Remove usage of "logger" and un-necessary comments wrt the same

Logging is used to introspect variables or notify the commencement of
a given operation.  Logging should only be used to log errors.  Also,
most of the logging is either "logger.debug" or "logger.info"; and
this won't show up in production/testing since we need a logging level
above "WARNING" for them to show up.

* wqflask/base/data_set.py (create_datasets_list): Remove logger.
(Markers.add_pvalues): Ditto.
(DataSet.retrieve_other_names): Ditto.
* wqflask/base/mrna_assay_tissue_data.py: Ditto.
* wqflask/base/webqtlCaseData.py: Ditto.
* wqflask/db/call.py (fetch1): Ditto.
(gn_server): Ditto.
* wqflask/db/gn_server.py: Ditto.
* wqflask/maintenance/set_resource_defaults.py: Ditto.
* wqflask/utility/Plot.py (find_outliers): Ditto.
* wqflask/utility/gen_geno_ob.py: Ditto.
* wqflask/utility/helper_functions.py: Ditto.
* wqflask/utility/pillow_utils.py: Ditto.
* wqflask/utility/redis_tools.py: Ditto.
* wqflask/wqflask/api/gen_menu.py (get_groups): Ditto.
* wqflask/wqflask/api/mapping.py: Ditto.
* wqflask/wqflask/api/router.py (get_dataset_info): Ditto.
* wqflask/wqflask/collect.py (report_change): Ditto.
* wqflask/wqflask/correlation/corr_scatter_plot.py: Ditto.
* wqflask/wqflask/ctl/ctl_analysis.py (CTL): Ditto.
(CTL.__init__): Ditto.
(CTL.run_analysis): Ditto.
(CTL.process_results): Ditto.
* wqflask/wqflask/db_info.py: Ditto.
* wqflask/wqflask/do_search.py (DoSearch.execute): Ditto.
(DoSearch.mescape): Ditto.
(DoSearch.get_search): Ditto.
(MrnaAssaySearch.run_combined): Ditto.
(MrnaAssaySearch.run): Ditto.
(PhenotypeSearch.run_combined): Ditto.
(GenotypeSearch.get_where_clause): Ditto.
(LrsSearch.get_where_clause): Ditto.
(MeanSearch.run): Ditto.
(RangeSearch.get_where_clause): Ditto.
(PvalueSearch.run): Ditto.
* wqflask/wqflask/docs.py: Ditto.
* wqflask/wqflask/export_traits.py: Ditto.
* wqflask/wqflask/external_tools/send_to_bnw.py: Ditto.
* wqflask/wqflask/external_tools/send_to_geneweaver.py: Ditto.
* wqflask/wqflask/external_tools/send_to_webgestalt.py: Ditto.
* wqflask/wqflask/gsearch.py (GSearch.__init__): Ditto.
* wqflask/wqflask/heatmap/heatmap.py: Ditto.
* wqflask/wqflask/marker_regression/display_mapping_results.py (DisplayMappingResults): Ditto.
* wqflask/wqflask/marker_regression/gemma_mapping.py: Ditto.
* wqflask/wqflask/marker_regression/plink_mapping.py (run_plink): Ditto.
* wqflask/wqflask/marker_regression/qtlreaper_mapping.py (run_reaper): Ditto.
* wqflask/wqflask/marker_regression/rqtl_mapping.py: Ditto.
* wqflask/wqflask/marker_regression/run_mapping.py (RunMapping.__init__): Ditto.
* wqflask/wqflask/parser.py (parse): Ditto.
* wqflask/wqflask/search_results.py (SearchResultPage.__init__): Ditto.
* wqflask/wqflask/update_search_results.py (GSearch.__init__): Ditto.
* wqflask/wqflask/user_login.py (send_email): Ditto.
(logout): Ditto.
(forgot_password_submit): Ditto.
(password_reset): Ditto.
(password_reset_step2): Ditto.
(register): Ditto.
* wqflask/wqflask/user_session.py (create_signed_cookie): Ditto.

5 files changed, 1 insertions, 15 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/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/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():