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Task #5551 (closed)

Opened 12 years ago

Closed 12 years ago

Bug: import fails if a user tries to visualize image???

Reported by: jamoore Owned by: jburel
Priority: blocker Milestone: OMERO-Beta4.3
Component: Insight Version: n.a.
Keywords: n.a. Cc: cxallan, jburel
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

  • Start directory import of "venu" (lim files)
  • 2 lim files import and say "Building pyramid, please wait before viewing"
  • While 3rd is importing, go to data browser and click on refresh
  • 3rd image states "invalid image" on double click
  • import fails with following (in comments)

Change History (5)

comment:1 Changed 12 years ago by jmoore

org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data. 
Cannot start the Raw pixels store.
	at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:875)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.isLargeImage(OMEROGateway.java:7644)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6154)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:179)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1185)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: omero.ResourceError
    serverStackTrace = "ome.conditions.ResourceError: FormatException: /OMERO/Pixels/Dir-016/16721_pyramid
                        Invalid TIFF file
                        	at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:72)
                        	at ome.io.bioformats.BfPixelBuffer.close(BfPixelBuffer.java:116)
                        	at ome.io.bioformats.BfPyramidPixelBuffer.close(BfPyramidPixelBuffer.java:572)
                        	at ome.services.RawPixelsBean.closePixelBuffer(RawPixelsBean.java:240)
                        	at ome.services.RawPixelsBean.clean(RawPixelsBean.java:225)
                        	at ome.services.RawPixelsBean.close(RawPixelsBean.java:217)
                        	at sun.reflect.GeneratedMethodAccessor973.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	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.EventHandler.invoke(EventHandler.java:150)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)
                        	at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)
                        	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:231)
                        	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 $Proxy84.close(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor973.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	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:83)
                        	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 $Proxy84.close(Unknown Source)
                        	at ome.services.blitz.impl.AbstractAmdServant.close_async(AbstractAmdServant.java:227)
                        	at omero.api._RawPixelsStoreTie.close_async(_RawPixelsStoreTie.java:330)
                        	at omero.api._StatefulServiceInterfaceDisp.___close(_StatefulServiceInterfaceDisp.java:142)
                        	at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1157)
                        	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.ResourceError"
    message = "FormatException: /OMERO/Pixels/Dir-016/16721_pyramid
               Invalid TIFF file"
	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._RawPixelsStoreDelM.close(_RawPixelsStoreDelM.java:1901)
	at omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:2642)
	at omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:2614)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.isLargeImage(OMEROGateway.java:7638)
	... 13 more

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6184)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:179)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1185)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data. 
Cannot start the Raw pixels store.
	at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:875)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.isLargeImage(OMEROGateway.java:7644)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6154)
	... 12 more
Caused by: omero.ResourceError
    serverStackTrace = "ome.conditions.ResourceError: FormatException: /OMERO/Pixels/Dir-016/16721_pyramid
                        Invalid TIFF file
                        	at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:72)
                        	at ome.io.bioformats.BfPixelBuffer.close(BfPixelBuffer.java:116)
                        	at ome.io.bioformats.BfPyramidPixelBuffer.close(BfPyramidPixelBuffer.java:572)
                        	at ome.services.RawPixelsBean.closePixelBuffer(RawPixelsBean.java:240)
                        	at ome.services.RawPixelsBean.clean(RawPixelsBean.java:225)
                        	at ome.services.RawPixelsBean.close(RawPixelsBean.java:217)
                        	at sun.reflect.GeneratedMethodAccessor973.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	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.EventHandler.invoke(EventHandler.java:150)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)
                        	at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)
                        	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:231)
                        	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 $Proxy84.close(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor973.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	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:83)
                        	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 $Proxy84.close(Unknown Source)
                        	at ome.services.blitz.impl.AbstractAmdServant.close_async(AbstractAmdServant.java:227)
                        	at omero.api._RawPixelsStoreTie.close_async(_RawPixelsStoreTie.java:330)
                        	at omero.api._StatefulServiceInterfaceDisp.___close(_StatefulServiceInterfaceDisp.java:142)
                        	at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1157)
                        	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.ResourceError"
    message = "FormatException: /OMERO/Pixels/Dir-016/16721_pyramid
               Invalid TIFF file"
	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._RawPixelsStoreDelM.close(_RawPixelsStoreDelM.java:1901)
	at omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:2642)
	at omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:2614)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.isLargeImage(OMEROGateway.java:7638)
	... 13 more

comment:2 Changed 12 years ago by jburel

Error seems related to #5549

comment:3 Changed 12 years ago by jburel

No longer use the RawPixelsStore to figure out if a pyramid is required or not.
This seems to be fixed the issue described above: 2 things

  • define max size as a constant somewhere.
  • when the image is not ready, I do not have the default thumbnail returned when I use the getThumbnailSet image.

comment:4 Changed 12 years ago by jmoore <josh@…>

(In [903bed3d0d759023c22613eecdd101a1d4dab881/ome.git] on branch develop) acquireLock in ctor for BfPyramidPixelBuffer (Fix #5433, See #5551)

comment:5 Changed 12 years ago by jburel

  • Resolution set to fixed
  • Status changed from new to closed

Yeah I think Josh and I have killed that with the locking changes.
Josh Moore
09:52
I'd think so as well. That was a part of a series of dupes when big images were just completely hosed.

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