[ome-users] Manual Mode Import of Flex Files
Melissa Linkert
melissa at glencoesoftware.com
Thu Jul 7 03:07:01 BST 2011
Hi Christophe,
I am sorry to hear that some of your files could not be imported into OMERO.
> 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:
Which version of OMERO are you using? A similar (perhaps identical)
problem was fixed some time ago, so if you are using something other
than 4.3.0 then most likely it is just a matter of upgrading.
If you are using 4.3.0, then would you be willing to send one of the
problematic files so that we can more thoroughly investigate the
problem? If so, you can either send the file that failed to import
directly from OMERO.insight (there should be a "Send Feedback" button or
similar when you see the error message) or upload it separately to
OMERO.qa by following the directions here:
http://qa.openmicroscopy.org.uk/qa/upload/
Regards,
-Melissa
On Wed, Jul 06, 2011 at 01:13:15PM +0000, Christophe TREFOIS wrote:
> 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
> CAMPUS LIMPERTSBERG
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> L-1511 Luxembourg
> T +352 46 66 44 6124
> F +352 46 66 44 6949
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>
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