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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 htmlgen import HTMLgen2 as HT
+
+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'],
+'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':['HSRBNF1', 'BNHSRF1', 'BN', 'HSR'],
+'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0','Shahdara'],
+'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0','Bur-0'],
+'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0','Cvi'],
+'SXM':['SMF1', 'MSF1', 'Steptoe','Morex']
+}
+
+
+# NL, 07/27/2010. moved from template.py
+IMGSTEP1 = HT.Image('/images/step1.gif', alt='STEP 1',border=0) #XZ, Only be used in inputPage.py
+IMGSTEP2 = HT.Image('/images/step2.gif', alt='STEP 2',border=0) #XZ, Only be used in inputPage.py
+IMGSTEP3 = HT.Image('/images/step3.gif', alt='STEP 3',border=0) #XZ, Only be used in inputPage.py
+IMGNEXT = HT.Image('/images/arrowdown.gif', alt='NEXT',border=0) #XZ, Only be used in inputPage.py
+
+IMGASC = HT.Image("/images/sortup.gif", border=0)
+IMGASCON = HT.Image("/images/sortupon.gif", border=0)
+IMGDESC = HT.Image("/images/sortdown.gif", border=0)
+IMGDESCON = HT.Image("/images/sortdownon.gif", border=0)
+
+"""
+IMGASC = HT.Image("/images/sortup_icon.gif", border=0)
+IMGASCON = HT.Image("/images/sortupon.gif", border=0)
+IMGDESC = HT.Image("/images/sortdown_icon.gif", border=0)
+IMGDESCON = HT.Image("/images/sortdownon.gif", border=0)
+IMG_UNSORTED = HT.Image("/images/unsorted_icon.gif", border=0)
+"""
+
+PROGRESSBAR = HT.Image('/images/waitAnima2.gif', alt='checkblue',align="middle",border=0)
+
+#########################################
+# Accessory Functions
+#########################################
+
+def decodeEscape(str):
+ a = str
+ pattern = re.compile('(%[0-9A-Fa-f][0-9A-Fa-f])')
+ match = pattern.findall(a)
+ matched = []
+ for item in match:
+ if item not in matched:
+ a = a.replace(item, '%c' % eval("0x"+item[-2:]))
+ matched.append(item)
+ return a
+
+def exportData(hddn, tdata, NP = None):
+ for key in tdata.keys():
+ _val, _var, _N = tdata[key].val, tdata[key].var, tdata[key].N
+ if _val != None:
+ hddn[key] = _val
+ if _var != None:
+ hddn['V'+key] = _var
+ if NP and _N != None:
+ hddn['N'+key] = _N
+
+def genShortStrainName(RISet='', input_strainName=''):
+ #aliasStrainDict = {'C57BL/6J':'B6','DBA/2J':'D2'}
+ strainName = input_strainName
+ if RISet != 'AXBXA':
+ if RISet == 'BXD300':
+ this_RISet = 'BXD'
+ elif RISet == 'BDF2-2005':
+ this_RISet = 'CASE05_'
+ else:
+ this_RISet = RISet
+ strainName = string.replace(strainName,this_RISet,'')
+ strainName = string.replace(strainName,'CASE','')
+ try:
+ strainName = "%02d" % int(strainName)
+ except:
+ pass
+ else:
+ strainName = string.replace(strainName,'AXB','A')
+ strainName = string.replace(strainName,'BXA','B')
+ try:
+ strainName = strainName[0] + "%02d" % int(strainName[1:])
+ except:
+ pass
+ return strainName
+
+def toInt(in_str):
+ "Converts an arbitrary string to an unsigned integer"
+ start = -1
+ end = -1
+ for i, char in enumerate(in_str):
+ if char >= '0' and char <= '9':
+ if start < 0:
+ start = i
+ end = i+1
+ else:
+ if start >= 0:
+ break
+ if start < end:
+ return int(in_str[start:end])
+ else:
+ return -1
+
+def transpose(m):
+ 'transpose a matrix'
+ n = len(m)
+ return [[m[j][i] for i in range(len(m[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m[0]))]
+
+def asymTranspose(m):
+ 'transpose a matrix'
+ t = max(map(len, m))
+ n = len(m)
+ m2 = [["-"]]*n
+ for i in range(n):
