Kasi created CTAKES-538:
---------------------------
Summary: DBCollectionReader throwing an exception while running a
piper file
Key: CTAKES-538
URL: https://issues.apache.org/jira/browse/CTAKES-538
Project: cTAKES
Issue Type: Bug
Affects Versions: 4.0.0
Environment: Windows 10 with Java 1.8.0_231
Reporter: Kasi
Attachments: ytexpipertest.piper
I have installed cTakes from
[https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide]
and followed the YTEX installations from
[https://cwiki.apache.org/confluence/display/CTAKES/YTEX+3.2]
I have tested the YTEXinstallation by running the CVD using YTEX Analysis
Engine and the results were what I expected.
I have UMLS installed in the Database. I have been trying to run a piper file
to write results back into the database.
I created a piper file using the pipercreator GUI and it was validated(please
see attachment for piper file)
I've been running into the following error when executing the piper file:
19 Nov 2019 13:15:48 INFO ApplicationContextHolder - loading ytex.properties
from:
[file:/C:/Users/kvegesan/Documents/cTakes_Home/resources/org/apache/ctakes/ytex/ytex.properties|file:///C:/Users/kvegesan/Documents/cTakes_Home/resources/org/apache/ctakes/ytex/ytex.properties]
19 Nov 2019 13:15:48 INFO ApplicationContextHolder -
beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml
19 Nov 2019 13:15:48 INFO ClassPathXmlApplicationContext - Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@2f879bab:
startup date [Tue Nov 19 13:15:48 CST 2019]; root of context hierarchy
19 Nov 2019 13:15:48 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from URL
[jar:file:/C:/Users/kvegesan/Documents/cTakes_Home/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]
19 Nov 2019 13:15:49 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from URL
[jar:file:/C:/Users/kvegesan/Documents/cTakes_Home/lib/ctakes-ytex-web-4.0.0-classes.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]
19 Nov 2019 13:15:49 INFO DefaultListableBeanFactory - Overriding bean
definition for bean 'ytexApplicationContext': replacing [Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[jar:file:/C:/Users/kvegesan/Documents/cTakes_Home/lib/ctakes-ytex-res-4.0.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]]
with [Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[jar:file:/C:/Users/kvegesan/Documents/cTakes_Home/lib/ctakes-ytex-web-4.0.0-classes.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]]
19 Nov 2019 13:15:49 INFO DefaultListableBeanFactory - Pre-instantiating
singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@66e889df:
defining beans [ytexApplicationContext]; root of factory hierarchy
19 Nov 2019 13:15:49 INFO ClassPathXmlApplicationContext - Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@3c017078:
startup date [Tue Nov 19 13:15:49 CST 2019]; root of context hierarchy
19 Nov 2019 13:15:49 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/beans-datasource.xml]
19 Nov 2019 13:15:49 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
19 Nov 2019 13:15:49 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel-sim.xml]
19 Nov 2019 13:15:49 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/uima/beans-uima.hbm.xml]
19 Nov 2019 13:15:49 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/uima/beans-uima-dao.xml]
19 Nov 2019 13:15:49 INFO XmlBeanDefinitionReader - Loading XML bean
definitions from class path resource
[org/apache/ctakes/ytex/uima/beans-uima-mapper.xml]
19 Nov 2019 13:15:49 INFO DefaultListableBeanFactory - Overriding bean
definition for bean 'mapperOperation': replacing [Root bean: class
[org.springframework.aop.aspectj.AspectJExpressionPointcut]; scope=prototype;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null] with [Root
bean: class [org.springframework.aop.aspectj.AspectJExpressionPointcut];
scope=prototype; abstract=false; lazyInit=false; autowireMode=0;
dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null]
19 Nov 2019 13:15:49 INFO PropertyPlaceholderConfigurer - Loading properties
file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
19 Nov 2019 13:15:49 INFO PropertyPlaceholderConfigurer - Loading properties
file from class path resource [org/apache/ctakes/ytex/ytex.properties]
19 Nov 2019 13:15:49 INFO PropertyPlaceholderConfigurer - Loading properties
file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
19 Nov 2019 13:15:49 INFO DefaultListableBeanFactory - Pre-instantiating
singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@71dfcf21:
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,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|#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,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
19 Nov 2019 13:15:49 INFO PropertiesFactoryBean - Loading properties file from
class path resource [org/apache/ctakes/ytex/ytex.properties]
19 Nov 2019 13:15:49 INFO Version - HCANN000001: Hibernate Commons Annotations
\{4.0.2.Final}
19 Nov 2019 13:15:49 INFO Version - HHH000412: Hibernate Core \{4.2.6.Final}
19 Nov 2019 13:15:49 INFO Environment - HHH000206: hibernate.properties not
found
19 Nov 2019 13:15:49 INFO Environment - HHH000021: Bytecode provider name :
javassist
19 Nov 2019 13:15:50 INFO Dialect - HHH000400: Using dialect:
org.hibernate.dialect.SQLServerDialect
19 Nov 2019 13:15:50 WARN RootClass - HHH000038: Composite-id class does not
override equals(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
19 Nov 2019 13:15:50 WARN RootClass - HHH000039: Composite-id class does not
override hashCode(): org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
19 Nov 2019 13:15:50 INFO TransactionFactoryInitiator - HHH000399: Using
default transaction strategy (direct JDBC transactions)
19 Nov 2019 13:15:50 INFO ASTQueryTranslatorFactory - HHH000397: Using
ASTQueryTranslatorFactory
19 Nov 2019 13:15:50 INFO UpdateTimestampsCache - HHH000250: Starting update
timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
19 Nov 2019 13:15:50 INFO StandardQueryCache - HHH000248: Starting query cache
at region: org.hibernate.cache.internal.StandardQueryCache
19 Nov 2019 13:15:50 INFO TableGenerator - HHH000398: Explicit segment value
for id generator [YTEX.hibernate_sequences.sequence_name] suggested; using
default [default]
19 Nov 2019 13:15:50 WARN AbstractEhcacheRegionFactory - HHH020003: Could not
find a specific ehcache configuration for cache named
[org.apache.ctakes.ytex.uima.model.UimaType]; using defaults.
