From b6ae09732c4fdeb40e7efe3a7380414051730263 Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Wed, 1 Apr 2026 14:01:33 +0200
Subject: [PATCH 01/18] Logging but request id context is not bound properly

---
 src/database/datasets.py |  2 ++
 src/main.py              | 42 +++++++++++++++++++++++++++++++++++++++-
 2 files changed, 43 insertions(+), 1 deletion(-)

diff --git a/src/database/datasets.py b/src/database/datasets.py
index 26eb33d..27f1f4e 100644
--- a/src/database/datasets.py
+++ b/src/database/datasets.py
@@ -3,6 +3,7 @@
 import datetime
 from collections import defaultdict
 
+from loguru import logger
 from sqlalchemy import text
 from sqlalchemy.engine import Row
 from sqlalchemy.ext.asyncio import AsyncConnection
@@ -11,6 +12,7 @@
 
 
 async def get(id_: int, connection: AsyncConnection) -> Row | None:
+    logger.info("Fetching dataset from database", dataset_id=id_)
     row = await connection.execute(
         text(
             """
diff --git a/src/main.py b/src/main.py
index 8ffecd0..1c2c341 100644
--- a/src/main.py
+++ b/src/main.py
@@ -1,10 +1,14 @@
 import argparse
 import logging
-from collections.abc import AsyncGenerator
+import uuid
+from collections.abc import AsyncGenerator, Awaitable, Callable
 from contextlib import asynccontextmanager
 
 import uvicorn
 from fastapi import FastAPI
+from loguru import logger
+from starlette.requests import Request
+from starlette.responses import Response
 
 from config import load_configuration
 from core.errors import ProblemDetailError, problem_detail_exception_handler
@@ -55,9 +59,45 @@ def _parse_args() -> argparse.Namespace:
     return parser.parse_args()
 
 
+async def add_request_context_to_log(
+    request: Request,
+    call_next: Callable[[Request], Awaitable[Response]],
+) -> Response:
+    identifier = uuid.uuid4().hex
+    host = request.client.host if request.client else "unknown host"
+    with logger.contextualize(request_id=identifier, client_ip=host):
+        return await call_next(request)
+
+
+async def request_response_logger(
+    request: Request,
+    call_next: Callable[[Request], Awaitable[Response]],
+) -> Response:
+    logger.info(
+        "request",
+        url=request.url,
+        headers=request.headers,
+        cookies=request.cookies,
+        path_params=request.path_params,
+        query_params=request.query_params,
+        body=await request.body(),
+    )
+    response: Response = await call_next(request)
+    logger.info(
+        "response",
+        status_code=response.status_code,
+        headers=response.headers,
+        media_type=response.media_type,
+    )
+    return response
+
+
 def create_api() -> FastAPI:
+    logger.add("log.log", serialize=True)
     fastapi_kwargs = load_configuration()["fastapi"]
     app = FastAPI(**fastapi_kwargs, lifespan=lifespan)
+    app.middleware("http")(add_request_context_to_log)
+    app.middleware("http")(request_response_logger)
 
     app.add_exception_handler(ProblemDetailError, problem_detail_exception_handler)  # type: ignore[arg-type]
 

From 346c97fed53e59e44cfac2598de628236949a556 Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Wed, 1 Apr 2026 14:11:36 +0200
Subject: [PATCH 02/18] Fix middleware order

---
 src/main.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/main.py b/src/main.py
index 1c2c341..5d3999a 100644
--- a/src/main.py
+++ b/src/main.py
@@ -96,8 +96,11 @@ def create_api() -> FastAPI:
     logger.add("log.log", serialize=True)
     fastapi_kwargs = load_configuration()["fastapi"]
     app = FastAPI(**fastapi_kwargs, lifespan=lifespan)
-    app.middleware("http")(add_request_context_to_log)
+
+    # Order matters! Each added middleware wraps the previous, creating a stack.
+    # See also: https://fastapi.tiangolo.com/tutorial/middleware/#multiple-middleware-execution-order
     app.middleware("http")(request_response_logger)
+    app.middleware("http")(add_request_context_to_log)
 
     app.add_exception_handler(ProblemDetailError, problem_detail_exception_handler)  # type: ignore[arg-type]
 

From 186d196385443a132ab1a10512c2e36dc2b6d89d Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Wed, 1 Apr 2026 16:26:22 +0200
Subject: [PATCH 03/18] Fully transition to Loguru and make it configurable

---
 pyproject.toml           |  1 +
 src/config.py            | 14 ++++++++------
 src/config.toml          | 15 +++++++++++++++
 src/database/datasets.py |  2 --
 src/main.py              | 15 ++++++++++++---
 5 files changed, 36 insertions(+), 11 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 54cab3c..596d5b2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,6 +14,7 @@ classifiers = [
 ]
 dependencies = [
     "fastapi",
+    "loguru",
     "cryptography",
     "pydantic",
     "uvicorn",
diff --git a/src/config.py b/src/config.py
index 4a234a5..0ff7a91 100644
--- a/src/config.py
+++ b/src/config.py
@@ -1,13 +1,11 @@
 import functools
-import logging
 import os
 import tomllib
 import typing
 from pathlib import Path
 
 from dotenv import load_dotenv
-
-logger = logging.getLogger(__name__)
+from loguru import logger
 
 TomlTable = dict[str, typing.Any]
 
@@ -27,9 +25,13 @@
 _dotenv_file = Path(os.getenv(DOTENV_FILE_ENV, _config_directory / ".env"))
 _dotenv_file = _dotenv_file.expanduser().absolute()
 