+ m2[i] = m[i] + [""]*(t- len(m[i]))
+ return [[m2[j][i] for i in range(len(m2[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m2[0]))]
+
+def genRandStr(prefix = "", length=8, chars=string.letters+string.digits):
+ from random import choice
+ _str = prefix[:]
+ for i in range(length):
+ _str += choice(chars)
+ return _str
+
+def generate_session():
+ import sha
+ return sha.new(str(time.time())).hexdigest()
+
+def cvt2Dict(x):
+ tmp = {}
+ for key in x.keys():
+ tmp[key] = x[key]
+ return tmp
+
+def dump_session(session_obj, filename):
+ "It seems mod python can only cPickle most basic data type"
+ import cPickle
+ session_file = open(filename, 'wb')
+ #try:
+ # pass
+ #except:
+ # pass
+ cPickle.dump(session_obj, session_file)
+ session_file.close()
+
+def StringAsFloat(str):
+ 'Converts string to float but catches any exception and returns None'
+ try:
+ return float(str)
+ except:
+ return None
+
+def IntAsFloat(str):
+ 'Converts string to Int but catches any exception and returns None'
+ try:
+ return int(str)
+ except:
+ return None
+
+def FloatAsFloat(flt):
+ 'Converts float to string but catches any exception and returns None'
+ try:
+ return float("%2.3f" % flt)
+ except:
+ return None
+
+def RemoveZero(flt):
+ 'Converts string to float but catches any exception and returns None'
+ try:
+ if abs(flt) < 1e-6:
+ return None
+ else:
+ return flt
+ except:
+ return None
+
+
+def SciFloat(d):
+ 'Converts string to float but catches any exception and returns None'
+
+ try:
+ if abs(d) <= 1.0e-4:
+ return "%1.2e" % d
+ else:
+ return "%1.5f" % d
+ except:
+ return None
+
+###To be removed
+def FloatList2String(lst):
+ 'Converts float list to string but catches any exception and returns None'
+ tt=''
+ try:
+ for item in lst:
+ if item == None:
+ tt += 'X '
+ else:
+ tt += '%f ' % item
+ return tt
+ except:
+ return ""
+
+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
+
+###To be removed
+def FileDataProcess(str):
+ 'Remove the description text from the input file if theres any'
+ i=0
+ while i<len(str):
+ if str[i]<'\x7f' and str[i]>'\x20':
+ break
+ else:
+ i+=1
+ str=str[i:]
+ str=string.join(string.split(str,'\000'),'')
+ i=string.find(str,"*****")
+ if i>-1:
+ return str[i+5:]
+ else:
+ return str
+
+def rank(a,lst,offset=0):
+ """Calculate the integer rank of a number in an array, can be used to calculate p-value"""
+ n = len(lst)
+ if n == 2:
+ if a <lst[0]:
+ return offset
+ elif a > lst[1]:
+ return offset + 2
+ else:
+ return offset +1
+ elif n == 1:
+ if a <lst[0]:
+ return offset
+ else:
+ return offset +1
+ elif n== 0:
+ return offset
+ else:
+ mid = n/2
+ if a < lst[mid]:
+ return rank(a,lst[:mid-1],offset)
+ else:
+ return rank(a,lst[mid:],offset+mid)
+
+def cmpScanResult(A,B):
+ try:
+ if A.LRS > B.LRS:
+ return 1
+ elif A.LRS == B.LRS:
+ return 0
+ else:
+ return -1
+ except:
+ return 0
+
+
+def cmpScanResult2(A,B):
+ try:
+ if A.LRS < B.LRS:
+ return 1
+ elif A.LRS == B.LRS:
+ return 0
+ else:
+ return -1
+ except:
+ return 0
+
+def cmpOrder(A,B):
+ try:
+ if A[1] < B[1]:
+ return -1
+ elif A[1] == B[1]:
+ return 0
+ else:
+ return 1
+ except:
+ return 0
+
+def cmpOrder2(A,B):
+ try:
+ if A[-1] < B[-1]:
+ return -1
+ elif A[-1] == B[-1]:
+ return 0
+ else:
+ return 1
+ except:
+ return 0
+
+
+
+
+def calRank(xVals, yVals, N): ### Zach Sloan, February 4 2010
+ """
+ Returns a ranked set of X and Y values. These are used when generating
+ a Spearman scatterplot. Bear in mind that this sets values equal to each
+ other as the same rank.
