[ENH] allow to query directly for tsv content (#555)

* silence some warnings * test error
bids-standard · Apr 28, 2023 · 786b562 · 786b562
1 parent f423ea6
commit 786b562
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Showing 4 changed files with 65 additions and 5 deletions.
diff --git a/+bids/File.m b/+bids/File.m
@@ -752,7 +752,9 @@ function validate_string(obj, str, type, pattern)
       if ~isempty(str)
         res = regexp(str, pattern, 'once');
         if isempty(res)
-          msg = sprintf('%s do not satisfy pattern %s', str, pattern);
+          msg = sprintf('%s do not satisfy pattern %s', ...
+                        str, ...
+                        strrep(pattern, '\', '\\'));
           obj.bids_file_error(['Invalid' type], msg);
         end
       end

diff --git a/+bids/query.m b/+bids/query.m
@@ -25,6 +25,7 @@
   % - ``'dependencies'``
   % - ``'extensions'``
   % - ``'prefixes'``
+  % - ``'tsv_content'``
   %
   % And any of the BIDS entities:
   %
@@ -163,7 +164,8 @@
                           'metafiles', ...
                           'dependencies', ...
                           'extensions', ...
-                          'prefixes'}, ...
+                          'prefixes', ...
+                          'tsv_content'}, ...
                       valid_entity_queries());
 
   if ~any(strcmp(query, VALID_QUERIES))
@@ -173,8 +175,6 @@
     bids.internal.error_handling(mfilename(), 'unknownQuery', msg, false, true);
   end
 
-  %   bids_entities = schema_entities();
-
   BIDS = bids.layout(BIDS);
 
   options = parse_query(varargin);
@@ -196,7 +196,11 @@
   % Get optional target option for metadata query
   [target, options] = get_target(query, options);
 
-  result = perform_query(BIDS, query, options, subjects, modalities, target);
+  if strcmp(query, 'tsv_content')
+    result = perform_query(BIDS, 'data', options, subjects, modalities, target);
+  else
+    result = perform_query(BIDS, query, options, subjects, modalities, target);
+  end
 
   %% Postprocessing output variable
   switch query
@@ -223,6 +227,25 @@
     case cat(2, {'suffixes',  'suffixes', 'extensions', 'prefixes'}, valid_entity_queries())
       result = unique(result);
       result(cellfun('isempty', result)) = [];
+
+    case 'tsv_content'
+      if isempty(result)
+        return
+      end
+      extensions = bids.internal.file_utils(result, 'ext');
+      if numel(unique(extensions)) > 1 || ~strcmp(unique(extensions), 'tsv')
+        msg = sprintf(['Queries for ''tsv_content'' must be done only on tsv files.\n', ...
+                       'Your query returned: %s'], ...
+                      bids.internal.create_unordered_list(result));
+        bids.internal.error_handling(mfilename(), 'notJustTsvFiles', msg, false);
+        return
+      end
+      tmp = {};
+      for i_tsv_file = 1:numel(result)
+        tmp{i_tsv_file} = bids.util.tsvread(result{i_tsv_file});
+      end
+      result = tmp;
+
   end
 
 end

diff --git a/tests/tests_query/test_bids_query.m b/tests/tests_query/test_bids_query.m
@@ -258,6 +258,39 @@ function test_query_modalities()
 
 end
 
+function test_query_tsv_content()
+
+  pth_bids_example = get_test_data_dir();
+
+  BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_ds003645s_hed_inheritance'));
+
+  tsv_content = bids.query(BIDS, 'tsv_content', 'suffix', 'events');
+
+  assertEqual(numel(tsv_content), 3);
+  assertEqual(fieldnames(tsv_content{1}), ...
+              {'onset'; ...
+               'duration'; ...
+               'sample'; ...
+               'event_type'; ...
+               'face_type'; ...
+               'rep_status'; ...
+               'trial'; ...
+               'rep_lag'; ...
+               'value'; ...
+               'stim_file'});
+
+end
+
+function test_query_tsv_content_error()
+
+  pth_bids_example = get_test_data_dir();
+
+  BIDS = bids.layout(fullfile(pth_bids_example, 'qmri_tb1tfl'));
+  assertExceptionThrown(@()bids.query(BIDS, 'tsv_content', 'extension', '.nii.gz'), ...
+                        'query:notJustTsvFiles');
+
+end
+
 function test_query_sessions()
 
   pth_bids_example = get_test_data_dir();

diff --git a/tests/tests_query/test_bids_query_eeg.m b/tests/tests_query/test_bids_query_eeg.m
@@ -22,6 +22,8 @@ function test_bids_query_eeg_basic()
   suffixes = {'channels', 'eeg', 'electrodes', 'events'};
   assertEqual(bids.query(BIDS, 'suffixes'), suffixes);
 
+  extension = bids.query(BIDS, 'data', 'extension', '.tsv');
+
   %%
   BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_ds000117'));