fix: store variation aliases in aliases not extensions (#460)

close #459

src/metakb/load_data.py

@@ -295,6 +295,10 @@ def _add_categorical_variant(
         _create_parameterized_query(cv, ("id", "name", "description", "type"))
     ]
 
+    if "aliases" in cv:
+        cv["aliases"] = json.dumps(cv["aliases"])
+        mp_nonnull_keys.append("aliases:$aliases")
+
     _add_mappings_and_exts_to_obj(cv, mp_nonnull_keys)
     mp_keys = ", ".join(mp_nonnull_keys)
 

src/metakb/query.py

@@ -650,6 +650,7 @@ def _get_cat_var(self, node: dict) -> CategoricalVariant:
         :return: Categorical Variant data
         """
         node["mappings"] = _deserialize_field(node, "mappings")
+        node["aliases"] = _deserialize_field(node, "aliases")
 
         extensions = []
         for node_key, ext_name in (
@@ -678,10 +679,6 @@ def _get_cat_var(self, node: dict) -> CategoricalVariant:
                 )
             )
 
-        aliases = node.pop("aliases", None)
-        if aliases:
-            extensions.append(Extension(name="aliases", value=json.loads(aliases)))
-
         node["extensions"] = extensions or None
         node["constraints"] = [
             DefiningAlleleConstraint(

src/metakb/transformers/civic.py

@@ -159,7 +159,7 @@ class _VariationCache(BaseModel):
     civic_gene_id: str
     variant_types: list[Coding] | None = None
     mappings: list[ConceptMapping] | None = None
-    aliases: list[Extension] | None = None
+    aliases: list[str] | None = None
     coordinates: dict | None = None
     members: list[Variation] | None = None
     extensions: list[Extension] | None = None
@@ -523,16 +523,11 @@ def _add_categorical_variants(
             extensions = civic_variation_data.extensions or []
 
             # Get aliases from MP and Variant record
-            if civic_variation_data.aliases:
-                aliases = civic_variation_data.aliases[0].value
-            else:
-                aliases = []
+            aliases = civic_variation_data.aliases or []
 
             for a in mp["aliases"] or []:
                 if not SNP_RE.match(a) and a not in aliases:
                     aliases.append(a)
-            if aliases:
-                extensions.append(Extension(name="aliases", value=aliases))
 
             # Get molecular profile score data
             mp_score = mp["molecular_profile_score"]
@@ -567,6 +562,7 @@ def _add_categorical_variants(
                 description=mp["description"],
                 name=mp["name"],
                 constraints=constraints,
+                aliases=aliases or None,
                 mappings=civic_variation_data.mappings,
                 extensions=extensions or None,
                 members=civic_variation_data.members,
@@ -669,7 +665,6 @@ async def _add_variations(self, variants: list[dict]) -> None:
             vrs_variation = None
             civic_variation = None
             extensions = []
-            aliases_extensions = []
 
             if self._is_supported_variant_query(variant_name, variant_id):
                 vrs_variation = await self.vicc_normalizers.normalize_variation(
@@ -763,9 +758,6 @@ async def _add_variations(self, variants: list[dict]) -> None:
                 else:
                     aliases.append(a)
 
-            if aliases:
-                aliases_extensions.append(Extension(name="aliases", value=aliases))
-
             if variant["coordinates"]:
                 coordinates = {
                     k: v for k, v in variant["coordinates"].items() if v is not None
@@ -781,7 +773,7 @@ async def _add_variations(self, variants: list[dict]) -> None:
                 civic_gene_id=f"civic.gid:{variant['gene_id']}",
                 variant_types=variant_types_value or None,
                 mappings=mappings or None,
-                aliases=aliases_extensions or None,
+                aliases=aliases or None,
                 extensions=extensions,
                 coordinates=coordinates or None,
                 members=members,

tests/conftest.py

@@ -408,8 +408,8 @@ def civic_mpid33(civic_vid33):
                 "relation": "exactMatch",
             },
         ],
+        "aliases": ["LEU858ARG", "L813R", "LEU813ARG"],
         "extensions": [
-            {"name": "aliases", "value": ["LEU858ARG", "L813R", "LEU813ARG"]},
             {
                 "name": "CIViC representative coordinate",
                 "value": {
@@ -679,8 +679,8 @@ def civic_mpid12(civic_vid12, braf_v600e_genomic):
                 "relation": "exactMatch",
             },
         ],
+        "aliases": ["VAL600GLU", "V640E", "VAL640GLU"],
         "extensions": [
-            {"name": "aliases", "value": ["VAL600GLU", "V640E", "VAL640GLU"]},
             {
                 "name": "CIViC representative coordinate",
                 "value": {
@@ -1558,8 +1558,8 @@ def civic_mpid65(civic_vid65):
                 "relation": "exactMatch",
             },
         ],
+        "aliases": ["ASP816VAL"],
         "extensions": [
-            {"name": "aliases", "value": ["ASP816VAL"]},
             {
                 "name": "CIViC representative coordinate",
                 "value": {

tests/unit/database/test_database.py

@@ -341,10 +341,7 @@ def test_categorical_variant_rules(
     assert cv["type"] == civic_mpid12["type"]
     assert cv["name"] == civic_mpid12["name"]
     assert cv["description"] == civic_mpid12["description"]
-    expected_aliases = next(
-        ext for ext in civic_mpid12["extensions"] if ext["name"] == "aliases"
-    )["value"]
-    assert set(json.loads(cv["aliases"])) == set(expected_aliases)
+    assert set(json.loads(cv["aliases"])) == set(civic_mpid12["aliases"])
     assert isinstance(cv["civic_molecular_profile_score"], float)
     crc = json.loads(cv["civic_representative_coordinate"])
     assert set(crc.keys()) == {

tests/unit/transformers/test_civic_transformer_diagnostic.py

@@ -143,8 +143,8 @@ def civic_mpid99():
                 "relation": "exactMatch",
             },
         ],
+        "aliases": ["ASP842VAL"],
         "extensions": [
-            {"name": "aliases", "value": ["ASP842VAL"]},
             {
                 "name": "CIViC representative coordinate",
                 "value": {
@@ -430,8 +430,8 @@ def civic_mpid113():
                 "relation": "exactMatch",
             },
         ],
+        "aliases": ["MET918THR"],
         "extensions": [
-            {"name": "aliases", "value": ["MET918THR"]},
             {
                 "name": "CIViC representative coordinate",
                 "value": {

tests/unit/transformers/test_civic_transformer_therapeutic.py

@@ -169,15 +169,12 @@ def civic_mpid473():
                 "relation": "exactMatch",
             },
         ],
+        "aliases": [
+            "3021INSTC",
+            "PRO968LEUFS",
+        ],
         "extensions": [
             get_vicc_normalizer_failure_ext(),
-            {
-                "name": "aliases",
-                "value": [
-                    "3021INSTC",
-                    "PRO968LEUFS",
-                ],
-            },
             {
                 "name": "CIViC representative coordinate",
                 "value": {