Error when opening certain SBML files

[tanio003]

@tpfau I'm getting an error using MATLAB 2015b and 2016b when I try to open a model (iNS934.xml). The SMBL file was download from here: https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-017-0441-1#Bib1 ("Additional File 3", just above References Section)

The model itself is valid on SBML checker. Error message get when I try to open this model is

>> model=readCbModel('iNS934.xml')
Error using cellfun
Non-scalar in Uniform output, at index 1, output 1.
Set 'UniformOutput' to false.

Error in readSBML>extractGPRRule (line 447)
    ruleGenes = cellfun(@(x) regexp(x,'[^ \[\]\(\)\{\}]*','match'),geneFields);

Error in readSBML (line 214)
        [rule,cgenes] = extractGPRRule(grRule{i},model.genes,0);

Error in readCbModel (line 206)
        model = readSBML(fileName,defaultBound);

I also attached the log file for COBRA toolbox as pdf. COBRAconfigReport-2.pdf

Thank you I hereby confirm that I have:

• [X] Tried to solve the issue on my own
• [X] Retried to run my code with the latest version of The COBRA Toolbox
• [X] Checked that a similar issue has not already been opened

(Note: You may replace [] with [X] to check the box)

[laurentheirendt]

Direct link to model file.

[tpfau]

Hi @tanio003 Thanks for the report. There are a few issues with this file: One issue is something we can solve. There is an empty GPR that only contains '()' - something that we did not accept (but I'll put in a PR to adapt that). However, there are two errors in the SBML (line 46837, 46902), where the GENE_ASSOCIATION contains a duplicated 'and', which is something we can't filter in the code as this would allow very odd things to happen.This is simply an mistake in the SBML where the SBML does not stick to the definition.

[laurentheirendt]

Thanks @tanio003 and @tpfau! :+1: