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

5 files changed, 0 insertions, 976 deletions

diff --git a/web/webqtl/maintainance/__init__.py b/web/webqtl/maintainance/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/web/webqtl/maintainance/__init__.py
+++ /dev/null
diff --git a/web/webqtl/maintainance/addRif.py b/web/webqtl/maintainance/addRif.py
deleted file mode 100755
index c7cdde7a..00000000
--- a/web/webqtl/maintainance/addRif.py
+++ /dev/null
@@ -1,107 +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 Lei Yan 2011/02/08
-
-# created by Lei Yan 02/08/2011
-
-import string
-import MySQLdb
-import time
-import os
-import sys
-
-path1 = os.path.abspath(os.path.dirname(__file__))
-path2 = path1 + "/.."
-path3 = path1 + "/../../tmp"
-sys.path.insert(0, path2)
-from base import webqtlConfig
-
-try:
-        con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
-        cursor = con.cursor()
-        print "You have successfully connected to mysql.\n"
-except:
-        print "You entered incorrect password.\n"
-        sys.exit(0)
-
-taxIds = {'10090':1, '9606':4, '10116':2, '3702':3}
-taxIdKeys = taxIds.keys()
-
-os.chdir(path3)
-cdict = {}
-
-os.system("rm -f gene_info")
-os.system("wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz")
-os.system("gunzip gene_info.gz")
-try:
-	fp = open("gene_info")
-except:
-	print "gene_info doesn't exit"
-	sys.exit(1)
-
-i=0
-line = fp.readline()
-while line:
-	line2 = map(string.strip, string.split(line.strip(), "\t"))
-	if line2[0] in taxIdKeys:
-		cdict[line2[1]] = line2[2]
-	line = fp.readline()
-	i += 1
-	if i%1000 == 0:
-		print "finished ",  i
-fp.close()
-
-os.system("rm -f generifs_basic")
-os.system("wget ftp://ftp.ncbi.nlm.nih.gov/gene/GeneRIF/generifs_basic.gz")
-os.system("gunzip generifs_basic.gz")
-try:
-	fp = open("generifs_basic")
-except:
-	print "generifs_basic doesn't exist"
-	sys.exit(1)
-
-cursor.execute("delete from GeneRIF_BASIC")
-count = 0
-line = fp.readline()
-while line:
-	line2 = map(string.strip, string.split(line.strip(), "\t"))
-	if line2[0] in taxIdKeys:
-		count += 1
-		line2[0] = taxIds[line2[0]]
-		if len(line2) !=5:
-			print line
-		else:
-			try:
-				symbol=cdict[line2[1]]
-			except:
-				symbol= ""
-			
-			line2 = line2[:2] + [symbol] + line2[2:]
-			cursor.execute("insert into GeneRIF_BASIC(SpeciesId, GeneId, Symbol, PubMed_ID, createtime, comment) values(%s, %s, %s, %s, %s, %s)", tuple(line2))
-	line = fp.readline()
-
-fp.close()
-print count, "\n"
-cursor.close()
diff --git a/web/webqtl/maintainance/checkInfoFile.py b/web/webqtl/maintainance/checkInfoFile.py
deleted file mode 100755
index 6aa0d771..00000000
--- a/web/webqtl/maintainance/checkInfoFile.py
+++ /dev/null
@@ -1,102 +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 NL 2011/01/28
-
-# created by Ning Liu 2011/01/27
-# This script is to check whether dataset related Info file exist or not; if not, the tempate Info file will be generated
-# This script should be only run at GeneNetwork production server
-
-import sys, os
-import MySQLdb
-
-current_file_name = __file__
-pathname = os.path.dirname( current_file_name )
-abs_path = os.path.abspath(pathname)
-sys.path.insert(0, abs_path + '/..')
-
-from base import template
-from base import webqtlConfig
-from base import header
-from base import footer
-
-# build MySql database connection
-con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
-cursor = con.cursor()
-
-InfoFilePath =webqtlConfig.HTMLPATH+'dbdoc/'
-		
-# create template for Info file
-def createTemplateForInfoFile(datasetId=None,datasetFullName=None,InfoFileURL=None):
-	#template.py has been changed with dynamic header and footer
-	userInfo=""
-	headerInfo=header.header_string % userInfo
-	serverInfo=""
-	footerInfo=footer.footer_string % serverInfo
-	
-	title =datasetFullName
-	contentTitle = '''
-	<P class="title">%s<A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A><BR><BR>
-	''' % datasetFullName	
-	content ='''
-	Accession number: <A HREF="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=%s">GN%s</A></P>
-	<br><br>
-	This page will be updated soon. 
