# 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