+ """
+ XX = []
+ YY = []
+ X = [0]*len(xVals)
+ Y = [0]*len(yVals)
+ j = 0
+
+ for i in range(len(xVals)):
+
+ if xVals[i] != None and yVals[i] != None:
+ XX.append((j, xVals[i]))
+ YY.append((j, yVals[i]))
+ j = j + 1
+
+ NN = len(XX)
+
+ XX.sort(cmpOrder2)
+ YY.sort(cmpOrder2)
+
+ j = 1
+ rank = 0.0
+
+ while j < NN:
+
+ if XX[j][1] != XX[j-1][1]:
+ X[XX[j-1][0]] = j
+ j = j+1
+
+ else:
+ jt = j+1
+ ji = j
+ for jt in range(j+1, NN):
+ if (XX[jt][1] != XX[j-1][1]):
+ break
+ rank = 0.5*(j+jt)
+ for ji in range(j-1, jt):
+ X[XX[ji][0]] = rank
+ if (jt == NN-1):
+ if (XX[jt][1] == XX[j-1][1]):
+ X[XX[NN-1][0]] = rank
+ j = jt+1
+
+ if j == NN:
+ if X[XX[NN-1][0]] == 0:
+ X[XX[NN-1][0]] = NN
+
+ j = 1
+ rank = 0.0
+
+ while j < NN:
+
+ if YY[j][1] != YY[j-1][1]:
+ Y[YY[j-1][0]] = j
+ j = j+1
+ else:
+ jt = j+1
+ ji = j
+ for jt in range(j+1, NN):
+ if (YY[jt][1] != YY[j-1][1]):
+ break
+ rank = 0.5*(j+jt)
+ for ji in range(j-1, jt):
+ Y[YY[ji][0]] = rank
+ if (jt == NN-1):
+ if (YY[jt][1] == YY[j-1][1]):
+ Y[YY[NN-1][0]] = rank
+ j = jt+1
+
+ if j == NN:
+ if Y[YY[NN-1][0]] == 0:
+ Y[YY[NN-1][0]] = NN
+
+ return (X,Y)
+
+def calCorrelationRank(xVals,yVals,N):
+ """
+ Calculated Spearman Ranked Correlation. The algorithm works
+ by setting all tied ranks to the average of those ranks (for
+ example, if ranks 5-10 all have the same value, each will be set
+ to rank 7.5).
+ """
+
+ XX = []
+ YY = []
+ j = 0
+
+ for i in range(len(xVals)):
+ if xVals[i]!= None and yVals[i]!= None:
+ XX.append((j,xVals[i]))
+ YY.append((j,yVals[i]))
+ j = j+1
+
+ NN = len(XX)
+ if NN <6:
+ return (0.0,NN)
+ XX.sort(cmpOrder2)
+ YY.sort(cmpOrder2)
+ X = [0]*NN
+ Y = [0]*NN
+
+ j = 1
+ rank = 0.0
+ t = 0.0
+ sx = 0.0
+
+ while j < NN:
+
+ if XX[j][1] != XX[j-1][1]:
+ X[XX[j-1][0]] = j
+ j = j+1
+
+ else:
+ jt = j+1
+ ji = j
+ for jt in range(j+1, NN):
+ if (XX[jt][1] != XX[j-1][1]):
+ break
+ rank = 0.5*(j+jt)
+ for ji in range(j-1, jt):
+ X[XX[ji][0]] = rank
+ t = jt-j
+ sx = sx + (t*t*t-t)
+ if (jt == NN-1):
+ if (XX[jt][1] == XX[j-1][1]):
+ X[XX[NN-1][0]] = rank
+ j = jt+1
+
+ if j == NN:
+ if X[XX[NN-1][0]] == 0:
+ X[XX[NN-1][0]] = NN
+
+ j = 1
+ rank = 0.0
+ t = 0.0
+ sy = 0.0
+
+ while j < NN:
+
+ if YY[j][1] != YY[j-1][1]:
+ Y[YY[j-1][0]] = j
+ j = j+1
+ else:
+ jt = j+1
+ ji = j
+ for jt in range(j+1, NN):
+ if (YY[jt][1] != YY[j-1][1]):
+ break
+ rank = 0.5*(j+jt)
+ for ji in range(j-1, jt):
+ Y[YY[ji][0]] = rank
+ t = jt - j
+ sy = sy + (t*t*t-t)
+ if (jt == NN-1):
+ if (YY[jt][1] == YY[j-1][1]):
+ Y[YY[NN-1][0]] = rank
+ j = jt+1
+
+ if j == NN:
+ if Y[YY[NN-1][0]] == 0:
+ Y[YY[NN-1][0]] = NN
+
+ D = 0.0
+
+ for i in range(NN):
+ D += (X[i]-Y[i])*(X[i]-Y[i])
+
+ fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN))
+
+ return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN)
+
+
+def calCorrelationRankText(dbdata,userdata,N): ### dcrowell = David Crowell, July 2008
+ """Calculates correlation ranks with data formatted from the text file.
