Merge pull request #634 from VisLab/dev_refactor

Updated bids tests
hed-standard · Mar 23, 2023 · f2455d8 · f2455d8
2 parents a1e61df + bc5c949
commit f2455d8
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Showing 5 changed files with 13 additions and 22 deletions.
diff --git a/hed/tools/bids/bids_dataset.py b/hed/tools/bids/bids_dataset.py
@@ -79,18 +79,14 @@ def validate(self, types=None, check_for_warnings=True):
             list:  List of issues encountered during validation. Each issue is a dictionary.
 
         """
-        validator = HedValidator(hed_schema=self.schema)
-        error_handler = ErrorHandler()
+
         if not types:
             types = list(self.tabular_files.keys())
         issues = []
         for tab_type in types:
             files = self.tabular_files[tab_type]
-            issues += files.validate_sidecars(self.schema,
-                                              check_for_warnings=check_for_warnings, error_handler=error_handler)
-            issues += files.validate_datafiles(self.schema,
-                                               check_for_warnings=check_for_warnings,
-                                               error_handler=error_handler)
+            issues += files.validate_sidecars(self.schema, check_for_warnings=check_for_warnings)
+            issues += files.validate_datafiles(self.schema, check_for_warnings=check_for_warnings)
         return issues
 
     def get_summary(self):

diff --git a/hed/tools/bids/bids_file_group.py b/hed/tools/bids/bids_file_group.py
@@ -132,7 +132,8 @@ def validate_sidecars(self, hed_schema, extra_def_dicts=None, check_for_warnings
 
         for sidecar in self.sidecar_dict.values():
             name = os.path.basename(sidecar.file_path)
-            issues += validator.validate(extra_def_dicts=extra_def_dicts, name=name, error_handler=error_handler)
+            issues += validator.validate(sidecar.contents, extra_def_dicts=extra_def_dicts, name=name, 
+                                         error_handler=error_handler)
         return issues
 
     def validate_datafiles(self, hed_schema, extra_def_dicts=None, check_for_warnings=True, keep_contents=False):
@@ -154,7 +155,7 @@ def validate_datafiles(self, hed_schema, extra_def_dicts=None, check_for_warning
         for data_obj in self.datafile_dict.values():
             data_obj.set_contents(overwrite=False)
             name = os.path.basename(data_obj.file_path)
-            issues += data_obj.contents.validate(data_obj.contents, extra_def_dicts=None, name=name, 
+            issues += data_obj.contents.validate(hed_schema, extra_def_dicts=None, name=name, 
                                                  error_handler=error_handler)
             if not keep_contents:
                 data_obj.clear_contents()

diff --git a/tests/tools/analysis/test_event_manager.py b/tests/tools/analysis/test_event_manager.py
@@ -36,7 +36,6 @@ def test_constructor(self):
                 self.assertEqual(event.start_time, manager1.data.dataframe.loc[index, "onset"])
                 if not event.end_time:
                     self.assertEqual(event.end_index, len(manager1.data.dataframe))
-        print("to here")
 
     # def test_constructor(self):
     #     with self.assertRaises(ValueError) as cont:

diff --git a/tests/tools/bids/test_bids_dataset.py b/tests/tools/bids/test_bids_dataset.py
@@ -68,21 +68,18 @@ def test_validator(self):
         self.assertTrue(issues, "BidsDataset validate should return issues when the default check_for_warnings is used")
         issues = bids.validate(check_for_warnings=True)
         self.assertTrue(issues, "BidsDataset validate should return issues when check_for_warnings is True")
-        # ToDO 
-        # issues = bids.validate(check_for_warnings=False)
-        # self.assertFalse(issues, "BidsDataset validate should return no issues when check_for_warnings is False")
+        issues = bids.validate(check_for_warnings=False)
+        self.assertFalse(issues, "BidsDataset validate should return no issues when check_for_warnings is False")
 
     def test_validator_libraries(self):
         bids = BidsDataset(self.library_path)
-        # ToDO check_for_warnings
-        # issues = bids.validate(check_for_warnings=False)
-        # self.assertFalse(issues, "BidsDataset with libraries should validate")
+        issues = bids.validate(check_for_warnings=False)
+        self.assertFalse(issues, "BidsDataset with libraries should validate")
 
     def test_validator_types(self):
         bids = BidsDataset(self.root_path, tabular_types=None)
-        # ToDO: check_for_warnings
-        # issues = bids.validate(check_for_warnings=False)
-        # self.assertFalse(issues, "BidsDataset with participants and events validates")
+        issues = bids.validate(check_for_warnings=False)
+        self.assertFalse(issues, "BidsDataset with participants and events validates")
 
     def test_with_schema_group(self):
         base_version = '8.0.0'

diff --git a/tests/tools/remodeling/cli/test_run_remodel.py b/tests/tools/remodeling/cli/test_run_remodel.py
@@ -97,9 +97,7 @@ def test_main_bids_no_sidecar_with_hed(self):
         os.remove(self.sidecar_path)
         with patch('sys.stdout', new=io.StringIO()) as fp:
             main(arg_list)
-            a = fp.getvalue()
-            print("to here")
-            #self.assertFalse(fp.getvalue())
+            self.assertFalse(fp.getvalue())
 
     def test_main_direct_no_sidecar(self):
         arg_list = [self.data_root, self.model_path, '-x', 'derivatives', 'stimuli']