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On 08/05/12 14:43, Nicolas Rodriguez wrote:
> 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.

Just checked it again using org.sbml.jsbml.ext.qual.BuildToyModelTest

And it is working fine for me.

Can you check which version of jsbml did you use to generate the models ?

Nico


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