+ dbdata, userdata are lists of strings. N is an int. Returns a float.
+ Used by correlationPage"""
+ XX = []
+ YY = []
+ j = 0
+ for i in range(N):
+ if (dbdata[i]!= None and userdata[i]!=None) and (dbdata[i]!= 'None' and userdata[i]!='None'):
+ XX.append((j,float(dbdata[i])))
+ YY.append((j,float(userdata[i])))
+ j += 1
+ NN = len(XX)
+ if NN <6:
+ return (0.0,NN)
+ XX.sort(cmpOrder2)
+ YY.sort(cmpOrder2)
+ X = [0]*NN
+ Y = [0]*NN
+
+ j = 1
+ rank = 0.0
+ t = 0.0
+ sx = 0.0
+
+ while j < NN:
+
+ if XX[j][1] != XX[j-1][1]:
+ X[XX[j-1][0]] = j
+ j = j+1
+
+ else:
+ jt = j+1
+ ji = j
+ for jt in range(j+1, NN):
+ if (XX[jt][1] != XX[j-1][1]):
+ break
+ rank = 0.5*(j+jt)
+ for ji in range(j-1, jt):
+ X[XX[ji][0]] = rank
+ t = jt-j
+ sx = sx + (t*t*t-t)
+ if (jt == NN-1):
+ if (XX[jt][1] == XX[j-1][1]):
+ X[XX[NN-1][0]] = rank
+ j = jt+1
+
+ if j == NN:
+ if X[XX[NN-1][0]] == 0:
+ X[XX[NN-1][0]] = NN
+
+ j = 1
+ rank = 0.0
+ t = 0.0
+ sy = 0.0
+
+ while j < NN:
+
+ if YY[j][1] != YY[j-1][1]:
+ Y[YY[j-1][0]] = j
+ j = j+1
+ else:
+ jt = j+1
+ ji = j
+ for jt in range(j+1, NN):
+ if (YY[jt][1] != YY[j-1][1]):
+ break
+ rank = 0.5*(j+jt)
+ for ji in range(j-1, jt):
+ Y[YY[ji][0]] = rank
+ t = jt - j
+ sy = sy + (t*t*t-t)
+ if (jt == NN-1):
+ if (YY[jt][1] == YY[j-1][1]):
+ Y[YY[NN-1][0]] = rank
+ j = jt+1
+
+ if j == NN:
+ if Y[YY[NN-1][0]] == 0:
+ Y[YY[NN-1][0]] = NN
+
+ D = 0.0
+
+ for i in range(NN):
+ D += (X[i]-Y[i])*(X[i]-Y[i])
+
+ fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN))
+
+ return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN)
+
+
+
+def calCorrelation(dbdata,userdata,N):
+ X = []
+ Y = []
+ for i in range(N):
+ if dbdata[i]!= None and userdata[i]!= None:
+ X.append(dbdata[i])
+ Y.append(userdata[i])
+ NN = len(X)
+ if NN <6:
+ return (0.0,NN)
+ sx = reduce(lambda x,y:x+y,X,0.0)
+ sy = reduce(lambda x,y:x+y,Y,0.0)
+ meanx = sx/NN
+ meany = sy/NN
+ xyd = 0.0
+ sxd = 0.0
+ syd = 0.0
+ for i in range(NN):
+ xyd += (X[i] - meanx)*(Y[i]-meany)
+ sxd += (X[i] - meanx)*(X[i] - meanx)
+ syd += (Y[i] - meany)*(Y[i] - meany)
+ try:
+ corr = xyd/(sqrt(sxd)*sqrt(syd))
+ except:
+ corr = 0
+ return (corr,NN)
+
+def calCorrelationText(dbdata,userdata,N): ### dcrowell July 2008
+ """Calculates correlation coefficients with values formatted from text files. dbdata, userdata are lists of strings. N is an int. Returns a float
+ Used by correlationPage"""
