bug #5211: Error when creating new taxon /problem with sortindex in taxon tree - EDIT - EDIT Project Management

Actions

Copy link

bug #5211

open

Error when creating new taxon /problem with sortindex in taxon tree

Added by Cherian Mathew over 8 years ago. Updated about 3 years ago.

Status:

In Progress

Priority:

Highest

Assignee:

Andreas Müller

Category:

cdmlib

Target version:

Release 5.46

Start date:

Due date:

% Done:

Estimated time:

Severity:

normal

Found in Version:

Description

Following error occurs sometimes when creating a taxon.

java.lang.Exception: login : admin
editor version : 3.8.0.qualifier
server : test.e-taxonomy.eu / edit-test
schema version : 3.6.0.0.201527040000
os : Linux 3.13.0-62-generic amd64
java : 1.7.0_60
eu.etaxonomy.taxeditor.remoting.CdmEagerLoadingException: java.lang.ArrayIndexOutOfBoundsException: -1
    at org.hibernate.collection.internal.AbstractPersistentCollection.remoteInitialize(AbstractPersistentCollection.java:1334)
    at org.hibernate.collection.internal.AbstractPersistentCollection.initialize(AbstractPersistentCollection.java:603)
    at org.hibernate.collection.internal.AbstractPersistentCollection.read(AbstractPersistentCollection.java:143)
    at org.hibernate.collection.internal.AbstractPersistentCollection.readSize(AbstractPersistentCollection.java:160)
    at org.hibernate.collection.internal.PersistentList.size(PersistentList.java:114)
    at eu.etaxonomy.taxeditor.navigation.navigator.TaxonNodePropertyTester.test(TaxonNodePropertyTester.java:32)
    at org.eclipse.core.internal.expressions.Property.test(Property.java:58)
    at org.eclipse.core.internal.expressions.TestExpression.evaluate(TestExpression.java:99)
    at org.eclipse.core.internal.expressions.CompositeExpression.evaluateAnd(CompositeExpression.java:53)
    at org.eclipse.core.internal.expressions.AndExpression.evaluate(AndExpression.java:29)
    at org.eclipse.core.internal.expressions.CompositeExpression.evaluateOr(CompositeExpression.java:68)
    at org.eclipse.core.internal.expressions.OrExpression.evaluate(OrExpression.java:21)
    at org.eclipse.ui.internal.navigator.NavigatorPlugin$Evaluator.run(NavigatorPlugin.java:245)
    at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
    at org.eclipse.ui.internal.navigator.CustomAndExpression.evaluate(CustomAndExpression.java:71)
    at org.eclipse.ui.internal.navigator.NavigatorPlugin$Evaluator.run(NavigatorPlugin.java:245)
    at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
    at org.eclipse.ui.internal.navigator.NavigatorPlugin.safeEvaluate(NavigatorPlugin.java:260)
    at org.eclipse.ui.internal.navigator.extensions.NavigatorContentDescriptor.isTriggerPoint(NavigatorContentDescriptor.java:426)
    at 
Caused by: java.lang.ArrayIndexOutOfBoundsException: -1
    at java.util.ArrayList.elementData(ArrayList.java:400)
    at java.util.ArrayList.set(ArrayList.java:428)
    at org.hibernate.collection.internal.PersistentList.readFrom(PersistentList.java:409)
    at org.hibernate.loader.Loader.readCollectionElement(Loader.java:1312)
    at org.hibernate.loader.Loader.readCollectionElements(Loader.java:872)
    at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:723)
    at org.hibernate.loader.Loader.processResultSet(Loader.java:940)
    at org.hibernate.loader.Loader.doQuery(Loader.java:910)
    at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:341)
    at org.hibernate.loader.Loader.doList(Loader.java:2516)
    at org.hibernate.loader.Loader.doList(Loader.java:2502)
    at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2332)
    at org.hibernate.loader.Loader.list(Loader.java:2327)
    at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:490)
    at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:355)
    at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:195)
    at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1247)
    at org.hibernate.internal.QueryImpl.list(QueryImpl.java:101)
    at eu.etaxonomy.cdm.persistence.dao.initializer.AdvancedBeanInitializer.bulkLoadLazies(AdvancedBeanInitializer.java:436)
    at eu.etaxonomy.cdm.persistence.dao.initializer.AdvancedBeanInitializer.initializeNodeNoWildcard(AdvancedBeanInitializer.java:246)
    at eu.etaxonomy.cdm.persistence.dao.initializer.AdvancedBeanInitializer.initializeNode(AdvancedBeanInitializer.java:120)
    at eu.etaxonomy.cdm.persistence.dao.initializer.AdvancedBeanInitializer.initializeNodeRecursive(AdvancedBeanInitializer.java:100)
    at eu.etaxonomy.cdm.persistence.dao.initializer.AdvancedBeanInitializer.initializeNodeRecursive(AdvancedBeanInitializer.java:102)
    at eu.etaxonomy.cdm.persistence.dao.initializer.AdvancedBeanInitializer.initializeAll(AdvancedBeanInitializer.java:80)
    at eu.etaxonomy.cdm.persistence.dao.initializer.AdvancedBeanInitializer.initialize(AdvancedBeanInitializer.java:52)
    at eu.etaxonomy.cdm.persistence.dao.hibernate.common.CdmEntityDaoBase.load(CdmEntityDaoBase.java:519)
    at eu.etaxonomy.cdm.persistence.dao.hibernate.common.CdmGenericDaoImpl.initializeCollection(CdmGenericDaoImpl.java:744)
    at eu.etaxonomy.cdm.api.service.CommonServiceImpl.initializeCollection(CommonServiceImpl.java:322)
    at sun.reflect.GeneratedMethodAccessor1840.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
    at com.sun.proxy.$Proxy5599.initializeCollection(Unknown Source)
    at sun.reflect.GeneratedMethodAccessor1840.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)...

