Merge pull request #169 from biolink/add-utility-predicate-methods

Added a couple of utility methods useful at my end but which seemed to belong in BMT

bmt/toolkit.py

@@ -1590,10 +1590,65 @@ def is_mixin(self, name: str) -> bool:
         is_mixin = element.mixin if isinstance(element, Definition) else False
         return is_mixin
 
+    def is_symmetric(self, name: str) -> bool:
+        """
+        Checks if a given element identified by name, is a symmetric (predicate) slot.
+
+        Parameters
+        ----------
+        name: str
+            The name or alias of an element in the Biolink Model
+
+        Returns
+        -------
+        bool
+            That the named element is tagged as symmetric: true in Biolink Model
+        """
+        if not name:
+            return False
+        element: Optional[Element] = self.get_element(name)
+        if element is not None and element['symmetric']:
+            return True
+        else:
+            return False
+
     @lru_cache(CACHE_SIZE)
     def get_inverse(self, slot_name: str):
         return self.view.inverse(slot_name)
 
+    @lru_cache(CACHE_SIZE)
+    def get_inverse_predicate(
+            self, predicate: Optional[str],
+            formatted: bool = False
+    ) -> Optional[str]:
+        """
+        Utility wrapper of logic to robustly test if a predicate exists and has an inverse.
+
+        Parameters
+        ----------
+        predicate: Optional[str]
+            CURIE or string name of predicate in the Biolink Model, for which the inverse is sought
+        formatted: bool
+            Whether to format element names as CURIEs
+
+        Returns
+        -------
+        Optional[str]
+            CURIE string of inverse predicate, if it exists; None otherwise
+        """
+        if predicate and self.is_predicate(predicate):
+            predicate_name = parse_name(predicate)
+            inverse_predicate_name = self.get_inverse(predicate_name)
+            if not inverse_predicate_name:
+                if self.is_symmetric(predicate_name):
+                    inverse_predicate_name = predicate_name
+                else:
+                    inverse_predicate_name = None
+            if inverse_predicate_name:
+                ip = self.get_element(inverse_predicate_name)
+                return format_element(ip) if formatted else str(ip.name)
+        return None
+
     @lru_cache(CACHE_SIZE)
     def has_inverse(self, name: str) -> bool:
         """

tests/unit/test_toolkit.py

@@ -92,6 +92,7 @@ def test_sv(toolkit):
     print(ancs)
     assert 'related to' in ancs
 
+
 def test_get_denormalized_association_slots(toolkit):
     annotations = toolkit.get_denormalized_association_slots(formatted=True)
     print(annotations)
@@ -667,9 +668,17 @@ def test_is_mixin(toolkit):
     assert not toolkit.is_mixin("this_does_not_exist")
 
 
+def test_is_symmetric(toolkit):
+    assert not toolkit.is_symmetric("")
+    assert not toolkit.is_symmetric("this_predicate_does_not_exist")
+    assert toolkit.is_symmetric(RELATED_TO)
+    assert toolkit.is_symmetric(INTERACTS_WITH)
+    assert not toolkit.is_symmetric(AFFECTS)
+
+
 def test_is_translator_canonical_predicate(toolkit):
     assert toolkit.is_translator_canonical_predicate("studied to treat")
-    assert not toolkit.is_translator_canonical_predicate("this_does_not_exist")
+    assert not toolkit.is_translator_canonical_predicate("this_predicate_does_not_exist")
     assert not toolkit.is_translator_canonical_predicate("completed by")
     assert toolkit.is_translator_canonical_predicate("regulates")
 
@@ -686,6 +695,13 @@ def test_get_inverse(toolkit):
     assert toolkit.get_inverse(sd.name) == HAS_ACTIVE_COMPONENT
 
 
+def test_get_get_inverse_predicate(toolkit):
+    assert toolkit.get_inverse_predicate(ACTIVE_IN) == HAS_ACTIVE_COMPONENT
+    assert toolkit.get_inverse_predicate(HAS_ACTIVE_COMPONENT) == ACTIVE_IN
+    assert toolkit.get_inverse_predicate(RELATED_TO) == RELATED_TO
+    assert toolkit.get_inverse_predicate(RELATED_TO, formatted=True) == BIOLINK_RELATED_TO
+
+
 def test_category(toolkit):
     assert toolkit.is_category(NAMED_THING)
     assert toolkit.is_category(GENE)
@@ -868,7 +884,11 @@ def test_permissible_value_ancestors(toolkit):
     )
     assert "increased" in toolkit.get_permissible_value_parent("upregulated", "DirectionQualifierEnum")
     assert "upregulated" in toolkit.get_permissible_value_children("increased", "DirectionQualifierEnum")
-    assert "synthesis" in toolkit.get_permissible_value_descendants("activity_or_abundance", "GeneOrGeneProductOrChemicalEntityAspectEnum")
+    assert "synthesis" in \
+           toolkit.get_permissible_value_descendants(
+               "activity_or_abundance",
+               "GeneOrGeneProductOrChemicalEntityAspectEnum"
+           )
 
 
 def test_ancestors_for_kgx(toolkit):