bug #8736: LazyInitializationException (LIE) during adding Specimens to Matrix Editor - Edit - Redmine

bug #8736

LazyInitializationException (LIE) during adding Specimens to Matrix Editor

Added by Andreas Kohlbecker 7 months ago. Updated 19 days ago.

Status:

Closed

Priority:

New

Assignee:

Patrick Plitzner

Category:

taxeditor

Target version:

Release 5.12

Start date:

11/29/2019

Due date:

% Done:

100%

Severity:

normal

Found in Version:

Tags:

additivity

Description

To reproduce:

use database: caryophyllales_spp (cactaceae)
create new Descriptive Dataset (non specimens so far!), add Character tree and Cactaceae, save it
open the Dataset in the Matrix Editor
open Select Specimen Dialog
Enter "Acantho" in the filter bar
Select all Specimens click OK
The dialog will be shown asking if you want to create IndividualsAssiociations, click OK --> LIE (see below)

The proplem only occures when creating the IndividualsAssiociations.

client stack trace:

login : 
editor version : 5.12.0.201911220001
server :  ()
schema version : 
os : Linux 5.0.0-36-generic amd64
java : 1.8.0_131
org.hibernate.LazyInitializationException: failed to lazily initialize a collection of role: eu.etaxonomy.cdm.model.taxon.Taxon.descriptions, could not initialize proxy - no Session
    at org.hibernate.collection.internal.AbstractPersistentCollection.throwLazyInitializationException(AbstractPersistentCollection.java:567)
    at org.hibernate.collection.internal.AbstractPersistentCollection.withTemporarySessionIfNeeded(AbstractPersistentCollection.java:205)
    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.PersistentSet.iterator(PersistentSet.java:163)
    at java.util.Spliterators$IteratorSpliterator.estimateSize(Spliterators.java:1821)
    at java.util.Spliterator.getExactSizeIfKnown(Spliterator.java:408)
    at java.util.stream.AbstractPipeline.copyIntoWithCancel(AbstractPipeline.java:497)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:485)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
    at java.util.stream.FindOps$FindOp.evaluateSequential(FindOps.java:152)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.util.stream.ReferencePipeline.findFirst(ReferencePipeline.java:464)
    at eu.etaxonomy.cdm.api.service.DescriptiveDataSetService.addRowWrapperToDataset(DescriptiveDataSetService.java:237)
    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:302)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
    at com.sun.proxy.$Proxy178.addRowWrapperToDataset(Unknown Source)
    at eu.etaxonomy.cdm.api.service.longrunningService.LongRunningTasksService$3.doRun(LongRunningTasksService.java:115)
    at eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread.run(RemotingProgressMonitorThread.java:42)

server stack trace:

[caryophyllales_spp] 17:04:58,498 INFO [Thread-390][eu.et.cd.co.mo.RemotingProgressMonitorThread] - Exception in RemotingProgressMonitorThread 
org.hibernate.LazyInitializationException: failed to lazily initialize a collection of role: eu.etaxonomy.cdm.model.taxon.Taxon.descriptions, could not initialize proxy - no Session
    at org.hibernate.collection.internal.AbstractPersistentCollection.throwLazyInitializationException(AbstractPersistentCollection.java:567)
    at org.hibernate.collection.internal.AbstractPersistentCollection.withTemporarySessionIfNeeded(AbstractPersistentCollection.java:205)
    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.PersistentSet.iterator(PersistentSet.java:163)
    at java.util.Spliterators$IteratorSpliterator.estimateSize(Spliterators.java:1821)
    at java.util.Spliterator.getExactSizeIfKnown(Spliterator.java:408)
    at java.util.stream.AbstractPipeline.copyIntoWithCancel(AbstractPipeline.java:497)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:485)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
    at java.util.stream.FindOps$FindOp.evaluateSequential(FindOps.java:152)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.util.stream.ReferencePipeline.findFirst(ReferencePipeline.java:464)
    at eu.etaxonomy.cdm.api.service.DescriptiveDataSetService.addRowWrapperToDataset(DescriptiveDataSetService.java:237)
    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:302)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
    at com.sun.proxy.$Proxy178.addRowWrapperToDataset(Unknown Source)
    at eu.etaxonomy.cdm.api.service.longrunningService.LongRunningTasksService$3.doRun(LongRunningTasksService.java:115)
    at eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread.run(RemotingProgressMonitorThread.java:42)

