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From: Rutger V. <rut...@gm...> - 2010-03-12 08:29:49
|
Yup, I can tell that the text isn't entirely final: * the proposed menu suggests there should be a "partnerships" page, but no text has been written for that (I think) * likewise for the "contact" page * the text for the "data access" page is still in flux Therefore, the ticket is still open. But we're closer than we were. I'll do some PhyloWS work bug fixing today. On Fri, Mar 12, 2010 at 3:05 AM, Hilmar Lapp <hl...@ne...> wrote: > Hi Rutger - > > I saw that from the commit messages. Sorry for the slightly misleading > language in the ticket - that text was close to but not exactly ready yet. > > However that doesn't hurt at all - the ticket was assigned to Youjun anyway, > and you doing that now enables us to do some of the testing by appointment > earlier than we had planned. > > -hilmar > > On Mar 11, 2010, at 7:19 PM, Rutger Vos wrote: > >> Hi all, >> >> I created most of the pages as suggested on the google doc >> >> http://docs.google.com/Doc?docid=0AXEQpupFgwYiZGg4bXF6bl82NmZwdm50cmRz&hl=en >> and I give the site a slight layout change. Can we have a rebuild and >> redeployment to see it in action? It's commit 547. >> >> Cheers, >> >> Rutger >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com >> >> >> ------------------------------------------------------------------------------ >> 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 : > =========================================================== > > > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Hilmar L. <hl...@ne...> - 2010-03-12 03:06:00
|
Hi Rutger - I saw that from the commit messages. Sorry for the slightly misleading language in the ticket - that text was close to but not exactly ready yet. However that doesn't hurt at all - the ticket was assigned to Youjun anyway, and you doing that now enables us to do some of the testing by appointment earlier than we had planned. -hilmar On Mar 11, 2010, at 7:19 PM, Rutger Vos wrote: > Hi all, > > I created most of the pages as suggested on the google doc > http://docs.google.com/Doc?docid=0AXEQpupFgwYiZGg4bXF6bl82NmZwdm50cmRz&hl=en > and I give the site a slight layout change. Can we have a rebuild and > redeployment to see it in action? It's commit 547. > > Cheers, > > Rutger > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > 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 : =========================================================== |
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From: William P. <wil...@ya...> - 2010-03-12 02:41:47
|
On Mar 11, 2010, at 2:25 PM, Vladimir Gapeyev wrote: > I believe, all these predate the migration. Let me know what to do: scrape them all out, update their nchar, ntax to the counts, or do something case-by-case. > Thanks Vladimir. The likely solution is to update nchar, ntax numbers to the correct amounts. When I get a chance, I'll try downloading reconstructed versions to verify that there are not other problems with these files. bp |
|
From: Rutger V. <rut...@gm...> - 2010-03-12 00:48:52
|
Hi all, I created most of the pages as suggested on the google doc http://docs.google.com/Doc?docid=0AXEQpupFgwYiZGg4bXF6bl82NmZwdm50cmRz&hl=en and I give the site a slight layout change. Can we have a rebuild and redeployment to see it in action? It's commit 547. Cheers, Rutger -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
|
From: Vladimir G. <vga...@ne...> - 2010-03-11 21:02:17
|
Since the most computationally intensive part of data migration is now over, it will be more convenient to finish the migration and data cleaning on the treebasestage instance. So, please be aware that - treebasestage DB will be dropped and rebuilt with the most recent copy of the migrated data sometime this afternoon; - any edits made to treebasestage after that, including via the web app at treebase-stage.nescent.org, will make their way into the release in production -- that is, use caution. --Vladimir |
|
From: Vladimir G. <vga...@ne...> - 2010-03-11 19:25:22
|
Bill,
Here are all the matrices (also attached) in the post-migration
instance that have a discrepancy between their ntax and the number of
associated matrixrows, or between nchar and the number of associated
matrixcolumns.
matrix_id | tb_matrixid | nexusfilename |
published | ntax | rows_counted | nchar | columns_counted
-----------+----------------------+--------------------------
+-----------+------+--------------+-------+-----------------
4090 | M1728 | M1728.nex |
f | | 26 | 30 | 30
4150 | | withstates.nex |
f | | 7 | | 28
4374 | M4524 | M4524.nex |
f | | 205 | 11335 | 11335
4050 | | 18S-28S |
f | | 72 | | 1818
4098 | M64c1x28x96c16c00c36 | M64c1x28x96c16c00c36.nex |
f | | 46 | 84 | 84
4110 | | M2496.nex |
f | | 34 | 16837 | 16837
4622 | M4460 | M4460.nex |
f | | 54 | 9173 | 9173
4092 | M2056 | M2056.nex |
f | | 49 | 161 | 161
4070 | | zztip |
f | | 12 | | 542
4095 | M2767 | M2767.nex |
f | | 66 | 806 | 806
4091 | M1729 | M1729.nex |
f | | 46 | 30 | 30
4099 | M76c1x29x96c15c31c23 | M76c1x29x96c15c31c23.nex |
f | | 15 | 31 | 31
4130 | | 12Tx432C.nex |
f | | 12 | | 432
4096 | M62c1x28x96c15c56c19 | M62c1x28x96c15c56c19.nex |
f | | 72 | 82 | 82
4094 | M2765 | M2765.nex |
f | | 74 | 2266 | 2266
4093 | M2313 | M2313.nex |
f | | 43 | 1902 | 1902
4097 | M644 | M644.nex |
f | | 28 | 86 | 86
(17 rows)
I believe, all these predate the migration. Let me know what to do:
scrape them all out, update their nchar, ntax to the counts, or do
something case-by-case.