-logger.info("Configuration directory is '%s'", _config_directory)
-logger.info("Loading configuration file from '%s'", _config_file)
-logger.info("Loading environment variables from '%s'", _dotenv_file)
+
+logger.info(
+    "Determined configuration sources.",
+    configuration_directory=_config_directory,
+    configuration_file=_config_file,
+    dotenv_file=_dotenv_file,
+)
 
 load_dotenv(dotenv_path=_dotenv_file)
 
diff --git a/src/config.toml b/src/config.toml
index f819ec9..384067d 100644
--- a/src/config.toml
+++ b/src/config.toml
@@ -4,6 +4,21 @@ minio_base_url="https://openml1.win.tue.nl"
 [development]
 allow_test_api_keys=true
 
+# Any number of logging.NAME configurations can be added.
+# NAME is for reference only, it has no meaning otherwise.
+# You can add any arguments to `loguru.logger.add`,
+# the `sink` variable will be used as first positional argument.
+# https://loguru.readthedocs.io/en/stable/api/logger.html
+[logging.develop]
+sink="develop.log"
+# One of loguru levels: TRACE, DEBUG, INFO, SUCCESS, WARNING, ERROR
+level="DEBUG"
+# Automatically create a new file by date or file size
+rotation="50 MB"
+# Retention specifies the timespan after which automatic cleanup occurs.
+retention="1 day"
+compression="gz"
+
 [fastapi]
 root_path=""
 
diff --git a/src/database/datasets.py b/src/database/datasets.py
index 27f1f4e..26eb33d 100644
--- a/src/database/datasets.py
+++ b/src/database/datasets.py
@@ -3,7 +3,6 @@
 import datetime
 from collections import defaultdict
 
-from loguru import logger
 from sqlalchemy import text
 from sqlalchemy.engine import Row
 from sqlalchemy.ext.asyncio import AsyncConnection
@@ -12,7 +11,6 @@
 
 
 async def get(id_: int, connection: AsyncConnection) -> Row | None:
-    logger.info("Fetching dataset from database", dataset_id=id_)
     row = await connection.execute(
         text(
             """
diff --git a/src/main.py b/src/main.py
index 5d3999a..dad7d02 100644
--- a/src/main.py
+++ b/src/main.py
@@ -1,5 +1,5 @@
 import argparse
-import logging
+import sys
 import uuid
 from collections.abc import AsyncGenerator, Awaitable, Callable
 from contextlib import asynccontextmanager
@@ -12,6 +12,7 @@
 
 from config import load_configuration
 from core.errors import ProblemDetailError, problem_detail_exception_handler
+from core.logging import setup_log_sinks
 from database.setup import close_databases
 from routers.mldcat_ap.dataset import router as mldcat_ap_router
 from routers.openml.datasets import router as datasets_router
@@ -93,10 +94,15 @@ async def request_response_logger(
 
 
 def create_api() -> FastAPI:
-    logger.add("log.log", serialize=True)
+    # Default logging configuration so we have logs during setup
+    setup_sink = logger.add(sys.stderr, serialize=True)
+    setup_log_sinks()
+
     fastapi_kwargs = load_configuration()["fastapi"]
+    logger.info("Creating FastAPI App", lifespan=lifespan, **fastapi_kwargs)
     app = FastAPI(**fastapi_kwargs, lifespan=lifespan)
 
+    logger.info("Setting up middleware and exception handlers.")
     # Order matters! Each added middleware wraps the previous, creating a stack.
     # See also: https://fastapi.tiangolo.com/tutorial/middleware/#multiple-middleware-execution-order
     app.middleware("http")(request_response_logger)
@@ -104,6 +110,7 @@ def create_api() -> FastAPI:
 
     app.add_exception_handler(ProblemDetailError, problem_detail_exception_handler)  # type: ignore[arg-type]
 
+    logger.info("Adding routers to app")
     app.include_router(datasets_router)
     app.include_router(qualities_router)
     app.include_router(mldcat_ap_router)
@@ -115,11 +122,13 @@ def create_api() -> FastAPI:
     app.include_router(study_router)
     app.include_router(setup_router)
     app.include_router(run_router)
+
+    logger.info("App setup completed.")
+    logger.remove(setup_sink)
     return app
 
 
 def main() -> None:
-    logging.basicConfig(level=logging.INFO)
     args = _parse_args()
     uvicorn.run(
         app="main:create_api",

From ee38e330c98fb6bb8f086f52c7f2b3ca0c4c5d8a Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Wed, 1 Apr 2026 16:27:51 +0200
Subject: [PATCH 04/18] ignore log files

---
 .gitignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitignore b/.gitignore
index a306cbd..5bcdce7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,6 @@
 docker/mysql/data
+*.log
+logs/
 .DS_Store
 
 # Byte-compiled / optimized / DLL files

From 964e55c8db33b514f6656c2e8a259e971ceeb9ff Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Wed, 1 Apr 2026 16:32:58 +0200
Subject: [PATCH 05/18] Add function to setup loguru sinks based on
 configuration

---
 src/core/logging.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 src/core/logging.py

diff --git a/src/core/logging.py b/src/core/logging.py
new file mode 100644
index 0000000..54d70ae
--- /dev/null
+++ b/src/core/logging.py
@@ -0,0 +1,14 @@
+"""Utility functions for logging."""
+
+from loguru import logger
+
+from config import load_configuration
+
+
+def setup_log_sinks() -> None:
+    """Configure loguru based on app configuration."""
+    configuration = load_configuration()
+    for nickname, sink_configuration in configuration.get("logging", {}).items():
+        logger.info("Configuring sink", nickname=nickname, **sink_configuration)
+        sink = sink_configuration.pop("sink")
+        logger.add(sink, serialize=True, **sink_configuration)

