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

1 files changed, 0 insertions, 225 deletions

diff --git a/web/webqtl/collection/BatchSubmitSelectionPage.py b/web/webqtl/collection/BatchSubmitSelectionPage.py
deleted file mode 100755
index 743606b2..00000000
--- a/web/webqtl/collection/BatchSubmitSelectionPage.py
+++ /dev/null
@@ -1,225 +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
-
-#BatchSubmitSelectionPage.py
-
-import string
-import time
-
-from base import webqtlConfig
-from base.templatePage import templatePage
-from utility import webqtlUtil
-from AddToSelectionPage import AddToSelectionPage
-	
-
-#########################################
-#     batch submission result Page
-#########################################
-class BatchSubmitSelectionPage(AddToSelectionPage):
-
-	def __init__(self, fd):
-
-		templatePage.__init__(self, fd)
-
-		if not self.openMysql():
-			return
-		if not fd.genotype:
-			fd.readGenotype()
-		
-		heading = 'Batch Submission'
-		
-		self.batchDataFile = fd.formdata.getvalue('batchdatafile')
-		if not self.batchDataFile:
-			templatePage.__init__(self, fd)
-			detail = ['The file you choose to import from doesn\'t exist.']
-			self.error(heading=heading,detail=detail)
-			return
-		self.batchDataFile = string.replace(self.batchDataFile, '\r', '\n')
-		self.batchDataFile = string.replace(self.batchDataFile, '\n\n', '\n')
-		self.batchDataFile = string.split(self.batchDataFile, '\n')
-		self.batchDataFile = map(string.strip, self.batchDataFile)
-		
-		traitNames, strainNames, traitValues, SE, NStrain = self.parseDataFile()
-		strainIds = []
-		
-		#print 'Content-type: text/html\n'
-		#print len(traitNames), len(strainNames) , len(strainIds), len(traitValues) , len(SE), "<BR><BR>", len(NStrain)
-		#return
-		
-		try:
-			
-			if not traitNames or not strainNames or not traitValues or len(traitNames) != len(traitValues) or len(traitNames) != len(SE) or len(traitNames) != len(NStrain):
-				raise 'ValueError'
-			for item in traitValues:
-				if len(strainNames) != len(item):
-					raise 'ValueError'
-			for item in SE:
-				if len(strainNames) != len(item):
-					raise 'ValueError'
-			for item in NStrain:
-				if len(strainNames) != len(item):
-					raise 'ValueError'
-			for item in strainNames:
- 				self.cursor.execute('''Select 
- 								Strain.Id 
- 							from Strain, StrainXRef,InbredSet 
- 							where 
- 								Strain.Name = "%s" AND
- 								StrainXRef.StrainId = Strain.Id AND
- 								StrainXRef.InbredSetId = InbredSet.Id AND
- 								InbredSet.Name = "%s"
- 							''' % (item, fd.RISet))
- 				strainId = self.cursor.fetchone()[0]
- 				strainIds.append(strainId)
- 		except:
-			templatePage.__init__(self, fd)
-			detail = ['The format of the file is incorrect, or it contains unknown strains.']
