Merge pull request #81 from TheJacksonLaboratory/G3-75-fix-user-depen…

…dency-function

G3 75 fix user dependency function

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.7.0a9"
+version = "0.7.0a10"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <alexander.berger@jax.org>",

src/geneweaver/api/controller/genesets.py

@@ -23,8 +23,8 @@
 
 @router.get("")
 def get_visible_genesets(
-    user: UserInternal = Security(deps.optional_full_user),
-    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+    cursor: deps.CursorDep,
+    user: deps.OptionalFullUserDep,
     gs_id: Annotated[
         Optional[int],
         Query(

src/geneweaver/api/dependencies.py

@@ -4,15 +4,15 @@
 import logging
 from contextlib import asynccontextmanager
 from tempfile import TemporaryDirectory
-from typing import Generator, Optional
+from typing import Annotated, Optional
 
 import psycopg
 from fastapi import Depends, FastAPI, Request
 from geneweaver.api.core.config import settings
 from geneweaver.api.core.exceptions import AuthenticationMismatch
 from geneweaver.api.core.security import Auth0, UserInternal
 from geneweaver.db import user as db_user
-from psycopg.rows import dict_row
+from psycopg.rows import DictRow, dict_row
 from psycopg_pool import ConnectionPool
 
 auth = Auth0(
@@ -34,7 +34,11 @@ async def lifespan(app: FastAPI) -> None:
     :param app: The FastAPI application (dependency injection).
     """
     logger.info("Opening DB Connection Pool.")
-    app.pool = ConnectionPool(settings.DB.URI)
+    app.pool = ConnectionPool(
+        settings.DB.URI,
+        connection_class=psycopg.Connection[DictRow],
+        kwargs={"row_factory": dict_row},
+    )
     app.pool.open()
     app.pool.wait()
     with app.pool.connection() as conn:
@@ -50,13 +54,17 @@ async def lifespan(app: FastAPI) -> None:
     app.pool.close()
 
 
-def cursor(request: Request) -> Generator:
+async def cursor(request: Request) -> Cursor:
     """Get a cursor from the connection pool."""
+    logger.debug("Getting cursor from pool.")
     with request.app.pool.connection() as conn:
-        with conn.cursor(row_factory=dict_row) as cur:
+        with conn.cursor() as cur:
             yield cur
 
 
+CursorDep = Annotated[Cursor, Depends(cursor)]
+
+
 def _get_user_details(cursor: Cursor, user: UserInternal) -> UserInternal:
     """Get the user details.
 
@@ -100,8 +108,11 @@ async def full_user(
     yield _get_user_details(cursor, user)
 
 
+FullUserDep = Annotated[UserInternal, Depends(full_user)]
+
+
 async def optional_full_user(
-    cursor: Cursor = Depends(cursor),
+    cursor: CursorDep,
     user: Optional[UserInternal] = Depends(auth.get_user),
 ) -> Optional[UserInternal]:
     """Get the full user object, if request is logged in.
@@ -115,8 +126,11 @@ async def optional_full_user(
     @param user: GW user.
     """
     if user is not None:
-        yield _get_user_details(cursor, user)
-    yield None
+        return _get_user_details(cursor, user)
+    return None
+
+
+OptionalFullUserDep = Annotated[Optional[UserInternal], Depends(optional_full_user)]
 
 
 async def get_temp_dir() -> TemporaryDirectory: