Merge pull request #117 from biolink/fix_uri_for

add class and slot uris in get_element method, fixes #116

bmt/toolkit.py

@@ -592,6 +592,11 @@ def get_element(self, name: str) -> Optional[Element]:
             for e, el in self.view.all_elements().items():
                 if el.name.lower() == name.lower():
                     element = el
+
+        if type(element) == ClassDefinition and element.class_uri is None:
+            element.class_uri = format_element(element)
+        if type(element) == SlotDefinition and element.slot_uri is None:
+            element.slot_uri = format_element(element)
         return element
 
     def get_slot_domain(

tests/unit/test_toolkit.py

@@ -71,7 +71,7 @@ def test_get_model_version(toolkit):
 
 def test_get_id_prefixes(toolkit):
     tclass = toolkit.get_element('biolink:Gene')
-    print(tclass.id_prefixes)
+    assert tclass.class_uri == "biolink:Gene"
 
 
 def test_get_element_via_alias(toolkit):
@@ -351,6 +351,10 @@ def test_is_permissible_value_of_enum(toolkit):
 
 def test_ancestors(toolkit):
     assert RELATED_TO in toolkit.get_ancestors(CAUSES)
+    a = toolkit.get_ancestors(GENE)
+    ancs = [toolkit.get_element(ai)['class_uri'] for ai in a]
+    assert "biolink:NamedThing" in ancs
+
     assert "biolink:ChemicalEntityOrGeneOrGeneProduct" in toolkit.get_ancestors(
         GENE, formatted=True
     )
@@ -381,6 +385,8 @@ def test_ancestors(toolkit):
     )
     assert THING_WITH_TAXON in toolkit.get_ancestors(PHENOTYPIC_FEATURE)
 
+    assert GENE not in toolkit.get_ancestors("biolink:ChemicalEntity", reflexive=False)
+
 
 def test_permissible_value_ancestors(toolkit):
     assert "increased" in toolkit.get_permissible_value_ancestors("upregulated", "DirectionQualifierEnum")