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Task #9595 (closed)

Opened 7 years ago

Closed 7 years ago

Bug: 1 OME-XML file fails to import

Reported by: sbesson Owned by: mlinkert
Priority: critical Milestone: OMERO-4.4.4
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: jburel, ajpatterson
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2012-09-25 (5)

Description

Using OMERO.insight-4.4.1-486-b319a8c-ice33-b3078-mac on OSX 10.7

Tried to import tubhiswt.ome from test_image_good/ome-xml/samples.

Import marked as failed.
All other OME-XML files import correctly but end up as orphaned (see ticket)

Change History (3)

comment:1 Changed 7 years ago by jburel

Do you have the error?

comment:2 Changed 7 years ago by mlinkert

  • Cc ajpatterson added
  • Component changed from Insight to Bio-Formats
  • Owner changed from jburel to mlinkert-x
  • Sprint set to 2012-09-25 (5)

Problem is that a LightSource? is referenced, but the LightSource? itself doesn't exist in the object graph. Not sure yet if this is a Bio-Formats problem or an upgrade stylesheet problem - I'll find out more in the morning.

Stack trace is:

java.lang.RuntimeException: omero.ApiUsageException
    serverStackTrace = "ome.conditions.ApiUsageException: Missing reference handler for urn:lsid:loci.wisc.edu:LightSource:OWS1(null) --> omero.model.LightSettings:0:0(ome.model.acquisition.LightSettings:Hash_1324513152) reference.
                        	at ome.formats.OMEROMetadataStore.updateReferences(OMEROMetadataStore.java:549)
                        	at ome.services.blitz.impl.MetadataStoreI$5.doWork(MetadataStoreI.java:237)
                        	at sun.reflect.GeneratedMethodAccessor256.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:508)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java: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 $Proxy65.doWork(Unknown Source)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:406)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:350)
                        	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:164)
                        	at ome.services.blitz.impl.MetadataStoreI.updateReferences_async(MetadataStoreI.java:232)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
                        	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 $Proxy97.updateReferences_async(Unknown Source)
                        	at omero.api._MetadataStoreTie.updateReferences_async(_MetadataStoreTie.java:106)
                        	at omero.api._MetadataStoreDisp.___updateReferences(_MetadataStoreDisp.java:201)
                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:378)
                        	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.ApiUsageException"
    message = "Missing reference handler for urn:lsid:loci.wisc.edu:LightSource:OWS1(null) --> omero.model.LightSettings:0:0(ome.model.acquisition.LightSettings:Hash_1324513152) reference."
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2159)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:356)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:538)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6324)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1248)
	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$1.doCall(ImagesImporter.java:110)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:679)
Caused by: omero.ApiUsageException
    serverStackTrace = "ome.conditions.ApiUsageException: Missing reference handler for urn:lsid:loci.wisc.edu:LightSource:OWS1(null) --> omero.model.LightSettings:0:0(ome.model.acquisition.LightSettings:Hash_1324513152) reference.
                        	at ome.formats.OMEROMetadataStore.updateReferences(OMEROMetadataStore.java:549)
                        	at ome.services.blitz.impl.MetadataStoreI$5.doWork(MetadataStoreI.java:237)
                        	at sun.reflect.GeneratedMethodAccessor256.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:508)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java: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 $Proxy65.doWork(Unknown Source)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:406)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:350)
                        	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:164)
                        	at ome.services.blitz.impl.MetadataStoreI.updateReferences_async(MetadataStoreI.java:232)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
                        	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 $Proxy97.updateReferences_async(Unknown Source)
                        	at omero.api._MetadataStoreTie.updateReferences_async(_MetadataStoreTie.java:106)
                        	at omero.api._MetadataStoreDisp.___updateReferences(_MetadataStoreDisp.java:201)
                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:378)
                        	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.ApiUsageException"
    message = "Missing reference handler for urn:lsid:loci.wisc.edu:LightSource:OWS1(null) --> omero.model.LightSettings:0:0(ome.model.acquisition.LightSettings:Hash_1324513152) reference."
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
	at java.lang.Class.newInstance0(Class.java:372)
	at java.lang.Class.newInstance(Class.java:325)
	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.updateReferences(_MetadataStoreDelM.java:315)
	at omero.api.MetadataStorePrxHelper.updateReferences(MetadataStorePrxHelper.java:460)
	at omero.api.MetadataStorePrxHelper.updateReferences(MetadataStorePrxHelper.java:432)
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2143)
	... 14 more

