Utilize app.logger everywhere.

app/__init__.py

@@ -24,14 +24,13 @@ app.config['UPLOAD_DIR'] = upload_dir
 formatter = logging.Formatter('%(asctime)s [%(levelname)s] %(module)s: %(message)s')
 handler = logging.FileHandler(filename="/tmp/rarefan.log")
 handler.setFormatter(formatter)
+handler.setLevel(logging.DEBUG)
 
 # Configure root logger (this config will trickle down to all module loggers.)
-logging.basicConfig(handlers=[handler], level=logging.DEBUG)
-
-logger = logging.getLogger(__name__)
+app.logger.addHandler(handler)
 
 if app.debug:
-    logger.debug("****************** Debug mode is active ******************")
+    app.logger.debug("****************** Debug mode is active ******************")
 
 
 # csrf = CSRFProtect()

app/callbacks/callbacks.py

@@ -4,9 +4,9 @@ from app.models import Job as DBJob
 from app.utilities.checkers import parse_results
 from app.tasks.email import email_task
 from app.tasks.zip import zip_task
+from app import app
 
-import logging
-logger = logging.getLogger('rarefan')
+logger = app.logger
 
 def rarefan_on_success(job, result):
     """ Callback for the 'rarefan' task if completed successfully. """

app/models.py

@@ -5,11 +5,8 @@ import os
 import sys
 import rq
 from rq.exceptions import NoSuchJobError
-import logging
-
-logger = logging.getLogger(__name__)
-
 from app import app, db
+logger = app.logger
 
 
 class Job(db.Document):

app/routes.py

@@ -34,7 +34,7 @@ import subprocess
 import tempfile
 import time
 
-logger = logging.getLogger(__name__)
+logger = app.logger
 
 def get_status_code(run_id_path):
     # Check if the run has finished.
@@ -520,7 +520,9 @@ def test_task():
 
 @app.route('/test_mail')
 def test_mail():
+    logger.debug("Attempting to send mail throug redis queue.")
     job = app.queue.enqueue(email_test)
+    logger.debug(job)
     time.sleep(3)
 
 

app/tasks/email.py

@@ -19,14 +19,15 @@ from app.views import AnalysisForm
 from app.models import Job as DBJob
 
 import jinja2
-import logging
-logger = logging.getLogger(__name__)
 
 app.app_context().push()
 
+logger = app.logger
+
 def email_test():
 
     recipients = ['grotec@evolbio.mpg.de']
+    logger.debug("Attempting to send email to %s", recipients[0])
 
     message = Message("Test from flask",
                       sender="rarefan@evolbio.mpg.de",
@@ -39,7 +40,7 @@ def email_test():
     logger.debug("Mail was sent: %s", str(success))
     logger.debug("Mail message was: %s", str(message))
 
-    return success, message
+    return success, str(message)
 
 
 def email_task(run_id):
@@ -99,3 +100,6 @@ def email_task(run_id):
     dbjob.save()
 
     logger.debug("Mail sent? %s", str(is_sent))
+
+if __name__ == "__main__":
+    email_test()

app/tasks/rarefan.py

@@ -7,8 +7,10 @@ import subprocess
 
 from app.models import Job as DBJob
 from rq import get_current_job
-import logging
-logger = logging.getLogger(__name__)
+from app import app
+
+app.app_context().push()
+logger = app.logger
 
 from app.utilities.rarefan_cli import rarefan_command
 

app/tasks/redis_tests.py

 # usage: $> rq enqueue -p app.tasks.redis_tests example 10
 import time
 
-import logging
-logger = logging.getLogger(__name__)
+from app import app
+app.app_context().push()
+
+logger = app.logger
 
 def example(seconds):
     seconds=int(seconds)

app/tasks/tree.py

@@ -5,9 +5,9 @@ import shlex
 import shutil
 from app.models import Job as DBJob
 from rq import get_current_job
-
-import logging
-logger = logging.getLogger(__name__)
+from app import app
+app.app_context().push()
+logger = app.logger
 
 def tree_task(run_dir, treefile=None):
     """ Generate a phylogenetic tree from all DNA sequence files in given directory.

app/tasks/zip.py

@@ -6,8 +6,9 @@ import shutil
 
 from app.models import Job as DBJob
 from rq import get_current_job
-import logging
-logger = logging.getLogger(__name__)
+from app import app
+app.app_context().push()
+logger = app.logger
 
 
 def zip_task(run_dir):