Update tests, validate script for default load ns

src/pynwb/__init__.py

@@ -227,7 +227,6 @@ def __init__(self, **kwargs):
             load_namespaces = False
 
         if load_namespaces:
-
             tm = get_type_map()
             super().load_namespaces(tm, path, file=file_obj, driver=driver)
             manager = BuildManager(tm)

src/pynwb/validate.py

@@ -156,6 +156,7 @@ def validate(**kwargs):
                         file=sys.stderr,
                     )
         else:
+            io_kwargs.update(load_namespaces=False)
             namespaces_to_validate = [CORE_NAMESPACE]
 
         if namespace is not None:

tests/back_compat/test_read.py

@@ -31,6 +31,16 @@ class TestReadOldVersions(TestCase):
                                "- expected an array of shape '[None]', got non-array data 'one publication'")],
     }
 
+    def get_io(self, path):
+        """Get an NWBHDF5IO object for the given path."""
+        with warnings.catch_warnings():
+            warnings.filterwarnings(
+                "ignore",
+                message=r"Ignoring cached namespace .*",
+                category=UserWarning,
+            )
+            return NWBHDF5IO(str(path), 'r')
+
     def test_read(self):
         """Test reading and validating all NWB files in the same folder as this file.
 
@@ -43,7 +53,7 @@ def test_read(self):
             with self.subTest(file=f.name):
                 with warnings.catch_warnings(record=True) as warnings_on_read:
                     warnings.simplefilter("always")
-                    with NWBHDF5IO(str(f), 'r') as io:
+                    with self.get_io(f) as io:
                         errors = validate(io)
                         io.read()
                         for w in warnings_on_read:
@@ -69,28 +79,28 @@ def test_read(self):
     def test_read_timeseries_no_data(self):
         """Test that a TimeSeries written without data is read with data set to the default value."""
         f = Path(__file__).parent / '1.5.1_timeseries_no_data.nwb'
-        with NWBHDF5IO(str(f), 'r') as io:
+        with self.get_io(f) as io:
             read_nwbfile = io.read()
             np.testing.assert_array_equal(read_nwbfile.acquisition['test_timeseries'].data, TimeSeries.DEFAULT_DATA)
 
     def test_read_timeseries_no_unit(self):
         """Test that an ImageSeries written without unit is read with unit set to the default value."""
         f = Path(__file__).parent / '1.5.1_timeseries_no_unit.nwb'
-        with NWBHDF5IO(str(f), 'r') as io:
+        with self.get_io(f) as io:
             read_nwbfile = io.read()
             self.assertEqual(read_nwbfile.acquisition['test_timeseries'].unit, TimeSeries.DEFAULT_UNIT)
 
     def test_read_imageseries_no_data(self):
         """Test that an ImageSeries written without data is read with data set to the default value."""
         f = Path(__file__).parent / '1.5.1_imageseries_no_data.nwb'
-        with NWBHDF5IO(str(f), 'r') as io:
+        with self.get_io(f) as io:
             read_nwbfile = io.read()
             np.testing.assert_array_equal(read_nwbfile.acquisition['test_imageseries'].data, ImageSeries.DEFAULT_DATA)
 
     def test_read_imageseries_no_unit(self):
         """Test that an ImageSeries written without unit is read with unit set to the default value."""
         f = Path(__file__).parent / '1.5.1_imageseries_no_unit.nwb'
-        with NWBHDF5IO(str(f), 'r') as io:
+        with self.get_io(f) as io:
             read_nwbfile = io.read()
             self.assertEqual(read_nwbfile.acquisition['test_imageseries'].unit, ImageSeries.DEFAULT_UNIT)
 
@@ -100,7 +110,7 @@ def test_read_imageseries_non_external_format(self):
         f = Path(__file__).parent / fbase
         expected_warning = self.expected_warnings[fbase][0]
         with self.assertWarnsWith(UserWarning, expected_warning):
-            with NWBHDF5IO(str(f), 'r') as io:
+            with self.get_io(f) as io:
                 read_nwbfile = io.read()
                 self.assertEqual(read_nwbfile.acquisition['test_imageseries'].format, "tiff")
 
@@ -110,13 +120,13 @@ def test_read_imageseries_nonmatch_starting_frame(self):
         f = Path(__file__).parent / fbase
         expected_warning = self.expected_warnings[fbase][0]
         with self.assertWarnsWith(UserWarning, expected_warning):
-            with NWBHDF5IO(str(f), 'r') as io:
+            with self.get_io(f) as io:
                 read_nwbfile = io.read()
                 np.testing.assert_array_equal(read_nwbfile.acquisition['test_imageseries'].starting_frame, [1, 2, 3])
 
     def test_read_subject_no_age__reference(self):
         """Test that reading a Subject without an age__reference set with NWB schema 2.5.0 sets the value to None"""
         f = Path(__file__).parent / '2.2.0_subject_no_age__reference.nwb'
-        with NWBHDF5IO(str(f), 'r') as io:
+        with self.get_io(f) as io:
             read_nwbfile = io.read()
             self.assertIsNone(read_nwbfile.subject.age__reference)

tests/validation/test_validate.py

@@ -199,64 +199,54 @@ class TestValidateFunction(TestCase):
     # 1.0.3_nwbfile.nwb has cached "core" specification
     # 1.1.2_nwbfile.nwb has cached "core" and "hdmf-common" specificaitions
 
