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

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

At 20:09 08/03/2006, Egon Willighagen wrote:

>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 now replaced this by:
<cml:molecule xmlns:cml="http://www.xml-cml.org/schema"
  xsi:schemaLocation="http://www.xml-cml.org/schema ../../schema.xsd"
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 >
<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>

in schema23/examples/complex/arrays.xml

and now it runs through ExamplesTest.

I think your Bioclipse environment is trying to validate it against 
something - not sure what. I have tried different elements and they 
all fail. So it is like trying to validate with an empty DTD or 
schema (or perhaps the wrong schema). I don't know *what* software is 
giving the error because XOM is not a validating parser. Do you have 
a validating parser bound into it?

Note that the (horrible) syntax above requires the schema.xsd to be 
in a relative directory.

Hope you can find

P,

P.



>--
>e.w...@sc...
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>Radboud University Nijmegen
>Blog: http://chem-bla-ics.blogspot.com/
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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