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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
from mod_python import Cookie
import string
import os
import reaper
import webqtlConfig
import cookieData
import sessionData
from cgiData import cgiData
from webqtlCaseData import webqtlCaseData
from utility import webqtlUtil
class webqtlFormData:
'Represents data from a WebQTL form page, needed to generate the next page'
attrs = ('formID','RISet','genotype','strainlist','allstrainlist',
'suggestive','significance','submitID','identification', 'enablevariance',
'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo')
#XZ: Attention! All attribute values must be picklable!
def __init__(self, req = None, mod_python_session=None, FieldStorage_formdata=None):
for item in self.attrs:
setattr(self,item, None)
try:
self.remote_ip = req.connection.remote_ip
except:
self.remote_ip = '1.2.3.4'
if req and req.headers_in.has_key('referer'):
self.refURL = req.headers_in['referer']
else:
self.refURL = None
self.cookies = cookieData.cookieData(Cookie.get_cookies(req)) #XZ: dictionary type. To hold values transfered from mod_python Cookie.
#XZ: dictionary type. To hold values transfered from mod_python Session object. We assume that it is always picklable.
self.input_session_data = sessionData.sessionData( mod_python_session )
#XZ: FieldStorage_formdata may contain item that can't be pickled. Must convert to picklable data.
self.formdata = cgiData( FieldStorage_formdata )
#get Form ID
self.formID = self.formdata.getfirst('FormID')
#get rest of the attributes
if self.formID:
for item in self.attrs:
value = self.formdata.getfirst(item)
if value != None:
setattr(self,item,string.strip(value))
self.ppolar = ""
self.mpolar = ""
if self.RISet:
try:
# NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
f1, f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.RISet]
except:
f1 = f12 = self.mpolar = self.ppolar = None
try:
self.nperm = int(self.nperm)
self.nboot = int(self.nboot)
except:
self.nperm = 2000 #XZ: Rob asked to change the default value to 2000
self.nboot = 2000 #XZ: Rob asked to change the default value to 2000
if self.allstrainlist:
self.allstrainlist = map(string.strip, string.split(self.allstrainlist))
#self.readGenotype()
#self.readData()
if self.RISet == 'BXD300':
self.RISet = 'BXD'
else:
pass
def __str__(self):
rstr = ''
for item in self.attrs:
if item != 'genotype':
rstr += '%s:%s\n' % (item,str(getattr(self,item)))
return rstr
def readGenotype(self):
'read genotype from .geno file'
if self.RISet == 'BXD300':
self.RISet = 'BXD'
else:
pass
assert self.RISet
#genotype_1 is Dataset Object without parents and f1
#genotype_2 is Dataset Object with parents and f1 (not for intercross)
self.genotype_1 = reaper.Dataset()
self.genotype_1.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno'))
try:
# NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
_f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet]
except:
_f1 = _f12 = _mat = _pat = None
self.genotype_2 =self.genotype_1
if self.genotype_1.type == "riset" and _mat and _pat:
self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1)
#determine default genotype object
if self.incparentsf1 and self.genotype_1.type != "intercross":
self.genotype = self.genotype_2
else:
self.incparentsf1 = 0
self.genotype = self.genotype_1
self.strainlist = list(self.genotype.prgy)
self.f1list = self.parlist = []
if _f1 and _f12:
self.f1list = [_f1, _f12]
if _mat and _pat:
self.parlist = [_mat, _pat]
def readData(self, strainlst=[], incf1=[]):
'read user input data or from trait data and analysis form'
if not self.genotype:
self.readGenotype()
if not strainlst:
if incf1:
strainlst = self.f1list + self.strainlist
else:
strainlst = self.strainlist
traitfiledata = self.formdata.getfirst('traitfile')
