ModelPolisher
ModelPolisher copied to clipboard
MP (probably: JSBML) gives wrong tags to render elements
Unlike expected, the render specification seems to specify the GlobalRenderInformation class to use a renderInformation tag, possibly because it derives from the RenderInformation tag. (Section 3.5.3)
https://raw.githubusercontent.com/combine-org/combine-specifications/main/specifications/files/sbml.level-3.version-1.render.version-1.release-1.pdf
However, after application of the ModelPolisher, these tags are named globalRenderInformation, yielding an SBML_ERROR in cobrapy validation.
This behaviour can be observed on the model https://www.ebi.ac.uk/biomodels/BIOMD0000000967 where
<render:listOfGlobalRenderInformation xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
<render:renderInformation name="Copasi simple style" render:backgroundColor="#FFFFFFFF" render:id="GlobalRenderInformation_0">
[...]
</render:renderInformation>
</render:listOfGlobalRenderInformation>
turns to
<render:listOfGlobalRenderInformation xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
<render:globalRenderInformation name="Copasi simple style" render:backgroundColor="#FFFFFFFF" render:id="GlobalRenderInformation_0">
[...]
</render:globalRenderInformation>
</render:listOfGlobalRenderInformation>
The MP does not concern itself with this package at all, so I assume this is an error in JSBML