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From Clayton Turner <caturn...@g.cofc.edu>
Subject Re: cTAKES 3.2 Analysis Batch Issue
Date Tue, 08 Jul 2014 19:36:43 GMT
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:
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Loading lexica.
Loading model:
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Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
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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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