Revert breaking change of TypeMap.get_container_cls function header (…

…#590)

* Revert breaking change of get_container_cls function header

* Update changelog

* Fix flake8

CHANGELOG.md

@@ -1,5 +1,11 @@
 # HDMF Changelog
 
+## HDMF 2.5.1 (April 23, 2021)
+
+### Bug fix
+- Revert breaking change in `TypeMap.get_container_cls`. While this function is returned to its original behavior,
+  it will be modified at the next major release. Please use the new `TypeMap.get_dt_container_cls` instead. @rly (#590)
+
 ## HDMF 2.5.0 (April 22, 2021)
 
 ### New features

src/hdmf/build/classgenerator.py

@@ -147,7 +147,7 @@ def _get_container_type(cls, type_name, type_map):
         """Search all namespaces for the container class associated with the given data type.
         Raises TypeDoesNotExistError if type is not found in any namespace.
         """
-        container_type = type_map.get_container_cls(type_name)
+        container_type = type_map.get_dt_container_cls(type_name)
         if container_type is None:  # pragma: no cover
             # this should never happen after hdmf#322
             raise TypeDoesNotExistError("Type '%s' does not exist." % type_name)

src/hdmf/build/manager.py

@@ -475,30 +475,46 @@ def load_namespaces(self, **kwargs):
         for new_ns, ns_deps in deps.items():
             for src_ns, types in ns_deps.items():
                 for dt in types:
-                    container_cls = self.get_container_cls(dt, src_ns, autogen=False)
+                    container_cls = self.get_dt_container_cls(dt, src_ns, autogen=False)
                     if container_cls is None:
                         container_cls = TypeSource(src_ns, dt)
                     self.register_container_type(new_ns, dt, container_cls)
         return deps
 
+    @docval({"name": "namespace", "type": str, "doc": "the namespace containing the data_type"},
+            {"name": "data_type", "type": str, "doc": "the data type to create a AbstractContainer class for"},
+            {"name": "autogen", "type": bool, "doc": "autogenerate class if one does not exist", "default": True},
+            returns='the class for the given namespace and data_type', rtype=type)
+    def get_container_cls(self, **kwargs):
+        """Get the container class from data type specification.
+        If no class has been associated with the ``data_type`` from ``namespace``, a class will be dynamically
+        created and returned.
+        """
+        # NOTE: this internally used function get_container_cls will be removed in favor of get_dt_container_cls
+        namespace, data_type, autogen = getargs('namespace', 'data_type', 'autogen', kwargs)
+        return self.get_dt_container_cls(data_type, namespace, autogen)
+
     @docval({"name": "data_type", "type": str, "doc": "the data type to create a AbstractContainer class for"},
             {"name": "namespace", "type": str, "doc": "the namespace containing the data_type", "default": None},
             {"name": "autogen", "type": bool, "doc": "autogenerate class if one does not exist", "default": True},
             returns='the class for the given namespace and data_type', rtype=type)
-    def get_container_cls(self, **kwargs):
+    def get_dt_container_cls(self, **kwargs):
         """Get the container class from data type specification.
         If no class has been associated with the ``data_type`` from ``namespace``, a class will be dynamically
         created and returned.
+
+        Replaces get_container_cls but namespace is optional. If namespace is unknown, it will be looked up from
+        all namespaces.
         """
         namespace, data_type, autogen = getargs('namespace', 'data_type', 'autogen', kwargs)
 
         # namespace is unknown, so look it up
         if namespace is None:
-            for key, val in self.__container_types.items():
+            for ns_key, ns_data_types in self.__container_types.items():
                 # NOTE that the type_name may appear in multiple namespaces based on how they were resolved
                 # but the same type_name should point to the same class
-                if data_type in val:
-                    namespace = key
+                if data_type in ns_data_types:
+                    namespace = ns_key
                     break
 
         cls = self.__get_container_cls(namespace, data_type)
@@ -517,18 +533,18 @@ def __check_dependent_types(self, spec, namespace):
         def __check_dependent_types_helper(spec, namespace):
             if isinstance(spec, (GroupSpec, DatasetSpec)):
                 if spec.data_type_inc is not None:
-                    self.get_container_cls(spec.data_type_inc, namespace)  # TODO handle recursive definitions
+                    self.get_dt_container_cls(spec.data_type_inc, namespace)  # TODO handle recursive definitions
                 if spec.data_type_def is not None:
-                    self.get_container_cls(spec.data_type_def, namespace)
+                    self.get_dt_container_cls(spec.data_type_def, namespace)
             elif isinstance(spec, LinkSpec):
                 if spec.target_type is not None:
-                    self.get_container_cls(spec.target_type, namespace)
+                    self.get_dt_container_cls(spec.target_type, namespace)
             if isinstance(spec, GroupSpec):
                 for child_spec in (spec.groups + spec.datasets + spec.links):
                     __check_dependent_types_helper(child_spec, namespace)
 