traitpastedata = self.formdata.getfirst('traitpaste')
variancefiledata = self.formdata.getfirst('variancefile')
variancepastedata = self.formdata.getfirst('variancepaste')
Nfiledata = self.formdata.getfirst('Nfile')
if traitfiledata:
tt = string.split(traitfiledata)
vals = map(webqtlUtil.StringAsFloat, tt)
elif traitpastedata:
tt = string.split(traitpastedata)
vals = map(webqtlUtil.StringAsFloat, tt)
else:
vals = map(self.FormDataAsFloat, strainlst)
if len(vals) < len(strainlst):
vals += [None]*(len(strainlst) - len(vals))
elif len(vals) > len(strainlst):
vals = vals[:len(strainlst)]
else:
pass
if variancefiledata:
tt = string.split(variancefiledata)
vars = map(webqtlUtil.StringAsFloat, tt)
elif variancepastedata:
tt = string.split(variancepastedata)
vars = map(webqtlUtil.StringAsFloat, tt)
else:
vars = map(self.FormVarianceAsFloat, strainlst)
if len(vars) < len(strainlst):
vars += [None]*(len(strainlst) - len(vars))
elif len(vars) > len(strainlst):
vars = vars[:len(strainlst)]
else:
pass
if Nfiledata:
tt = string.split(Nfiledata)
nstrains = map(webqtlUtil.IntAsFloat, tt)
if len(nstrains) < len(strainlst):
nstrains += [None]*(len(strainlst) - len(nstrains))
else:
nstrains = map(self.FormNAsFloat, strainlst)
##vals, vars, nstrains is obsolete
self.allTraitData = {}
for i, _strain in enumerate(strainlst):
if vals[i] != None:
self.allTraitData[_strain] = webqtlCaseData(vals[i], vars[i], nstrains[i])
def informativeStrains(self, strainlst=[], incVars = 0):
'''if readData was called, use this to output the informative strains
(strain with values)'''
if not strainlst:
strainlst = self.strainlist
strains = []
vals = []
vars = []
for _strain in strainlst:
if self.allTraitData.has_key(_strain):
_val, _var = self.allTraitData[_strain].val, self.allTraitData[_strain].var
if _val != None:
if incVars:
if _var != None:
strains.append(_strain)
vals.append(_val)
vars.append(_var)
else:
strains.append(_strain)
vals.append(_val)
vars.append(None)
return strains, vals, vars, len(strains)
def FormDataAsFloat(self, key):
try:
return float(self.formdata.getfirst(key))
except:
return None
def FormVarianceAsFloat(self, key):
try:
return float(self.formdata.getfirst('V' + key))
except:
return None
def FormNAsFloat(self, key):
try:
return int(self.formdata.getfirst('N' + key))
except:
return None
def Sample(self):
'Create some dummy data for testing'
self.RISet = 'BXD'
self.incparentsf1 = 'on'
#self.display = 9.2
#self.significance = 16.1
self.readGenotype()
self.identification = 'BXD : Coat color example by Lu Lu, et al'
#self.readGenotype()
#self.genotype.ReadMM('AXBXAforQTL')
#self.strainlist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy)
#self.strainlist.sort()
self.allTraitData = {'BXD29': webqtlCaseData(3), 'BXD28': webqtlCaseData(2),
'BXD25': webqtlCaseData(2), 'BXD24': webqtlCaseData(2), 'BXD27': webqtlCaseData(2),
'BXD21': webqtlCaseData(1), 'BXD20': webqtlCaseData(4), 'BXD23': webqtlCaseData(4),
'BXD22': webqtlCaseData(3), 'BXD14': webqtlCaseData(4), 'BXD15': webqtlCaseData(2),
'BXD16': webqtlCaseData(3), 'BXD11': webqtlCaseData(4), 'BXD12': webqtlCaseData(3),
'BXD13': webqtlCaseData(2), 'BXD18': webqtlCaseData(3), 'BXD19': webqtlCaseData(3),
'BXD38': webqtlCaseData(3), 'BXD39': webqtlCaseData(3), 'BXD36': webqtlCaseData(2),
'BXD34': webqtlCaseData(4), 'BXD35': webqtlCaseData(4), 'BXD32': webqtlCaseData(4),
'BXD33': webqtlCaseData(3), 'BXD30': webqtlCaseData(1), 'BXD31': webqtlCaseData(4),
'DBA/2J': webqtlCaseData(1), 'BXD8': webqtlCaseData(3), 'BXD9': webqtlCaseData(1),
'BXD6': webqtlCaseData(3), 'BXD5': webqtlCaseData(3), 'BXD2': webqtlCaseData(4),
'BXD1': webqtlCaseData(1), 'C57BL/6J': webqtlCaseData(4), 'B6D2F1': webqtlCaseData(4),
'BXD42': webqtlCaseData(4), 'BXD40': webqtlCaseData(3)}
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