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[cellml-dev] Errors in CellML files


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  • From: lpsmith at spod-central.org (Lucian Smith)
  • Subject: [cellml-dev] Errors in CellML files
  • Date: Thu, 22 Sep 2011 23:11:03 +0100
I don't know which release included the change (it was some release prior
to 1.10) but it was a change since I originally wrote it, which might have
been up to a year ago. (I have old translated versions of files that now
refuse to translate.)

-Lucian

* David Nickerson <david.nickerson at gmail.com> [2011-09-22 22:56] writes:
> 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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> >
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