[ome-devel] OME-XML Schema (Mis-?)Use of ID token?

[Isaak Berg]

Greetings all,
 
I am fairly new to XML and have been working with validating via the OME
xsd's.  While using Microsoft Visual Studio .NET 2003 for XML validation
of the XML from some of the sample documents, the validator used by that
development environment pointed out ever so politely that identical ID
values were being used multiple times.
 
Within XML, there is some mention of a validity constraint that each
element type in an XML document can only be assigned a given ID once.
If my understanding of the constraint is accurate, (a big IF), the
sample documents I have seen thus far violate it by using an attribute
name of "ID" everywhere, instead of using "ID" only in the element
defining the information  that the particular LSID actually refers to,
and "IDRef" everywhere else that only refers to, rather than defines,
that information. See 
http://www.w3.org/TR/2000/WD-xml-2e-20000814#one-id-per-el.
 
I am not sure whether the validator in use by VS.NET2003 is
product-specific or an implementation of the .NET or MS_XML validation
APIs, but it sure would be nice (for both developers and users) if OME
could update the schema to use IDRefs, so that documents can be
generated in compliance with the validity constraint and still validate
correctly with ome.xsd.
 
Note that I did check against the "definitive" validator referenced by
Ilya in April '05
<http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2005-April/00037
5.html>  (version 2.9.1 of the Windows version).
" The definitive XML Validator is http://www.w3.org/2001/03/webdata/xsv,
though validation should pass in TurboXML as well." 
While that validator is indeed very nice,  it did not flag the multiple
ID assignments.... (Neither does XML Notepad 2006).
However if the schema is updated to use IDRefs instead of ID's, all
instance documents already generated to date will be invalid on t
 
 I hope we all agree that it is beneficial to everyone to ensure that
either OME-XML (and OME_TIFF) documents and schemas
 can be used together in a manner compliant with the XML specification.

 
I've attached a version of ome.xsd with the proposed changes made so
that you can difference it versus
http://www.openmicroscopy.org/XMLschemas/OME/FC/ome.xsd.
 
Incidentally, I also noticed that when validating the sample OME-TIFFs
data (against my version of ome.xsd modified for the proposed OME-TIFF
spec)
validating parser gave me an error for the "Locked" attribute of the
Dataset element when its value was the empty string.
Is this a schema deficiency (i.e. was an empty value intended to be
permitted (if so, the type of Locked should be some other type than
boolean)?) or
the document (was a default value intended to be indicated, if so, I
believe the entire attribute should have been omitted)?), or is the
validating parser
I am using being too strict on this point?
 
Could someone please provide a ue-case scenario of how the "Locked"
attribute is intended to be used?
 
The sample OME-TIFFs are also missing a Filter child element of the
Image element.
Needless to say, we are anxiously awaiting the publication of an
OME-TIFF schema!
 
 
 
Isaak Berg

Software Developer

isaak at cimaging.net

 

Compix Inc., Imaging Systems

109 Nicholson Road

Sewickley, PA 15143

412-741-7920

412-741-7930 Fax

www.cimaging.net <http://www.cimaging.net/> 

 

 
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