Pass parent properties to extended dataset/attribute

src/hdmf/spec/spec.py

@@ -376,6 +376,24 @@ def resolve_spec(self, **kwargs):
         for attribute in inc_spec.attributes:
             self.__new_attributes.discard(attribute)
             if attribute.name in self.__attributes:
+                # copy over the fields 'shape' and 'dims' of the parent attribute to this spec's attribute
+                # NOTE: because the default value for the 'required' field is True, it is not possible to know whether
+                # the 'required' field was explicitly set. thus, 'required' defaults to True no matter what the parent
+                # specification defines.
+                # NOTE: the value and default value of a parent attribute are also not copied to the child spec
+                my_attribute = self.get_attribute(attribute.name)
+                if attribute.shape is not None:
+                    if my_attribute.shape is None:
+                        my_attribute['shape'] = attribute.shape
+                    else:
+                        # TODO: test whether child shape is compatible with parent shape
+                        pass
+                if attribute.dims is not None:
+                    if my_attribute.dims is None:
+                        my_attribute['dims'] = attribute.dims
+                    else:
+                        # TODO: test whether child dims is compatible with parent dims
+                        pass
                 self.__overridden_attributes.add(attribute.name)
                 continue
             self.set_attribute(attribute)
@@ -695,6 +713,30 @@ def __is_sub_dtype(cls, orig, new):
     @docval({'name': 'inc_spec', 'type': 'DatasetSpec', 'doc': 'the data type this specification represents'})
     def resolve_spec(self, **kwargs):
         inc_spec = getargs('inc_spec', kwargs)
+        # copy over fields of the parent dataset to this spec
+        # NOTE: because the default value for the 'quantity' field is 1, it is not possible to know whether
+        # the 'quantity' field was explicitly set. thus, 'quantity' defaults to 1 no matter what the parent
+        # specification defines.
+        # NOTE: the default value of a parent attribute is also not copied to the child spec
+        if inc_spec.dtype is not None:
+            if self.dtype is None:
+                self['dtype'] = inc_spec.dtype
+            else:
+                # TODO: test whether child dtype is compatible with parent dtype
+                # e.g., if parent dtype is int, child dtype cannot be text
+                pass
+        if inc_spec.shape is not None:
+            if self.shape is None:
+                self['shape'] = inc_spec.shape
+            elif inc_spec.shape is not None:
+                # TODO: test whether child shape is compatible with parent shape
+                pass
+        if inc_spec.dims is not None:
+            if self.dims is None:
+                self['dims'] = inc_spec.dims
+            elif inc_spec.dims is not None:
+                # TODO: test whether child dims is compatible with parent dims
+                pass
         if isinstance(self.dtype, list):
             # merge the new types
             inc_dtype = inc_spec.dtype

tests/unit/spec_tests/test_load_namespace.py

@@ -223,3 +223,192 @@ def test_get_namespace_missing_version(self):
         namespace['version'] = None  # work around lack of setter to remove version key
 
