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On 09/05/12 19:42, Andreas Dräger wrote:
> 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.

Not sure of what is going on there !!

The unit of the first astnode is reset somewhere.

if I print the value of the units in
MathMLXMLStreamCompiler.compileInteger(ASTNode), the first astnode
return 'null'.

The sbml namespace is not added because the method
FindUnitsCompiler.compile(int, String) is never called by the
ASTNodeCompiler.
Again, not sure why it would work sometimes and not others.

Nico

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