use objects for levels (#630)

bids-standard · Sep 11, 2023 · 64b4613 · 64b4613
1 parent 2efd714
commit 64b4613
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Showing 2 changed files with 105 additions and 88 deletions.
diff --git a/+bids/+util/create_data_dict.m b/+bids/+util/create_data_dict.m
@@ -99,6 +99,12 @@
                            'new_level_name', {{}});
 
   for i = 1:numel(headers)
+    if strcmp(bids.internal.file_utils(tsv_file{1}, ...
+                                       'basename'), ...
+              'participants') && ...
+        strcmp(headers{i}, 'participant_id')
+      continue
+    end
     data_dict.(headers{i}) = set_dict(headers{i}, schema);
     [data_dict, modified_levels] = add_levels_desc(data_dict, ...
                                                    headers{i}, ...
@@ -242,7 +248,8 @@
       warning_modified_level_name(level_name_before, hdr, this_level, verbose);
     end
 
-    json.(hdr).Levels.(this_level) = 'TODO';
+    json.(hdr).Levels.(this_level) = struct('Description', level_name_before, ...
+                                            'TermURL', 'TODO');
 
   end
 

diff --git a/tests/tests_utils/test_create_data_dict.m b/tests/tests_utils/test_create_data_dict.m
@@ -6,6 +6,103 @@
   initTestSuite;
 end
 
+function test_create_data_dict_several_tsv()
+
+  %% WITH SCHEMA
+  % data      time (sec)
+  % eeg_face13      0.387
+  % ds003     0.480
+  % eeg_cbm     0.636
+  % ds101     0.963
+  % genetics_ukbb     0.989
+  % ieeg_visual_multimodal      1.014
+  % ds005     1.060
+  % ds105     1.064
+  % ds102     1.281
+  % ds052     1.293
+  % eeg_rishikesh     1.486
+  % ds008     1.498
+  % ds011     1.654
+  % ds114     1.667
+  % ds109     1.767
+  % ds002     1.855
+  % ds051     1.873
+  % eeg_ds000117      1.900
+  % ds116     1.975
+  % ds007     2.356
+  % ds107     2.386
+  % ds113b      2.554
+  % ds009     2.732
+  % ds210     2.820
+  % ds110     3.263
+  % ds006     3.378
+  % ds108     3.897
+  % ds000117      5.958
+
+  datasets = {'ds000248'; ...
+              'ds000246'; ...
+              'ieeg_visual'; ...
+              'ieeg_epilepsy_ecog'; ...
+              'eeg_matchingpennies'; ...
+              'ds000247'; ...
+              'ieeg_filtered_speech'; ...
+              'eeg_face13'; ...
+              'ds005'; ...
+              'ds105'; ...
+              'ds102'; ...
+              'ds052'; ...
+              'eeg_rishikesh'; ...
+              'ds008'; ...
+              'ds011'; ...
+              'ds114'; ...
+              'ds109'; ...
+              'ds002'; ...
+              'ds051'  };
+
+  schema = bids.Schema();
+  schema.load_schema_metadata = true;
+  schema = schema.load();
+
+  pth_bids_example = get_test_data_dir();
+
+  for i_dataset = 1:numel(datasets)
+
+    dataset = datasets{i_dataset};
+
+    BIDS = bids.layout(fullfile(pth_bids_example, dataset), ...
+                       'index_dependencies', false);
+
+    tasks =  bids.query(BIDS, 'tasks');
+
+    for i_task = 1:numel(tasks)
+
+      tsv_files = bids.query(BIDS, 'data', ...
+                             'task', tasks{i_task}, ...
+                             'suffix', 'events');
+
+      data_dict = bids.util.create_data_dict(tsv_files, ...
+                                             'output', [dataset '_' tasks{i_task} '.json'], ...
+                                             'schema', schema, ...
+                                             'level_limit', 50, ...
+                                             'verbose', false);
+      teardown([dataset '_' tasks{i_task} '.json']);
+
+    end
+
+  end
+
+end
+
+function test_create_data_dict_participants_tsv()
+
+  pth_bids_example = get_test_data_dir();
+
+  tsv_file = fullfile(pth_bids_example, 'ds008', 'participants.tsv');
+  data_dict = bids.util.create_data_dict(tsv_file, 'output', [], 'schema', true);
+  assertEqual(fieldnames(data_dict), {'sex'; 'age'});
+
+end
+
 function test_create_data_dict_basic()
 
   pth_bids_example = get_test_data_dir();
@@ -94,93 +191,6 @@ function test_create_data_dict_schema()
 
 end
 
-function test_create_data_dict_several_tsv()
-
-  %% WITH SCHEMA
-  % data      time (sec)
-  % eeg_face13      0.387
-  % ds003     0.480
-  % eeg_cbm     0.636
-  % ds101     0.963
-  % genetics_ukbb     0.989
-  % ieeg_visual_multimodal      1.014
-  % ds005     1.060
-  % ds105     1.064
-  % ds102     1.281
-  % ds052     1.293
-  % eeg_rishikesh     1.486
-  % ds008     1.498
-  % ds011     1.654
-  % ds114     1.667
-  % ds109     1.767
-  % ds002     1.855
-  % ds051     1.873
-  % eeg_ds000117      1.900
-  % ds116     1.975
-  % ds007     2.356
-  % ds107     2.386
-  % ds113b      2.554
-  % ds009     2.732
-  % ds210     2.820
-  % ds110     3.263
-  % ds006     3.378
-  % ds108     3.897
-  % ds000117      5.958
-
-  datasets = {'ds000248'; ...
-              'ds000246'; ...
-              'ieeg_visual'; ...
-              'ieeg_epilepsy_ecog'; ...
-              'eeg_matchingpennies'; ...
-              'ds000247'; ...
-              'ieeg_filtered_speech'; ...
-              'eeg_face13'; ...
-              'ds005'; ...
-              'ds105'; ...
-              'ds102'; ...
-              'ds052'; ...
-              'eeg_rishikesh'; ...
-              'ds008'; ...
-              'ds011'; ...
-              'ds114'; ...
-              'ds109'; ...
-              'ds002'; ...
-              'ds051'  };
-
-  schema = bids.Schema();
-  schema.load_schema_metadata = true;
-  schema = schema.load();
-
-  pth_bids_example = get_test_data_dir();
-
-  for i_dataset = 1:numel(datasets)
-
-    dataset = datasets{i_dataset};
-
-    BIDS = bids.layout(fullfile(pth_bids_example, dataset), ...
-                       'index_dependencies', false);
-
-    tasks =  bids.query(BIDS, 'tasks');
-
-    for i_task = 1:numel(tasks)
-
-      tsv_files = bids.query(BIDS, 'data', ...
-                             'task', tasks{i_task}, ...
-                             'suffix', 'events');
-
-      data_dict = bids.util.create_data_dict(tsv_files, ...
-                                             'output', [dataset '_' tasks{i_task} '.json'], ...
-                                             'schema', schema, ...
-                                             'level_limit', 50, ...
-                                             'verbose', false);
-      teardown([dataset '_' tasks{i_task} '.json']);
-
-    end
-
-  end
-
-end
-
 function teardown(files)
   if nargin < 1
     files = [];