checkpoint/remove field_name

src/hdmf/common/resources.py

@@ -414,7 +414,7 @@ def _get_file_from_container(self, **kwargs):
     def __check_termset_wrapper(self, **kwargs):
         """
         Takes a list of objects and checks the fields for TermSetWrapper.
-        :return: [[object, wrapper1], [object, wrapper2], ...]
+        :return: [[object, attribute_name, wrapper1], [object, attribute_name, wrapper2], ...]
         """
         objects = kwargs['objects']
 
@@ -423,11 +423,14 @@ def __check_termset_wrapper(self, **kwargs):
         for obj in objects:
             # Get all the fields, parse out the methods and internal variables
             obj_fields = [a for a in dir(obj) if not a.startswith('_') and not callable(getattr(obj, a))]
+
             for attribute in obj_fields:
                 attr = getattr(obj, attribute)
                 if isinstance(attr, TermSetWrapper):
+                    # breakpoint()
                     # Search objects that are wrapped
-                    ret.append([obj, attr])
+                    ret.append([obj, attribute, attr])
+        # breakpoint()
         return ret
 
     @docval({'name': 'root_container', 'type': HERDManager,
@@ -443,8 +446,8 @@ def add_ref_term_set(self, **kwargs):
         all_objects = root_container.all_children() # list of child objects and the container itslef
 
         add_ref_items = self.__check_termset_wrapper(objects=all_objects)
-        for ref_pairs in add_ref_items:
-            container, wrapper = ref_pairs
+        for ref in add_ref_items:
+            container, attr_name, wrapper = ref
             if isinstance(wrapper.value, (list, np.ndarray, tuple)):
                 values = wrapper.value
             else:
@@ -456,7 +459,7 @@ def add_ref_term_set(self, **kwargs):
                 entity_uri = term_info[2]
                 self.add_ref(file=root_container,
                              container=container,
-                             attribute=wrapper.field_name,
+                             attribute=attr_name,
                              key=term,
                              entity_id=entity_id,
                              entity_uri=entity_uri)
@@ -544,8 +547,12 @@ def add_ref(self, **kwargs):
         ###############################################################
         container = kwargs['container']
         attribute = kwargs['attribute']
-        if attribute == 'data':
+        if container.__class__.__name__ == 'VectorData':
             attribute = None
+        # if attribute == 'my_data':
+        #     attribute = None
+        # if attribute == 'data':
+        #     attribute = None
         key = kwargs['key']
         field = kwargs['field']
         entity_id = kwargs['entity_id']
@@ -599,13 +606,20 @@ def add_ref(self, **kwargs):
                                                             relative_path=relative_path,
                                                             field=field)
 
+        # try:
+        #     # key_name, container, relative_path, field
+        #     key = self.get_key(key_name=key, container=container)
+        # except ValueError:
+        #     pass
+
         if not isinstance(key, Key):
             key_idx_matches = self.keys.which(key=key)
         # if same key is used multiple times, determine
         # which instance based on the Container
             for row_idx in self.object_keys.which(objects_idx=object_field.idx):
                 key_idx = self.object_keys['keys_idx', row_idx]
                 if key_idx in key_idx_matches:
+                    breakpoint()
                     msg = "Use Key Object when referencing an existing (container, relative_path, key)"
                     raise ValueError(msg)
 

src/hdmf/term_set.py

@@ -185,13 +185,10 @@ class TermSetWrapper:
             {'name': 'value',
              'type': (list, np.ndarray, dict, str, tuple),
              'doc': 'The target item that is wrapped, either data or attribute.'},
-            {'name': 'field_name',
-             'type': str,
-             'doc': 'The name of the field being wrapped.'})
+            )
     def __init__(self, **kwargs):
         self.__value = kwargs['value']
         self.__termset = kwargs['termset']
-        self.__field_name = kwargs['field_name']
         self.__validate()
 
     def __validate(self):
@@ -220,10 +217,6 @@ def value(self):
     def termset(self):
         return self.__termset
 
-    @property
-    def field_name(self):
-        return self.__field_name
-
     @property
     def dtype(self):
         return self.__getattr__('dtype')

tests/unit/common/test_resources.py

@@ -276,15 +276,16 @@ def test_check_termset_wrapper(self):
         col1 = VectorData(
             name='Species_1',
             description='...',
-            data=TermSetWrapper(value=['Homo sapiens'], field_name='data', termset=terms)
+            data=TermSetWrapper(value=['Homo sapiens'], termset=terms)
         )
         species = DynamicTable(name='species', description='My species', columns=[col1])
         objs = species.all_children()
 
