[ome-devel] import into Omero server fails

[Peter Schregle]

Hi Chris,

thank you very much for the investigation and the detailed answer. This is
indeed very helpful.

I've contacted Aleksandra Tarkowska to see if and when they will upgrade the
demo server. Alternatively we think about installing our own server to
continue our testing.

Just one more question that is unclear to me: the validator on the website
did say that our files were ok (which indeed seems to be correct). What
exactly is the validator doing? Just checking the schema? Or more?

Thanks again and best regards

mfg

Peter Schregle
Geschäftsführer



Impuls computergestützte Bildanalyse GmbH
Carl-Benz-Str. 13
82205 Gilching
Germany/European Union

Phone: +49 8105 773640
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Fax: +49 8105 773642
E-Mail: p.schregle at impuls-imaging.com
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Geschäftsführer: Peter Hengel, Peter Schregle
Handelsregister: Amtsgericht München, HRB 110818


> -----Ursprüngliche Nachricht-----
> Von: Chris Allan [mailto:callan at lifesci.dundee.ac.uk]
> Gesendet: Donnerstag, 16. September 2010 11:11
> An: Peter Schregle
> Cc: ome-devel Development; pierre.menard at till-photonics.com
> Betreff: Re: [ome-devel] import into Omero server fails
> 
> Hi Peter,
> 
> There are a few issues at play here:
> 
> 1) A bug in Bio-Formats 4.2.0 with certain types of Light Source handling
in OME-
> XML and OME-TIFF files. If you're interested the overarching ticket is
here:
> 
> http://trac.openmicroscopy.org.uk/omero/ticket/2757
> 
> 2) A lack of correct OTF handling in OMERO 4.2.0. Again if you're
interested the
> OTF ticket is here:
> 
> http://trac.openmicroscopy.org.uk/omero/ticket/2830
> 
> 3) Incorrect Experiment type populated in the max-sample-2008-02.ome
> example.
> 
> Both (1) and (2) have been fixed and (3) will be rectified as soon as
possible.
> What this means for the import of your TILL OME-TIFF files is that in
order to do
> so you must upgrade your server and OMERO.importer to the latest available
on
> the Beta 4.2.x branch. The downloads are available here:
> 
> http://hudson.openmicroscopy.org.uk/view/Beta4.2/job/OMERO-Beta4.2/23/
> 
> The OMERO.importer upgrade is quite obvious, just grab the build for your
> particular platform. The server upgrade is slightly more tricky but the
general
> upgrade preparations from the following apply:
> 
> http://www.openmicroscopy.org/site/support/omero4/server/upgrade
> 
> Once you have prepared (done a database backup, etc.) you should be able
to
> follow the following loose procedure:
> 
> OMERO_DIR/bin/omero admin stop
> cp OMERO_DIR/etc/grid/config.xml NEW_OMERO_DIR/etc/grid/ cp
> var/lib/custom_settings.py NEW_OMERO_DIR/var/lib/
> NEW_OMERO_DIR/bin/omero web syncmedia NEW_OMERO_DIR/bin/omero
> admin start
> 
> 
> Let us know if anything is unclear or you have any problems.
> 
> -Chris
> 
> 
> On 15 Sep 2010, at 12:38, Peter Schregle wrote:
> 
> > Hello Andrew,
> >
> > thanks for your answer.
> >
> > I understand it partly, only. If the max_sample... does create an
> > error because the image data is missing, why does the min_sample...
> > import properly? It doesn't have image data either.
> >
> > The real problem is not the max_sample, but other files created by a
> > TILL microscope that currently cannot be imported. I've uploaded these
> > images from the OMERO importer in the last hour.
> >
> > I've looked into the max_sample in order to find out if there might be
> > problems in the metadata section of the TILL files, but because of the
> > loading errors I was led to believe that the problem is not in the
> > TILL files but in the OME importer.
> >
> > However, your pointer to the sample files in
> > http://www.ome-xml.org/browser/Documentation/Samples/OmeFiles is very
> > helpful, I will look into these.
> >
> > Best regards
> > Peter
> >
> >> -----Ursprüngliche Nachricht-----
> >> Von: Andrew Patterson [mailto:ajpatterson at lifesci.dundee.ac.uk]
> >> Gesendet: Mittwoch, 15. September 2010 13:16
> >> An: Peter Schregle
> >> Cc: ome-devel at lists.openmicroscopy.org.uk
> >> Betreff: Re: [ome-devel] import into Omero server fails
> >>
> >> Hello Peter,
> >>
> >> The file max-sample-2008-02.ome is not real data. It and
> >> min-sample-2008- 02.ome were created to show the XML structure that an
> ome file can have.
> >>
> >> If you open max-sample-2008-02.ome in a text editor you will see the
> > matadata
> >> side of the file has been "maxed out", that is it has at "least one"
> >> of
> > everything
> >> possible, but has no real image data in it.
> >>
> >> I created them to go with an old documentation page, now removed.
> >>
> >> If you want files that should import fine look in the sub-folder of
> > samples:
> >> http://www.ome-xml.org/browser/Documentation/Samples/OmeFiles
> >>
> >> I will move the other files into a new folder and add a note
> >> describing
> > there
> >> purpose.
> >>
> >> Hope this helps,
> >>
> >> Andrew
> >>
> >> On 15 Sep 2010, at 10:52, Peter Schregle wrote:
> >>
> >>> Hi,
> >>>
> >>> we are having problems with the OME import functionality.
> >>>
> >>> We tried to import the max-sample-2008-02.ome (which we downloaded
> >> somewhere on the OME site as giving a real-world example of an OME
> >> file),
> > but
> >> we got an error message. The trivial-sized min-sample
 worked.
> >>>
> >>> There seems to be a serious problem with import. Can you help somehow?
> > Or
> >> provide some contact to someone who can help?
> >>>
> >>> Thanks and best regards
> >>>
> >>> Peter
> >>> _______________________________________________
> >>> ome-devel mailing list
> >>> ome-devel at lists.openmicroscopy.org.uk
> >>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
> >
> >
> > _______________________________________________
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> > ome-devel at lists.openmicroscopy.org.uk
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