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[Treebase-devel] Deleting Childless treeblocks
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From: William P. <wil...@ya...> - 2010-01-08 16:15:41
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One of the unit tests that is giving Youjun trouble is one that checks for orphans (or in this case "childless" records) in the following chain of tables: study --- submission --- sub_treeblock --- treeblock >-- phylotree Frankly, I'm not clear why we have sub_* tables to begin with, but it turns out that there are about 4,500 orphaned treeblocks (i.e. treeblock records that lack any related phylotree records) that each have a sub_treeblock id, and almost all of them belong to a submission that belongs to a study with study_id 22. So for some strange reason, study_id 22 has thousands of sub_treeblock records that each have a treeblock record, yet they lack phylotrees. Looks to me like these were created as part of Mark Jason's last migration effort -- probably purely spurious. I tried deleting these simply by deleting study_id 22, but after many hours that resulted in the "data access failure" (below). Don't know if anyone has some ideas re. why they doesn't work. The other approach is to run a SQL query like so: DELETE FROM treeblock WHERE treeblock_id IN ( SELECT tb.treeblock_id FROM phylotree pt RIGHT JOIN treeblock tb ON (pt.treeblock_id = tb.treeblock_id) JOIN sub_treeblock stb ON (tb.treeblock_id = stb.treeblock_id) JOIN submission sub ON (stb.submission_id = sub.submission_id) JOIN study st ON (sub.study_id = st.study_id) WHERE pt.phylotree_id IS NULL AND st.study_id = 22 ) ... but the trouble is that foreign key constraints don't allow these to be deleted (and postgres does not support CASCADE DELETE unless the tables are altered to do this automatically). One way around this would be to first build a list of orphaned sub_treeblock, treeblock, etc, records, and then delete them from the list of IDs flowing with the cascade. Anyway... I wanted to touch base with everyone in case there's an easy way to do this the proper way -- i.e. to have our java code & hibernate delete study_id 22 without running into the "DataIntegrityViolationException" below. bp Data Access Failure could not delete: [org.cipres.treebase.domain.taxon.TaxonLabel#67521]; nested exception is org.hibernate.exception.ConstraintViolationException: could not delete: [org.cipres.treebase.domain.taxon.TaxonLabel#67521] org.springframework.dao.DataIntegrityViolationException: could not delete: [org.cipres.treebase.domain.taxon.TaxonLabel#67521]; nested exception is org.hibernate.exception.ConstraintViolationException: could not delete: [org.cipres.treebase.domain.taxon.TaxonLabel#67521] Caused by: org.hibernate.exception.ConstraintViolationException: could not delete: [org.cipres.treebase.domain.taxon.TaxonLabel#67521] at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:71) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.persister.entity.AbstractEntityPersister.delete(AbstractEntityPersister.java:2546) at org.hibernate.persister.entity.AbstractEntityPersister.delete(AbstractEntityPersister.java:2702) at org.hibernate.action.EntityDeleteAction.execute(EntityDeleteAction.java:77) 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:172) 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.springframework.orm.hibernate3.HibernateTemplate$27.doInHibernate(HibernateTemplate.java:811) at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:372) at org.springframework.orm.hibernate3.HibernateTemplate.flush(HibernateTemplate.java:809) at org.cipres.treebase.dao.AbstractDAO.flush(AbstractDAO.java:158) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:198) at $Proxy50.flush(Unknown Source) at org.cipres.treebase.service.study.SubmissionServiceImpl.deleteSubmission(SubmissionServiceImpl.java:428) at org.cipres.treebase.service.study.SubmissionServiceImpl.deleteSubmission(SubmissionServiceImpl.java:900) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy80.deleteSubmission(Unknown Source) at org.cipres.treebase.web.controllers.DeleteStudyController.onSubmit(DeleteStudyController.java:71) 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:710) at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) 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$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:210) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:151) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685) at java.lang.Thread.run(Thread.java:636) Caused by: java.sql.BatchUpdateException: Batch entry 13 delete from TAXONLABEL where TAXONLABEL_ID=71834 and VERSION=2 was aborted. Call getNextException to see the cause. at org.postgresql.jdbc2.AbstractJdbc2Statement$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 com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeBatch(NewProxyPreparedStatement.java:1723) at org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48) at org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34) at org.hibernate.persister.entity.AbstractEntityPersister.delete(AbstractEntityPersister.java:2525) ... 85 more « Back |
