Add SQL databases for CLEM workflow to Murfey (#321)

* Added SQLModel tables to record CLEM data
* Added FastAPI endpoints to facilitate registration of CLEM data into the Murfey database
* Refactored API endpoint files to move towards increased modularity

pyproject.toml

@@ -65,6 +65,7 @@ server = [
     "pillow",
     "prometheus_client",
     "python-jose[cryptography]",
+    "sqlalchemy[postgresql]", # Add as explicit dependency
     "sqlmodel",
     "stomp-py<=8.1.0", # 8.1.1 (released 2024-04-06) doesn't work with our project
     "uvicorn[standard]",

src/murfey/cli/add_user.py

@@ -3,7 +3,7 @@
 
 from sqlmodel import Session, create_engine
 
-from murfey.server.auth import hash_password
+from murfey.server.api.auth import hash_password
 from murfey.server.config import get_machine_config
 from murfey.server.murfey_db import url
 from murfey.util.db import MurfeyUser as User

src/murfey/server/api.py → src/murfey/server/api/__init__.py

@@ -45,11 +45,11 @@
     sanitise,
     templates,
 )
-from murfey.server.auth import validate_token
+from murfey.server.api.auth import validate_token
+from murfey.server.api.spa import _cryolo_model_path
 from murfey.server.config import from_file, settings
 from murfey.server.gain import Camera, prepare_eer_gain, prepare_gain
 from murfey.server.murfey_db import murfey_db
-from murfey.server.spa.api import _cryolo_model_path
 from murfey.util.db import (
     AutoProcProgram,
     ClientEnvironment,

src/murfey/server/auth/__init__.py → src/murfey/server/api/auth.py

@@ -1,25 +1,39 @@
+from __future__ import annotations
+
 import secrets
+from logging import getLogger
 from typing import Annotated
 
-from fastapi import Depends, HTTPException, status
-from fastapi.security import OAuth2PasswordBearer
+from fastapi import APIRouter, Depends, HTTPException, status
+from fastapi.security import OAuth2PasswordBearer, OAuth2PasswordRequestForm
 from jose import JWTError, jwt
 from passlib.context import CryptContext
+from pydantic import BaseModel
 from sqlmodel import Session, create_engine, select
 
 from murfey.server.config import get_machine_config
 from murfey.server.murfey_db import url
 from murfey.util.db import MurfeyUser as User
 
+# Set up logger
+logger = getLogger("murfey.server.api.auth")
+
+# Set up router
+router = APIRouter()
+
+# Set up variables used for authentication
 machine_config = get_machine_config()
 ALGORITHM = machine_config.auth_algorithm or "HS256"
 SECRET_KEY = machine_config.auth_key or secrets.token_hex(32)
-
 oauth2_scheme = OAuth2PasswordBearer(tokenUrl="token")
-
 pwd_context = CryptContext(schemes=["bcrypt"], deprecated="auto")
 
 
+"""
+HELPER FUNCTIONS
+"""
+
+
 def verify_password(plain_password: str, hashed_password: str) -> bool:
     return pwd_context.verify(plain_password, hashed_password)
 
@@ -28,6 +42,7 @@ def hash_password(password: str) -> str:
     return pwd_context.hash(password)
 
 
+# Set up database engine
 try:
     _url = url(get_machine_config())
     engine = create_engine(_url)
@@ -65,3 +80,37 @@ async def validate_token(token: Annotated[str, Depends(oauth2_scheme)]):
             headers={"WWW-Authenticate": "Bearer"},
         )
     return None
+
+
+class Token(BaseModel):
+    access_token: str
+    token_type: str
+
+
+def create_access_token(data: dict):
+    to_encode = data.copy()
+
+    encoded_jwt = jwt.encode(to_encode, SECRET_KEY, algorithm=ALGORITHM)
+    return encoded_jwt
+
+
+"""
+API ENDPOINTS
+"""
+
+
+@router.post("/token")
+def generate_token(
+    form_data: Annotated[OAuth2PasswordRequestForm, Depends()],
+) -> Token:
+    validated = validate_user(form_data.username, form_data.password)
+    if not validated:
+        raise HTTPException(
+            status_code=status.HTTP_401_UNAUTHORIZED,
+            detail="Incorrect username or password",
+            headers={"WWW-Authenticate": "Bearer"},
+        )
+    access_token = create_access_token(
+        data={"user": form_data.username},
+    )
+    return Token(access_token=access_token, token_type="bearer")

src/murfey/server/bootstrap.py → src/murfey/server/api/bootstrap.py

@@ -41,7 +41,7 @@
 cygwin = APIRouter(prefix="/cygwin", tags=["bootstrap"])
 version = APIRouter(prefix="/version", tags=["bootstrap"])
 
-log = logging.getLogger("murfey.server.bootstrap")
+log = logging.getLogger("murfey.server.api.bootstrap")
 
 
 def _validate_package_name(package: str) -> bool: