Changed BidsDataset to not include participants for HED by default

hed/tools/bids/bids_dataset.py

@@ -21,16 +21,16 @@ class BidsDataset:
 
     """
 
-    def __init__(self, root_path, schema=None, tabular_types=None,
-                 exclude_dirs=['sourcedata', 'derivatives', 'code', 'stimuli']):
+    def __init__(self, root_path, schema=None, tabular_types=['events'],
+                 exclude_dirs=['sourcedata', 'derivatives', 'code', 'stimuli', 'phenotype']):
         """ Constructor for a BIDS dataset.
 
         Parameters:
             root_path (str):  Root path of the BIDS dataset.
             schema (HedSchema or HedSchemaGroup):  A schema that overrides the one specified in dataset.
             tabular_types (list or None):  List of strings specifying types of tabular types to include.
                 If None or empty, then ['events'] is assumed.
-            exclude_dirs=['sourcedata', 'derivatives', 'code']:
+            exclude_dirs=['sourcedata', 'derivatives', 'code', 'phenotype']:
 
         """
         self.root_path = os.path.realpath(root_path)
@@ -42,7 +42,7 @@ def __init__(self, root_path, schema=None, tabular_types=None,
             self.schema = load_schema_version(self.dataset_description.get("HEDVersion", None))
 
         self.exclude_dirs = exclude_dirs
-        self.tabular_files = {"participants": BidsFileGroup(root_path, suffix="participants", obj_type="tabular")}
+        self.tabular_files = {}
         if not tabular_types:
             self.tabular_files["events"] = BidsFileGroup(root_path, suffix="events", obj_type="tabular",
                                                          exclude_dirs=exclude_dirs)

tests/tools/bids/test_bids_dataset.py

@@ -20,6 +20,9 @@ def test_constructor(self):
         bids = BidsDataset(Test.root_path)
         self.assertIsInstance(bids, BidsDataset, "BidsDataset should create a valid object from valid dataset")
         parts = bids.get_tabular_group("participants")
+        self.assertFalse(parts)
+        bids = BidsDataset(Test.root_path, tabular_types=['participants', 'events'])
+        parts = bids.get_tabular_group("participants")
         self.assertIsInstance(parts, BidsFileGroup, "BidsDataset participants should be a BidsFileGroup")
         self.assertEqual(len(parts.sidecar_dict), 1, "BidsDataset should have one participants.json file")
         self.assertEqual(len(parts.datafile_dict), 1, "BidsDataset should have one participants.tsv file")
@@ -30,7 +33,7 @@ def test_constructor(self):
         self.assertIsInstance(bids.schema, HedSchema, "BidsDataset schema should be HedSchema")
 
     def test_constructor_libraries(self):
-        bids = BidsDataset(self.library_path)
+        bids = BidsDataset(self.library_path, tabular_types=['participants', 'events'])
         self.assertIsInstance(bids, BidsDataset,
                               "BidsDataset with libraries should create a valid object from valid dataset")
         parts = bids.get_tabular_group("participants")
@@ -48,9 +51,11 @@ def test_constructor_tabular(self):
         self.assertIsInstance(bids, BidsDataset,
                               "BidsDataset with libraries should create a valid object from valid dataset")
         parts = bids.get_tabular_group("participants")
-        self.assertIsInstance(parts, BidsFileGroup, "BidsDataset participants should be a BidsFileGroup")
-        self.assertEqual(len(parts.sidecar_dict), 1, "BidsDataset should have one participants.json file")
-        self.assertEqual(len(parts.datafile_dict), 1, "BidsDataset should have one participants.tsv file")
+        self.assertFalse(parts)
+        chans = bids.get_tabular_group("channels")
+        self.assertIsInstance(chans, BidsFileGroup, "BidsDataset participants should be a BidsFileGroup")
+        self.assertFalse(chans.sidecar_dict)
+        self.assertEqual(len(chans.datafile_dict), 6, "BidsDataset should have one participants.tsv file")
         self.assertIsInstance(bids.dataset_description, dict, "BidsDataset dataset_description should be a dict")
         for group in bids.tabular_files.values():
             self.assertIsInstance(group, BidsFileGroup, "BidsDataset event files should be in a BidsFileGroup")
@@ -87,12 +92,12 @@ def test_with_schema_group(self):
                        "library_schemas/score/hedxml/HED_score_1.0.0.xml"
         library2_url = "https://raw.githubusercontent.com/hed-standard/hed-schemas/main/" + \
                        "library_schemas/testlib/hedxml/HED_testlib_1.0.2.xml"
-        schema_list = [load_schema_version(xml_version=base_version)]
-        schema_list.append(load_schema(library1_url, schema_namespace="sc"))
-        schema_list.append(load_schema(library2_url, schema_namespace="test"))
+        schema_list = [load_schema_version(xml_version=base_version),
+                       load_schema(library1_url, schema_namespace="sc"),
+                       load_schema(library2_url, schema_namespace="test")]
         x = HedSchemaGroup(schema_list)
-        bids = BidsDataset(self.library_path, schema=x)
-        self.assertIsInstance(bids, BidsDataset,
+        bids = BidsDataset(self.library_path, schema=x, tabular_types=["participants"] )
+        self.assertIsInstance(bids, BidsDataset, 
                               "BidsDataset with libraries should create a valid object from valid dataset")
         parts = bids.get_tabular_group("participants")
         self.assertIsInstance(parts, BidsFileGroup, "BidsDataset participants should be a BidsFileGroup")
@@ -105,7 +110,7 @@ def test_with_schema_group(self):
         self.assertIsInstance(bids.schema, HedSchemaGroup,
                               "BidsDataset with libraries should have schema that is a HedSchemaGroup")
         issues = bids.validate(check_for_warnings=True)
-        self.assertTrue(issues, "BidsDataset validate should return issues when check_for_warnings is True")
+        self.assertFalse(issues)
 
     def test_get_summary(self):
         bids1 = BidsDataset(self.root_path)