treebase-devel

[Treebase-devel] Data access failure for dev.

[William P. <wil...@ya...>]

When we try to upload a rowsegment metadata, we're getting a data access failure. 


http://treebasedb-dev.nescent.org/treebase-web/user/rowSegmentDataTable.html



Data Access Failure

could not insert: [org.cipres.treebase.domain.matrix.RowSegment]; nested exception is org.hibernate.exception.ConstraintViolationException: could not insert: [org.cipres.treebase.domain.matrix.RowSegment]

org.springframework.dao.DataIntegrityViolationException: could not insert: [org.cipres.treebase.domain.matrix.RowSegment]; nested exception is org.hibernate.exception.ConstraintViolationException: could not insert: [org.cipres.treebase.domain.matrix.RowSegment] Caused by: org.hibernate.exception.ConstraintViolationException: could not insert: [org.cipres.treebase.domain.matrix.RowSegment] at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:71) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2272) at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2665) at org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:60) at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279) at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:263) at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:167) at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298) at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338) at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106) at org.springframework.orm.hibernate3.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:578) at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:662) at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:632) at org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:314) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:116) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy75.createSegments(Unknown Source) at org.cipres.treebase.web.controllers.RowSegmentDataTableController.onSubmit(RowSegmentDataTableController.java:112) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286) at java.lang.Thread.run(Thread.java:636) Caused by: java.sql.BatchUpdateException: Batch entry 0 insert into ROWSEGMENT (VERSION, EndIndex, MATRIXROW_ID, CatalogNum, CollectionCode, Collector, Country, Elevation, GenBAccession, InstAcronym, Latitude, Locality, Longitude, Notes, OtherAccession, SampleDate, State, StartIndex, TAXONLABEL_ID, Title, ROWSEGMENT_ID) values (0, 4485, 224329, NULL, NULL, NULL, NULL, NULL, AY3242354, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, 54) was aborted. Call getNextException to see the cause. at org.postgresql.jdbc2.AbstractJdbc2Statement$BatchResultHandler.handleError(AbstractJdbc2Statement.java:2537) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1328) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:351) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java:2674) at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java:297) at org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48) at org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34) at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2252) ... 69 more « Back

Re: [Treebase-devel] Data access failure for dev.

[Hilmar L. <hl...@ne...>]

It seems that hibernate assigned the primary key (54 here). I thought  
the database would do that, not hibernate?

	-hilmar

On Mar 10, 2010, at 3:15 PM, William Piel wrote:

>
>
> When we try to upload a rowsegment metadata, we're getting a data  
> access failure.
>
>
> http://treebasedb-dev.nescent.org/treebase-web/user/rowSegmentDataTable.html
>
>
>
> Data Access Failure
>
> could not insert: [org.cipres.treebase.domain.matrix.RowSegment];  
> nested exception is  
> org.hibernate.exception.ConstraintViolationException: could not  
> insert: [org.cipres.treebase.domain.matrix.RowSegment]
>
> org.springframework.dao.DataIntegrityViolationException: could not  
> insert: [org.cipres.treebase.domain.matrix.RowSegment]; nested  
> exception is org.hibernate.exception.ConstraintViolationException:  
> could not insert: [org.cipres.treebase.domain.matrix.RowSegment]  
> Caused by: org.hibernate.exception.ConstraintViolationException:  
> could not insert: [org.cipres.treebase.domain.matrix.RowSegment] at  
> org 
> .hibernate 
> .exception.SQLStateConverter.convert(SQLStateConverter.java:71) at  
> org 
> .hibernate 
> .exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)  
> at  
> org 
> .hibernate 
> .persister 
> .entity.AbstractEntityPersister.insert(AbstractEntityPersister.java: 
> 2272) at  
> org 
> .hibernate 
> .persister 
> .entity.AbstractEntityPersister.insert(AbstractEntityPersister.java: 
> 2665) at  
> org 
> .hibernate.action.EntityInsertAction.execute(EntityInsertAction.java: 
> 60) at org.hibernate.engine.ActionQueue.execute(ActionQueue.java: 
> 279) at  
> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
> 263) at  
> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
> 167) at  
> org 
> .hibernate 
> .event 
> .def 
> .AbstractFlushingEventListener 
> .performExecutions(AbstractFlushingEventListener.java:298) at  
> org 
> .hibernate 
> .event 
> .def 
> .DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java: 
> 27) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)  
> at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)  
> at  
> org 
> .hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java: 
> 106) at  
> org 
> .springframework 
> .orm 
> .hibernate3 
> .HibernateTransactionManager 
> .doCommit(HibernateTransactionManager.java:578) at  
> org 
> .springframework 
> .transaction 
> .support 
> .AbstractPlatformTransactionManager 
> .processCommit(AbstractPlatformTransactionManager.java:662) at  
> org 
> .springframework 
> .transaction 
> .support 
> .AbstractPlatformTransactionManager 
> .commit(AbstractPlatformTransactionManager.java:632) at  
> org 
> .springframework 
> .transaction 
> .interceptor 
> .TransactionAspectSupport 
> .commitTransactionAfterReturning(TransactionAspectSupport.java:314)  
> at  
> org 
> .springframework 
> .transaction 
> .interceptor 
> .TransactionInterceptor.invoke(TransactionInterceptor.java:116) at  
> org 
> .springframework 
> .aop 
> .framework 
> .ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java: 
> 171) at  
> org 
> .springframework 
> .aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java: 
> 204) at $Proxy75.createSegments(Unknown Source) at  
> org.cipres.treebase.web.controllers.RowSegmentDataTableController.onSubmit 
> (RowSegmentDataTableController.java:112) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission 
> (SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission 
> (CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal 
> (AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest 
> (AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle 
> (SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch 
> (DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService 
> (DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest 
> (FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost 
> (FrameworkServlet.java:441) at  
> javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at  
> javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at  
> org 
> .apache 
> .catalina 
> .core 
> .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 
> 269) at  
> org 
> .apache 
> .catalina 
> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
> 188) at  
> org 
> .displaytag 
> .filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java: 
> 125) at  
> org 
> .apache 
> .catalina 
> .core 
> .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 
> 215) at  
> org 
> .apache 
> .catalina 
> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
> 188) at  
> org 
> .springframework 
> .orm 
> .hibernate3 
> .support 
> .OpenSessionInViewFilter 
> .doFilterInternal(OpenSessionInViewFilter.java:198) at  
> org 
> .springframework 
> .web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: 
> 75) at  
> org 
> .apache 
> .catalina 
> .core 
> .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 
> 215) at  
> org 
> .apache 
> .catalina 
> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
> 188) at  
> com 
> .opensymphony 
> .module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at  
> com 
> .opensymphony 
> .module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at  
> org 
> .apache 
> .catalina 
> .core 
> .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 
> 215) at  
> org 
> .apache 
> .catalina 
> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
> 188) at org.acegisecurity.util.FilterChainProxy 
> $VirtualFilterChain.doFilter(FilterChainProxy.java:264) at  
> org 
> .acegisecurity 
> .intercept 
> .web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java: 
> 107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter 
> (FilterSecurityInterceptor.java:72) at  
> org.acegisecurity.util.FilterChainProxy 
> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
> org 
> .acegisecurity 
> .ui 
> .ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java: 
> 110) at org.acegisecurity.util.FilterChainProxy 
> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
> org 
> .acegisecurity 
> .wrapper 
> .SecurityContextHolderAwareRequestFilter 
> .doFilter(SecurityContextHolderAwareRequestFilter.java:81) at  
> org.acegisecurity.util.FilterChainProxy 
> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
> org 
> .acegisecurity 
> .ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java: 
> 217) at org.acegisecurity.util.FilterChainProxy 
> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
> org 
> .acegisecurity 
> .context 
> .HttpSessionContextIntegrationFilter 
> .doFilter(HttpSessionContextIntegrationFilter.java:191) at  
> org.acegisecurity.util.FilterChainProxy 
> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
> org 
> .acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java: 
> 148) at  
> org 
> .acegisecurity 
> .util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at  
> org 
> .apache 
> .catalina 
> .core 
> .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 
> 215) at  
> org 
> .apache 
> .catalina 
> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
> 188) at  
> org 
> .apache 
> .catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java: 
> 213) at  
> org 
> .apache 
> .catalina.core.StandardContextValve.invoke(StandardContextValve.java: 
> 172) at  
> org 
> .apache 
> .catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)  
> at  
> org 
> .apache 
> .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)  
> at  
> org 
> .apache 
> .catalina.core.StandardEngineValve.invoke(StandardEngineValve.java: 
> 108) at  
> org 
> .apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java: 
> 174) at  
> org 
> .apache 
> .coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java: 
> 837) at org.apache.coyote.http11.Http11AprProtocol 
> $Http11ConnectionHandler.process(Http11AprProtocol.java:640) at  
> org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java: 
> 1286) at java.lang.Thread.run(Thread.java:636) Caused by:  
> java.sql.BatchUpdateException: Batch entry 0 insert into ROWSEGMENT  
> (VERSION, EndIndex, MATRIXROW_ID, CatalogNum, CollectionCode,  
> Collector, Country, Elevation, GenBAccession, InstAcronym, Latitude,  
> Locality, Longitude, Notes, OtherAccession, SampleDate, State,  
> StartIndex, TAXONLABEL_ID, Title, ROWSEGMENT_ID) values (0, 4485,  
> 224329, NULL, NULL, NULL, NULL, NULL, AY3242354, NULL, NULL, NULL,  
> NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, 54) was aborted. Call  
> getNextException to see the cause. at  
> org.postgresql.jdbc2.AbstractJdbc2Statement 
> $BatchResultHandler.handleError(AbstractJdbc2Statement.java:2537) at  
> org 
> .postgresql 
> .core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java: 
> 1328) at  
> org 
> .postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java: 
> 351) at  
> org 
> .postgresql 
> .jdbc2 
> .AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java: 
> 2674) at  
> org 
> .apache 
> .tomcat 
> .dbcp.dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java: 
> 297) at  
> org 
> .hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java: 
> 48) at  
> org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java: 
> 34) at  
> org 
> .hibernate 
> .persister 
> .entity.AbstractEntityPersister.insert(AbstractEntityPersister.java: 
> 2252) ... 69 more « Back
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] Data access failure for dev.

