| Author | Topic |
|---|
Posts: 273
Registered:
June 2006
|
|
|
Posts: 307
Location:
Cambridge UK
Registered:
February 2005
|
|
|
Posts: 307
Location:
Cambridge UK
Registered:
February 2005
|
|
Re: Problems when parsing an SBML document
|
30 Nov '10 02:37
 
|
 |
|
On 11/30/2010 08:54 AM, Andreas Draeger wrote:
> Hello everybody,
>
> I just tried to parse the SBML model
> http://docs.u003f.com/murabito_normal.xml using JSBML. It works, but
> although the SBML online validator says that besides some unit problems
> this is totally proper SBML,
That seems strange to me. In fact, there is no namespace on the math
element, that is why the parser
say that the math elements are not recognized.
It seems to be a bug on the libsbml validator.
> our SBML parser displays plenty of warnings
> and I don't know why we have so different results. Nico, can you please
> have a look on it?
>
Apart for the math elements warning which are normal, it seems that some
of the
cellDesigner annotation are send to the SBMLCoreParser which is a bug in
jsbml.
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
|
|
|
Posts: 307
Location:
Cambridge UK
Registered:
February 2005
|
|
|
Posts: 273
Registered:
June 2006
|
|
|
Posts: 307
Location:
Cambridge UK
Registered:
February 2005
|
|
|
Posts: 307
Location:
Cambridge UK
Registered:
February 2005
|
|
|
Posts: 413
Registered:
May 2004
|
|
|
Posts: 273
Registered:
June 2006
|
|
Re: Problems when parsing an SBML document
|
14 Dec '10 05:37
|
|
|
>>>> http://docs.u003f.com/murabito_normal.xml using JSBML. It works, but
>>> There is also this warning :
>>>
>>> WARN (SBMLCoreParser.java:561) - No UnitDefinition matches the unitsID
>>> 'dimensionless'of the parameter Keqv5.
>> Yes,
>>
>> I will. Please give me some time.
>>
> No rush. But I think, it is only missing from the predefinedUnit list in
> the Model.
Hello everybody,
This problem is now solved as well. The method isSetUnitsInstance() in
QuantityWithDefineUnit did not return true if the unitsID refered to a
simple base unit kind, but only if the associated model contained a
UnitDefinition with the given ID. Now it also returns true if we can
directly create an instance of Unit for the given unitsID in the
element's Level/Version combination, i.e., if an instance of Units can
be addressed by the unitsID. The warning then dissapears.
Cheers
Andreas
--
Dipl.-Bioinform. Andreas Dräger
Eberhard Karls University Tübingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 Tübingen
Germany
Phone: +49-7071-29-70436
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
|
|
|
