* Catherine Lloyd c.ll...@auckland.ac.nz [2010-02-23 22:50] writes:
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.
I can at least put the answers I got; here they are:
Begin forwarded message:
From: Lucian Smith lpsm...@spod-central.org
-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?
The short answer is 'yes'; the longer answer is 'look at the OpenCell
Installer'. I may need some help here, but it's at least a start.
-In the model bertram_satin_pedersen_luciani_sherman_2007.cellml,
'lambda'
gets translated into infix with a '$' before it. Is this because
'lambda'
is also a function name? Does this happen with any other variables?
Yes. Any variable may be prepended with the '$'; it's *required* for any
variable that is also a reserved word. There may be a list of reserved
words somewhere; someone said they'd look into forwarding me a copy.
-Is there documentation about how you define your infix?
Not externally, but it's inside the help in OpenCell.
-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(nsCOMPtrcellml_apiIModel model)
{
if (model == NULL) return true;
nsresult rv;
nsCOMPtrcellml_servicesICeVASBootstrap
cevasboot(do_GetService(CEVAS_BOOTSTRAP_CONTRACTID, rv));
NS_ENSURE_SUCCESS(rv, true);
nsCOMPtrcellml_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 ()
Basically, this is a bug, so I submitted a tracker item for it. Andrew
had a workaround (I believe), but I don't remember what it was; it's a
low enough priority item for me I think I'll just wait for the fix.
-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?
This turned out to also be a bug in the example CellML file (the file in
question was named 'CompletedImportExample.cellml'). I submitted a
different tracker item for that. Basically, the answer was 'use / and not
\'.
-Can I get a zip file of all the cellml models on cellml.org from
anywhere?
The short answer was What? and the long answer was Um, maybe? There
may be a script that uses mercurial that could work for this. I still
think such a zip file would be very useful for anyone who wants to
translate models or just test their own systems. Biomodels does this
(albeit with a lower number of models), and that's what I always grab when
I'm testing things. If in the future I wanted to provide Antimony
versions of CellML models, it would be great if I could update those
translations with the current versions at the repository.
One possibility would be to download the cellml files grouped by their
curation status: cellml_threestar_models.tar.gz, etc.
-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));
}
There are API calls you can use to get the number of times the current
component has been imported--I think I can use this so I don't try to
re-create the basic model again. The trick then will be to make sure I
implement the multiple instantiations needed for the full model.
This does bring up a different point that wasn't quite appropriate for the
hackathon, but might be worth discussing here: if a model like
faville_model_2008 has shown that it is helpful to 'clone'
