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sbmlteam / libsbml

LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It offers language bindings for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R and Ruby.
https://sbml.org/software/libsbml
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File 99107-fail-01-06-10102 not actually wrong #367

Open luciansmith opened 4 months ago

luciansmith commented 4 months ago

We test for error 99107 in the file 99107-fail-01-06-10102.xml, but the problem it detects is, I believe, not actually an error. The file defines a new namespace 'appear' and adds a listOfShapes in that namespace, but I believe this is perfectly legal XML, and doesn't impact the SBML specification at all.

<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core"  level="3" version="2"
xmlns:appear1="http://www.sbml.org/sbml/level3/version1/appear/version1"
      appear1:required="true" xmlns:appear="http://anything">
  <model>
    <listOfCompartments>
      <compartment id="c" constant="true" units="litre"/>
    </listOfCompartments>
    <appear:listOfShapes>
      <appear:shape appear:id="circle"/>
    </appear:listOfShapes>
  </model>
</sbml>

Tagging @daemontus for bringing this to our attention.