Task #5551 (closed)
Opened 8 years ago
Closed 8 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 8 years ago by jmoore
comment:2 Changed 8 years ago by jburel
Error seems related to #5549
comment:3 Changed 8 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 8 years ago by jmoore <josh@…>
(In [903bed3d0d759023c22613eecdd101a1d4dab881/ome.git] on branch develop) acquireLock in ctor for BfPyramidPixelBuffer (Fix #5433, See #5551)
comment:5 Changed 8 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.
Note: See
TracTickets for help on using
tickets.
You may also have a look at Agilo extensions to the ticket.
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