[ome-users] Manual Mode Import of Flex Files

[Christophe TREFOIS]

Hi all,

I'm new to Omero so forgive me if I'm bringing up a "trivial" topic.

I am able to successfully a series of .flex files that were taken using the "automated" acquisition mode on the Opera Microscope.

However, I also have .flex files that do not come with a .mea or .res file and are around 1 GB in size each.
These were taken in the so called "manual" mode.

When I use Omero Insight to import those .flex files, I get the following error:

2011-07-06 13:42:46,054 205839     [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.DetectorSettings:74:0 == Detector:0:0
2011-07-06 13:42:46,057 205842     [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - containerCache contains 1826 entries.
2011-07-06 13:42:46,059 205844     [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - referenceCache contains 1261 entries.
2011-07-06 13:42:46,657 206442     [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - INTERNAL_EXCEPTION: D:\Opera Demo\OperaDB\life cells long term\fast kin\B5_1 GFP RFP Draq5 20times 7planes step1.flex
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$100(ThreadPool.jva:12)
                                at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
                       and few more errors of the sort.

Does anybody of you have any clue or tip on how to proceed in getting those pictures imported successfully?

Maybe something went wrong during export ? Is there a big in the Importer?

Thank you for any help!

--
Christophe
................................................................................

Dipl.-Ing. Christophe TREFOIS
PhD Student

Ing. Sys. Com. Dipl. EPF

[Description: cid:image001.jpg at 01CACC35.07191DE0]
Luxembourg Centre for Systems Biomedicine
UNIVERSITY OF LUXEMBOURG
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162a, avenue de la Faïencerie
L-1511 Luxembourg
T +352 46 66 44 6124
F +352 46 66 44 6949
www.lcsb.lu<http://www.uni.lu/>

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