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Task #3000 (closed)

Opened 9 years ago

Closed 9 years ago

Example File Error

Reported by: bwzloranger Owned by: cxallan
Priority: major Milestone: OMERO-Beta4.2.1
Component: Import Version: n.a.
Keywords: n.a. Cc: ajpatterson, cxallan
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2010-09-30 (17)

Description (last modified by jmoore)

Getting a format validation exception from SVN/Documentation/Samples/OmeFiles/2010-06/6x4y1z1t1c8b-swatch-2s2p4w2ws.ome

ormats.importer.gui.LoggingImportMonitor  - INTERNAL_EXCEPTION: /Users/andrew/Work/SVN/Documentation/Samples/OmeFiles/2010-06/6x4y1z1t1c8b-swatch-2s2p4w2ws.ome
...

Change History (5)

comment:1 Changed 9 years ago by jmoore

  • Description modified (diff) 
ormats.importer.gui.LoggingImportMonitor  - INTERNAL_EXCEPTION: /Users/andrew/Work/SVN/Documentation/Samples/OmeFiles/2010-06/6x4y1z1t1c8b-swatch-2s2p4w2ws.ome
java.lang.RuntimeException: omero.ValidationException
   serverStackTrace = "ome.conditions.ValidationException: not-null property references a null or transient value: ome.model.screen.WellSample._wellSamplesBackref; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.screen.WellSample._wellSamplesBackref
                       	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:648)
                       	at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)
                       	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)
                       	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                       	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                       	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                       	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:222)
                       	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                       	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:111)
                       	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                       	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                       	at $Proxy56.doWork(Unknown Source)
                       	at ome.services.util.Executor$Impl.execute(Executor.java:339)
                       	at ome.services.throttling.Adapter.run(Adapter.java:51)
                       	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)
                       	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:147)
                       	at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:167)
                       	at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:85)
                       	at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:211)
                       	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:333)
                       	at IceInternal.Incoming.invoke(Incoming.java:159)
                       	at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
                       	at Ice.ConnectionI.message(ConnectionI.java:972)
                       	at IceInternal.ThreadPool.run(ThreadPool.java:577)
                       	at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
                       	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
                       "
   serverExceptionClass = "ome.conditions.ValidationException"
   message = "not-null property references a null or transient value: ome.model.screen.WellSample._wellSamplesBackref; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.screen.WellSample._wellSamplesBackref"
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2030)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:290)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:520)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:433)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:376)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:216)
	at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:59)
	at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
	at java.lang.Thread.run(Thread.java:637)
Caused by: omero.ValidationException
   serverStackTrace = "ome.conditions.ValidationException: not-null property references a null or transient value: ome.model.screen.WellSample._wellSamplesBackref; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.screen.WellSample._wellSamplesBackref
                       	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:648)
                       	at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)
                       	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)
                       	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                       	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                       	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                       	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:222)
                       	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                       	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:111)
                       	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                       	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                       	at $Proxy56.doWork(Unknown Source)
                       	at ome.services.util.Executor$Impl.execute(Executor.java:339)
                       	at ome.services.throttling.Adapter.run(Adapter.java:51)
                       	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)
                       	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:147)
                       	at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:167)
                       	at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:85)
                       	at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:211)
                       	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:333)
                       	at IceInternal.Incoming.invoke(Incoming.java:159)
                       	at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
                       	at Ice.ConnectionI.message(ConnectionI.java:972)
                       	at IceInternal.ThreadPool.run(ThreadPool.java:577)
                       	at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
                       	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
                       "
   serverExceptionClass = "ome.conditions.ValidationException"
   message = "not-null property references a null or transient value: ome.model.screen.WellSample._wellSamplesBackref; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.screen.WellSample._wellSamplesBackref"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:355)
	at java.lang.Class.newInstance(Class.java:308)
	at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
	at IceInternal.BasicStream.throwException(BasicStream.java:1632)
	at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
	at omero.api._MetadataStoreDelM.saveToDB(_MetadataStoreDelM.java:162)
	at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:254)
	at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:226)
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2015)
	... 15 more

comment:2 Changed 9 years ago by ajpatterson

The file does have extra Well Samples, but removing them does not help. Same Error. The version with only 1 Screen and 1 Plate does work.

comment:3 Changed 9 years ago by cxallan

  • Owner set to cxallan
  • Status changed from new to assigned

comment:4 Changed 9 years ago by cxallan

  • Remaining Time set to 0.25

comment:5 Changed 9 years ago by cxallan

  • Remaining Time changed from 0.25 to 0
  • Resolution set to fixed
  • Status changed from assigned to closed

(In [8235]) More robust handling of index based referencing for multiple Plate and multiple Screen object hierarchies. (Fixes #3000)

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