[ome-users] Manual Mode Import of Flex Files
Melissa Linkert
melissa at glencoesoftware.com
Fri Jul 8 15:53:07 BST 2011
Hi Christophe,
> I used the Submit Feedback in Insight and the ticket is here with the problematic file
Thank you very much. I have filed a ticket for this problem on our issue
tracking system:
https://trac.openmicroscopy.org.uk/ome/ticket/6191
You have been CC'd on the ticket, and so will receive an automated email
with "[OME #6191]" in the subject line whenever we update the status of the
ticket.
Regards,
-Melissa
On Fri, Jul 08, 2011 at 08:57:36AM +0000, Christophe TREFOIS wrote:
> 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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