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MP (probably: JSBML) gives wrong tags to render elements #135

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Schmoho opened this issue Dec 1, 2024 · 0 comments
Open

MP (probably: JSBML) gives wrong tags to render elements #135

Schmoho opened this issue Dec 1, 2024 · 0 comments
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2.1 Issue in the 2.1 branch bug upstream Bug or issue in upstream, ticket might be kept while issue is not resolved.

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@Schmoho
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Schmoho commented Dec 1, 2024

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

@Schmoho Schmoho added bug 2.1 Issue in the 2.1 branch upstream Bug or issue in upstream, ticket might be kept while issue is not resolved. labels Dec 1, 2024
@Schmoho Schmoho changed the title render elements receive wrong names (possible JSBML bug) MP (probably: JSBML) gives wrong tags to render elements Dec 1, 2024
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Labels
2.1 Issue in the 2.1 branch bug upstream Bug or issue in upstream, ticket might be kept while issue is not resolved.
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