PyCml - CellML Tools in Python

Web-based validation

Known limitations

• Metadata validation does not assert anything about the content of <rdf:RDF> elements.
• Units checking will try to evaluate the <degree> qualifier and the exponent of an application of <power>, and will generate a warning if it is unable to do so. Generally it only supports the CellML subset of MathML.
• User-defined relationship types are not well supported.
• The specification doesn't require models to be dimensionally consistent. By default this validator will declare inconsistent models to be invalid, however. There is an option to demote units errors to warnings, which is more consistent with the specification.
• Queries on the specification:
  • Rule 2.5.2 conflicts with the standard interpretation of attribute namespaces. Attributes without an explicit namespace are considered to be in the null (local) namespace, not the namespace of the parent element.
  • Paragraph 3 of section 4.2.1 is misleading, and conflicts with section 7.2. In particular, “These expressions may make use of any variable declared in the current component but must only modify the value of the variable referenced by the ancestor <cellml:variable_ref> element” implies the opposite of “In all other cases, the equations relate an intermediate variable used in the rate calculation to the variable referenced by the containing <variable_ref> element. For instance, it would be appropriate to calculate an effective concentration of a catalyst inside the <role> element contained by the <variable_ref> element that references the variable representing the actual concentration of the catalyst.” I go with the latter.
  • Equation (14) in appendix C.3.4 appears to be missing "o₁ +"
  • Appendix C.3.5 step 1 suggests that the algorithm of C.3.4 performs simplification, whereas it is the algorithm of C.3.1 that is described as simplifying units, and that algorithm is not appropriate for use in a units conversion context as it discards multipliers. This could perhaps be made clearer.
  • The operand of <exp> is required to have units of dimensionless, but many ionic models have membrane potentials as operands. This software follows the spec at present, and will likely continue to do so.
  • The specification of units checking doesn't mention the <piecewise> element. I require all the cases to have dimensionally equivalent units, and the tests to have units of cellml:boolean.

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