From 48a73efc690f50707faaffccb09fc04041664edd Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Wed, 1 Apr 2026 16:37:58 +0200
Subject: [PATCH 06/18] Move logging middleware to logging module

---
 src/core/logging.py | 40 ++++++++++++++++++++++++++++++++++++++++
 src/main.py         | 40 ++--------------------------------------
 2 files changed, 42 insertions(+), 38 deletions(-)

diff --git a/src/core/logging.py b/src/core/logging.py
index 54d70ae..c575d79 100644
--- a/src/core/logging.py
+++ b/src/core/logging.py
@@ -1,6 +1,11 @@
 """Utility functions for logging."""
 
+import uuid
+from collections.abc import Awaitable, Callable
+
 from loguru import logger
+from starlette.requests import Request
+from starlette.responses import Response
 
 from config import load_configuration
 
@@ -12,3 +17,38 @@ def setup_log_sinks() -> None:
         logger.info("Configuring sink", nickname=nickname, **sink_configuration)
         sink = sink_configuration.pop("sink")
         logger.add(sink, serialize=True, **sink_configuration)
+
+
+async def add_request_context_to_log(
+    request: Request,
+    call_next: Callable[[Request], Awaitable[Response]],
+) -> Response:
+    """Add a unique request id and client ip address to each log call."""
+    identifier = uuid.uuid4().hex
+    host = request.client.host if request.client else "unknown host"
+    with logger.contextualize(request_id=identifier, client_ip=host):
+        return await call_next(request)
+
+
+async def request_response_logger(
+    request: Request,
+    call_next: Callable[[Request], Awaitable[Response]],
+) -> Response:
+    """Log the incoming request and outgoing response."""
+    logger.info(
+        "request",
+        url=request.url,
+        headers=request.headers,
+        cookies=request.cookies,
+        path_params=request.path_params,
+        query_params=request.query_params,
+        body=await request.body(),
+    )
+    response: Response = await call_next(request)
+    logger.info(
+        "response",
+        status_code=response.status_code,
+        headers=response.headers,
+        media_type=response.media_type,
+    )
+    return response
diff --git a/src/main.py b/src/main.py
index dad7d02..fe09177 100644
--- a/src/main.py
+++ b/src/main.py
@@ -1,18 +1,15 @@
 import argparse
 import sys
-import uuid
-from collections.abc import AsyncGenerator, Awaitable, Callable
+from collections.abc import AsyncGenerator
 from contextlib import asynccontextmanager
 
 import uvicorn
 from fastapi import FastAPI
 from loguru import logger
-from starlette.requests import Request
-from starlette.responses import Response
 
 from config import load_configuration
 from core.errors import ProblemDetailError, problem_detail_exception_handler
-from core.logging import setup_log_sinks
+from core.logging import add_request_context_to_log, request_response_logger, setup_log_sinks
 from database.setup import close_databases
 from routers.mldcat_ap.dataset import router as mldcat_ap_router
 from routers.openml.datasets import router as datasets_router
@@ -60,39 +57,6 @@ def _parse_args() -> argparse.Namespace:
     return parser.parse_args()
 
 
-async def add_request_context_to_log(
-    request: Request,
-    call_next: Callable[[Request], Awaitable[Response]],
-) -> Response:
-    identifier = uuid.uuid4().hex
-    host = request.client.host if request.client else "unknown host"
-    with logger.contextualize(request_id=identifier, client_ip=host):
-        return await call_next(request)
-
-
-async def request_response_logger(
-    request: Request,
-    call_next: Callable[[Request], Awaitable[Response]],
-) -> Response:
-    logger.info(
-        "request",
-        url=request.url,
-        headers=request.headers,
-        cookies=request.cookies,
-        path_params=request.path_params,
-        query_params=request.query_params,
-        body=await request.body(),
-    )
-    response: Response = await call_next(request)
-    logger.info(
-        "response",
-        status_code=response.status_code,
-        headers=response.headers,
-        media_type=response.media_type,
-    )
-    return response
-
-
 def create_api() -> FastAPI:
     # Default logging configuration so we have logs during setup
     setup_sink = logger.add(sys.stderr, serialize=True)

From dd806b1050b1f2dcd0e2c262797ef2274766cfeb Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Wed, 1 Apr 2026 16:47:21 +0200
Subject: [PATCH 07/18] Remove automated logging of client ip address

---
 src/core/logging.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/core/logging.py b/src/core/logging.py
index c575d79..5d1d093 100644
--- a/src/core/logging.py
+++ b/src/core/logging.py
@@ -23,10 +23,9 @@ async def add_request_context_to_log(
     request: Request,
     call_next: Callable[[Request], Awaitable[Response]],
 ) -> Response:
-    """Add a unique request id and client ip address to each log call."""
+    """Add a unique request id to each log call."""
     identifier = uuid.uuid4().hex
-    host = request.client.host if request.client else "unknown host"
-    with logger.contextualize(request_id=identifier, client_ip=host):
+    with logger.contextualize(request_id=identifier):
         return await call_next(request)
 
 

From 37e974a62bd12cf95da235e25882d17a9b9df691 Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Wed, 1 Apr 2026 17:02:27 +0200
Subject: [PATCH 08/18] Disable logging to file with pytest

