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Task #7398 (closed)

Opened 8 years ago

Closed 7 years ago

BUG:NPE import ims file

Reported by:	omero-qa	Owned by:	cxallan
Priority:	critical	Milestone:	OMERO-4.4
Component:	Import	Version:	n.a.
Keywords:	n.a.	Cc:	squire0104@…, mlinkert
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	n.a.

Description

http://qa.openmicroscopy.org.uk/qa/feedback/4083/

java.lang.RuntimeException: omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.NullPointerException):
                        null
                        	at ome.formats.OMEROMetadataStore.getPixels(OMEROMetadataStore.java:1416)
                        	at ome.formats.OMEROMetadataStore.getChannel(OMEROMetadataStore.java:1463)
                        	at ome.formats.OMEROMetadataStore.getLogicalChannel(OMEROMetadataStore.java:1476)
                        	at ome.formats.OMEROMetadataStore.handle(OMEROMetadataStore.java:788)
                        	at ome.formats.OMEROMetadataStore.updateObject(OMEROMetadataStore.java:214)
                        	at ome.services.blitz.impl.MetadataStoreI$4.doWork(MetadataStoreI.java:221)
                        	at sun.reflect.GeneratedMethodAccessor259.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:440)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:150)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy64.doWork(Unknown Source)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:371)
                        	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:150)
                        	at ome.services.blitz.impl.MetadataStoreI.updateObjects_async(MetadataStoreI.java:206)
                        	at omero.api._MetadataStoreTie.updateObjects_async(_MetadataStoreTie.java:99)
                        	at omero.api._MetadataStoreDisp.___updateObjects(_MetadataStoreDisp.java:180)
                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:374)
                        	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.InternalException"
    message = " Wrapped Exception: (java.lang.NullPointerException):
               null"
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2163)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:355)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:537)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6402)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:180)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1377)
	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$1.doCall(ImagesImporter.java:111)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Unknown Source)
Caused by: omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.NullPointerException):
                        null
                        	at ome.formats.OMEROMetadataStore.getPixels(OMEROMetadataStore.java:1416)
                        	at ome.formats.OMEROMetadataStore.getChannel(OMEROMetadataStore.java:1463)
                        	at ome.formats.OMEROMetadataStore.getLogicalChannel(OMEROMetadataStore.java:1476)
                        	at ome.formats.OMEROMetadataStore.handle(OMEROMetadataStore.java:788)
                        	at ome.formats.OMEROMetadataStore.updateObject(OMEROMetadataStore.java:214)
                        	at ome.services.blitz.impl.MetadataStoreI$4.doWork(MetadataStoreI.java:221)
                        	at sun.reflect.GeneratedMethodAccessor259.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:440)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:150)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy64.doWork(Unknown Source)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:371)
                        	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:150)
                        	at ome.services.blitz.impl.MetadataStoreI.updateObjects_async(MetadataStoreI.java:206)
                        	at omero.api._MetadataStoreTie.updateObjects_async(_MetadataStoreTie.java:99)
                        	at omero.api._MetadataStoreDisp.___updateObjects(_MetadataStoreDisp.java:180)
                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:374)
                        	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.InternalException"
    message = " Wrapped Exception: (java.lang.NullPointerException):
               null"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at java.lang.Class.newInstance0(Unknown Source)
	at java.lang.Class.newInstance(Unknown Source)
	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.updateObjects(_MetadataStoreDelM.java:267)
	at omero.api.MetadataStorePrxHelper.updateObjects(MetadataStorePrxHelper.java:391)
	at omero.api.MetadataStorePrxHelper.updateObjects(MetadataStorePrxHelper.java:363)
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2146)
	... 15 more

References

Change History (2)

comment:1 Changed 7 years ago by jburel

Component changed from from QA to Import
Milestone changed from Unscheduled to OMERO-Beta4.4
Priority changed from minor to critical

to check during import testing phase.

comment:2 Changed 7 years ago by cxallan

Cc mlinkert-x added
Resolution set to worksforme
Status changed from new to closed

Imaris import has been updated for 4.4.0. As we don't have the source data or the import log files it's very difficult to be any more confident that the problem has been addressed. Closing as worksforme. If we need to re-open Imaris related tickets during the import testing phase we can.

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