convertSBMLToCobra - bug SBML models without kineticLaws about cobratoolbox HOT 2 CLOSED

I believe this is the same as #3584901 on the old sourceforge site. I had reported that as:

"When attempting to load the iAZ900 model of yeast (which you can get at https://www.biomedcentral.com/content/supplementary/1752-0509-4-178-s3.xml), ReadCbModel gives the following error:

Too many outputs requested. Most likely cause is missing [] around left hand side that has a comma separated list expansion.

Error in convertSBMLToCobra (line 122)
parameters = modelSBML.reaction(i).kineticLaw.parameter;

This error has been reported on the google group a few times, too.

Digging into it, convertSBMLToCobra uses isfield(modelSBML.reaction(i).kineticLaw, 'parameter'), which returns true even if there's no modelSBML.reaction(i).kineticLaw.parameter field (I think this is because there is a modelSBML.parameter field).

To fix this, the loop beginning at line 122 with "if isfield" can be replaced with the following loop:
if isempty(modelSBML.reaction(i).kineticLaw) % added by BH
parameters = []; %added by BH
else
parameters = modelSBML.reaction(i).kineticLaw.parameter; % added by BH
end % added by BH

I have tested this with the iND750 model and the Yeast 5 model, and readCbModel still works for these models. There may be a better solution, though. (and yes, python is one of them)

Daniel had added the try/catch statements around the loop in response to this bug. Does the try/catch not work (I haven't tested it).

-b

from cobratoolbox.

I'm guessing that it might be due to the bug possibly being present in the zip file vs the repository. After we take care of #13, I'll push out another zip file for download and then we can use @bheavner's CORBAVersion command to sort out future issues.

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