unintended prefix for compartment i

[mihai-sysbio]

Description of the issue:

When exporting Human-GEM from yml to xml, the compartment i becomes c_i. It is the only compartment that gets prefixed with c_. The root cause is likely in the lines

RAVEN/io/exportModel.m

Lines 224 to 231 in 800362e

	if isfield(modelSBML.compartment,'metaid')
	if ~isnan(str2double(model.comps(i)))
	EM='The compartment IDs are in numeric format. For the compliance with SBML specifications, compartment IDs will be preceded with "c_" string';
	dispEM(EM,false);
	model.comps(i)=strcat('c_',model.comps(i));
	end
	modelSBML.compartment(i).metaid=model.comps{i};
	end

Maybe due to the unintended interpretation of i as an imaginary unit?

Reproducing this issue:

Below is a test case that demonstrates the bug:

compartment = 'i';
if ~isnan(str2double(compartment))
compartment=strcat('c_',compartment);
end
disp(compartment)

c_i

System information

The bug is based on the latest release of RAVEN, demonstrated above in Matlab 2019b on macOS.

I hereby confirm that I have:

• Followed the guidelines to install RAVEN.
• Checked that a similar issue does not already exist
• If suitable, needed, asked first in the Gitter chat room about the issue

[edkerk]

You're right. Checking whether something is numeric using str2double is very sloppy, this is fixed by changing line 225 as:

        if any(regexp(model.comps(i),'^\d'))

Will make a PR for this asap. Meanwhile, exportModel from #360, together with the extended checkModelStruct from #353 would prevent these issues.

[mihai-sysbio]

Will make a PR for this asap. Meanwhile, exportModel from #360, together with the extended checkModelStruct from #353 would prevent these issues.

Thanks @edkerk for the quick action and good advice.