Merge pull request #102 from biolink/support_predicate_maps

add test for and fixes #93, fixes #86

Author: sierra-moxon

bmt/toolkit.py

@@ -18,7 +18,6 @@
 
 from bmt.utils import format_element, parse_name
 
-
 Url = str
 Path = str
 
@@ -30,7 +29,6 @@
 ASSOCIATION_SLOT = "association slot"
 RELATED_TO = "related to"
 
-
 CACHE_SIZE = 1024
 
 logger = logging.getLogger(__name__)
@@ -48,7 +46,7 @@ class Toolkit(object):
     """
 
     def __init__(
-        self, schema: Union[Url, Path, TextIO, SchemaDefinition] = REMOTE_PATH,
+            self, schema: Union[Url, Path, TextIO, SchemaDefinition] = REMOTE_PATH,
             predicate_map: Url = PREDICATE_MAP,
             infores_map: Url = INFORES_MAP
     ) -> None:
@@ -292,7 +290,8 @@ def _filter_secondary(self, elements: List[str]) -> List[str]:
         return filtered_elements
 
     @lru_cache(CACHE_SIZE)
-    def get_permissible_value_ancestors(self, permissible_value: str, enum_name: str, formatted: bool = False) -> List[str]:
+    def get_permissible_value_ancestors(self, permissible_value: str, enum_name: str, formatted: bool = False) -> List[
+        str]:
         """
         Get ancestors of a permissible value.
 
@@ -394,11 +393,11 @@ def get_permissible_value_parent(self, permissible_value: str, enum_name: str) -
 
     @lru_cache(CACHE_SIZE)
     def get_ancestors(
-        self,
-        name: str,
-        reflexive: bool = True,
-        formatted: bool = False,
-        mixin: bool = True,
+            self,
+            name: str,
+            reflexive: bool = True,
+            formatted: bool = False,
+            mixin: bool = True,
     ) -> List[str]:
         """
         Gets a list of names of ancestors.
@@ -444,11 +443,11 @@ def _get_mixin_descendants(self, ancestors: List[ElementName]) -> List[ElementNa
 
     @lru_cache(CACHE_SIZE)
     def get_descendants(
-        self,
-        name: str,
-        reflexive: bool = True,
-        formatted: bool = False,
-        mixin: bool = True,
+            self,
+            name: str,
+            reflexive: bool = True,
+            formatted: bool = False,
+            mixin: bool = True,
     ) -> List[str]:
         """
         Gets a list of names of descendants.
@@ -487,9 +486,27 @@ def get_descendants(
 
         return self._format_all_elements(filtered_desc, formatted)
 
+    @lru_cache(CACHE_SIZE)
+    def get_all_multivalued_slots(self) -> List[str]:
+        """
+        Gets a list of names of all multivalued slots.
+
+        Returns
+        -------
+        List[str]
+            The names of all multivalued slots
+
+        """
+        multivalued_slots = []
+        slots = self.view.all_slots()
+        for slot_name, slot_def in slots.items():
+            if self.view.is_multivalued(slot_name):
+                multivalued_slots.append(slot_name)
+        return multivalued_slots
+
     @lru_cache(CACHE_SIZE)
     def get_children(
-        self, name: str, formatted: bool = False, mixin: bool = True
+            self, name: str, formatted: bool = False, mixin: bool = True
     ) -> List[str]:
         """
         Gets a list of names of children.
@@ -568,7 +585,6 @@ def get_element(self, name: str) -> Optional[Element]:
                 if name in self.view.all_aliases()[e]:
                     element = self.view.get_element(e)
         if element is None and "_" in name:
-            print("has a _")
             element = self.get_element(name.replace("_", " "))
         if element is None:
             for e, el in self.view.all_elements().items():
@@ -577,11 +593,11 @@ def get_element(self, name: str) -> Optional[Element]:
         return element
 
     def get_slot_domain(
-        self,
-        slot_name,
-        include_ancestors: bool = False,
-        formatted: bool = False,
-        mixin: bool = True,
+            self,
+            slot_name,
+            include_ancestors: bool = False,
+            formatted: bool = False,
+            mixin: bool = True,
     ) -> List[str]:
         """
         Get the domain for a given slot.
@@ -625,11 +641,11 @@ def get_slot_domain(
         return self._format_all_elements(slot_domain, formatted)
 