---
 tests/conftest.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/conftest.py b/tests/conftest.py
index 89a7bcb..2b8ac7a 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,5 +1,6 @@
 import contextlib
 import json
+import sys
 from collections.abc import AsyncIterator, Iterable, Iterator
 from pathlib import Path
 from typing import Any, NamedTuple
@@ -9,6 +10,7 @@
 import pytest
 from _pytest.config import Config
 from _pytest.nodes import Item
+from loguru import logger
 from sqlalchemy import text
 from sqlalchemy.ext.asyncio import AsyncConnection, AsyncEngine
 
@@ -74,6 +76,8 @@ async def py_api(
     expdb_test: AsyncConnection, user_test: AsyncConnection
 ) -> AsyncIterator[httpx.AsyncClient]:
     app = create_api()
+    logger.remove()
+    logger.add(sys.stderr, serialize=True)
 
     # We use async generator functions because fixtures may not be called directly.
     # The async generator returns the test connections for FastAPI to handle properly

From c62218c77697430401c7971eb2653d22da02458e Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Thu, 2 Apr 2026 12:35:09 +0200
Subject: [PATCH 09/18] Use a different configuration for the tests

---
 src/config.py          |  3 ++-
 src/core/logging.py    |  8 ++++++--
 src/main.py            |  7 ++++---
 tests/config.test.toml | 28 ++++++++++++++++++++++++++++
 tests/conftest.py      |  6 +-----
 5 files changed, 41 insertions(+), 11 deletions(-)
 create mode 100644 tests/config.test.toml

diff --git a/src/config.py b/src/config.py
index 0ff7a91..ffc4fb8 100644
--- a/src/config.py
+++ b/src/config.py
@@ -79,5 +79,6 @@ def load_database_configuration(file: Path = _config_file) -> TomlTable:
     return database_configuration
 
 
-def load_configuration(file: Path = _config_file) -> TomlTable:
+def load_configuration(file: Path | None = None) -> TomlTable:
+    file = file or _config_file
     return tomllib.loads(file.read_text())
diff --git a/src/core/logging.py b/src/core/logging.py
index 5d1d093..0878b8e 100644
--- a/src/core/logging.py
+++ b/src/core/logging.py
@@ -1,7 +1,9 @@
 """Utility functions for logging."""
 
+import sys
 import uuid
 from collections.abc import Awaitable, Callable
+from pathlib import Path
 
 from loguru import logger
 from starlette.requests import Request
@@ -10,12 +12,14 @@
 from config import load_configuration
 
 
-def setup_log_sinks() -> None:
+def setup_log_sinks(configuration_file: Path | None = None) -> None:
     """Configure loguru based on app configuration."""
-    configuration = load_configuration()
+    configuration = load_configuration(configuration_file)
     for nickname, sink_configuration in configuration.get("logging", {}).items():
         logger.info("Configuring sink", nickname=nickname, **sink_configuration)
         sink = sink_configuration.pop("sink")
+        if sink == "sys.stderr":
+            sink = sys.stderr
         logger.add(sink, serialize=True, **sink_configuration)
 
 
diff --git a/src/main.py b/src/main.py
index fe09177..93acd5d 100644
--- a/src/main.py
+++ b/src/main.py
@@ -2,6 +2,7 @@
 import sys
 from collections.abc import AsyncGenerator
 from contextlib import asynccontextmanager
+from pathlib import Path
 
 import uvicorn
 from fastapi import FastAPI
@@ -57,12 +58,12 @@ def _parse_args() -> argparse.Namespace:
     return parser.parse_args()
 
 
-def create_api() -> FastAPI:
+def create_api(configuration_file: Path | None = None) -> FastAPI:
     # Default logging configuration so we have logs during setup
     setup_sink = logger.add(sys.stderr, serialize=True)
-    setup_log_sinks()
+    setup_log_sinks(configuration_file)
 
-    fastapi_kwargs = load_configuration()["fastapi"]
+    fastapi_kwargs = load_configuration(configuration_file)["fastapi"]
     logger.info("Creating FastAPI App", lifespan=lifespan, **fastapi_kwargs)
     app = FastAPI(**fastapi_kwargs, lifespan=lifespan)
 
diff --git a/tests/config.test.toml b/tests/config.test.toml
new file mode 100644
index 0000000..6942c90
--- /dev/null
+++ b/tests/config.test.toml
@@ -0,0 +1,28 @@
+arff_base_url="https://test.openml.org"
+minio_base_url="https://openml1.win.tue.nl"
+
+[development]
+allow_test_api_keys=true
+
+[logging.develop]
+sink="sys.stderr"
+level="DEBUG"
+
+[fastapi]
+root_path=""
+
+[databases.defaults]
+host="database"
+port="3306"
+# SQLAlchemy `dialect` and `driver`: https://docs.sqlalchemy.org/en/20/dialects/index.html
+drivername="mysql+aiomysql"
+
+[databases.expdb]
+database="openml_expdb"
+
+[databases.openml]
+database="openml"
+
+[routing]
+minio_url="http://minio:9000/"
+server_url="http://php-api:80/"
diff --git a/tests/conftest.py b/tests/conftest.py
index 2b8ac7a..163e4e7 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,6 +1,5 @@
 import contextlib
 import json
-import sys
 from collections.abc import AsyncIterator, Iterable, Iterator
 from pathlib import Path
 from typing import Any, NamedTuple
@@ -10,7 +9,6 @@
 import pytest
 from _pytest.config import Config
 from _pytest.nodes import Item
-from loguru import logger
 from sqlalchemy import text
 from sqlalchemy.ext.asyncio import AsyncConnection, AsyncEngine
 
