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

1 files changed, 0 insertions, 309 deletions

diff --git a/web/webqtl/genomeGraph/genAllDbResultPage.py b/web/webqtl/genomeGraph/genAllDbResultPage.py
deleted file mode 100755
index f0663a7c..00000000
--- a/web/webqtl/genomeGraph/genAllDbResultPage.py
+++ /dev/null
@@ -1,309 +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
-
-import string
-import os
-import time
-
-from htmlgen import HTMLgen2 as HT
-
-from base import webqtlConfig
-from utility import webqtlUtil
-from base.webqtlDataset import webqtlDataset
-from base.templatePage import templatePage
-			
-
-######################################### 
-#      Genome Scan PAGE
-#########################################
-class genAllDbResultPage(templatePage):
-
-	def __init__(self,fd):
-
-		templatePage.__init__(self,fd)
-
-		if not self.openMysql():
-			return
-
-		self.database = fd.formdata.getvalue('database', '')
-		db = webqtlDataset(self.database, self.cursor)
-
-		try:
-			if db.type != "ProbeSet" or not db.id:
-				raise DbNameError
-		except:
-			print 'Content-type: text/html\n'
-			heading = "Download Results"
-			detail = ["Only results of microarray database are available to download."]
-			self.error(heading=heading,detail=detail)
-			self.write()
-			return
-
-
-                #XZ, protect confidential dataset.
-		userExist = None
-                self.cursor.execute('SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM ProbeSetFreeze WHERE Name = "%s"' %  self.database)
-                indId, indName, indFullName, indConfid, AuthorisedUsers = self.cursor.fetchall()[0]
-                if indConfid == 1 and userExist == None:
-                    try:
-
-                        userExist = self.userName
-
-                        #for the dataset that confidentiality is 1
-                        #1. 'admin' and 'root' can see all of the dataset
-                        #2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
-                        if webqtlConfig.USERDICT[self.privilege] < webqtlConfig.USERDICT['admin']:
-                            if not AuthorisedUsers:
-                                userExist=None
-                            else:
-                                AuthorisedUsersList=AuthorisedUsers.split(',')
-                                if not AuthorisedUsersList.__contains__(self.userName):
-                                    userExist=None
-                    except:
-                        pass
-
-                    if not userExist:
-                        #Error, Confidential Database
-                        heading = "Correlation Table"
-                        detail = ["The %s database you selected is not open to the public at this time, please go back and select other database." % indFullName]
-                        self.error(heading=heading,detail=detail,error="Confidential Database")
-                        return
-	
-		self.cursor.execute("""
-				Select 
-					InbredSet.Name
-				From
-					ProbeSetFreeze, ProbeFreeze, InbredSet
-				whERE
-					ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
-					ProbeFreeze.InbredSetId = InbredSet.Id AND
-					ProbeSetFreeze.Id = %d
-				""" % db.id)
-		thisRISet = self.cursor.fetchone()[0]
-		if thisRISet =='BXD300':
-			thisRISet = 'BXD'
-
-		#XZ, 06/26/2009: It seems that this query is not neccessary. It doesn't return any result.
-		#XZ: It seems it is just for test purpose. The next try-except block does the real work.
-		#XZ: I think it should be deleted to shorten the response time.	
-		#self.cursor.execute("""
-		#		Select 
-		#			ProbeSet.Name, ProbeSet.symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSetXRef.Locus, 
-		#			ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive, ProbeSetXRef.mean
-		#		From
-		#			ProbeSet, ProbeSetXRef
-		#		whERE
-		#			ProbeSetXRef.ProbeSetFreezeId = %d AND
-		#			ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-		#			ProbeSetXRef.Locus is not NULL 
-		#		Order by
-		#			ProbeSet.name_num
-		#		""" % db.id)
-		
-		filename = os.path.join(webqtlConfig.SECUREDIR, db.name+'.result.xls')
-
-		try:
-			import random234
-			if random.choice(range(10)) == 0:
-				raise "ReCalculate"
-			fp = open(filename, 'rb')
-			text = fp.read()
-			fp.close()
-		except:
-			self.cursor.execute("Select ProbeSetXRef.ProbeSetId from ProbeSetXRef where ProbeSetFreezeId=%d" % db.id)
-			ProbeSetIds = self.cursor.fetchall()
-			self.mouseChrLengthDict, sum = self.readMouseGenome(thisRISet)
-
-			if ProbeSetIds:
-				import reaper
-				markerGMb = {}
-				genotype_1 = reaper.Dataset()
-				genotype_1.read(os.path.join(webqtlConfig.GENODIR, thisRISet + '.geno'))
-				for chr in genotype_1:
-					chrlen = self.mouseChrLengthDict[chr.name]
-					for locus in chr:	
-						markerGMb[locus.name] = [chr.name, locus.Mb, locus.Mb + chrlen]
-				
-				text = []
-				text.append(['ProbeSetId', 'Symbol', 'Description', 'Target Description', 'Chr', 'TMb', 'TGMb', 'Locus', 'LRS', 'Additive', 'pvalue', 'markerChr', 'markerMb', 'markerGMb', 'meanExpression'])
-				ProbeSetIdList = []
-				for ProbeSetId in ProbeSetIds:
-					ProbeSetIdList.append(ProbeSetId[0])
-					if len(ProbeSetIdList)==1000:
-						ProbeSetIdStr = ','.join(map(str, ProbeSetIdList))
-						ProbeSetIdList = []
-
-						cmd = """
-							Select 
-								ProbeSet.Name, ProbeSet.symbol, ProbeSet.description,ProbeSet.Probe_Target_Description,ProbeSet.Chr, ProbeSet.Mb, 
-								ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, 
-								ProbeSetXRef.additive, ProbeSetXRef.mean
-							From
-								ProbeSet, ProbeSetXRef
-							Where
-								ProbeSetXRef.ProbeSetFreezeId = %s AND
-								ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-								ProbeSetXRef.Locus is not NULL AND
-								ProbeSet.Id in (%s)
-							Order by
-								ProbeSet.name_num
-						""" % (db.id, ProbeSetIdStr)
-
-						self.cursor.execute(cmd)
-						results = self.cursor.fetchall()
-
-						for result in results:
-							_Id, _symbol, _desc,_targetDesc, _chr, _TMb, _marker, _lrs, _pvalue, _additive, _mean = result
-							if _marker == "-":
-								continue
-							if not _additive:
-								_additive = ""
-						
-							try:
-								_TGMb = _TMb + self.mouseChrLengthDict[string.strip(_chr)]
-							except:
-								_TGMb = ""
-
-							result2 = [_Id, _symbol, _desc, _targetDesc, _chr, _TMb, _TGMb, _marker, _lrs, _additive, _pvalue]
-							try:
-								result2 += markerGMb[_marker]
-							except:
-								result2 += ['', '', '']
-							result2 += [_mean]
-							text.append(map(str, result2))
-
-				#XZ, 06/29/2007: This block is dealing with the last several probesets that fall out of the 1000-probeset block. 
