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|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?

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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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.

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

____________________________________________________________
To manage your jsbml-development list subscription, visit
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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.

Nico

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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

____________________________________________________________
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

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

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On 10/05/12 12:57, Nicolas Rodriguez wrote:
> 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 ?

ok, both fixes are commited now and it should be working fine.

I suppose this a good case to de-freeze the 0.8 branch.

Should I commit there (in the 0.8 branch) the changes to
Model.registerIds as well ?

Nico


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