Add all the source codes into the github.

1 files changed, 289 insertions, 0 deletions

diff --git a/web/webqtl/base/webqtlFormData.py b/web/webqtl/base/webqtlFormData.py
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+++ b/web/webqtl/base/webqtlFormData.py
@@ -0,0 +1,289 @@
+# 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)}
+