TermSet minor test updates, _repr_html_, name field

CHANGELOG.md

@@ -1,5 +1,10 @@
 # HDMF Changelog
 
+## HDMF 3.10.1 (Upcoming)
+
+### Enhancements
+- Updated `TermSet` to include `_repr_html_` for easy to read notebook representation. @mavaylon1 [967](https://github.com/hdmf-dev/hdmf/pull/967)
+
 ## HDMF 3.10.0 (October 3, 2023)
 
 Since version 3.9.1 should have been released as 3.10.0 but failed to release on PyPI and conda-forge, this release

docs/gallery/plot_term_set.py

@@ -92,7 +92,7 @@
 # spreadsheet, the spreadsheet needs to be saved as individual tsv files, i.e., one tsv file per spreadsheet tab. Please
 # refer to the Schemasheets tutorial link above for more details on the required syntax structure within the sheets.
 # Once the tsv files are in a folder, the user simply provides the path to the folder with ``schemasheets_folder``.
-termset = TermSet(schemasheets_folder=schemasheets_folder)
+termset = TermSet(name='example', schemasheets_folder=schemasheets_folder)
 
 # Use Dynamic Enumerations to populate TermSet
 # --------------------------------------------
@@ -102,7 +102,7 @@
 # Please refer to the LinkMl Dynamic Enumeration tutorial for more information on these sources and how to setup Dynamic
 # Enumerations within the schema. Once the schema is ready, the user provides a path to the schema and set
 # ``dynamic=True``. A new schema, with the populated permissible values, will be created in the same directory.
-termset = TermSet(term_schema_path=dynamic_schema_path, dynamic=True)
+termset = TermSet(name='example', term_schema_path=dynamic_schema_path, dynamic=True)
 
 ######################################################
 # Viewing TermSet values
@@ -111,7 +111,7 @@
 # method will return a dictionary of all the terms and the corresponding information for each term.
 # Users can index specific terms from the :py:class:`~hdmf.term_set.TermSet`. LinkML runtime will need to be installed.
 # You can do so by first running ``pip install linkml-runtime``.
-terms = TermSet(term_schema_path=yaml_file)
+terms = TermSet(name='example', term_schema_path=yaml_file)
 print(terms.view_set)
 
 # Retrieve a specific term

src/hdmf/term_set.py

@@ -19,11 +19,13 @@ class TermSet:
     :ivar expanded_termset_path: The path to the schema with the expanded enumerations
     """
     def __init__(self,
+                 name: str,
                  term_schema_path: str=None,
                  schemasheets_folder: str=None,
                  dynamic: bool=False
                  ):
         """
+        :param name: The name of the TermSet
         :param term_schema_path: The path to the LinkML YAML enumeration schema
         :param schemasheets_folder: The path to the folder containing the LinkML TSV files
         :param dynamic: Boolean parameter denoting whether the schema uses Dynamic Enumerations
@@ -35,6 +37,7 @@ def __init__(self,
             msg = "Install linkml_runtime"
             raise ValueError(msg)
 
+        self.name = name
         self.term_schema_path = term_schema_path
         self.schemasheets_folder = schemasheets_folder
 
@@ -55,9 +58,14 @@ def __init__(self,
 
         self.sources = self.view.schema.prefixes
 
-    def __repr__(self):
-        re = "class: %s\n" % str(self.__class__)
-        re += "term_schema_path: %s\n" % self.term_schema_path
+    def __repr__(self): # pragma: no cover
+        re = "Class: %s\n" % str(self.__class__.__name__)
+        re += "Schema Path: %s\n" % self.term_schema_path
+        return re
+
+    def _repr_html_(self): # pragma: no cover
+        re = "<p><b>" + "Schema Path: " + "</b>" + self.term_schema_path + "<br>" + "</p>"
+        re += "<p><b>" + "Sources: " + "</b>" + ", ".join(list(self.sources.keys())) + "</p>"
         return re
 
     def __perm_value_key_info(self, perm_values_dict: dict, key: str):

tests/unit/common/test_resources.py

@@ -270,7 +270,7 @@ def test_add_ref_search_for_file_error(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_check_termset_wrapper(self):
-        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(name='example', term_schema_path='tests/unit/example_test_term_set.yaml')
 
