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

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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 Could this be due to the treebase-dev instance being out of date re:  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&#174; Parallel Studio Eval
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>>>> 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
>>
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>