package logger

cellarium/cas/__init__.py

@@ -1,6 +1,6 @@
 from cellarium.cas.client import CASClient
 
-from . import constants, exceptions, postprocessing, preprocessing, service, settings, version, visualization
+from . import constants, exceptions, logging, postprocessing, preprocessing, service, settings, version, visualization
 
 __version__ = version.get_version()
 
@@ -15,4 +15,5 @@
     "service",
     "settings",
     "version",
+    "logging",
 ]

cellarium/cas/client.py

@@ -1,7 +1,6 @@
 import asyncio
 import datetime
 import functools
-import logging
 import math
 import operator
 import pkgutil
@@ -15,6 +14,7 @@
 from anndata import ImplicitModificationWarning
 from deprecated import deprecated
 
+from cellarium.cas.logging import logger
 from cellarium.cas.service import action_context_manager
 
 from . import _io, constants, exceptions, models, preprocessing, service, settings, version
@@ -71,7 +71,7 @@ def __init__(
             api_token=api_token, api_url=api_url, client_session_id=self.client_session_id
         )
 
-        logging.info(f"Connecting to the Cellarium Cloud backend with session {self.client_session_id}...")
+        logger.info(f"Connecting to the Cellarium Cloud backend with session {self.client_session_id}...")
         self.user_info = self.cas_api_service.validate_token()
         username = self.user_info["username"]
         self.__print(f"User is {username}")

cellarium/cas/logging.py

@@ -0,0 +1,17 @@
+import logging
+
+from cellarium.cas import settings
+
+# Create a custom logger for the package
+logger = logging.getLogger("cellarium.cas")
+logger.setLevel(settings.LOGGING_LEVEL)
+
+# Create a handler
+handler = logging.StreamHandler()
+
+# Create a formatter and set it for the handler
+formatter = logging.Formatter(fmt=settings.LOGGING_FORMAT, datefmt=settings.LOGGING_DATE_FORMAT)
+handler.setFormatter(formatter)
+
+# Add the handler to the logger
+logger.addHandler(handler)

cellarium/cas/postprocessing/cell_ontology/cell_ontology_cache.py

@@ -1,4 +1,3 @@
-import logging
 import typing as t
 from functools import lru_cache
 
@@ -8,6 +7,7 @@
 
 from cellarium.cas import settings  # noqa
 from cellarium.cas._io import suppress_stderr
+from cellarium.cas.logging import logger
 
 # Used in CZ CELLxGENE schema v5:
 # https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.0.0/schema.md
@@ -56,7 +56,7 @@ def __init__(self, cl_owl_path: str = DEFAULT_CL_OWL_PATH):
         """
 
         with suppress_stderr():
-            logging.info(f"Loading cell ontology OWL from: {cl_owl_path}")
+            logger.info(f"Loading cell ontology OWL from: {cl_owl_path}")
             cl = owlready2.get_ontology(cl_owl_path).load()
 
         # only keep CL classes with a singleton label

cellarium/cas/service.py

@@ -1,6 +1,5 @@
 import asyncio
 import json
-import logging
 import ssl
 import typing as t
 from contextlib import ContextDecorator
@@ -14,9 +13,10 @@
 from aiohttp import client_exceptions
 
 from cellarium.cas import constants, endpoints, exceptions, settings
+from cellarium.cas.logging import logger
 
 if settings.is_interactive_environment():
-    logging.debug("Running in an interactive environment, applying nest_asyncio")
+    logger.debug("Running in an interactive environment, applying nest_asyncio")
     nest_asyncio.apply()
 
 # Context variable to track the action id for the current context
@@ -211,7 +211,7 @@ async def _aiohttp_async_post(
                         except (json.decoder.JSONDecodeError, client_exceptions.ClientResponseError):
                             response_detail = await response.text()
                         except KeyError:
-                            logging.warning("Response body doesn't have a 'detail' key, returning full response body")
+                            logger.warning("Response body doesn't have a 'detail' key, returning full response body")
                             response_detail = str(await response.json())
 
                         self.raise_response_exception(status_code=status_code, detail=response_detail)

cellarium/cas/settings.py

@@ -8,8 +8,9 @@
 AIOHTTP_READ_TIMEOUT_SECONDS = 730
 MAX_CHUNK_SIZE_SEARCH_METHOD = 500
 CELLARIUM_CLOUD_BACKEND_URL = "https://cellarium-cloud-api.cellarium.ai"
-
-logging.basicConfig(level=logging.INFO, format="* [%(asctime)s.%(msecs)03d] %(message)s", datefmt="%H:%M:%S")
+LOGGING_LEVEL = logging.INFO
+LOGGING_FORMAT = "* [%(asctime)s.%(msecs)03d] %(message)s"
+LOGGING_DATE_FORMAT = "%H:%M:%S"
 
 
 def is_interactive_environment() -> bool:

cellarium/cas/visualization/__init__.py

@@ -1,12 +1,12 @@
-import logging
+from cellarium.cas.logging import logger
 
 try:
     from .circular_tree_plot_umap_dash_app.app import CASCircularTreePlotUMAPDashApp  # noqa
     from .ui_utils import find_and_kill_process  # noqa
 
     __all__ = ["CASCircularTreePlotUMAPDashApp", "find_and_kill_process"]
 except ImportError:
-    logging.warn(
+    logger.warning(
         """
 Visualization dependencies not installed.
 To install the Cellarium CAS Client with visualation dependencies, please run:

cellarium/cas/visualization/circular_tree_plot_umap_dash_app/app.py

@@ -14,7 +14,7 @@
 from dash.development.base_component import Component
 from plotly.express.colors import sample_colorscale
 
-from cellarium.cas import settings  # noqa
+from cellarium.cas.logging import logger
 from cellarium.cas.postprocessing import (
     CAS_CL_SCORES_ANNDATA_OBSM_KEY,
     CAS_METADATA_ANNDATA_UNS_KEY,
@@ -264,7 +264,7 @@ def run(self, port: int = 8050, jupyter_mode: str = "inline", **kwargs):
         :param port: The port on which to run the Dash application. |br|
             `Default:` ``8050``
         """
-        logging.info(f"Starting Dash application on port {port}...")
+        logger.info(f"Starting Dash application on port {port}...")
         try:
             self.app.run_server(port=port, jupyter_mode=jupyter_mode, jupyter_height=self.height + 100, **kwargs)
         except OSError:  # Dash raises OSError if the port is already in use