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bug #8064
closedNPE in AbstractHibernateTaxonGraphProcessor.assureSingleTaxon() on saving new name for new registration with new genus
Status:
Closed
Priority:
Highest
Assignee:
Category:
cdm-vaadin
Target version:
Start date:
Due date:
% Done:
100%
Estimated time:
Severity:
normal
Found in Version:
Description
This happened while entering the registration data for http://phycobank.org/100474 from scratch
Heidari, F., Zima, J., Riahi, H. & al., New simple trichal cyanobacterial taxa isolated from radioactive thermal springs in Fottea 18(2): 137–149. 2018
Nodosilinea radiophila Heidari & Hauer Type: Iran, Talesh Mahalleh, Ramsar., alt. 20 m, 36°52'58.8"N, 50°40'58.8"E. Holotype, (CBFS A–83–1). http://phycobank.org/100474 Registration on 2018-11-27 11:27:52
- create citation
- registration for new name
- add genus for new name "Nodosilinea Perkerson & Casamatta, 2011" with nom ref = Perkerson, III, R.B.; Johansen, J.R.; Kovácik, L.; Brand, J.; Kastovsky, J.; Casamatta, D.A. (2011). A unique pseudanabaenalean (cyanobacteria) genus Nodosilinea gen. nov. based on morphological and molecular data. Journal of Phycology, 47(6): 1397-1412.
- enter specific epithet, nom ref and ref detail for Nodosilinea radiophila and save ==> Error
eu.etaxonomy.vaadin.mvp.PopupEditorException: Error saving popup editor - context [user=admin] :Edit registration (TypedEntityReference: Registration#null) > New taxon name (TaxonNameDTO: TaxonName#0<0158be2b-d8c5-42a5-a8ae-47c7b814169e>) at eu.etaxonomy.vaadin.mvp.AbstractPopupEditor.save(AbstractPopupEditor.java:448) at eu.etaxonomy.vaadin.mvp.AbstractPopupEditor.lambda$0(AbstractPopupEditor.java:174) at sun.reflect.GeneratedMethodAccessor110.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at com.vaadin.event.ListenerMethod.receiveEvent(ListenerMethod.java:510) at com.vaadin.event.EventRouter.fireEvent(EventRouter.java:200) at com.vaadin.event.EventRouter.fireEvent(EventRouter.java:163) at com.vaadin.server.AbstractClientConnector.fireEvent(AbstractClientConnector.java:1015) at com.vaadin.ui.Button.fireClick(Button.java:377) at com.vaadin.ui.Button$1.click(Button.java:54) at sun.reflect.GeneratedMethodAccessor109.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at com.vaadin.server.ServerRpcManager.applyInvocation(ServerRpcManager.java:158) at com.vaadin.server.ServerRpcManager.applyInvocation(ServerRpcManager.java:119) at com.vaadin.server.communication.ServerRpcHandler.handleInvocation(ServerRpcHandler.java:437) at com.vaadin.server.communication.ServerRpcHandler.handleInvocations(ServerRpcHandler.java:402) at com.vaadin.server.communication.ServerRpcHandler.handleRpc(ServerRpcHandler.java:273) at com.vaadin.server.communication.UidlRequestHandler.synchronizedHandleRequest(UidlRequestHandler.java:90) at com.vaadin.server.SynchronizedRequestHandler.handleRequest(SynchronizedRequestHandler.java:41) at com.vaadin.server.VaadinService.handleRequest(VaadinService.java:1435) at com.vaadin.server.VaadinServlet.service(VaadinServlet.java:380) at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:841) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1634) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:316) at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:126) at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:90) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:114) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:122) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:169) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:48) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:158) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.oauth2.provider.authentication.OAuth2AuthenticationProcessingFilter.doFilter(OAuth2AuthenticationProcessingFilter.java:176) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:120) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:64) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:91) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:53) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:213) at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:176) at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:346) at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:262) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1621) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:121) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1613) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:541) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1584) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1228) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:481) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1553) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1130) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.Server.handle(Server.java:564) at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:320) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:251) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:112) at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:124) at