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diff --git a/web/webqtl/base/webqtlFormData.py b/web/webqtl/base/webqtlFormData.py
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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 2024-10-21 06:31:37 +0000