bug #9360: Parsed hybrids can not be persisted - EDIT - EDIT Project Management

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5.33
cdm-dataportal (open)
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phycobank
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Taxeditor-UX (Platform Etablierung)

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bug #9360

open

Parsed hybrids can not be persisted

Added by Andreas Müller over 3 years ago. Updated almost 3 years ago.

Status:

Feedback

Priority:

Highest

Assignee:

Katja Luther

Category:

taxeditor

Target version:

Release 5.19

Start date:

Due date:

% Done:

50%

Estimated time:

Severity:

normal

Found in Version:

Description

In Flora of Cyprus I tried to persist a hybrid formula (Aegilops biuncialis × geniculata) but got an NPE in TaxonName.isBotanical() during persisting the taxon.
Looks like ther is a name without type which should not exist.

I did override an existing unparsed name. Not sure if this is relevant here.

Once this is fixed we should fix data in databases (or wait until they can also be edited in TaxEditor as otherwise there may be some confusion especially if the parents are names that exist elsewhere in the database and need deduplication. There should be a ticket for this.)

Related issues

Related to EDIT - bug #7711: Bugs in media gallery

Resolved

Katja Luther

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Has duplicate EDIT - bug #9149: NPE when saving hybrid formula

Duplicate

Andreas Müller

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Issue # Delay: days Cancel

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Updated by Andreas Müller about 3 years ago

Status changed from New to In Progress
Priority changed from New to Highest

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Updated by Andreas Müller about 3 years ago

Related to bug #9149: NPE when saving hybrid formula added

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Updated by Andreas Müller about 3 years ago

maybe a duplicate for #9149

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Updated by Andreas Müller about 3 years ago

