[ome-users] Manual Mode Import of Flex Files
Melissa Linkert
melissa at glencoesoftware.com
Thu Jul 7 15:34:15 BST 2011
Hi Christophe,
> I will indeed try to upload one of those files so that you can investigate,
> The file is relatively big though, around 1 GB, I hope that will be OK?
That should be no problem - if I recall, the QA system handles files up to 2 GB.
If you experience any trouble uploading the file, though, please let us know.
Regards,
-Melissa
On Thu, Jul 07, 2011 at 06:01:53AM +0000, Christophe TREFOIS wrote:
> Hi Melissa,
>
> I indeed face the same problems both on 4.2 and on the 4.3 Beta (the latest release I guess) that I installed yesterday.
>
> I will indeed try to upload one of those files so that you can investigate,
> The file is relatively big though, around 1 GB, I hope that will be OK?
>
> Thank you for our help,
>
> Kind Regards,
>
> --
> Christophe
> ................................................................................
>
> Christophe TREFOIS
> PhD Student
> Ing. Sys. Com. Dipl. EPF
> Luxembourg Centre for Systems Biomedicine
>
> UNIVERSITY OF LUXEMBOURG
> CAMPUS LIMPERTSBERG
> 162a, avenue de la Faïencerie
> L-1511 Luxembourg
>
> T +352 46 66 44 6124
> F +352 46 66 44 6949
> www.lcsb.lu
>
>
>
> ________________________________________
> From: Melissa Linkert [melissa.linkert at gmail.com] on behalf of Melissa Linkert [melissa at glencoesoftware.com]
> Sent: Thursday, July 07, 2011 4:07 AM
> To: Christophe TREFOIS
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Manual Mode Import of Flex Files
>
> 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
> > 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/>
> >
>
>
>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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