refactor: add worker to app lifespan to avoid running when importing

pyproject.toml

@@ -6,7 +6,7 @@ authors = [
     { name = "zietzm", email = "michael.zietz@gmail.com" }
 ]
 dependencies = [
-    "fastapi>=0.111.0",
+    "fastapi[standard]>=0.111.0",
     "boto3>=1.34.145",
     "botocore>=1.34.145",
     "pydantic>=2.8.2",
@@ -50,3 +50,10 @@ packages = ["src/webgwas_backend"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"
+
+[tool.uv]
+dev-dependencies = [
+    "pytest>=8.3.2",
+    "ruff>=0.6.2",
+    "httpx>=0.27.2",
+]

requirements-dev.lock

@@ -53,28 +53,36 @@ idna==3.7
     # via anyio
     # via email-validator
     # via httpx
+igwas @ git+https://github.com/tatonetti-lab/indirect-gwas@e0546ff0fe39624cfab9bd02cec80dcdd14e5af7
+    # via webgwas
 iniconfig==2.0.0
     # via pytest
 jinja2==3.1.4
     # via fastapi
 jmespath==1.0.1
     # via boto3
     # via botocore
+joblib==1.4.2
+    # via scikit-learn
 markdown-it-py==3.0.0
     # via rich
 markupsafe==2.1.5
     # via jinja2
 mdurl==0.1.2
     # via markdown-it-py
-numpy==2.0.1
+numpy==2.1.0
+    # via igwas
     # via pandas
     # via pyarrow
+    # via scikit-learn
+    # via scipy
     # via webgwas
 orjson==3.10.6
     # via fastapi
 packaging==24.1
     # via pytest
 pandas==2.2.2
+    # via igwas
     # via webgwas
     # via webgwas-backend
 pluggy==1.5.0
@@ -114,6 +122,10 @@ rich==13.7.1
 ruff==0.6.2
 s3transfer==0.10.2
     # via boto3
+scikit-learn==1.5.1
+    # via webgwas-backend
+scipy==1.14.1
+    # via scikit-learn
 shellingham==1.5.4
     # via typer
 six==1.16.0
@@ -127,6 +139,8 @@ sqlmodel==0.0.21
     # via webgwas-backend
 starlette==0.37.2
     # via fastapi
+threadpoolctl==3.5.0
+    # via scikit-learn
 typer==0.12.3
     # via fastapi-cli
     # via webgwas-backend
@@ -148,9 +162,10 @@ uvloop==0.19.0
     # via uvicorn
 watchfiles==0.22.0
     # via uvicorn
-webgwas @ git+https://github.com/zietzm/webgwas.git@bb627b570e507222accd2fdf08a896565835db0d
+webgwas @ git+https://github.com/zietzm/webgwas.git@fa93c0bbb02ab92c03af5975bbb36770f7c70445
     # via webgwas-backend
 websockets==12.0
     # via uvicorn
 zstandard==0.23.0
+    # via igwas
     # via webgwas-backend

requirements.lock

@@ -53,24 +53,32 @@ idna==3.7
     # via anyio
     # via email-validator
     # via httpx
+igwas @ git+https://github.com/tatonetti-lab/indirect-gwas@e0546ff0fe39624cfab9bd02cec80dcdd14e5af7
+    # via webgwas
 jinja2==3.1.4
     # via fastapi
 jmespath==1.0.1
     # via boto3
     # via botocore
+joblib==1.4.2
+    # via scikit-learn
 markdown-it-py==3.0.0
     # via rich
 markupsafe==2.1.5
     # via jinja2
 mdurl==0.1.2
     # via markdown-it-py
-numpy==2.0.1
+numpy==2.1.0
+    # via igwas
     # via pandas
     # via pyarrow
+    # via scikit-learn
+    # via scipy
     # via webgwas
 orjson==3.10.6
     # via fastapi
 pandas==2.2.2
+    # via igwas
     # via webgwas
     # via webgwas-backend
 polars==1.3.0
@@ -106,6 +114,10 @@ rich==13.7.1
     # via webgwas-backend
 s3transfer==0.10.2
     # via boto3
+scikit-learn==1.5.1
+    # via webgwas-backend
+scipy==1.14.1
+    # via scikit-learn
 shellingham==1.5.4
     # via typer
 six==1.16.0
@@ -119,6 +131,8 @@ sqlmodel==0.0.21
     # via webgwas-backend
 starlette==0.37.2
     # via fastapi
+threadpoolctl==3.5.0
+    # via scikit-learn
 typer==0.12.3
     # via fastapi-cli
     # via webgwas-backend
@@ -140,9 +154,10 @@ uvloop==0.19.0
     # via uvicorn
 watchfiles==0.22.0
     # via uvicorn
-webgwas @ git+https://github.com/zietzm/webgwas.git@bb627b570e507222accd2fdf08a896565835db0d
+webgwas @ git+https://github.com/zietzm/webgwas.git@fa93c0bbb02ab92c03af5975bbb36770f7c70445
     # via webgwas-backend
 websockets==12.0
     # via uvicorn
 zstandard==0.23.0
+    # via igwas
     # via webgwas-backend

src/webgwas_backend/main.py

@@ -1,10 +1,13 @@
 import logging
 from collections.abc import Generator
+from contextlib import asynccontextmanager
+from functools import lru_cache
 from typing import Annotated
 
 import webgwas.phenotype_definitions
 from fastapi import Depends, FastAPI, HTTPException
 from fastapi.middleware.cors import CORSMiddleware
+from sqlalchemy import Engine
 from sqlmodel import Session, select
 from webgwas.phenotype_definitions import Field, KnowledgeBase
 
@@ -27,22 +30,35 @@
 from webgwas_backend.worker import Worker
 
 logger = logging.getLogger("uvicorn")
-logger.setLevel(logging.INFO)
+logger.setLevel(logging.DEBUG)
 
 init_db()
-worker_group = Worker(settings)
 
+worker: Worker | None = None
 
+
+@asynccontextmanager
+async def lifespan(app: FastAPI):  # noqa: ARG001
+    global worker
+    worker = Worker(settings)
+    yield
+
+
+@lru_cache(maxsize=1)
 def get_worker() -> Worker:
-    return worker_group
+    return Worker(settings)
+
+
+def get_engine() -> Engine:
+    return engine
 
 
-def get_session() -> Generator[Session]:
+def get_session(engine: Annotated[Engine, Depends(get_engine)]) -> Generator[Session]:
     with Session(engine) as session:
         yield session
 
 
-app = FastAPI()
+app = FastAPI(lifespan=lifespan)
 app.add_middleware(
     CORSMiddleware,
     allow_origins=["*"],