[Vladimir G. <vla...@du...>]

That's strange...  I checked the definition of the RowSegment class  
and it is about the same as, say Study.  That is both should pick PK  
from their own sequences.  The current rowsegment_sequence_id is 98.

How about trying once more -- does the generated id change from 54 (it  
should, if it is picked from a sequence).

--VG


On Mar 10, 2010, at 3:19 PM, Hilmar Lapp wrote:

> It seems that hibernate assigned the primary key (54 here). I  
> thought the database would do that, not hibernate?
>
> 	-hilmar
>
> On Mar 10, 2010, at 3:15 PM, William Piel wrote:
>
>>
>>
>> When we try to upload a rowsegment metadata, we're getting a data  
>> access failure.
>>
>>
>> http://treebasedb-dev.nescent.org/treebase-web/user/rowSegmentDataTable.html
>>
>>
>>
>> Data Access Failure
>>
>> could not insert: [org.cipres.treebase.domain.matrix.RowSegment];  
>> nested exception is  
>> org.hibernate.exception.ConstraintViolationException: could not  
>> insert: [org.cipres.treebase.domain.matrix.RowSegment]
>>
>> org.springframework.dao.DataIntegrityViolationException: could not  
>> insert: [org.cipres.treebase.domain.matrix.RowSegment]; nested  
>> exception is org.hibernate.exception.ConstraintViolationException:  
>> could not insert: [org.cipres.treebase.domain.matrix.RowSegment]  
>> Caused by: org.hibernate.exception.ConstraintViolationException:  
>> could not insert: [org.cipres.treebase.domain.matrix.RowSegment] at  
>> org 
>> .hibernate 
>> .exception.SQLStateConverter.convert(SQLStateConverter.java:71) at  
>> org 
>> .hibernate 
>> .exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)  
>> at  
>> org 
>> .hibernate 
>> .persister 
>> .entity.AbstractEntityPersister.insert(AbstractEntityPersister.java: 
>> 2272) at  
>> org 
>> .hibernate 
>> .persister 
>> .entity.AbstractEntityPersister.insert(AbstractEntityPersister.java: 
>> 2665) at  
>> org 
>> .hibernate 
>> .action.EntityInsertAction.execute(EntityInsertAction.java:60) at  
>> org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279) at  
>> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
>> 263) at  
>> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
>> 167) at  
>> org 
>> .hibernate 
>> .event 
>> .def 
>> .AbstractFlushingEventListener 
>> .performExecutions(AbstractFlushingEventListener.java:298) at  
>> org 
>> .hibernate 
>> .event 
>> .def 
>> .DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java: 
>> 27) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)  
>> at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java: 
>> 338) at  
>> org 
>> .hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java: 
>> 106) at  
>> org 
>> .springframework 
>> .orm 
>> .hibernate3 
>> .HibernateTransactionManager 
>> .doCommit(HibernateTransactionManager.java:578) at  
>> org 
>> .springframework 
>> .transaction 
>> .support 
>> .AbstractPlatformTransactionManager 
>> .processCommit(AbstractPlatformTransactionManager.java:662) at  
>> org 
>> .springframework 
>> .transaction 
>> .support 
>> .AbstractPlatformTransactionManager 
>> .commit(AbstractPlatformTransactionManager.java:632) at  
>> org 
>> .springframework 
>> .transaction 
>> .interceptor 
>> .TransactionAspectSupport 
>> .commitTransactionAfterReturning(TransactionAspectSupport.java:314)  
>> at  
>> org 
>> .springframework 
>> .transaction 
>> .interceptor 
>> .TransactionInterceptor.invoke(TransactionInterceptor.java:116) at  
>> org 
>> .springframework 
>> .aop 
>> .framework 
>> .ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java: 
>> 171) at  
>> org 
>> .springframework 
>> .aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java: 
>> 204) at $Proxy75.createSegments(Unknown Source) at  
>> org.cipres.treebase.web.controllers.RowSegmentDataTableController.onSubmit 
>> (RowSegmentDataTableController.java:112) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission 
>> (SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission 
>> (CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal 
>> (AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest 
>> (AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle 
>> (SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch 
>> (DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService 
>> (DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest 
>> (FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost 
>> (FrameworkServlet.java:441) at  
>> javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at  
>> javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at  
>> org 
>> .apache 
>> .catalina 
>> .core 
>> .ApplicationFilterChain 
>> .internalDoFilter(ApplicationFilterChain.java:269) at  
>> org 
>> .apache 
>> .catalina 
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>> 188) at  
>> org 
>> .displaytag 
>> .filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java: 
>> 125) at  
>> org 
>> .apache 
>> .catalina 
>> .core 
>> .ApplicationFilterChain 
>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>> org 
>> .apache 
>> .catalina 
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>> 188) at  
>> org 
>> .springframework 
>> .orm 
>> .hibernate3 
>> .support 
>> .OpenSessionInViewFilter 
>> .doFilterInternal(OpenSessionInViewFilter.java:198) at  
>> org 
>> .springframework 
>> .web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: 
>> 75) at  
>> org 
>> .apache 
>> .catalina 
>> .core 
>> .ApplicationFilterChain 
>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>> org 
>> .apache 
>> .catalina 
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>> 188) at  
>> com 
>> .opensymphony 
>> .module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)  
>> at  
>> com 
>> .opensymphony 
>> .module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at  
>> org 
>> .apache 
>> .catalina 
>> .core 
>> .ApplicationFilterChain 
>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>> org 
>> .apache 
>> .catalina 
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>> 188) at org.acegisecurity.util.FilterChainProxy 
>> $VirtualFilterChain.doFilter(FilterChainProxy.java:264) at  
>> org 
>> .acegisecurity 
>> .intercept 
>> .web 
>> .FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java: 
>> 107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter 
>> (FilterSecurityInterceptor.java:72) at  
>> org.acegisecurity.util.FilterChainProxy 
>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>> org 
>> .acegisecurity 
>> .ui 
>> .ExceptionTranslationFilter 
>> .doFilter(ExceptionTranslationFilter.java:110) at  
>> org.acegisecurity.util.FilterChainProxy 
>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>> org 
>> .acegisecurity 
>> .wrapper 
>> .SecurityContextHolderAwareRequestFilter 
>> .doFilter(SecurityContextHolderAwareRequestFilter.java:81) at  
>> org.acegisecurity.util.FilterChainProxy 
>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>> org 
>> .acegisecurity 
>> .ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java: 
>> 217) at org.acegisecurity.util.FilterChainProxy 
>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>> org 
>> .acegisecurity 
>> .context 
>> .HttpSessionContextIntegrationFilter 
>> .doFilter(HttpSessionContextIntegrationFilter.java:191) at  
>> org.acegisecurity.util.FilterChainProxy 
>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>> org 
>> .acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java: 
>> 148) at  
>> org 
>> .acegisecurity 
>> .util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at  
>> org 
>> .apache 
>> .catalina 
>> .core 
>> .ApplicationFilterChain 
>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>> org 
>> .apache 
>> .catalina 
>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>> 188) at  
>> org 
>> .apache 
>> .catalina 
>> .core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at  
>> org 
>> .apache 
>> .catalina 
>> .core.StandardContextValve.invoke(StandardContextValve.java:172) at  
>> org 
>> .apache 
>> .catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)  
>> at  
>> org 
>> .apache 
>> .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)  
>> at  
>> org 
>> .apache 
>> .catalina.core.StandardEngineValve.invoke(StandardEngineValve.java: 
>> 108) at  
>> org 
>> .apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java: 
>> 174) at  
>> org 
>> .apache 
>> .coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java: 
>> 837) at org.apache.coyote.http11.Http11AprProtocol 
>> $Http11ConnectionHandler.process(Http11AprProtocol.java:640) at  
>> org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java: 
>> 1286) at java.lang.Thread.run(Thread.java:636) Caused by:  
>> java.sql.BatchUpdateException: Batch entry 0 insert into ROWSEGMENT  
>> (VERSION, EndIndex, MATRIXROW_ID, CatalogNum, CollectionCode,  
>> Collector, Country, Elevation, GenBAccession, InstAcronym,  
>> Latitude, Locality, Longitude, Notes, OtherAccession, SampleDate,  
>> State, StartIndex, TAXONLABEL_ID, Title, ROWSEGMENT_ID) values (0,  
>> 4485, 224329, NULL, NULL, NULL, NULL, NULL, AY3242354, NULL, NULL,  
>> NULL, NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, 54) was aborted.  
>> Call getNextException to see the cause. at  
>> org.postgresql.jdbc2.AbstractJdbc2Statement 
>> $BatchResultHandler.handleError(AbstractJdbc2Statement.java:2537)  
>> at  
>> org 
>> .postgresql 
>> .core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java: 
>> 1328) at  
>> org 
>> .postgresql 
>> .core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:351) at  
>> org 
>> .postgresql 
>> .jdbc2 
>> .AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java: 
>> 2674) at  
>> org 
>> .apache 
>> .tomcat 
>> .dbcp 
>> .dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java: 
>> 297) at  
>> org 
>> .hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java: 
>> 48) at  
>> org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java: 
>> 34) at  
>> org 
>> .hibernate 
>> .persister 
>> .entity.AbstractEntityPersister.insert(AbstractEntityPersister.java: 
>> 2252) ... 69 more « Back
>> ------------------------------------------------------------------------------
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

