Merge pull request #30 from hdmf-dev/fix/nested_get_class

add support for nested get_class

src/hdmf/build/map.py

@@ -1290,11 +1290,11 @@ def __get_type(self, spec):
                     container_type = val.get(tgttype)
                     if container_type is not None:
                         return container_type
-                return (Data, Container)
+                return Data, Container
             elif spec.shape is None and spec.dims is None:
                 return self._type_map.get(spec.dtype)
             else:
-                return ('array_data',)
+                return 'array_data',
         elif isinstance(spec, LinkSpec):
             return Container
         else:
@@ -1306,19 +1306,21 @@ def __get_type(self, spec):
             elif spec.shape is None and spec.dims is None:
                 return self._type_map.get(spec.dtype)
             else:
-                return ('array_data', 'data',)
+                return 'array_data', 'data'
 
-    def __get_constructor(self, base, addl_fields):
+    def __get_cls_dict(self, base, addl_fields):
         # TODO: fix this to be more maintainable and smarter
+        if base is None:
+            raise ValueError('cannot generate class without base class')
         existing_args = set()
         docval_args = list()
         new_args = list()
-        if base is not None:
-            for arg in get_docval(base.__init__):
-                existing_args.add(arg['name'])
-                if arg['name'] in addl_fields:
-                    continue
-                docval_args.append(arg)
+        fields = list()
+        for arg in get_docval(base.__init__):
+            existing_args.add(arg['name'])
+            if arg['name'] in addl_fields:
+                continue
+            docval_args.append(arg)
         for f, field_spec in addl_fields.items():
             if not f == 'help':
                 dtype = self.__get_type(field_spec)
@@ -1330,20 +1332,19 @@ def __get_constructor(self, base, addl_fields):
                 docval_args.append(docval_arg)
                 if f not in existing_args:
                     new_args.append(f)
-        if base is None:
-            @docval(*docval_args)
-            def __init__(self, **kwargs):
-                for f in new_args:
-                    setattr(self, f, kwargs.get(f, None))
-            return __init__
-        else:
-            @docval(*docval_args)
-            def __init__(self, **kwargs):
-                pargs, pkwargs = fmt_docval_args(base.__init__, kwargs)
-                super(type(self), self).__init__(*pargs, **pkwargs)
-                for f in new_args:
-                    setattr(self, f, kwargs.get(f, None))
-            return __init__
+                if issubclass(dtype, (Container, Data, DataRegion)):
+                    fields.append({'name': f, 'child': True})
+                else:
+                    fields.append(f)
+
+        @docval(*docval_args)
+        def __init__(self, **kwargs):
+            pargs, pkwargs = fmt_docval_args(base.__init__, kwargs)
+            super(type(self), self).__init__(*pargs, **pkwargs)
+            for f in new_args:
+                setattr(self, f, kwargs.get(f, None))
+
+        return {'__init__': __init__, base._fieldsname: tuple(fields)}
 
     @docval({"name": "namespace", "type": str, "doc": "the namespace containing the data_type"},
             {"name": "data_type", "type": str, "doc": "the data type to create a Container class for"},
@@ -1364,7 +1365,6 @@ def get_container_cls(self, **kwargs):
                 parent_cls = self.__get_container_cls(namespace, t)
                 if parent_cls is not None:
                     break
-            bases = tuple()
             if parent_cls is not None:
                 bases = (parent_cls,)
             else:
@@ -1375,14 +1375,16 @@ def get_container_cls(self, **kwargs):
                 else:
                     raise ValueError("Cannot generate class from %s" % type(spec))
                 parent_cls = bases[0]
+            if type(parent_cls) is not ExtenderMeta:
+                raise ValueError("parent class %s is not of type ExtenderMeta - %s" % (parent_cls, type(parent_cls)))
             name = data_type
             attr_names = self.__default_mapper_cls.get_attr_names(spec)
             fields = dict()
             for k, field_spec in attr_names.items():
                 if not spec.is_inherited_spec(field_spec):
                     fields[k] = field_spec
-            d = {'__init__': self.__get_constructor(parent_cls, fields)}
-            cls = type(str(name), bases, d)
+            d = self.__get_cls_dict(parent_cls, fields)
+            cls = ExtenderMeta(str(name), bases, d)
             self.register_container_type(namespace, data_type, cls)
         return cls
 

src/hdmf/container.py

@@ -1,9 +1,11 @@
 import abc
 from six import with_metaclass
-from .utils import docval, getargs
+from .utils import docval, getargs, ExtenderMeta
 
 
-class Container(with_metaclass(abc.ABCMeta, object)):
+class Container(with_metaclass(ExtenderMeta, object)):
+
+    _fieldsname = '__fields__'
 
     @docval({'name': 'name', 'type': str, 'doc': 'the name of this container'},
             {'name': 'parent', 'type': 'Container', 'doc': 'the Container that holds this Container', 'default': None},

src/hdmf/utils.py

@@ -549,7 +549,7 @@ def get_data_shape(data, strict_no_data_load=False):
 
     :param data: Array for which we should determine the shape.
     :type data: List, numpy.ndarray, DataChunkIterator, any object that support __len__ or .shape.
-    :param strict_no_data_load: In order to determin the shape of nested tuples and lists, this function
+    :param strict_no_data_load: In order to determine the shape of nested tuples and lists, this function
                 recursively inspects elements along the dimensions, assuming that the data has a regular,
                 rectangular shape. In the case of out-of-core iterators this means that the first item
                 along each dimensions would potentially be loaded into memory. By setting this option
@@ -580,7 +580,7 @@ def __get_shape_helper(local_data):
 
 def pystr(s):
     """
-    Cross-version support for convertin a string of characters to Python str object
+    Cross-version support for converting a string of characters to Python str object
     """
     if six.PY2 and isinstance(s, six.text_type):
         return s.encode('ascii', 'ignore')