         # create children and add parent
         col1 = VectorData(
@@ -290,7 +290,7 @@ def test_check_termset_wrapper(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_ref_termset_data(self):
-        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(name='example', term_schema_path='tests/unit/example_test_term_set.yaml')
         er = HERD()
         em = HERDManagerContainer()
         em.link_resources(er)
@@ -313,7 +313,7 @@ def test_add_ref_termset_data(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_ref_termset_attr(self):
-        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(name='example', term_schema_path='tests/unit/example_test_term_set.yaml')
         er = HERD()
         em = HERDManagerContainer()
         em.link_resources(er)

tests/unit/common/test_table.py

@@ -120,7 +120,7 @@ def test_constructor_all_columns_are_iterators(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_col_validate(self):
-        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(name='example', term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
             name='Species_1',
             description='...',
@@ -139,7 +139,7 @@ def test_add_col_validate(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_col_validate_bad_data(self):
-        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(name='example', term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
             name='Species_1',
             description='...',
@@ -154,7 +154,7 @@ def test_add_col_validate_bad_data(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_row_validate(self):
-        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(name='example', term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
             name='Species_1',
             description='...',
@@ -176,7 +176,7 @@ def test_add_row_validate(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_row_validate_bad_data_one_col(self):
-        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(name='example', term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
             name='Species_1',
             description='...',
@@ -193,7 +193,7 @@ def test_add_row_validate_bad_data_one_col(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_row_validate_bad_data_all_col(self):
-        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(name='example', term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
             name='Species_1',
             description='...',

tests/unit/test_io_hdf5_h5tools.py

@@ -149,7 +149,7 @@ def test_write_dataset_string(self):
     ##########################################
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_write_dataset_TermSetWrapper(self):
-        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(name='example', term_schema_path='tests/unit/example_test_term_set.yaml')
         a = TermSetWrapper(value=['Homo sapiens'], termset=terms)
         self.io.write_dataset(self.f, DatasetBuilder('test_dataset', a, attributes={}))
         dset = self.f['test_dataset']
@@ -826,7 +826,7 @@ def test_roundtrip_pathlib_path(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_roundtrip_TermSetWrapper_dataset(self):
-        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(name='example', 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))
@@ -845,7 +845,7 @@ def test_roundtrip_TermSetWrapper_dataset(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_roundtrip_TermSetWrapper_attribute(self):
-        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(name='example', term_schema_path='tests/unit/example_test_term_set.yaml')
         foo = Foo(name="species", attr1=TermSetWrapper(value='Homo sapiens', termset=terms),
                   attr2=0, my_data=[1,2,3])
         foobucket = FooBucket('bucket1', [foo])
@@ -1076,7 +1076,7 @@ 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')
+        terms = TermSet(name='example', term_schema_path='tests/unit/example_test_term_set.yaml')
         foo = Foo(name="species", attr1='attr1', attr2=0,
                   my_data=TermSetWrapper(value=['Homo sapiens'],
                                                          termset=terms))

tests/unit/test_term_set.py

@@ -25,50 +25,51 @@ def setUp(self):
             self.skipTest("optional LinkML module is not installed")
 
     def test_termset_setup(self):
-        termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        termset = TermSet(name='test', term_schema_path='tests/unit/example_test_term_set.yaml')
+        self.assertEqual(termset.name, 'test')
         self.assertEqual(list(termset.sources), ['NCBI_TAXON'])
 
     def test_view_set(self):
-        termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        termset = TermSet(name='test', term_schema_path='tests/unit/example_test_term_set.yaml')
         expected = ['Homo sapiens', 'Mus musculus', 'Ursus arctos horribilis', 'Myrmecophaga tridactyla']
         self.assertEqual(list(termset.view_set), expected)
         self.assertIsInstance(termset.view, SchemaView)
 
