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Task #6191 (closed)

Opened 8 years ago

Closed 8 years ago

Last modified 8 years ago

BUG: Flex file does not have Plane.TheC populated

Reported by: omero-qa Owned by: mlinkert
Priority: major Milestone: OMERO-Beta4.3.2
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: christophe.trefois@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2011-08-04 (2)

Description (last modified by mlinkert)

​http://qa.openmicroscopy.org.uk/qa/feedback/3857/

Comment: I get an import failure when I try to import .flex files captured in "Manual" Mode on an Opera microscope.

Can anyone provide any hints, tips or directions to follow in order to successfully import those?

Note: .flex files with .mea files captured in "Automatic" Mode import without problems...

Change History (5)

comment:1 Changed 8 years ago by mlinkert

  • Component changed from from QA to Bio-Formats
  • Description modified (diff)
  • Milestone changed from Unscheduled to OMERO-Beta4.3.2
  • Priority changed from minor to major
  • Remaining Time set to 0.25
  • Sprint set to 2011-08-04 (2)

The stack trace is:

java.lang.RuntimeException: omero.ValidationException
    serverStackTrace = "ome.conditions.ValidationException: not-null property references a null or transient value: ome.model.core.PlaneInfo.theC; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.core.PlaneInfo.theC

                        	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:648)

                        	at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)

                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)

                        	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.saveToDB_async(MetadataStoreI.java:190)

                        	at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:85)

                        	at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:218)

                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:366)

                        	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.ValidationException"
    message = "not-null property references a null or transient value: ome.model.core.PlaneInfo.theC; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.core.PlaneInfo.theC"
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2174)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:293)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:452)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6288)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1137)
	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.ValidationException
    serverStackTrace = "ome.conditions.ValidationException: not-null property references a null or transient value: ome.model.core.PlaneInfo.theC; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.core.PlaneInfo.theC

                        	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:648)

                        	at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)

                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)

                        	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.saveToDB_async(MetadataStoreI.java:190)

                        	at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:85)

                        	at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:218)

                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:366)

                        	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.ValidationException"
    message = "not-null property references a null or transient value: ome.model.core.PlaneInfo.theC; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.core.PlaneInfo.theC"
	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.saveToDB(_MetadataStoreDelM.java:162)
	at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:254)
	at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:226)
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2159)
	... 14 more

comment:2 Changed 8 years ago by Melissa Linkert <melissa@…>

  • Remaining Time changed from 0.25 to 0
  • Resolution set to fixed
  • Status changed from new to closed

(In [d43071a4cc01507e8c2457e40127bd12ce196981/bioformats.git]) Prevent Plane.* from being populated for planes that do not exist.

Closes #6191.

comment:3 Changed 8 years ago by Melissa Linkert <melissa@…>

(In [d43071a4cc01507e8c2457e40127bd12ce196981/bioformats.git]) Prevent Plane.* from being populated for planes that do not exist.

Closes #6191.

comment:4 Changed 8 years ago by Melissa Linkert <melissa@…>

(In [10ffa0774b49935cca53e98c6ab05336c0c298ce/bioformats.git]) Prevent Plane.* from being populated for planes that do not exist.

Closes #6191.
(cherry picked from commit d43071a4cc01507e8c2457e40127bd12ce196981)

comment:5 Changed 8 years ago by Melissa Linkert <melissa@…>

(In [10ffa0774b49935cca53e98c6ab05336c0c298ce/bioformats.git]) Prevent Plane.* from being populated for planes that do not exist.

Closes #6191.
(cherry picked from commit d43071a4cc01507e8c2457e40127bd12ce196981)

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