Related issues

Actions

Copy link

Updated by Cherian Mathew over 8 years ago

The actual reason for this error is that one of the taxon nodes to be loaded in the navigator has sortIndex -1.

Not really sure why this happens but correcting the sortIndex in the db fixes the problem.

Actions

Copy link

Updated by Cherian Mathew over 8 years ago

Status changed from New to Resolved
Assignee changed from c.mathew - to Andreas Müller

Actions

Copy link

Updated by Andreas Müller over 8 years ago

Assignee changed from Andreas Müller to c.mathew -

Should we just close this ticket and wait if the sortindex issue comes up again. I currently can't reproduce.

Or should we try to create a handler for this exception to give better feedback to the user such as "Please ask your database administrator to fix this"?

Actions

Copy link

Updated by Cherian Mathew over 8 years ago

Assignee changed from c.mathew - to Andreas Müller

Actions

Copy link

Updated by Andreas Müller over 8 years ago

Status changed from Resolved to In Progress
Target version changed from Remoting 5.0 to Unassigned CDM tickets

Actions

Copy link

Updated by Andreas Müller over 8 years ago

Status changed from In Progress to New

Actions

Copy link

Updated by Andreas Müller over 7 years ago

Description updated (diff)
Status changed from New to Worksforme

Probably fixed with better handling for null values in merge.

Actions

Copy link

Updated by Andreas Müller over 7 years ago

Target version deleted (~~Unassigned CDM tickets~~)

Actions

Copy link

Updated by Katja Luther about 7 years ago

Status changed from Worksforme to New
Assignee changed from Andreas Müller to Katja Luther

we have to reopen this ticket.
Henning created a new taxon, which had the sortindex -1.

