[FIX] failing to return file index during dependencies indexing thorw…

… warning and not error (#546)

* no file index throws warning and not error

* silence octave warning

+bids/+internal/return_file_index.m

@@ -1,7 +1,7 @@
 function file_idx = return_file_index(BIDS, modality, filename)
   %
   % For a given filename and modality, it returns the file index
-  % in the subject sub-structure of the BIDS structure
+  % in the subject sub-structure of the BIDS structure.
   %
   % UISAGE::
   %
@@ -13,18 +13,22 @@
   sub_idx = bids.internal.return_subject_index(BIDS, filename);
   try
     file_idx = strcmp(filename, {BIDS.subjects(sub_idx).(modality).filename}');
-  catch ME
-    warning(['An error occurred when processing', ...
-             '\n\t- dataset: %s', ...
-             '\n\t- subject: %s', ...
-             '\n\t- modality: %s', ...
-             '\n\t- file: %s', ...
-             '\nThis may happen if your dataset is not valid.'], ...
-            BIDS.pth, ...
-            BIDS.subjects(sub_idx).name, ...
-            modality, ...
-            filename);
-    rethrow(ME);
+  catch
+    msg = sprintf(['An error occurred when processing', ...
+                   '\n\t- dataset: %s', ...
+                   '\n\t- subject: %s', ...
+                   '\n\t- modality: %s', ...
+                   '\n\t- file: %s', ...
+                   '\nThis may happen if your dataset is not valid.'], ...
+                  BIDS.pth, ...
+                  BIDS.subjects(sub_idx).name, ...
+                  modality, ...
+                  filename);
+    tolerant = true;
+    verbose = true;
+    bids.internal.error_handling(mfilename(), 'noFileIndex', msg, tolerant, verbose);
+    file_idx = [];
+    return
   end
   file_idx = find(file_idx);
 

+bids/+internal/return_file_info.m

@@ -17,8 +17,9 @@
   end
 
   file_info.modality = bids.internal.file_utils(file_info.path, 'filename');
-  file_info.file_idx = bids.internal.return_file_index(BIDS, ...
-                                                       file_info.modality, ...
-                                                       file_info.filename);
+  file_idx = bids.internal.return_file_index(BIDS, ...
+                                             file_info.modality, ...
+                                             file_info.filename);
+  file_info.file_idx = file_idx;
 
 end

+bids/copy_to_derivative.m

@@ -241,7 +241,8 @@ function copy_file(BIDS, derivatives_folder, data_file, unzip_files, force, skip
 
   info = bids.internal.return_file_info(BIDS, data_file);
 
-  if ~isfield(info, 'sub_idx') || ~isfield(info, 'modality')
+  if ~isfield(info, 'sub_idx') || ~isfield(info, 'modality') ||  ...
+      isempty(info.sub_idx) || isempty(info.file_idx)
     % TODO: for we do not copy files in the root directory that have been indexed.
     return
   end

+bids/layout.m

@@ -713,7 +713,7 @@
 
     info_src = bids.internal.return_file_info(BIDS, file_list{iFile});
     % skip files in the root folder with no sub entity
-    if isempty(info_src.sub_idx)
+    if isempty(info_src.sub_idx) || isempty(info_src.file_idx)
       continue
     end
     file = BIDS.subjects(info_src.sub_idx).(info_src.modality)(info_src.file_idx);

tests/tests_private/test_return_file_index.m

@@ -26,3 +26,23 @@ function test_return_file_index_basic()
   assertEqual(file_idx, 2);
 
 end
+
+function test_return_file_index_warning()
+
+  if bids.internal.is_octave
+    return
+  end
+
+  pth_bids_example = get_test_data_dir();
+
+  bids_dir = fullfile(pth_bids_example, 'qmri_tb1tfl');
+
+  unindexable_file = fullfile(bids_dir, 'sub-01_task-foo_events.tsv');
+  content = struct('onset', 1, 'duration', 1, 'trial_type', 'bar');
+  bids.util.tsvwrite(unindexable_file, content);
+
+  assertWarning(@()bids.layout(bids_dir), 'return_file_index:noFileIndex');
+
+  delete(unindexable_file);
+
+end