Module level logging and basicConfig in __init__.

app/__init__.py

@@ -21,16 +21,15 @@ app.config.from_object(Config)
 app.config['UPLOAD_DIR'] = upload_dir
 
 # Logging
-logger = logging.getLogger('rarefan')
 formatter = logging.Formatter('%(asctime)s [%(levelname)s] %(module)s: %(message)s')
-handler = logging.FileHandler("/tmp/rarefan.log")
+handler = logging.FileHandler(filename="/tmp/rarefan.log")
 handler.setFormatter(formatter)
-if app.debug:
-    logger.setLevel(logging.DEBUG)
-else:
-    logger.setLevel(logging.INFO)
 
-logger.addHandler(handler)
+# Configure root logger (this config will trickle down to all module loggers.)
+logging.basicConfig(handlers=[handler], filemode='a', level=logging.DEBUG)
+
+logger = logging.getLogger(__name__)
+
 if app.debug:
     logger.debug("****************** Debug mode is active ******************")
 

app/models.py

@@ -7,7 +7,7 @@ import rq
 from rq.exceptions import NoSuchJobError
 import logging
 
-logger = logging.getLogger('rarefan')
+logger = logging.getLogger(__name__)
 
 from app import app, db
 

app/routes.py

@@ -34,7 +34,7 @@ import subprocess
 import tempfile
 import time
 
-logger = logging.getLogger('rarefan')
+logger = logging.getLogger(__name__)
 
 def get_status_code(run_id_path):
     # Check if the run has finished.

app/tasks/email.py

@@ -20,7 +20,7 @@ from app.models import Job as DBJob
 
 import jinja2
 import logging
-logger = logging.getLogger('rarefan')
+logger = logging.getLogger(__name__)
 
 app.app_context().push()
 

app/tasks/rarefan.py

@@ -8,7 +8,7 @@ import subprocess
 from app.models import Job as DBJob
 from rq import get_current_job
 import logging
-logger = logging.getLogger('rarefan')
+logger = logging.getLogger(__name__)
 
 from app.utilities.rarefan_cli import rarefan_command
 

app/tasks/redis_tests.py

@@ -2,7 +2,7 @@
 import time
 
 import logging
-logger = logging.getLogger()
+logger = logging.getLogger(__name__)
 
 def example(seconds):
     seconds=int(seconds)

app/tasks/tree.py

@@ -7,7 +7,7 @@ from app.models import Job as DBJob
 from rq import get_current_job
 
 import logging
-logger = logging.getLogger('rarefan')
+logger = logging.getLogger(__name__)
 
 def tree_task(run_dir, treefile=None):
     """ Generate a phylogenetic tree from all DNA sequence files in given directory.

app/tasks/zip.py

@@ -7,7 +7,7 @@ import shutil
 from app.models import Job as DBJob
 from rq import get_current_job
 import logging
-logger = logging.getLogger('rarefan')
+logger = logging.getLogger(__name__)
 
 
 def zip_task(run_dir):

app/utilities/checkers.py

 import sys
 import os
 import logging
-logger = logging.getLogger('rarefan')
+logger = logging.getLogger(__name__)
 
 
 def count_lines(fname):