From 968eb8c1d8703c3d5c84f2162eae365b930c008d Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 23 Jun 2016 05:33:20 +0000
Subject: Backend: moved methods into call module

---
 wqflask/base/data_set.py             |  7 ++++---
 wqflask/db/call.py                   | 38 ++++++++++++++++++++++++++++++++++++
 wqflask/db/webqtlDatabaseFunction.py | 27 +++----------------------
 3 files changed, 45 insertions(+), 27 deletions(-)
 create mode 100644 wqflask/db/call.py

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index a7b6e402..02018dd3 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -114,9 +114,10 @@ def create_datasets_list():
             for dataset_type in type_dict:
                 query = "SELECT Name FROM {}".format(type_dict[dataset_type])
                 for result in g.db.execute(query).fetchall():
-                    #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))
+                    #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)
 
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
new file mode 100644
index 00000000..6b15abb3
--- /dev/null
+++ b/wqflask/db/call.py
@@ -0,0 +1,38 @@
+# Module for calling the backend
+
+from flask import g
+
+# import MySQLdb
+import string
+import urllib2
+import json
+# from base import webqtlConfig
+from utility.tools import USE_GN_SERVER, LOG_SQL
+from utility.benchmark import Bench
+
+from utility.logger import getLogger
+logger = getLogger(__name__ )
+
+from inspect import stack
+
+def fetchone(query):
+    """Return tuple containing one row by calling SQL directly
+
+    """
+    with Bench("SQL",LOG_SQL):
+        def helper(query):
+            res = g.db.execute(query)
+            return res.fetchone()
+        callername = stack()[1][3]
+        return logger.sql(callername, query, helper)
+
+def gn_server(path):
+    """Return JSON record by calling GN_SERVER
+
+    """
+    with Bench("GN_SERVER",LOG_SQL):
+        res = urllib2.urlopen("http://localhost:8880/"+path)
+        rest = res.read()
+        res2 = json.loads(rest)
+        logger.info(res2)
+        return res2
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index e30929d2..bdc3eeb2 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -20,7 +20,6 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from inspect import stack
 from flask import Flask, g
 
 import MySQLdb
@@ -31,6 +30,8 @@ from base import webqtlConfig
 from utility.tools import USE_GN_SERVER, LOG_SQL
 from utility.benchmark import Bench
 
+from db.call import fetchone, gn_server
+
 from utility.logger import getLogger
 logger = getLogger(__name__ )
 
@@ -40,35 +41,13 @@ logger = getLogger(__name__ )
 ###########################################################################
 def getCursor():
     try:
-        logger.warning("Creating new MySQLdb cursor")
+        logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)")
         con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD)
         cursor = con.cursor()
         return cursor
     except:
         return None
 
-def fetchone(query):
-    """Return tuple containing one row by calling SQL directly
-
-    """
-    with Bench("SQL",LOG_SQL):
-        def helper(query):
-            res = g.db.execute(query)
-            return res.fetchone()
-        callername = stack()[1][3]
-        return logger.sql(callername, query, helper)
-
-def gn_server(path):
-    """Return JSON record by calling GN_SERVER
-
-    """
-    with Bench("GN_SERVER",LOG_SQL):
-        res = urllib2.urlopen("http://localhost:8880/"+path)
-        rest = res.read()
-        res2 = json.loads(rest)
-        logger.info(res2)
-        return res2
-
 def retrieve_species(group):
     """Get the species of a group (e.g. returns string "mouse" on "BXD"
 
-- 
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