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After application of the polisher the cobrapy validator gives this SBML_ERROR:
"E0 (Error): MathML consistency (core, L40425); A ci element in this context must refer to a model component; Outside of a functionDefinition, if a ci element is not the first element within a MathML apply, then the ci's value can only be chosen from the set of identifiers of (in L2V1) species, compartment, or parameter objects; (in L2V2-L2V5), species, compartment, parameter or reaction objects; (in L3V1) species, compartment, parameter, reaction or speciesReference objects and (in L3V2) species, compartment, parameter, reaction, speciesReference objects or L3 package objects with defined mathematical meaning.
Reference: L3V1 Section 3.4.3
The formula 'FLUX_VALUE' in the math element of the kineticLaw uses 'FLUX_VALUE' that is not the id of a species/compartment/parameter/reaction/speciesReference."
In the following are the unpolished and polished versions. As far as I can tell, the only difference is that the whitespace on the element in the kinetic law has been removed by the polisher (most likely by JSBML, since I don't think we actually touch kinetic laws at all).
The question is whether we should consider this a bug (@draeger):
Schmoho
changed the title
Application of the Polisher leads to cobrapy validation errors on kinetic laws
MP introduces to cobrapy validation errors on kinetic laws
Dec 1, 2024
Schmoho
changed the title
MP introduces to cobrapy validation errors on kinetic laws
MP introduces cobrapy validation errors on kinetic laws
Dec 1, 2024
Schmoho
changed the title
MP introduces cobrapy validation errors on kinetic laws
MP introduces (or: reveals) cobrapy validation errors on kinetic laws
Dec 1, 2024
The issue can be observed on this model: https://www.ebi.ac.uk/biomodels/MODEL1604280030
After application of the polisher the cobrapy validator gives this
SBML_ERROR
:In the following are the unpolished and polished versions. As far as I can tell, the only difference is that the whitespace on the element in the kinetic law has been removed by the polisher (most likely by JSBML, since I don't think we actually touch kinetic laws at all).
The question is whether we should consider this a bug (@draeger):
This is the unpolished original version:
this is the polished version:
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