@@ -75,9 +73,7 @@ async def php_api() -> AsyncIterator[httpx.AsyncClient]:
 async def py_api(
     expdb_test: AsyncConnection, user_test: AsyncConnection
 ) -> AsyncIterator[httpx.AsyncClient]:
-    app = create_api()
-    logger.remove()
-    logger.add(sys.stderr, serialize=True)
+    app = create_api(Path(__file__).parent / "config.test.toml")
 
     # We use async generator functions because fixtures may not be called directly.
     # The async generator returns the test connections for FastAPI to handle properly

From 26592193090c5a9c4808dd88715fd8b03f39279d Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Thu, 2 Apr 2026 16:02:25 +0200
Subject: [PATCH 10/18] Do not log the request body

---
 src/core/logging.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/core/logging.py b/src/core/logging.py
index 0878b8e..d36df1e 100644
--- a/src/core/logging.py
+++ b/src/core/logging.py
@@ -45,7 +45,6 @@ async def request_response_logger(
         cookies=request.cookies,
         path_params=request.path_params,
         query_params=request.query_params,
-        body=await request.body(),
     )
     response: Response = await call_next(request)
     logger.info(

From f7c6ff68ceb5b126b52d30c07bf6819b2932dae8 Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Thu, 2 Apr 2026 16:25:29 +0200
Subject: [PATCH 11/18] Disable loguru

---
 src/config.py       | 14 +++++++-------
 src/core/logging.py |  7 ++++++-
 src/main.py         | 20 ++++++++++----------
 3 files changed, 23 insertions(+), 18 deletions(-)

diff --git a/src/config.py b/src/config.py
index ffc4fb8..894e755 100644
--- a/src/config.py
+++ b/src/config.py
@@ -5,7 +5,7 @@
 from pathlib import Path
 
 from dotenv import load_dotenv
-from loguru import logger
+# from loguru import logger
 
 TomlTable = dict[str, typing.Any]
 
@@ -26,12 +26,12 @@
 _dotenv_file = _dotenv_file.expanduser().absolute()
 
 
-logger.info(
-    "Determined configuration sources.",
-    configuration_directory=_config_directory,
-    configuration_file=_config_file,
-    dotenv_file=_dotenv_file,
-)
+# logger.info(
+#    "Determined configuration sources.",
+#    configuration_directory=_config_directory,
+#    configuration_file=_config_file,
+#    dotenv_file=_dotenv_file,
+# )
 
 load_dotenv(dotenv_path=_dotenv_file)
 
diff --git a/src/core/logging.py b/src/core/logging.py
index d36df1e..698e787 100644
--- a/src/core/logging.py
+++ b/src/core/logging.py
@@ -5,7 +5,6 @@
 from collections.abc import Awaitable, Callable
 from pathlib import Path
 
-from loguru import logger
 from starlette.requests import Request
 from starlette.responses import Response
 
@@ -14,6 +13,8 @@
 
 def setup_log_sinks(configuration_file: Path | None = None) -> None:
     """Configure loguru based on app configuration."""
+    from loguru import logger
+
     configuration = load_configuration(configuration_file)
     for nickname, sink_configuration in configuration.get("logging", {}).items():
         logger.info("Configuring sink", nickname=nickname, **sink_configuration)
@@ -28,6 +29,8 @@ async def add_request_context_to_log(
     call_next: Callable[[Request], Awaitable[Response]],
 ) -> Response:
     """Add a unique request id to each log call."""
+    from loguru import logger
+
     identifier = uuid.uuid4().hex
     with logger.contextualize(request_id=identifier):
         return await call_next(request)
@@ -38,6 +41,8 @@ async def request_response_logger(
     call_next: Callable[[Request], Awaitable[Response]],
 ) -> Response:
     """Log the incoming request and outgoing response."""
+    from loguru import logger
+
     logger.info(
         "request",
         url=request.url,
diff --git a/src/main.py b/src/main.py
index 93acd5d..dee397e 100644
--- a/src/main.py
+++ b/src/main.py
@@ -6,7 +6,7 @@
 
 import uvicorn
 from fastapi import FastAPI
-from loguru import logger
+# from loguru import logger
 
 from config import load_configuration
 from core.errors import ProblemDetailError, problem_detail_exception_handler
@@ -60,22 +60,22 @@ def _parse_args() -> argparse.Namespace:
 
 def create_api(configuration_file: Path | None = None) -> FastAPI:
     # Default logging configuration so we have logs during setup
-    setup_sink = logger.add(sys.stderr, serialize=True)
-    setup_log_sinks(configuration_file)
+    # setup_sink = logger.add(sys.stderr, serialize=True)
+    # setup_log_sinks(configuration_file)
 
     fastapi_kwargs = load_configuration(configuration_file)["fastapi"]
-    logger.info("Creating FastAPI App", lifespan=lifespan, **fastapi_kwargs)
+    # logger.info("Creating FastAPI App", lifespan=lifespan, **fastapi_kwargs)
     app = FastAPI(**fastapi_kwargs, lifespan=lifespan)
 
-    logger.info("Setting up middleware and exception handlers.")
+    # logger.info("Setting up middleware and exception handlers.")
     # Order matters! Each added middleware wraps the previous, creating a stack.
     # See also: https://fastapi.tiangolo.com/tutorial/middleware/#multiple-middleware-execution-order
-    app.middleware("http")(request_response_logger)
-    app.middleware("http")(add_request_context_to_log)
+    # app.middleware("http")(request_response_#logger)
+    # app.middleware("http")(add_request_context_to_log)
 
     app.add_exception_handler(ProblemDetailError, problem_detail_exception_handler)  # type: ignore[arg-type]
 
