categorical variation -> categorical variant

src/metakb/load_data.py

@@ -261,21 +261,21 @@ def _add_variation(tx: ManagedTransaction, variation_in: dict) -> None:
     tx.run(query, **v)
 
 
-def _add_categorical_variation(
+def _add_categorical_variant(
     tx: ManagedTransaction,
-    categorical_variation_in: dict,
+    categorical_variant_in: dict,
     ids_in_studies: set[str],
 ) -> None:
-    """Add categorical variation objects to DB.
+    """Add categorical variant objects to DB.
 
     :param tx: Transaction object provided to transaction functions
-    :param categorical_variation_in: Categorical variation CDM object
+    :param categorical_variant_in: Categorical variant CDM object
     :param ids_in_studies: IDs found in studies
     """
-    if categorical_variation_in["id"] not in ids_in_studies:
+    if categorical_variant_in["id"] not in ids_in_studies:
         return
 
-    cv = categorical_variation_in.copy()
+    cv = categorical_variant_in.copy()
 
     mp_nonnull_keys = [
         _create_parameterized_query(
@@ -476,7 +476,7 @@ def add_transformed_data(driver: Driver, data: dict) -> None:
         loaded_study_count = 0
 
         for cv in data.get("categorical_variants", []):
-            session.execute_write(_add_categorical_variation, cv, ids_in_studies)
+            session.execute_write(_add_categorical_variant, cv, ids_in_studies)
 
         for doc in data.get("documents", []):
             session.execute_write(_add_document, doc, ids_in_studies)

src/metakb/query.py

@@ -47,7 +47,7 @@ class PaginationParamError(Exception):
 
 class VariationRelation(str, Enum):
     """Constrain possible values for the relationship between variations and
-    categorical variations.
+    categorical variants.
     """
 
     HAS_MEMBERS = "HAS_MEMBERS"
@@ -575,11 +575,11 @@ def _get_disease(self, node: dict) -> Disease:
         return Disease(**node)
 
     def _get_variations(self, cv_id: str, relation: VariationRelation) -> list[dict]:
-        """Get list of variations associated to categorical variation
+        """Get list of variations associated to categorical variant
 
-        :param cv_id: ID for categorical variation
-        :param relation: Relation type for categorical variation and variation
-        :return: List of variations with `relation` to categorical variation. If
+        :param cv_id: ID for categorical variant
+        :param relation: Relation type for categorical variant and variation
+        :return: List of variations with `relation` to categorical variant. If
             VariationRelation.HAS_MEMBERS, returns at least one variation. Otherwise,
             returns exactly one variation
         """
@@ -615,10 +615,10 @@ def _get_variations(self, cv_id: str, relation: VariationRelation) -> list[dict]
         return variations
 
     def _get_cat_var(self, node: dict) -> CategoricalVariant:
-        """Get categorical variation data from a node with relationship ``HAS_VARIANT``
+        """Get categorical variant data from a node with relationship ``HAS_VARIANT``
 
         :param node: Variant node data. This will be mutated.
-        :return: Categorical Variation data
+        :return: Categorical Variant data
         """
         node["mappings"] = _deserialize_field(node, "mappings")
 

src/metakb/transformers/civic.py

@@ -209,7 +209,7 @@ async def transform(self, harvested_data: CivicHarvestedData) -> None:
             for mp in molecular_profiles
             if f"civic.vid:{mp['variant_ids'][0]}" in able_to_normalize_vids
         ]
-        self._add_protein_consequences(mps, mp_id_to_v_id_mapping)
+        self._add_categorical_variants(mps, mp_id_to_v_id_mapping)
 
         # Add variant therapeutic response study data. Will update `studies`
         self._add_variant_therapeutic_response_studies(
@@ -366,10 +366,10 @@ def _get_predicate(
                 predicate = TherapeuticResponsePredicate.RESISTANCE
         return predicate
 
-    def _add_protein_consequences(
+    def _add_categorical_variants(
         self, molecular_profiles: list[dict], mp_id_to_v_id_mapping: dict
     ) -> None:
-        """Create Protein Sequence Consequence objects for all supported MP records.
+        """Create Categorical Variant objects for all supported MP records.
         Mutates instance variables ``able_to_normalize['categorical_variants']`` and
         ``processed_data.categorical_variants``.
 

src/metakb/transformers/moa.py

@@ -81,7 +81,7 @@ async def transform(self, harvested_data: MoaHarvestedData) -> None:
         # Add gene, variant, and source data to ``processed_data`` instance variable
         # (``genes``, ``variations``, and ``documents``)
         self._add_genes(harvested_data.genes)
-        await self._add_protein_consequences(harvested_data.variants)
+        await self._add_categorical_variants(harvested_data.variants)
         self._add_documents(harvested_data.sources)
 
         # Add variant therapeutic response study data. Will update `studies`
@@ -215,8 +215,8 @@ async def _add_variant_therapeutic_response_studies(
             )
             self.processed_data.studies.append(statement)
 
-    async def _add_protein_consequences(self, variants: list[dict]) -> None:
-        """Create Protein Sequence Consequence objects for all MOA variant records.
+    async def _add_categorical_variants(self, variants: list[dict]) -> None:
+        """Create Categorical Variant objects for all MOA variant records.
         Mutates instance variables ``able_to_normalize['variations']`` and
         ``processed_data.variations``, if the variation-normalizer can successfully
         normalize the variant

tests/unit/database/test_database.py

@@ -310,14 +310,14 @@ def test_variation_rules(
     assert v["expression_hgvs_p"] == expected_p
 
 
-def test_categorical_variation_rules(
+def test_categorical_variant_rules(
     check_unique_property,
     check_relation_count,
     check_node_labels,
     get_node_by_id,
     civic_mpid12,
 ):
-    """Verify property and relationship rules for Categorical Variation nodes."""
+    """Verify property and relationship rules for Categorical Variant nodes."""
     check_unique_property("CategoricalVariant", "id")
     check_relation_count(
         "CategoricalVariant", "Variation", "HAS_DEFINING_CONTEXT", max_rels=1