[Miase-discuss] Schema annotations

[Richard A. <ra...@st...>]

Sorry, probably didn't explain very well - the .xsd schema definition  
allows application specific annotations. The changes to the schema I'm  
proposing would
not be included in .miase files, but in the schema itself, inside the  
notes and annotation element  definitions.

  The problem arises, as JAXB comes across 'notes' and 'annotation'  
defined in both sbml-mathml and sedml schemas. When generating classes  
from the schema, it gets confused as it attempts to create classes of  
the same name twice. To prevent this happening, you  can add a  
processing instruction in the notes element declaration in the sedml  
schema, saying 'don't create another notes class for this notes  
element, create a class called 'SedmlNotes instead'.

Just looking through the JAXB docs, there doesn't seem to be an  
obvious solution readily available, e.g., to make the classes in two  
different packages,
which would prevent the need for these annotations.

Basically, there are a quite a lot of processing instructions which  
could be included, for example, specifying java collection classes,  
method names, class names, javadoc. Some of these, but not all, can be  
put in an external file, called a binding file, so I'm just thinking  
that these schema annotations  could pollute the schema definition  
somewhat.

Cheers
  Richard



> I'm sorry, i don't quite see the issue ... the schema right now says
> that you are free to put under the annotation element pretty much
> anything, and as far as MIASE goes, it will be ignored. The same goes
> for the notes section.

> i've never used jaxb so I'm not sure what the issues are. Could you
> explain further?

best
Frank

On Feb 14, 2009, at 2:28 PM, Richard Adams wrote:

>
> Hi all,
> Just wondering, it is possible to add <xsd:annotation><xsd:appinfo>
> elements
> into a schema for tool-specific customization of schema processing.
> Is this tolerable in the sed-ml schema, or would it clutter up the
> schema too much?
>
> Just wondered as Dagmar's last change ( to add the notes/annotation
> elements) causes a namespace conflict to the JAXB schema parser with
> the elements of the same name defined in sbml-mathml. One way round
> this is to add this jaxb specific annotations in the .xsd file to
> produce classes with different names. An alternative is to specify
> instructions in a separate 'binding' file, this would be ideal but
> I've not got it to work yet.
>
> Basically it would add:
>
> <xs:annotation>
> <xs:appinfo>
> <jxb:class name="SedMLNotes">
> </jxb:class>
> </xs:appinfo>

-- 
Dr Richard Adams
Senior Software Developer,
Computational Systems Biology Group,
University of Edinburgh
Tel: 0131 650 8281/8285
email : ric...@ed...

-- 
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Scotland, with registration number SC005336.