarityServiceImpl - could not
> initialize cui-tui map: could not extract ResultSet.  This is expected if
> you do not have umls installed in your db.
> 08 Jul 2014 15:28:00  INFO ConceptSimilarityServiceImpl - end
> initialization for concept graph: sct-msh-csp-aod
> 08 Jul 2014 15:28:00  INFO Dialect - HHH000400: Using dialect:
> org.hibernate.dialect.MySQLMyISAMDialect
> 08 Jul 2014 15:28:00  INFO DocumentMapperServiceImpl - document table name
> = ytex.document
> 08 Jul 2014 15:28:00  INFO SentenceDetector - [SegmentsToSkip,
> SentenceModelFile]
> 08 Jul 2014 15:28:00  INFO SentenceDetector - Sentence detector model
> file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
> 08 Jul 2014 15:28:01  INFO POSTagger - POS tagger model file:
> org/apache/ctakes/postagger/models/mayo-pos.zip
> Loading configuration.
> Loading feature templates.
> Loading model:
> .
> Loading configuration.
> Loading feature templates.
> Loading lexica.
> Loading model:
> ...
> Loading model:
> .
> Loading model:
> .
> Loading model:
> .
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> .
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> .......
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> ..........
> Loading model:
> .
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> ...
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> ...
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> ....
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> ...
> Loading model:
> .
> Loading configuration.
> Loading feature templates.
> Loading lexica.
> Loading model:
> ................................
> Loading model:
> .............................
> 08 Jul 2014 15:28:07  INFO Chunker - Chunker model file:
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT\resources\org\apache\ctakes\chunker\models\chunker-model.zip
> 08 Jul 2014 15:28:07  INFO InitableJdbcConnectionResourceImpl - Connection
> established to: jdbc:mysql://localhost:3306/ytex?autoReconnect=true
> 08 Jul 2014 15:28:07  INFO DictionaryLookupAnnotator - Parsing descriptor:
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT\resources\org\apache\ctakes\ytex\dictionary\lookup\LookupDesc_SNOMED.xml
> 08 Jul 2014 15:28:07  INFO FirstTokenPermLookupInitializerImpl - Exclusion
> tagset loaded: [dt, to, rp, ls, pos, md, vbd, vbg, vb, ex, vbp, vbn, pdt,
> vbz, wp, wrb, in, wps, pp$, prp$, wdt, prp, pp, cc, cd]
> 08 Jul 2014 15:28:08  INFO AssertionAnalysisEngine - scope model file:
> /C:/ctakes/ctakes-distribution/target/apache-ctakes-3.1.2-SNAPSHOT/resources/org/apache/ctakes/assertion/models/scope.model
> 08 Jul 2014 15:28:08  INFO AssertionAnalysisEngine - cue model file:
> /C:/ctakes/ctakes-distribution/target/apache-ctakes-3.1.2-SNAPSHOT/resources/org/apache/ctakes/assertion/models/cue.model
> scope model:
> /C:/ctakes/ctakes-distribution/target/apache-ctakes-3.1.2-SNAPSHOT/resources/org/apache/ctakes/assertion/models/scope.model
> 08 Jul 2014 15:28:09  INFO AssertionAnalysisEngine - pos model file:
> /C:/ctakes/ctakes-distribution/target/apache-ctakes-3.1.2-SNAPSHOT/resources/org/apache/ctakes/assertion/models/pos.model
> Jul 08, 2014 3:28:21 PM org.mitre.medfacts.i2b2.cli.BatchRunner
> loadEnabledFeaturesFromFile
> INFO: opening enabled features file:
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT\resources\org\apache\ctakes\assertion\models\featureFile11b
>
> Jul 08, 2014 3:28:24 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.
> Jul 08, 2014 3:28:24 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.
> Jul 08, 2014 3:28:24 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.
> Jul 08, 2014 3:28:24 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.