-				if ProbeSetIdList:
-					ProbeSetIdStr = ','.join(map(str, ProbeSetIdList))
-
-					cmd = """
-						Select 
-							ProbeSet.Name, ProbeSet.symbol, ProbeSet.description,ProbeSet.Probe_Target_Description, ProbeSet.Chr, ProbeSet.Mb, 
-							ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, 
-							ProbeSetXRef.additive, ProbeSetXRef.mean
-						From
-							ProbeSet, ProbeSetXRef
-						Where
-							ProbeSetXRef.ProbeSetFreezeId = %s AND
-							ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-							ProbeSetXRef.Locus is not NULL AND
-							ProbeSet.Id in (%s)
-						Order by
-							ProbeSet.name_num
-					""" % (db.id, ProbeSetIdStr)
-
-					self.cursor.execute(cmd)
-					results = self.cursor.fetchall()
-
-					for result in results:
-						_Id, _symbol, _desc, _targetDesc,_chr, _TMb, _marker, _lrs, _pvalue, _additive, _mean = result
-						if _marker == "-":
-							continue
-						if not _additive:
-							_additive = ""
-					
-						try:
-							_TGMb = _TMb + self.mouseChrLengthDict[string.strip(_chr)]
-						except:
-							_TGMb = ""
-
-						result2 = [_Id, _symbol, _desc,_targetDesc,  _chr, _TMb, _TGMb, _marker, _lrs, _additive, _pvalue]
-						try:
-							result2 += markerGMb[_marker]
-						except:
-							result2 += ['', '', '']
-						result2 += [_mean]
-						text.append(map(str, result2))
-
-				
-				import pyXLWriter as xl
-				# Create a new Excel workbook
-				workbook = xl.Writer(filename)
-				worksheet = workbook.add_worksheet()
-				heading = workbook.add_format(align = 'center', bold = 1, size=13, color = 'red')
-				titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray")
-
-				worksheet.write([0, 0], "Data source: The GeneNetwork at http://www.genenetwork.org", titleStyle)
-				worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
-				worksheet.write([2, 0], "Database : %s" % db.fullname, titleStyle)
-				worksheet.write([3, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle)
-				worksheet.write([4, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle)
-				worksheet.write([5, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle)
-
-				table_row_start_index = 7
-				nrow = table_row_start_index
-				for row in text:
-				    for ncol, cell in enumerate(row):
-				    	if nrow == table_row_start_index:
-				        	worksheet.write([nrow, ncol], cell.strip(), heading)
-				        	worksheet.set_column([ncol, ncol], 20)
-				    	else:
-				        	worksheet.write([nrow, ncol], cell.strip())
-				    nrow += 1
-
-				worksheet.write([1+nrow, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)", titleStyle)
-				worksheet.write([2+nrow, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle)
-
-				workbook.close()
-								
-				fp = open(filename, 'rb')
-				text = fp.read()
-				fp.close()
-			else:
-				heading = "Download Results"
-				detail = ["Database calculation is not finished."]
-				self.error(heading=heading,detail=detail)
-				return
-				
-		self.content_type = 'application/xls'
-		self.content_disposition = 'attachment; filename=%s' % ('export-%s.xls' % time.strftime("%y-%m-%d-%H-%M"))
-		self.attachment = text
-			
-	def readMouseGenome(self, RISet):
-		ldict = {}
-		lengths = []
-		sum = 0
-		#####################################
-		# Retrieve Chr Length Information
-		#####################################
-		self.cursor.execute("""
-			Select 
-				Chr_Length.Name, Length from Chr_Length, InbredSet 
-			where 
-				Chr_Length.SpeciesId = InbredSet.SpeciesId AND
-				InbredSet.Name = '%s'
-			Order by 
-				OrderId
-			""" % RISet)
-		lengths = self.cursor.fetchall()
-		ldict[lengths[0][0]] = 0
-		prev = lengths[0][1]/1000000.0
-		sum += lengths[0][1]/1000000.0
-		for item in lengths[1:]:
-			ldict[item[0]] = prev
-			prev += item[1]/1000000.0
-			sum += item[1]/1000000.0
-		return ldict, sum