Always use parent names in autogenerated child spec names (#130)

* Always use parent names in autogenerated child spec names, use __

* Add custom object mapper in tests

src/hdmf/build/map.py

@@ -598,12 +598,12 @@ def __get_fields(cls, name_stack, all_names, spec):
         if spec.name is None:
             name = cls.convert_dt_name(spec)
         name_stack.append(name)
-        if name in all_names:
-            name = "_".join(name_stack)
+        name = '__'.join(name_stack)
         all_names[name] = spec
         if isinstance(spec, BaseStorageSpec):
             if not (spec.data_type_def is None and spec.data_type_inc is None):
                 # don't get names for components in data_types
+                name_stack.pop()
                 return
             for subspec in spec.attributes:
                 cls.__get_fields(name_stack, all_names, subspec)
@@ -643,10 +643,6 @@ def __map_spec(self, spec):
     def map_attr(self, **kwargs):
         """ Map an attribute to spec. Use this to override default behavior """
         attr_name, spec = getargs('attr_name', 'spec', kwargs)
-        if hasattr(spec, 'name') and spec.name is not None:
-            n = spec.name
-        elif hasattr(spec, 'data_type_def') and spec.data_type_def is not None:
-            n = spec.data_type_def  # noqa: F841
         self.__spec2attr[spec] = attr_name
         self.__attr2spec[attr_name] = spec
 

tests/unit/build_tests/test_io_manager.py

@@ -11,6 +11,16 @@
 from tests.unit.test_utils import Foo, FooBucket, CORE_NAMESPACE
 
 
+class FooMapper(ObjectMapper):
+    """Maps nested 'attr2' attribute on dataset 'my_data' to Foo.attr2 in constructor and attribute map
+    """
+
+    def __init__(self, spec):
+        super(FooMapper, self).__init__(spec)
+        my_data_spec = spec.get_dataset('my_data')
+        self.map_spec('attr2', my_data_spec.get_attribute('attr2'))
+
+
 class TestBase(unittest.TestCase):
 
     def setUp(self):
@@ -37,7 +47,7 @@ def setUp(self):
         self.namespace_catalog.add_namespace(CORE_NAMESPACE, self.namespace)
         self.type_map = TypeMap(self.namespace_catalog)
         self.type_map.register_container_type(CORE_NAMESPACE, 'Foo', Foo)
-        self.type_map.register_map(Foo, ObjectMapper)
+        self.type_map.register_map(Foo, FooMapper)
         self.manager = BuildManager(self.type_map)
 
 
@@ -130,7 +140,7 @@ def setUp(self):
 
         self.spec_catalog.register_spec(self.bucket_spec, 'test.yaml')
         self.type_map.register_container_type(CORE_NAMESPACE, 'FooBucket', FooBucket)
-        self.type_map.register_map(FooBucket, ObjectMapper)
+        self.type_map.register_map(FooBucket, self.setUpBucketMapper())
         self.manager = BuildManager(self.type_map)
 
     def setUpBucketBuilder(self):
@@ -139,6 +149,9 @@ def setUpBucketBuilder(self):
     def setUpBucketSpec(self):
         raise unittest.SkipTest('Abstract Base Class')
 
+    def setUpBucketMapper(self):
+        raise unittest.SkipTest('Abstract Base Class')
+
     def test_build(self):
         ''' Test default mapping for an Container that has an Container as an attribute value '''
         builder = self.manager.build(self.foo_bucket)
@@ -171,6 +184,9 @@ def setUpBucketSpec(self):
                                          data_type_inc='Foo',
                                          quantity=ZERO_OR_MANY)])
 
+    def setUpBucketMapper(self):
+        return ObjectMapper
+
 
 class TestNestedContainersSubgroup(TestNestedBase):
     '''
@@ -197,6 +213,14 @@ def setUpBucketSpec(self):
                                      data_type_def='FooBucket',
                                      groups=[tmp_spec])
 