org.eclipse.jetty.util.thread.Invocable.invokePreferred(Invocable.java:122) at org.eclipse.jetty.util.thread.strategy.ExecutingExecutionStrategy.invoke(ExecutingExecutionStrategy.java:58) at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.produceConsume(ExecuteProduceConsume.java:201) at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.run(ExecuteProduceConsume.java:133) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:672) at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:590) at java.lang.Thread.run(Thread.java:748) Caused by: com.vaadin.data.fieldgroup.FieldGroup$CommitException: Commit failed at com.vaadin.data.fieldgroup.FieldGroup.commit(FieldGroup.java:509) at eu.etaxonomy.vaadin.mvp.AbstractPopupEditor.save(AbstractPopupEditor.java:428) ... 90 more Caused by: com.vaadin.data.fieldgroup.FieldGroup$CommitException: Failed to store data to backend at eu.etaxonomy.vaadin.mvp.AbstractPopupEditor$SaveHandler.postCommit(AbstractPopupEditor.java:374) at com.vaadin.data.fieldgroup.FieldGroup.firePostCommitEvent(FieldGroup.java:625) at com.vaadin.data.fieldgroup.FieldGroup.commit(FieldGroup.java:501) ... 91 more Caused by: org.hibernate.AssertionFailure: Unable to perform beforeTransactionCompletion callback at org.hibernate.engine.spi.ActionQueue$BeforeTransactionCompletionProcessQueue.beforeTransactionCompletion(ActionQueue.java:905) at org.hibernate.engine.spi.ActionQueue.beforeTransactionCompletion(ActionQueue.java:481) at org.hibernate.internal.SessionImpl.beforeTransactionCompletion(SessionImpl.java:2340) at org.hibernate.engine.jdbc.internal.JdbcCoordinatorImpl.beforeTransactionCompletion(JdbcCoordinatorImpl.java:485) at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcResourceLocalTransactionCoordinatorImpl.beforeCompletionCallback(JdbcResourceLocalTransactionCoordinatorImpl.java:147) at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcResourceLocalTransactionCoordinatorImpl.access$100(JdbcResourceLocalTransactionCoordinatorImpl.java:38) at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcResourceLocalTransactionCoordinatorImpl$TransactionDriverControlImpl.commit(JdbcResourceLocalTransactionCoordinatorImpl.java:231) at org.hibernate.engine.transaction.internal.TransactionImpl.commit(TransactionImpl.java:65) at org.springframework.orm.hibernate5.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:581) at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:761) at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:730) at eu.etaxonomy.cdm.api.application.CdmRepository.commitTransaction(CdmRepository.java:468) at eu.etaxonomy.cdm.service.CdmStore.commitTransaction(CdmStore.java:245) at eu.etaxonomy.cdm.service.CdmStore.saveBean(CdmStore.java:167) at eu.etaxonomy.vaadin.mvp.CdmEditorPresenterBase.onEditorSaveEvent(CdmEditorPresenterBase.java:231) at sun.reflect.GeneratedMethodAccessor159.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.vaadin.spring.events.internal.MethodListenerWrapper.publish(MethodListenerWrapper.java:78) at org.vaadin.spring.events.internal.ListenerCollection.publish(ListenerCollection.java:167) at org.vaadin.spring.events.internal.ScopedEventBus.publish(ScopedEventBus.java:116) at org.vaadin.spring.events.internal.ScopedEventBus.publish(ScopedEventBus.java:109) at eu.etaxonomy.vaadin.mvp.AbstractPopupEditor$SaveHandler.postCommit(AbstractPopupEditor.java:366) ... 93 more Caused by: java.lang.NullPointerException at eu.etaxonomy.cdm.persistence.dao.hibernate.taxonGraph.AbstractHibernateTaxonGraphProcessor.assureSingleTaxon(AbstractHibernateTaxonGraphProcessor.java:222) at eu.etaxonomy.cdm.persistence.dao.hibernate.taxonGraph.AbstractHibernateTaxonGraphProcessor.assureSingleTaxon(AbstractHibernateTaxonGraphProcessor.java:209) at eu.etaxonomy.cdm.persistence.dao.hibernate.taxonGraph.AbstractHibernateTaxonGraphProcessor.updateEdges(AbstractHibernateTaxonGraphProcessor.java:129) at eu.etaxonomy.cdm.api.service.taxonGraph.TaxonGraphBeforeTransactionCompleteProcess.onNameOrRankChange(TaxonGraphBeforeTransactionCompleteProcess.java:175) at eu.etaxonomy.cdm.api.service.taxonGraph.TaxonGraphBeforeTransactionCompleteProcess.onNewTaxonName(TaxonGraphBeforeTransactionCompleteProcess.java:163) at eu.etaxonomy.cdm.api.service.taxonGraph.TaxonGraphBeforeTransactionCompleteProcess.doBeforeTransactionCompletion(TaxonGraphBeforeTransactionCompleteProcess.java:90) at org.hibernate.engine.spi.ActionQueue$BeforeTransactionCompletionProcessQueue.beforeTransactionCompletion(ActionQueue.java:899) ... 115 more
Related issues
Updated by Andreas Kohlbecker about 5 years ago
- Related to feature request #7648: Create taxonrelation to genus or species when subordinate names are created added
Updated by Andreas Kohlbecker about 5 years ago
- Status changed from New to Resolved
- % Done changed from 0 to 50
Applied in changeset cdmlib|a53c0e28c0e061f1abf2837042f1a933c7fdba50.
Updated by Andreas Kohlbecker about 5 years ago
- Status changed from Resolved to Closed
- % Done changed from 50 to 100
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