[ome-users] Manual Mode Import of Flex Files

Christophe TREFOIS christophe.trefois at uni.lu
Fri Jul 8 09:57:36 BST 2011


Hi Melissa,

I used the Submit Feedback in Insight and the ticket is here with the problematic file

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

Let me know if you guys need more "sample" files to improve the Opera importer.

Kind Regards,

--
Christophe
................................................................................
Dipl.-Ing. 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


-----Original Message-----
From: Melissa Linkert [mailto:melissa.linkert at gmail.com] On Behalf Of Melissa Linkert
Sent: Thursday, July 07, 2011 4:34 PM
To: Christophe TREFOIS
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Manual Mode Import of Flex Files

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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