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From "Alex Zbarcea (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-334) GramMatrixExporterImpl initialization failed
Date Wed, 11 Oct 2017 20:54:01 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-334?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16200942#comment-16200942
] 

Alex Zbarcea commented on CTAKES-334:
-------------------------------------

Looking more in depth about this issue, it seems that the script was intended to be more of
a UTest. In order to unlock the issue: 

{code}
$ cp ./target/test-classes/org/apache/ctakes/ytex/ytex.properties ./target/classes/org/apache/ctakes/ytex/ytex.properties

$ mkdir -p ctakes-ytex-uima/target/classes/org/apache/ctakes/ytex/umls/model
mkdir: created directory 'ctakes-ytex-uima/target/classes/org/apache/ctakes/ytex/umls'
mkdir: created directory 'ctakes-ytex-uima/target/classes/org/apache/ctakes/ytex/umls/model'

$ cp ./ctakes-ytex-uima/target/test-classes/org/apache/ctakes/ytex/umls/model/UMLS.hbm.xml
\
        ./ctakes-ytex-uima/target/classes/org/apache/ctakes/ytex/umls/model/UMLS.hbm.xml
{code}

After these steps I got into, which looks more like an issue with the resource.

{code}
Exception in thread "main" org.hibernate.exception.SQLGrammarException: could not prepare
statement
	at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:82)
	at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49)
	at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:125)
	at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:188)
	at org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(StatementPreparerImpl.java:159)
	at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1859)
	at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1836)
	at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1816)
	at org.hibernate.loader.Loader.doQuery(Loader.java:900)
	at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:342)
	at org.hibernate.loader.Loader.doList(Loader.java:2526)
	at org.hibernate.loader.Loader.doList(Loader.java:2512)
	at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2342)
	at org.hibernate.loader.Loader.list(Loader.java:2337)
	at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:495)
	at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:357)
	at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:195)
	at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1269)
	at org.hibernate.internal.QueryImpl.list(QueryImpl.java:101)
	at org.hibernate.internal.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:909)
	at org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl.getLastAui(UMLSDaoImpl.java:144)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:319)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:90)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
	at com.sun.proxy.$Proxy9.getLastAui(Unknown Source)
	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:202)
	at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
Caused by: java.sql.SQLSyntaxErrorException: user lacks privilege or object not found: UMLS_AUI_FWORD
	at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
	at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
	at org.hsqldb.jdbc.JDBCPreparedStatement.<init>(Unknown Source)
	at org.hsqldb.jdbc.JDBCConnection.prepareStatement(Unknown Source)
	at org.apache.commons.dbcp.DelegatingConnection.prepareStatement(DelegatingConnection.java:281)
	at org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.prepareStatement(PoolingDataSource.java:313)
	at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(StatementPreparerImpl.java:161)
	at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:182)
	... 32 more
Caused by: org.hsqldb.HsqlException: user lacks privilege or object not found: UMLS_AUI_FWORD
	at org.hsqldb.error.Error.error(Unknown Source)
	at org.hsqldb.error.Error.error(Unknown Source)
	at org.hsqldb.SchemaManager.getTable(Unknown Source)
	at org.hsqldb.ParserDQL.readTableName(Unknown Source)
	at org.hsqldb.ParserDQL.readTableOrSubquery(Unknown Source)
	at org.hsqldb.ParserDQL.XreadTableReference(Unknown Source)
	at org.hsqldb.ParserDQL.XreadFromClause(Unknown Source)
	at org.hsqldb.ParserDQL.XreadTableExpression(Unknown Source)
	at org.hsqldb.ParserDQL.XreadQuerySpecification(Unknown Source)
	at org.hsqldb.ParserDQL.XreadSimpleTable(Unknown Source)
	at org.hsqldb.ParserDQL.XreadQueryPrimary(Unknown Source)
	at org.hsqldb.ParserDQL.XreadQueryTerm(Unknown Source)
	at org.hsqldb.ParserDQL.XreadQueryExpressionBody(Unknown Source)
	at org.hsqldb.ParserDQL.XreadQueryExpression(Unknown Source)
	at org.hsqldb.ParserDQL.compileCursorSpecification(Unknown Source)
	at org.hsqldb.ParserCommand.compilePart(Unknown Source)
	at org.hsqldb.ParserCommand.compileStatement(Unknown Source)
	at org.hsqldb.Session.compileStatement(Unknown Source)
	at org.hsqldb.StatementManager.compile(Unknown Source)
	at org.hsqldb.Session.execute(Unknown Source)
	... 38 more