-    logger.info("Adding routers to app")
+    # logger.info("Adding routers to app")
     app.include_router(datasets_router)
     app.include_router(qualities_router)
     app.include_router(mldcat_ap_router)
@@ -88,8 +88,8 @@ def create_api(configuration_file: Path | None = None) -> FastAPI:
     app.include_router(setup_router)
     app.include_router(run_router)
 
-    logger.info("App setup completed.")
-    logger.remove(setup_sink)
+    # logger.info("App setup completed.")
+    # logger.remove(setup_sink)
     return app
 
 

From 38d1d8dc4a017961857a1adf3cf79012abc2c043 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 2 Apr 2026 14:25:52 +0000
Subject: [PATCH 12/18] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/config.py | 1 +
 src/main.py   | 4 +---
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/config.py b/src/config.py
index 894e755..2e1872a 100644
--- a/src/config.py
+++ b/src/config.py
@@ -5,6 +5,7 @@
 from pathlib import Path
 
 from dotenv import load_dotenv
+
 # from loguru import logger
 
 TomlTable = dict[str, typing.Any]
diff --git a/src/main.py b/src/main.py
index dee397e..3618e88 100644
--- a/src/main.py
+++ b/src/main.py
@@ -1,16 +1,14 @@
 import argparse
-import sys
 from collections.abc import AsyncGenerator
 from contextlib import asynccontextmanager
 from pathlib import Path
 
 import uvicorn
 from fastapi import FastAPI
-# from loguru import logger
 
+# from loguru import logger
 from config import load_configuration
 from core.errors import ProblemDetailError, problem_detail_exception_handler
-from core.logging import add_request_context_to_log, request_response_logger, setup_log_sinks
 from database.setup import close_databases
 from routers.mldcat_ap.dataset import router as mldcat_ap_router
 from routers.openml.datasets import router as datasets_router

From 1f1fa5581c9520f96de967eda2aabe95c8b9b643 Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Thu, 2 Apr 2026 16:36:12 +0200
Subject: [PATCH 13/18] Add back import statements

---
 src/config.py       | 2 +-
 src/core/logging.py | 4 +---
 src/main.py         | 3 ++-
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/config.py b/src/config.py
index 2e1872a..dabc5b2 100644
--- a/src/config.py
+++ b/src/config.py
@@ -6,7 +6,7 @@
 
 from dotenv import load_dotenv
 
-# from loguru import logger
+from loguru import logger
 
 TomlTable = dict[str, typing.Any]
 
diff --git a/src/core/logging.py b/src/core/logging.py
index 698e787..0d463d7 100644
--- a/src/core/logging.py
+++ b/src/core/logging.py
@@ -7,13 +7,13 @@
 
 from starlette.requests import Request
 from starlette.responses import Response
+from loguru import logger
 
 from config import load_configuration
 
 
 def setup_log_sinks(configuration_file: Path | None = None) -> None:
     """Configure loguru based on app configuration."""
-    from loguru import logger
 
     configuration = load_configuration(configuration_file)
     for nickname, sink_configuration in configuration.get("logging", {}).items():
@@ -29,7 +29,6 @@ async def add_request_context_to_log(
     call_next: Callable[[Request], Awaitable[Response]],
 ) -> Response:
     """Add a unique request id to each log call."""
-    from loguru import logger
 
     identifier = uuid.uuid4().hex
     with logger.contextualize(request_id=identifier):
@@ -41,7 +40,6 @@ async def request_response_logger(
     call_next: Callable[[Request], Awaitable[Response]],
 ) -> Response:
     """Log the incoming request and outgoing response."""
-    from loguru import logger
 
     logger.info(
         "request",
diff --git a/src/main.py b/src/main.py
index 3618e88..7fbb190 100644
--- a/src/main.py
+++ b/src/main.py
@@ -5,10 +5,11 @@
 
 import uvicorn
 from fastapi import FastAPI
+from loguru import logger
 
-# from loguru import logger
 from config import load_configuration
 from core.errors import ProblemDetailError, problem_detail_exception_handler
+from core.logging import add_request_context_to_log, request_response_logger, setup_log_sinks
 from database.setup import close_databases
 from routers.mldcat_ap.dataset import router as mldcat_ap_router
 from routers.openml.datasets import router as datasets_router

From 9c81a9af7785434ff07ada38cc8e28a69831a0a1 Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Thu, 2 Apr 2026 16:40:53 +0200
Subject: [PATCH 14/18] Startup logging

---
 src/config.py | 12 ++++++------
 src/main.py   | 12 ++++++------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/config.py b/src/config.py
index dabc5b2..2c5beeb 100644
--- a/src/config.py
+++ b/src/config.py
@@ -27,12 +27,12 @@
 _dotenv_file = _dotenv_file.expanduser().absolute()
 