Re: [Treebase-devel] Data access failure for dev.

[Hilmar L. <hl...@ne...>]

Could this be due to the treebase-dev instance being out of date re:  
updates to the codebase?

	-hilmar

On Mar 10, 2010, at 3:36 PM, Vladimir Gapeyev wrote:

> That's strange...  I checked the definition of the RowSegment class  
> and it is about the same as, say Study.  That is both should pick PK  
> from their own sequences.  The current rowsegment_sequence_id is 98.
>
> How about trying once more -- does the generated id change from 54  
> (it should, if it is picked from a sequence).
>
> --VG
>
>
> On Mar 10, 2010, at 3:19 PM, Hilmar Lapp wrote:
>
>> It seems that hibernate assigned the primary key (54 here). I  
>> thought the database would do that, not hibernate?
>>
>> 	-hilmar
>>
>> On Mar 10, 2010, at 3:15 PM, William Piel wrote:
>>
>>>
>>>
>>> When we try to upload a rowsegment metadata, we're getting a data  
>>> access failure.
>>>
>>>
>>> http://treebasedb-dev.nescent.org/treebase-web/user/rowSegmentDataTable.html
>>>
>>>
>>>
>>> Data Access Failure
>>>
>>> could not insert: [org.cipres.treebase.domain.matrix.RowSegment];  
>>> nested exception is  
>>> org.hibernate.exception.ConstraintViolationException: could not  
>>> insert: [org.cipres.treebase.domain.matrix.RowSegment]
>>>
>>> org.springframework.dao.DataIntegrityViolationException: could not  
>>> insert: [org.cipres.treebase.domain.matrix.RowSegment]; nested  
>>> exception is org.hibernate.exception.ConstraintViolationException:  
>>> could not insert: [org.cipres.treebase.domain.matrix.RowSegment]  
>>> Caused by: org.hibernate.exception.ConstraintViolationException:  
>>> could not insert: [org.cipres.treebase.domain.matrix.RowSegment]  
>>> at  
>>> org 
>>> .hibernate 
>>> .exception.SQLStateConverter.convert(SQLStateConverter.java:71) at  
>>> org 
>>> .hibernate 
>>> .exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java: 
>>> 43) at  
>>> org 
>>> .hibernate 
>>> .persister 
>>> .entity 
>>> .AbstractEntityPersister.insert(AbstractEntityPersister.java:2272)  
>>> at  
>>> org 
>>> .hibernate 
>>> .persister 
>>> .entity 
>>> .AbstractEntityPersister.insert(AbstractEntityPersister.java:2665)  
>>> at  
>>> org 
>>> .hibernate 
>>> .action.EntityInsertAction.execute(EntityInsertAction.java:60) at  
>>> org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279) at  
>>> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
>>> 263) at  
>>> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
>>> 167) at  
>>> org 
>>> .hibernate 
>>> .event 
>>> .def 
>>> .AbstractFlushingEventListener 
>>> .performExecutions(AbstractFlushingEventListener.java:298) at  
>>> org 
>>> .hibernate 
>>> .event 
>>> .def 
>>> .DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java: 
>>> 27) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)  
>>> at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java: 
>>> 338) at  
>>> org 
>>> .hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java: 
>>> 106) at  
>>> org 
>>> .springframework 
>>> .orm 
>>> .hibernate3 
>>> .HibernateTransactionManager 
>>> .doCommit(HibernateTransactionManager.java:578) at  
>>> org 
>>> .springframework 
>>> .transaction 
>>> .support 
>>> .AbstractPlatformTransactionManager 
>>> .processCommit(AbstractPlatformTransactionManager.java:662) at  
>>> org 
>>> .springframework 
>>> .transaction 
>>> .support 
>>> .AbstractPlatformTransactionManager 
>>> .commit(AbstractPlatformTransactionManager.java:632) at  
>>> org 
>>> .springframework 
>>> .transaction 
>>> .interceptor 
>>> .TransactionAspectSupport 
>>> .commitTransactionAfterReturning(TransactionAspectSupport.java: 
>>> 314) at  
>>> org 
>>> .springframework 
>>> .transaction 
>>> .interceptor 
>>> .TransactionInterceptor.invoke(TransactionInterceptor.java:116) at  
>>> org 
>>> .springframework 
>>> .aop 
>>> .framework 
>>> .ReflectiveMethodInvocation 
>>> .proceed(ReflectiveMethodInvocation.java:171) at  
>>> org 
>>> .springframework 
>>> .aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java: 
>>> 204) at $Proxy75.createSegments(Unknown Source) at  
>>> org.cipres.treebase.web.controllers.RowSegmentDataTableController.onSubmit 
>>> (RowSegmentDataTableController.java:112) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission 
>>> (SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission 
>>> (CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal 
>>> (AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest 
>>> (AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle 
>>> (SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch 
>>> (DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService 
>>> (DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest 
>>> (FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost 
>>> (FrameworkServlet.java:441) at  
>>> javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at  
>>> javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core 
>>> .ApplicationFilterChain 
>>> .internalDoFilter(ApplicationFilterChain.java:269) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>> 188) at  
>>> org 
>>> .displaytag 
>>> .filter 
>>> .ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125)  
>>> at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core 
>>> .ApplicationFilterChain 
>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>> 188) at  
>>> org 
>>> .springframework 
>>> .orm 
>>> .hibernate3 
>>> .support 
>>> .OpenSessionInViewFilter 
>>> .doFilterInternal(OpenSessionInViewFilter.java:198) at  
>>> org 
>>> .springframework 
>>> .web 
>>> .filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: 
>>> 75) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core 
>>> .ApplicationFilterChain 
>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>> 188) at  
>>> com 
>>> .opensymphony 
>>> .module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)  
>>> at  
>>> com 
>>> .opensymphony 
>>> .module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core 
>>> .ApplicationFilterChain 
>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>> 188) at org.acegisecurity.util.FilterChainProxy 
>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:264) at  
>>> org 
>>> .acegisecurity 
>>> .intercept 
>>> .web 
>>> .FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java: 
>>> 107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter 
>>> (FilterSecurityInterceptor.java:72) at  
>>> org.acegisecurity.util.FilterChainProxy 
>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>> org 
>>> .acegisecurity 
>>> .ui 
>>> .ExceptionTranslationFilter 
>>> .doFilter(ExceptionTranslationFilter.java:110) at  
>>> org.acegisecurity.util.FilterChainProxy 
>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>> org 
>>> .acegisecurity 
>>> .wrapper 
>>> .SecurityContextHolderAwareRequestFilter 
>>> .doFilter(SecurityContextHolderAwareRequestFilter.java:81) at  
>>> org.acegisecurity.util.FilterChainProxy 
>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>> org 
>>> .acegisecurity 
>>> .ui 
>>> .AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java: 
>>> 217) at org.acegisecurity.util.FilterChainProxy 
>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>> org 
>>> .acegisecurity 
>>> .context 
>>> .HttpSessionContextIntegrationFilter 
>>> .doFilter(HttpSessionContextIntegrationFilter.java:191) at  
>>> org.acegisecurity.util.FilterChainProxy 
>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>> org 
>>> .acegisecurity 
>>> .util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at  
>>> org 
>>> .acegisecurity 
>>> .util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core 
>>> .ApplicationFilterChain 
>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>> 188) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)  
>>> at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.StandardContextValve.invoke(StandardContextValve.java:172)  
>>> at  
>>> org 
>>> .apache 
>>> .catalina.core.StandardHostValve.invoke(StandardHostValve.java: 
>>> 127) at  
>>> org 
>>> .apache 
>>> .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java: 
>>> 117) at  
>>> org 
>>> .apache 
>>> .catalina.core.StandardEngineValve.invoke(StandardEngineValve.java: 
>>> 108) at  
>>> org 
>>> .apache 
>>> .catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)  
>>> at  
>>> org 
>>> .apache 
>>> .coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java: 
>>> 837) at org.apache.coyote.http11.Http11AprProtocol 
>>> $Http11ConnectionHandler.process(Http11AprProtocol.java:640) at  
>>> org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java: 
>>> 1286) at java.lang.Thread.run(Thread.java:636) Caused by:  
>>> java.sql.BatchUpdateException: Batch entry 0 insert into  
>>> ROWSEGMENT (VERSION, EndIndex, MATRIXROW_ID, CatalogNum,  
>>> CollectionCode, Collector, Country, Elevation, GenBAccession,  
>>> InstAcronym, Latitude, Locality, Longitude, Notes, OtherAccession,  
>>> SampleDate, State, StartIndex, TAXONLABEL_ID, Title,  
>>> ROWSEGMENT_ID) values (0, 4485, 224329, NULL, NULL, NULL, NULL,  
>>> NULL, AY3242354, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL,  
>>> 1, NULL, NULL, 54) was aborted. Call getNextException to see the  
>>> cause. at org.postgresql.jdbc2.AbstractJdbc2Statement 
>>> $BatchResultHandler.handleError(AbstractJdbc2Statement.java:2537)  
>>> at  
>>> org 
>>> .postgresql 
>>> .core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java: 
>>> 1328) at  
>>> org 
>>> .postgresql 
>>> .core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:351) at  
>>> org 
>>> .postgresql 
>>> .jdbc2 
>>> .AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java: 
>>> 2674) at  
>>> org 
>>> .apache 
>>> .tomcat 
>>> .dbcp 
>>> .dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java: 
>>> 297) at  
>>> org 
>>> .hibernate 
>>> .jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48) at  
>>> org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java: 
>>> 34) at  
>>> org 
>>> .hibernate 
>>> .persister 
>>> .entity 
>>> .AbstractEntityPersister.insert(AbstractEntityPersister.java: 
>>> 2252) ... 69 more « Back
>>> ------------------------------------------------------------------------------
>>> Download Intel® Parallel Studio Eval
>>> Try the new software tools for yourself. Speed compiling, find bugs
>>> proactively, and fine-tune applications for parallel performance.
>>> See why Intel Parallel Studio got high marks during beta.
>>> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
>>> Treebase-devel mailing list
>>> Tre...@li...
>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
>> ===========================================================
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] Data access failure for dev.

