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Am 5/8/12 3:43 PM, schrieb Nicolas Rodriguez:
> On 08/05/12 14:30, Nicolas Rodriguez wrote:
>> On 08/05/12 14:20, Andreas Dräger wrote:
>>> 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.
>> It should be enough but it was probably not tested much until now.
>>
>> We should probably check how the reader is setting things up.
> So, the reader is not doing anything specific, just using the setUnits()
> method ( I suppose it was a typo error on your code as I don't see a
> method setUnit().
>
> Strange, it was working fine before.
>
>

Hi all,

here is a minimal example that doesn't work properly with the current
version of JSBML:

public static void main(String[] args) throws Throwable {
SBMLDocument doc = new SBMLDocument(3, 1);
Model m = doc.createModel("m1");
Compartment c = m.createCompartment("c1");
Species s1 = m.createSpecies("s1", c);
Species s2 = m.createSpecies("s2", c);
Reaction r = m.createReaction("r1");
r.createReactant(s1).setStoichiometry(1d);
r.createProduct(s2).setStoichiometry(1d);
KineticLaw kl = r.createKineticLaw();
ASTNode one = new ASTNode(1, kl);
ASTNode two = new ASTNode(2, kl);
one.setUnits(Unit.Kind.MOLE.toString().toLowerCase());
two.setUnits(Unit.Kind.SECOND.toString().toLowerCase());
ASTNode ast = ASTNode.frac(one, two);
kl.setMath(ast);
SBMLWriter.write(doc, System.out, ' ', (short) 2);
}

You'll see that the first unit is not written to SBML at all. The second
unit is written, but the namespace declaration is missing. I already
found what is probably the reason, but can't fix it at the moment: The
recursive check if the ASTNode contains unit declarations doesn't work.

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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