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.

3 files changed, 0 insertions, 20 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 211c6752..8206b67c 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -22,7 +22,6 @@ from dataclasses import field
 from dataclasses import InitVar
 from typing import Optional, Dict, List
 from db.call import fetchall, fetchone, fetch1
-from utility.logger import getLogger
 from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
 from db.gn_server import menu_main
 from pprint import pformat as pf
@@ -60,8 +59,6 @@ from redis import Redis
 
 r = Redis()
 
-logger = getLogger(__name__)
-
 # Used by create_database to instantiate objects
 # Each subclass will add to this
 DS_NAME_MAP = {}
@@ -200,7 +197,6 @@ def create_datasets_list():
         result = r.get(key)
 
         if result:
-            logger.debug("Redis cache hit")
             datasets = pickle.loads(result)
 
     if result is None:
@@ -213,10 +209,6 @@ def create_datasets_list():
             for dataset_type in type_dict:
                 query = "SELECT Name FROM {}".format(type_dict[dataset_type])
                 for result in fetchall(query):
-                    # The query at the beginning of this function isn't
-                    # necessary here, but still would rather just reuse
-                    # it logger.debug("type: {}\tname:
-                    # {}".format(dataset_type, result.Name))
                     dataset = create_dataset(result.Name, dataset_type)
                     datasets.append(dataset)
 
@@ -259,9 +251,6 @@ class Markers:
         self.markers = markers
 
     def add_pvalues(self, p_values):
-        logger.debug("length of self.markers:", len(self.markers))
-        logger.debug("length of p_values:", len(p_values))
-
         if isinstance(p_values, list):
             # THIS IS only needed for the case when we are limiting the number of p-values calculated
             # if len(self.markers) > len(p_values):
@@ -664,8 +653,6 @@ class DataSet:
                     """ % (query_args))
 
         except TypeError:
-            logger.debug(
-                "Dataset {} is not yet available in GeneNetwork.".format(self.name))
             pass
 
     def chunk_dataset(self, dataset, n):
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 8f8e2b0a..d7e747aa 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -9,10 +9,6 @@ from utility.db_tools import escape
 from gn3.db_utils import database_connector
 
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-
 class MrnaAssayTissueData:
 
     def __init__(self, gene_symbols=None):
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 25b6cb8a..dd6fad04 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -21,9 +21,6 @@
 # Created by GeneNetwork Core Team 2010/08/10
 
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
 import utility.tools
 
 utility.tools.show_settings()