[Vladimir G. <vla...@du...>]

Only if anyone committed code related to RowSegment in the past week.   
Does Youjun recall anything like that?
Just in case, I'll rebuild and ask Jon to redeploy.

If you are currently stuck on this, I would not mind to stop by to see  
how to reproduce this.

--VG


On Mar 10, 2010, at 3:47 PM, Hilmar Lapp wrote:

> Could this be due to the treebase-dev instance being out of date re:  
> updates to the codebase?
>
> 	-hilmar
>
> On Mar 10, 2010, at 3:36 PM, Vladimir Gapeyev wrote:
>
>> That's strange...  I checked the definition of the RowSegment class  
>> and it is about the same as, say Study.  That is both should pick  
>> PK from their own sequences.  The current rowsegment_sequence_id is  
>> 98.
>>
>> How about trying once more -- does the generated id change from 54  
>> (it should, if it is picked from a sequence).
>>
>> --VG
>>
>>
>> On Mar 10, 2010, at 3:19 PM, Hilmar Lapp wrote:
>>
>>> It seems that hibernate assigned the primary key (54 here). I  
>>> thought the database would do that, not hibernate?
>>>
>>> 	-hilmar
>>>
>>> On Mar 10, 2010, at 3:15 PM, William Piel wrote:
>>>
>>>>
>>>>
>>>> When we try to upload a rowsegment metadata, we're getting a data  
>>>> access failure.
>>>>
>>>>
>>>> http://treebasedb-dev.nescent.org/treebase-web/user/rowSegmentDataTable.html
>>>>
>>>>
>>>>
>>>> Data Access Failure
>>>>
>>>> could not insert: [org.cipres.treebase.domain.matrix.RowSegment];  
>>>> nested exception is  
>>>> org.hibernate.exception.ConstraintViolationException: could not  
>>>> insert: [org.cipres.treebase.domain.matrix.RowSegment]
>>>>
>>>> org.springframework.dao.DataIntegrityViolationException: could  
>>>> not insert: [org.cipres.treebase.domain.matrix.RowSegment];  
>>>> nested exception is  
>>>> org.hibernate.exception.ConstraintViolationException: could not  
>>>> insert: [org.cipres.treebase.domain.matrix.RowSegment] Caused by:  
>>>> org.hibernate.exception.ConstraintViolationException: could not  
>>>> insert: [org.cipres.treebase.domain.matrix.RowSegment] at  
>>>> org 
>>>> .hibernate 
>>>> .exception.SQLStateConverter.convert(SQLStateConverter.java:71)  
>>>> at  
>>>> org 
>>>> .hibernate 
>>>> .exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java: 
>>>> 43) at  
>>>> org 
>>>> .hibernate 
>>>> .persister 
>>>> .entity 
>>>> .AbstractEntityPersister.insert(AbstractEntityPersister.java: 
>>>> 2272) at  
>>>> org 
>>>> .hibernate 
>>>> .persister 
>>>> .entity 
>>>> .AbstractEntityPersister.insert(AbstractEntityPersister.java: 
>>>> 2665) at  
>>>> org 
>>>> .hibernate 
>>>> .action.EntityInsertAction.execute(EntityInsertAction.java:60) at  
>>>> org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279) at  
>>>> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
>>>> 263) at  
>>>> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
>>>> 167) at  
>>>> org 
>>>> .hibernate 
>>>> .event 
>>>> .def 
>>>> .AbstractFlushingEventListener 
>>>> .performExecutions(AbstractFlushingEventListener.java:298) at  
>>>> org 
>>>> .hibernate 
>>>> .event 
>>>> .def 
>>>> .DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java: 
>>>> 27) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java: 
>>>> 1000) at  
>>>> org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)  
>>>> at  
>>>> org 
>>>> .hibernate 
>>>> .transaction.JDBCTransaction.commit(JDBCTransaction.java:106) at  
>>>> org 
>>>> .springframework 
>>>> .orm 
>>>> .hibernate3 
>>>> .HibernateTransactionManager 
>>>> .doCommit(HibernateTransactionManager.java:578) at  
>>>> org 
>>>> .springframework 
>>>> .transaction 
>>>> .support 
>>>> .AbstractPlatformTransactionManager 
>>>> .processCommit(AbstractPlatformTransactionManager.java:662) at  
>>>> org 
>>>> .springframework 
>>>> .transaction 
>>>> .support 
>>>> .AbstractPlatformTransactionManager 
>>>> .commit(AbstractPlatformTransactionManager.java:632) at  
>>>> org 
>>>> .springframework 
>>>> .transaction 
>>>> .interceptor 
>>>> .TransactionAspectSupport 
>>>> .commitTransactionAfterReturning(TransactionAspectSupport.java: 
>>>> 314) at  
>>>> org 
>>>> .springframework 
>>>> .transaction 
>>>> .interceptor 
>>>> .TransactionInterceptor.invoke(TransactionInterceptor.java:116)  
>>>> at  
>>>> org 
>>>> .springframework 
>>>> .aop 
>>>> .framework 
>>>> .ReflectiveMethodInvocation 
>>>> .proceed(ReflectiveMethodInvocation.java:171) at  
>>>> org 
>>>> .springframework 
>>>> .aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java: 
>>>> 204) at $Proxy75.createSegments(Unknown Source) at  
>>>> org.cipres.treebase.web.controllers.RowSegmentDataTableController.onSubmit 
>>>> (RowSegmentDataTableController.java:112) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission 
>>>> (SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission 
>>>> (CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal 
>>>> (AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest 
>>>> (AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle 
>>>> (SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch 
>>>> (DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService 
>>>> (DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest 
>>>> (FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost 
>>>> (FrameworkServlet.java:441) at  
>>>> javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at  
>>>> javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core 
>>>> .ApplicationFilterChain 
>>>> .internalDoFilter(ApplicationFilterChain.java:269) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>>> 188) at  
>>>> org 
>>>> .displaytag 
>>>> .filter 
>>>> .ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125)  
>>>> at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core 
>>>> .ApplicationFilterChain 
>>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>>> 188) at  
>>>> org 
>>>> .springframework 
>>>> .orm 
>>>> .hibernate3 
>>>> .support 
>>>> .OpenSessionInViewFilter 
>>>> .doFilterInternal(OpenSessionInViewFilter.java:198) at  
>>>> org 
>>>> .springframework 
>>>> .web 
>>>> .filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: 
>>>> 75) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core 
>>>> .ApplicationFilterChain 
>>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>>> 188) at  
>>>> com 
>>>> .opensymphony 
>>>> .module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)  
