Forums

On 10/05/12 12:49, Nicolas Rodriguez wrote:
> 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 unit that get deleted is probably due to the code from
org.sbml.jsbml.ASTNode.arithmeticOperation(Type, ASTNode) ??

The swap node does not copy the units ?

Nico

____________________________________________________________
To manage your jsbml-development list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/jsbml-development

For a web interface to the jsbml-development mailing list, visit
http://sbml.org/Forums/

For questions or feedback about the jsbml-development list,
contact sbml-team@caltech.edu