# 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        logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)")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):
    return g.db.execute("select SpeciesId from InbredSet where Name = %s", (group)).fetchone()[0]