[ome-devel] Problem with OMERO.importer when using the new OME/2009-09 schema

Dominik Langer langer at hifo.uzh.ch
Thu Oct 29 12:34:00 GMT 2009


Dear ome-devel list members

I am trying to import an OME-TIFF file (see attachment)  into OMERO 4.1 
using OMERO.importer. However, the import fails with the Error message 
"java.lang.IllegalArgumentException: Invalid series: 0".

- The OME header of the file is according to the newest OME schema 
(http://www.openmicroscopy.org/Schemas/OME/2009-09/ome.xsd).
- XML is valid according to http://www.validome.org/xml/validate/
- The OME validator at http://validator.openmicroscopy.org.uk/ tells 
that the file is invalid and gives the following error message:

"File schema: No schema found - using 
http://www.openmicroscopy.org/Schemas/OME/2008-09 (Standard V1)

    * The file is *invalid*.
    * The file is an OME-TIFF.
    * The file's xml could be parsed.
    * The file was not checked for internal consistency.
    * The OME-TIFF data appears consistent with the OME-TIFF metadata.
    * No custom attributes were found.

Element '{http://www.openmicroscopy.org/Schemas/OME/2009-09}OME': No 
matching global declaration available for the validation root."

Now I wonder why the validator says that it does not find the schema. Is 
there a mistake in the way I define the use of the new 2009-09 schema in 
my XML? This is my OME header of the OME-TIFF file (also see attachment):

<?xml version="1.0" encoding="UTF-8"?><OME 
xmlns="http://www.openmicroscopy.org/Schemas/OME/2009-09" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2009-09 
http://www.openmicroscopy.org/Schemas/OME/2009-09/ome.xsd"><Image 
ID="urn:lsid:hifo.uzh.ch:Image:943704370950:0"><AcquiredDate>1988-04-07T18:39:09</AcquiredDate><Description>Hello 
World</Description><Pixels 
ID="urn:lsid:hifo.uzh.ch:Pixels:691459359378:0" Type="uint16" 
DimensionOrder="XYZTC" SizeC="1" SizeX="256" SizeY="256" SizeZ="1" 
SizeT="1"><TiffData></TiffData></Pixels></Image></OME>


Thank you in advance for any help!

Best regards,
Dominik

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