         self.assertEqual(namespace.version, SpecNamespace.UNVERSIONED)
+
+
+class TestLoadSpecInheritProperties(TestCase):
+    NS_NAME = 'test_ns'
+
+    def setUp(self):
+        self.specs_path = 'test_load_spec_inherit.specs.yaml'
+        self.namespace_path = 'test_load_spec_inherit.namespace.yaml'
+
+        ns_dict = {
+            'doc': 'a test namespace',
+            'name': self.NS_NAME,
+            'schema': [
+                {'source': self.specs_path}
+            ],
+            'version': '0.1.0'
+        }
+        self.namespace = SpecNamespace.build_namespace(**ns_dict)
+        to_dump = {'namespaces': [self.namespace]}
+        with open(self.namespace_path, 'w') as tmp:
+            yaml.safe_dump(json.loads(json.dumps(to_dump)), tmp, default_flow_style=False)
+        self.ns_catalog = NamespaceCatalog()
+
+    def tearDown(self):
+        if os.path.exists(self.namespace_path):
+            os.remove(self.namespace_path)
+        if os.path.exists(self.specs_path):
+            os.remove(self.specs_path)
+
+    def test_inherited_shape(self):
+        """Test that an extended dataset/attribute inherits the dims and shape of the original dataset/attribute"""
+        attributes = [
+            AttributeSpec(
+                'attribute1',
+                'my first attribute',
+                'text',
+                dims=['my_dims'],
+                shape=[None]
+            )
+        ]
+        datasets = [
+            DatasetSpec(
+                'my first dataset',
+                'int',
+                name='dataset1',
+                dims=['my_dims'],
+                shape=[None]
+            )
+        ]
+        group_spec = GroupSpec(
+            'A test group',
+            name='root_constructor_datatype',
+            datasets=datasets,
+            attributes=attributes,
+            data_type_def='MyGroup'
+        )
+
+        # same name, same dtype, change docstring, omit dims and shape specifications
+        ext_attributes = [
+            AttributeSpec(
+                'attribute1',
+                'my first attribute extension',
+                'text',
+            )
+        ]
+        # same name, same dtype, change docstring, omit dims and shape specifications
+        ext_datasets = [
+            DatasetSpec(
+                'my first dataset extension',
+                'int',
+                name='dataset1'
+            )
+        ]
+        ext_group_spec = GroupSpec(
+            'A test group extension',
+            name='root_constructor_datatype',
+            datasets=ext_datasets,
+            attributes=ext_attributes,
+            data_type_inc='MyGroup',
+            data_type_def='MyExtGroup'
+        )
+        to_dump = {'groups': [group_spec, ext_group_spec]}
+        with open(self.specs_path, 'w') as tmp:
+            yaml.safe_dump(json.loads(json.dumps(to_dump)), tmp, default_flow_style=False)
+
+        self.ns_catalog.load_namespaces(self.namespace_path)
+
+        # first test that shape of the original dataset/attribute is set correctly
+        read_group_spec = self.ns_catalog.get_spec(self.NS_NAME, 'MyGroup')
+        read_dset_spec = read_group_spec.datasets[0]
+        read_attr_spec = read_group_spec.attributes[0]
+        self.assertEqual(read_dset_spec.dims, ['my_dims'])
+        self.assertEqual(read_attr_spec.dims, ['my_dims'])
+        self.assertEqual(read_dset_spec.shape, [None])
+        self.assertEqual(read_attr_spec.shape, [None])
+
+        # then test that shape of the extended dataset/attribute is set correctly
+        read_group_spec = self.ns_catalog.get_spec(self.NS_NAME, 'MyExtGroup')
+        read_dset_spec = read_group_spec.datasets[0]
+        read_attr_spec = read_group_spec.attributes[0]
+        self.assertEqual(read_dset_spec.dims, ['my_dims'])
+        self.assertEqual(read_attr_spec.dims, ['my_dims'])
+        self.assertEqual(read_dset_spec.shape, [None])
+        self.assertEqual(read_attr_spec.shape, [None])
+
+    def test_inherited_dtype(self):
+        """Test that an extended dataset inherits the dtype of the original dataset"""
+        # NOTE: we do not need to test whether dtype of attributes are extended because attribute dtype is required
+        datasets = [
+            DatasetSpec(
+                'my first dataset',
+                'int',
+                name='dataset1',
+            )
+        ]
+        group_spec = GroupSpec(
+            'A test group',
+            name='root_constructor_datatype',
+            datasets=datasets,
+            data_type_def='MyGroup'
+        )
+
+        # same name, omit dtype, change docstring
+        ext_datasets = [
+            DatasetSpec(
+                'my first dataset extension',
+                name='dataset1'
+            )
+        ]
+        ext_group_spec = GroupSpec(
+            'A test group extension',
+            name='root_constructor_datatype',
+            datasets=ext_datasets,
+            data_type_inc='MyGroup',
+            data_type_def='MyExtGroup'
+        )
+        to_dump = {'groups': [group_spec, ext_group_spec]}
+        with open(self.specs_path, 'w') as tmp:
+            yaml.safe_dump(json.loads(json.dumps(to_dump)), tmp, default_flow_style=False)
+
+        self.ns_catalog.load_namespaces(self.namespace_path)
+
+        # first test that dtype of the original dataset is set correctly
+        read_group_spec = self.ns_catalog.get_spec(self.NS_NAME, 'MyGroup')
+        read_dset_spec = read_group_spec.datasets[0]
+        self.assertEqual(read_dset_spec.dtype, 'int')
+
+        # then test that dtype of the extended dataset is set correctly
+        read_group_spec = self.ns_catalog.get_spec(self.NS_NAME, 'MyExtGroup')
+        read_dset_spec = read_group_spec.datasets[0]
+        self.assertEqual(read_dset_spec.dtype, 'int')
+
+    def test_inherited_incompatible_dtype(self):
+        """Test that an extended dataset cannot change the dtype of the original dataset to an incompatible dtype"""
+        datasets = [
+            DatasetSpec(
+                'my first dataset',
+                'int',
+                name='dataset1',
+            )
+        ]
+        group_spec = GroupSpec(
+            'A test group',
+            name='root_constructor_datatype',
+            datasets=datasets,
+            data_type_def='MyGroup'
+        )
+
+        # same name, change dtype, change docstring
+        ext_datasets = [
+            DatasetSpec(
+                'my first dataset extension',
+                'text',
+                name='dataset1'
+            )
+        ]
+        ext_group_spec = GroupSpec(
+            'A test group extension',
+            name='root_constructor_datatype',
+            datasets=ext_datasets,
+            data_type_inc='MyGroup',
+            data_type_def='MyExtGroup'
+        )
+        to_dump = {'groups': [group_spec, ext_group_spec]}
+        with open(self.specs_path, 'w') as tmp:
+            yaml.safe_dump(json.loads(json.dumps(to_dump)), tmp, default_flow_style=False)
+
+        # TODO this test should fail but currently succeeds
+        self.ns_catalog.load_namespaces(self.namespace_path)