+ X = []
+ Y = []
+ for i in range(N):
+ #if (dbdata[i]!= None and userdata[i]!= None) and (dbdata[i]!= 'None' and userdata[i]!= 'None'):
+ # X.append(float(dbdata[i]))
+ # Y.append(float(userdata[i]))
+ if dbdata[i] == None or dbdata[i] == 'None' or userdata[i] == None or userdata[i] == 'None':
+ continue
+ else:
+ X.append(float(dbdata[i]))
+ Y.append(float(userdata[i]))
+ NN = len(X)
+ if NN <6:
+ return (0.0,NN)
+ sx = sum(X)
+ sy = sum(Y)
+ meanx = sx/float(NN)
+ meany = sy/float(NN)
+ xyd = 0.0
+ sxd = 0.0
+ syd = 0.0
+ for i in range(NN):
+ x1 = X[i]-meanx
+ y1 = Y[i]-meany
+ xyd += x1*y1
+ sxd += x1**2
+ syd += y1**2
+ try:
+ corr = xyd/(sqrt(sxd)*sqrt(syd))
+ except:
+ corr = 0
+ return (corr,NN)
+
+
+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 cmpCorr(A,B):
+ try:
+ if abs(A[1]) < abs(B[1]):
+ return 1
+ elif abs(A[1]) == abs(B[1]):
+ return 0
+ else:
+ return -1
+ except:
+ return 0
+
+def cmpLitCorr(A,B):
+ try:
+ if abs(A[3]) < abs(B[3]): return 1
+ elif abs(A[3]) == abs(B[3]):
+ if abs(A[1]) < abs(B[1]): return 1
+ elif abs(A[1]) == abs(B[1]): return 0
+ else: return -1
+ else: return -1
+ except:
+ return 0
+
+def cmpPValue(A,B):
+ try:
+ if A.corrPValue < B.corrPValue:
+ return -1
+ elif A.corrPValue == B.corrPValue:
+ if abs(A.corr) > abs(B.corr):
+ return -1
+ elif abs(A.corr) < abs(B.corr):
+ return 1
+ else:
+ return 0
+ else:
+ return 1
+ except:
+ return 0
+
+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 cmpLRSFull(A,B):
+ try:
+ if A[0] < B[0]:
+ return -1
+ elif A[0] == B[0]:
+ return 0
+ else:
+ return 1
+ except:
+ return 0
+
+def cmpLRSInteract(A,B):
+ try:
+ if A[1] < B[1]:
+ return -1
+ elif A[1] == B[1]:
+ return 0
+ else:
+ return 1
+ except:
+ return 0
+
+
+def cmpPos(A,B):
+ try:
+ try:
+ AChr = int(A.chr)
+ except:
+ AChr = 20
+ try:
+ BChr = int(B.chr)
+ except:
+ BChr = 20
+ if AChr > BChr:
+ return 1
+ elif AChr == BChr:
+ if A.mb > B.mb:
+ return 1
+ if A.mb == B.mb:
+ return 0
+ else:
+ return -1
+ else:
+ return -1
+ except:
+ return 0
+
+def cmpGenoPos(A,B):
+ try:
+ A1 = A.chr
+ B1 = B.chr
+ try:
+ A1 = int(A1)
+ except:
+ A1 = 25
+ try:
+ B1 = int(B1)
+ except:
+ B1 = 25
+ if A1 > B1:
+ return 1
+ elif A1 == B1:
+ if A.mb > B.mb:
+ return 1
+ if A.mb == B.mb:
+ return 0
+ else:
+ return -1
+ else:
+ return -1
+ except:
+ return 0
+
+#XZhou: Must use "BINARY" to enable case sensitive comparison.
