[ome-devel] import into Omero server fails

[Chris Allan]

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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