Task #6191 (closed)
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 13 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)
comment:2 Changed 13 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 13 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 13 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 13 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)
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