+def authUser(name,password,db, encrypt=None):
+ try:
+ if encrypt:
+ query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY \'%s\'' % (name,password)
+ else:
+ query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY SHA(\'%s\')' % (name,password)
+ db.execute(query)
+ records = db.fetchone()
+ if not records:
+ raise ValueError
+ return records#(privilege,id,name,password,grpName)
+ except:
+ return (None, None, None, None, None)
+
+
+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=map(string.strip, string.split(authorized_users, ','))
+ if AuthorizedUsersList.__contains__(userName):
+ access_to_confidential_phenotype_trait = 1
+ return access_to_confidential_phenotype_trait
+
+
+class VisualizeException(Exception):
+ def __init__(self, message):
+ self.message = message
+ def __str__(self):
+ return self.message
+
+# safeConvert : (string -> A) -> A -> A
+# to convert a string to type A, using the supplied default value
+# if the given conversion function doesn't work
+def safeConvert(f, value, default):
+ try:
+ return f(value)
+ except:
+ return default
+
+# safeFloat : string -> float -> float
+# to convert a string to a float safely
+def safeFloat(value, default):
+ return safeConvert(float, value, default)
+
+# safeInt: string -> int -> int
+# to convert a string to an int safely
+def safeInt(value, default):
+ return safeConvert(int, value, default)
+
+# safeString : string -> (arrayof string) -> string -> string
+# if a string is not in a list of strings to pick a default value
+# for that string
+def safeString(value, validChoices, default):
+ if value in validChoices:
+ return value
+ else:
+ return default
+
+# yesNoToInt: string -> int
+# map "yes" -> 1 and "no" -> 0
+def yesNoToInt(value):
+ if value == "yes":
+ return 1
+ elif value == "no":
+ return 0
+ else:
+ return None
+
+# IntToYesNo: int -> string
+# map 1 -> "yes" and 0 -> "no"
+def intToYesNo(value):
+ if value == 1:
+ return "yes"
+ elif value == 0:
+ return "no"
+ else:
+ return None
+
+def formatField(name):
+ name = name.replace("_", " ")
+ name = name.title()
+ #name = name.replace("Mb Mm6", "Mb");
+ return name.replace("Id", "ID")
+
+#XZ, 03/27/2009: This function is very specific.
+#It is used by AJAX_table.py, correlationPage.py and dataPage.py
+
+
+def genTableObj(tblobj=None, file="", sortby = ("", ""), tableID = "sortable", addIndex = "1", hiddenColumns=[]):
+ header = tblobj['header']
+ body = tblobj['body']
+ field, order = sortby
+
+ #ZAS 9/12/2011 - The hiddenColumns array needs to be converted into a string so they can be placed into the javascript of each up/down button
+ hiddenColumnsString = ",".join(hiddenColumns)
+
+ tbl = HT.TableLite(Class="collap b2", cellspacing=1, cellpadding=5)
+
+ hiddenColumnIdx = [] #indices of columns to hide
+ idx = -1
+ last_idx = 0 #ZS: This is the index of the last item in the regular table header (without any extra parameters). It is used to determine the index of each extra parameter.
+ for row in header:
+ hr = HT.TR()
+ for i, item in enumerate(row):
+ if (item.text == '') or (item.text not in hiddenColumns):
+ if item.sort and item.text:
+ down = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=down&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGDESC)
+ up = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=up&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGASC)
+ if item.text == field:
+ idx = item.idx
+ last_idx = idx
+ if order == 'up':
+ up = IMGASCON
+ elif order == 'down':
+ down = IMGDESCON
+ item.html.append(HT.Div(up, down, style="float: bottom;"))
+ hr.append(item.html)
+ else:
+ hiddenColumnIdx.append(i)
+ tbl.append(hr)
+
+ for i, row in enumerate(body):
+ for j, item in enumerate(row):
+ if order == 'down':
+ if (item.val == '' or item.val == 'x' or item.val == 'None'):
+ item.val = 0
+ if order == 'up':
+ if (item.val == '' or item.val == 'x' or item.val == 'None'):
+ item.val = 'zzzzz'
+
+ if idx >= 0:
+ if order == 'down':
+ body.sort(lambda A, B: cmp(B[idx].val, A[idx].val), key=natsort_key)
+ elif order == 'up':
+ body.sort(lambda A, B: cmp(A[idx].val, B[idx].val), key=natsort_key)
+ else:
+ pass
+
+ for i, row in enumerate(body):
+ hr = HT.TR(Id = row[0].text)
+ for j, item in enumerate(row):
+ if (j not in hiddenColumnIdx):
+ if j == 0:
+ if addIndex == "1":
+ item.html.contents = [i+1] + item.html.contents
+ hr.append(item.html)
+ tbl.append(hr)
+
+ return tbl
+
+def natsort_key(string):
+ r = []
+ for c in string:
+ try:
+ c = int(c)
+ try: r[-1] = r[-1] * 10 + c
+ except: r.append(c)
+ except:
+ r.append(c)
+ return r
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 00:02:31 +0000