# 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)
#
# Created by GeneNetwork Core Team 2010/08/10
#
# Last updated by GeneNetwork Core Team 2010/10/20

import string
import time
import re
import math
from math import *

from base import webqtlConfig

# NL, 07/27/2010. moved from webqtlForm.py
# Dict of Parents and F1 information, In the order of [F1, Mat, Pat]
ParInfo = {
    'BXH': ['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'],
    'AKXD': ['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'],
    'BXD': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
    'C57BL-6JxC57BL-6NJF2': ['', '', 'C57BL/6J', 'C57BL/6NJ'],
    'BXD300': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
    'B6BTBRF2': ['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
    'BHHBF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
    'BHF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
    'B6D2F2': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
    'BDF2-1999': ['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'],
    'BDF2-2005': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
    'CTB6F2': ['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'],
    'CXB': ['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'],
    'AXBXA': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
    'AXB': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
    'BXA': ['BAF1', 'ABF1', 'C57BL/6J', 'A/J'],
    'LXS': ['LSF1', 'SLF1', 'ISS', 'ILS'],
    'HXBBXH': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'],
    'BayXSha': ['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'],
    'ColXBur': ['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'],
    'ColXCvi': ['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'],
    'SXM': ['SMF1', 'MSF1', 'Steptoe', 'Morex'],
    'HRDP': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv']
}

#########################################
#      Accessory Functions
#########################################


def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits):
    from random import choice
    _str = prefix[:]
    for i in range(length):
        _str += choice(chars)
    return _str


def ListNotNull(lst):
    '''Obsolete - Use built in function any (or all or whatever)


    Determine if the elements in a list are all null

    '''
    for item in lst:
        if item is not None:
            return 1
    return None


def readLineCSV(line):  # dcrowell July 2008
    """Parses a CSV string of text and returns a list containing each element as a string.
    Used by correlationPage"""
    returnList = line.split('","')
    returnList[-1] = returnList[-1][:-2]
    returnList[0] = returnList[0][1:]
    return returnList


def cmpEigenValue(A, B):
    try:
        if A[0] > B[0]:
            return -1
        elif A[0] == B[0]:
            return 0
        else:
            return 1
    except:
        return 0


def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users):
    access_to_confidential_phenotype_trait = 0
    if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']:
        access_to_confidential_phenotype_trait = 1
    else:
        AuthorizedUsersList = [x.strip() for x in authorized_users.split(',')]
        if userName in AuthorizedUsersList:
            access_to_confidential_phenotype_trait = 1
    return access_to_confidential_phenotype_trait