 
-# logger.info(
-#    "Determined configuration sources.",
-#    configuration_directory=_config_directory,
-#    configuration_file=_config_file,
-#    dotenv_file=_dotenv_file,
-# )
+logger.info(
+    "Determined configuration sources.",
+    configuration_directory=_config_directory,
+    configuration_file=_config_file,
+    dotenv_file=_dotenv_file,
+)
 
 load_dotenv(dotenv_path=_dotenv_file)
 
diff --git a/src/main.py b/src/main.py
index 7fbb190..cee152a 100644
--- a/src/main.py
+++ b/src/main.py
@@ -2,6 +2,7 @@
 from collections.abc import AsyncGenerator
 from contextlib import asynccontextmanager
 from pathlib import Path
+import sys
 
 import uvicorn
 from fastapi import FastAPI
@@ -9,7 +10,6 @@
 
 from config import load_configuration
 from core.errors import ProblemDetailError, problem_detail_exception_handler
-from core.logging import add_request_context_to_log, request_response_logger, setup_log_sinks
 from database.setup import close_databases
 from routers.mldcat_ap.dataset import router as mldcat_ap_router
 from routers.openml.datasets import router as datasets_router
@@ -59,11 +59,11 @@ def _parse_args() -> argparse.Namespace:
 
 def create_api(configuration_file: Path | None = None) -> FastAPI:
     # Default logging configuration so we have logs during setup
-    # setup_sink = logger.add(sys.stderr, serialize=True)
+    setup_sink = logger.add(sys.stderr, serialize=True)
     # setup_log_sinks(configuration_file)
 
     fastapi_kwargs = load_configuration(configuration_file)["fastapi"]
-    # logger.info("Creating FastAPI App", lifespan=lifespan, **fastapi_kwargs)
+    logger.info("Creating FastAPI App", lifespan=lifespan, **fastapi_kwargs)
     app = FastAPI(**fastapi_kwargs, lifespan=lifespan)
 
     # logger.info("Setting up middleware and exception handlers.")
@@ -74,7 +74,7 @@ def create_api(configuration_file: Path | None = None) -> FastAPI:
 
     app.add_exception_handler(ProblemDetailError, problem_detail_exception_handler)  # type: ignore[arg-type]
 
-    # logger.info("Adding routers to app")
+    logger.info("Adding routers to app")
     app.include_router(datasets_router)
     app.include_router(qualities_router)
     app.include_router(mldcat_ap_router)
@@ -87,8 +87,8 @@ def create_api(configuration_file: Path | None = None) -> FastAPI:
     app.include_router(setup_router)
     app.include_router(run_router)
 
-    # logger.info("App setup completed.")
-    # logger.remove(setup_sink)
+    logger.info("App setup completed.")
+    logger.remove(setup_sink)
     return app
 
 

From 6b276ded992b9fa19136b0b2a21e306893befa56 Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Thu, 2 Apr 2026 16:46:11 +0200
Subject: [PATCH 15/18] Add back the context middleware

---
 src/config.py | 1 -
 src/main.py   | 7 ++++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/config.py b/src/config.py
index 2c5beeb..ffc4fb8 100644
--- a/src/config.py
+++ b/src/config.py
@@ -5,7 +5,6 @@
 from pathlib import Path
 
 from dotenv import load_dotenv
-
 from loguru import logger
 
 TomlTable = dict[str, typing.Any]
diff --git a/src/main.py b/src/main.py
index cee152a..a8aa6f9 100644
--- a/src/main.py
+++ b/src/main.py
@@ -1,11 +1,12 @@
 import argparse
+import sys
 from collections.abc import AsyncGenerator
 from contextlib import asynccontextmanager
 from pathlib import Path
-import sys
 
 import uvicorn
 from fastapi import FastAPI
+from core.logging import add_request_context_to_log
 from loguru import logger
 
 from config import load_configuration
@@ -66,11 +67,11 @@ def create_api(configuration_file: Path | None = None) -> FastAPI:
     logger.info("Creating FastAPI App", lifespan=lifespan, **fastapi_kwargs)
     app = FastAPI(**fastapi_kwargs, lifespan=lifespan)
 
-    # logger.info("Setting up middleware and exception handlers.")
+    logger.info("Setting up middleware and exception handlers.")
     # Order matters! Each added middleware wraps the previous, creating a stack.
     # See also: https://fastapi.tiangolo.com/tutorial/middleware/#multiple-middleware-execution-order
     # app.middleware("http")(request_response_#logger)
-    # app.middleware("http")(add_request_context_to_log)
+    app.middleware("http")(add_request_context_to_log)
 
     app.add_exception_handler(ProblemDetailError, problem_detail_exception_handler)  # type: ignore[arg-type]
 

From 9f5862341dcac560718feb133565562d031a14f9 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 2 Apr 2026 14:48:15 +0000
Subject: [PATCH 16/18] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/core/logging.py | 5 +----
 src/main.py         | 2 +-
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/core/logging.py b/src/core/logging.py
index 0d463d7..d36df1e 100644
--- a/src/core/logging.py
+++ b/src/core/logging.py
@@ -5,16 +5,15 @@
 from collections.abc import Awaitable, Callable
 from pathlib import Path
 
+from loguru import logger
 from starlette.requests import Request
 from starlette.responses import Response
-from loguru import logger
 
 from config import load_configuration
 
 
 def setup_log_sinks(configuration_file: Path | None = None) -> None:
     """Configure loguru based on app configuration."""
-
     configuration = load_configuration(configuration_file)
     for nickname, sink_configuration in configuration.get("logging", {}).items():
         logger.info("Configuring sink", nickname=nickname, **sink_configuration)
@@ -29,7 +28,6 @@ async def add_request_context_to_log(
     call_next: Callable[[Request], Awaitable[Response]],
 ) -> Response:
     """Add a unique request id to each log call."""
-
     identifier = uuid.uuid4().hex
     with logger.contextualize(request_id=identifier):
         return await call_next(request)
@@ -40,7 +38,6 @@ async def request_response_logger(
     call_next: Callable[[Request], Awaitable[Response]],
 ) -> Response:
     """Log the incoming request and outgoing response."""
-
     logger.info(
         "request",
         url=request.url,
diff --git a/src/main.py b/src/main.py
index a8aa6f9..4825547 100644
--- a/src/main.py
+++ b/src/main.py
@@ -6,11 +6,11 @@
 
 import uvicorn
 from fastapi import FastAPI
-from core.logging import add_request_context_to_log
 from loguru import logger
 
 from config import load_configuration
 from core.errors import ProblemDetailError, problem_detail_exception_handler
+from core.logging import add_request_context_to_log
 from database.setup import close_databases
 from routers.mldcat_ap.dataset import router as mldcat_ap_router
 from routers.openml.datasets import router as datasets_router

