fix: remove batch_size

settings.toml

@@ -4,4 +4,3 @@ sqlite_db = "sqlite:///backend.db"
 n_workers = 1
 
 [indirect_gwas]
-batch_size = 10000

src/webgwas_backend/config.py

@@ -4,12 +4,12 @@
 from typing import Any
 
 from dynaconf import Dynaconf
-from pydantic import BaseModel, Field
+from pydantic import BaseModel
 from pydantic_settings import BaseSettings
 
 
 class IndirectGWASSettings(BaseModel):
-    batch_size: int = Field(10000, description="Batch size (in variants)")
+    pass
 
 
 class Settings(BaseSettings):

src/webgwas_backend/igwas_handler.py

@@ -49,7 +49,7 @@ def get_igwas_coef(request: WebGWASRequestID) -> Series:
 
 
 def handle_igwas(
-    request: WebGWASRequestID, dry_run: bool, s3_bucket: str, batch_size: int
+    request: WebGWASRequestID, dry_run: bool, s3_bucket: str
 ) -> WebGWASResult:
     beta_series = get_igwas_coef(request)
     cov_path = pathlib.Path(request.cohort.root_directory).joinpath(
@@ -69,7 +69,6 @@ def handle_igwas(
                 gwas_result_path=gwas_path.as_posix(),
                 output_file_path=output_file_path.as_posix(),
                 num_covar=request.cohort.num_covar,
-                batch_size=batch_size,
             )
         except Exception as e:
             raise HTTPException(

src/webgwas_backend/test_main.py

@@ -135,7 +135,7 @@ def client():
         s3_bucket="TEST",
         sqlite_db=":memory:",
         n_workers=2,
-        indirect_gwas=IndirectGWASSettings(batch_size=10000),
+        indirect_gwas=IndirectGWASSettings(),
     )
     worker = TestWorker(settings)
 

src/webgwas_backend/worker.py

@@ -15,7 +15,6 @@ class Worker:
     def __init__(self, settings: Settings):
         self.s3_dry_run = settings.dry_run
         self.s3_bucket = settings.s3_bucket
-        self.batch_size = settings.indirect_gwas.batch_size
 
         self.manager = Manager()
         self.lock = self.manager.Lock()
@@ -30,16 +29,13 @@ def submit(self, request: WebGWASRequestID):
                 request,
                 self.s3_dry_run,
                 self.s3_bucket,
-                self.batch_size,
             )
         logger.info(f"Queued request: {request.id}")
 
     @staticmethod
-    def handle_request(
-        request: WebGWASRequestID, dry_run: bool, s3_bucket: str, batch_size: int
-    ):
+    def handle_request(request: WebGWASRequestID, dry_run: bool, s3_bucket: str):
         try:
-            return handle_igwas(request, dry_run, s3_bucket, batch_size)
+            return handle_igwas(request, dry_run, s3_bucket)
         except Exception as e:
             return WebGWASResult(
                 request_id=request.id, status="error", error_msg=f"{e}"
@@ -67,14 +63,11 @@ class TestWorker(Worker):
     def __init__(self, settings: Settings):
         self.s3_dry_run = settings.dry_run
         self.s3_bucket = settings.s3_bucket
-        self.batch_size = settings.indirect_gwas.batch_size
         self.id_to_result: dict[str, WebGWASResult] = {}
 
     def submit(self, request: WebGWASRequestID):
         logger.info(f"Submitting request: {request}")
-        result = self.handle_request(
-            request, self.s3_dry_run, self.s3_bucket, self.batch_size
-        )
+        result = self.handle_request(request, self.s3_dry_run, self.s3_bucket)
         self.id_to_result[request.id] = result
         logger.info(f"Queued request: {request.id}")