A similar issue in test DB

last remote method : http://test.e-taxonomy.eu:80/cdmserver/rem_conf_am/remoting/taxonnode.service
last remote request client time : 2021-01-26T09:06:01.138
last remote request response header time : Tue, 26 Jan 2021 09:06:01 GMT
client error time : 2021-01-26T09:06:01.341
login : admin
editor version : 5.19.0.202101252350
server : test.e-taxonomy.eu (edit-test) / rem_conf_am
schema version : 5.18.6.0.20201124
os : Windows Server 2012 R2 6.3 amd64
java : 1.8.0_121
org.eclipse.e4.core.di.InjectionException: java.lang.NullPointerException
    at org.eclipse.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:65)
    at org.eclipse.e4.core.internal.di.InjectorImpl.invokeUsingClass(InjectorImpl.java:282)
    at org.eclipse.e4.core.internal.di.InjectorImpl.invoke(InjectorImpl.java:247)
    at org.eclipse.e4.core.contexts.ContextInjectionFactory.invoke(ContextInjectionFactory.java:90)
    at org.eclipse.e4.ui.internal.workbench.PartServiceSaveHandler.save(PartServiceSaveHandler.java:57)
    at org.eclipse.ui.internal.WorkbenchWindow$7.save(WorkbenchWindow.java:594)
    at org.eclipse.e4.ui.internal.workbench.PartServiceImpl.savePart(PartServiceImpl.java:1390)
    at eu.etaxonomy.taxeditor.workbench.SaveHandler.execute(SaveHandler.java:42)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.eclipse.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:55)
    at org.eclipse.e4.core.internal.di.InjectorImpl.invokeUsingClass(InjectorImpl.java:282)
    at org.eclipse.e4.core.internal.di.InjectorImpl.invoke(InjectorImpl.java:264)
    at org.eclipse.e4.core.contexts.ContextInjectionFactory.invoke(ContextInjectionFactory.java:132)
    at org.eclipse.e4.core.commands.internal.HandlerServiceHandler.execute(HandlerServiceHandler.java:152)
    at org.eclipse.core.commands.Command.executeWithChecks(Command.java:494)
    at org.eclipse.core.commands.ParameterizedCommand.executeWithChecks(ParameterizedCommand.java:488)
    at org.eclipse.e4.core.commands.internal.HandlerServiceImpl.executeHandler(HandlerServiceImpl.java:210)
    at org.eclipse.e4.ui.workbench.renderers.swt.HandledContributionItem.executeItem(HandledContributionItem.java:433)
    at org.eclipse.e4.ui.workbench.renderers.swt.AbstractContributionItem.handleWidgetSelection(AbstractContributionItem.java:454)
    at org.eclipse.e4.ui.workbench.renderers.swt.AbstractContributionItem$3.handleEvent(AbstractContributionItem.java:482)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
    at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4418)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1079)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4236)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3824)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$4.run(PartRenderingEngine.java:1121)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1022)
    at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:150)
    at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:693)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336)
    at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:610)
    at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:148)
    at eu.etaxonomy.taxeditor.Application.start(Application.java:20)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:673)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:610)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1519)
Caused by: java.lang.NullPointerException
    at eu.etaxonomy.cdm.model.name.TaxonName.isBotanical(TaxonName.java:3536)
    at eu.etaxonomy.cdm.model.name.TaxonName.isAutonym(TaxonName.java:1411)
    at eu.etaxonomy.cdm.strategy.cache.name.TaxonNameDefaultCacheStrategy.getTaggedTitle(TaxonNameDefaultCacheStrategy.java:397)
    at eu.etaxonomy.cdm.strategy.cache.name.TaxonNameDefaultCacheStrategy.getTaggedTitle(TaxonNameDefaultCacheStrategy.java:394)
    at eu.etaxonomy.cdm.strategy.cache.name.TaxonNameDefaultCacheStrategy.getTaggedFullTitle(TaxonNameDefaultCacheStrategy.java:299)
    at eu.etaxonomy.cdm.strategy.cache.name.NameCacheStrategyBase.getFullTitleCache(NameCacheStrategyBase.java:58)
    at eu.etaxonomy.cdm.strategy.cache.name.NameCacheStrategyBase.getFullTitleCache(NameCacheStrategyBase.java:69)
    at eu.etaxonomy.cdm.model.name.TaxonName.generateFullTitle(TaxonName.java:1385)
    at eu.etaxonomy.cdm.model.name.TaxonName.getFullTitleCache(TaxonName.java:1448)
    at eu.etaxonomy.cdm.persistence.hibernate.CdmPreDataChangeListener.generateCaches(CdmPreDataChangeListener.java:119)
    at eu.etaxonomy.cdm.persistence.hibernate.CacheStrategyGenerator.saveOrUpdateOrMerge(CacheStrategyGenerator.java:47)
    at eu.etaxonomy.cdm.persistence.hibernate.CacheStrategyGenerator.onSaveOrUpdate(CacheStrategyGenerator.java:32)
    at org.hibernate.internal.SessionImpl.fireSaveOrUpdate(SessionImpl.java:651)
    at org.hibernate.internal.SessionImpl.saveOrUpdate(SessionImpl.java:643)
    at org.hibernate.engine.spi.CascadingActions$5.cascade(CascadingActions.java:218)
    at org.hibernate.engine.internal.Cascade.cascadeToOne(Cascade.java:423)
    at org.hibernate.engine.internal.Cascade.cascadeAssociation(Cascade.java:348)
    at org.hibernate.engine.internal.Cascade.cascadeProperty(Cascade.java:187)
    at org.hibernate.engine.internal.Cascade.cascade(Cascade.java:136)
    at org.hibernate.event.internal.AbstractFlushingEventListener.cascadeOnFlush(AbstractFlushingEventListener.java:150)
    at org.hibernate.event.internal.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:141)
    at org.hibernate.event.internal.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:74)
    at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:38)
    at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1295)
    at org.hibernate.internal.SessionImpl.managedFlush(SessionImpl.java:468)
    at org.hibernate.internal.SessionImpl.flushBeforeTransactionCompletion(SessionImpl.java:3159)
    at org.hibernate.internal.SessionImpl.beforeTransactionCompletion(SessionImpl.java:2352)
    at org.hibernate.engine.jdbc.internal.JdbcCoordinatorImpl.beforeTransactionCompletion(JdbcCoordinatorImpl.java:491)
    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:582)
    at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:765)
    at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:734)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:522)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:293)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
    at com.sun.proxy.$Proxy688.merge(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    at org.springframework.remoting.support.RemoteInvocationTraceInterceptor.invoke(RemoteInvocationTraceInterceptor.java:78)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
    at com.sun.proxy.$Proxy1048.merge(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.springframework.remoting.support.RemoteInvocation.invoke(RemoteInvocation.java:212)
    at eu.etaxonomy.cdm.api.remoting.DebuggingRemoteInvocationExecutor.invoke(DebuggingRemoteInvocationExecutor.java:52)
    at org.springframework.remoting.support.RemoteInvocationBasedExporter.invoke(RemoteInvocationBasedExporter.java:78)
    at org.springframework.remoting.support.RemoteInvocationBasedExporter.invokeAndCreateResult(RemoteInvocationBasedExporter.java:114)
    at org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter.handleRequest(HttpInvokerServiceExporter.java:80)
    at org.springframework.web.servlet.mvc.HttpRequestHandlerAdapter.handle(HttpRequestHandlerAdapter.java:51)
    at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:967)
    at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:901)
    at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
    at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:872)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
    at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
    at org.eclipse.jetty.servlet.ServletHolder$NotAsyncServlet.service(ServletHolder.java:1395)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:755)
    at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1617)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:317)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:127)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
    at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:114)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
    at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
    at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
    at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
    at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:215)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
    at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
    at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:66)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
    at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
...

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Updated by Andreas Müller about 3 years ago

Assignee changed from Andreas Müller to Katja Luther
% Done changed from 0 to 20

Probably the reason is that in TaxEditorInputE4.merge() only the hybrid parents for new parents are pre-saved. But the concept is not new, only the name has been changed therefore this save does not take place.
Or is there a reason why only the new concepts and synonyms are checked for hybrid parents? Do we can lazyloading issues otherwise?

Katja, can you have a look?

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Updated by Andreas Müller about 3 years ago

Related to deleted (bug #9149: NPE when saving hybrid formula)

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Updated by Andreas Müller about 3 years ago

Has duplicate bug #9149: NPE when saving hybrid formula added

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Updated by Andreas Müller about 3 years ago

Related to bug #7711: Bugs in media gallery added

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Updated by Katja Luther about 3 years ago

Status changed from In Progress to Resolved
% Done changed from 20 to 50

Applied in changeset taxeditor|f8decba5d7a4bc8ec562b380190b1534a31c069a.

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#10

Updated by Katja Luther about 3 years ago

Concepts with hybrid names are already handled correctly, because the list toSaveNewConcepts contains all concepts, I would rename it to toSaveConcepts.

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#11

Updated by Andreas Müller about 3 years ago

Katja Luther wrote:

Concepts with hybrid names are already handled correctly, because the list toSaveNewConcepts contains all concepts, I would rename it to toSaveConcepts.

But why did we get the save issue for accepted taxa yesterday when editing accepted taxa?

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#12