     def get_slot_range(
-        self,
-        slot_name,
-        include_ancestors: bool = False,
-        formatted: bool = False,
-        mixin: bool = True,
+            self,
+            slot_name,
+            include_ancestors: bool = False,
+            formatted: bool = False,
+            mixin: bool = True,
     ) -> List[str]:
         """
         Get the range for a given slot.
@@ -662,11 +678,11 @@ def get_slot_range(
         return self._format_all_elements(slot_range, formatted)
 
     def get_all_slots_with_class_domain(
-        self,
-        class_name,
-        check_ancestors: bool = False,
-        formatted: bool = False,
-        mixin: bool = True,
+            self,
+            class_name,
+            check_ancestors: bool = False,
+            formatted: bool = False,
+            mixin: bool = True,
     ) -> List[str]:
         """
         Given a class, get all the slots where the class is the domain.
@@ -694,11 +710,11 @@ def get_all_slots_with_class_domain(
         return self._format_all_elements(slot_names, formatted)
 
     def get_all_slots_with_class_range(
-        self,
-        class_name,
-        check_ancestors: bool = False,
-        formatted: bool = False,
-        mixin: bool = True,
+            self,
+            class_name,
+            check_ancestors: bool = False,
+            formatted: bool = False,
+            mixin: bool = True,
     ) -> List[str]:
         """
         Given a class, get all the slots where the class is the range.
@@ -726,11 +742,11 @@ def get_all_slots_with_class_range(
         return self._format_all_elements(slot_names, formatted)
 
     def get_all_predicates_with_class_domain(
-        self,
-        class_name,
-        check_ancestors: bool = False,
-        formatted: bool = False,
-        mixin: bool = True,
+            self,
+            class_name,
+            check_ancestors: bool = False,
+            formatted: bool = False,
+            mixin: bool = True,
     ) -> List[str]:
         """
         Given a class, get all Biolink predicates where the class is the domain.
@@ -764,11 +780,11 @@ def get_all_predicates_with_class_domain(
         return self._format_all_elements(filtered_slots, formatted)
 
     def get_all_predicates_with_class_range(
-        self,
-        class_name,
-        check_ancestors: bool = False,
-        formatted: bool = False,
-        mixin: bool = True,
+            self,
+            class_name,
+            check_ancestors: bool = False,
+            formatted: bool = False,
+            mixin: bool = True,
     ):
         """
         Given a class, get all Biolink predicates where the class is the range.
@@ -802,11 +818,11 @@ def get_all_predicates_with_class_range(
         return self._format_all_elements(filtered_slots, formatted)
 
     def get_all_properties_with_class_domain(
-        self,
-        class_name,
-        check_ancestors: bool = False,
-        formatted: bool = False,
-        mixin: bool = True,
+            self,
+            class_name,
+            check_ancestors: bool = False,
+            formatted: bool = False,
+            mixin: bool = True,
     ) -> List[str]:
         """
         Given a class, get all Biolink properties where the class is the domain.
@@ -840,11 +856,11 @@ def get_all_properties_with_class_domain(
         return self._format_all_elements(filtered_slots, formatted)
 
     def get_all_properties_with_class_range(
-        self,
-        class_name,
-        check_ancestors: bool = False,
-        formatted: bool = False,
-        mixin: bool = True,
+            self,
+            class_name,
+            check_ancestors: bool = False,
+            formatted: bool = False,
+            mixin: bool = True,
     ) -> List[str]:
         """
         Given a class, get all Biolink properties where the class is the range.
@@ -911,7 +927,7 @@ def get_value_type_for_slot(self, slot_name, formatted: bool = False) -> str:
         return element_type
 
     def _get_all_slots_with_class_domain(
-        self, element: Element, check_ancestors: bool, mixin: bool = True
+            self, element: Element, check_ancestors: bool, mixin: bool = True
     ) -> List[Element]:
         """
         Given a class, get all the slots where the class is the domain.
@@ -944,7 +960,7 @@ def _get_all_slots_with_class_domain(
         return slots
 
     def _get_all_slots_with_class_range(
-        self, element: Element, check_ancestors: bool, mixin: bool = True
+            self, element: Element, check_ancestors: bool, mixin: bool = True
     ) -> List[Element]:
         """
         Given a class, get all the slots where the class is the range.
@@ -968,7 +984,7 @@ def _get_all_slots_with_class_range(
         for k, v in self.view.schema.slots.items():
             if check_ancestors:
                 if v.range == element.name or v.range in self.get_ancestors(
-                    element.name, mixin
+                        element.name, mixin
                 ):
                     slots.append(v)
             else:
@@ -1200,11 +1216,11 @@ def get_element_by_prefix(
 
