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Am 5/8/12 3:17 PM, schrieb Nicolas Rodriguez:
> On 08/05/12 13:57, Andreas Dräger wrote:
>> |Hi all,
>>
>> It seems the SBML writer does currently write invalid SBML code when
>> making use of the ability of SBML Level 3 to associate plain numbers
>> with units:
>>
>> <cn type="integer" sbml:units="dimensionless"> 1</cn>
>>
>> The above code is only valid if the namespace declaration of the math
>> element also defines
>>
>> xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"
>>
>> Currently, it does only declare the regular MathML namesapce. As a
>> result, JSBML is currently unable to parse models that itself wrote into
>> a file before. Where can we fix this problem?
> The check is in
> org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler.isSBMLNamespaceNeeded(ASTNode)
>
> the namespace is added in
> org.sbml.jsbml.xml.stax.SBMLWriter.writeMathML(MathContainer,
> SMOutputElement, XMLStreamWriter, int)
>
> line 1084 to 1106.
>
> The compiler org.sbml.jsbml.util.compilers.FindUnitsCompiler is used to
> say if there is a unit declaration or not in the mathML.
>
> This is probably there that the problem happen, and the value returned
> is probably false.
> It is probably due to the way you are declaring the units and then how
> the mathML compiler is calling the methods.
>
> If I read a model with units, then the writing is fine so there is may
> be something missing when we declare units from scratch.
>
>
Hi Nico,

Yes, it is probably because I simply say

myASTNode.setUnit(Unit.Kind.DIMENSIONLESS.getName());

or something similar. I thought this would be enough and didn't care
about namespaces at the moment.

Cheers
Andreas

--
Dr. Andreas Dräger
University of Tuebingen
Center for Bioinformatics Tuebingen (ZBIT)
Sand 1
72076 Tübingen
Germany

Phone: +49-7071-29-78982
Fax: +49-7071-29-5091

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