>>>> at  
>>>> com 
>>>> .opensymphony 
>>>> .module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55)  
>>>> at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core 
>>>> .ApplicationFilterChain 
>>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>>> 188) at org.acegisecurity.util.FilterChainProxy 
>>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:264) at  
>>>> org 
>>>> .acegisecurity 
>>>> .intercept 
>>>> .web 
>>>> .FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java: 
>>>> 107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter 
>>>> (FilterSecurityInterceptor.java:72) at  
>>>> org.acegisecurity.util.FilterChainProxy 
>>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>>> org 
>>>> .acegisecurity 
>>>> .ui 
>>>> .ExceptionTranslationFilter 
>>>> .doFilter(ExceptionTranslationFilter.java:110) at  
>>>> org.acegisecurity.util.FilterChainProxy 
>>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>>> org 
>>>> .acegisecurity 
>>>> .wrapper 
>>>> .SecurityContextHolderAwareRequestFilter 
>>>> .doFilter(SecurityContextHolderAwareRequestFilter.java:81) at  
>>>> org.acegisecurity.util.FilterChainProxy 
>>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>>> org 
>>>> .acegisecurity 
>>>> .ui 
>>>> .AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java: 
>>>> 217) at org.acegisecurity.util.FilterChainProxy 
>>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>>> org 
>>>> .acegisecurity 
>>>> .context 
>>>> .HttpSessionContextIntegrationFilter 
>>>> .doFilter(HttpSessionContextIntegrationFilter.java:191) at  
>>>> org.acegisecurity.util.FilterChainProxy 
>>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>>> org 
>>>> .acegisecurity 
>>>> .util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at  
>>>> org 
>>>> .acegisecurity 
>>>> .util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core 
>>>> .ApplicationFilterChain 
>>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>>> 188) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)  
>>>> at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.StandardContextValve.invoke(StandardContextValve.java:172)  
>>>> at  
>>>> org 
>>>> .apache 
>>>> .catalina.core.StandardHostValve.invoke(StandardHostValve.java: 
>>>> 127) at  
>>>> org 
>>>> .apache 
>>>> .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java: 
>>>> 117) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.StandardEngineValve.invoke(StandardEngineValve.java:108) at  
>>>> org 
>>>> .apache 
>>>> .catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)  
>>>> at  
>>>> org 
>>>> .apache 
>>>> .coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java: 
>>>> 837) at org.apache.coyote.http11.Http11AprProtocol 
>>>> $Http11ConnectionHandler.process(Http11AprProtocol.java:640) at  
>>>> org.apache.tomcat.util.net.AprEndpoint 
>>>> $Worker.run(AprEndpoint.java:1286) at  
>>>> java.lang.Thread.run(Thread.java:636) Caused by:  
>>>> java.sql.BatchUpdateException: Batch entry 0 insert into  
>>>> ROWSEGMENT (VERSION, EndIndex, MATRIXROW_ID, CatalogNum,  
>>>> CollectionCode, Collector, Country, Elevation, GenBAccession,  
>>>> InstAcronym, Latitude, Locality, Longitude, Notes,  
>>>> OtherAccession, SampleDate, State, StartIndex, TAXONLABEL_ID,  
>>>> Title, ROWSEGMENT_ID) values (0, 4485, 224329, NULL, NULL, NULL,  
>>>> NULL, NULL, AY3242354, NULL, NULL, NULL, NULL, NULL, NULL, NULL,  
>>>> NULL, 1, NULL, NULL, 54) was aborted. Call getNextException to  
>>>> see the cause. at org.postgresql.jdbc2.AbstractJdbc2Statement 
>>>> $BatchResultHandler.handleError(AbstractJdbc2Statement.java:2537)  
>>>> at  
>>>> org 
>>>> .postgresql 
>>>> .core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java: 
>>>> 1328) at  
>>>> org 
>>>> .postgresql 
>>>> .core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:351) at  
>>>> org 
>>>> .postgresql 
>>>> .jdbc2 
>>>> .AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java: 
>>>> 2674) at  
>>>> org 
>>>> .apache 
>>>> .tomcat 
>>>> .dbcp 
>>>> .dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java: 
>>>> 297) at  
>>>> org 
>>>> .hibernate 
>>>> .jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48) at  
>>>> org 
>>>> .hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java: 
>>>> 34) at  
>>>> org 
>>>> .hibernate 
>>>> .persister 
>>>> .entity 
>>>> .AbstractEntityPersister.insert(AbstractEntityPersister.java: 
>>>> 2252) ... 69 more « Back
>>>> ------------------------------------------------------------------------------
>>>> Download Intel® Parallel Studio Eval
>>>> Try the new software tools for yourself. Speed compiling, find bugs
>>>> proactively, and fine-tune applications for parallel performance.
>>>> See why Intel Parallel Studio got high marks during beta.
>>>> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
>>>> Treebase-devel mailing list
>>>> Tre...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>>
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
>>> ===========================================================
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Download Intel® Parallel Studio Eval
>>> Try the new software tools for yourself. Speed compiling, find bugs
>>> proactively, and fine-tune applications for parallel performance.
>>> See why Intel Parallel Studio got high marks during beta.
>>> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
>>> Treebase-devel mailing list
>>> Tre...@li...
>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>

Re: [Treebase-devel] Data access failure for dev.

[Hilmar L. <hl...@ne...>]

On Mar 10, 2010, at 3:54 PM, Vladimir Gapeyev wrote:

> Just in case, I'll rebuild and ask Jon to redeploy.

That'd be great. We're seeing other things as well that Bill thinks  
should have been fixed.

> If you are currently stuck on this, I would not mind to stop by to  
> see how to reproduce this.


We've already moved on. But Bill can show it to you later.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] Data access failure for dev.

[youjun g. <you...@ya...>]

Bill tried the same operation one more time and hibernate get 101 as PK from
rowsegment_id_sequence, which is correct and everything is fine. I met same
problem on table 'person' two days ago.

Youjun

On Wed, Mar 10, 2010 at 3:36 PM, Vladimir Gapeyev <vla...@du...
> wrote:

