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FIX: copyfile()/symlinks on Linux, Matlab < R2020a #22

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FIX: copyfile()/symlinks on Linux, Matlab < R2020a #22

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61b8523
FIX: copyfile()/symlinks on Linux, Matlab < R2020a
octomike May 6, 2020
3cf147e
Fix comment
octomike May 10, 2020
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25 changes: 21 additions & 4 deletions spm_BIDS_App.m
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Original file line number Diff line number Diff line change
Expand Up @@ -223,10 +223,27 @@
%-Copy participants' data
%------------------------------------------------------------------
for s=1:numel(BIDS_App.participants)
%fprintf('Temporary directory: %s\n',...
% fullfile(BIDS_App.tmpdir,BIDS_App.participants{s}));
sts = copyfile(fullfile(BIDS_App.dir,BIDS_App.participants{s}),...
fullfile(BIDS_App.tmpdir,BIDS_App.participants{s}));
%
% Datasets may be managed with symlinks (e.g. datalad/git-annex)
%
% Prior to Matlab 2020, copyfile() on Linux will not dereference
% the symlink, which can easily break if the target is relative.
% To save space keeping the symblic would be the better choice, but
% it's much harder to determine the correct location for all
% platforms, so we resort to cp -L in that special case and always
% dereference.
%
% https://www.mathworks.com/help/matlab/ref/copyfile.html
%
matlab_ver = str2num(erase(ver('MATLAB').('Version'), '.'));
if isunix && matlab_ver <= 98 % We should always be on Linux, but still
sts = system(sprintf('cp -rL "%s" "%s"', fullfile(BIDS_App.dir, BIDS_App.participants{s}),...
fullfile(BIDS_App.tmpdir, BIDS_App.participants{s})));
sts = ~ sts; % exit semantic is inverted in shell
else
sts = copyfile(fullfile(BIDS_App.dir,BIDS_App.participants{s}),...
fullfile(BIDS_App.tmpdir,BIDS_App.participants{s}));
end
if ~sts
error('Data could not be temporarily copied.');
end
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