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/gn_server.py | 3 ---
1 file changed, 3 deletions(-)
(limited to 'wqflask/db/gn_server.py')
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 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/gn_server.py')
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)
--
cgit v1.2.3