From db898648a7f3a26b96638fd74fd3a6bdb75c8995 Mon Sep 17 00:00:00 2001 From: zietzm Date: Thu, 29 Aug 2024 08:50:34 -0700 Subject: [PATCH] refactor: add worker to app lifespan to avoid running when importing --- pyproject.toml | 9 +- requirements-dev.lock | 19 +- requirements.lock | 19 +- src/webgwas_backend/main.py | 26 ++- uv.lock | 398 ++++++++++++++++++++++++++++++++++-- 5 files changed, 444 insertions(+), 27 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 0e78d4e..ef1dced 100644 --- a/pyproject.toml +++ b/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", +] diff --git a/requirements-dev.lock b/requirements-dev.lock index fc01265..b77aab7 100644 --- a/requirements-dev.lock +++ b/requirements-dev.lock @@ -53,6 +53,8 @@ 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 @@ -60,21 +62,27 @@ jinja2==3.1.4 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 diff --git a/requirements.lock b/requirements.lock index 9488afe..910e08c 100644 --- a/requirements.lock +++ b/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 diff --git a/src/webgwas_backend/main.py b/src/webgwas_backend/main.py index c101f59..19222ab 100644 --- a/src/webgwas_backend/main.py +++ b/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 = 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