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Argh, I really wish it had been a problem with my code! Well, if anything,
thanks for reminding me about that tracker item, I had clearly forgotten
about it. I have changed its priority so that it is now set to "Highest
priority".



Alan



From: cellml-tools-developers-bounces at cellml.org
[mailto:cellml-tools-developers-bounces at cellml.org] On Behalf Of Jonathan
Cooper
Sent: 25 September 2009 11:14
To: A list for the developers of CellML tools
Subject: Re: [cellml-dev] CellML API - GetAlternateVersion from the Model
interface



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>
"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>
"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/









_____




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• [cellml-dev] CellML API - GetAlternateVersion from the Model interface, Alan Garny, 09/25/2009
  • [cellml-dev] CellML API - GetAlternateVersion from the Model interface, Jonathan Cooper, 09/25/2009
    • [cellml-dev] CellML API - GetAlternateVersion from the Model interface, Alan Garny, 09/25/2009
  • <Possible follow-up(s)>
  • [cellml-dev] CellML API - GetAlternateVersion from the Model interface, David Nickerson, 09/25/2009
    • [cellml-dev] CellML API - GetAlternateVersion from the Model interface, Alan Garny, 09/25/2009
    • [cellml-dev] CellML API - GetAlternateVersion from the Model interface, Alan Garny, 09/25/2009
      • [cellml-dev] CellML API - GetAlternateVersion from the Model interface, Jonathan Cooper, 09/25/2009

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