From 8c06a9534d3340ff0287b5c70f63b2000b6eb612 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Mon, 29 Aug 2022 12:11:41 +0300
Subject: 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.
---
 wqflask/db/call.py      | 4 ----
 wqflask/db/gn_server.py | 3 ---
 2 files changed, 7 deletions(-)

(limited to 'wqflask/db')

diff --git a/wqflask/db/call.py b/wqflask/db/call.py
index 1fe0772b..a6bbda54 100644
--- a/wqflask/db/call.py
+++ b/wqflask/db/call.py
@@ -31,9 +31,6 @@ GN_SERVER result when set (which should return a Tuple)
             res2 = func(result)
         else:
             res2 = result,
-        if LOG_SQL:
-            logger.debug("Replaced SQL call", query)
-        logger.debug(path, res2)
         return res2
     else:
         return fetchone(query)
@@ -75,5 +72,4 @@ def gn_server(path):
             res = urllib2.urlopen(GN_SERVER_URL + path)
         rest = res.read()
         res2 = json.loads(rest)
-        logger.debug(res2)
         return res2
diff --git a/wqflask/db/gn_server.py b/wqflask/db/gn_server.py
index f9b01658..af6682ba 100644
--- a/wqflask/db/gn_server.py
+++ b/wqflask/db/gn_server.py
@@ -2,9 +2,6 @@
 
 from db.call import gn_server
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
 
 def menu_main():
     return gn_server("/int/menu/main.json")
-- 
cgit v1.2.3


From 9d0f492d8a999c1a3eb6525b0ae72bbbcaad4279 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Tue, 30 Aug 2022 11:36:58 +0300
Subject: Remove "with Bench ..." calls

"with Bench" instruments how long a function takes and generates time
reports on as INFO logs.  This should be done on a developer server.
Should the log level be low enough, this bench marks will generate a
lot of noise.  Instrumentation should be done during development.

* wqflask/base/data_set.py (create_datasets_list): Remove "with
Bench...".
* wqflask/db/call.py (fetchone): Ditto.
(fetchall): Ditto.
(gn_server): Ditto.
* wqflask/wqflask/gsearch.py (GSearch.__init__): Ditto.
* wqflask/wqflask/marker_regression/display_mapping_results.py (DisplayMappingResults.__init__): Ditto.
* wqflask/wqflask/marker_regression/run_mapping.py
(RunMapping.__init__): Ditto.
* wqflask/wqflask/update_search_results.py (GSearch.__init__): Ditto.
* wqflask/wqflask/views.py (search_page): Ditto.
(heatmap_page): Ditto.
(mapping_results_page): Ditto.
---
 wqflask/base/data_set.py                           |  20 +-
 wqflask/db/call.py                                 |  38 ++--
 wqflask/wqflask/gsearch.py                         | 240 ++++++++++-----------
 .../marker_regression/display_mapping_results.py   |   6 +-
 wqflask/wqflask/marker_regression/run_mapping.py   |  62 +++---
 wqflask/wqflask/update_search_results.py           |  34 ++-
 wqflask/wqflask/views.py                           |  68 +++---
 7 files changed, 216 insertions(+), 252 deletions(-)

(limited to 'wqflask/db')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 8206b67c..33e6f353 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -32,7 +32,6 @@ from maintenance import get_group_samplelists
 from utility.tools import locate, locate_ignore_error, flat_files
 from utility import gen_geno_ob
 from utility import chunks
-from utility.benchmark import Bench
 from utility import webqtlUtil
 from db import webqtlDatabaseFunction
 from base import species
@@ -201,16 +200,15 @@ def create_datasets_list():
 
     if result is None:
         datasets = list()
-        with Bench("Creating DataSets object"):
-            type_dict = {'Publish': 'PublishFreeze',
-                         'ProbeSet': 'ProbeSetFreeze',
-                         'Geno': 'GenoFreeze'}
-
-            for dataset_type in type_dict:
-                query = "SELECT Name FROM {}".format(type_dict[dataset_type])
-                for result in fetchall(query):
-                    dataset = create_dataset(result.Name, dataset_type)
-                    datasets.append(dataset)
+        type_dict = {'Publish': 'PublishFreeze',
+                     'ProbeSet': 'ProbeSetFreeze',
+                     'Geno': 'GenoFreeze'}
+
+        for dataset_type in type_dict:
+            query = "SELECT Name FROM {}".format(type_dict[dataset_type])
+            for result in fetchall(query):
+                dataset = create_dataset(result.Name, dataset_type)
+                datasets.append(dataset)
 
         if USE_REDIS:
             r.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
index a6bbda54..c27e0326 100644
--- a/wqflask/db/call.py
+++ b/wqflask/db/call.py
@@ -11,13 +11,10 @@ except:
     import urllib2
 import json
 from utility.tools import USE_GN_SERVER, LOG_SQL, GN_SERVER_URL
-from utility.benchmark import Bench
 
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
-# from inspect import stack
-
 
 def fetch1(query, path=None, func=None):
     """Fetch one result as a Tuple using either a SQL query or the URI
@@ -41,11 +38,10 @@ def fetchone(query):
 original fetchone, but with logging)
 
     """
-    with Bench("SQL", LOG_SQL):
-        def helper(query):
-            res = g.db.execute(query)
-            return res.fetchone()
-        return logger.sql(query, helper)
+    def helper(query):
+        res = g.db.execute(query)
+        return res.fetchone()
+    return logger.sql(query, helper)
 
 
 def fetchall(query):
@@ -53,23 +49,21 @@ def fetchall(query):
 original fetchall, but with logging)
 
     """
-    with Bench("SQL", LOG_SQL):
-        def helper(query):
-            res = g.db.execute(query)
-            return res.fetchall()
-        return logger.sql(query, helper)
+    def helper(query):
+        res = g.db.execute(query)
+        return res.fetchall()
+    return logger.sql(query, helper)
 
 
 def gn_server(path):
     """Return JSON record by calling GN_SERVER
 
     """
-    with Bench("GN_SERVER", LOG_SQL):
-        res = ()
-        try:
-            res = urllib.request.urlopen(GN_SERVER_URL + path)
-        except:
-            res = urllib2.urlopen(GN_SERVER_URL + path)
-        rest = res.read()
-        res2 = json.loads(rest)
-        return res2
+    res = ()
+    try:
+        res = urllib.request.urlopen(GN_SERVER_URL + path)
+    except:
+        res = urllib2.urlopen(GN_SERVER_URL + path)
+    rest = res.read()
+    res2 = json.loads(rest)
+    return res2
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 74964297..6d49bc79 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -11,7 +11,6 @@ from base import webqtlConfig
 
 from utility import hmac
 
-from utility.benchmark import Bench
 from utility.authentication_tools import check_resource_availability
 from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
 
@@ -61,74 +60,72 @@ class GSearch:
                 ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
                 LIMIT 6000
                 """ % (self.terms)
-            with Bench("Running query"):
-                re = g.db.execute(sql).fetchall()
+            re = g.db.execute(sql).fetchall()
 
             trait_list = []
             dataset_to_permissions = {}
-            with Bench("Creating trait objects"):
-                for i, line in enumerate(re):
-                    this_trait = {}
-                    this_trait['index'] = i + 1
-                    this_trait['name'] = line[5]
-                    this_trait['dataset'] = line[3]
-                    this_trait['dataset_fullname'] = line[4]
-                    this_trait['hmac'] = hmac.data_hmac(
-                        '{}:{}'.format(line[5], line[3]))
-                    this_trait['species'] = line[0]
-                    this_trait['group'] = line[1]
-                    this_trait['tissue'] = line[2]
-                    this_trait['symbol'] = "N/A"
-                    if line[6]:
-                        this_trait['symbol'] = line[6]
-                    this_trait['description'] = "N/A"
-                    if line[7]:
-                        this_trait['description'] = line[7].decode(
-                            'utf-8', 'replace')
-                    this_trait['location_repr'] = "N/A"
-                    if (line[8] != "NULL" and line[8] != "") and (line[9] != 0):
-                        this_trait['location_repr'] = 'Chr%s: %.6f' % (
-                            line[8], float(line[9]))
+            for i, line in enumerate(re):
+                this_trait = {}
+                this_trait['index'] = i + 1
+                this_trait['name'] = line[5]
+                this_trait['dataset'] = line[3]
+                this_trait['dataset_fullname'] = line[4]
+                this_trait['hmac'] = hmac.data_hmac(
+                    '{}:{}'.format(line[5], line[3]))
+                this_trait['species'] = line[0]
+                this_trait['group'] = line[1]
+                this_trait['tissue'] = line[2]
+                this_trait['symbol'] = "N/A"
+                if line[6]:
+                    this_trait['symbol'] = line[6]
+                this_trait['description'] = "N/A"
+                if line[7]:
+                    this_trait['description'] = line[7].decode(
+                        'utf-8', 'replace')
+                this_trait['location_repr'] = "N/A"
+                if (line[8] != "NULL" and line[8] != "") and (line[9] != 0):
+                    this_trait['location_repr'] = 'Chr%s: %.6f' % (
+                        line[8], float(line[9]))
 
-                    this_trait['LRS_score_repr'] = "N/A"
-                    this_trait['additive'] = "N/A"
-                    this_trait['mean'] = "N/A"
+                this_trait['LRS_score_repr'] = "N/A"
+                this_trait['additive'] = "N/A"
+                this_trait['mean'] = "N/A"
 
-                    if line[11] != "" and line[11] != None:
-                        this_trait['LRS_score_repr'] = f"{line[11]:.3f}"
-                    if line[14] != "" and line[14] != None:
-                        this_trait['additive'] = f"{line[14]:.3f}"
-                    if line[10] != "" and line[10] != None:
-                        this_trait['mean'] = f"{line[10]:.3f}"
+                if line[11] != "" and line[11] != None:
+                    this_trait['LRS_score_repr'] = f"{line[11]:.3f}"
+                if line[14] != "" and line[14] != None:
+                    this_trait['additive'] = f"{line[14]:.3f}"
+                if line[10] != "" and line[10] != None:
+                    this_trait['mean'] = f"{line[10]:.3f}"
 
