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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)}
+
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 16:22:25 +0000