Avoid uvicorn logger and use __main__ logger and remove logger from multiprocessing code

CHANGELOG.md

@@ -10,6 +10,7 @@
 - Updated PR template
 - Generalised issue templates to make them more user-friendly for people outside our organisation
 - Moved logging setup out of app lifespan and db initialisation logic
+- Switch to __main__ logger and removed unused logger from multiprocessing code
 ### Fixed
 - Updated version of external images used in GitHub actions
 

src/chanjo2/crud/intervals.py

@@ -14,7 +14,7 @@
     TranscriptTag,
 )
 
-LOG = logging.getLogger("uvicorn.access")
+LOG = logging.getLogger(__name__)
 
 
 def delete_intervals_for_build(

src/chanjo2/crud/samples.py

@@ -1,4 +1,4 @@
-from typing import List, Optional, Tuple, Union
+from typing import List, Optional, Tuple
 
 from fastapi import HTTPException, status
 from sqlalchemy import delete

src/chanjo2/endpoints/coverage.py

@@ -34,7 +34,7 @@
 )
 
 router = APIRouter()
-LOG = logging.getLogger("uvicorn.access")
+LOG = logging.getLogger(__name__)
 
 
 @router.post("/coverage/d4/interval/", response_model=IntervalCoverage)

src/chanjo2/endpoints/overview.py

@@ -1,4 +1,3 @@
-import logging
 from os import path
 
 from fastapi import APIRouter, Depends, HTTPException, Request, status
@@ -17,8 +16,6 @@
 )
 from chanjo2.models.pydantic_models import GeneCoverage, GeneReportForm, ReportQuery
 
-LOG = logging.getLogger("uvicorn.access")
-
 
 def get_templates_path() -> str:
     """Returns the absolute path to the templates folder of this app."""

src/chanjo2/endpoints/report.py

@@ -21,7 +21,7 @@ def get_templates_path() -> str:
     return path.join(APP_ROOT, "templates")
 
 
-LOG = logging.getLogger("uvicorn.access")
+LOG = logging.getLogger(__name__)
 templates: Jinja2Templates = Jinja2Templates(directory=get_templates_path())
 router = APIRouter()
 

src/chanjo2/logger.py

@@ -2,13 +2,15 @@
 
 import uvicorn
 
-LOG = logging.getLogger("uvicorn.access")
+LOG = logging.getLogger(__name__)
 
 
-console_formatter = uvicorn.logging.ColourizedFormatter(
-    "{levelprefix} {asctime} : {message}", style="{", use_colors=True
-)
-if LOG.handlers:
-    LOG.handlers[0].setFormatter(console_formatter)
-else:
-    logging.basicConfig()
+def configure_log():
+    """Configure logging."""
+    console_formatter = uvicorn.logging.ColourizedFormatter(
+        "{levelprefix} {asctime} : {message}", style="{", use_colors=True
+    )
+    if LOG.handlers:
+        LOG.handlers[0].setFormatter(console_formatter)
+    else:
+        logging.basicConfig()

src/chanjo2/main.py

@@ -1,3 +1,4 @@
+import logging
 import os
 from contextlib import asynccontextmanager
 from typing import List, Tuple
@@ -8,10 +9,11 @@
 from chanjo2 import __version__
 from chanjo2.dbutil import engine
 from chanjo2.endpoints import cases, coverage, intervals, overview, report, samples
-from chanjo2.logger import LOG
+from chanjo2.logger import configure_log
 from chanjo2.models.sql_models import Base
 from chanjo2.populate_demo import load_demo_data
 
+LOG = logging.getLogger(__name__)
 APP_ROUTER_TAGS: List[Tuple] = [
     (intervals.router, "intervals"),
     (coverage.router, "coverage"),
@@ -28,6 +30,7 @@ def create_db_and_tables():
 
 @asynccontextmanager
 async def lifespan(app_: FastAPI):
+    configure_log()
     LOG.info("Starting up...")
     await startup_db()
     yield

src/chanjo2/meta/handle_completeness_tasks.py

@@ -1,9 +1,7 @@
-import logging
 import subprocess
 from multiprocessing import Manager, Pool
 from typing import Dict, List, Tuple
 
-LOG = logging.getLogger("uvicorn.access")
 INTERVAL_CHUNKS = 50
 CHROM_INDEX = 0
 START_INDEX = 1

src/chanjo2/meta/handle_d4.py

@@ -1,4 +1,3 @@
-import logging
 import subprocess
 import tempfile
 from statistics import mean
@@ -17,7 +16,6 @@
     TranscriptTag,
 )
 
-LOG = logging.getLogger("uvicorn.access")
 CHROM_INDEX = 0
 START_INDEX = 1
 STOP_INDEX = 2

src/chanjo2/meta/handle_load_intervals.py

@@ -28,7 +28,7 @@
     TranscriptBase,
 )
 
-LOG = logging.getLogger("uvicorn.access")
+LOG = logging.getLogger(__name__)
 MAX_NR_OF_RECORDS = 10_000
 END_OF_PARSED_FILE: str = "[success]"
 

src/chanjo2/meta/handle_report_contents.py

@@ -1,4 +1,3 @@
-import logging
 from collections import OrderedDict
 from typing import Dict, List, Optional, Tuple, Union
 
@@ -22,8 +21,6 @@
     TranscriptTag,
 )
 
-LOG = logging.getLogger("uvicorn.access")
-
 INTERVAL_TYPE_SQL_TYPE: Dict[IntervalType, Union[SQLGene, SQLTranscript, SQLExon]] = {
     IntervalType.GENES: SQLGene,
     IntervalType.TRANSCRIPTS: SQLTranscript,

src/chanjo2/models/pydantic_models.py

@@ -1,5 +1,4 @@
 import json
-import logging
 import os
 from datetime import datetime
 from enum import Enum
@@ -18,8 +17,6 @@
     WRONG_COVERAGE_FILE_MSG,
 )
 
-LOG = logging.getLogger("uvicorn.access")
-
 
 def default_report_coverage_levels() -> List[int]:
     """Sets the coverage thresholds to be used for report metrics whenever a request doesn't contain 'completeness_thresholds' values."""