create valid participants and sessions tsv during dataset init

bids-standard · Apr 7, 2024 · 67d014f · 67d014f
1 parent 6e2a3fb
commit 67d014f
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Showing 5 changed files with 68 additions and 52 deletions.
diff --git a/+bids/+util/create_participants_tsv.m b/+bids/+util/create_participants_tsv.m
@@ -64,12 +64,12 @@
   % in case the query returns empty in case no file was indexed
   if isempty(subjects_list) && ~use_schema
     subjects_list = cellstr(bids.internal.file_utils('List', layout.pth, 'dir', '^sub-.*$'));
+    output_structure = struct('participant_id', {subjects_list});
+  else
+    subjects_list = [repmat('sub-', numel(subjects_list), 1), char(subjects_list')];
+    output_structure = struct('participant_id', subjects_list);
   end
 
-  subjects_list = [repmat('sub-', numel(subjects_list), 1), char(subjects_list')];
-
-  output_structure = struct('participant_id', subjects_list);
-
   output_filename = fullfile(layout.pth, 'participants.tsv');
 
   bids.util.tsvwrite(fullfile(layout.pth, 'participants.tsv'), output_structure);

diff --git a/+bids/+util/create_sessions_tsv.m b/+bids/+util/create_sessions_tsv.m
@@ -89,7 +89,7 @@
                                                        fullfile(layout.pth, ...
                                                                 ['sub-' subjects_list{i_sub}]), ...
                                                        'dir', ...
-                                                       '^sub-.*$'));
+                                                       '^ses-.*$'));
       sessions_list = regexprep(sessions_list, 'ses-', '');
     end
 

diff --git a/tests/test_bids_init.m b/tests/test_bids_init.m
@@ -11,17 +11,16 @@ function test_basic()
 
   set_test_cfg();
 
-  dataset_description = fullfile(pwd, 'dummy_ds', 'dataset_description.json');
+  output_dir = fullfile(temp_dir(), 'dummy_ds');
 
-  bids.init('dummy_ds');
-  assertEqual(exist(fullfile(pwd, 'dummy_ds'), 'dir'), 7);
+  bids.init(output_dir);
+  assertEqual(exist(output_dir, 'dir'), 7);
 
+  dataset_description = fullfile(output_dir, 'dataset_description.json');
   assertEqual(exist(dataset_description, 'file'), 2);
   ds_metadata = bids.util.jsondecode(dataset_description);
   assertEqual(ds_metadata.DatasetType, 'raw');
 
-  clean_up();
-
 end
 
 function test_no_folder_smoke_test()
@@ -30,102 +29,116 @@ function test_no_folder_smoke_test()
 
   bids.init('dummy_ds', 'folders', struct(), 'is_derivative', true);
 
-  clean_up();
+end
+
+function test_valid_tsv()
+  set_test_cfg();
+
+  output_dir = fullfile(temp_dir(), 'dummy_ds');
 
+  folders.subjects = 'a';
+  folders.sessions = '1';
+  folders.modalities = 'beh';
+
+  bids.init(output_dir, 'folders', folders);
+  assertEqual(exist(fullfile(output_dir, 'sub-a', 'ses-1', 'beh'), 'dir'), 7);
+  assertEqual(exist(fullfile(output_dir, 'sub-a', 'sub-a_sessions.tsv'), 'file'), 2);
+
+  participants = bids.util.tsvread(fullfile(output_dir, 'participants.tsv'));
+  assertEqual(participants.participant_id, {'sub-a'});
+
+  sessions = bids.util.tsvread(fullfile(output_dir, 'sub-a', 'sub-a_sessions.tsv'));
+  assertEqual(sessions.session_id, {'ses-1'});
 end
 
 function test_folders()
 
   set_test_cfg();
 
+  output_dir = fullfile(temp_dir(), 'dummy_ds');
+
   folders.subjects = {'01', '02'};
   folders.sessions = {'test', 'retest', ''};
   folders.modalities = {'anat', 'func', 'fizz', ''};
 
-  bids.init('dummy_ds', 'folders', folders);
-  assertEqual(exist(fullfile(pwd, 'dummy_ds', 'sub-02', 'ses-retest', 'func'), 'dir'), 7);
-  assertEqual(exist(fullfile(pwd, 'dummy_ds', 'sub-02', 'sub-02_sessions.tsv'), 'file'), 2);
+  bids.init(output_dir, 'folders', folders);
+  assertEqual(exist(fullfile(output_dir, 'sub-02', 'ses-retest', 'func'), 'dir'), 7);
+  assertEqual(exist(fullfile(output_dir, 'sub-02', 'sub-02_sessions.tsv'), 'file'), 2);
 
-  clean_up();
+  sessions = bids.util.tsvread(fullfile(output_dir, 'sub-01', 'sub-01_sessions.tsv'));
+  assertEqual(sessions.session_id, {'ses-retest'; 'ses-test'});
 
 end
 
 function test_folders_no_session()
 
   set_test_cfg();
 
+  output_dir = fullfile(temp_dir(), 'dummy_ds');
+
   folders.subjects = {'01', '02'};
   folders.modalities = {'anat', 'func'};
 
-  bids.init('dummy_ds', 'folders', folders);
-  assertEqual(exist(fullfile(pwd, 'dummy_ds', 'sub-02', 'func'), 'dir'), 7);
-  assertEqual(exist(fullfile(pwd, 'dummy_ds', 'sub-02', 'sub-02_sessions.tsv'), 'file'), 0);
+  bids.init(output_dir, 'folders', folders);
+  assertEqual(exist(fullfile(output_dir, 'sub-02', 'func'), 'dir'), 7);
+  assertEqual(exist(fullfile(output_dir, 'sub-02', 'sub-02_sessions.tsv'), 'file'), 0);
 