         er = HERD()
         ret = er._HERD__check_termset_wrapper(objs)
         self.assertEqual(ret[0][0].__class__.__name__, 'VectorData')
-        self.assertEqual(ret[0][1].__class__.__name__, 'TermSetWrapper')
+        self.assertEqual(ret[0][1], 'data')
+        self.assertEqual(ret[0][2].__class__.__name__, 'TermSetWrapper')
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_ref_termset_data(self):
@@ -297,7 +298,7 @@ def test_add_ref_termset_data(self):
         col1 = VectorData(
             name='Species_1',
             description='...',
-            data=TermSetWrapper(value=['Homo sapiens'], field_name='data', termset=terms)
+            data=TermSetWrapper(value=['Homo sapiens'], termset=terms)
         )
         species = DynamicTable(name='species', description='My species', columns=[col1])
 
@@ -319,7 +320,7 @@ def test_add_ref_termset_attr(self):
         # create children and add parent
         col1 = VectorData(
             name='Species_1',
-            description=TermSetWrapper(value='Homo sapiens', field_name='description', termset=terms),
+            description=TermSetWrapper(value='Homo sapiens', termset=terms),
             data=['Human']
         )
         species = DynamicTable(name='species', description='My species', columns=[col1])

tests/unit/common/test_table.py

@@ -124,12 +124,12 @@ def test_add_col_validate(self):
         col1 = VectorData(
             name='Species_1',
             description='...',
-            data=TermSetWrapper(value=['Homo sapiens'], field_name='data', termset=terms)
+            data=TermSetWrapper(value=['Homo sapiens'], termset=terms)
         )
         species = DynamicTable(name='species', description='My species', columns=[col1])
         species.add_column(name='Species_2',
                            description='Species data',
-                           data=TermSetWrapper(value=['Mus musculus'], field_name='data', termset=terms))
+                           data=TermSetWrapper(value=['Mus musculus'], termset=terms))
         expected_df_data = \
             {'Species_1': {0: 'Homo sapiens'},
              'Species_2': {0: 'Mus musculus'}}
@@ -143,14 +143,13 @@ def test_add_col_validate_bad_data(self):
         col1 = VectorData(
             name='Species_1',
             description='...',
-            data=TermSetWrapper(value=['Homo sapiens'], field_name='data', termset=terms)
+            data=TermSetWrapper(value=['Homo sapiens'], termset=terms)
         )
         species = DynamicTable(name='species', description='My species', columns=[col1])
         with self.assertRaises(ValueError):
             species.add_column(name='Species_2',
                                description='Species data',
                                data=TermSetWrapper(value=['bad data'],
-                                                   field_name='data',
                                                    termset=terms))
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
@@ -159,12 +158,12 @@ def test_add_row_validate(self):
         col1 = VectorData(
             name='Species_1',
             description='...',
-            data=TermSetWrapper(value=['Homo sapiens'], field_name='data', termset=terms)
+            data=TermSetWrapper(value=['Homo sapiens'], termset=terms)
         )
         col2 = VectorData(
             name='Species_2',
             description='...',
-            data=TermSetWrapper(value=['Mus musculus'], field_name='data', termset=terms)
+            data=TermSetWrapper(value=['Mus musculus'], termset=terms)
         )
         species = DynamicTable(name='species', description='My species', columns=[col1,col2])
         species.add_row(Species_1='Myrmecophaga tridactyla', Species_2='Ursus arctos horribilis')
@@ -181,12 +180,12 @@ def test_add_row_validate_bad_data_one_col(self):
         col1 = VectorData(
             name='Species_1',
             description='...',
-            data=TermSetWrapper(value=['Homo sapiens'], field_name='data', termset=terms)
+            data=TermSetWrapper(value=['Homo sapiens'], termset=terms)
         )
         col2 = VectorData(
             name='Species_2',
             description='...',
-            data=TermSetWrapper(value=['Mus musculus'], field_name='data', termset=terms)
+            data=TermSetWrapper(value=['Mus musculus'], termset=terms)
         )
         species = DynamicTable(name='species', description='My species', columns=[col1,col2])
         with self.assertRaises(ValueError):
@@ -198,12 +197,12 @@ def test_add_row_validate_bad_data_all_col(self):
         col1 = VectorData(
             name='Species_1',
             description='...',
-            data=TermSetWrapper(value=['Homo sapiens'], field_name='data', termset=terms)
+            data=TermSetWrapper(value=['Homo sapiens'], termset=terms)
         )
         col2 = VectorData(
             name='Species_2',
             description='...',
-            data=TermSetWrapper(value=['Mus musculus'], field_name='data', termset=terms)
+            data=TermSetWrapper(value=['Mus musculus'], termset=terms)
         )
         species = DynamicTable(name='species', description='My species', columns=[col1,col2])
         with self.assertRaises(ValueError):

tests/unit/helpers/utils.py

@@ -72,9 +72,9 @@ def __str__(self):
     def my_data(self):
         return self.__data
 
