Interface for Model manipulation

[skeating]

Remaining items from this section of #21

• Look up variable(s) by RDF annotation
  • Actually by cmeta:id - RDF library will handle finding the ID from property + object
  • No variable found - can be OK or not (chosen by caller)
  • One variable found
  • Multiple variables found - can be OK or not (chosen by caller)
• Look up RDF annotation(s) for a given variable
• Get the free variable
• Iterate over state variables
• Iterate over all variables
• Get the equation defining a variable / derivative
  • Get the RHS of the equation
• Get variables referenced by an equation
• Get equations needed to compute a set of variables, recursively
  • Where 'variables' can include ODE RHSs, i.e. the definition of a derivative
• Given an equation, tell easily if it's an ODE or simple assignment
  • Get the variable assigned to, state var, or free var
• Add a variable (optionally with units, annotations) Model.add_number and add_variable now allow unit objects as well as strings #172 allows adding a variable with units
  • Add an annotation for a variable
  • Units may be unknown when variable is first added, and calculated later from its definition. We need to be able to find all such variables easily.
• Remove an equation from the system Replaced Model.set_equation(lhs, rhs) with Model.remove_equation(equation) #171 adds this functionality
• Add an equation to the system Replace a variable's equation #118
  • Variable names in new equations can be things like oxmeta:membrane_voltage - these need to be mapped to names suitable for code generation at some point, and identified with other variables having that annotation Replace a variable's equation #118
• Replace part of an equation
  • E.g. to replace an 'original_definition' symbol with the equation originally defining it
  • This needs to be a 'clone' of the inserted equation
• Allow 'special' operations, so we can represent 'linear interpolation on a data file'
• Handle time units conversion issue (Adding unit conversion for code generation #77 should deal with this)
  • RHS gets assigned to new variable with original units; change references to original derivative to this new variable; add another version of this variable with desired units, assigned from this one; use that to define the ODE.
• Handle [state] variable units conversion (Adding unit conversion for code generation #77 should deal with this)
  • See _replace_variable logic, and perhaps _add_converted_variable - should be able to merge these
• Construct an equation on the fly
• Track which equations were added to the system
• Redo model consistency checks & units conversions after all modifications done

[MichaelClerx]

What's "replace part of an equation" and why do we want to do that?

[MichaelClerx]

I think we've done a lot of the unchecked ones, @jonc125 ?
A few could also be crossed out, as they're more part of chaste-codegen / fc? For example "linear interpolation on a data file" or "Redo model consistency checks & units conversions after all modifications done" ?

[jonc125]

Remaining items don't need special support here I think; can be done in weblab-fc.