scratch work

src/hdmf/backends/hdf5/h5tools.py

@@ -1106,6 +1106,7 @@ def write_dataset(self, **kwargs):  # noqa: C901
         if isinstance(data, TermSetWrapper):
             # This is for when the wrapped item is a dataset
             # (refer to objectmapper.py for wrapped attributes)
+            breakpoint()
             data = data.value
         attributes = builder.attributes
         options['dtype'] = builder.dtype

src/hdmf/backends/io.py

@@ -91,12 +91,13 @@ def write(self, **kwargs):
 
             # add_ref_container to search for and resolve the TermSetWrapper
             herd.add_ref_container(root_container=container,
-                                   unwrap=True) # container would be the NWBFile
+                                   unwrap=False) # container would be the NWBFile
             # write HERD
             herd.to_zip(path=self.herd_path)
 
         """Write a container to the IO source."""
         f_builder = self.__manager.build(container, source=self.__source, root=True)
+        breakpoint()
         self.write_builder(f_builder, **kwargs)
 
     @docval({'name': 'src_io', 'type': 'hdmf.backends.io.HDMFIO',

src/hdmf/build/objectmapper.py

@@ -566,6 +566,7 @@ def get_attr_value(self, **kwargs):
                        % (container.__class__.__name__, container.name, attr_name, spec))
                 raise ContainerConfigurationError(msg)
             if isinstance(attr_val, TermSetWrapper):
+                breakpoint()
                 attr_val = attr_val.value
             if attr_val is not None:
                 attr_val = self.__convert_string(attr_val, spec)

tests/unit/common/test_resources.py

@@ -352,26 +352,29 @@ def test_add_ref_container_attr(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_ref_termset(self):
-        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
-        er = HERD()
-        em = HERDManagerContainer()
-
         col1 = VectorData(name='Species_Data',
                           description='species from NCBI and Ensemble',
                           data=['Homo sapiens'])
-
-        species = DynamicTable(name='species', description='My species', columns=[col1],)
-
-        er.add_ref_termset(file=em,
-                    container=species,
-                    attribute='Species_Data',
-                    key='Homo sapiens',
-                    termset=terms
-                   )
-        self.assertEqual(er.keys.data, [('Homo sapiens',)])
-        self.assertEqual(er.entities.data, [('NCBI_TAXON:9606',
-        'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606')])
-        self.assertEqual(er.objects.data, [(0, col1.object_id, 'VectorData', '', '')])
+        # terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        # er = HERD()
+        # em = HERDManagerContainer()
+        #
+        # col1 = VectorData(name='Species_Data',
+        #                   description='species from NCBI and Ensemble',
+        #                   data=['Homo sapiens'])
+        #
+        # species = DynamicTable(name='species', description='My species', columns=[col1],)
+        #
+        # er.add_ref_termset(file=em,
+        #             container=species,
+        #             attribute='Species_Data',
+        #             key='Homo sapiens',
+        #             termset=terms
+        #            )
+        # self.assertEqual(er.keys.data, [('Homo sapiens',)])
+        # self.assertEqual(er.entities.data, [('NCBI_TAXON:9606',
+        # 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606')])
+        # self.assertEqual(er.objects.data, [(0, col1.object_id, 'VectorData', '', '')])
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_ref_termset_data_object_error(self):

tests/unit/helpers/utils.py

@@ -73,10 +73,18 @@ def __str__(self):
     def my_data(self):
         return self.__data
 
+    @my_data.setter
+    def my_data(self, value):
+        self.__data = value
+
     @property
     def attr1(self):
         return self.__attr1
 
+    @attr1.setter
+    def attr1(self, value):
+        self.__attr1 = value
+
     @property
     def attr2(self):
         return self.__attr2

tests/unit/test_io_hdf5_h5tools.py

@@ -830,7 +830,7 @@ def test_roundtrip_TermSetWrapper_dataset(self):
         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])
 
@@ -839,7 +839,7 @@ def test_roundtrip_TermSetWrapper_dataset(self):
 
         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,
+            self.assertListEqual(foofile.buckets['bucket1'].foos['species'].my_data,
                                  read_foofile.buckets['bucket1'].foos['species'].my_data[:].tolist())
         remove_test_file('./HERD.zip')
 
@@ -856,7 +856,7 @@ def test_roundtrip_TermSetWrapper_attribute(self):
 
         with HDF5IO(self.path, manager=self.manager, mode='r') as io:
             read_foofile = io.read()
-            self.assertEqual(foofile.buckets['bucket1'].foos['species'].attr1.value,
+            self.assertEqual(foofile.buckets['bucket1'].foos['species'].attr1,
                              read_foofile.buckets['bucket1'].foos['species'].attr1)
             remove_test_file('./HERD.zip')