-                    locus_chr = line[16]
-                    locus_mb = line[17]
+                locus_chr = line[16]
+                locus_mb = line[17]
 
-                    max_lrs_text = "N/A"
-                    if locus_chr and locus_mb:
-                        max_lrs_text = f"Chr{locus_chr}: {locus_mb}"
-                    this_trait['max_lrs_text'] = max_lrs_text
+                max_lrs_text = "N/A"
+                if locus_chr and locus_mb:
+                    max_lrs_text = f"Chr{locus_chr}: {locus_mb}"
+                this_trait['max_lrs_text'] = max_lrs_text
 
-                    this_trait['additive'] = "N/A"
-                    if line[14] != "" and line[14] != None:
-                        this_trait['additive'] = '%.3f' % line[14]
-                    this_trait['dataset_id'] = line[15]
+                this_trait['additive'] = "N/A"
+                if line[14] != "" and line[14] != None:
+                    this_trait['additive'] = '%.3f' % line[14]
+                this_trait['dataset_id'] = line[15]
 
-                    dataset_ob = SimpleNamespace(
-                        id=this_trait["dataset_id"], type="ProbeSet", name=this_trait["dataset"], species=this_trait["species"])
-                    if dataset_ob.id not in dataset_to_permissions:
-                        permissions = check_resource_availability(dataset_ob)
-                        dataset_to_permissions[dataset_ob.id] = permissions
-                    else:
-                        pemissions = dataset_to_permissions[dataset_ob.id]
-                    if type(permissions['data']) is list:
-                        if "view" not in permissions['data']:
-                            continue
-                    else:
-                        if permissions['data'] == 'no-access':
-                            continue
+                dataset_ob = SimpleNamespace(
+                    id=this_trait["dataset_id"], type="ProbeSet", name=this_trait["dataset"], species=this_trait["species"])
+                if dataset_ob.id not in dataset_to_permissions:
+                    permissions = check_resource_availability(dataset_ob)
+                    dataset_to_permissions[dataset_ob.id] = permissions
+                else:
+                    pemissions = dataset_to_permissions[dataset_ob.id]
+                if type(permissions['data']) is list:
+                    if "view" not in permissions['data']:
+                        continue
+                else:
+                    if permissions['data'] == 'no-access':
+                        continue
 
-                    trait_list.append(this_trait)
+                trait_list.append(this_trait)
 
             self.trait_count = len(trait_list)
             self.trait_list = trait_list
@@ -208,76 +205,75 @@ class GSearch:
                 """.format(group_clause, search_term)
             re = g.db.execute(sql).fetchall()
             trait_list = []
-            with Bench("Creating trait objects"):
-                for i, line in enumerate(re):
-                    this_trait = {}
-                    this_trait['index'] = i + 1
-                    this_trait['name'] = str(line[4])
-                    if len(str(line[12])) == 3:
-                        this_trait['display_name'] = str(
-                            line[12]) + "_" + this_trait['name']
-                    else:
-                        this_trait['display_name'] = this_trait['name']
-                    this_trait['dataset'] = line[2]
-                    this_trait['dataset_fullname'] = line[3]
-                    this_trait['hmac'] = hmac.data_hmac(
-                        '{}:{}'.format(line[4], line[2]))
-                    this_trait['species'] = line[0]
-                    this_trait['group'] = line[1]
-                    if line[9] != None and line[6] != None:
-                        this_trait['description'] = line[6].decode(
-                            'utf-8', 'replace')
-                    elif line[5] != None:
-                        this_trait['description'] = line[5].decode(
-                            'utf-8', 'replace')
-                    else:
-                        this_trait['description'] = "N/A"
-                    this_trait['dataset_id'] = line[14]
+            for i, line in enumerate(re):
+                this_trait = {}
+                this_trait['index'] = i + 1
+                this_trait['name'] = str(line[4])
+                if len(str(line[12])) == 3:
+                    this_trait['display_name'] = str(
+                        line[12]) + "_" + this_trait['name']
+                else:
+                    this_trait['display_name'] = this_trait['name']
+                this_trait['dataset'] = line[2]
+                this_trait['dataset_fullname'] = line[3]
+                this_trait['hmac'] = hmac.data_hmac(
+                    '{}:{}'.format(line[4], line[2]))
+                this_trait['species'] = line[0]
+                this_trait['group'] = line[1]
+                if line[9] != None and line[6] != None:
+                    this_trait['description'] = line[6].decode(
+                        'utf-8', 'replace')
+                elif line[5] != None:
+                    this_trait['description'] = line[5].decode(
+                        'utf-8', 'replace')
+                else:
+                    this_trait['description'] = "N/A"
+                this_trait['dataset_id'] = line[14]
 
-                    this_trait['LRS_score_repr'] = "N/A"
-                    this_trait['additive'] = "N/A"
-                    this_trait['mean'] = "N/A"
+                this_trait['LRS_score_repr'] = "N/A"
+                this_trait['additive'] = "N/A"
+                this_trait['mean'] = "N/A"
 