     def test_termset_validate(self):
-        termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        termset = TermSet(name='test', term_schema_path='tests/unit/example_test_term_set.yaml')
         self.assertEqual(termset.validate('Homo sapiens'), True)
 
     def test_termset_validate_false(self):
-        termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        termset = TermSet(name='test', term_schema_path='tests/unit/example_test_term_set.yaml')
         self.assertEqual(termset.validate('missing_term'), False)
 
     def test_get_item(self):
-        termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        termset = TermSet(name='test', term_schema_path='tests/unit/example_test_term_set.yaml')
         self.assertEqual(termset['Homo sapiens'].id, 'NCBI_TAXON:9606')
         self.assertEqual(termset['Homo sapiens'].description, 'the species is human')
         self.assertEqual(termset['Homo sapiens'].meaning, 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606')
 
     def test_get_item_key_error(self):
-        termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        termset = TermSet(name='test', term_schema_path='tests/unit/example_test_term_set.yaml')
         with self.assertRaises(ValueError):
             termset['Homo Ssapiens']
 
     def test_schema_sheets_and_path_provided_error(self):
         folder = os.path.join(CUR_DIR, "test_term_set_input", "schemasheets")
         with self.assertRaises(ValueError):
-            TermSet(term_schema_path='tests/unit/example_test_term_set.yaml', schemasheets_folder=folder)
+            TermSet(name='test', term_schema_path='tests/unit/example_test_term_set.yaml', schemasheets_folder=folder)
 
     def test_view_set_sheets(self):
         folder = os.path.join(CUR_DIR, "test_term_set_input", "schemasheets")
-        termset = TermSet(schemasheets_folder=folder)
+        termset = TermSet(name='name', schemasheets_folder=folder)
         expected = ['ASTROCYTE', 'INTERNEURON', 'MICROGLIAL_CELL', 'MOTOR_NEURON',
                     'OLIGODENDROCYTE', 'PYRAMIDAL_NEURON']
         self.assertEqual(list(termset.view_set), expected)
         self.assertIsInstance(termset.view, SchemaView)
 
     def test_enum_expander(self):
         schema_path = 'tests/unit/example_dynamic_term_set.yaml'
-        termset = TermSet(term_schema_path=schema_path, dynamic=True)
+        termset = TermSet(name='test', term_schema_path=schema_path, dynamic=True)
         # check that interneuron term is in materialized schema
         self.assertIn("CL:0000099", termset.view_set)
         # check that motor neuron term is in materialized schema
@@ -88,7 +89,7 @@ def test_enum_expander(self):
 
     def test_enum_expander_output(self):
         schema_path = 'tests/unit/example_dynamic_term_set.yaml'
-        termset = TermSet(term_schema_path=schema_path, dynamic=True)
+        termset = TermSet(name='test', term_schema_path=schema_path, dynamic=True)
         convert_path = termset._TermSet__enum_expander()
         convert_path = os.path.normpath(convert_path)
 
@@ -102,7 +103,7 @@ def test_enum_expander_output(self):
 
     def test_folder_output(self):
         folder = os.path.join(CUR_DIR, "test_term_set_input", "schemasheets")
-        termset = TermSet(schemasheets_folder=folder)
+        termset = TermSet(name='test', schemasheets_folder=folder)
         actual_path = termset._TermSet__schemasheets_convert()
         expected_path = os.path.normpath(os.path.join(os.path.dirname(folder), "schemasheets/nwb_static_enums.yaml"))
         self.assertEqual(actual_path, expected_path)
@@ -114,7 +115,7 @@ def setUp(self):
         if not REQUIREMENTS_INSTALLED:
             self.skipTest("optional LinkML module is not installed")
 
-        self.termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        self.termset = TermSet(name='test', term_schema_path='tests/unit/example_test_term_set.yaml')
 
         self.wrapped_array = TermSetWrapper(value=np.array(['Homo sapiens']), termset=self.termset)
         self.wrapped_list = TermSetWrapper(value=['Homo sapiens'], termset=self.termset)