         if spec.data_type_inc is not None:
-            self.get_container_cls(spec.data_type_inc, namespace)
+            self.get_dt_container_cls(spec.data_type_inc, namespace)
         if isinstance(spec, GroupSpec):
             for child_spec in (spec.groups + spec.datasets + spec.links):
                 __check_dependent_types_helper(child_spec, namespace)
@@ -560,7 +576,7 @@ def __get_container_cls(self, namespace, data_type):
             return None
         ret = self.__container_types[namespace][data_type]
         if isinstance(ret, TypeSource):  # data_type is a dependency from ret.namespace
-            cls = self.get_container_cls(ret.data_type, ret.namespace)  # get class / generate class
+            cls = self.get_dt_container_cls(ret.data_type, ret.namespace)  # get class / generate class
             # register the same class into this namespace (replaces TypeSource)
             self.register_container_type(namespace, data_type, cls)
             ret = cls
@@ -619,7 +635,7 @@ def get_cls(self, **kwargs):
         namespace = self.get_builder_ns(builder)
         if namespace is None:
             raise ValueError("No namespace found for builder %s" % builder.path)
-        return self.get_container_cls(data_type, namespace)
+        return self.get_dt_container_cls(data_type, namespace)
 
     @docval({'name': 'spec', 'type': (DatasetSpec, GroupSpec), 'doc': 'the parent spec to search'},
             {'name': 'builder', 'type': (DatasetBuilder, GroupBuilder, LinkBuilder),

src/hdmf/common/__init__.py

@@ -101,6 +101,18 @@ def available_namespaces():
     return __TYPE_MAP.namespace_catalog.namespaces
 
 
+# a function to get the container class for a give type
+@docval({'name': 'data_type', 'type': str,
+         'doc': 'the data_type to get the Container class for'},
+        {'name': 'namespace', 'type': str, 'doc': 'the namespace the data_type is defined in'},
+        is_method=False)
+def get_class(**kwargs):
+    """Get the class object of the Container subclass corresponding to a given neurdata_type.
+    """
+    data_type, namespace = getargs('data_type', 'namespace', kwargs)
+    return __TYPE_MAP.get_dt_container_cls(data_type, namespace)
+
+
 # load the hdmf-common namespace
 __resources = __get_resources()
 if os.path.exists(__resources['namespace_path']):
@@ -129,16 +141,16 @@ def available_namespaces():
     raise RuntimeError("Unable to load a TypeMap - no namespace file found")
 
 
-DynamicTable = __TYPE_MAP.get_container_cls('DynamicTable', CORE_NAMESPACE)
-VectorData = __TYPE_MAP.get_container_cls('VectorData', CORE_NAMESPACE)
-VectorIndex = __TYPE_MAP.get_container_cls('VectorIndex', CORE_NAMESPACE)
-ElementIdentifiers = __TYPE_MAP.get_container_cls('ElementIdentifiers', CORE_NAMESPACE)
-DynamicTableRegion = __TYPE_MAP.get_container_cls('DynamicTableRegion', CORE_NAMESPACE)
-EnumData = __TYPE_MAP.get_container_cls('EnumData', EXP_NAMESPACE)
-CSRMatrix = __TYPE_MAP.get_container_cls('CSRMatrix', CORE_NAMESPACE)
-ExternalResources = __TYPE_MAP.get_container_cls('ExternalResources', EXP_NAMESPACE)
-SimpleMultiContainer = __TYPE_MAP.get_container_cls('SimpleMultiContainer', CORE_NAMESPACE)
-AlignedDynamicTable = __TYPE_MAP.get_container_cls('AlignedDynamicTable', CORE_NAMESPACE)
+DynamicTable = get_class('DynamicTable', CORE_NAMESPACE)
+VectorData = get_class('VectorData', CORE_NAMESPACE)
+VectorIndex = get_class('VectorIndex', CORE_NAMESPACE)
+ElementIdentifiers = get_class('ElementIdentifiers', CORE_NAMESPACE)
+DynamicTableRegion = get_class('DynamicTableRegion', CORE_NAMESPACE)
+EnumData = get_class('EnumData', EXP_NAMESPACE)
+CSRMatrix = get_class('CSRMatrix', CORE_NAMESPACE)
+ExternalResources = get_class('ExternalResources', EXP_NAMESPACE)
+SimpleMultiContainer = get_class('SimpleMultiContainer', CORE_NAMESPACE)
+AlignedDynamicTable = get_class('AlignedDynamicTable', CORE_NAMESPACE)
 
 
 @docval({'name': 'extensions', 'type': (str, TypeMap, list),
@@ -190,18 +202,6 @@ def get_manager(**kwargs):
     return BuildManager(type_map)
 
 
-# a function to get the container class for a give type
-@docval({'name': 'data_type', 'type': str,
-         'doc': 'the data_type to get the Container class for'},
-        {'name': 'namespace', 'type': str, 'doc': 'the namespace the data_type is defined in'},
-        is_method=False)
-def get_class(**kwargs):
-    """Get the class object of the Container subclass corresponding to a given neurdata_type.
-    """
-    data_type, namespace = getargs('data_type', 'namespace', kwargs)
-    return __TYPE_MAP.get_container_cls(data_type, namespace)
-
-
 @docval({'name': 'io', 'type': HDMFIO,
          'doc': 'the HDMFIO object to read from'},
         {'name': 'namespace', 'type': str,