feedback

hdmf-dev · Jun 30, 2023 · 6f9e3c6 · 6f9e3c6
1 parent 3e8cd3d
commit 6f9e3c6
Show file tree

Hide file tree

Showing 8 changed files with 24 additions and 30 deletions.
diff --git a/docs/gallery/example_term_set.yaml b/docs/gallery/example_term_set.yaml
@@ -1,5 +1,6 @@
 id: pynert/termset/species_example
 name: Species
+version: 0.0.1
 prefixes:
   NCBI_TAXON: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=
 imports:

diff --git a/docs/gallery/plot_term_set.py b/docs/gallery/plot_term_set.py
@@ -67,7 +67,7 @@
 # Users can index specific terms from the :py:class:`~hdmf.TermSet`.
 if LINKML_INSTALLED:
     terms = TermSet(name='Species', term_schema_path='docs/gallery/example_term_set.yaml')
-    terms.view_set
+    print(terms.view_set)
 
     # Retrieve a specific term
     terms['Homo sapiens']

diff --git a/src/hdmf/term_set.py b/src/hdmf/term_set.py
@@ -12,32 +12,24 @@ class TermSet():
     :ivar ontology_source_uri: The uri of the ontology
     """
     def __init__(self,
-                 name: str,
                  term_schema_path: str,
-                 # ontology_version: str,
                  ):
         """
-        :param name: The name of the TermSet
         :param term_schema_path: The path to LinkML YAML enumeration schema
-        :param ontology_version: The version of the ontology
-        :param ontology_source_name: The name of the ontology
-        :param ontology_source_uri: The uri of the ontology
+
         """
         try:
             from linkml_runtime.utils.schemaview import SchemaView
         except ImportError:
             msg = "Install linkml_runtime"
             raise ValueError(msg)
-        self.name = name
         self.term_schema_path = term_schema_path
         self.view = SchemaView(self.term_schema_path)
         self.sources = self.view.schema.prefixes
 
     def __repr__(self):
         re = "class: %s\n" % str(self.__class__)
-        re += "name: %s\n" % self.name
         re += "term_schema_path: %s\n" % self.term_schema_path
-        re += "ontology_source_name: %s\n" % self.sources
         return re
 
     def _perm_value_key_info(self, perm_values_dict: dict, key: str):

diff --git a/tests/unit/common/test_resources.py b/tests/unit/common/test_resources.py
@@ -271,7 +271,7 @@ def test_add_ref_search_for_file_error(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_ref_termset(self):
-        terms = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         er = ExternalResources()
         em = ExternalResourcesManagerContainer()
         em.link_resources(er)
@@ -324,7 +324,7 @@ def test_add_ref_termset_missing_attribute_termset_value(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_ref_termset_missing_terms(self):
-        terms = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         er = ExternalResources()
         em = ExternalResourcesManagerContainer()
         em.link_resources(er)
@@ -348,7 +348,7 @@ def test_add_ref_termset_missing_terms(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_ref_termset_missing_file_error(self):
-        terms = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         er = ExternalResources()
 
         col1 = VectorData(name='Species_Data',

diff --git a/tests/unit/common/test_table.py b/tests/unit/common/test_table.py
@@ -105,7 +105,7 @@ def test_constructor_ids_bad_ids(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_add_col_validate(self):
-        terms = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
             name='Species_1',
             description='...',
@@ -126,7 +126,7 @@ 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(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
             name='Species_1',
             description='...',
@@ -142,7 +142,7 @@ 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(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
             name='Species_1',
             description='...',
@@ -166,7 +166,7 @@ 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(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
             name='Species_1',
             description='...',
@@ -185,7 +185,7 @@ 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(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         col1 = VectorData(
             name='Species_1',
             description='...',

diff --git a/tests/unit/example_test_term_set.yaml b/tests/unit/example_test_term_set.yaml
@@ -1,5 +1,6 @@
 id: pynert/termset/species_example
 name: Species
+version: 0.0.1
 prefixes:
   NCBI_TAXON: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=
 imports:

diff --git a/tests/unit/test_container.py b/tests/unit/test_container.py
@@ -307,54 +307,54 @@ def test_shape_list(self):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_validate_data(self):
-        terms = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         data_obj = Data(name='species', data=['Homo sapiens'])
         bool = data_obj.validate_data(term='Homo sapiens', term_set=terms)
         self.assertEqual(bool, True)
     #
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_validate_data_error(self):
-        terms = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         data_obj = Data(name='species', data=['Homo sapiens'])
         bool = data_obj.validate_data(term='term', term_set=terms)
         self.assertEqual(bool, False)
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_validate(self):
-        terms = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         data_obj = Data(name='species', data=['Homo sapiens'], term_set=terms)
         self.assertEqual(data_obj.data, ['Homo sapiens'])
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_validate_value_error(self):
-        terms = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         with self.assertRaises(ValueError):
             Data(name='species', data=['Macaca mulatta'], term_set=terms)
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_append_validate(self):
-        terms = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         data_obj = Data(name='species', data=['Homo sapiens'], term_set=terms)
         data_obj.append('Mus musculus')
         self.assertEqual(data_obj.data, ['Homo sapiens', 'Mus musculus'])
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_append_validate_error(self):
-        terms = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         data_obj = Data(name='species', data=['Homo sapiens'], term_set=terms)
         with self.assertRaises(ValueError):
             data_obj.append('Macaca mulatta')
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_extend_validate(self):
-        terms = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         data_obj = Data(name='species', data=['Homo sapiens'], term_set=terms)
         data_obj.extend(['Mus musculus', 'Ursus arctos horribilis'])
         self.assertEqual(data_obj.data, ['Homo sapiens', 'Mus musculus', 'Ursus arctos horribilis'])
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_extend_validate_bad_data_error(self):
-        terms = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         data_obj = Data(name='species', data=['Homo sapiens'], term_set=terms)
         with self.assertRaises(ValueError):
             data_obj.extend(['Mus musculus', 'Oryctolagus cuniculus'])

diff --git a/tests/unit/test_term_set.py b/tests/unit/test_term_set.py
@@ -13,24 +13,24 @@ class TestTermSet(TestCase):
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_termset_setup(self):
-        termset = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         self.assertEqual(list(termset.sources), ['NCBI_TAXON'])
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_view_set(self):
-        termset = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        termset = TermSet(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)
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_get_item(self):
-        termset = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        termset = TermSet(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, 'description')
         self.assertEqual(termset['Homo sapiens'].meaning, 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606')
 
     @unittest.skipIf(not LINKML_INSTALLED, "optional LinkML module is not installed")
     def test_get_item_key_error(self):
-        termset = TermSet(name='species', term_schema_path='tests/unit/example_test_term_set.yaml')
+        termset = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
         with self.assertRaises(ValueError):
             termset['Homo Ssapiens']