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[cellml-dev] CellML API - GetAlternateVersion from the Model interface


Chronological Thread 
  • From: jonathan.cooper at comlab.ox.ac.uk (Jonathan Cooper)
  • Subject: [cellml-dev] CellML API - GetAlternateVersion from the Model interface
  • Date: Fri, 25 Sep 2009 11:13:37 +0100
Hi Alan,

See https://tracker.physiomeproject.org/show_bug.cgi?id=1331

Best wishes,
Jonathan

Alan Garny wrote:
>
> Hi,
>
>
>
> I have just been reminded about this mailing list for my
> CellML-related 'problems', so here goes...
>
>
>
> I am currently working on generating a CellML object from the COR-like
> view in OpenCell. Right now, I am able to create an empty CellML 1.0
> object. However, should the user specify an import statement in the
> COR-like view, I would like to 'convert' that CellML 1.0 object to a
> CellML 1.1 object.
>
>
>
> Unless I am mistaken, I believe that one should be able to do that
> using the GetAlternateVersion method from the Model interface. At the
> moment, I have a Bison rule that reads as follows:
>
>
>
> ------------------------------------------------------------------------
>
> importstart: T_IMPORT T_URI T_AS {
>
> // We are importing something, which means the model should be a
> CellML 1.1
>
> // model (as opposed to a CellML 1.0 model, which is what it is by
> default)
>
>
>
> nsString cellMLVersion;
>
>
>
> (*aCellMLOutput)->GetCellmlVersion(cellMLVersion);
>
>
>
> if (cellMLVersion.Equals(NS_LITERAL_STRING("1.0")))
>
> (*aCellMLOutput)->GetAlternateVersion(NS_LITERAL_STRING("1.1"),
> aCellMLOutput);
>
> };
>
> ------------------------------------------------------------------------
>
>
>
> The above code works fine in that the CellML 1.0 model does become a
> CellML 1.1 model (as can be seen in the XML view), BUT the whole
> contents of the CellML model disappears in the process. Say that I
> initially had the following COR code:
>
>
>
> ------------------------------------------------------------------------
>
> def model my_model as
>
> enddef;
>
> ------------------------------------------------------------------------
>
>
>
> This corresponds to the following CellML code:
>
>
>
> ------------------------------------------------------------------------
>
> <?xml version="1.0"?>
>
> <model xmlns="http://www.cellml.org/cellml/1.0#"; xml:base=""
> name="my_model"/>
>
> ------------------------------------------------------------------------
>
>
>
> Then, say that I edit the COR-like view to read:
>
>
>
> ------------------------------------------------------------------------
>
> def model my_model as
>
> def import {uri: cellml.org} as
>
> comp A as B;
>
> unit C as D;
>
> enddef;
>
> enddef;
>
> ------------------------------------------------------------------------
>
>
>
> This requires the CellML object to be 'converted to' CellML 1.1.
> However, when switching to the XML view (something that will trigger
> the 'conversion'), I get:
>
>
>
> ------------------------------------------------------------------------
>
> <?xml version="1.0"?>
>
> <model xmlns="http://www.cellml.org/cellml/1.1#"; xml:base=""/>
>
> ------------------------------------------------------------------------
>
>
>
> So, the model has been 'converted to' CellML 1.1, but everything is
> gone and indeed, if you switch back to the COR-like view, you will (as
> you would expect) get the following:
>
>
>
> ------------------------------------------------------------------------
>
> def model as
>
> enddef;
>
> ------------------------------------------------------------------------
>
>
>
> So, does anyone know what I have done wrong, if anything? I have
> checked the CellML test for GetAlternateVersion and it 'only' checks
> the CellML version, a test which my current code would also pass, but
> which should in fact fail (if we consider that the contents of the
> model has gone)... It seems like RecursivelyChangeVersionCopy might
> not be working? (I am currently looking into it.)
>
>
>
> Anyway, if any of you had some comments on the above or, most
> importantly, a working solution to my problem, then please feel free
> to make yourself heard... J
>
>
>
> Cheers, Alan.
>
>
>
> *Dr Alan Garny*
>
> University of Oxford, Department of Physiology, Anatomy & Genetics
>
> Sherrington Building, Parks Road, Oxford, OX1 3PT, England
>
> http://noble.physiol.ox.ac.uk/people/agarny/
>
> http://cor.physiol.ox.ac.uk/
>
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> cellml-tools-developers mailing list
> cellml-tools-developers at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-tools-developers
>

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