-			self.error(heading=heading,detail=detail)
-			return
-		
-		self.searchResult = []	
-		self.addToTable(traitNames, strainNames,strainIds, traitValues,SE, NStrain, fd)
-		
-		if self.genSelection(fd=fd):
-			self.writeHTML(fd)
-	
-	def parseDataFile(self):
-		rchSartPos = 0
-		header = []
-		traits = []
-		data = []
-		se = []
-		nstrain = []
-		strains = []
-		
-		if 1:
-			for line in  self.batchDataFile:
-				line = line.strip()
-				if line == '' or line[0] == '#':
-					continue
-					
-				columns = string.split(line, '\t')
-				columns = map(string.strip, columns)
-				
-				if rchSartPos == 'column':
-					strains.append(columns[0])
-					tdata = map(webqtlUtil.StringAsFloat,columns[1:])
-					for j, item in enumerate(tdata):
-						if  posIdx[j][0] == 'data':
-							data[posIdx[j][1]].append(item)
-						elif  posIdx[j][0] == 'n':
-							if item != None:
-								nstrain[posIdx[j][1]].append(int(item))
-							else:
-								nstrain[posIdx[j][1]].append(item)
-						else:
-							se[posIdx[j][1]].append(item)
-							
-				elif rchSartPos == 'row':
-					if columns[0].lower() == 'se':
-						se.append(map(webqtlUtil.StringAsFloat,columns[1:]))
-					elif columns[0].lower() == 'n':
-						nstrain.append(map(webqtlUtil.IntAsFloat,columns[1:]))
-					else:
-						while (len(data) > len(se)):
-							se.append([None] * len(data[-1]))
-						while (len(data) > len(nstrain)):
-							nstrain.append([None] * len(data[-1]))
-						header.append(columns[0])
-						data.append(map(webqtlUtil.StringAsFloat,columns[1:]))
- 				elif columns[0] == '@format=column':
-					rchSartPos = 'column'
-					posIdx = []
-					j = 0
-					for item in columns[1:]:
-						#assign column type
-						if string.lower(item) == 'se':
-							posIdx.append(('se',j-1))
-						elif string.lower(item) == 'n':
-							posIdx.append(('n',j-1))
-						else:
-							header.append(item)
-							posIdx.append(('data',j))
-							j += 1
-					
-					for i in range(len(header)):
-						data.append([])
-						se.append([])
-						nstrain.append([])
- 				elif columns[0] == '@format=row':
-					rchSartPos = 'row'
-					strains = columns[1:]
-				else:
-					pass
-			#modify
-			for i in range(len(se)):
-				if se[i] == []:
-					se[i] = [None] * len(data[-1])
-			for i in range(len(nstrain)):
-				if nstrain[i] == []:
-					nstrain[i] = [None] * len(data[-1])
-			if len(data) > len(se):
-				se.append([None] * len(data[-1]))
-			if len(data) > len(nstrain):
-				nstrain.append([None] * len(data[-1]))
-			
-			return header,strains,data,se, nstrain
-		else:
-			return [],[],[],[], []
-
-
-	#XZ, add items to self.searchResult	
-	def addToTable(self, traitNames, strainNames,strainIds, traitValues, SE, NStrain, fd):
-		self.cursor.execute('delete Temp, TempData from Temp, TempData where Temp.DataId = TempData.Id and UNIX_TIMESTAMP()-UNIX_TIMESTAMP(CreateTime)>%d;' % webqtlConfig.MAXLIFE)
-		
-		i = 0
-		for trait in traitNames:
-			ct0 = time.localtime(time.time())
-			ct = time.strftime("%B/%d %H:%M:%S",ct0)
-			if trait == '':
-				trait = "Unnamed Trait"
-			user_ip = fd.remote_ip
-			newDescription = '%s entered at %s from IP %s' % (trait,ct,user_ip)
-			newProbeSetID = webqtlUtil.genRandStr('Usr_TMP_')
-			
-			self.cursor.execute('SelecT max(id) from TempData')
-			try:
-				DataId = self.cursor.fetchall()[0][0] + 1
-			except:
-				DataId = 1
-			
-			self.cursor.execute('Select Id  from InbredSet where Name = "%s"' % fd.RISet)
-			InbredSetId = self.cursor.fetchall()[0][0]
-					
-			self.cursor.execute('insert into Temp(Name,description, createtime,DataId,InbredSetId,IP) values(%s,%s,Now(),%s,%s,%s)' ,(newProbeSetID, newDescription, DataId,InbredSetId,user_ip))
-			
-			for k in range(len(traitValues[i])):
-				if traitValues[i][k] != None:
-					self.cursor.execute('insert into TempData(Id, StrainId, value, SE, NStrain) values(%s, %s, %s, %s, %s)' , (DataId, strainIds[k], traitValues[i][k],SE[i][k],NStrain[i][k]))
-			
-			self.searchResult.append('Temp::%s'	% newProbeSetID)
-			i += 1
-