Re: [Miase-discuss] Schema annotations

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

Quoting Frank Bergmann <fbergman@u.washington.edu>:

> Personally I don't mind, as I would not consume the schema as such. Though
> your concerns are valid at which point would we stop adding non-critical
> elements. For the problem at hand it might make more sense to take 'notes'
> and 'annotation' out from the sbml-math schema. I would prefer to have the
> sed-ml file annotated, rather than the math-ml ...

>
> If that won't work, perhaps you could keep the JAXB annotations separate
> from the miase schema in jlibsedml, perhaps having your ant script merge the
> two.
  I think that could be the best all round solution for now, it keeps  
the main schema nice and clean - while 'notes' and 'annotation' may  
not be essential for the mathml elements it probably sets a bad  
precedent to start altering the schema to fit in with the whims of  
implementations.
>

  Richard

> What do you think?
>
> Best
> Frank
>
>> -----Original Message-----
>> From: Richard Adams [mailto:ra...@st...]
>> Sent: Monday, February 16, 2009 8:08 AM
>> To: mia...@li...
>> Subject: [Miase-discuss] Schema annotations
>>
>>
>> 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...
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>>
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>
>
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-- 
Dr Richard Adams
Senior Software Developer,
Computational Systems Biology Group,
University of Edinburgh
Tel: 0131 650 8281/8285
email : ric...@ed...

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.