-	<br><br>
-	''' % (datasetId,datasetId)	
-	
-	body=contentTitle+content
-	# Note: 'templateParameters' includes parameters required for template.py
-	# templateParameters = ['title','basehref','js1','js2','layer','header','body', 'footer']
-	templateParameters =[title,'','','','',headerInfo,body,footerInfo]
-	
-	# build template file
-	templateFile=template.template % tuple(templateParameters)		
-	InfoFileHandler = open(InfoFileURL, 'w')
-	# write template file into Info .html file
-	InfoFileHandler.write(templateFile)
-	InfoFileHandler.close()
-	
-	
-# select all ProbeSet names from datatable 'ProbeSetFreeze'
-cursor.execute("select Id, Name, FullName from  ProbeSetFreeze ")		
-results = cursor.fetchall()
-for item in results:
-	datasetId = item[0]
-	datasetName =item[1]
-	datasetFullName =item[2]
-	InfoFileURL = InfoFilePath+datasetName+".html"
-	# check Info html file exist or not
-	if not os.path.exists(InfoFileURL):
-		createTemplateForInfoFile(datasetId=datasetId,datasetFullName=datasetFullName,InfoFileURL=InfoFileURL)
-
-		
-
-
-
-
-
-
-
- 
diff --git a/web/webqtl/maintainance/genSelectDatasetJS.py b/web/webqtl/maintainance/genSelectDatasetJS.py
deleted file mode 100755
index d03cc7af..00000000
--- a/web/webqtl/maintainance/genSelectDatasetJS.py
+++ /dev/null
@@ -1,640 +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 NL 2011/01/27
-
-# created by Ning Liu 07/01/2010
-# This script is to generate selectDatasetMenu.js file for cascade menu in the main search page http://www.genenetwork.org/.
-# This script will be run automatically every one hour or manually when database has been changed .
-
-from __future__ import print_function, division
-
-import sys, os
-
-current_file_name = __file__
-pathname = os.path.dirname( current_file_name )
-abs_path = os.path.abspath(pathname)
-sys.path.insert(0, abs_path + '/..')
-
-import MySQLdb
-import os
-import string
-import time
-import datetime
-
-from base import template
-from base import webqtlConfig
-
-#################################################################################
-# input: searchArray, targetValue
-# function: retrieve index info of target value in designated array (searchArray)
-# output: return index info
-##################################################################################
-def getIndex(searchArray=None, targetValue=None):
-	for index in range(len(searchArray)):
-		if searchArray[index][0]==targetValue:
-			return index
-
-# build MySql database connection
-con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
-cursor = con.cursor()
-
-# create js_select.js file
-fileHandler = open(webqtlConfig.HTMLPATH + 'javascript/selectDatasetMenu.js', 'w')
-
-# define SpeciesString, GroupString, TypeString, DatabasingString, LinkageString for output
-# outputSpeciesStr is for building Species Array(sArr) in js file; outputGroupStr is for Group Array(gArr)
-# outputTypeStr is for Type Array(tArr); outputDatabaseStr is for Database Array(dArr)
-# outputLinkStr is for Linkage Array(lArr)
-outputTimeStr ="/* Generated Date : %s , Time : %s */ \n" % (datetime.date.today(),time.strftime("%H:%M ", time.localtime()))
-outputTimeStr =""
-outputSpeciesStr ='var sArr = [\n{txt:\'\',val:\'\'},\n'
-outputGroupStr ='var gArr = [\n{txt:\'\',val:\'\'},\n'
-outputTypeStr ='var tArr = [\n{txt:\'\',val:\'\'},\n'
-outputDatabaseStr ='var dArr = [\n{txt:\'\',val:\'\'},\n'
-outputLinkStr ='var lArr = [\n null,\n'
-
-# built speices array in js file for select menu in the main search page http://www.genenetwork.org/
-cursor.execute("select Name, MenuName from Species order by OrderId")		
-speciesResult = cursor.fetchall()
-speciesTotalResult = list(speciesResult)
-speciesResultsTotalNum = cursor.rowcount
-if speciesResultsTotalNum >0:
-	for speciesItem in speciesResult:
-		speciesVal = speciesItem[0]
-		speciesTxt = speciesItem[1]
-		outputSpeciesStr += '{txt:\'%s\',val:\'%s\'},\n'%(speciesTxt,speciesVal)
-# 'All Species' option for 'Species' select menu		
