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# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
from flask import Flask, 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 db.call import fetch1
from utility.logger import getLogger
logger = getLogger(__name__ )
###########################################################################
#output: cursor instance
#function: connect to database and return cursor instance
###########################################################################
def getCursor():
try:
logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)")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 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)
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)
return result
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