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MP deletes empty fbc:objectives [COBRA_WARNING] #134

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

MP deletes empty fbc:objectives [COBRA_WARNING] #134

Schmoho opened this issue Dec 1, 2024 · 0 comments
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2.1 Issue in the 2.1 branch bug

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@Schmoho
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Schmoho commented Dec 1, 2024

We actually have a test for this specific behaviour:

https://github.com/draeger-lab/ModelPolisher/blob/113b46764b2df15a0333e6a1244fa1215cee7c39/lib/src/test/java/de/uni_halle/informatik/biodata/mp/fixing/fbc/ListOfObjectivesFixerTest.java#L99C1-L117C6

Evaluation of cobrapy validator results for the Biomodels dataset however revealed this yields a COBRA_WARNING.

This behaviour can be seen on https://www.ebi.ac.uk/biomodels/MODEL2403010004 with this listOfObjectives:

    <fbc:listOfObjectives fbc:activeObjective="obj">
      <fbc:objective fbc:id="obj" fbc:type="maximize"/>
    </fbc:listOfObjectives>

@draeger is this behaviour intended? FBC v2 spec says

  1. section 3.3 the listOfObjectives is optional
  2. section 3.3.1 says the listOfObjectives must contain at least one objective
  3. section 3.6 says an objective must contain a listOfFluxObjectives with at least one fluxObjective

So in this case, we cannot actually do much. However, I wonder if the more conservative approach - leaving the invalid SBML as is - wouldn't be the better choice.

@Schmoho Schmoho added bug 2.1 Issue in the 2.1 branch labels Dec 1, 2024
@Schmoho Schmoho changed the title ModelPolisher deletes empty fbc:objectives [COBRA_WARNING] MP deletes empty fbc:objectives [COBRA_WARNING] Dec 1, 2024
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