Re: [cml/ccml-discuss] Namespaces [was: CMLRSS plugin]

[peter murray-r. <pm...@ca...>]

At 20:09 08/03/2006, Egon Willighagen wrote:
>On Tuesday 07 March 2006 14:35, peter murray-rust wrote:
> > At 12:52 07/03/2006, Egon Willighagen wrote:
> > > > Namespaces are a problem since we haven't been very consistent in
> > > > CML. The current suggestion is that we always use
> > > > "http://www.xml-cml.org/schema". What we could then do is strip off
> > > > all other old CML namespaces at start of parse and replace by this one.
> > >
> > >Yes, stripping might be a good idea. At least they have the above in
> > > common.
> >
> > I have had quite a lot of discussion on the XOM list about namespaces
> > - they are not trivial. So my current idea is:
> > - read in a potential CML file.
> > - does if have namespace http://www.xml-cml.org/schema on the root
> > - if not use heuristics to judge whether it is a CML file (if there
> > is an obsolete CML namespace on root? or whether all elements have
> > local names in CML. Then strip old CML namespaces and replace by current
> > one.
>
>This is the error I now have... the CML goes to the builder as plain text. It
>looks good:
>
>CML source for entry:
><cml:molecule xmlns:cml="http://www.xml-cml.org/schema">
><cml:atomArray atomID="a1 a2 a3 a4" elementType="C C O O" formalCharge="0 0 0
>0" />
><cml:bondArray atomRef1="a1 a2 a2" atomRef2="a2 a3 a4" order="1 2 1" />
></cml:molecule>
>General error with resourceString from: null
>java.lang.ClassCastException: nu.xom.Element
>         at
>net.bioclipse.model.FeedEntryResource.parseResource(FeedEntryResource.java:109)

I have cut and pasted your example into:
schema23/examples/complex/arrays.xml

and run it through ExamplesTest in JUMBO5.1 and got:
Error: URI=file:C:/pmr/schema23/examples/complex/arrays.xml Line=1: 
cvc-elt.1: Cannot find the declaration of element 'cml:molecule'.

(this is a Xerces message). So there is clearly a problem and I'm 
completely mystified! I shall now have to hack it!

Thanks - keep the bugs coming.

P.



>Egon
>
>--
>e.w...@sc...
>PhD student on Molecular Representation in Chemometrics
>Radboud University Nijmegen
>Blog: http://chem-bla-ics.blogspot.com/
>http://www.cac.science.ru.nl/people/egonw/
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>
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Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road,  Cambridge CB2 1EW, UK
+44-1223-763069