Merge branch 'testing' into feature/generalize_tables

9 files changed, 2 insertions, 72 deletions

diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index d4256a46..df7156b4 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -33,8 +33,7 @@ from math import *
 import utility.corestats as corestats
 from base import webqtlConfig
 from utility.pillow_utils import draw_rotated_text
-import utility.logger
-logger = utility.logger.getLogger(__name__)
+
 
 # ---- Define common colours ---- #
 BLUE = ImageColor.getrgb("blue")
@@ -105,7 +104,6 @@ def find_outliers(vals):
     """
 
     if vals:
-        #logger.debug("vals is:", pf(vals))
         stats = corestats.Stats(vals)
         low_hinge = stats.percentile(25)
         up_hinge = stats.percentile(75)
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
deleted file mode 100644
index 6ece2f21..00000000
--- a/wqflask/utility/benchmark.py
+++ /dev/null
@@ -1,52 +0,0 @@
-import collections
-import inspect
-import time
-from utility.tools import LOG_BENCH
-
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-
-class Bench:
-    entries = collections.OrderedDict()
-
-    def __init__(self, name=None, write_output=LOG_BENCH):
-        self.name = name
-        self.write_output = write_output
-
-    def __enter__(self):
-        if self.write_output:
-            if self.name:
-                logger.debug("Starting benchmark: %s" % (self.name))
-            else:
-                logger.debug("Starting benchmark at: %s [%i]" % (
-                    inspect.stack()[1][3], inspect.stack()[1][2]))
-        self.start_time = time.time()
-
-    def __exit__(self, type, value, traceback):
-        time_taken = time.time() - self.start_time
-        if self.write_output:
-            if self.name:
-                name = self.name
-            else:
-                name = "That"
-
-            logger.info("  %s took: %f seconds" % (name, (time_taken)))
-
-        if self.name:
-            Bench.entries[self.name] = Bench.entries.get(
-                self.name, 0) + time_taken
-
-    @classmethod
-    def report(cls):
-        total_time = sum(
-            (time_taken for time_taken in list(cls.entries.values())))
-        print("\nTiming report\n")
-        for name, time_taken in list(cls.entries.items()):
-            percent = int(round((time_taken / total_time) * 100))
-            print("[{}%] {}: {}".format(percent, name, time_taken))
-        print()
-
-    def reset(cls):
-        """Reset the entries"""
-        cls.entries = collections.OrderedDict()
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index e619b7b6..c7a1ea59 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -1,7 +1,3 @@
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
-
 class genotype:
     """
     Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 27dd0729..4229a91f 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -6,9 +6,6 @@ from utility import hmac
 
 from flask import g
 
-import logging
-logger = logging.getLogger(__name__)
-
 
 def get_species_dataset_trait(self, start_vars):
     if "temp_trait" in list(start_vars.keys()):
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index d706e32a..65f2f1ee 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -27,7 +27,6 @@
 # We'll add more overrides soon.
 
 import logging
-import string
 from inspect import isfunction
 from pprint import pformat as pf
 from inspect import stack
diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py
index 5713e155..e302df18 100644
--- a/wqflask/utility/pillow_utils.py
+++ b/wqflask/utility/pillow_utils.py
@@ -2,9 +2,6 @@ from PIL import Image, ImageColor, ImageDraw, ImageFont
 
 from utility.tools import TEMPDIR
 
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
 BLACK = ImageColor.getrgb("black")
 WHITE = ImageColor.getrgb("white")
 
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 641d973e..945efbbd 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -5,8 +5,6 @@ import datetime
 import redis  # used for collections
 
 from utility.hmac import hmac_creation
-from utility.logger import getLogger
-logger = getLogger(__name__)
 
 
 def get_redis_conn():
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index 778fb64d..59923fa1 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -23,12 +23,9 @@ def app_config():
     if mode in ["DEV", "DEBUG"]:
         app.config['TEMPLATES_AUTO_RELOAD'] = True
         if mode == "DEBUG":
-            from flask_debugtoolbar import DebugToolbarExtension
             app.debug = True
-            toolbar = DebugToolbarExtension(app)
 
     print("==========================================")
-
     show_settings()
 
     port = get_setting_int("SERVER_PORT")
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index db0b4320..19bf686b 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -50,7 +50,7 @@ def get_setting(command_id, guess=None):
             app_set(command_id, command)
             return command
         else:
-            return None
+            return app.config.get(command_id)
 
     # ---- Check whether environment exists
     # print("Looking for "+command_id+"\n")