-                    if line[10] != "" and line[10] != None:
-                        this_trait['LRS_score_repr'] = f"{line[10]:.3f}"
-                        # Some Max LRS values in the DB are wrongly listed as 0.000, but shouldn't be displayed
-                        if this_trait['LRS_score_repr'] == "0.000":
-                            this_trait['LRS_score_repr'] = "N/A"
-                    if line[11] != "" and line[11] != None:
-                        this_trait['additive'] = f"{line[11]:.3f}"
-                    if line[13] != "" and line[13] != None:
-                        this_trait['mean'] = f"{line[13]:.3f}"
+                if line[10] != "" and line[10] != None:
+                    this_trait['LRS_score_repr'] = f"{line[10]:.3f}"
+                    # Some Max LRS values in the DB are wrongly listed as 0.000, but shouldn't be displayed
+                    if this_trait['LRS_score_repr'] == "0.000":
+                        this_trait['LRS_score_repr'] = "N/A"
+                if line[11] != "" and line[11] != None:
+                    this_trait['additive'] = f"{line[11]:.3f}"
+                if line[13] != "" and line[13] != None:
+                    this_trait['mean'] = f"{line[13]:.3f}"
 
-                    locus_chr = line[15]
-                    locus_mb = line[16]
+                locus_chr = line[15]
+                locus_mb = line[16]
 
-                    max_lrs_text = "N/A"
-                    if locus_chr and locus_mb:
-                        max_lrs_text = f"Chr{locus_chr}: {locus_mb}"
-                    this_trait['max_lrs_text'] = max_lrs_text
+                max_lrs_text = "N/A"
+                if locus_chr and locus_mb:
+                    max_lrs_text = f"Chr{locus_chr}: {locus_mb}"
+                this_trait['max_lrs_text'] = max_lrs_text
 
-                    this_trait['authors'] = line[7]
-                    this_trait['year'] = line[8]
-                    this_trait['pubmed_text'] = "N/A"
-                    this_trait['pubmed_link'] = "N/A"
-                    if this_trait['year'].isdigit():
-                        this_trait['pubmed_text'] = this_trait['year']
-                    if line[9] != "" and line[9] != None:
-                        this_trait['pubmed_link'] = webqtlConfig.PUBMEDLINK_URL % line[8]
-                        if line[12]:
-                            this_trait['display_name'] = line[12] + \
-                                "_" + str(this_trait['name'])
+                this_trait['authors'] = line[7]
+                this_trait['year'] = line[8]
+                this_trait['pubmed_text'] = "N/A"
+                this_trait['pubmed_link'] = "N/A"
+                if this_trait['year'].isdigit():
+                    this_trait['pubmed_text'] = this_trait['year']
+                if line[9] != "" and line[9] != None:
+                    this_trait['pubmed_link'] = webqtlConfig.PUBMEDLINK_URL % line[8]
+                    if line[12]:
+                        this_trait['display_name'] = line[12] + \
+                            "_" + str(this_trait['name'])
 
-                    dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="Publish", species=this_trait["species"])
-                    permissions = check_resource_availability(dataset_ob, this_trait['name'])
-                    if type(permissions['data']) is list:
-                        if "view" not in permissions['data']:
-                            continue
-                    else:
-                        if permissions['data'] == 'no-access':
-                            continue
+                dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="Publish", species=this_trait["species"])
+                permissions = check_resource_availability(dataset_ob, this_trait['name'])
+                if type(permissions['data']) is list:
+                    if "view" not in permissions['data']:
+                        continue
+                else:
+                    if permissions['data'] == 'no-access':
+                        continue
 
-                    trait_list.append(this_trait)
+                trait_list.append(this_trait)
 
             self.trait_count = len(trait_list)
             self.trait_list = trait_list
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 278d8a6b..ef0c357e 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -42,7 +42,6 @@ from base import webqtlConfig
 from base.GeneralObject import GeneralObject
 from utility import webqtlUtil
 from utility import Plot
-from utility.benchmark import Bench
 from wqflask.interval_analyst import GeneUtil
 from base.webqtlConfig import GENERATED_IMAGE_DIR
 from utility.pillow_utils import draw_rotated_text, draw_open_polygon
@@ -587,9 +586,8 @@ class DisplayMappingResults:
         ################################################################
         showLocusForm = ""
         intCanvas = Image.new("RGBA", size=(self.graphWidth, self.graphHeight))
-        with Bench("Drawing Plot"):
-            gifmap = self.plotIntMapping(
-                intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm=showLocusForm)
+        gifmap = self.plotIntMapping(
+            intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm=showLocusForm)
 
         self.gifmap = gifmap.__str__()
 
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 7a424b17..c57596e9 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -33,7 +33,6 @@ from utility import webqtlUtil
 from utility import helper_functions
 from utility import Plot, Bunch
 from utility import temp_data
-from utility.benchmark import Bench
 from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping
 from wqflask.show_trait.SampleList import SampleList
 