Hallo, beim Überarbeiten des ungespreicherten Taxoneintrags: „Surirella chasei“ passiert,

VG
Henning

login : henning
editor version : 4.6.0
server : 160.45.63.173 (edit-prod) / phycobank
schema version : 4.1.0.0.201607300000
os : Windows 7 6.1 x86
java : 1.8.0_121
java.lang.ArrayIndexOutOfBoundsException: -1
                at java.util.ArrayList.elementData(ArrayList.java:418)
                at java.util.ArrayList.set(ArrayList.java:446)
                at org.hibernate.collection.internal.PersistentList.readFrom(PersistentList.java:390)
                at org.hibernate.loader.plan.exec.process.internal.CollectionReferenceInitializerImpl.finishUpRow(CollectionReferenceInitializerImpl.java:77)
                at org.hibernate.loader.plan.exec.process.internal.AbstractRowReader.readRow(AbstractRowReader.java:121)
                at org.hibernate.loader.plan.exec.process.internal.ResultSetProcessorImpl.extractResults(ResultSetProcessorImpl.java:112)
                at org.hibernate.loader.plan.exec.internal.AbstractLoadPlanBasedLoader.executeLoad(AbstractLoadPlanBasedLoader.java:122)
                at org.hibernate.loader.plan.exec.internal.AbstractLoadPlanBasedLoader.executeLoad(AbstractLoadPlanBasedLoader.java:86)
                at org.hibernate.loader.collection.plan.AbstractLoadPlanBasedCollectionInitializer.initialize(AbstractLoadPlanBasedCollectionInitializer.java:88)
                at org.hibernate.persister.collection.AbstractCollectionPersister.initialize(AbstractCollectionPersister.java:682)
                at org.hibernate.event.internal.DefaultInitializeCollectionEventListener.onInitializeCollection(DefaultInitializeCollectionEventListener.java:75)
                at org.hibernate.internal.SessionImpl.initializeCollection(SessionImpl.java:1991)
                at org.hibernate.collection.internal.AbstractPersistentCollection$4.doWork(AbstractPersistentCollection.java:550)
                at org.hibernate.collection.internal.AbstractPersistentCollection.withTemporarySessionIfNeeded(AbstractPersistentCollection
                at org.hibernate.collection.internal.AbstractPersistentCollection.initialize(AbstractPersistentCollection.java:546)
                at org.hibernate.collection.internal.AbstractPersistentCollection.read(AbstractPersistentCollection.java:133)
                at org.hibernate.collection.internal.AbstractPersistentCollection$1.doWork(AbstractPersistentCollection.java:162)
                at org.hibernate.collection.internal.AbstractPersistentCollection$1.doWork(AbstractPersistentCollection.java:147)
                at org.hibernate.collection.internal.AbstractPersistentCollection.withTemporarySessionIfNeeded(AbstractPersistentCollection.java:248)
                at org.hibernate.collection.internal.AbstractPersistentCollection.readSize(AbstractPersistentCollection.java:146)
                at org.hibernate.collection.internal.PersistentList.size(PersistentList.java:114)
                at eu.etaxonomy.cdm.model.taxon.TaxonNode.hasChildNodes(TaxonNode.java:950)
                at eu.etaxonomy.cdm.model.taxon.TaxonNode.updateSortIndex(TaxonNode.java:762)
                at eu.etaxonomy.cdm.model.taxon.TaxonNode.removeNullValueFromChildren(TaxonNode.java:969)
                at eu.etaxonomy.cdm.persistence.hibernate.PostMergeEntityListener.removeNullFromCollections(PostMergeEntityListener.java:87)
                at eu.etaxonomy.cdm.persistence.hibernate.PostMergeEntityListener.onMerge(PostMergeEntityListener.java:64)

Actions

Copy link

#10

Updated by Andreas Müller about 7 years ago

Target version set to Release 4.7

Actions

Copy link

#11

Updated by Andreas Müller about 7 years ago

Subject changed from Error when creating new taxon to Error when creating new taxon /problem with sortindex in taxon tree
Private changed from Yes to No

The main problem here is that the hibernate implementation of List (PersistentList) has a strange behavior in the size() method when an object is added. Size() does not change its value though a new abject is added. Instead only an ADD object is remembered in the list. As we use size for computing the sortindex this leads to problems and incorrect sortindexes.

Actions

Copy link

#12