fix: update ga4gh.vrs version + add back VRS type anno in models (#95)

close #91 --------- Co-authored-by: Eugene Clark <[email protected]>
biocommons · Aug 26, 2024 · e4c112f · e4c112f
1 parent 4cb87ae
commit e4c112f
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Showing 3 changed files with 11 additions and 11 deletions.
diff --git a/setup.cfg b/setup.cfg
@@ -7,7 +7,7 @@ install_requires =
     fastapi>=0.95.0
     python-multipart
     uvicorn
-    ga4gh.vrs[extras]~=2.0.0a5
+    ga4gh.vrs[extras]~=2.0.0a10
     psycopg[binary]
     snowflake-sqlalchemy~=1.5.1
 

diff --git a/src/anyvar/restapi/main.py b/src/anyvar/restapi/main.py
@@ -105,7 +105,7 @@ def get_location_by_id(
         )
 
     if location:
-        return {"location": location.model_dump(exclude_none=True)}
+        return {"location": location}
     else:
         raise HTTPException(
             status_code=HTTPStatus.NOT_FOUND, detail=f"Location {location_id} not found"
@@ -147,7 +147,7 @@ def register_variation(
     else:
         if translated_variation:
             v_id = av.put_object(translated_variation)
-            result["object"] = translated_variation.model_dump(exclude_none=True)
+            result["object"] = translated_variation
             result["object_id"] = v_id
         else:
             result["messages"].append(f"Translation of {definition} failed.")
@@ -200,7 +200,7 @@ def register_vrs_object(
 
     variation_object = variation_class_map[variation_type](**variation.dict())
     v_id = av.put_object(variation_object)
-    result["object"] = variation_object.model_dump(exclude_none=True)
+    result["object"] = variation_object
     result["object_id"] = v_id
     return result
 
@@ -286,7 +286,7 @@ def get_variation_by_id(
         )
 
     if variation:
-        return {"messages": [], "data": variation.model_dump(exclude_none=True)}
+        return {"messages": [], "data": variation}
     else:
         raise HTTPException(
             status_code=HTTPStatus.NOT_FOUND, detail=f"Variation {variation_id} not found"
@@ -341,7 +341,7 @@ def search_variations(
             var_object = av.get_object(allele["id"], deref=True)
             if not var_object:
                 continue
-            inline_alleles.append(var_object.model_dump(exclude_none=True))
+            inline_alleles.append(var_object)
 
     return {"variations": inline_alleles}
 

diff --git a/src/anyvar/restapi/schema.py b/src/anyvar/restapi/schema.py
@@ -50,7 +50,7 @@ def schema_extra(schema: Dict[str, Any], model: Type["InfoResponse"]) -> None:
 class GetSequenceLocationResponse(BaseModel):
     """Describe response for the /locations/ endpoint"""
 
-    location: Optional[Dict]
+    location: Optional[models.SequenceLocation]
 
 
 class RegisterVariationRequest(BaseModel):
@@ -78,7 +78,7 @@ class RegisterVariationResponse(BaseModel):
     """Describe response for the variation registry endpoint"""
 
     messages: List[str]
-    object: Optional[Dict]
+    object: Optional[models.Variation]
     object_id: Optional[str]
 
     class Config:
@@ -116,15 +116,15 @@ class RegisterVrsVariationResponse(BaseModel):
     """Describe response for VRS object registration endpoint"""
 
     messages: List[str]
-    object: Optional[Dict]
+    object: Optional[models.Variation]
     object_id: Optional[str]
 
 
 class GetVariationResponse(BaseModel):
     """Describe response for the /variation get endpoint"""
 
     messages: List[StrictStr]
-    data: Dict
+    data: models.Variation
 
     class Config:
         """Configure GetVariationResponse class"""
@@ -161,7 +161,7 @@ def schema_extra(schema: Dict[str, Any], model: Type["GetVariationResponse"]) ->
 class SearchResponse(BaseModel):
     """Describe response for the /search endpoint"""
 
-    variations: List[Dict]
+    variations: List[models.Variation]
 
 
 class VariationStatisticType(str, Enum):