@@ -204,13 +203,12 @@ class RunMapping:
                 self.first_run = False
             self.score_type = "-logP"
             self.manhattan_plot = True
-            with Bench("Running GEMMA"):
-                if self.use_loco == "True":
-                    marker_obs, self.output_files = gemma_mapping.run_gemma(
-                        self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files)
-                else:
-                    marker_obs, self.output_files = gemma_mapping.run_gemma(
-                        self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files)
+            if self.use_loco == "True":
+                marker_obs, self.output_files = gemma_mapping.run_gemma(
+                    self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files)
+            else:
+                marker_obs, self.output_files = gemma_mapping.run_gemma(
+                    self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files)
             results = marker_obs
         elif self.mapping_method == "rqtl_plink":
             results = self.run_rqtl_plink()
@@ -372,33 +370,29 @@ class RunMapping:
                             self.qtl_results.append(marker)
 
                 total_markers = len(self.qtl_results)
+                export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path,
+                                       self.mapping_method, self.mapping_scale, self.score_type,
+                                       self.transform, self.covariates, self.n_samples, self.vals_hash)
+
+                if len(self.qtl_results) > 30000:
+                    self.qtl_results = trim_markers_for_figure(
+                        self.qtl_results)
+                    self.results_for_browser = trim_markers_for_figure(
+                        self.results_for_browser)
+                    filtered_annotations = []
+                    for marker in self.results_for_browser:
+                        for annot_marker in self.annotations_for_browser:
+                            if annot_marker['rs'] == marker['rs']:
+                                filtered_annotations.append(annot_marker)
+                                break
+                    self.annotations_for_browser = filtered_annotations
+                    browser_files = write_input_for_browser(
+                        self.dataset, self.results_for_browser, self.annotations_for_browser)
+                else:
+                    browser_files = write_input_for_browser(
+                        self.dataset, self.results_for_browser, self.annotations_for_browser)
 
-                with Bench("Exporting Results"):
-                    export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path,
-                                           self.mapping_method, self.mapping_scale, self.score_type,
-                                           self.transform, self.covariates, self.n_samples, self.vals_hash)
-
-                with Bench("Trimming Markers for Figure"):
-                    if len(self.qtl_results) > 30000:
-                        self.qtl_results = trim_markers_for_figure(
-                            self.qtl_results)
-                        self.results_for_browser = trim_markers_for_figure(
-                            self.results_for_browser)
-                        filtered_annotations = []
-                        for marker in self.results_for_browser:
-                            for annot_marker in self.annotations_for_browser:
-                                if annot_marker['rs'] == marker['rs']:
-                                    filtered_annotations.append(annot_marker)
-                                    break
-                        self.annotations_for_browser = filtered_annotations
-                        browser_files = write_input_for_browser(
-                            self.dataset, self.results_for_browser, self.annotations_for_browser)
-                    else:
-                        browser_files = write_input_for_browser(
-                            self.dataset, self.results_for_browser, self.annotations_for_browser)
-
-                with Bench("Trimming Markers for Table"):
-                    self.trimmed_markers = trim_markers_for_table(results)
+                self.trimmed_markers = trim_markers_for_table(results)
 
                 chr_lengths = get_chr_lengths(
                     self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results)
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 6b1b4e97..f132e2c6 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -5,8 +5,6 @@ from base.data_set import create_dataset
 from base.trait import GeneralTrait
 from db import webqtlDatabaseFunction
 
-from utility.benchmark import Bench
-
 
 class GSearch:
 
@@ -43,18 +41,15 @@ class GSearch:
                 ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
                 LIMIT 6000
                 """ % (self.terms)
-            with Bench("Running query"):
-                re = g.db.execute(sql).fetchall()
+            re = g.db.execute(sql).fetchall()
             self.trait_list = []
-            with Bench("Creating trait objects"):
-                for line in re:
-                    dataset = create_dataset(
-                        line[3], "ProbeSet", get_samplelist=False)
-                    trait_id = line[4]
-                    # with Bench("Building trait object"):
-                    this_trait = GeneralTrait(
-                        dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
-                    self.trait_list.append(this_trait)
+            for line in re:
+                dataset = create_dataset(
+                    line[3], "ProbeSet", get_samplelist=False)
+                trait_id = line[4]
+                this_trait = GeneralTrait(
+                    dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+                self.trait_list.append(this_trait)
 
         elif self.type == "phenotype":
             sql = """
@@ -90,13 +85,12 @@ class GSearch:
                 """ % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms)
             re = g.db.execute(sql).fetchall()
             self.trait_list = []
-            with Bench("Creating trait objects"):
-                for line in re:
-                    dataset = create_dataset(line[2], "Publish")
-                    trait_id = line[3]
-                    this_trait = GeneralTrait(
-                        dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
-                    self.trait_list.append(this_trait)
+            for line in re:
+                dataset = create_dataset(line[2], "Publish")
+                trait_id = line[3]
+                this_trait = GeneralTrait(
+                    dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+                self.trait_list.append(this_trait)
 
         self.results = self.convert_to_json()
 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index d80d557b..acd65587 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -95,7 +95,6 @@ from utility.redis_tools import get_redis_conn
 
 
 from base.webqtlConfig import GENERATED_IMAGE_DIR, DEFAULT_PRIVILEGES
-from utility.benchmark import Bench
 