     @lru_cache(CACHE_SIZE)
     def get_element_by_mapping(
-        self,
-        identifier: str,
-        most_specific: bool = False,
-        formatted: bool = False,
-        mixin: bool = True,
+            self,
+            identifier: str,
+            most_specific: bool = False,
+            formatted: bool = False,
+            mixin: bool = True,
     ) -> Optional[str]:
         """
         Get a Biolink Model element by mapping.
@@ -1297,7 +1313,7 @@ def _get_element_by_mapping(self, identifier: str) -> List[str]:
 
     @lru_cache(CACHE_SIZE)
     def get_element_by_exact_mapping(
-        self, identifier: str, formatted: bool = False
+            self, identifier: str, formatted: bool = False
     ) -> List[str]:
         """
         Given an identifier as IRI/CURIE, find a Biolink element that corresponds
@@ -1324,7 +1340,7 @@ def get_element_by_exact_mapping(
 
     @lru_cache(CACHE_SIZE)
     def get_element_by_close_mapping(
-        self, identifier: str, formatted: bool = False
+            self, identifier: str, formatted: bool = False
     ) -> List[str]:
         """
         Given an identifier as IRI/CURIE, find a Biolink element that corresponds
@@ -1350,7 +1366,7 @@ def get_element_by_close_mapping(
 
     @lru_cache(CACHE_SIZE)
     def get_element_by_related_mapping(
-        self, identifier: str, formatted: bool = False
+            self, identifier: str, formatted: bool = False
     ) -> List[str]:
         """
         Given an identifier as IRI/CURIE, find a Biolink element that corresponds
@@ -1376,7 +1392,7 @@ def get_element_by_related_mapping(
 
     @lru_cache(CACHE_SIZE)
     def get_element_by_narrow_mapping(
-        self, identifier: str, formatted: bool = False
+            self, identifier: str, formatted: bool = False
     ) -> List[str]:
         """
         Given an identifier as IRI/CURIE, find a Biolink element that corresponds
@@ -1402,7 +1418,7 @@ def get_element_by_narrow_mapping(
 
     @lru_cache(CACHE_SIZE)
     def get_element_by_broad_mapping(
-        self, identifier: str, formatted: bool = False
+            self, identifier: str, formatted: bool = False
     ) -> List[str]:
         """
         Given an identifier as IRI/CURIE, find a Biolink element that corresponds
@@ -1428,7 +1444,7 @@ def get_element_by_broad_mapping(
 
     @lru_cache(CACHE_SIZE)
     def get_all_elements_by_mapping(
-        self, identifier: str, formatted: bool = False
+            self, identifier: str, formatted: bool = False
     ) -> List[str]:
         """
         Given an identifier as IRI/CURIE, find all Biolink elements that correspond
@@ -1451,7 +1467,7 @@ def get_all_elements_by_mapping(
         return self._format_all_elements(mappings, formatted)
 
     def _format_all_elements(
-        self, elements: List[str], formatted: bool = False
+            self, elements: List[str], formatted: bool = False
     ) -> List[str]:
         """
         Format all the elements in a given list.

tests/unit/test_toolkit.py

@@ -460,3 +460,27 @@ def test_get_value_type_for_slot(toolkit):
     assert "biolink:CategoryType" in toolkit.get_value_type_for_slot(
         "category", formatted=True
     )
+
+
+def test_get_all_types(toolkit):
+    basic_descendants = {}
+
+    # get_all_types()
+    types = toolkit.get_all_types()
+
+    for element in types:
+        try:
+            basic_descendants.update({
+                element: toolkit.get_descendants(
+                    element,
+                    reflexive=False,
+                    mixin=False,
+                )
+            })
+        except Exception as e:
+            assert False, f"Error getting descendants for {element}: {e}"
+
+
+def test_get_all_multivalued_slots(toolkit):
+    assert "synonym" in toolkit.get_all_multivalued_slots()
+    assert "id" not in toolkit.get_all_multivalued_slots()