-    @property
-    def data(self):
-        return self.__data
+    # @property
+    # def data(self):
+    #     return self.__data
 
     @property
     def attr1(self):

tests/unit/test_io_hdf5_h5tools.py

@@ -143,7 +143,7 @@ def test_write_dataset_string(self):
     ##########################################
     def test_write_dataset_TermSetWrapper(self):
         terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
-        a = TermSetWrapper(value=['Homo sapiens'], field_name='data', termset=terms)
+        a = TermSetWrapper(value=['Homo sapiens'], termset=terms)
         self.io.write_dataset(self.f, DatasetBuilder('test_dataset', a, attributes={}))
         dset = self.f['test_dataset']
         self.assertEqual(dset[0].decode('utf-8'), a.value[0])
@@ -821,15 +821,12 @@ def test_roundtrip_TermSetWrapper_dataset(self):
         terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         foo = Foo(name="species", attr1='attr1', attr2=0,
                   my_data=TermSetWrapper(value=['Homo sapiens', 'Mus musculus'],
-                                                         field_name='data',
                                                          termset=terms))
         foobucket = FooBucket('bucket1', [foo])
         foofile = FooFile(buckets=[foobucket])
 
-        # with HDF5IO(self.path, manager=self.manager, mode='w') as io:
-        #     io.write(foofile)
         with HDF5IO(self.path, manager=self.manager, mode='w', herd_path='./HERD.zip') as io:
-            io.write(foofile, herd=er)
+            io.write(foofile)
         #
         # with HDF5IO(self.path, manager=self.manager, mode='r') as io:
         #     read_foofile = io.read()
@@ -1059,9 +1056,7 @@ def test_io_write_extend_herd(self):
         terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         foo = Foo(name="foo", attr1='attr1', attr2=0,
                   my_data=TermSetWrapper(value=['Homo sapiens', 'Mus musculus'],
-                                                         field_name='my_data',
                                                          termset=terms))
-        # breakpoint()
         foobucket = FooBucket('bucket1', [foo])
         file = FooFile(buckets=[foobucket])
 
@@ -1088,7 +1083,6 @@ def test_io_write_create_herd(self):
         terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         foo = Foo(name="my_data", attr1='attr1', attr2=0,
                   my_data=TermSetWrapper(value=['Homo sapiens', 'Mus musculus'],
-                                                         field_name='data',
                                                          termset=terms))
         foobucket = FooBucket('bucket1', [foo])
         file = FooFile(buckets=[foobucket])

tests/unit/test_term_set.py

@@ -111,8 +111,8 @@ class TestTermSetWrapper(TestCase):
     def setUp(self):
         self.termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
 
-        self.wrapped_array = TermSetWrapper(value=np.array(['Homo sapiens']), termset=self.termset, field_name='data')
-        self.wrapped_list = TermSetWrapper(value=['Homo sapiens'], termset=self.termset, field_name='data')
+        self.wrapped_array = TermSetWrapper(value=np.array(['Homo sapiens']), termset=self.termset)
+        self.wrapped_list = TermSetWrapper(value=['Homo sapiens'], termset=self.termset)
 
         self.np_data = VectorData(
             name='Species_1',
@@ -128,7 +128,6 @@ def setUp(self):
     def test_properties(self):
         self.assertEqual(self.wrapped_array.value, ['Homo sapiens'])
         self.assertEqual(self.wrapped_array.termset.view_set, self.termset.view_set)
-        self.assertEqual(self.wrapped_list.field_name, 'data')
         self.assertEqual(self.wrapped_array.dtype, 'U12') # this covers __getattr__
 
     def test_get_item(self):
@@ -148,14 +147,12 @@ def test_validate_error(self):
             data = VectorData(name='Species_1',
                               description='...',
                               data=TermSetWrapper(value=['Missing Term'],
-                                                  termset=self.termset,
-                                                  field_name='data'))
+                                                  termset=self.termset))
 
     def test_wrapper_validate_attribute(self):
         col1 = VectorData(
             name='Species_1',
             description=TermSetWrapper(value='Homo sapiens',
-                                       field_name='description',
                                        termset=self.termset),
             data=['Human']
         )
@@ -166,7 +163,6 @@ def test_wrapper_validate_dataset(self):
             name='Species_1',
             description='...',
             data=TermSetWrapper(value=['Homo sapiens'],
-                                field_name='data',
                                 termset=self.termset)
         )
         self.assertTrue(isinstance(col1.data, TermSetWrapper))