Merge pull request #183 from biolink/fix_descendents

fixes tests associated with get_descendents

Author: sierra-moxon

bmt/toolkit.py

@@ -1061,7 +1061,13 @@ def get_element(self, name: str) -> Optional[Element]:
             element = self.get_element(name.replace("_", " "))
         if element is None:
             for e, el in self.view.all_elements().items():
-                if el.name.lower() == name.lower():
+                el_normalized = el.name.lower().replace(' ', '').replace('_', '')
+                name_normalized = name.lower().replace(' ', '').replace('_', '')
+                parsed_normalized = parsed_name.lower().replace(' ', '').replace('_', '')
+                if (el.name.lower() == name.lower() or 
+                    el.name.lower() == parsed_name.lower() or
+                    el_normalized == name_normalized or
+                    el_normalized == parsed_normalized):
                     element = el
 
         if isinstance(element, ClassDefinition) and element.class_uri is None:

poetry.lock

@@ -1258,3 +1258,52 @@ def test_get_all_types(toolkit):
 def test_get_all_multivalued_slots(toolkit):
     assert "synonym" in toolkit.get_all_multivalued_slots()
     assert "id" not in toolkit.get_all_multivalued_slots()
+
+
+def test_get_descendants_with_biolink_prefix(toolkit):
+    assert 'noncoding RNA product' in toolkit.get_descendants("noncoding RNA product")
+    assert 'microRNA' in toolkit.get_descendants("noncoding RNA product")
+    assert 'siRNA' in toolkit.get_descendants("noncoding RNA product")
+    
+    assert 'noncoding RNA product' in toolkit.get_descendants("biolink:NoncodingRNAProduct")
+    assert 'microRNA' in toolkit.get_descendants("biolink:NoncodingRNAProduct")
+    assert 'siRNA' in toolkit.get_descendants("biolink:NoncodingRNAProduct")
+    
+    assert 'microRNA' in toolkit.get_descendants("biolink:MicroRNA")
+    assert 'siRNA' in toolkit.get_descendants("biolink:SiRNA")
+
+
+def test_get_element_with_biolink_prefix_edge_cases(toolkit):
+    elem = toolkit.get_element("biolink:NoncodingRNAProduct")
+    assert elem is not None
+    assert elem.name == "noncoding RNA product"
+    
+    elem = toolkit.get_element("biolink:MicroRNA")
+    assert elem is not None
+    assert elem.name == "microRNA"
+    
+    elem = toolkit.get_element("biolink:SiRNA")
+    assert elem is not None
+    assert elem.name == "siRNA"
+    
+    elem = toolkit.get_element("biolink:gene_fusion_with")
+    assert elem is not None
+    assert elem.name == "gene_fusion_with"
+    
+    elem = toolkit.get_element("biolink:genetic_neighborhood_of")
+    assert elem is not None
+    assert elem.name == "genetic_neighborhood_of"
+
+
+def test_get_parent_with_biolink_prefix(toolkit):
+    parent = toolkit.get_parent('microRNA')
+    assert parent == 'noncoding RNA product'
+    
+    parent_curie = toolkit.get_parent('microRNA', formatted=True)
+    assert parent_curie == 'biolink:NoncodingRNAProduct'
+    
+    parent_from_curie = toolkit.get_parent('biolink:microRNA')
+    assert parent_from_curie == 'noncoding RNA product'
+    
+    parent_from_curie_formatted = toolkit.get_parent('biolink:microRNA', formatted=True)
+    assert parent_from_curie_formatted == 'biolink:NoncodingRNAProduct'