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Task #10256 (new)

Opened 7 years ago

Last modified 4 years ago

Bug: deleting ManagedRepo directories can cause imports to fail

Reported by: cblackburn Owned by:
Priority: major Milestone: Unscheduled
Component: Import Version: n.a.
Keywords: FS Cc: jamoore
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by cblackburn)

If directories under ManagedRepository are rmdir'ed imports can fail after OriginalFile objects have been created as files cannot be successfully uploaded. This may simply be a case of managing the Exception since messing around in the ManagedRepository shouldn't be undertaken lightly.

Change History (8)

comment:1 Changed 7 years ago by cblackburn

  • Description modified (diff)

comment:2 Changed 7 years ago by cblackburn

After deleting an entire directory tree system/root/2013-1-28/Users/cblackburn/Desktop/Images/dv/

2013-01-28 10:17:48,597 1544       [      main] INFO   ormats.importer.cli.LoggingImportMonitor  - FILE_UPLOAD_STARTED
2013-01-28 10:17:48,627 1574       [      main] ERROR        ome.formats.importer.ImportLibrary  - Error on import
omero.ResourceError
    serverStackTrace = "ome.conditions.ResourceError: /OMERO/ManagedRepository/system/root/2013-1-28/Users/cblackburn/Desktop/Images/dv/IAGFP-Noc01_R3D.dv (No such file or directory)
                        	at ome.services.RawFileBean.write(RawFileBean.java:414)
                        	at sun.reflect.GeneratedMethodAccessor396.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:154)
                        	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 $Proxy84.write(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor396.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: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 $Proxy84.write(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor398.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	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.RawFileStoreI.write_async(RawFileStoreI.java:117)
                        	at sun.reflect.GeneratedMethodAccessor397.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 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 $Proxy85.write_async(Unknown Source)
                        	at omero.api._RawFileStoreTie.write_async(_RawFileStoreTie.java:106)
                        	at omero.api._RawFileStoreDisp.___write(_RawFileStoreDisp.java:248)
                        	at omero.api._RawFileStoreDisp.__dispatch(_RawFileStoreDisp.java:379)
                        	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 = "/OMERO/ManagedRepository/system/root/2013-1-28/Users/cblackburn/Desktop/Images/dv/IAGFP-Noc01_R3D.dv (No such file or directory)"
	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._RawFileStoreDelM.write(_RawFileStoreDelM.java:330)
	at omero.api.RawFileStorePrxHelper.write(RawFileStorePrxHelper.java:457)
	at omero.api.RawFileStorePrxHelper.write(RawFileStorePrxHelper.java:429)
	at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:288)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:390)
	at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:167)
	at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:143)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:479)
2013-01-28 10:17:48,652 1599       [      main] INFO         ome.formats.importer.ImportLibrary  - Exiting on error

comment:3 Changed 7 years ago by cblackburn

This might also be mitigated by cleaning up such directories and the corresponding OriginalFile entries on delet.

comment:4 Changed 7 years ago by jburel

  • Sprint changed from 2013-02-12 (5) to 2013-03-12 (6))

Moved from sprint 2013-02-12 (5)

comment:5 Changed 7 years ago by jburel

  • Sprint changed from 2013-03-12 (6)) to 2013-04-09 (7))

Moved from sprint 2013-03-12 (6))

comment:6 Changed 7 years ago by jmoore

  • Milestone changed from OMERO-4.5 to OMERO-5
  • Sprint changed from 2013-04-09 (7)) to FS Demo 3

comment:7 Changed 7 years ago by jamoore

  • Sprint changed from FS Demo 3 to FS Demo 4

comment:8 Changed 4 years ago by jamoore

  • Milestone changed from 5.x to Unscheduled
  • Sprint FS demo 4.x deleted
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