build: update ga4gh.vrsatile.pydantic version (#281)

- Upgrades to pydantic v2

Pipfile

@@ -9,7 +9,7 @@ fastapi = "*"
 uvicorn = "*"
 click = "*"
 boto3 = "*"
-"ga4gh.vrsatile.pydantic" = "~=0.0.12"
+"ga4gh.vrsatile.pydantic" = "~=0.2.0"
 "ga4gh.vrs" = "~=0.8.1"
 
 [dev-packages]

docs/scripts/generate_normalize_figure.py

@@ -49,7 +49,7 @@ def create_gjgf(result: UnmergedNormalizationService) -> Dict:
                 "metadata": {
                     "color": COLORS[i],
                     "hover": f"{match.concept_id}\n{match.symbol}\n<i>{match.label}</i>",  # noqa: E501
-                    "click": f"<p color='black'>{json.dumps(match.dict(), indent=2)}</p>",  # noqa: E501
+                    "click": f"<p color='black'>{json.dumps(match.model_dump(), indent=2)}</p>",  # noqa: E501
                 }
             }
             for xref in match.xrefs:

pyproject.toml

@@ -30,7 +30,7 @@ dependencies = [
     "uvicorn",
     "click",
     "boto3",
-    "ga4gh.vrsatile.pydantic~=0.0.12",
+    "ga4gh.vrsatile.pydantic~=0.2.0",
     "ga4gh.vrs~=0.8.1"
 ]
 dynamic = ["version"]

src/gene/database/dynamodb.py

@@ -356,7 +356,7 @@ def add_source_metadata(self, src_name: SourceName, metadata: SourceMeta) -> Non
         :raise DatabaseWriteException: if write fails
         """
         src_name_value = src_name.value
-        metadata_item = metadata.dict()
+        metadata_item = metadata.model_dump()
         metadata_item["src_name"] = src_name_value
         metadata_item["label_and_type"] = f"{str(src_name_value).lower()}##source"
         metadata_item["concept_id"] = f"source:{str(src_name_value).lower()}"

src/gene/etl/vrs_locations/chromosome_location.py

@@ -32,7 +32,7 @@ def get_location(self, location: Dict, gene: Dict) -> Optional[Dict]:
             try:
                 chr_location = GeneChromosomeLocation(
                     chr=location["chr"], start=location["start"], end=location["end"]
-                ).dict()
+                ).model_dump()
             except ValidationError as e:
                 logger.info(f"{e} for {gene['symbol']}")
             else:

src/gene/etl/vrs_locations/sequence_location.py

@@ -52,7 +52,7 @@ def add_location(
                     start=gene.start - 1,  # type: ignore
                     end=gene.end,  # type: ignore
                     sequence_id=sequence_id,
-                ).dict()  # type: ignore
+                ).model_dump()  # type: ignore
             else:
                 logger.info(
                     f"{params['concept_id']} has invalid interval:"

src/gene/main.py

@@ -61,6 +61,7 @@
     summary=read_query_summary,
     response_description=response_description,
     response_model=SearchService,
+    response_model_exclude_none=True,
     description=search_description,
     tags=["Query"],
 )
@@ -99,6 +100,7 @@ def search(
     summary=normalize_summary,
     response_description=normalize_response_descr,
     response_model=NormalizeService,
+    response_model_exclude_none=True,
     description=normalize_descr,
     tags=["Query"],
 )
@@ -134,6 +136,7 @@ def normalize(q: str = Query(..., description=normalize_q_descr)) -> NormalizeSe
     operation_id="getUnmergedRecords",
     response_description=unmerged_response_descr,
     response_model=UnmergedNormalizationService,
+    response_model_exclude_none=True,
     description=unmerged_normalize_description,
     tags=["Query"],
 )

src/gene/query.py

@@ -24,6 +24,7 @@
     RefType,
     SearchService,
     ServiceMeta,
+    SourceMeta,
     SourceName,
     SourcePriority,
     UnmergedNormalizationService,
@@ -370,7 +371,8 @@ def _add_merged_meta(self, response: NormalizeService) -> NormalizeService:
             prefix = concept_id.split(":")[0]
             src_name = PREFIX_LOOKUP[prefix.lower()]
             if src_name not in sources_meta:
-                sources_meta[src_name] = self.db.get_source_metadata(src_name)
+                _sources_meta = self.db.get_source_metadata(src_name)
+                sources_meta[SourceName(src_name)] = SourceMeta(**_sources_meta)
         response.source_meta_ = sources_meta
         return response