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Re: [[cellml-dev] ] libCellML handling of non-valid CellML - discussion request


Chronological Thread 
  • From: David Nickerson <david.nickerson AT gmail.com>
  • To: cellml-tools-developers AT lists.cellml.org
  • Subject: Re: [[cellml-dev] ] libCellML handling of non-valid CellML - discussion request
  • Date: Fri, 16 Jan 2015 22:22:12 +1300
> Regarding connections: first and foremost, I am all in favour of an API that
> looks like what David described (i.e. “[provide] a much cleaner, more
> intuitive, and flexible interface for application developers”). However, I
> have typical cases where access to a DOM-based structure would also be
> useful.

My view would be that if you want a DOM based representation of a
CellML XML file then you should probably use an XML library directly
rather than an abstracted DOM view via libCellML :) Exactly as you
have said for working with your pretty CellML view in OpenCOR, which
is really a pretty view of CellML XML.

> One such case is the CellML Annotation view in OpenCOR. In that view, we
> want to be able to annotate any CellML element and, whether we/I like it or
> not, that includes connection elements.

LibCellML won't be doing anything with RDF or annotations, so not too
much of a problem for libCellML. One issue that might be worth
discussing is how to assign cmeta:id's to serialised XML elements that
are not directly represented in the object model - if that is even
something that should be in the scope of libCellML.

> Now, assuming we cannot access connections, what would happen in the
> following scenario: say that you have 4 components (A1, A2, B1 and B2) that
> are all siblings. Say that both A1 and B1 define the exact same variable V

I think you mean to say that A1.V and B1.V have the same name, they
are obviously not the same variable and would each have distinct
objects.

> and that this variable contains the result of some calculation (with
> different results for A1.V and B1.V). Next, say that A2 and B2 need to use
> the result of A1.V and B1.V, respectively. Now, since I don’t have access to
> connections, how would I tell libCellML that A2.V is connected to A1.V and
> that B2.V is connected to B1.V?

I would imagine something along the lines of either A1.V = A2.V or
A1.v.isEquivalentTo(A2.V). It is important to remember that a
connection is nothing more than an equivalency relationship (with unit
conversion) between two variables and I believe it is that
relationship that is the important piece of information to represent
in the libCellML object model and API. I see that relationship being a
property of the variables. Also, when talking about the result of a
calculation or using the value of any variable you are really meaning
the instantiation of the model into a simulation, which is also
something that is currently out of scope for libCellML.


Cheers,
Andre.

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