19 Nov 2019 13:15:50 WARN EhcacheAccessStrategyFactoryImpl - HHH020007:
read-only cache configured for mutable entity
[org.apache.ctakes.ytex.uima.model.UimaType]
19 Nov 2019 13:15:51 INFO HibernateTransactionManager - Using DataSource
[org.apache.commons.dbcp.BasicDataSource@5c931134] of Hibernate SessionFactory
for HibernateTransactionManager
19 Nov 2019 13:15:51 INFO EhCacheManagerFactoryBean - Initializing EHCache
CacheManager
19 Nov 2019 13:15:51 WARN CacheManager - Creating a new instance of
CacheManager using the diskStorePath "C:\Users\kvegesan\AppData\Local\Temp\"
which is already used by an existing CacheManager.
The source of the configuration was
net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurationSource@7675c171.
The diskStore path for this CacheManager will be set to
C:\Users\kvegesan\AppData\Local\Temp
ehcache_auto_created_1574190951530.
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.
19 Nov 2019 13:15:51 INFO ConceptSimilarityServiceImpl - begin initialization
for concept graph: sct-umls
19 Nov 2019 13:15:51 INFO ConceptDaoImpl - loading concept graph from
[file:/C:/Users/kvegesan/Documents/cTakes_Home/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls.gz|file:///C:/Users/kvegesan/Documents/cTakes_Home/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls.gz]
19 Nov 2019 13:15:53 INFO ConceptDaoImpl - concept graph sct-umls, vertices:
387110
19 Nov 2019 13:15:53 INFO ConceptSimilarityServiceImpl - initializing
similarity measures
19 Nov 2019 13:15:53 INFO ConceptSimilarityServiceImpl - loading corpus
infocontent for corpusName=, conceptGraphName=sct-umls, conceptSetName=
19 Nov 2019 13:15:53 WARN ConceptSimilarityServiceImpl - IC not found
19 Nov 2019 13:15:53 INFO ConceptSimilarityServiceImpl - end initialization
for concept graph: sct-umls
19 Nov 2019 13:15:54 INFO Dialect - HHH000400: Using dialect:
org.hibernate.dialect.SQLServerDialect
19 Nov 2019 13:15:54 INFO DocumentMapperServiceImpl - document table name =
YTEX.document
Exception in thread "main" java.lang.IllegalArgumentException: SQL must not be
null
at org.springframework.util.Assert.notNull(Assert.java:112)
at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:432)
at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:464)
at
org.springframework.jdbc.core.JdbcTemplate.queryForList(JdbcTemplate.java:495)
at
org.springframework.jdbc.core.simple.SimpleJdbcTemplate.queryForList(SimpleJdbcTemplate.java:238)
at
org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCollectionReader.java:179)
at
org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCollectionReader.java:173)
at
org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:130)
at
org.apache.ctakes.ytex.uima.DBCollectionReader.loadDocumentIds(DBCollectionReader.java:173)
at
org.apache.ctakes.ytex.uima.DBCollectionReader.initialize(DBCollectionReader.java:116)
at
org.apache.uima.collection.CollectionReader_ImplBase.initialize(CollectionReader_ImplBase.java:70)
at
org.apache.uima.impl.CollectionReaderFactory_impl.produceResource(CollectionReaderFactory_impl.java:103)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:331)
at
org.apache.uima.UIMAFramework.produceCollectionReader(UIMAFramework.java:812)
at
org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:133)
at
org.apache.ctakes.core.pipeline.PipelineBuilder.run(PipelineBuilder.java:293)
at
org.apache.ctakes.core.pipeline.PiperFileRunner.main(PiperFileRunner.java:81)
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