fix log imports

api/common/__init__.py

@@ -1,5 +1,5 @@
 from .decorators import data_decorator, router_decorator, async_router_decorator, name_to_fns_map
 from .siibra_api_typing import ROLE_TYPE
-from .logger import logger, access_logger
+from .logger import logger as general_logger, access_logger
 from .exceptions import *
 from .storage import get_filename

api/common/data_handlers/features/types.py

@@ -1,4 +1,4 @@
-from api.common import data_decorator, InsufficientParameters, NotFound, AmbiguousParameters, logger
+from api.common import data_decorator, InsufficientParameters, NotFound, AmbiguousParameters, general_logger
 from api.siibra_api_config import ROLE, SIIBRA_API_SHARED_DIR
 from typing import List, Type, Any, Dict
 from hashlib import md5
@@ -108,13 +108,13 @@ def get_single_feature_download_zip_path(feature_id: str, **kwargs):
     try:
         feat = siibra.features.Feature._get_instance_by_id(feature_id)
     except Exception as e:
-        logger.error(f"Error finding single feature {feature_id=}, {str(e)}")
+        general_logger.error(f"Error finding single feature {feature_id=}, {str(e)}")
         raise NotFound from e
     try:
         feat.export(str(full_filename))
         return str(full_filename)
     except Exception as e:
-        logger.error(f"Error export single feature {feature_id=}, {str(e)}")
+        general_logger.error(f"Error export single feature {feature_id=}, {str(e)}")
         error_filename = full_filename.with_suffix(".error.zip")
         with ZipFile(error_filename, "w") as zf:
             zf.writestr("error.txt", f"Error exporting file for feature_id: {feature_id}: {str(e)}")
@@ -153,7 +153,7 @@ def get_all_all_features(*, space_id: str=None, parcellation_id: str=None, regio
             )
         except Exception as e:
             err_str = str(e).replace('\n', ' ')
-            logger.warning(f"feature failed to be serialized. Params: space_id={space_id}, parcellation_id={parcellation_id}, region_id={region_id}. feature id: {f.id}. error: {err_str}")
+            general_logger.warning(f"feature failed to be serialized. Params: space_id={space_id}, parcellation_id={parcellation_id}, region_id={region_id}. feature id: {f.id}. error: {err_str}")
     return re_features
 
 
@@ -184,7 +184,7 @@ def all_features(*, space_id: str, parcellation_id: str, region_id: str, type: s
             )
         except Exception as e:
             err_str = str(e).replace('\n', ' ')
-            logger.warning(f"feature failed to be serialized. Params: space_id={space_id}, parcellation_id={parcellation_id}, region_id={region_id}. feature id: {f.id}, error: {err_str}")
+            general_logger.warning(f"feature failed to be serialized. Params: space_id={space_id}, parcellation_id={parcellation_id}, region_id={region_id}. feature id: {f.id}, error: {err_str}")
     return re_features
 
 

api/common/decorators.py

@@ -1,13 +1,14 @@
-from .siibra_api_typing import ROLE_TYPE
-from api.common import logger
 from functools import wraps, partial
 import inspect
 import asyncio
 import time
-from api.common.exceptions import (
+from typing import Dict, Callable, Tuple
+
+from .siibra_api_typing import ROLE_TYPE
+from .logger import logger as general_logger
+from .exceptions import (
     FaultyRoleException,
 )
-from typing import Dict, Callable, Tuple
 
 name_to_fns_map: Dict[str, Tuple[Callable, Callable]] = {}
 
@@ -33,15 +34,15 @@ def outer_wrapper(fn):
 
                 def celery_task_wrapper(self, *args, **kwargs):
                     if role == "worker":
-                        logger.info(f"Task Received: {fn.__name__=}, {args=}, {kwargs=}")
+                        general_logger.info(f"Task Received: {fn.__name__=}, {args=}, {kwargs=}")
                     return fn(*args, **kwargs)
 
                 return app.task(bind=True)(
                     wraps(fn)(celery_task_wrapper)
                 )
             except ImportError as e:
                 errmsg = f"For worker role, celery must be installed as a dep"
-                logger.critical(errmsg)
+                general_logger.critical(errmsg)
                 raise ImportError(errmsg) from e
         raise FaultyRoleException(f"role must be 'all', 'server' or 'worker', but it is {role}")
     return outer_wrapper

api/serialization/core/region.py

@@ -12,7 +12,7 @@
     instance_to_model
 )
 from api.serialization.util.siibra import Region, Space, parcellations, RegionRelationAssessments
-from api.common.logger import logger
+from api.common import general_logger
 
