Fix problems introduced by project configuration changes and dependen…

…cy upgrades (#101)

* Add sqlalchemy to list of main dependencies

* Add response_model=None to pass FastAPI validation

* Update batch_add_mode setting to work properly

* Change test data from "efo:" to "EFO:" to make Pydantic happy

* Bump VRS to 2.0.0a11

* Code formatting

pyproject.toml

@@ -19,7 +19,8 @@ dependencies = [
     "fastapi>=0.95.0",
     "python-multipart",  # required for fastapi file uploads
     "uvicorn",
-    "ga4gh.vrs[extras]~=2.0.0a10",
+    "ga4gh.vrs[extras]~=2.0.0a11",
+    "sqlalchemy~=1.4.54",
 ]
 dynamic = ["version"]
 

src/anyvar/restapi/main.py

@@ -216,6 +216,7 @@ def register_vrs_object(
     summary="Register alleles from a VCF",
     description="Provide a valid VCF. All reference and alternate alleles will be registered with AnyVar. The file is annotated with VRS IDs and returned.",
     tags=[EndpointTag.VARIATIONS],
+    response_model=None,
 )
 async def annotate_vcf(
     request: Request,

src/anyvar/storage/snowflake.py

@@ -56,7 +56,7 @@ def sf_create_connect_args_override(self, url: URL) -> tuple[list, dict]:  # noq
 #
 
 
-class SnowflakeBatchAddMode(str, Enum):
+class SnowflakeBatchAddMode(Enum):
     """Define values for snowflake batch add modes"""
 
     merge = auto()
@@ -88,10 +88,13 @@ def __init__(
             max_pending_batches,
             flush_on_batchctx_exit,
         )
-        self.batch_add_mode = batch_add_mode or os.environ.get(
-            "ANYVAR_SNOWFLAKE_BATCH_ADD_MODE", SnowflakeBatchAddMode.merge
+        env_batch_mode_name = os.environ.get(
+            "ANYVAR_SNOWFLAKE_BATCH_ADD_MODE", SnowflakeBatchAddMode.merge.name
         )
-        if self.batch_add_mode not in SnowflakeBatchAddMode.__members__:
+        self.batch_add_mode = (
+            batch_add_mode or SnowflakeBatchAddMode[env_batch_mode_name]
+        )
+        if self.batch_add_mode not in SnowflakeBatchAddMode:
             msg = "batch_add_mode must be one of 'merge', 'insert_notin', or 'insert'"
             raise Exception(msg)
 

tests/data/variations.json

@@ -63,7 +63,7 @@
     "ga4gh:CX.TvAhuGK6HYf53mXoUnon60cZ7DC_UgM3": {
       "params": {
         "definition": "NC_000013.11:g.26440969_26443305del",
-        "copy_change": "efo:0030069",
+        "copy_change": "EFO:0030069",
         "input_type": "CopyNumberChange"
       },
       "copy_number_response": {
@@ -82,7 +82,7 @@
             },
             "type": "SequenceLocation"
           },
-          "copyChange": "efo:0030069",
+          "copyChange": "EFO:0030069",
           "type": "CopyNumberChange"
         }
       },