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-rw-r--r--wqflask/base/data_set.py7
-rw-r--r--wqflask/db/call.py38
-rw-r--r--wqflask/db/webqtlDatabaseFunction.py27
3 files changed, 45 insertions, 27 deletions
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"