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-rw-r--r--wqflask/db/webqtlDatabaseFunction.py27
1 files changed, 3 insertions, 24 deletions
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+ logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)")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"