> That's strange...  I checked the definition of the RowSegment class and it
> is about the same as, say Study.  That is both should pick PK from their own
> sequences.  The current rowsegment_sequence_id is 98.
>
> How about trying once more -- does the generated id change from 54 (it
> should, if it is picked from a sequence).
>
> --VG
>
>
> On Mar 10, 2010, at 3:19 PM, Hilmar Lapp wrote:
>
> It seems that hibernate assigned the primary key (54 here). I thought the
> database would do that, not hibernate?
>
> -hilmar
>
> On Mar 10, 2010, at 3:15 PM, William Piel wrote:
>
>
>
> When we try to upload a rowsegment metadata, we're getting a data access
> failure.
>
>
>
> http://treebasedb-dev.nescent.org/treebase-web/user/rowSegmentDataTable.html
>
>
>
> Data Access Failure
>
> could not insert: [org.cipres.treebase.domain.matrix.RowSegment]; nested
> exception is org.hibernate.exception.ConstraintViolationException: could not
> insert: [org.cipres.treebase.domain.matrix.RowSegment]
> org.springframework.dao.DataIntegrityViolationException: could not insert:
> [org.cipres.treebase.domain.matrix.RowSegment]; nested exception is
> org.hibernate.exception.ConstraintViolationException: could not insert:
> [org.cipres.treebase.domain.matrix.RowSegment] Caused by:
> org.hibernate.exception.ConstraintViolationException: could not insert:
> [org.cipres.treebase.domain.matrix.RowSegment] at
> org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:71)
> at
> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
> at
> org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2272)
> at
> org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2665)
> at
> org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:60)
> at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279) at
> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:263) at
> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:167) at
> org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
> at
> org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
> at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) at
> org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338) at
> org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
> at
> org.springframework.orm.hibernate3.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:578)
> at
> org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:662)
> at
> org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:632)
> at
> org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:314)
> at
> org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:116)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
> at
> org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
> at $Proxy75.createSegments(Unknown Source) at org.cipres.treebase.
> web.controllers.RowSegmentDataTableController.onSubmit(RowSegmentDataTableController.java:112)
> at org.springframework.
> web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267)
> at org.springframework.
> web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140)
> at org.springframework.
> web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265)
> at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
> at org.springframework.
> web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48)
> at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858)
> at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792)
> at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476)
> at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at
> javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
> at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
> at
> org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125)
> at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
> at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
> at
> org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198)
> at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
> at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
> at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
> at
> com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)
> at
> com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55)
> at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
> at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
> at
> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264)
> at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107)
> at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72)
> at
> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
> at
> org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110)
> at
> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
> at
> org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81)
> at
> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
> at
> org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217)
> at
> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
> at
> org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191)
> at
> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
> at
> org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148)
> at
> org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90)
> at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
> at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
> at
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
> at
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
> at
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
> at
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
> at
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
> at
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
> at
> org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837)
> at
> org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640)
> at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286)
> at java.lang.Thread.run(Thread.java:636) Caused by:
> java.sql.BatchUpdateException: Batch entry 0 insert into ROWSEGMENT
> (VERSION, EndIndex, MATRIXROW_ID, CatalogNum, CollectionCode, Collector,
> Country, Elevation, GenBAccession, InstAcronym, Latitude, Locality,
> Longitude, Notes, OtherAccession, SampleDate, State, StartIndex,
> TAXONLABEL_ID, Title, ROWSEGMENT_ID) values (0, 4485, 224329, NULL, NULL,
> NULL, NULL, NULL, AY3242354, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL,
> 1, NULL, NULL, 54) was aborted. Call getNextException to see the cause. at
> org.postgresql.jdbc2.AbstractJdbc2Statement$BatchResultHandler.handleError(AbstractJdbc2Statement.java:2537)
> at
> org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1328)
> at
> org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:351)
> at
> org.postgresql.jdbc2.AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java:2674)
> at
> org.apache.tomcat.dbcp.dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java:297)
> at
> org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
> at org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34) at
> org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2252)
> ... 69 more « Back<http://treebasedb-dev.nescent.org/user/submissionList.html>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
>
> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
>
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
>
> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
>
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
>

Re: [Treebase-devel] Data access failure for dev.

[Vladimir G. <vla...@du...>]

Jon has just re-deployed treebase-dev.  This should have all commits  
up to an hour ago.
--VG

Re: [Treebase-devel] Data access failure for dev.

[Vladimir G. <vla...@du...>]

A guess: Could this be related to "caching" that hibernate does?  Does  
anyone understand how that work?
If the cache is persisted in files or in the DB, could Hibernate got  
confused when we suddenly dropped and restored the database last week?
--VG


On Mar 10, 2010, at 4:15 PM, youjun guo wrote:

> Bill tried the same operation one more time and hibernate get 101 as  
> PK from rowsegment_id_sequence, which is correct and everything is  
> fine. I met same problem on table 'person' two days ago.
>
> Youjun
>
> On Wed, Mar 10, 2010 at 3:36 PM, Vladimir Gapeyev <vla...@du... 
> > wrote:
> That's strange...  I checked the definition of the RowSegment class  
> and it is about the same as, say Study.  That is both should pick PK  
> from their own sequences.  The current rowsegment_sequence_id is 98.
>
> How about trying once more -- does the generated id change from 54  
> (it should, if it is picked from a sequence).
>
> --VG
>
>
> On Mar 10, 2010, at 3:19 PM, Hilmar Lapp wrote:
>
>> It seems that hibernate assigned the primary key (54 here). I  
>> thought the database would do that, not hibernate?
>>
>> 	-hilmar
>>
>> On Mar 10, 2010, at 3:15 PM, William Piel wrote:
>>
>>>
>>>
>>> When we try to upload a rowsegment metadata, we're getting a data  
>>> access failure.
>>>
>>>
>>> http://treebasedb-dev.nescent.org/treebase-web/user/rowSegmentDataTable.html
>>>
>>>
>>>
>>> Data Access Failure
>>>
>>> could not insert: [org.cipres.treebase.domain.matrix.RowSegment];  
>>> nested exception is  
>>> org.hibernate.exception.ConstraintViolationException: could not  
>>> insert: [org.cipres.treebase.domain.matrix.RowSegment]
>>>
>>> org.springframework.dao.DataIntegrityViolationException: could not  
