fix system cp flags problem on macs

[marcobarilari]

to check if this works on linux

fix #90

[codecov]

Codecov Report

Merging #105 into dev will increase coverage by 1.95%.
The diff coverage is 60.00%.

@@            Coverage Diff             @@
##              dev     #105      +/-   ##
==========================================
+ Coverage   41.83%   43.78%   +1.95%     
==========================================
  Files          56       56              
  Lines        1310     1311       +1     
==========================================
+ Hits          548      574      +26     
+ Misses        762      737      -25     

Impacted Files	Coverage Δ
src/spmBatching/bidsCopyRawFolder.m	62.50% <60.00%> (+62.50%)	⬆️
src/getData.m	100.00% <0.00%> (+2.56%)	⬆️

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[marcobarilari]

in case we want to track any errors from system we may want to use this (from help section in matlab)

returns status = 0 and, in result, a MATLAB character vector containing
    a list of files in the current directory (assuming your operating
    system knows about the "dir" or "ls" command). If "dir" or "ls" fails
    or does not exist on your system, system returns a nonzero value in
    status, and an explanatory message in result.

so it will be

try
    status =  system( ...
        sprintf('cp -R -L %s %s', ...
        fullfile(rawDir, subDir), ...
        fullfile(derivativesDir, subDir)));
    
    if status > 0
        error('...')
    end
    
catch
    message = [ ...
        'Copying data with system command failed: ' ...
        'are you running Windows?\n', ...
        'Will use matlab/octave copyfile command instead.\n', ...
        'Could be an issue if your data set contains symbolic links' ...
        '(e.g. if you use datalad or git-annex.'];
    warning(message);
    
    copyfile(fullfile(rawDir, subDir), ...
        fullfile(derivativesDir, subDir));
end

[Remi-Gau]

Added a VERY simple that relies on the fact that I download an SPM example BIDS dataset as part of the travis CI, so I can try this very test on it.

@CerenB have you confirmed that this fixed your problem #90 ?

[marcobarilari]

btw, let me know what you think about the 'error' thing, we can change it in the fly like

try
    status =  system( ...
        sprintf('cp -R -L %s %s', ...
        fullfile(rawDir, subDir), ...
        fullfile(derivativesDir, subDir)));
    
    if status > 0
        message = [ ...
             'Copying data with system command failed: ' ...
             'are you running Windows?\n', ...
             'Will use matlab/octave copyfile command instead.\n', ...
             'Could be an issue if your data set contains symbolic links' ...
              '(e.g. if you use datalad or git-annex.'];
        error(message)
    end
    
catch
    copyfile(fullfile(rawDir, subDir), ...
        fullfile(derivativesDir, subDir));
end

[CerenB]

yup looks good!

[Remi-Gau]

btw, let me know what you think about the 'error' thing, we can change it in the fly like

I am tired.

I thought we had added it: go ahead and add it. 🚀

[marcobarilari]

done