Re: Bug in SBMLWriter
08 May '12 06:20
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
>> 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
> the namespace is added in
> 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.
Yes, it is probably because I simply say
or something similar. I thought this would be enough and didn't care
about namespaces at the moment.
Dr. Andreas Dräger
University of Tuebingen
Center for Bioinformatics Tuebingen (ZBIT)
To manage your jsbml-development list subscription, visit
For a web interface to the jsbml-development mailing list, visit
For questions or feedback about the jsbml-development list,
Powered by FUDforum. (Copyright Advanced Internet Designs Inc.)