-outputSpeciesStr +='{txt:\'All Species\',val:\'All Species\'}];\n\n'
-#speciesTotalResult is a list which inclues all species' options
-speciesTotalResult.append(('All Species','All Species'))  
-
-# built group array in js file for select menu in the main search page http://www.genenetwork.org/
-cursor.execute("select distinct InbredSet.Name, InbredSet.FullName from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze where InbredSet.SpeciesId= Species.Id and InbredSet.Name != 'BXD300' and (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) order by InbredSet.Name")
-groupResults = cursor.fetchall()
-groupTotalResults = list(groupResults)
-groupResultsTotalNum = cursor.rowcount
-if groupResultsTotalNum > 0:
-	for groupItem in groupResults:
-		groupVal = groupItem[0]
-		groupTxt = groupItem[1]
-		outputGroupStr += '{txt:\'%s\',val:\'%s\'},\n'%(groupTxt,groupVal)
-# add 'All Groups' option for 'Group' select menu	
-outputGroupStr +='{txt:\'All Groups\',val:\'all groups\'}];\n\n'  
-# groupTotalResults is a list which inclues all groups' options
-groupTotalResults.append(('all groups','All Groups'))
-							
-# built type array in js file for select menu in the main search page http://www.genenetwork.org/			
-cross = groupVal
-cursor.execute("select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.public > %d order by Tissue.Name" % (webqtlConfig.PUBLICTHRESH))
-typeResults = cursor.fetchall()
-typeTotalResults = list(typeResults)
-typeResultsTotalNum = cursor.rowcount
-if typeResultsTotalNum > 0:		
-	for typeItem in typeResults:
-		typeVal = typeItem[0]
-		typeTxt = typeItem[1]
-		outputTypeStr += '{txt:\'%s\',val:\'%s\'},\n'%(typeTxt,typeVal)
-# add 'Phenotypes' and 'Genotypes' options for 'Type' select menu
-outputTypeStr +='{txt:\'Phenotypes\',val:\'Phenotypes\'},\n'
-outputTypeStr +='{txt:\'Genotypes\',val:\'Genotypes\'}];\n\n'
-# typeTotalResults is a list which inclues all types' options
-typeTotalResults.append(('Phenotypes','Phenotypes'))	
-typeTotalResults.append(('Genotypes','Genotypes'))
-		
-# built dataset array in js file for select menu in the main search page http://www.genenetwork.org/			
-tissue = typeVal
-cursor.execute("select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime desc" % (webqtlConfig.PUBLICTHRESH))
-datasetResults = cursor.fetchall()
-datasetTotalResults = list(datasetResults)
-datasetResultsTotalNum = cursor.rowcount
-if datasetResultsTotalNum > 0:	
-	for datasetItem in datasetResults:
-		datasetVal = datasetItem[0]
-		datasetTxt = datasetItem[1]
-		outputDatabaseStr += '{txt:\'%s\',val:\'%s\'},\n'%(datasetTxt,datasetVal)
-
-# This part is to built linkage array in js file, the linkage is among Species, Group, Type and Database.
-# The format of linkage array is [speciesIndex, groupIndex, typeIndex, databaseIndex]
-if speciesResultsTotalNum >0:
-	for speciesItem in speciesResult:
-		speciesVal = speciesItem[0]
-		sIndex = getIndex(searchArray=speciesTotalResult,targetValue=speciesVal)+1
-	 			
-		# retrieve group info based on specie
-		cursor.execute("select distinct InbredSet.Name, InbredSet.FullName from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze where InbredSet.SpeciesId= Species.Id and Species.Name='%s' and InbredSet.Name != 'BXD300' and (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) order by InbredSet.Name" % speciesVal)
-		groupResults = cursor.fetchall()
-		groupResultsNum = cursor.rowcount
-		
-		if groupResultsNum > 0:
-			for groupItem in groupResults:
-				groupVal = groupItem[0]
-				gIndex = getIndex(searchArray=groupTotalResults, targetValue=groupVal)+1						
-		
-				cross = groupVal
-				# if group also exists in PublishFreeze table, then needs to add related Published Phenotypes in Database Array(dArr) and Linkage Array(lArr)
-				# 'MDP' case is related to 'Mouse Phenome Database'
-				cursor.execute("select PublishFreeze.Id from PublishFreeze, InbredSet where PublishFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s'" % cross)