-  clean_up();
+  participants = bids.util.tsvread(fullfile(output_dir, 'participants.tsv'));
+  assertEqual(participants.participant_id, {'sub-01'; 'sub-02'});
 
 end
 
 function test_validate()
 
   set_test_cfg();
 
+  output_dir = fullfile(temp_dir(), 'dummy_ds');
+
   folders.subjects = {'01-bla', '02_foo'};
   folders.sessions = {'te-st', 'ret$est'};
   folders.modalities = {'a#nat', 'fu*nc', '45^['};
 
-  assertExceptionThrown(@() bids.init('dummy_ds', 'folders', folders), ...
+  assertExceptionThrown(@() bids.init(output_dir, 'folders', folders), ...
                         'init:nonAlphaNumFodler');
 
   folders.subjects = {'01', '02'};
   folders.sessions = {'te-st', 'ret$est'};
   folders.modalities = {'a#nat', 'fu*nc', '45^['};
 
-  assertExceptionThrown(@() bids.init('dummy_ds', 'folders', folders), ...
+  assertExceptionThrown(@() bids.init(output_dir, 'folders', folders), ...
                         'init:nonAlphaNumFodler');
 
   folders.subjects = {'01', '02'};
   folders.sessions = {'test', 'retest'};
   folders.modalities = {'a#nat', 'fu*nc', '45^['};
 
-  assertExceptionThrown(@() bids.init('dummy_ds', 'folders', folders), ...
+  assertExceptionThrown(@() bids.init(output_dir, 'folders', folders), ...
                         'init:nonAlphaNumFodler');
 
-  clean_up();
-
 end
 
 function test_derivatives()
 
   set_test_cfg();
 
+  output_dir = fullfile(temp_dir(), 'dummy_ds');
+
   folders.subjects = {'01', '02'};
   folders.sessions = {'test', 'retest'};
   folders.modalities = {'anat', 'func'};
 
-  dataset_description = fullfile(pwd, 'dummy_ds', 'dataset_description.json');
+  dataset_description = fullfile(output_dir, 'dataset_description.json');
 
-  bids.init('dummy_ds', 'folders', folders, 'is_derivative', true);
-  assertEqual(exist(fullfile(pwd, 'dummy_ds', 'sub-02', 'ses-retest', 'func'), 'dir'), 7);
+  bids.init(output_dir, 'folders', folders, 'is_derivative', true);
+  assertEqual(exist(fullfile(output_dir, 'sub-02', 'ses-retest', 'func'), 'dir'), 7);
 
   ds_metadata = bids.util.jsondecode(dataset_description);
   assertEqual(ds_metadata.DatasetType, 'derivative');
 
   % smoke test
-  bids.init('dummy_ds',  ...
+  bids.init(output_dir,  ...
             'folders', folders, ...
             'is_derivative', true, ...
             'is_datalad_ds', true);
 
-  clean_up();
-
-end
-
-function clean_up()
-
-  pause(0.5);
-
-  if isdir(fullfile(pwd, 'dummy_ds'))
-    rmdir(fullfile(pwd, 'dummy_ds'), 's');
-  end
-
 end
diff --git a/tests/tests_utils/test_create_participants_tsv.m b/tests/tests_utils/test_create_participants_tsv.m
@@ -8,12 +8,17 @@
 
 function test_create_participants_tsv_basic()
 
-  bids_path = fullfile(get_test_data_dir(), 'asl001');
+  bids_path = temp_dir();
+
+  copyfile(fullfile(get_test_data_dir(), 'asl001'), bids_path);
 
   validate_dataset(bids_path);
 
   output_filename = bids.util.create_participants_tsv(bids_path, 'verbose', false);
 
+  participants = bids.util.tsvread(output_filename);
+  assertEqual(participants.participant_id, {'sub-Sub103'});
+
   validate_dataset(bids_path);
 
   delete(output_filename);
@@ -24,7 +29,9 @@ function test_create_participants_tsv_already_exist()
 
   skip_if_octave('mixed-string-concat warning thrown');
 
-  bids_path = fullfile(get_test_data_dir(), 'ds210');
+  bids_path = temp_dir();
+
+  copyfile(fullfile(get_test_data_dir(), 'ds210'), bids_path);
 
   output_filename = bids.util.create_participants_tsv(bids_path);
 

diff --git a/tests/tests_utils/test_create_sessions_tsv.m b/tests/tests_utils/test_create_sessions_tsv.m
@@ -8,7 +8,9 @@
 
 function test_create_sessions_tsv_no_session()
 
-  bids_path = fullfile(get_test_data_dir(), 'ds210');
+  bids_path = temp_dir();
+
+  copyfile(fullfile(get_test_data_dir(), 'ds210'), bids_path);
 
   validate_dataset(bids_path);
 
@@ -27,7 +29,9 @@ function test_create_sessions_tsv_no_session()
 
 function test_create_sessions_tsv_basic()
 
-  bids_path = fullfile(get_test_data_dir(), 'ieeg_epilepsy');
+  bids_path = temp_dir();
+
+  copyfile(fullfile(get_test_data_dir(), 'ieeg_epilepsy'), bids_path);
 
   validate_dataset(bids_path);
 
@@ -41,12 +45,4 @@ function test_create_sessions_tsv_basic()
 
   validate_dataset(bids_path);
 
-  teardown(bids_path, output_filenames);
-
-end
-
-function teardown(pth, filelist)
-  for i = 1:numel(filelist)
-    delete(fullfile(pth, filelist{i}));
-  end
 end