 from pprint import pformat as pf
 
@@ -217,12 +216,11 @@ def twitter(filename):
 def search_page():
     result = None
     if USE_REDIS:
-        with Bench("Trying Redis cache"):
-            key = "search_results:v1:" + \
-                json.dumps(request.args, sort_keys=True)
-            result = Redis.get(key)
-            if result:
-                result = pickle.loads(result)
+        key = "search_results:v1:" + \
+            json.dumps(request.args, sort_keys=True)
+        result = Redis.get(key)
+        if result:
+            result = pickle.loads(result)
     the_search = SearchResultPage(request.args)
     result = the_search.__dict__
     valid_search = result['search_term_exists']
@@ -529,12 +527,10 @@ def heatmap_page():
         version = "v5"
         key = "heatmap:{}:".format(
             version) + json.dumps(start_vars, sort_keys=True)
-        with Bench("Loading cache"):
-            result = Redis.get(key)
+        result = Redis.get(key)
 
         if result:
-            with Bench("Loading results"):
-                result = pickle.loads(result)
+            result = pickle.loads(result)
 
         else:
             template_vars = heatmap.Heatmap(request.form, temp_uuid)
@@ -547,9 +543,7 @@ def heatmap_page():
             pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
             Redis.set(key, pickled_result)
             Redis.expire(key, 60 * 60)
-
-        with Bench("Rendering template"):
-            rendered_template = render_template("heatmap.html", **result)
+        rendered_template = render_template("heatmap.html", **result)
 
     else:
         rendered_template = render_template(
@@ -762,40 +756,36 @@ def mapping_results_page():
     version = "v3"
     key = "mapping_results:{}:".format(
         version) + json.dumps(start_vars, sort_keys=True)
-    with Bench("Loading cache"):
-        result = None  # Just for testing
+    result = None  # Just for testing
 
     if result:
-        with Bench("Loading results"):
-            result = pickle.loads(result)
+        result = pickle.loads(result)
     else:
-        with Bench("Total time in RunMapping"):
-            try:
-                template_vars = run_mapping.RunMapping(start_vars, temp_uuid)
-                if template_vars.no_results:
-                    rendered_template = render_template("mapping_error.html")
-                    return rendered_template
-            except:
+        try:
+            template_vars = run_mapping.RunMapping(start_vars, temp_uuid)
+            if template_vars.no_results:
                 rendered_template = render_template("mapping_error.html")
                 return rendered_template
+        except:
+            rendered_template = render_template("mapping_error.html")
+            return rendered_template
 
-            if not template_vars.pair_scan:
-                template_vars.js_data = json.dumps(template_vars.js_data,
-                                                   default=json_default_handler,
-                                                   indent="   ")
+        if not template_vars.pair_scan:
+            template_vars.js_data = json.dumps(template_vars.js_data,
+                                               default=json_default_handler,
+                                               indent="   ")
 
-            result = template_vars.__dict__
+        result = template_vars.__dict__
 
-            if result['pair_scan']:
-                with Bench("Rendering template"):
-                    rendered_template = render_template(
-                        "pair_scan_results.html", **result)
-            else:
-                gn1_template_vars = display_mapping_results.DisplayMappingResults(
-                    result).__dict__
+        if result['pair_scan']:
+            rendered_template = render_template(
+                "pair_scan_results.html", **result)
+        else:
+            gn1_template_vars = display_mapping_results.DisplayMappingResults(
+                result).__dict__
 
-                rendered_template = render_template(
-                    "mapping_results.html", **gn1_template_vars)
+            rendered_template = render_template(
+                "mapping_results.html", **gn1_template_vars)
 
     return rendered_template
 
-- 
cgit v1.2.3


From d9a6e9433e4fd5cc20ed45a53c34cab4357eac8e Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Tue, 30 Aug 2022 21:39:38 +0300
Subject: Replace fetchall, fetchone, fetch1 with database_connection

* wqflask/base/data_set.py: Replace "db.call" import with
"database_connection".
(create_datasets_list): Use "database_connection" to fetch data.
(DatasetGroup.__init__): Ditto.
(DataSet.retrieve_other_names): Ditto.
(PhenotypeDataSet.setup): Remove query escaping in string and format
the string.
(GenotypeDataSet.setup): Ditto.
(MrnaAssayDataSet.setup): Ditto.
* wqflask/db/webqtlDatabaseFunction.py: Remove db.call import.
(retrieve_species): Use database_connection() to fetch data.
(retrieve_species_id): Ditto.
---
 wqflask/base/data_set.py             | 115 ++++++++++++++---------------------
 wqflask/db/webqtlDatabaseFunction.py |  16 +++--
 2 files changed, 55 insertions(+), 76 deletions(-)