From 8e5c56125fc0601eba372d8445b226eb69656d58 Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Thu, 2 Apr 2026 16:57:29 +0200
Subject: [PATCH 17/18] Add back in logging, but with placeholder messages

---
 src/core/logging.py | 30 ++++++++++++++++--------------
 src/main.py         |  7 ++++---
 2 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/src/core/logging.py b/src/core/logging.py
index d36df1e..37b0b4a 100644
--- a/src/core/logging.py
+++ b/src/core/logging.py
@@ -38,19 +38,21 @@ async def request_response_logger(
     call_next: Callable[[Request], Awaitable[Response]],
 ) -> Response:
     """Log the incoming request and outgoing response."""
-    logger.info(
-        "request",
-        url=request.url,
-        headers=request.headers,
-        cookies=request.cookies,
-        path_params=request.path_params,
-        query_params=request.query_params,
-    )
+    # logger.info(
+    #    "request",
+    #    url=request.url,
+    #    headers=request.headers,
+    #    cookies=request.cookies,
+    #    path_params=request.path_params,
+    #    query_params=request.query_params,
+    # )
+    logger.info("before request")
     response: Response = await call_next(request)
-    logger.info(
-        "response",
-        status_code=response.status_code,
-        headers=response.headers,
-        media_type=response.media_type,
-    )
+    logger.info("after request")
+    # logger.info(
+    #    "response",
+    #    status_code=response.status_code,
+    #    headers=response.headers,
+    #    media_type=response.media_type,
+    # )
     return response
diff --git a/src/main.py b/src/main.py
index 4825547..696c09b 100644
--- a/src/main.py
+++ b/src/main.py
@@ -10,7 +10,7 @@
 
 from config import load_configuration
 from core.errors import ProblemDetailError, problem_detail_exception_handler
-from core.logging import add_request_context_to_log
+from core.logging import add_request_context_to_log, request_response_logger, setup_log_sinks
 from database.setup import close_databases
 from routers.mldcat_ap.dataset import router as mldcat_ap_router
 from routers.openml.datasets import router as datasets_router
@@ -60,8 +60,9 @@ def _parse_args() -> argparse.Namespace:
 
 def create_api(configuration_file: Path | None = None) -> FastAPI:
     # Default logging configuration so we have logs during setup
+    logger.remove()
     setup_sink = logger.add(sys.stderr, serialize=True)
-    # setup_log_sinks(configuration_file)
+    setup_log_sinks(configuration_file)
 
     fastapi_kwargs = load_configuration(configuration_file)["fastapi"]
     logger.info("Creating FastAPI App", lifespan=lifespan, **fastapi_kwargs)
@@ -70,7 +71,7 @@ def create_api(configuration_file: Path | None = None) -> FastAPI:
     logger.info("Setting up middleware and exception handlers.")
     # Order matters! Each added middleware wraps the previous, creating a stack.
     # See also: https://fastapi.tiangolo.com/tutorial/middleware/#multiple-middleware-execution-order
-    # app.middleware("http")(request_response_#logger)
+    app.middleware("http")(request_response_logger)
     app.middleware("http")(add_request_context_to_log)
 
     app.add_exception_handler(ProblemDetailError, problem_detail_exception_handler)  # type: ignore[arg-type]

From 4e5d3da21b5cac917b21b7bdd93834cce6e25188 Mon Sep 17 00:00:00 2001
From: PGijsbers <p.gijsbers@tue.nl>
Date: Thu, 2 Apr 2026 20:04:27 +0200
Subject: [PATCH 18/18] Add back in full logging of requests

---
 src/core/logging.py | 30 ++++++++++++++----------------
 1 file changed, 14 insertions(+), 16 deletions(-)

diff --git a/src/core/logging.py b/src/core/logging.py
index 37b0b4a..d36df1e 100644
--- a/src/core/logging.py
+++ b/src/core/logging.py
@@ -38,21 +38,19 @@ async def request_response_logger(
     call_next: Callable[[Request], Awaitable[Response]],
 ) -> Response:
     """Log the incoming request and outgoing response."""
-    # logger.info(
-    #    "request",
-    #    url=request.url,
-    #    headers=request.headers,
-    #    cookies=request.cookies,
-    #    path_params=request.path_params,
-    #    query_params=request.query_params,
-    # )
-    logger.info("before request")
+    logger.info(
+        "request",
+        url=request.url,
+        headers=request.headers,
+        cookies=request.cookies,
+        path_params=request.path_params,
+        query_params=request.query_params,
+    )
     response: Response = await call_next(request)
-    logger.info("after request")
-    # logger.info(
-    #    "response",
-    #    status_code=response.status_code,
-    #    headers=response.headers,
-    #    media_type=response.media_type,
-    # )
+    logger.info(
+        "response",
+        status_code=response.status_code,
+        headers=response.headers,
+        media_type=response.media_type,
+    )
     return response