Merge branch 'testing' of github.com:genenetwork/genenetwork2 into feature/remove_trait_creation_from_search

3 files changed, 16 insertions, 18 deletions

diff --git a/wqflask/db/call.py b/wqflask/db/call.py
index 0971d2a2..1fe0772b 100644
--- a/wqflask/db/call.py
+++ b/wqflask/db/call.py
@@ -4,7 +4,9 @@ from flask import g
 
 import string
 try:  # Python2 support
-    import urllib.request, urllib.error, urllib.parse
+    import urllib.request
+    import urllib.error
+    import urllib.parse
 except:
     import urllib2
 import json
@@ -12,10 +14,11 @@ 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__ )
+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
 path to GN_SERVER (when USE_GN_SERVER is True). Apply func to
@@ -35,6 +38,7 @@ GN_SERVER result when set (which should return a Tuple)
     else:
         return fetchone(query)
 
+
 def fetchone(query):
     """Return tuple containing one row by calling SQL directly (the
 original fetchone, but with logging)
@@ -46,6 +50,7 @@ original fetchone, but with logging)
             return res.fetchone()
         return logger.sql(query, helper)
 
+
 def fetchall(query):
     """Return row iterator by calling SQL directly (the
 original fetchall, but with logging)
@@ -57,6 +62,7 @@ original fetchall, but with logging)
             return res.fetchall()
         return logger.sql(query, helper)
 
+
 def gn_server(path):
     """Return JSON record by calling GN_SERVER
 
@@ -64,9 +70,9 @@ def gn_server(path):
     with Bench("GN_SERVER", LOG_SQL):
         res = ()
         try:
-            res = urllib.request.urlopen(GN_SERVER_URL+path)
+            res = urllib.request.urlopen(GN_SERVER_URL + path)
         except:
-            res = urllib2.urlopen(GN_SERVER_URL+path)
+            res = urllib2.urlopen(GN_SERVER_URL + path)
         rest = res.read()
         res2 = json.loads(rest)
         logger.debug(res2)
diff --git a/wqflask/db/gn_server.py b/wqflask/db/gn_server.py
index da224112..f9b01658 100644
--- a/wqflask/db/gn_server.py
+++ b/wqflask/db/gn_server.py
@@ -3,7 +3,8 @@
 from db.call import gn_server
 
 from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
+
 
 def menu_main():
     return gn_server("/int/menu/main.json")
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 2805febd..9ec650a4 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -21,27 +21,18 @@
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
 from db.call import fetch1
-from utility.tools import USE_GN_SERVER
 
-from utility.logger import getLogger
-logger = getLogger(__name__ )
-
-###########################################################################
-#output: cursor instance
-#function: connect to database and return cursor instance
-###########################################################################
 
 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]
-    logger.debug("retrieve_species result:", result)
+    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]
     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]
-    logger.debug("retrieve_species_id result:", result)
+    result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (
+        group), "/cross/" + group + ".json", lambda r: (r["species_id"],))[0]
     return result