refactoring logging, metrics and new tests

src/endpoints/default.py

@@ -1,10 +1,10 @@
 
 from fastapi import APIRouter, Depends, Request, HTTPException
 from fastapi.responses import FileResponse, JSONResponse
-from loguru import logger
 from sqlalchemy.orm import Session
 
 from core.config import VERSION, BREAKING_CHANGES
+from core.logging import log_error
 from db import crud
 from db.database import get_db_dependency, get_db
 from web.security import get_user_auth, bearer_security
@@ -21,7 +21,7 @@ async def home(request: Request):
         with get_db() as db:
             status["groups"] = crud.get_user_groups(db, email)
     except HTTPException: pass  # not authenticated is fine
-    except Exception as e: logger.error(e)
+    except Exception as e: log_error(e)
     return JSONResponse(status)
 
 

src/endpoints/interoperability.py

@@ -7,6 +7,7 @@ import sqlalchemy
 from web.security import token_api_key_auth
 from db import models, schemas
 from worker import insert_result_into_db
+from core.logging import log_error
 
 
 interoperability_router = APIRouter(prefix="/interop", tags=["Interoperability endpoints."])
@@ -21,6 +22,6 @@ def submit_manual_archive(manual: schemas.SubmitManual, auth=Depends(token_api_k
     try:
         archive_id = insert_result_into_db(result, manual.tags, manual.public, manual.group_id, manual.author_id, models.generate_uuid())
     except sqlalchemy.exc.IntegrityError as e:
-        logger.error(e)
+        log_error(e)
         raise HTTPException(status_code=422, detail=f"Cannot insert into DB due to integrity error")
     return JSONResponse({"id": archive_id}, status_code=201)

src/endpoints/task.py

@@ -1,4 +1,3 @@
-import traceback
 from celery.result import AsyncResult
 from fastapi import APIRouter, Depends
 from fastapi.encoders import jsonable_encoder
@@ -8,7 +7,7 @@ from loguru import logger
 from web.security import get_token_or_user_auth
 
 from db import schemas
-
+from core.logging import log_error
 from worker import celery
 
 
@@ -25,8 +24,6 @@ def get_status(task_id, email=Depends(get_token_or_user_auth)):
             # The :attr:`result` attribute then contains the exception raised by the task.
             # https://docs.celeryq.dev/en/stable/_modules/celery/result.html#AsyncResult
             raise task.result
-        # TODO: refactor to use schema?
-        # response = schemas.TaskResult(id=task_id, status=task.status, result=task.result)
 
         response = {
             "id": task_id,
@@ -36,10 +33,7 @@ def get_status(task_id, email=Depends(get_token_or_user_auth)):
         return JSONResponse(jsonable_encoder(response, exclude_unset=True))
 
     except Exception as e:
-        logger.error(e)
-        logger.error(traceback.format_exc())
-        # TODO: refactor to use schema?
-        # response = schemas.TaskResult(id=task_id, status="FAILURE", result={"error": str(e)})
+        log_error(e)
         return JSONResponse({
             "id": task_id,
             "status": "FAILURE",