[
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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