[FIX] copy to derivatives handles bids filter file and minimize re copying files that already exist (#1015)

* set overwrite to false by default when copying

* split tests

* better handle using bids filter file for copy

* fix boilerplate cli errors

* fix boilerplate cli errors

* properly skip tests

* fix path

* skip the correct test

* style

* skip octave test

Author: Remi-Gau

bidspm.m

@@ -42,6 +42,9 @@
   addParameter(args, 'fwhm', 6, isPositiveScalar);
   addParameter(args, 'space', {}, isCellStr);
 
+  % copy only
+  addParameter(args, 'force', false, isLogical);
+
   % create_roi only
   addParameter(args, 'roi_dir', '', isChar);
   addParameter(args, 'hemisphere', {'L', 'R'}, isCellStr);
@@ -193,7 +196,30 @@ function copy(args)
   opt.query.desc = {'preproc', 'brain'};
   opt.query.suffix = {'T1w', 'bold', 'mask'};
   opt.query.space = opt.space;
-  bidsCopyInputFolder(opt);
+
+  bidsFilterFile = get_bidsFilterFile(args);
+  if ~isempty(bidsFilterFile)
+    suffixes = fieldnames(bidsFilterFile);
+    modalities = {};
+    for i = 1:numel(suffixes)
+      modalities{end + 1} = bidsFilterFile.(suffixes{i}).modality; %#ok<*AGROW>
+      if isfield(bidsFilterFile.(suffixes{i}), 'suffix')
+        opt.query.suffix = cat(2, ...
+                               opt.query.suffix, ...
+                               bidsFilterFile.(suffixes{i}).suffix);
+      end
+      if isfield(bidsFilterFile.(suffixes{i}), 'desc')
+        opt.query.desc = cat(2, ...
+                             opt.query.desc, ...
+                             bidsFilterFile.(suffixes{i}).desc);
+      end
+    end
+    opt.query.modality = unique(modalities);
+  end
+  opt.query.suffix = unique(opt.query.suffix);
+  opt.query.desc = unique(opt.query.desc);
+
+  bidsCopyInputFolder(opt, 'unzip', true, 'force', args.Results.force);
 
 end
 
@@ -657,6 +683,16 @@ function update()
 
 %% helpers functions
 
+function bidsFilterFile = get_bidsFilterFile(args)
+
+  if isstruct(args.Results.bids_filter_file)
+    bidsFilterFile = args.Results.bids_filter_file;
+  else
+    bidsFilterFile = bids.util.jsondecode(args.Results.bids_filter_file);
+  end
+
+end
+
 function detectBidspm()
 
   workflowsDir = cellstr(which('bidsSpatialPrepro.m', '-ALL'));

src/messages/bidspmHelp.m

@@ -140,7 +140,8 @@ function bidspmHelp()
   %
   % **COPY:**
   %
-  % Copies fmriprep data for smoothing.
+  % Copies and unzips input data to output dir.
+  % For example for fmriprep data before smoothing.
   %
   % .. code-block:: matlab
   %
@@ -152,8 +153,11 @@ function bidspmHelp()
   %           'space', {'individual', 'IXI549Space'}, ...
   %           'options', struct([]), ...
   %           'task', {}, ...
-  %           'skip_validation', false)
+  %           'skip_validation', false, ...
+  %           'force', false)
   %
+  % :param force:   overwrites previous data if true
+  % :type  force:   logical
   %
   % **CREATE_ROI:**
   %
@@ -189,6 +193,8 @@ function bidspmHelp()
   %
   % **SMOOTH:**
   %
+  % Copies files to output dir and smooths them.
+  %
   % .. code-block:: matlab
   %
   %   bidspm(bids_dir, output_dir, 'subject', ...
@@ -201,7 +207,11 @@ function bidspmHelp()
   %           'options', struct([]), ...
   %           'task', {}, ...
   %           'fwhm', 6, ...
-  %           'skip_validation', false)
+  %           'skip_validation', false
+  %           'force', false)
+  %
+  % :param force:   overwrites previous data if true
+  % :type  force:   logical
   %
   %
   % **DEFAULT_MODEL:**

src/workflows/bidsCopyInputFolder.m

@@ -16,8 +16,8 @@ function bidsCopyInputFolder(varargin)
   % :param unzip: defaults to true
   % :type unzip: boolean
   %
-  % :param unzip: defaults to true
-  % :type unzip: boolean
+  % :param force: defaults to true
+  % :type force: boolean
   %
   % See also: bids.copy_to_derivative
   %
@@ -31,7 +31,7 @@ function bidsCopyInputFolder(varargin)
 
   addRequired(args, 'opt', @isstruct);
   addParameter(args, 'unzip', true, @islogical);
-  addParameter(args, 'force', true, @islogical);
+  addParameter(args, 'force', false, @islogical);
 
   parse(args, varargin{:});
 
@@ -52,7 +52,6 @@ function bidsCopyInputFolder(varargin)
   % raw directory and derivatives directory
   createDerivativeDir(opt);
 
-  %% Loop through the groups, subjects, sessions
   [BIDS, opt] = getData(opt, opt.dir.input);
 
   use_schema = true;

tests/tests_batches/stats/test_setBatchSubjectLevelResults.m

@@ -53,8 +53,7 @@ function test_setBatchSubjectLevelResults_basic()
 function test_setBatchSubjectLevelResults_missing_contrast_name()
 
   if bids.internal.is_octave()
-    %       'Octave:mixed-string-concat'
-    return
+    moxunit_throw_test_skipped_exception('Octave:mixed-string-concat warning thrown');
   end
 
   [subLabel, opt, result] = setUp('vismotion');
@@ -73,8 +72,7 @@ function test_setBatchSubjectLevelResults_missing_contrast_name()
 function test_setBatchSubjectLevelResults_error_no_matching_contrast()
 
   if bids.internal.is_octave()
-    %       'Octave:mixed-string-concat'
-    return
+    moxunit_throw_test_skipped_exception('Octave:mixed-string-concat warning thrown');
   end
 
   contrast_name = 'NotAContrast';