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

[Chris Allan]

On 29 Oct 2009, at 12:34, Dominik Langer wrote:

> Dear ome-devel list members

Hi Dominik.

>
> 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".

This is because Bio-Formats and OMERO do not yet support the latest  
schema. We're working on this for Beta 4.2 as it requires significant  
changes to our infrastructure. Your best bet for compatibility is to  
use the 2008-09 schema.

>
> - 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."

This is because the validator has not been updated to support the  
newest schema yet. We are in the process of doing this as we speak.

>
> 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

Thanks for pushing this support in your software!

-Chris