-				if (cursor.fetchall()):
-					typeVal = "Phenotypes"
-					if cross=='MDP':
-						datasetTxt = "Mouse Phenome Database"
-					else: 
-						datasetTxt = "%s Published Phenotypes" % cross
-					datasetVal = "%sPublish" % cross
-					outputDatabaseStr += '{txt:\'%s\',val:\'%s\'},\n'% (datasetTxt,datasetVal)
-					datasetTotalResults.append(('%s'% datasetVal,'%s' % datasetTxt)) 
-					
-					tIndex = getIndex(searchArray=typeTotalResults,targetValue=typeVal)+1
-					dIndex = getIndex(searchArray=datasetTotalResults, targetValue=datasetVal)+1
-					outputLinkStr +='[%d,%d,%d,%d],\n'%(sIndex,gIndex,tIndex,dIndex)
-					
-				# if group also exists in GenoFreeze table, then needs to add related Genotypes in database Array(dArr)					
-				cursor.execute("select GenoFreeze.Id from GenoFreeze, InbredSet where GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s'" % cross)
-				if (cursor.fetchall()):
-					typeVal = "Genotypes"
-					datasetTxt = "%s Genotypes" % cross
-					datasetVal = "%sGeno" % cross
-					outputDatabaseStr += '{txt:\'%s\',val:\'%s\'},\n'%(datasetTxt,datasetVal)
-					typeTotalResults.append(('Genotypes','Genotypes'))
-					datasetTotalResults.append(('%s'% datasetVal,'%s' % datasetTxt))
-					
-					tIndex = getIndex(searchArray=typeTotalResults,targetValue=typeVal)+1
-					dIndex = getIndex(searchArray=datasetTotalResults, targetValue=datasetVal)+1
-					outputLinkStr +='[%d,%d,%d,%d],\n'%(sIndex,gIndex,tIndex,dIndex)
-				
-				# retrieve type(tissue) info based on group
-				# if cross is equal to 'BXD', then need to seach for 'BXD' and 'BXD300' InbredSet
-				if cross == "BXD":
-					cross2 = "BXD', 'BXD300"
-				else:
-					cross2 = cross
-				cursor.execute("select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.public > %d order by Tissue.Name" % (cross2, webqtlConfig.PUBLICTHRESH))
-				typeResults = cursor.fetchall()					
-				typeResultsNum = cursor.rowcount
-				
-				if typeResultsNum > 0:		
-					for typeItem in typeResults:
-						typeVal = typeItem[0]
-						tIndex = getIndex(searchArray=typeTotalResults, targetValue=typeVal)+1					
-						# retrieve database(dataset) info based on group(InbredSet) and type(Tissue)
-						tissue = typeVal
-						cursor.execute("select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and Tissue.name = '%s' and ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime desc" % (cross2, tissue, webqtlConfig.PUBLICTHRESH))
-						datasetResults = cursor.fetchall()
-						datasetResultsNum = cursor.rowcount
-						
-						if datasetResultsNum > 0:					
-							for datasetItem in datasetResults:
-								datasetVal = datasetItem[0]
-								dIndex = getIndex(searchArray=datasetTotalResults, targetValue=datasetVal)+1
-								outputLinkStr +='[%d,%d,%d,%d],\n'%(sIndex,gIndex,tIndex,dIndex)	
-
-# add 'All Phenotypes' option for 'Database' select menu
-# for 'All Species'option in 'Species' select menu, 'Database' select menu will show 'All Phenotypes' option								
-outputDatabaseStr += '{txt:\'%s\',val:\'%s\'}];\n\n'%('All Phenotypes','_allPublish')
-datasetTotalResults.append(('_allPublish','All Phenotypes'))
-
-sIndex = getIndex(searchArray=speciesTotalResult,targetValue='All Species')+1
-gIndex = getIndex(searchArray=groupTotalResults, targetValue='all groups')+1
-tIndex = getIndex(searchArray=typeTotalResults,targetValue='Phenotypes')+1
-dIndex = getIndex(searchArray=datasetTotalResults, targetValue='_allPublish')+1
-outputLinkStr +='[%d,%d,%d,%d]];\n\n'%(sIndex,gIndex,tIndex,dIndex)
-
-# Combine sArr, gArr, tArr, dArr and lArr output string together
-outputStr = outputTimeStr+outputSpeciesStr+outputGroupStr+outputTypeStr+outputDatabaseStr+outputLinkStr		
-outputStr +='''
-
-/* 
-*  function: based on different browser use, will have different initial actions; 
-*  Once the index.html page is loaded, this function will be called
-*/
-function initialDatasetSelection()
-{		
-	defaultSpecies =getDefaultValue('species');
