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[cellml-discussion] Fwd: Evo connection


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  • From: c.lloyd at auckland.ac.nz (Catherine Lloyd)
  • Subject: [cellml-discussion] Fwd: Evo connection
  • Date: Wed, 24 Feb 2010 11:49:27 +1300
Dear Andrew

I am forwarding Lucian's questions onto you in case you feel you have
to file tracker items for any of them or need to get in touch with
Lucian again.

I am also opening it up to the discussion list in case anyone else
would like to comment.

Best wishes
Catherine


Begin forwarded message:

> From: Lucian Smith <lpsmith at spod-central.org>
> Date: 24 February 2010 9:38:13 AM
> To: Catherine Lloyd <c.lloyd at auckland.ac.nz>
> Subject: Re: [cellml-discussion] Evo connection
>
> -Currently, I must run my program from the directory with the
> 'components/'
> subdirectory. Is there a way I can set things up so I can run my
> program
> from anywhere?
>
> -In the model bertram_satin_pedersen_luciani_sherman_2007.cellml,
> 'lambda'
> gets translated into infix with a '$' before it. Is this because
> 'lambda'
> is also a function name? Does this happen with any other variables?
>
> -Is there documentation about how you define your infix?
>
> -If I get a 'failed to load external entity' exception, it SIGABRTs
> me,
> despite being supposedly wrapped in one of those 'nsresult'
> thingummies, and
> try/catch doesn't seem to work. What do I need to do to catch this?
>
> code:
> bool Registry::LoadCellML(nsCOMPtr<cellml_apiIModel> model)
> {
> if (model == NULL) return true;
> nsresult rv;
> nsCOMPtr<cellml_servicesICeVASBootstrap>
> cevasboot(do_GetService(CEVAS_BOOTSTRAP_CONTRACTID, &rv));
> NS_ENSURE_SUCCESS(rv, true);
>
> nsCOMPtr<cellml_servicesICeVAS> cevas;
> try {
> rv = cevasboot->CreateCeVASForModel(model, getter_AddRefs(cevas));
> }
> catch (...){
> return true;
> }
>
>
> result:
> I/O warning : failed to load external entity "/home/lpsmith/CellML/
> models/.\ImportExample2.cellml"
> terminate called after throwing an instance of
> 'iface::cellml_api::CellMLException'
> what(): std::exception
>
> Program received signal SIGABRT, Aborted.
> 0xb7f5b430 in __kernel_vsyscall ()
>
> -Speaking of, the above problem was due to the imported file name
> being
> called ".\ImportedExample2.cellml" instead of "./
> ImportedExample2.cellml"
> (and me running on a unix platform). Is there a good cross-platform
> method
> for fixing this problem?
>
> -Can I get a zip file of all the cellml models on cellml.org from
> anywhere?
>
> -hypertrophy_or_deterioration_parent.cellml
> -faville_model_2008: This model is recursive. When I loop over its
> components, some components come up multiple times, every time under
> the
> original name. My code then sees the same thing again, and fails.
> How
> would I get the *new* name for the component? Here's the current
> code:
>
> while (component != NULL) {
> numcomps++;
> //Each CellML 'component' becomes its own Antimony 'module'
> nsString cellmltext;
> rv = component->GetName(cellmltext);
> string cellmlname = "cellmlmod_" + ToThinString(cellmltext.get());
> NewCurrentModule(&cellmlname);
> CurrentModule()->LoadCellMLComponent(component);
> RevertToPreviousModule();
> rv = cmpi->NextComponent(getter_AddRefs(component));
> }

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