>>> insert: [org.cipres.treebase.domain.matrix.RowSegment]; nested  
>>> exception is org.hibernate.exception.ConstraintViolationException:  
>>> could not insert: [org.cipres.treebase.domain.matrix.RowSegment]  
>>> Caused by: org.hibernate.exception.ConstraintViolationException:  
>>> could not insert: [org.cipres.treebase.domain.matrix.RowSegment]  
>>> at  
>>> org 
>>> .hibernate 
>>> .exception.SQLStateConverter.convert(SQLStateConverter.java:71) at  
>>> org 
>>> .hibernate 
>>> .exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java: 
>>> 43) at  
>>> org 
>>> .hibernate 
>>> .persister 
>>> .entity 
>>> .AbstractEntityPersister.insert(AbstractEntityPersister.java:2272)  
>>> at  
>>> org 
>>> .hibernate 
>>> .persister 
>>> .entity 
>>> .AbstractEntityPersister.insert(AbstractEntityPersister.java:2665)  
>>> at  
>>> org 
>>> .hibernate 
>>> .action.EntityInsertAction.execute(EntityInsertAction.java:60) at  
>>> org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279) at  
>>> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
>>> 263) at  
>>> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
>>> 167) at  
>>> org 
>>> .hibernate 
>>> .event 
>>> .def 
>>> .AbstractFlushingEventListener 
>>> .performExecutions(AbstractFlushingEventListener.java:298) at  
>>> org 
>>> .hibernate 
>>> .event 
>>> .def 
>>> .DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java: 
>>> 27) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)  
>>> at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java: 
>>> 338) at  
>>> org 
>>> .hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java: 
>>> 106) at  
>>> org 
>>> .springframework 
>>> .orm 
>>> .hibernate3 
>>> .HibernateTransactionManager 
>>> .doCommit(HibernateTransactionManager.java:578) at  
>>> org 
>>> .springframework 
>>> .transaction 
>>> .support 
>>> .AbstractPlatformTransactionManager 
>>> .processCommit(AbstractPlatformTransactionManager.java:662) at  
>>> org 
>>> .springframework 
>>> .transaction 
>>> .support 
>>> .AbstractPlatformTransactionManager 
>>> .commit(AbstractPlatformTransactionManager.java:632) at  
>>> org 
>>> .springframework 
>>> .transaction 
>>> .interceptor 
>>> .TransactionAspectSupport 
>>> .commitTransactionAfterReturning(TransactionAspectSupport.java: 
>>> 314) at  
>>> org 
>>> .springframework 
>>> .transaction 
>>> .interceptor 
>>> .TransactionInterceptor.invoke(TransactionInterceptor.java:116) at  
>>> org 
>>> .springframework 
>>> .aop 
>>> .framework 
>>> .ReflectiveMethodInvocation 
>>> .proceed(ReflectiveMethodInvocation.java:171) at  
>>> org 
>>> .springframework 
>>> .aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java: 
>>> 204) at $Proxy75.createSegments(Unknown Source) at  
>>> org.cipres.treebase.web.controllers.RowSegmentDataTableController.onSubmit 
>>> (RowSegmentDataTableController.java:112) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission 
>>> (SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission 
>>> (CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal 
>>> (AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest 
>>> (AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle 
>>> (SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch 
>>> (DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService 
>>> (DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest 
>>> (FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost 
>>> (FrameworkServlet.java:441) at  
>>> javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at  
>>> javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core 
>>> .ApplicationFilterChain 
>>> .internalDoFilter(ApplicationFilterChain.java:269) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>> 188) at  
>>> org 
>>> .displaytag 
>>> .filter 
>>> .ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125)  
>>> at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core 
>>> .ApplicationFilterChain 
>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>> 188) at  
>>> org 
>>> .springframework 
>>> .orm 
>>> .hibernate3 
>>> .support 
>>> .OpenSessionInViewFilter 
>>> .doFilterInternal(OpenSessionInViewFilter.java:198) at  
>>> org 
>>> .springframework 
>>> .web 
>>> .filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: 
>>> 75) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core 
>>> .ApplicationFilterChain 
>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>> 188) at  
>>> com 
>>> .opensymphony 
>>> .module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)  
>>> at  
>>> com 
>>> .opensymphony 
>>> .module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core 
>>> .ApplicationFilterChain 
>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>> 188) at org.acegisecurity.util.FilterChainProxy 
>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:264) at  
>>> org 
>>> .acegisecurity 
>>> .intercept 
>>> .web 
>>> .FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java: 
>>> 107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter 
>>> (FilterSecurityInterceptor.java:72) at  
>>> org.acegisecurity.util.FilterChainProxy 
>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>> org 
>>> .acegisecurity 
>>> .ui 
>>> .ExceptionTranslationFilter 
>>> .doFilter(ExceptionTranslationFilter.java:110) at  
>>> org.acegisecurity.util.FilterChainProxy 
>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>> org 
>>> .acegisecurity 
>>> .wrapper 
>>> .SecurityContextHolderAwareRequestFilter 
>>> .doFilter(SecurityContextHolderAwareRequestFilter.java:81) at  
>>> org.acegisecurity.util.FilterChainProxy 
>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>> org 
>>> .acegisecurity 
>>> .ui 
>>> .AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java: 
>>> 217) at org.acegisecurity.util.FilterChainProxy 
>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>> org 
>>> .acegisecurity 
>>> .context 
>>> .HttpSessionContextIntegrationFilter 
>>> .doFilter(HttpSessionContextIntegrationFilter.java:191) at  
>>> org.acegisecurity.util.FilterChainProxy 
>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>> org 
>>> .acegisecurity 
>>> .util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at  
>>> org 
>>> .acegisecurity 
>>> .util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core 
>>> .ApplicationFilterChain 
>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>> 188) at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)  
>>> at  
>>> org 
>>> .apache 
>>> .catalina 
>>> .core.StandardContextValve.invoke(StandardContextValve.java:172)  
>>> at  
>>> org 
>>> .apache 
>>> .catalina.core.StandardHostValve.invoke(StandardHostValve.java: 
>>> 127) at  
>>> org 
>>> .apache 
>>> .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java: 
>>> 117) at  
>>> org 
>>> .apache 
>>> .catalina.core.StandardEngineValve.invoke(StandardEngineValve.java: 
>>> 108) at  
>>> org 
>>> .apache 
>>> .catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)  
>>> at  
>>> org 
>>> .apache 
>>> .coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java: 
>>> 837) at org.apache.coyote.http11.Http11AprProtocol 
>>> $Http11ConnectionHandler.process(Http11AprProtocol.java:640) at  
>>> org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java: 
>>> 1286) at java.lang.Thread.run(Thread.java:636) Caused by:  
>>> java.sql.BatchUpdateException: Batch entry 0 insert into  
>>> ROWSEGMENT (VERSION, EndIndex, MATRIXROW_ID, CatalogNum,  
>>> CollectionCode, Collector, Country, Elevation, GenBAccession,  
>>> InstAcronym, Latitude, Locality, Longitude, Notes, OtherAccession,  
>>> SampleDate, State, StartIndex, TAXONLABEL_ID, Title,  
>>> ROWSEGMENT_ID) values (0, 4485, 224329, NULL, NULL, NULL, NULL,  
>>> NULL, AY3242354, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL,  
>>> 1, NULL, NULL, 54) was aborted. Call getNextException to see the  
>>> cause. at org.postgresql.jdbc2.AbstractJdbc2Statement 
>>> $BatchResultHandler.handleError(AbstractJdbc2Statement.java:2537)  
>>> at  
>>> org 
>>> .postgresql 
>>> .core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java: 
>>> 1328) at  
>>> org 
>>> .postgresql 
>>> .core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:351) at  
>>> org 
>>> .postgresql 
>>> .jdbc2 
>>> .AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java: 
>>> 2674) at  
>>> org 
>>> .apache 
>>> .tomcat 
>>> .dbcp 
>>> .dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java: 
>>> 297) at  
>>> org 
>>> .hibernate 
>>> .jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48) at  
>>> org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java: 
>>> 34) at  
>>> org 
>>> .hibernate 
>>> .persister 
>>> .entity 
>>> .AbstractEntityPersister.insert(AbstractEntityPersister.java: 
>>> 2252) ... 69 more « Back
>>> ------------------------------------------------------------------------------
>>> Download Intel&#174; Parallel Studio Eval
>>> Try the new software tools for yourself. Speed compiling, find bugs
>>> proactively, and fine-tune applications for parallel performance.
>>> See why Intel Parallel Studio got high marks during beta.
>>> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
>>> Treebase-devel mailing list
>>> Tre...@li...
>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
>> ===========================================================
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel&#174; Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
>

