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[cellml-dev] Errors in CellML files


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  • From: david.nickerson at gmail.com (David Nickerson)
  • Subject: [cellml-dev] Errors in CellML files
  • Date: Fri, 23 Sep 2011 09:55:56 +1200
Hi Lucian,

Just to be clear, are you saying that your code hasn't changed but
something in the new 1.10 release of the CellML API has changed in
such a way that your code no longer behaves the same?

Cheers,
David.

On Fri, Sep 23, 2011 at 9:46 AM, Lucian Smith <lpsmith at spod-central.org>
wrote:
> * Andrew Miller <ak.miller at auckland.ac.nz> [2011-09-22 22:37] writes:
>> On 23/09/11 06:05, Lucian Smith wrote:
>> >Out of the approximately 2,000 cellml model files on models.cellml.org,
>> >over half of them give me an error when I read them in with the CellML
>> >API, of the form:
>> >
>> > ? CellML Variable Po in component TempRLC has in interfaces, but is not
>> > ? connected (directly or indirectly) to any variable with no in
>> > ? interfaces;
>> >
>> >The thing is, I don't actually care about this error at all--I'm not
>> >trying to simulate anything, I'm only trying to translate the model, and
>> >it should be perfectly possible to translate a model like this.
>>
>> Hi Lucian,
>>
>> Can you remind me why you need to be using CeVAS? The whole point of
>> CeVAS is to map variables in components to their 'source' (that is, the
>> variable which is connected to them but is not an in variable).
>>
>> Therefore, CeVAS, in its current form, is only useful for variables that
>> are ultimately connected up to a variable with no in interfaces.
>
> It looks like I use CeVAS for the function 'iterateRelevantComponents'.
>
>> This should apply for any complete models, but it won't apply to, say, a
>> model that is not a complete model, but is designed as a component to be
>> imported into another model.
>>
>> If Antimony can't deal with these component models, then there is little
>> benefit to trying to translate them. If it can, I'd suggest doing a more
>> direct translation and letting Antimony work out the connections rather
>> than using CeVAS to flatten all the parts of the model into one.
>
> Antimony can indeed deal with thse component models just fine, as it does
> not have any concept of under-specification of a variable. ?It simply
> writes out what it has.
>
> I do indeed work out the connections on my own. I think. ?It's been a
> while since I wrote that code. ?At the very least, the only times I call
> 'cevas->' anything is to call 'modelError' and
> 'iterateRelevantComponents'.
>
> -Lucian
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