Here is the query used for the report:
select m.matrix_id, m.tb_matrixid, m.nexusfilename, m.published,
m.nTax, r.rows_counted,
nChar, c.columns_counted
from matrix as m,
(select matrix_id, count(*) as rows_counted
from matrixrow group by matrix_id) as r,
(select matrix_id, count(*) as columns_counted
from matrixcolumn group by matrix_id) as c
where m.matrix_id = r.matrix_id and m.matrix_id = c.matrix_id
and ((m.ntax is null or m.ntax <> r.rows_counted) or
(m.nchar is null or m.nchar <> c.columns_counted))
|
|
From: Hilmar L. <hl...@ne...> - 2010-03-10 23:12:44
|
On Mar 10, 2010, at 5:40 PM, Vladimir Gapeyev wrote: > in my Safari, but not in Firefox What is the error message? I.e., is there evidence of the version of PhyloWidget having a problem under Firefox, or a problem with accessing the jar itself? Does the applet itself start and then crash? Firefox has a nice error console - any hints you can find there? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: Vladimir G. <vga...@ne...> - 2010-03-10 22:40:10
|
I work on the PhyloWidget issue http://sourceforge.net/tracker/?func=detail&aid=2960910&group_id=248804&atid=1126676 As I suggested earlier, putting PhyloWidget.jar inside treebase- web.war seems to work -- in my Safari, but not in Firefox (I do have "Java and Javascript enabled"). If this is normal, I'll consider the issue closed. --VG |
|
From: Vladimir G. <vla...@du...> - 2010-03-10 21:29:11
|
Jon has just re-deployed treebase-dev. This should have all commits up to an hour ago. --VG |
|
From: Hilmar L. <hl...@ne...> - 2010-03-10 21:28:25
|
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® 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 >> >> >> ------------------------------------------------------------------------------ >> 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 : =========================================================== |
|
From: Vladimir G. <vla...@du...> - 2010-03-10 21:27:08
|
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® 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 > > > ------------------------------------------------------------------------------ > 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 > > |
|
From: youjun g. <you...@ya...> - 2010-03-10 21:15:50
|
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® 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 > > > > > ------------------------------------------------------------------------------ > 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 > > |
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From: Hilmar L. <hl...@ne...> - 2010-03-10 20:56:17
|
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 : =========================================================== |
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From: Vladimir G. <vla...@du...> - 2010-03-10 20:54:37
|
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 : > =========================================================== > > > |
|
From: Hilmar L. <hl...@ne...> - 2010-03-10 20:47:58
|
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 : =========================================================== |
|
From: Vladimir G. <vla...@du...> - 2010-03-10 20:36:52
|
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 |
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From: Hilmar L. <hl...@ne...> - 2010-03-10 20:19:18
|
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 : =========================================================== |
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From: William P. <wil...@ya...> - 2010-03-10 20:16:17
|
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 |
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From: Hilmar L. <hl...@ne...> - 2010-03-10 19:51:37
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This is mostly an FYI, as we had said before that we were going to do that. Jon is doing this such that the instance can be brought up again w/o too much hassle if we need it to answer whether the port 6666 instance had a particular feature working that is broken on production, staging, or dev. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2010-03-10 19:49:27
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I changed the PURL base path to redirect to http://treebase.nescent.org/treebase-web/phylows instead of the 6666 instance. Let me know if you encounter issues, or if you want them to redirect elsewhere (dev or staging). -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Vladimir G. <vga...@ne...> - 2010-03-10 18:34:59
|
Rutger, Could you point me to where data consistency checkers are located and to any relevant information about them? It would make sense to check the data now again, as we are done with the data migration. This is the stuff you used to do in SF bugs #2899240 and #2717395 Thanks, --Vladimir |
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From: Hilmar L. <hl...@ne...> - 2010-03-10 16:26:45
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The API documentation right now states for example that "tb:identifier.ubio inherits from dcterms:identifier and so any of the latter's semantics apply to the former." Where is this formalized? The namespace URI given in the spreadsheet [1] yields a 404. Has the vocabulary been published as RDF or OWL? If not, we need to revise the above statement. -hilmar [1] http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw&single=true&gid=0&output=html -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Vladimir G. <vga...@ne...> - 2010-03-10 15:51:32
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Looking through the loading logs, I notice something that may indicate a trouble (during loading Studies dump): Fixing tree 6763 Unknown TreeType 'single'; skipping it Fixing tree 6868 Unknown TreeType 'consensus'; skipping it Indeed, the treetype_id field is null in the newly uploaded matrices. Is this bad? This was likely caused by a lower/upper case mismatch: the values in the DB are 'Consensus' and 'Single'. As we are into this, the fields treekind_id and treequality_id are also null, but I do not see entries in the dump file that could fill them. --VG |
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From: Hilmar L. <hl...@ne...> - 2010-03-10 15:32:26
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Rutger - can you elaborate on how we are using RSS technically? You say in your comments to the website text draft that it is being used for search results that are lists. Is this the native response format of the web-application then and an XSLT is used to convert to HTML? I think not, right? So I'm still pretty confused. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Vladimir G. <vla...@du...> - 2010-03-10 15:21:41
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On Mar 8, 2010, at 9:28 PM, William Piel wrote: > At any rate, we have the last migration dump here: > > http://treebase.peabody.yale.edu/treebase/migration/Mar-10/ > > The citations and TI are not there yet, but Vladimir can start > migrating the trees, characters, and the dump file. Meanwhile I'll > be working on the TI mapping -- that's critical for release. For > now, citations can be stored in title field as one-liners (this is > not critical for release, so I'll be working on them after the TI is > done). Matrices, trees, and studies are now in the production instance. I'll wait on asking Jon to copy this instance to treebasestage, until TI and, perhaps, citations are loaded as well. The scripts reported loading 223 matrices and 257 trees -- is this about right? --Vladimir |
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