Re: [Treebase-devel] Data access failure for dev.

[Hilmar L. <hl...@ne...>]

It should not be an issue if you fully undeploy and redeploy. You  
should definitely do that each time you change the database underneath  
its feet.

	-hilmar

On Mar 10, 2010, at 4:26 PM, Vladimir Gapeyev wrote:

> A guess: Could this be related to "caching" that hibernate does?   
> Does anyone understand how that work?
> If the cache is persisted in files or in the DB, could Hibernate got  
> confused when we suddenly dropped and restored the database last week?
> --VG
>
>
> On Mar 10, 2010, at 4:15 PM, youjun guo wrote:
>
>> Bill tried the same operation one more time and hibernate get 101  
>> as PK from rowsegment_id_sequence, which is correct and everything  
>> is fine. I met same problem on table 'person' two days ago.
>>
>> Youjun
>>
>> On Wed, Mar 10, 2010 at 3:36 PM, Vladimir Gapeyev <vla...@du... 
>> > wrote:
>> That's strange...  I checked the definition of the RowSegment class  
>> and it is about the same as, say Study.  That is both should pick  
>> PK from their own sequences.  The current rowsegment_sequence_id is  
>> 98.
>>
>> How about trying once more -- does the generated id change from 54  
>> (it should, if it is picked from a sequence).
>>
>> --VG
>>
>>
>> On Mar 10, 2010, at 3:19 PM, Hilmar Lapp wrote:
>>
>>> It seems that hibernate assigned the primary key (54 here). I  
>>> thought the database would do that, not hibernate?
>>>
>>> 	-hilmar
>>>
>>> On Mar 10, 2010, at 3:15 PM, William Piel wrote:
>>>
>>>>
>>>>
>>>> When we try to upload a rowsegment metadata, we're getting a data  
>>>> access failure.
>>>>
>>>>
>>>> http://treebasedb-dev.nescent.org/treebase-web/user/rowSegmentDataTable.html
>>>>
>>>>
>>>>
>>>> Data Access Failure
>>>>
>>>> could not insert: [org.cipres.treebase.domain.matrix.RowSegment];  
>>>> nested exception is  
>>>> org.hibernate.exception.ConstraintViolationException: could not  
>>>> insert: [org.cipres.treebase.domain.matrix.RowSegment]
>>>>
>>>> org.springframework.dao.DataIntegrityViolationException: could  
>>>> not insert: [org.cipres.treebase.domain.matrix.RowSegment];  
>>>> nested exception is  
>>>> org.hibernate.exception.ConstraintViolationException: could not  
>>>> insert: [org.cipres.treebase.domain.matrix.RowSegment] Caused by:  
>>>> org.hibernate.exception.ConstraintViolationException: could not  
>>>> insert: [org.cipres.treebase.domain.matrix.RowSegment] at  
>>>> org 
>>>> .hibernate 
>>>> .exception.SQLStateConverter.convert(SQLStateConverter.java:71)  
>>>> at  
>>>> org 
>>>> .hibernate 
>>>> .exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java: 
>>>> 43) at  
>>>> org 
>>>> .hibernate 
>>>> .persister 
>>>> .entity 
>>>> .AbstractEntityPersister.insert(AbstractEntityPersister.java: 
>>>> 2272) at  
>>>> org 
>>>> .hibernate 
>>>> .persister 
>>>> .entity 
>>>> .AbstractEntityPersister.insert(AbstractEntityPersister.java: 
>>>> 2665) at  
>>>> org 
>>>> .hibernate 
>>>> .action.EntityInsertAction.execute(EntityInsertAction.java:60) at  
>>>> org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279) at  
>>>> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
>>>> 263) at  
>>>> org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 
>>>> 167) at  
>>>> org 
>>>> .hibernate 
>>>> .event 
>>>> .def 
>>>> .AbstractFlushingEventListener 
>>>> .performExecutions(AbstractFlushingEventListener.java:298) at  
>>>> org 
>>>> .hibernate 
>>>> .event 
>>>> .def 
>>>> .DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java: 
>>>> 27) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java: 
>>>> 1000) at  
>>>> org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)  
>>>> at  
>>>> org 
>>>> .hibernate 
>>>> .transaction.JDBCTransaction.commit(JDBCTransaction.java:106) at  
>>>> org 
>>>> .springframework 
>>>> .orm 
>>>> .hibernate3 
>>>> .HibernateTransactionManager 
>>>> .doCommit(HibernateTransactionManager.java:578) at  
>>>> org 
>>>> .springframework 
>>>> .transaction 
>>>> .support 
>>>> .AbstractPlatformTransactionManager 
>>>> .processCommit(AbstractPlatformTransactionManager.java:662) at  
>>>> org 
>>>> .springframework 
>>>> .transaction 
>>>> .support 
>>>> .AbstractPlatformTransactionManager 
>>>> .commit(AbstractPlatformTransactionManager.java:632) at  
>>>> org 
>>>> .springframework 
>>>> .transaction 
>>>> .interceptor 
>>>> .TransactionAspectSupport 
>>>> .commitTransactionAfterReturning(TransactionAspectSupport.java: 
>>>> 314) at  
>>>> org 
>>>> .springframework 
>>>> .transaction 
>>>> .interceptor 
>>>> .TransactionInterceptor.invoke(TransactionInterceptor.java:116)  
>>>> at  
>>>> org 
>>>> .springframework 
>>>> .aop 
>>>> .framework 
>>>> .ReflectiveMethodInvocation 
>>>> .proceed(ReflectiveMethodInvocation.java:171) at  
>>>> org 
>>>> .springframework 
>>>> .aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java: 
>>>> 204) at $Proxy75.createSegments(Unknown Source) at  
>>>> org.cipres.treebase.web.controllers.RowSegmentDataTableController.onSubmit 
>>>> (RowSegmentDataTableController.java:112) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission 
>>>> (SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission 
>>>> (CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal 
>>>> (AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest 
>>>> (AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle 
>>>> (SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch 
>>>> (DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService 
>>>> (DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest 
>>>> (FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost 
>>>> (FrameworkServlet.java:441) at  
>>>> javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at  
>>>> javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core 
>>>> .ApplicationFilterChain 
>>>> .internalDoFilter(ApplicationFilterChain.java:269) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>>> 188) at  
>>>> org 
>>>> .displaytag 
>>>> .filter 
>>>> .ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125)  
>>>> at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core 
>>>> .ApplicationFilterChain 
>>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>>> 188) at  
>>>> org 
>>>> .springframework 
>>>> .orm 
>>>> .hibernate3 
>>>> .support 
>>>> .OpenSessionInViewFilter 
>>>> .doFilterInternal(OpenSessionInViewFilter.java:198) at  
>>>> org 
>>>> .springframework 
>>>> .web 
>>>> .filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: 
>>>> 75) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core 
>>>> .ApplicationFilterChain 
>>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>>> 188) at  
>>>> com 
>>>> .opensymphony 
>>>> .module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)  
>>>> at  
>>>> com 
>>>> .opensymphony 
>>>> .module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55)  
>>>> at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core 
>>>> .ApplicationFilterChain 
>>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>>> 188) at org.acegisecurity.util.FilterChainProxy 
>>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:264) at  
>>>> org 
>>>> .acegisecurity 
>>>> .intercept 
>>>> .web 
>>>> .FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java: 
>>>> 107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter 
>>>> (FilterSecurityInterceptor.java:72) at  
>>>> org.acegisecurity.util.FilterChainProxy 
>>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>>> org 
>>>> .acegisecurity 
>>>> .ui 
>>>> .ExceptionTranslationFilter 
>>>> .doFilter(ExceptionTranslationFilter.java:110) at  
>>>> org.acegisecurity.util.FilterChainProxy 
>>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>>> org 
>>>> .acegisecurity 
>>>> .wrapper 
>>>> .SecurityContextHolderAwareRequestFilter 
>>>> .doFilter(SecurityContextHolderAwareRequestFilter.java:81) at  
>>>> org.acegisecurity.util.FilterChainProxy 
>>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>>> org 
>>>> .acegisecurity 
>>>> .ui 
>>>> .AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java: 
>>>> 217) at org.acegisecurity.util.FilterChainProxy 
>>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>>> org 
>>>> .acegisecurity 
>>>> .context 
>>>> .HttpSessionContextIntegrationFilter 
>>>> .doFilter(HttpSessionContextIntegrationFilter.java:191) at  
>>>> org.acegisecurity.util.FilterChainProxy 
>>>> $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at  
>>>> org 
>>>> .acegisecurity 
>>>> .util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at  
>>>> org 
>>>> .acegisecurity 
>>>> .util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core 
>>>> .ApplicationFilterChain 
>>>> .internalDoFilter(ApplicationFilterChain.java:215) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: 
>>>> 188) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)  
>>>> at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.StandardContextValve.invoke(StandardContextValve.java:172)  
>>>> at  
>>>> org 
>>>> .apache 
>>>> .catalina.core.StandardHostValve.invoke(StandardHostValve.java: 
>>>> 127) at  
>>>> org 
>>>> .apache 
>>>> .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java: 
>>>> 117) at  
>>>> org 
>>>> .apache 
>>>> .catalina 
>>>> .core.StandardEngineValve.invoke(StandardEngineValve.java:108) at  
>>>> org 
>>>> .apache 
>>>> .catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)  
>>>> at  
>>>> org 
>>>> .apache 
>>>> .coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java: 
>>>> 837) at org.apache.coyote.http11.Http11AprProtocol 
>>>> $Http11ConnectionHandler.process(Http11AprProtocol.java:640) at  
>>>> org.apache.tomcat.util.net.AprEndpoint 
>>>> $Worker.run(AprEndpoint.java:1286) at  
>>>> java.lang.Thread.run(Thread.java:636) Caused by:  
>>>> java.sql.BatchUpdateException: Batch entry 0 insert into  
>>>> ROWSEGMENT (VERSION, EndIndex, MATRIXROW_ID, CatalogNum,  
>>>> CollectionCode, Collector, Country, Elevation, GenBAccession,  
>>>> InstAcronym, Latitude, Locality, Longitude, Notes,  
>>>> OtherAccession, SampleDate, State, StartIndex, TAXONLABEL_ID,  
>>>> Title, ROWSEGMENT_ID) values (0, 4485, 224329, NULL, NULL, NULL,  
>>>> NULL, NULL, AY3242354, NULL, NULL, NULL, NULL, NULL, NULL, NULL,  
>>>> NULL, 1, NULL, NULL, 54) was aborted. Call getNextException to  
>>>> see the cause. at org.postgresql.jdbc2.AbstractJdbc2Statement 
>>>> $BatchResultHandler.handleError(AbstractJdbc2Statement.java:2537)  
>>>> at  
>>>> org 
>>>> .postgresql 
>>>> .core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java: 
>>>> 1328) at  
>>>> org 
>>>> .postgresql 
>>>> .core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:351) at  
>>>> org 
>>>> .postgresql 
>>>> .jdbc2 
>>>> .AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java: 
>>>> 2674) at  
>>>> org 
>>>> .apache 
>>>> .tomcat 
>>>> .dbcp 
>>>> .dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java: 
>>>> 297) at  
>>>> org 
>>>> .hibernate 
>>>> .jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48) at  
>>>> org 
>>>> .hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java: 
>>>> 34) at  
>>>> org 
>>>> .hibernate 
>>>> .persister 
>>>> .entity 
>>>> .AbstractEntityPersister.insert(AbstractEntityPersister.java: 
>>>> 2252) ... 69 more « Back
>>>> ------------------------------------------------------------------------------
>>>> Download Intel&#174; Parallel Studio Eval
>>>> Try the new software tools for yourself. Speed compiling, find bugs
>>>> proactively, and fine-tune applications for parallel performance.
>>>> See why Intel Parallel Studio got high marks during beta.
>>>> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
>>>> Treebase-devel mailing list
>>>> Tre...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>>
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
>>> ===========================================================
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Download Intel&#174; Parallel Studio Eval
>>> Try the new software tools for yourself. Speed compiling, find bugs
>>> proactively, and fine-tune applications for parallel performance.
>>> See why Intel Parallel Studio got high marks during beta.
>>> http://p.sf.net/sfu/intel-sw-dev_______________________________________________
>>> Treebase-devel mailing list
>>> Tre...@li...
>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel&#174; Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>>
>>
>

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================