+    def get_io(self, path):
+        """Get an NWBHDF5IO object for the given path, ignoring the warning about ignoring cached namespaces."""
+        with warnings.catch_warnings():
+            warnings.filterwarnings(
+                "ignore",
+                message=r"Ignoring cached namespace .*",
+                category=UserWarning,
+            )
+            return NWBHDF5IO(str(path), 'r')
+
     def test_validate_io_no_cache(self):
         """Test that validating a file with no cached spec against the core namespace succeeds."""
-        with NWBHDF5IO('tests/back_compat/1.0.2_nwbfile.nwb', 'r') as io:
+        with self.get_io('tests/back_compat/1.0.2_nwbfile.nwb') as io:
             errors = validate(io)
             self.assertEqual(errors, [])
 
     def test_validate_io_no_cache_bad_ns(self):
         """Test that validating a file with no cached spec against a specified, unknown namespace fails."""
-        with NWBHDF5IO('tests/back_compat/1.0.2_nwbfile.nwb', 'r') as io:
+        with self.get_io('tests/back_compat/1.0.2_nwbfile.nwb') as io:
             with self.assertRaisesWith(KeyError, "\"'notfound' not a namespace\""):
                 validate(io, 'notfound')
 
     def test_validate_io_cached(self):
         """Test that validating a file with cached spec against its cached namespace succeeds."""
-        with NWBHDF5IO('tests/back_compat/1.1.2_nwbfile.nwb', 'r') as io:
+        with self.get_io('tests/back_compat/1.1.2_nwbfile.nwb') as io:
             errors = validate(io)
             self.assertEqual(errors, [])
 
     def test_validate_io_cached_extension(self):
         """Test that validating a file with cached spec against its cached namespaces succeeds."""
-        with warnings.catch_warnings(record=True):
-            warnings.filterwarnings(
-                "ignore",
-                message=r"Ignoring cached namespace .*",
-                category=UserWarning,
-            )
-            with NWBHDF5IO('tests/back_compat/2.1.0_nwbfile_with_extension.nwb', 'r') as io:
-                errors = validate(io)
-                self.assertEqual(errors, [])
+        with self.get_io('tests/back_compat/2.1.0_nwbfile_with_extension.nwb') as io:
+            errors = validate(io)
+            self.assertEqual(errors, [])
 
     def test_validate_io_cached_extension_pass_ns(self):
         """Test that validating a file with cached extension spec against the extension namespace succeeds."""
-        with warnings.catch_warnings(record=True):
-            warnings.filterwarnings(
-                "ignore",
-                message=r"Ignoring cached namespace .*",
-                category=UserWarning,
-            )
-            with NWBHDF5IO('tests/back_compat/2.1.0_nwbfile_with_extension.nwb', 'r') as io:
-                errors = validate(io, 'ndx-testextension')
-                self.assertEqual(errors, [])
+        with self.get_io('tests/back_compat/2.1.0_nwbfile_with_extension.nwb') as io:
+            errors = validate(io, 'ndx-testextension')
+            self.assertEqual(errors, [])
 
     def test_validate_io_cached_core_with_io(self):
         """
         For back-compatability, test that validating a file with cached extension spec against the core
         namespace succeeds when using the `io` + `namespace` keywords.
         """
-        with warnings.catch_warnings(record=True):
-            warnings.filterwarnings(
-                "ignore",
-                message=r"Ignoring cached namespace .*",
-                category=UserWarning,
-            )
-            with NWBHDF5IO(
-                path='tests/back_compat/2.1.0_nwbfile_with_extension.nwb', mode='r'
-            ) as io:
-                results = validate(io=io, namespace="core")
-                self.assertEqual(results, [])
+        with self.get_io(path='tests/back_compat/2.1.0_nwbfile_with_extension.nwb') as io:
+            results = validate(io=io, namespace="core")
+            self.assertEqual(results, [])
 
     def test_validate_file_cached_extension(self):
         """
@@ -310,13 +300,13 @@ def test_validate_file_cached_no_cache_bad_ns(self):
 
     def test_validate_io_cached_bad_ns(self):
         """Test that validating a file with cached spec against a specified, unknown namespace fails."""
-        with NWBHDF5IO('tests/back_compat/1.1.2_nwbfile.nwb', 'r') as io:
+        with self.get_io('tests/back_compat/1.1.2_nwbfile.nwb') as io:
             with self.assertRaisesWith(KeyError, "\"'notfound' not a namespace\""):
                 validate(io, 'notfound')
 
     def test_validate_io_cached_hdmf_common(self):
         """Test that validating a file with cached spec against the hdmf-common namespace fails."""
-        with NWBHDF5IO('tests/back_compat/1.1.2_nwbfile.nwb', 'r') as io:
+        with self.get_io('tests/back_compat/1.1.2_nwbfile.nwb') as io:
             # TODO this error should not be different from the error when using the validate script above
             msg = "builder must have data type defined with attribute 'data_type'"
             with self.assertRaisesWith(ValueError, msg):