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Hi Andrew,

> Also, I fixed one of your tests which was not testing the correct thing;
> it applies to a few of them, but removeResource was the only one where
> they failed. Checking the length of getCVTerms(model) is not sufficient
> - there can be empty CVTerms (this means the bag exists but it has no
> contents), so I instead changed the tests to test for the size of the
> first bag. For example, removeResource does not cause the bag to be
> deleted, only the contents of the bag to be removed.

Thanks, I've applied the same idea to the rest of my tests. All of the
tests pass now and I'll be using it in Saint hopefully before the day is
done.

There's a few things that I'm curious about. I notice in the file that's
produced, all of the RDF is in a single block with no newlines. It's not
supposed to be human-readable anyway, I guess, but it makes it a little
bit difficult to test to see if the URIs actually made it into the file.

Also, you annotate the model in the following way:


<rdf:Description rdf:about="#aguda_1999">
<is xmlns="http://biomodels.net/model-qualifiers/";>
<rdf:Description rdf:nodeID="n2"/>
</is>
</rdf:Description>
...
<rdf:Description rdf:nodeID="n2">
<rdf:type>
<rdf:Description
rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
</rdf:type>
<rdf:_1>
<rdf:Description rdf:about="http://www.example.com/"/>
</rdf:_1>
</rdf:Description>


I thought the standard way to use Bags was like this:

<rdf:Description rdf:about="#aguda_1999">
<is xmlns="http://biomodels.net/model-qualifiers/";>
<rdf:Bag>
<rdf:li rdf:resource="http://www.example.com/"/>
</rdf:Bag>
</is>
</rdf:Description>


Or to keep to the same format:

<rdf:Description rdf:about="#aguda_1999">
<is xmlns="http://biomodels.net/model-qualifiers/";>
<rdf:Description rdf:nodeID="n2"/>
</is>
</rdf:Description>
...
<rdf:Description rdf:nodeId="n2">
<rdf:Bag>
<rdf:li rdf:resource="http://www.example.com/"/>
</rdf:Bag>
</rdf:Description>


It doesn't really make a difference to us as long as the API and CVTerm
can parse it, but I was wondering if the way you did it was better for
re-use or was conforming to CellML specification.

Thanks for all of your help on this. We really appreciate the time
you've taken to write this class and the extensions to the CellML API.


Cheers,
Morgan

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• [cellml-dev] Java CVTerm implementation, Andrew Miller, 04/07/2010
  • [cellml-dev] Java CVTerm implementation, Morgan Taschuk, 04/10/2010
  • Message not available
    • [cellml-dev] Java CVTerm implementation, Andrew Miller, 04/14/2010
      • [cellml-dev] Java CVTerm implementation, Morgan Taschuk, 04/15/2010
        • [cellml-dev] Java CVTerm implementation, Andrew Miller, 04/15/2010
          • [cellml-dev] Java CVTerm implementation, Morgan Taschuk, 04/16/2010
            • [cellml-dev] Java CVTerm implementation, David Nickerson, 04/16/2010
              • [cellml-dev] Java CVTerm implementation, Andrew Miller, 04/16/2010
              • [cellml-dev] Java CVTerm implementation, David Nickerson, 04/16/2010
            • [cellml-dev] Java CVTerm implementation, Andrew Miller, 04/16/2010

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