> 08 Jul 2014 15:28:24  INFO LvgCmdApiResourceImpl - Loading NLM Norm and
> Lvg with config file =
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT\resources\org\apache\ctakes\lvg\data\config\lvg.properties
> 08 Jul 2014 15:28:24  INFO LvgCmdApiResourceImpl -   config file absolute
> path =
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT\resources\org\apache\ctakes\lvg\data\config\lvg.properties
> 08 Jul 2014 15:28:24  INFO LvgCmdApiResourceImpl - cwd =
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT
> 08 Jul 2014 15:28:24  INFO LvgCmdApiResourceImpl - cd
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT\resources\org\apache\ctakes\lvg\
> 08 Jul 2014 15:28:26  INFO LvgCmdApiResourceImpl - cd
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT
> 08 Jul 2014 15:28:27  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=1}
> 08 Jul 2014 15:28:27  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=2}
> 08 Jul 2014 15:28:27  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:28:27  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=3}
> 08 Jul 2014 15:28:27  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:28:27  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:28:32  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:28:32  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:28:32  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:28:32  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:28:32  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:28:32  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:28:32  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:28:32  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:28:39  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:28:39  INFO ConceptConverterAnalysisEngine -     total
> annotation count 329
> 08 Jul 2014 15:28:39  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 18
> 08 Jul 2014 15:28:39  INFO ConceptConverterAnalysisEngine -     total
> annotation count 347
> 08 Jul 2014 15:28:39  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:28:39  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:28:39 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:28:39 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:28:41 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:28:42 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:28:43  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=4}
> 08 Jul 2014 15:28:43  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:28:43  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:28:43  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:28:46  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:28:46  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:28:46  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:28:47  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:28:47  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:28:47  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:28:47  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:28:47  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:28:52  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:28:52  INFO ConceptConverterAnalysisEngine -     total
> annotation count 239
> 08 Jul 2014 15:28:52  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 19
> 08 Jul 2014 15:28:52  INFO ConceptConverterAnalysisEngine -     total
> annotation count 258
> 08 Jul 2014 15:28:52  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:28:52  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:28:52 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:28:52 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:28:53 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:28:53 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:28:53  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=5}
> 08 Jul 2014 15:28:53  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:28:53  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:28:53  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:28:54  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:28:54  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:28:54  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:28:54  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:28:54  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:28:54  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:28:54  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:28:54  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:28:55  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:28:55  INFO ConceptConverterAnalysisEngine -     total
> annotation count 120
> 08 Jul 2014 15:28:55  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 11
> 08 Jul 2014 15:28:55  INFO ConceptConverterAnalysisEngine -     total
> annotation count 131
> 08 Jul 2014 15:28:55  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:28:55  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:28:55 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:28:55 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:28:56 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:28:56 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:28:56  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=6}
> 08 Jul 2014 15:28:56  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:28:56  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:28:56  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:28:57  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:28:57  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:28:57  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:28:57  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:28:57  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:28:57  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:28:57  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:28:57  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:28:58  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:28:58  INFO ConceptConverterAnalysisEngine -     total
> annotation count 252
> 08 Jul 2014 15:28:58  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 9
> 08 Jul 2014 15:28:58  INFO ConceptConverterAnalysisEngine -     total
> annotation count 261
> 08 Jul 2014 15:28:58  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:28:58  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:28:58 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:28:58 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:28:59 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:28:59 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:28:59  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:28:59  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:28:59  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:28:59  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=7}
> 08 Jul 2014 15:29:00  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:00  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:00  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:00  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:00  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:00  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:00  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:00  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:00  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:00  INFO ConceptConverterAnalysisEngine -     total
> annotation count 155
> 08 Jul 2014 15:29:00  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 5
> 08 Jul 2014 15:29:00  INFO ConceptConverterAnalysisEngine -     total
> annotation count 160
> 08 Jul 2014 15:29:00  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:00  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:00 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:00 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:01 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:01 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:01  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=8}
> 08 Jul 2014 15:29:01  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:01  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:01  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:04  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:04  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:04  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:04  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:04  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:04  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:04  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:04  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:06  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:06  INFO ConceptConverterAnalysisEngine -     total
> annotation count 216
> 08 Jul 2014 15:29:06  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 20
> 08 Jul 2014 15:29:06  INFO ConceptConverterAnalysisEngine -     total
> annotation count 236
> 08 Jul 2014 15:29:06  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:06  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:06 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:06 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:07 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:07 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:07  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=9}
> 08 Jul 2014 15:29:07  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:07  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:07  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:07  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:07  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:07  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:07  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:07  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:07  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:07  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:07  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:08  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:08  INFO ConceptConverterAnalysisEngine -     total
> annotation count 233
> 08 Jul 2014 15:29:08  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 12
> 08 Jul 2014 15:29:08  INFO ConceptConverterAnalysisEngine -     total
> annotation count 245
> 08 Jul 2014 15:29:08  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:08  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:08 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:08 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:09 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:09 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:09  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=10}