Related issues

Associated revisions

Revision 9e899760 (diff)
Added by Patrick Plitzner 7 months ago

fix #8736 Fix LIE when adding specimens to matrix

Revision 034ce108 (diff)
Added by Patrick Plitzner 7 months ago

ref #8736 minor performance improvement when adding specimens to matrix

History

#1 Updated by Andreas Kohlbecker 7 months ago

Description updated (diff)

#2 Updated by Andreas Kohlbecker 7 months ago

Description updated (diff)

#3 Updated by Andreas Müller 7 months ago

Assignee changed from Katja Luther to Patrick Plitzner

#4 Updated by Patrick Plitzner 7 months ago

Tags set to additivity

#5 Updated by Patrick Plitzner 7 months ago

Status changed from New to Resolved
% Done changed from 0 to 50

Applied in changeset cdmlib|9e89976076d8a735426f40e4cebb49c42bd5ab33.

#6 Updated by Patrick Plitzner 7 months ago

Assignee changed from Patrick Plitzner to Andreas Kohlbecker
Target version changed from 287 to Release 5.12

#7 Updated by Andreas Kohlbecker 6 months ago

Status changed from Resolved to In Progress
Assignee changed from Andreas Kohlbecker to Katja Luther

The LIE is apparently fixed but I received another exception:

Server side:

[caryophyllales_spp] 11:42:48,590 INFO [Thread-24][eu.et.cd.co.mo.RemotingProgressMonitorThread] - Exception in RemotingProgressMonitorThread 
java.util.NoSuchElementException
    at java.util.HashMap$HashIterator.nextNode(HashMap.java:1439)
    at java.util.HashMap$KeyIterator.next(HashMap.java:1461)
    at org.hibernate.collection.internal.AbstractPersistentCollection$IteratorProxy.next(AbstractPersistentCollection.java:829)
    at eu.etaxonomy.cdm.api.service.DescriptiveDataSetService.findTaxonNodeForDescription(DescriptiveDataSetService.java:196)
    at eu.etaxonomy.cdm.api.service.DescriptiveDataSetService.findDefaultDescription(DescriptiveDataSetService.java:171)
    at eu.etaxonomy.cdm.api.service.DescriptiveDataSetService.createSpecimenRowWrapper(DescriptiveDataSetService.java:319)
    at eu.etaxonomy.cdm.api.service.DescriptiveDataSetService.addRowWrapperToDataset(DescriptiveDataSetService.java:263)
    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:302)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
    at com.sun.proxy.$Proxy178.addRowWrapperToDataset(Unknown Source)
    at eu.etaxonomy.cdm.api.service.longrunningService.LongRunningTasksService$3.doRun(LongRunningTasksService.java:116)
    at eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread.run(RemotingProgressMonitorThread.java:42)
[caryophyllales_spp] 11:42:48,598 INFO [Thread-24][eu.et.cd.co.mo.DefaultProgressMonitor] - No task name... Done

Taxeditor:

login : 
editor version : 5.12.0.202001141551
server :  ()
schema version : 
os : Linux 5.0.0-37-generic amd64
java : 1.8.0_131
java.util.NoSuchElementException
    at java.util.HashMap$HashIterator.nextNode(HashMap.java:1439)
    at java.util.HashMap$KeyIterator.next(HashMap.java:1461)
    at org.hibernate.collection.internal.AbstractPersistentCollection$IteratorProxy.next(AbstractPersistentCollection.java:829)
    at eu.etaxonomy.cdm.api.service.DescriptiveDataSetService.findTaxonNodeForDescription(DescriptiveDataSetService.java:196)
    at eu.etaxonomy.cdm.api.service.DescriptiveDataSetService.findDefaultDescription(DescriptiveDataSetService.java:171)
    at eu.etaxonomy.cdm.api.service.DescriptiveDataSetService.createSpecimenRowWrapper(DescriptiveDataSetService.java:319)
    at eu.etaxonomy.cdm.api.service.DescriptiveDataSetService.addRowWrapperToDataset(DescriptiveDataSetService.java:263)
    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:302)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
    at com.sun.proxy.$Proxy178.addRowWrapperToDataset(Unknown Source)
    at eu.etaxonomy.cdm.api.service.longrunningService.LongRunningTasksService$3.doRun(LongRunningTasksService.java:116)
    at eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread.run(RemotingProgressMonitorThread.java:42)

this issue is moved to #8816