bug #8736
LazyInitializationException (LIE) during adding Specimens to Matrix Editor
Start date:
11/29/2019
Due date:
% Done:
100%
Severity:
normal
Found in Version:
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$3.doRun(LongRunningTasksService.java:115) at eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread.run(RemotingProgressMonitorThread.java:42)
Related issues
Associated revisions
fix #8736 Fix LIE when adding specimens to matrix
ref #8736 minor performance improvement when adding specimens to matrix
History
#1 Updated by Andreas Kohlbecker about 1 year ago
- Description updated (diff)
#2 Updated by Andreas Kohlbecker about 1 year ago
- Description updated (diff)
#3 Updated by Andreas Müller about 1 year ago
- Assignee changed from Katja Luther to Patrick Plitzner
#4 Updated by Patrick Plitzner about 1 year ago
- Tags set to additivity
#5 Updated by Patrick Plitzner about 1 year ago
- Status changed from New to Resolved
- % Done changed from 0 to 50
Applied in changeset cdmlib|9e89976076d8a735426f40e4cebb49c42bd5ab33.
#6 Updated by Patrick Plitzner about 1 year ago
- Assignee changed from Patrick Plitzner to Andreas Kohlbecker
- Target version changed from 287 to Release 5.12
#7 Updated by Andreas Kohlbecker about 1 year ago
- Status changed from Resolved to In Progress
- Assignee changed from Andreas Kohlbecker to Katja Luther
The LIE is apparently fixed but I received another exception:
Server side:
[caryophyllales_spp] 11:42:48,590 INFO [Thread-24][eu.et.cd.co.mo.RemotingProgressMonitorThread] - Exception in RemotingProgressMonitorThread java.util.NoSuchElementException at java.util.HashMap$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
#8 Updated by Katja Luther about 1 year ago
- Target version changed from Release 5.12 to Release 5.13
#9 Updated by Katja Luther about 1 year ago
- Related to bug #8816: NoSuchElementException during adding Specimens to Matrix Editor added
#10 Updated by Andreas Kohlbecker about 1 year ago
- Related to deleted (bug #8816: NoSuchElementException during adding Specimens to Matrix Editor)
#11 Updated by Andreas Kohlbecker about 1 year ago
- Copied to bug #8816: NoSuchElementException during adding Specimens to Matrix Editor added
#12 Updated by Andreas Müller about 1 year ago
- Status changed from In Progress to Feedback
- Target version changed from Release 5.13 to Release 5.12
I guess this can be closed in 5.12 as there is a follow up ticket in 5.13?
#13 Updated by Katja Luther about 1 year ago
- Status changed from Feedback to Closed
- Assignee changed from Katja Luther to Patrick Plitzner
#14 Updated by Andreas Müller about 1 year ago
- % Done changed from 50 to 100
#15 Updated by Andreas Kohlbecker 7 months ago
- Description updated (diff)