fix system cp flags problem on macs

src/spmBatching/bidsCopyRawFolder.m

@@ -70,19 +70,22 @@ function bidsCopyRawFolder(opt, deleteZippedNii)
             % use a call to system cp function to use the derefence option (-L)
             % to get the data 'out' of an eventual datalad dataset
             try
-                system( ...
-                       sprintf('cp -Lr %s %s', ...
+                status = system( ...
+                                sprintf('cp -R -L %s %s', ...
                                fullfile(rawDir, subDir), ...
                                fullfile(derivativesDir, subDir)));
-            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);
 
+                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

tests/test_bidsCopyRawFolder.m

@@ -0,0 +1,45 @@
+function test_suite = test_bidsCopyRawFolder %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
+
+function test_bidsCopyRawFolderBasic()
+
+    % directory with this script becomes the current directory
+    opt.dataDir = fullfile( ...
+                           fileparts(mfilename('fullpath')), ...
+                           '..', 'demos',  'MoAE', 'output', 'MoAEpilot');
+
+    % group of subjects to analyze
+    opt.groups = {''};
+    % suject to run in each group
+    opt.subjects = {[]};
+    % task to analyze
+    opt.taskName = 'auditory';
+
+    checkDependencies();
+    opt = checkOptions(opt);
+
+    bidsCopyRawFolder(opt, 1);
+
+    assertEqual(exist( ...
+                      fullfile(opt.dataDir, '..', ...
+                               'derivatives', 'SPM12_CPPL', ...
+                               'dataset_description.json'), 'file'), ...
+                2);
+
+    assertEqual(exist( ...
+                      fullfile(opt.dataDir, '..', ...
+                               'derivatives', 'SPM12_CPPL', 'sub-01', 'func', ...
+                               'sub-01_task-auditory_bold.nii'), 'file'), ...
+                2);
+
+    assertEqual(exist( ...
+                      fullfile(opt.dataDir, '..', ...
+                               'derivatives', 'SPM12_CPPL', 'sub-01', 'anat', ...
+                               'sub-01_T1w.nii'), 'file'), ...
+                2);
+end