> 08 Jul 2014 15:29:09  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:09  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:09  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:10  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:10  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:10  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:10  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:10  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:10  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:10  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:10  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:11  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:11  INFO ConceptConverterAnalysisEngine -     total
> annotation count 79
> 08 Jul 2014 15:29:11  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 5
> 08 Jul 2014 15:29:11  INFO ConceptConverterAnalysisEngine -     total
> annotation count 84
> 08 Jul 2014 15:29:11  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:11  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:11 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:11 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:12 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:12 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:12  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=11}
> 08 Jul 2014 15:29:12  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:12  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:12  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:12  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:12  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:12  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:12  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:12  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:12  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:12  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:12  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:13  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:13  INFO ConceptConverterAnalysisEngine -     total
> annotation count 194
> 08 Jul 2014 15:29:13  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 9
> 08 Jul 2014 15:29:13  INFO ConceptConverterAnalysisEngine -     total
> annotation count 203
> 08 Jul 2014 15:29:13  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:13  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:13 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:13 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:13 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:13 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:13  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=12}
> 08 Jul 2014 15:29:13  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:13  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:13  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:15  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:15  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:15  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:15  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:15  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:15  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:15  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:15  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:16  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:16  INFO ConceptConverterAnalysisEngine -     total
> annotation count 249
> 08 Jul 2014 15:29:16  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 19
> 08 Jul 2014 15:29:16  INFO ConceptConverterAnalysisEngine -     total
> annotation count 268
> 08 Jul 2014 15:29:16  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:16  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:16 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:16 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:17 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:17 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:17  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=13}
> 08 Jul 2014 15:29:17  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:17  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:17  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:18  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:18  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:18  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:18  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:18  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:18  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:18  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:18  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:18  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:18  INFO ConceptConverterAnalysisEngine -     total
> annotation count 254
> 08 Jul 2014 15:29:18  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 16
> 08 Jul 2014 15:29:18  INFO ConceptConverterAnalysisEngine -     total
> annotation count 270
> 08 Jul 2014 15:29:18  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:18  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:18 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:18 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:19 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:19 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:19  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=14}
> 08 Jul 2014 15:29:19  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:19  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:19  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:21  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:21  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:21  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:21  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:21  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:21  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:21  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:21  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:23  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:23  INFO ConceptConverterAnalysisEngine -     total
> annotation count 332
> 08 Jul 2014 15:29:23  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 13
> 08 Jul 2014 15:29:23  INFO ConceptConverterAnalysisEngine -     total
> annotation count 345
> 08 Jul 2014 15:29:23  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:23  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:23 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:23 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:24 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:24 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:24  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=15}
> 08 Jul 2014 15:29:24  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:24  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:24  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:25  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:25  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:25  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:25  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:25  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:25  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:25  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:25  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:25  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:25  INFO ConceptConverterAnalysisEngine -     total
> annotation count 245
> 08 Jul 2014 15:29:25  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 11
> 08 Jul 2014 15:29:25  INFO ConceptConverterAnalysisEngine -     total
> annotation count 256
> 08 Jul 2014 15:29:25  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:25  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:25 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:25 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:26 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:26 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:26  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=16}
> 08 Jul 2014 15:29:26  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:26  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:26  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:27  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:27  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:27  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:27  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:27  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:27  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:27  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:27  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:27  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:27  INFO ConceptConverterAnalysisEngine -     total
> annotation count 178
> 08 Jul 2014 15:29:27  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 10
> 08 Jul 2014 15:29:27  INFO ConceptConverterAnalysisEngine -     total
> annotation count 188
> 08 Jul 2014 15:29:27  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:27  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:27 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:27 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:28 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:28 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:28  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=17}
> 08 Jul 2014 15:29:28  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:28  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:28  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:31  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:31  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:31  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:31  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:31  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:31  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:31  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:31  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:32  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:32  INFO ConceptConverterAnalysisEngine -     total
> annotation count 487
> 08 Jul 2014 15:29:32  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 24
