Error when using writeCbModel

RieCo432 commented 1 year ago

I've been working with the COBRA Toolbox for almost a year now. Today, the writeCbModel function stopped working. I've tried reading and then saving various models I have been using for months and every time I try to save it, I get the following error:

Error using matlab.internal.math.uniqueCellstrHelper
Cell array input must be a cell array of character vectors.

Error in cell/unique (line 86)
    [varargout{1:nlhs}] = matlab.internal.math.uniqueCellstrHelper(A,[false true false true false]);

Error in getModelSubSystems (line 31)
        subSystems = unique(model.subSystems);

Error in writeSBML (line 453)
modelSubSystems = getModelSubSystems(model);

Error in writeCbModel (line 226)
        outmodel = writeSBML(model, fileName, input.compSymbols, input.compNames);

Error in enhance_iBsu1103v3 (line 152)
    outmodel = writeCbModel(model, 'format', 'sbml', 'filename', [filename '.xml']);

I have tried calling writeCbModel with the bare minimum of parameters (i.e. the model and a char array as a filename), but no luck.

I've had a look at the commit history for the source files that are involved in this, but there hasn't been any commits in about 3 weeks.

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

RieCo432 commented 1 year ago

Turns out my model.subSystems was filled with empty char arrays. It worked fine after fixing that. Still wondering how that's never been an issue before though.

rmtfleming commented 1 year ago

What extra option would be needed here to make it fail gracefully?

if all(charBool)
    subSystems = unique(model.subSystems);
elseif all(cellBool)
    orderedSubs = cellfun(@(x)

columnVector(x),model.subSystems,'UniformOUtput',false); subSystems = setdiff(vertcat(orderedSubs{:}),''); else subSystems = unique(model.subSystems); end

On Sun, 20 Nov 2022 at 19:18, Colin Ries @.***> wrote:

Turns out my model.subSystems was filled with empty char arrays. It worked fine after fixing that. Still wondering how that's never been an issue before though.

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