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6373)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1248)
	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$1.doCall(ImagesImporter.java:110)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:679)
Caused by: java.lang.RuntimeException: omero.ApiUsageException
    serverStackTrace = "ome.conditions.ApiUsageException: Missing reference handler for urn:lsid:loci.wisc.edu:LightSource:OWS1(null) --> omero.model.LightSettings:0:0(ome.model.acquisition.LightSettings:Hash_1324513152) reference.
                        	at ome.formats.OMEROMetadataStore.updateReferences(OMEROMetadataStore.java:549)
                        	at ome.services.blitz.impl.MetadataStoreI$5.doWork(MetadataStoreI.java:237)
                        	at sun.reflect.GeneratedMethodAccessor256.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:508)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java: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 $Proxy65.doWork(Unknown Source)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:406)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:350)
                        	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:164)
                        	at ome.services.blitz.impl.MetadataStoreI.updateReferences_async(MetadataStoreI.java:232)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
                        	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 $Proxy97.updateReferences_async(Unknown Source)
                        	at omero.api._MetadataStoreTie.updateReferences_async(_MetadataStoreTie.java:106)
                        	at omero.api._MetadataStoreDisp.___updateReferences(_MetadataStoreDisp.java:201)
                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:378)
                        	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.ApiUsageException"
    message = "Missing reference handler for urn:lsid:loci.wisc.edu:LightSource:OWS1(null) --> omero.model.LightSettings:0:0(ome.model.acquisition.LightSettings:Hash_1324513152) reference."
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2159)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:356)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:538)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6324)
	... 11 more
Caused by: omero.ApiUsageException
    serverStackTrace = "ome.conditions.ApiUsageException: Missing reference handler for urn:lsid:loci.wisc.edu:LightSource:OWS1(null) --> omero.model.LightSettings:0:0(ome.model.acquisition.LightSettings:Hash_1324513152) reference.
                        	at ome.formats.OMEROMetadataStore.updateReferences(OMEROMetadataStore.java:549)
                        	at ome.services.blitz.impl.MetadataStoreI$5.doWork(MetadataStoreI.java:237)
                        	at sun.reflect.GeneratedMethodAccessor256.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:508)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java: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 $Proxy65.doWork(Unknown Source)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:406)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:350)
                        	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:164)
                        	at ome.services.blitz.impl.MetadataStoreI.updateReferences_async(MetadataStoreI.java:232)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
                        	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 $Proxy97.updateReferences_async(Unknown Source)
                        	at omero.api._MetadataStoreTie.updateReferences_async(_MetadataStoreTie.java:106)
                        	at omero.api._MetadataStoreDisp.___updateReferences(_MetadataStoreDisp.java:201)
                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:378)
                        	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.ApiUsageException"
    message = "Missing reference handler for urn:lsid:loci.wisc.edu:LightSource:OWS1(null) --> omero.model.LightSettings:0:0(ome.model.acquisition.LightSettings:Hash_1324513152) reference."
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
	at java.lang.Class.newInstance0(Class.java:372)
	at java.lang.Class.newInstance(Class.java:325)
	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.updateReferences(_MetadataStoreDelM.java:315)
	at omero.api.MetadataStorePrxHelper.updateReferences(MetadataStorePrxHelper.java:460)
	at omero.api.MetadataStorePrxHelper.updateReferences(MetadataStorePrxHelper.java:432)
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2143)
	... 14 more

comment:3 Changed 7 years ago by mlinkert

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

The problem is that this file has a LightSource? with no Laser, Arc, Filament, etc. underneath it. Discussing with Andrew in devteam, this is not and has never been valid, which means that the problem is with the file itself.

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