> 08 Jul 2014 15:29:32  INFO ConceptConverterAnalysisEngine -     total
> annotation count 511
> 08 Jul 2014 15:29:32  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:32  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:32 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:32 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:33 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:33 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:33  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:33  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:33  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:33  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=18}
> 08 Jul 2014 15:29:35  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:35  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:35  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:36  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:36  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:36  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:36  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:36  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:37  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:37  INFO ConceptConverterAnalysisEngine -     total
> annotation count 630
> 08 Jul 2014 15:29:37  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 35
> 08 Jul 2014 15:29:37  INFO ConceptConverterAnalysisEngine -     total
> annotation count 665
> 08 Jul 2014 15:29:37  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:37  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:37 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:38 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:38 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:38 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:39  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:39  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=19}
> 08 Jul 2014 15:29:39  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:39  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:39  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:39  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:39  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:39  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:39  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:39  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:39  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:39  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:39  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:39  INFO ConceptConverterAnalysisEngine -     total
> annotation count 179
> 08 Jul 2014 15:29:39  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 9
> 08 Jul 2014 15:29:39  INFO ConceptConverterAnalysisEngine -     total
> annotation count 188
> 08 Jul 2014 15:29:39  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:39  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:39 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:39 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:40 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:40 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:40  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=20}
> 08 Jul 2014 15:29:40  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:40  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:40  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:40  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:40  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:40  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:40  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:40  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:40  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:40  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:40  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:40  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:40  INFO ConceptConverterAnalysisEngine -     total
> annotation count 110
> 08 Jul 2014 15:29:40  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 6
> 08 Jul 2014 15:29:40  INFO ConceptConverterAnalysisEngine -     total
> annotation count 116
> 08 Jul 2014 15:29:40  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:40  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:40 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:40 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:41 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:41 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:41  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=21}
> 08 Jul 2014 15:29:41  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:41  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:41  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:41  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:41  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:41  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:41  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:41  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:41  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:41  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:41  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:42  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:42  INFO ConceptConverterAnalysisEngine -     total
> annotation count 38
> 08 Jul 2014 15:29:42  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 5
> 08 Jul 2014 15:29:42  INFO ConceptConverterAnalysisEngine -     total
> annotation count 43
> 08 Jul 2014 15:29:42  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:42  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:42 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:42 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:42 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:42 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:42  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=22}
> 08 Jul 2014 15:29:42  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:42  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:42  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:43  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:43  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:43  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:43  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:43  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:43  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:43  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:43  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:43  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:43  INFO ConceptConverterAnalysisEngine -     total
> annotation count 162
> 08 Jul 2014 15:29:43  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 14
> 08 Jul 2014 15:29:43  INFO ConceptConverterAnalysisEngine -     total
> annotation count 176
> 08 Jul 2014 15:29:43  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:43  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:43 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:43 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:44 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:44 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:44  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=23}
> 08 Jul 2014 15:29:44  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:44  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:44  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:45  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:45  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:45  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:45  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:45  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:45  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:45  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:45  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:46  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:46  INFO ConceptConverterAnalysisEngine -     total
> annotation count 261
> 08 Jul 2014 15:29:46  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 22
> 08 Jul 2014 15:29:46  INFO ConceptConverterAnalysisEngine -     total
> annotation count 283
> 08 Jul 2014 15:29:46  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:46  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:46 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:46 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:47 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:47 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:47  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=24}
> 08 Jul 2014 15:29:47  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:47  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:47  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:48  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:48  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:48  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:48  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:48  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:48  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:48  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:48  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:48  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:48  INFO ConceptConverterAnalysisEngine -     total
> annotation count 308
> 08 Jul 2014 15:29:48  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 19
> 08 Jul 2014 15:29:48  INFO ConceptConverterAnalysisEngine -     total
> annotation count 327
> 08 Jul 2014 15:29:48  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:48  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:48 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:48 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:49 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:49 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:49  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=25}
> 08 Jul 2014 15:29:49  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:49  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:49  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:50  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:50  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:50  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:50  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:50  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:50  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:50  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:50  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:50  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:50  INFO ConceptConverterAnalysisEngine -     total
> annotation count 352
> 08 Jul 2014 15:29:50  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 21
> 08 Jul 2014 15:29:50  INFO ConceptConverterAnalysisEngine -     total
> annotation count 373
> 08 Jul 2014 15:29:50  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:50  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:50 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:50 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:51 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:51 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:51  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=26}
> 08 Jul 2014 15:29:51  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:51  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:51  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:51  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:51  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:51  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:51  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:51  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:51  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:51  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:51  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:51  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:51  INFO ConceptConverterAnalysisEngine -     total
> annotation count 306
> 08 Jul 2014 15:29:51  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 22
> 08 Jul 2014 15:29:51  INFO ConceptConverterAnalysisEngine -     total
> annotation count 328
> 08 Jul 2014 15:29:51  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:51  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:51 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:51 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:52 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:52 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:52  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=27}
> 08 Jul 2014 15:29:52  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:52  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:52  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:54  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:54  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:54  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:54  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:54  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:54  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:54  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:54  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:56  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:56  INFO ConceptConverterAnalysisEngine -     total
> annotation count 497
> 08 Jul 2014 15:29:56  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 41
> 08 Jul 2014 15:29:56  INFO ConceptConverterAnalysisEngine -     total
> annotation count 538
> 08 Jul 2014 15:29:56  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:56  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:56 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:56 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:57 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:57 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:57  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=28}
> 08 Jul 2014 15:29:57  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:57  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:57  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:57  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:57  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:57  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:57  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:57  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:57  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:57  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:57  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:58  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:58  INFO ConceptConverterAnalysisEngine -     total
> annotation count 273
> 08 Jul 2014 15:29:58  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 14
> 08 Jul 2014 15:29:58  INFO ConceptConverterAnalysisEngine -     total
> annotation count 287
> 08 Jul 2014 15:29:58  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:58  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:58 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:58 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:58 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:58 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:58  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=29}
> 08 Jul 2014 15:29:58  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:58  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:58  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:29:58  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:29:58  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:29:58  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:29:58  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:58  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:29:58  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:29:58  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:29:58  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:29:58  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:29:58  INFO ConceptConverterAnalysisEngine -     total
> annotation count 199
> 08 Jul 2014 15:29:58  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 7
> 08 Jul 2014 15:29:58  INFO ConceptConverterAnalysisEngine -     total
> annotation count 206
> 08 Jul 2014 15:29:58  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:29:58  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:29:58 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:29:58 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:29:59 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:29:59 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:29:59  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=30}
> 08 Jul 2014 15:29:59  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:29:59  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:29:59  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:30:00  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:30:00  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:30:00  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:30:00  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:30:00  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:30:00  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:30:00  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:30:00  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:30:00  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:30:00  INFO ConceptConverterAnalysisEngine -     total
> annotation count 198
> 08 Jul 2014 15:30:00  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 12
> 08 Jul 2014 15:30:00  INFO ConceptConverterAnalysisEngine -     total
> annotation count 210
> 08 Jul 2014 15:30:00  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:30:00  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:30:00 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:30:00 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:30:01 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:30:01 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:30:01  INFO DBCollectionReader - loading document with id =
> {INSTANCE_ID=31}
> 08 Jul 2014 15:30:01  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:30:01  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:30:01  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:30:02  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:30:02  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:30:02  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:30:02  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:30:02  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:30:02  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:30:02  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:30:02  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:30:03  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:30:03  INFO ConceptConverterAnalysisEngine -     total
> annotation count 351
> 08 Jul 2014 15:30:03  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 16
> 08 Jul 2014 15:30:03  INFO ConceptConverterAnalysisEngine -     total
> annotation count 367
> 08 Jul 2014 15:30:03  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:30:03  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:30:03 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:30:03 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:30:04 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:30:04 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:30:04  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:30:04  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:30:04  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:30:04  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:30:04  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:30:04  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:30:04  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:30:04  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:30:04  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:30:04  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:30:04  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:30:04  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:30:04  INFO ConceptConverterAnalysisEngine -     total
> annotation count 74
> 08 Jul 2014 15:30:04  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 7
> 08 Jul 2014 15:30:04  INFO ConceptConverterAnalysisEngine -     total
> annotation count 81
> 08 Jul 2014 15:30:04  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:30:04  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:30:04 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:30:04 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:30:05 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:30:05 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
> 08 Jul 2014 15:30:05  INFO SentenceDetector - Starting processing.
