Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 289 deletions

diff --git a/web/webqtl/base/webqtlFormData.py b/web/webqtl/base/webqtlFormData.py
deleted file mode 100755
index 84e41cae..00000000
--- a/web/webqtl/base/webqtlFormData.py
+++ /dev/null
@@ -1,289 +0,0 @@
-# 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)}
-