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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)
+#
+# 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 gn2.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