> 08 Jul 2014 15:30:05  INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 08 Jul 2014 15:30:05  INFO LvgAnnotator - process(JCas)
> 08 Jul 2014 15:30:06  INFO ContextDependentTokenizerAnnotator -
> process(JCas)
> 08 Jul 2014 15:30:06  INFO POSTagger - process(JCas)
> 08 Jul 2014 15:30:06  INFO Chunker -  process(JCas)
> 08 Jul 2014 15:30:06  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:30:06  INFO ChunkAdjuster -  process(JCas)
> 08 Jul 2014 15:30:06  INFO CopyAnnotator - process(JCas)
> 08 Jul 2014 15:30:06  INFO OverlapAnnotator - process(JCas)
> 08 Jul 2014 15:30:06  INFO DictionaryLookupAnnotator - process(JCas)
> 08 Jul 2014 15:30:06  INFO ConceptConverterAnalysisEngine - beginning of
> ConceptConverterAnalysisEngine.process()
> 08 Jul 2014 15:30:06  INFO ConceptConverterAnalysisEngine -     total
> annotation count 419
> 08 Jul 2014 15:30:06  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EntityMention annotation count 23
> 08 Jul 2014 15:30:06  INFO ConceptConverterAnalysisEngine -     total
> annotation count 442
> 08 Jul 2014 15:30:06  INFO ConceptConverterAnalysisEngine -
> org.apache.ctakes.typesystem.type.textsem.EventMention annotation count 0
> 08 Jul 2014 15:30:06  INFO ConceptConverterAnalysisEngine - end of
> ConceptConverterAnalysisEngine.process()
> Jul 08, 2014 3:30:06 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> BEGIN
> (stdout statement) SingleDocumentProcessor.processSingleDocument() BEGIN
> Jul 08, 2014 3:30:06 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() BEGIN
> (logging statement) SingleDocumentProcessor.processZones() BEGIN
> Jul 08, 2014 3:30:07 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processZones
> INFO: (logging statement) SingleDocumentProcessor.processZones() END
> (logging statement) SingleDocumentProcessor.processZones() END
> Jul 08, 2014 3:30:07 PM
> org.mitre.medfacts.i2b2.api.SingleDocumentProcessor processSingleDocument
> INFO: (logging statement) SingleDocumentProcessor.processSingleDocument()
> END
> (stdout statement) SingleDocumentProcessor.processSingleDocument() END
>
> C:\ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT>ENDLOCAL
>
>
>
> On Tue, Jul 8, 2014 at 2:55 PM, vijay garla <vngarla@gmail.com> wrote:
>
>> My bad, the default log4j config just sends everything to the console.
>>  Can
>> you run the cpe, can you redirect the output to a file like this:
>> runctakesCPE.bat > cpe.log 2>&1
>>
>> vj
>>
>>
>> On Tue, Jul 8, 2014 at 6:01 PM, Clayton Turner <caturner3@g.cofc.edu>
>> wrote:
>>
>> > I don't see a log file when running the CPE. When running the CVD I have
>> > access to a log file within the gui, but that does not seem to be
>> present
>> > here. Is there a specific place that this log file is saved?
>> >
>> >
>> > On Tue, Jul 8, 2014 at 3:14 AM, vijay garla <vngarla@gmail.com> wrote:
>> >
>> > > Hi Clayton,
>> > >
>> > > The screenshot is not coming through via the newsgroup emails.  can
>> you
>> > > attach the log file?
>> > >
>> > > vj
>> > >
>> > >
>> > > On Mon, Jul 7, 2014 at 5:38 PM, Clayton Turner <caturner3@g.cofc.edu>
>> > > wrote:
>> > >
>> > > > Any update on this issue? I have this problem even if I don't use
>> the
>> > > ytex
>> > > > version of the aggregate text processor (UMLS-independent as well).
>> > > >
>> > > >
>> > > > On Thu, Jul 3, 2014 at 2:33 PM, Clayton Turner <
>> caturner3@g.cofc.edu>
>> > > > wrote:
>> > > >
>> > > >> Yes, I am running the fracture_demo.xml cpe.
>> > > >>
>> > > >> There is no option for the analysis batch (that's the main issue).
>> I
>> > > also
>> > > >> get no response in my MySQL database (umls installed - not sure if
>> > that
>> > > can
>> > > >> be related).