+    def setUpBucketMapper(self):
+        class BucketMapper(ObjectMapper):
+            def __init__(self, spec):
+                super(BucketMapper, self).__init__(spec)
+                self.map_spec('foos', spec.get_group('foo_holder').get_data_type('Foo'))
+
+        return BucketMapper
+
 
 class TestNestedContainersSubgroupSubgroup(TestNestedBase):
     '''
@@ -225,6 +249,14 @@ def setUpBucketSpec(self):
                                      data_type_def='FooBucket',
                                      groups=[tmp_spec])
 
+    def setUpBucketMapper(self):
+        class BucketMapper(ObjectMapper):
+            def __init__(self, spec):
+                super(BucketMapper, self).__init__(spec)
+                self.map_spec('foos', spec.get_group('foo_holder_holder').get_group('foo_holder').get_data_type('Foo'))
+
+        return BucketMapper
+
 
 class TestTypeMap(TestBase):
 

tests/unit/build_tests/test_io_map.py

@@ -348,6 +348,7 @@ def test_build(self):
         expected = GroupBuilder('my_bar', datasets={'data': DatasetBuilder(
             'data', list(range(10)), attributes={'attr2': 10})},
                                 attributes={'attr1': 'value1'})
+        self._remap_nested_attr()
         builder = self.mapper.build(container_inst, self.manager)
         self.assertDictEqual(builder, expected)
 
@@ -359,15 +360,27 @@ def test_construct(self):
             'data', list(range(10)), attributes={'attr2': 10})},
                                attributes={'attr1': 'value1', 'data_type': 'Bar', 'namespace': CORE_NAMESPACE,
                                            'object_id': expected.object_id})
+        self._remap_nested_attr()
         container = self.mapper.construct(builder, self.manager)
         self.assertEqual(container, expected)
 
     def test_default_mapping_keys(self):
         attr_map = self.mapper.get_attr_names(self.bar_spec)
         keys = set(attr_map.keys())
-        expected = {'attr1', 'data', 'attr2'}
+        expected = {'attr1', 'data', 'data__attr2'}
         self.assertSetEqual(keys, expected)
 
+    def test_remap_keys(self):
+        self._remap_nested_attr()
+        self.assertEqual(self.mapper.get_attr_spec('attr2'),
+                         self.mapper.spec.get_dataset('data').get_attribute('attr2'))
+        self.assertEqual(self.mapper.get_attr_spec('attr1'), self.mapper.spec.get_attribute('attr1'))
+        self.assertEqual(self.mapper.get_attr_spec('data'), self.mapper.spec.get_dataset('data'))
+
+    def _remap_nested_attr(self):
+        data_spec = self.mapper.spec.get_dataset('data')
+        self.mapper.map_spec('attr2', data_spec.get_attribute('attr2'))
+
 
 class TestObjectMapperNoNesting(TestObjectMapper):
 

tests/unit/test_io_hdf5_h5tools.py

@@ -424,6 +424,12 @@ def _get_manager():
                             data_type_def='FooBucket',
                             groups=[tmp_spec])
 
+    class FooMapper(ObjectMapper):
+        def __init__(self, spec):
+            super(FooMapper, self).__init__(spec)
+            my_data_spec = spec.get_dataset('my_data')
+            self.map_spec('attr2', my_data_spec.get_attribute('attr2'))
+
     class BucketMapper(ObjectMapper):
         def __init__(self, spec):
             super(BucketMapper, self).__init__(spec)
@@ -461,6 +467,7 @@ def __init__(self, spec):
     type_map.register_container_type(CORE_NAMESPACE, 'FooBucket', FooBucket)
     type_map.register_container_type(CORE_NAMESPACE, 'FooFile', FooFile)
 
+    type_map.register_map(Foo, FooMapper)
     type_map.register_map(FooBucket, BucketMapper)
     type_map.register_map(FooFile, FileMapper)