(limited to 'wqflask/db')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 33e6f353..57bd6be3 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -21,7 +21,6 @@ from dataclasses import dataclass
 from dataclasses import field
 from dataclasses import InitVar
 from typing import Optional, Dict, List
-from db.call import fetchall, fetchone, fetch1
 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
@@ -40,6 +39,7 @@ from flask import Flask, g
 from base.webqtlConfig import TMPDIR
 from urllib.parse import urlparse
 from utility.tools import SQL_URI
+from wqflask.database import database_connection
 import os
 import math
 import string
@@ -205,11 +205,14 @@ def create_datasets_list():
                      'Geno': 'GenoFreeze'}
 
         for dataset_type in type_dict:
-            query = "SELECT Name FROM {}".format(type_dict[dataset_type])
-            for result in fetchall(query):
-                dataset = create_dataset(result.Name, dataset_type)
-                datasets.append(dataset)
-
+            with database_connection() as conn, conn.cursor() as cursor:
+                cursor.execute("SELECT Name FROM %s",
+                               (type_dict[dataset_type],))
+                results = cursor.fetchall(query)
+                if results:
+                    for result in results:
+                        datasets.append(
+                            create_dataset(result.Name, dataset_type))
         if USE_REDIS:
             r.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
             r.expire(key, 60 * 60)
@@ -319,12 +322,16 @@ class DatasetGroup:
 
     def __init__(self, dataset, name=None):
         """This sets self.group and self.group_id"""
-        if name == None:
-            self.name, self.id, self.genetic_type, self.code = fetchone(
-                dataset.query_for_group)
-        else:
-            self.name, self.id, self.genetic_type, self.code = fetchone(
-                "SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode FROM InbredSet where Name='%s'" % name)
+        query = """SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType,
+ InbredSet.InbredSetCode FROM InbredSet where Name=%s
+        """
+        if not name:
+            query, name = dataset.query_for_group, self.name
+        with database_connection() as conn, conn.cursor() as cursor:
+            cursor.execute(query, (name,))
+            results = cursor.fetchone()
+            if results:
+                self.name, self.id, self.genetic_type, self.code = results
         if self.name == 'BXD300':
             self.name = "BXD"
 
@@ -620,36 +627,25 @@ class DataSet:
         """
 
         try:
+            query = ""
+            _vars = None
             if self.type == "ProbeSet":
-                query_args = tuple(escape(x) for x in (
-                    self.name,
-                    self.name,
-                    self.name))
-
-                self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetch1("""
-    SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
-    FROM ProbeSetFreeze, ProbeFreeze, Tissue
-    WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
-    AND ProbeFreeze.TissueId = Tissue.Id
-    AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
-                """ % (query_args), "/dataset/" + self.name + ".json",
-                    lambda r: (r["id"], r["name"], r["full_name"],
-                               r["short_name"], r["data_scale"], r["tissue"])
-                )
+                query = """
+SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
+FROM ProbeSetFreeze, ProbeFreeze, Tissue
+WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
+AND ProbeFreeze.TissueId = Tissue.Id
+AND (ProbeSetFreeze.Name = %s OR ProbeSetFreeze.FullName = %s OR ProbeSetFreeze.ShortName = %s"""
+                _vars = (self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue,)
             else:
-                query_args = tuple(escape(x) for x in (
-                    (self.type + "Freeze"),
-                    self.name,
-                    self.name,
-                    self.name))
-
+                query = """
+SELECT Id, Name, FullName, ShortName FROM %s
+WHERE (Name = %s OR FullName = '%s' OR ShortName = %s)"""
                 self.tissue = "N/A"
-                self.id, self.name, self.fullname, self.shortname = fetchone("""
-                        SELECT Id, Name, FullName, ShortName
-                        FROM %s
-                        WHERE (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
-                    """ % (query_args))
-
+                _vars = (self.id, self.name, self.fullname, self.shortname,)
+            with database_connection() as conn, conn.cursor() as cursor:
+                cursor.execute(query, (query_args,))
+                _vars = cursor.fetchone()
         except TypeError:
             pass
 
@@ -848,16 +844,8 @@ class PhenotypeDataSet(DataSet):
                               'Additive Effect']
 
         self.type = 'Publish'
-
-        self.query_for_group = '''
-                            SELECT
-                                    InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
-                            FROM
-                                    InbredSet, PublishFreeze
-                            WHERE
-                                    PublishFreeze.InbredSetId = InbredSet.Id AND
-                                    PublishFreeze.Name = "%s"
-                    ''' % escape(self.name)
+        self.query_for_group = """
+SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode FROM InbredSet, PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id AND PublishFreeze.Name = %s"""
 
     def check_confidentiality(self):
         # (Urgently?) Need to write this
@@ -964,16 +952,10 @@ class GenotypeDataSet(DataSet):
 
         # Todo: Obsolete or rename this field
         self.type = 'Geno'
-
-        self.query_for_group = '''
-                SELECT
-                        InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
-                FROM
-                        InbredSet, GenoFreeze
-                WHERE
-                        GenoFreeze.InbredSetId = InbredSet.Id AND
-                        GenoFreeze.Name = "%s"
-                ''' % escape(self.name)
+        self.query_for_group = """
+SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
+FROM InbredSet, GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id AND
+GenoFreeze.Name = %s"""
 
     def check_confidentiality(self):
         return geno_mrna_confidentiality(self)
@@ -1072,17 +1054,10 @@ class MrnaAssayDataSet(DataSet):
 
