feat: Add application log config and initialize in app entrypoints

Author: bencap

src/api/server_main.py

@@ -1,8 +1,16 @@
 """FastAPI server file"""
+import logging
+
 import uvicorn
 from fastapi import FastAPI
 
 from api.routers import map
+from application_logging import init_logging
+from dcd_mapping.version import dcd_mapping_version
+
+init_logging()
+_logger = logging.getLogger(__name__)
+_logger.info("dcd-mapping API: %s", dcd_mapping_version)
 
 app = FastAPI()
 

src/application_logging/__init__.py

@@ -0,0 +1,19 @@
+"""Application logging initialization"""
+
+import logging
+import os
+
+LOG_LEVEL = os.getenv("LOG_LEVEL", "INFO").upper()
+
+
+def init_logging() -> None:
+    """Initialize application-wide logging with configured log level and format.
+
+    This sets the root logger's level based on the LOG_LEVEL environment variable
+    and applies a consistent log message format across the application.
+    """
+    logging.basicConfig(
+        format="%(asctime)s %(levelname)s %(name)s: %(message)s",
+        level=getattr(logging, LOG_LEVEL, logging.INFO),
+        force=True,
+    )

src/dcd_mapping/__init__.py

@@ -5,12 +5,20 @@
 See the mapping manuscript for more information:
 https://www.biorxiv.org/content/10.1101/2023.06.20.545702v1
 """
+import logging
+
 from dotenv import load_dotenv
 
+from application_logging import init_logging
+
 from .main import map_scoreset, map_scoreset_urn
 from .version import dcd_mapping_version
 
 __all__ = ["map_scoreset", "map_scoreset_urn"]
 __version__ = dcd_mapping_version
 
 load_dotenv()
+
+init_logging()
+_logger = logging.getLogger(__name__)
+_logger.info("dcd-mapping: %s", dcd_mapping_version)

src/dcd_mapping/cli.py

@@ -6,6 +6,7 @@
 
 import click
 
+from application_logging import init_logging
 from dcd_mapping.exceptions import (
     AlignmentError,
     ResourceAcquisitionError,
@@ -15,8 +16,6 @@
 from dcd_mapping.main import map_scoreset_urn
 from dcd_mapping.schemas import VrsVersion
 
-_logger = logging.getLogger(__name__)
-
 
 @click.command(no_args_is_help=True)
 @click.argument("urn", nargs=1)
@@ -66,14 +65,13 @@ def cli(
     :param urn: scoreset URN
     :param debug: if True, enable debug logging
     """  # noqa: D301
-    log_level = logging.DEBUG if debug else logging.INFO
-    logging.basicConfig(
-        filename="dcd-mapping.log",
-        format="%(asctime)s %(levelname)s:%(name)s:%(message)s",
-        level=log_level,
-        force=True,
-    )
-    _logger.debug("debug logging enabled")
+    init_logging()
+    _logger = logging.getLogger(__name__)
+
+    if debug:
+        logging.getLogger().setLevel(logging.DEBUG)
+        _logger.debug("debug logging enabled")
+
     try:
         asyncio.run(
             map_scoreset_urn(urn, output, vrs_version, prefer_genomic, silent=False)