Task #9726 (closed)
Opened 12 years ago
Closed 11 years ago
Bug: No thumbnails for JPEG with FS
Reported by: | rleigh | Owned by: | jburel |
---|---|---|---|
Priority: | critical | Milestone: | 5.0.0-beta1 |
Component: | Insight | Version: | n.a. |
Keywords: | FS | Cc: | fs@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | FS demo 4.4 |
Description
See attached image.
No thumbnails for big images, small image, or clocks for big images needing pyramids generating. Images are viewable however.
Attachments (3)
Change History (11)
Changed 12 years ago by rleigh
comment:1 Changed 12 years ago by rleigh
comment:2 Changed 12 years ago by bpindelski
Tested on gretzky. 8k x 8k JPEG still causes the mentioned exception. Thumbnails are still not generated in the Data Manager - images are viewable though.
comment:3 Changed 11 years ago by rleigh
- Keywords FS added
comment:4 Changed 11 years ago by rleigh
Thumbnails still fail to be created on import. I can't see the above exceptions in any of the logs though, so the cause of the present failure is not obvious. Attached screenshot and logfile.
Note that it looks like every other image fails, and the exception is due to a hibernate failure. Looks exactly like the black/duplicate thumbnail issue. Maybe we're reusing the id from the previous import and this leads to the database error.
2013-01-28 09:56:48,471 WARN [ ome.services.util.ServiceHandler] (l.Server-0) Unknown exception thrown. org.hibernate.NonUniqueObjectException: a different object with the same identifier value was already associated with the session: [ome.model.meta.Experimenter#4] at org.hibernate.engine.StatefulPersistenceContext.checkUniqueness(StatefulPersistenceContext.java:637) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performUpdate(DefaultSaveOrUpdateEventListener.java:305) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsDetached(DefaultSaveOrUpdateEventListener.java:246) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:112) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:93) at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:679) at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:671) at org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:252) at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:392) at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:335) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204) at org.hibernate.engine.Cascade.cascade(Cascade.java:161) at org.hibernate.engine.Cascade.cascade(Cascade.java:127) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.cascadeOnUpdate(DefaultSaveOrUpdateEventListener.java:376) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performUpdate(DefaultSaveOrUpdateEventListener.java:350) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsDetached(DefaultSaveOrUpdateEventListener.java:246) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:112) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:93) at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:679) at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:671) at org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:252) at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:392) at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:335) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204) at org.hibernate.engine.Cascade.cascadeComponent(Cascade.java:313) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:215) at org.hibernate.engine.Cascade.cascade(Cascade.java:161) at org.hibernate.event.def.AbstractFlushingEventListener.cascadeOnFlush(AbstractFlushingEventListener.java:154) at org.hibernate.event.def.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:145) at org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:88) at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1208) at ome.logic.UpdateImpl.afterUpdate(UpdateImpl.java:294) at ome.logic.UpdateImpl.doAction(UpdateImpl.java:312) at ome.logic.UpdateImpl.doAction(UpdateImpl.java:302) at ome.logic.UpdateImpl.saveAndReturnObject(UpdateImpl.java:118) at ome.security.basic.BasicSecuritySystem.loadEventContext(BasicSecuritySystem.java:430) at ome.security.basic.EventHandler.doLogin(EventHandler.java:210) at ome.security.basic.EventHandler.invoke(EventHandler.java:146) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:218) at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:202) 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:241) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at $Proxy89.setPixelsId(Unknown Source) at sun.reflect.GeneratedMethodAccessor1697.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at $Proxy89.setPixelsId(Unknown Source) at sun.reflect.GeneratedMethodAccessor1729.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179) at ome.services.throttling.Callback.run(Callback.java:56) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:150) at ome.services.blitz.impl.ThumbnailStoreI.setPixelsId_async(ThumbnailStoreI.java:142) at sun.reflect.GeneratedMethodAccessor1728.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at omero.cmd.CallContext.invoke(CallContext.java:59) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at $Proxy90.setPixelsId_async(Unknown Source) at omero.api._ThumbnailStoreTie.setPixelsId_async(_ThumbnailStoreTie.java:190) at omero.api._ThumbnailStoreDisp.___setPixelsId(_ThumbnailStoreDisp.java:232) at omero.api._ThumbnailStoreDisp.__dispatch(_ThumbnailStoreDisp.java:728) 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) 2013-01-28 09:56:48,471 INFO [ ome.services.util.ServiceHandler] (l.Server-0) Excp: org.hibernate.NonUniqueObjectException: a different object with the same identifier value was already associated with the session: [ome.model.meta.Experimenter#4] 2013-01-28 09:56:48,473 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Meth: interface ome.api.StatefulServiceInterface.close 2013-01-28 09:56:48,473 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Args: () 2013-01-28 09:56:48,474 INFO [ ome.security.basic.EventHandler] (l.Server-3) Auth: user=4,group=7,event=null(User),sess=1b787284-8a02-4d91-98e3-816f3b01ed5a 2013-01-28 09:56:48,475 INFO [ loci.formats.FormatHandler] (l.Server-3) Populating metadata 2013-01-28 09:56:48,717 INFO [ org.perf4j.TimingLogger] (l.Server-3) start[1359367008473] time[244] tag[omero.call.success.ome.services.ThumbnailBean.close] 2013-01-28 09:56:48,717 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Rslt: null 2013-01-28 09:56:48,717 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Cleanup: ome.services.ThumbnailBean@2021eda4 2013-01-28 09:56:48,717 INFO [ omero.cmd.SessionI] (l.Server-3) Unregistered servant:1b787284-8a02-4d91-98e3-816f3b01ed5a/86:24:41:e3:-637f1f0a:13c7f988fd1:-7eafomero.api.ThumbnailStore(omero.api._ThumbnailStoreTie@7d2884d2)
comment:5 Changed 11 years ago by mlinkert
The OOM from comment 1 is definitely not an FS issue - it has to do with the fact that the current JPEG reader has no way to retrieve individual tiles. Leaving the keyword for now, though, since the last exception may be FS-related.
comment:6 Changed 11 years ago by jburel
- Cc fs@… added
- Milestone changed from OMERO-4.4.9 to OMERO-5
- Sprint set to FS Demo 4.3
Moving back 4.3 to assess the status of this ticket. Only for the last part of the ticket. The out of memory is not FS related.
comment:7 Changed 11 years ago by jburel
- Sprint changed from FS Demo 4.3 to FS demo 4.4
Moved from sprint FS Demo 4.3
comment:8 Changed 11 years ago by jburel
- Resolution set to fixed
- Status changed from new to closed
Problem in thumbnail bean
see https://github.com/openmicroscopy/openmicroscopy/pull/1257
Closing.
Importing jpeg/8kx8k.jpg: