tests

src/hdmf/build/objectmapper.py

@@ -911,7 +911,7 @@ def __add_attributes(self, builder, attributes, container, build_manager, source
             if spec.value is not None:
                 attr_value = spec.value
             else:
-                attr_value = self.get_attr_value(spec, container, build_manager) #
+                attr_value = self.get_attr_value(spec, container, build_manager)
                 if attr_value is None:
                     attr_value = spec.default_value
 

src/hdmf/common/resources.py

@@ -548,10 +548,6 @@ def add_ref(self, **kwargs):
         if isinstance(container, Data):
             if attribute == 'data':
                 attribute = None
-        # if attribute == 'my_data':
-        #     attribute = None
-        # if attribute == 'data':
-        #     attribute = None
         key = kwargs['key']
         field = kwargs['field']
         entity_id = kwargs['entity_id']

src/hdmf/common/table.py

@@ -586,23 +586,9 @@ def add_row(self, **kwargs):
         extra_columns = set(list(data.keys())) - set(list(self.__colids.keys()))
         missing_columns = set(list(self.__colids.keys())) - set(list(data.keys()))
 
-        bad_data = []
         for colname, colnum in self.__colids.items():
             if colname not in data:
                 raise ValueError("column '%s' missing" % colname)
-            col = self.__df_cols[colnum]
-            if isinstance(col, VectorIndex):
-                continue
-            else:
-                if isinstance(col.data, TermSetWrapper):
-                    if col.data.termset.validate(term=data[colname]):
-                        continue
-                    else:
-                        bad_data.append(data[colname])
-
-        if len(bad_data)!=0:
-            msg = ('"%s" is not in the term set.' % ', '.join([str(item) for item in bad_data]))
-            raise ValueError(msg)
 
         # check to see if any of the extra columns just need to be added
         if extra_columns:

tests/unit/common/test_resources.py

@@ -283,9 +283,10 @@ def test_check_termset_wrapper(self):
 
         er = HERD()
         ret = er._HERD__check_termset_wrapper(objs)
-        self.assertEqual(ret[0][0].__class__.__name__, 'VectorData')
+
+        self.assertTrue(isinstance(ret[0][0], VectorData))
         self.assertEqual(ret[0][1], 'data')
-        self.assertEqual(ret[0][2].__class__.__name__, 'TermSetWrapper')
+        self.assertTrue(isinstance(ret[0][2], TermSetWrapper))
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_ref_termset_data(self):

tests/unit/test_io_hdf5_h5tools.py

@@ -837,7 +837,7 @@ def test_roundtrip_TermSetWrapper_dataset(self):
         with HDF5IO(self.path, manager=get_foo_buildmanager("text"), mode='w', herd_path='./HERD.zip') as io:
             io.write(foofile)
 
-        with HDF5IO(self.path, manager=self.manager, mode='r') as io:
+        with HDF5IO(self.path, manager=get_foo_buildmanager("text"), mode='r') as io:
             read_foofile = io.read()
             self.assertListEqual(foofile.buckets['bucket1'].foos['species'].my_data.value,
                                  read_foofile.buckets['bucket1'].foos['species'].my_data[:].tolist())
@@ -1071,52 +1071,34 @@ def test_io_read_herd_value_warn(self):
 
         self.remove_er_files()
 
-    # def test_io_write_extend_herd(self):
-    #     """
-    #     Test the optional write of HERD with extending an existing HERD instance.
-    #     """
-    #     # create a container that uses TermSetWrapper
-    #     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'],
-    #                                                      termset=terms))
-    #     foobucket = FooBucket('bucket1', [foo])
-    #     file = FooFile(buckets=[foobucket])
-    #
-    #     er = HERD()
-    #     er.add_ref(file=file,
-    #                container=file,
-    #                key='special',
-    #                entity_id="id11",
-    #                entity_uri='url11')
-    #
-    #     with HDF5IO(self.path, manager=self.manager, mode='w', herd_path='./HERD.zip') as io:
-    #         io.write(file, herd=er)
-    #     with HDF5IO(self.path, manager=self.manager, mode='r', herd_path='./HERD.zip') as io:
-    #         container = io.read()
-    #         self.assertIsInstance(io.herd, HERD)
-    #
-    #     self.remove_er_files()
-    #
-    # def test_io_write_create_herd(self):
-    #     """
-    #     Test the optional write of HERD with an new instance.
-    #     """
-    #     # create a container that uses TermSetWrapper
-    #     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'],
-    #                                                      termset=terms))
-    #     foobucket = FooBucket('bucket1', [foo])
-    #     file = FooFile(buckets=[foobucket])
-    #
-    #     with HDF5IO(self.path, manager=self.manager, mode='w', herd_path='./HERD.zip') as io:
-    #         io.write(file)
-    #     with HDF5IO(self.path, manager=self.manager, mode='r', herd_path='./HERD.zip') as io:
-    #         container = io.read()
-    #         self.assertIsInstance(io.herd, HERD)
-    #
-    #     self.remove_er_files()
+    def test_io_write_extend_herd(self):
+        """
+        Test the optional write of HERD with extending an existing HERD instance.
+        """
+        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'],
+                                                         termset=terms))
+
+        foobucket = FooBucket('bucket1', [foo])
+        foofile = FooFile(buckets=[foobucket])
+
+        er = HERD()
+        er.add_ref(file=foofile,
+                   container=foofile,
+                   key='special',
+                   entity_id="id11",
+                   entity_uri='url11')
+
+        with HDF5IO(self.path, manager=get_foo_buildmanager("text"), mode='w', herd_path='./HERD.zip') as io:
+            io.write(foofile)
+
+        with HDF5IO(self.path, manager=get_foo_buildmanager("text"), mode='r') as io:
+            read_foofile = io.read()
+            self.assertListEqual(foofile.buckets['bucket1'].foos['species'].my_data.value,
+                                 read_foofile.buckets['bucket1'].foos['species'].my_data[:].tolist())
+
+        self.remove_er_files()
 
 
 class TestMultiWrite(TestCase):