You are viewing a plain text version of this content. The canonical link for it is here.
Posted to notifications@ctakes.apache.org by "Sean Finan (Jira)" <ji...@apache.org> on 2022/12/30 22:33:00 UTC
[jira] [Commented] (CTAKES-538) DBCollectionReader throwing an exception while running a piper file
[ https://issues.apache.org/jira/browse/CTAKES-538?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17653203#comment-17653203 ]
Sean Finan commented on CTAKES-538:
-----------------------------------
Parameters cannot have spaces between the parameter name and value.
From your piper:
reader org.apache.ctakes.ytex.uima.DBCollectionReader queryGetDocumentKeys = "select note_id instance_id from kasi.ytex.fracture_demo" queryGetDocument = "select note_text from kasi.ytex.fracture_demo where note_id in (:instance_id)"
add org.apache.ctakes.ytex.uima.annotators.DBConsumer analysisBatch = "test"
> 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
> Priority: Major
> Labels: piper, sql
> 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)
>
>
--
This message was sent by Atlassian Jira
(v8.20.10#820010)