>> > > >>
>> > > >> Here's a screenshot of my CPE (using ytex):
>> > > >> [image: Inline image 1]
>> > > >>
>> > > >>
>> > > >>
>> > > >>
>> > > >> On Wed, Jul 2, 2014 at 10:48 PM, vijay garla <vngarla@gmail.com>
>> > wrote:
>> > > >>
>> > > >>> Hi clayton,
>> > > >>>
>> > > >>> I assume you are running the fracture_demo.xml cpe - is that
>> correct?
>> > > >>>  The CPE GUI should give you the option to set the analysis batch.
>> > (see
>> > > >>> attached screenshot).  That being said, the analysis_batch is not
>> > > required
>> > > >>> (it will default to the current date).  Can you attach the log
>> file?
>> > > >>>
>> > > >>> -vj
>> > > >>>
>> > > >>> [image: Inline image 1]
>> > > >>>
>> > > >>>
>> > > >>> On Wed, Jul 2, 2014 at 12:22 PM, Clayton Turner <
>> > caturner3@g.cofc.edu>
>> > > >>> wrote:
>> > > >>>
>> > > >>>> Hi, I'm a relatively new user of cTAKES.
>> > > >>>>
>> > > >>>> I recently cloned cTAKES from the repository and I am using UMLS
>> > > >>>> installed
>> > > >>>> in my mysql database. I have recently noticed an issue, though.
>> When
>> > > >>>> conducting the bone fracture demo, In the CPE, I use the
>> > > >>>> DBCollectionReader
>> > > >>>> and Analysis Engine from the ctakes-ytex-uima directory within my
>> > > >>>> CTAKES_HOME.
>> > > >>>>
>> > > >>>> I can get this to run successfully, but I am not able to specify
>> an
>> > > >>>> "analysis batch" in the CPE. Because of this, my ytex database is
>> > not
>> > > >>>> being
>> > > >>>> updated with results of the CPE run (in the v_document tables).
>> Any
>> > > >>>> ideas
>> > > >>>> why the analysis batch field is missing?
>> > > >>>>
>> > > >>>> Side question: Any update on when cTAKES 3.2 will be officially
>> > > >>>> released? I
>> > > >>>> see we're passed the expected release and was curious on how
>> long it
>> > > >>>> will
>> > > >>>> be until it will officially come out.
>> > > >>>>
>> > > >>>> Thanks a lot,
>> > > >>>> --
>> > > >>>> Clayton Turner
>> > > >>>>
>> > > >>>
>> > > >>>
>> > > >>
>> > > >>
>> > > >> --
>> > > >> --
>> > > >> Clayton Turner
>> > > >> email: caturner3@g.cofc.edu
>> > > >> phone: (843)-424-3784
>> > > >> web: claytonturner.blogspot.com
>> > > >>
>> > > >>
>> > >
>> >
>> -------------------------------------------------------------------------------------------------
>> > > >> “When scientifically investigating the natural world, the only
>> thing
>> > > >> worse than a blind believer is a seeing denier.”
>> > > >> - Neil deGrasse Tyson
>> > > >>
>> > > >
>> > > >
>> > > >
>> > > > --
>> > > > --
>> > > > Clayton Turner
>> > > > email: caturner3@g.cofc.edu
>> > > > phone: (843)-424-3784
>> > > > web: claytonturner.blogspot.com
>> > > >
>> > > >
>> > >
>> >
>> -------------------------------------------------------------------------------------------------
>> > > > “When scientifically investigating the natural world, the only thing
>> > > worse
>> > > > than a blind believer is a seeing denier.”
>> > > > - Neil deGrasse Tyson
>> > > >
>> > >
>> >
>> >
>> >
>> > --
>> > --
>> > Clayton Turner
>> > email: caturner3@g.cofc.edu
>> > phone: (843)-424-3784
>> > web: claytonturner.blogspot.com
>> >
>> >
>> -------------------------------------------------------------------------------------------------
>> > “When scientifically investigating the natural world, the only thing
>> worse
>> > than a blind believer is a seeing denier.”
>> > - Neil deGrasse Tyson
>> >
>>
>
>
>
> --
> --
> Clayton Turner
> email: caturner3@g.cofc.edu
> phone: (843)-424-3784
> web: claytonturner.blogspot.com
>
> -------------------------------------------------------------------------------------------------
> “When scientifically investigating the natural world, the only thing worse
> than a blind believer is a seeing denier.”
> - Neil deGrasse Tyson
>

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