Process finished with exit code 1
{code}

> GramMatrixExporterImpl initialization failed
> --------------------------------------------
>
>                 Key: CTAKES-334
>                 URL: https://issues.apache.org/jira/browse/CTAKES-334
>             Project: cTAKES
>          Issue Type: Bug
>          Components: ctakes-ytex
>    Affects Versions: 3.2.0, 3.1.1
>            Reporter: vijay
>             Fix For: 3.2.1
>
>         Attachments: ctakes-334.patch
>
>
> Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl];
nested exception is java.beans.IntrospectionException: type mismatch between read and write
methods
> {code}
>  Exception in thread "main" java.lang.ExceptionInInitializerError
>      [java]     at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.setupAuiFirstWord(SetupAuiFirstWord.java:190)
>      [java]     at org.apache.ctakes.ytex.tools.SetupAuiFirstWord.main(SetupAuiFirstWord.java:186)
>      [java] Caused by: org.springframework.beans.factory.access.BootstrapException: Unable
to initialize group definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml],
factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/media/nino/Dati/apache-ctakes-3.2.0/lib/ctakes-ytex-web-3.2.0-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]:
Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException:
Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]:
Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]:
Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException:
Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl];
nested exception is java.beans.IntrospectionException: type mismatch between read and write
methods
>      [java]     at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:386)
>      [java]     at org.apache.ctakes.ytex.kernel.KernelContextHolder.<clinit>(KernelContextHolder.java:28)
>      [java]     ... 2 more
>      [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'kernelApplicationContext' defined in URL [jar:file:/media/nino/Dati/apache-ctakes-3.2.0/lib/ctakes-ytex-web-3.2.0-classes.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]:
Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException:
Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]:
Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]:
Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException:
Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl];
nested exception is java.beans.IntrospectionException: type mismatch between read and write
methods
>      [java]     at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:288)
>      [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1035)
>      [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:939)
>      [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
>      [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
>      [java]     at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
>      [java]     at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
>      [java]     at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
>      [java]     at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
>      [java]     at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
>      [java]     at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
>      [java]     at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
>      [java]     at org.springframework.context.access.ContextSingletonBeanFactoryLocator.initializeDefinition(ContextSingletonBeanFactoryLocator.java:143)
>      [java]     at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:381)
>      [java]     ... 3 more
>      [java] Caused by: org.springframework.beans.BeanInstantiationException: Could not
instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]:
Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]:
Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException:
Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl];
nested exception is java.beans.IntrospectionException: type mismatch between read and write
methods
>      [java]     at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:162)
>      [java]     at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:110)
>      [java]     at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:280)
>      [java]     ... 16 more
>      [java] Caused by: org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]:
Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException:
Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl];
nested exception is java.beans.IntrospectionException: type mismatch between read and write
methods
>      [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:527)
>      [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
>      [java]     at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
>      [java]     at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
>      [java]     at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
>      [java]     at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
>      [java]     at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
>      [java]     at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
>      [java]     at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
>      [java]     at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
>      [java]     at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
>      [java]     at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>      [java]     at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>      [java]     at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>      [java]     at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
>      [java]     at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
>      [java]     ... 18 more
>      [java] Caused by: org.springframework.beans.FatalBeanException: Failed to obtain
BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl]; nested exception
is java.beans.IntrospectionException: type mismatch between read and write methods
>      [java]     at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:262)
>      [java]     at org.springframework.beans.CachedIntrospectionResults.forClass(CachedIntrospectionResults.java:149)
>      [java]     at org.springframework.beans.BeanWrapperImpl.getCachedIntrospectionResults(BeanWrapperImpl.java:324)
>      [java]     at org.springframework.beans.BeanWrapperImpl.getPropertyDescriptors(BeanWrapperImpl.java:331)
>      [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.filterPropertyDescriptorsForDependencyCheck(AbstractAutowireCapableBeanFactory.java:1242)
>      [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1101)
>      [java]     at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
>      [java]     ... 33 more
>      [java] Caused by: java.beans.IntrospectionException: type mismatch between read
and write methods
>      [java]     at java.beans.PropertyDescriptor.findPropertyType(PropertyDescriptor.java:659)
>      [java]     at java.beans.PropertyDescriptor.setReadMethod(PropertyDescriptor.java:256)
>      [java]     at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:282)
>      [java]     at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:180)
>      [java]     at org.springframework.beans.ExtendedBeanInfo.<init>(ExtendedBeanInfo.java:100)
>      [java]     at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:224)
>      [java]     ... 39 more
> {code}



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