         # Todo: Obsolete or rename this field
         self.type = 'ProbeSet'
-
-        self.query_for_group = '''
-                        SELECT
-                                InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
-                        FROM
-                                InbredSet, ProbeSetFreeze, ProbeFreeze
-                        WHERE
-                                ProbeFreeze.InbredSetId = InbredSet.Id AND
-                                ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
-                                ProbeSetFreeze.Name = "%s"
-                ''' % escape(self.name)
+        self.query_for_group = """
+SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode
+FROM InbredSet, ProbeSetFreeze, ProbeFreeze WHERE ProbeFreeze.InbredSetId = InbredSet.Id AND
+ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND ProbeSetFreeze.Name = %s"""
 
     def check_confidentiality(self):
         return geno_mrna_confidentiality(self)
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 9ec650a4..122c546f 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -20,19 +20,23 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from db.call import fetch1
+from wqflask.database import database_connection
 
 
 def retrieve_species(group):
     """Get the species of a group (e.g. returns string "mouse" on "BXD"
 
     """
-    result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (
-        group), "/cross/" + group + ".json", lambda r: (r["species"],))[0]
+    with database_connection() as conn, conn.cursor() as cursor:
+        cursor.execute(
+            "SELECT Species.Name FROM Species, InbredSet WHERE InbredSet.Name = %s AND InbredSet.SpeciesId = Species.Id",
+            (group,))
+        return cursor.fetchone()[0]
     return result
 
 
 def retrieve_species_id(group):
-    result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (
-        group), "/cross/" + group + ".json", lambda r: (r["species_id"],))[0]
-    return result
+    with database_connection() as conn, conn.cursor() as cursor:
+        cursor.execute("SELECT SpeciesId FROM InbredSet WHERE Name = %s",
+                       (group,))
+        return cursor.fetchone()[0]
-- 
cgit v1.2.3


From 327506abbc9b4a368f5785b8f90086cc5e038eb8 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Tue, 30 Aug 2022 21:49:28 +0300
Subject: Delete unused modules

* wqflask/base/data_set.py: Delete "menu_main" import.
* wqflask/db/call.py: Delete it.
* wqflask/db/gn_server.py: Ditto.
* wqflask/wqflask/submit_bnw.py: Ditto.
---
 wqflask/base/data_set.py      |  1 -
 wqflask/db/call.py            | 69 -------------------------------------------
 wqflask/db/gn_server.py       |  7 -----
 wqflask/wqflask/submit_bnw.py | 10 -------
 4 files changed, 87 deletions(-)
 delete mode 100644 wqflask/db/call.py
 delete mode 100644 wqflask/db/gn_server.py
 delete mode 100644 wqflask/wqflask/submit_bnw.py

(limited to 'wqflask/db')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 57bd6be3..433365fc 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 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
 from utility.db_tools import escape
 from utility.db_tools import mescape
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
deleted file mode 100644
index c27e0326..00000000
--- a/wqflask/db/call.py
+++ /dev/null
@@ -1,69 +0,0 @@
-# Module for calling the backend
-
-from flask import g
-
-import string
-try:  # Python2 support
-    import urllib.request
-    import urllib.error
-    import urllib.parse
-except:
-    import urllib2
-import json
-from utility.tools import USE_GN_SERVER, LOG_SQL, GN_SERVER_URL
-
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-
-def fetch1(query, path=None, func=None):
-    """Fetch one result as a Tuple using either a SQL query or the URI
-path to GN_SERVER (when USE_GN_SERVER is True). Apply func to
-GN_SERVER result when set (which should return a Tuple)
-
-    """
-    if USE_GN_SERVER and path:
-        result = gn_server(path)
-        if func != None:
-            res2 = func(result)
-        else:
-            res2 = result,
-        return res2
-    else:
-        return fetchone(query)
-
-
-def fetchone(query):
-    """Return tuple containing one row by calling SQL directly (the
-original fetchone, but with logging)
-
-    """
-    def helper(query):
-        res = g.db.execute(query)
-        return res.fetchone()
-    return logger.sql(query, helper)
-
-
-def fetchall(query):
-    """Return row iterator by calling SQL directly (the
-original fetchall, but with logging)
-
-    """
-    def helper(query):
-        res = g.db.execute(query)
-        return res.fetchall()
-    return logger.sql(query, helper)
-
-
-def gn_server(path):
-    """Return JSON record by calling GN_SERVER
-
-    """
-    res = ()
-    try:
-        res = urllib.request.urlopen(GN_SERVER_URL + path)
-    except:
-        res = urllib2.urlopen(GN_SERVER_URL + path)
-    rest = res.read()
-    res2 = json.loads(rest)
-    return res2
diff --git a/wqflask/db/gn_server.py b/wqflask/db/gn_server.py
deleted file mode 100644
index af6682ba..00000000
--- a/wqflask/db/gn_server.py
+++ /dev/null
@@ -1,7 +0,0 @@
-# Backend query functions (logic)
-
-from db.call import gn_server
-
-
-def menu_main():
-    return gn_server("/int/menu/main.json")
diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py
deleted file mode 100644
index b21a88cc..00000000
--- a/wqflask/wqflask/submit_bnw.py
+++ /dev/null
@@ -1,10 +0,0 @@
-from base.trait import GeneralTrait
-from base import data_set
-from utility import helper_functions
-
-import utility.logger
-logger = utility.logger.getLogger(__name__)
-
-
-def get_bnw_input(start_vars):
-    logger.debug("BNW VARS:", start_vars)
-- 
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