 
 
@@ -149,7 +149,7 @@ def region_to_model(region: Region, *, min_flag: bool=False, detail: bool=False,
         if centroids is not None and len(centroids) > 0:
             centroid = centroids[0]
             if len(centroids) > 1:
-                logger.warn(f"region {region.name!r} returned multiple centroids in space {space.name!r}. Returning the first one.")
+                general_logger.warn(f"region {region.name!r} returned multiple centroids in space {space.name!r}. Returning the first one.")
 
     pev.has_annotation = HasAnnotation(
         best_view_point=BestViewPoint(

api/server/api.py

@@ -22,7 +22,7 @@
 from .metrics import prom_metrics_resp, on_startup as metrics_on_startup, on_terminate as metrics_on_terminate
 from .code_snippet import get_sourcecode
 
-from ..common import logger, access_logger, NotFound, SapiBaseException, name_to_fns_map
+from ..common import general_logger, access_logger, NotFound, SapiBaseException, name_to_fns_map
 from ..siibra_api_config import GIT_HASH
 
 siibra_version_header = "x-siibra-api-version"
@@ -295,15 +295,15 @@ async def middleware_access_log(request: Request, call_next):
             "hit_cache": "cache_miss"
         })
     except Exception as e:
-        logger.critical(e)
+        general_logger.critical(e)
 
 @siibra_api.exception_handler(RuntimeError)
 async def exception_runtime(request: Request, exc: RuntimeError) -> JSONResponse:
     """Handling RuntimeErrors.
     Most of the RuntimeErrors are thrown by the siibra-python library when other Services are not responding.
     To be more resilient and not throw a simple and unplanned HTTP 500 response, this handler will return an HTTP 503
     status."""
-    logger.warning(f"Error handler: exception_runtime: {str(exc)}")
+    general_logger.warning(f"Error handler: exception_runtime: {str(exc)}")
     return JSONResponse(
         status_code=503,
         content={
@@ -315,13 +315,13 @@ async def exception_runtime(request: Request, exc: RuntimeError) -> JSONResponse
 @siibra_api.exception_handler(SapiBaseException)
 def exception_sapi(request: Request, exc: SapiBaseException):
     """Handle sapi errors"""
-    logger.warning(f"Error handler: exception_sapi: {str(exc)}")
+    general_logger.warning(f"Error handler: exception_sapi: {str(exc)}")
     raise HTTPException(400, str(exc))
 
 @siibra_api.exception_handler(Exception)
 async def exception_other(request: Request, exc: Exception):
     """Catch all exception handler"""
-    logger.warning(f"Error handler: exception_other: {str(exc)}")
+    general_logger.warning(f"Error handler: exception_other: {str(exc)}")
     return JSONResponse(
         status_code=500,
         content={

api/server/metrics.py

@@ -6,7 +6,7 @@
 from pathlib import Path
 from api.siibra_api_config import ROLE, CELERY_CONFIG, NAME_SPACE, MONITOR_FIRSTLVL_DIR
 from api.common.timer import RepeatTimer
-from api.common import logger
+from api.common import general_logger
 
 class Singleton:
     """Timer singleton"""
@@ -27,7 +27,7 @@ def timed_du():
             try:
                 dirs = os.listdir(MONITOR_FIRSTLVL_DIR)
             except Exception as e:
-                logger.warn(f"Failed to listdir of {MONITOR_FIRSTLVL_DIR}: {str(e)}")
+                general_logger.warn(f"Failed to listdir of {MONITOR_FIRSTLVL_DIR}: {str(e)}")
                 return
 
             for dir in dirs:
@@ -37,7 +37,7 @@ def timed_du():
                     size_b, *_ = result.stdout.split("\t")
                     Singleton.cached_du[dir] = int(size_b)
                 except Exception as e:
-                    logger.warn(f"Failed to check du of {str(path_to_dir)}: {str(e)}")
+                    general_logger.warn(f"Failed to check du of {str(path_to_dir)}: {str(e)}")
 
 
 def on_startup():

api/server/volumes/parcellationmap.py

@@ -9,7 +9,7 @@
 from api.models.volumes.parcellationmap import MapModel
 from api.models.volumes.volume import MapType
 from api.models._commons import DataFrameModel
-from api.common import router_decorator, get_filename, logger, NotFound
+from api.common import router_decorator, get_filename, NotFound
 from api.common.data_handlers.volumes.parcellationmap import get_map, get_region_statistic_map, get_region_statistic_map_info, get_parcellation_labelled_map, assign_point, get_resampled_map
 from api.server.util import SapiCustomRoute
 import os