-	defaultSet =getDefaultValue('cross');
-	defaultType =getDefaultValue('tissue');
-	defaultDB =getDefaultValue('database');
-	
-	if (navigator.userAgent.indexOf('MSIE')>=0)
-	{
-		sOptions = fillOptionsForIE(null,defaultSpecies);
-		var menu0 ="<SELECT NAME='species' ID='species' SIZE='1' onChange='fillOptions(\\"species\\");'>"+sOptions+"</Select>";
-		document.getElementById('menu0').innerHTML = menu0;
-		
-		gOptions = fillOptionsForIE('species',defaultSet);
-		var menu1 ="<Select NAME='cross' size=1 id='cross' onchange='fillOptions(\\"cross\\");'>"+gOptions+"</Select><input type=\\"button\\" class=\\"button\\" value=\\"Info\\" onCLick=\\"javascript:crossinfo();\\">";
-		document.getElementById('menu1').innerHTML =menu1;
-		
-		tOptions = fillOptionsForIE('cross',defaultType);
-		var menu2 ="<Select NAME='tissue' size=1 id='tissue' onchange='fillOptions(\\"tissue\\");'>"+tOptions+"</Select>";
-		document.getElementById('menu2').innerHTML =menu2;
-		
-		dOptions = fillOptionsForIE('tissue',defaultDB);
-		var menu3 ="<Select NAME='database' size=1 id='database'>"+dOptions+"</Select><input type=\\"button\\" class=\\"button\\" value=\\"Info\\" onCLick=\\"javascript:databaseinfo();\\">";
-		document.getElementById('menu3').innerHTML =menu3;
-		
-	}else{
-		fillOptions(null);
-    }
-	searchtip();
-}
-
-/* 
-*  input: selectObjId (designated select menu, such as species, cross, etc... )
-*  defaultValue (default Value of species, cross,tissue or database)
-*  function: special for IE browser,setting options value for select menu dynamically based on linkage array(lArr), 
-*  output: options string
-*/
-function fillOptionsForIE(selectObjId,defaultValue)
-{	
-	var options='';	
-	if(selectObjId==null)
-	{	
-		var len = sArr.length;
-		for (var i=1; i < len; i++) { 
-		    // setting Species' option			
-			if( sArr[i].val==defaultValue){
-				options =options+"<option selected=\\"selected\\" value='"+sArr[i].val+"'>"+sArr[i].txt+"</option>";
-			}else{
-				options =options+"<option value='"+sArr[i].val+"'>"+sArr[i].txt+"</option>";
-			}
-		}	
-	}else if(selectObjId=='species')
-	{
-		var speciesObj = document.getElementById('species');
-		var len = lArr.length;
-		var arr = [];
-		var idx = 0;
-		for (var i=1; i < len; i++) {
-			//get group(cross) info from lArr
-			if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&!Contains(arr,lArr[i][1]))
-			{
-				arr[idx++]=lArr[i][1];
-			}  
-		}
-		idx=0;
-		len = arr.length;
-		removeOptions("cross");
-		for (var i=0; i < len; i++) {
-			// setting Group's option
-			if( gArr[arr[i]].val==defaultValue){
-				options =options+"<option selected=\\"selected\\" value='"+gArr[arr[i]].val+"'>"+gArr[arr[i]].txt+"</option>";
-			}else{
-				options =options+"<option value='"+gArr[arr[i]].val+"'>"+gArr[arr[i]].txt+"</option>";
-			}
-			
-		}
-	}else if(selectObjId=='cross')
-	{
-		var speciesObj = document.getElementById('species');
-		var groupObj = document.getElementById('cross');
-		var len = lArr.length;
-		var arr = [];
-		var idx = 0;
-		for (var i=1; i < len; i++) {
-			//get type(tissue) info from lArr
-			if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&!Contains(arr,lArr[i][2]))
-			{
-				arr[idx++]=lArr[i][2];
-			}  
-		}
-		idx=0;
-		len = arr.length;
-		removeOptions("tissue");
-		for (var i=0; i < len; i++) {
-			// setting Type's option
-			if( tArr[arr[i]].val==defaultValue){
-				options =options+"<option selected=\\"selected\\" value='"+tArr[arr[i]].val+"'>"+tArr[arr[i]].txt+"</option>";
-			}else{
-				options =options+"<option value='"+tArr[arr[i]].val+"'>"+tArr[arr[i]].txt+"</option>";
-			}
-		}
-
-	}else if(selectObjId=='tissue')
-	{
-		var speciesObj = document.getElementById('species');
-		var groupObj = document.getElementById('cross');
-		var typeObj = document.getElementById('tissue');
-
-		var len = lArr.length;
-		var arr = [];
-		var idx = 0;
-		for (var i=1; i < len; i++) {
-			//get dataset(database) info from lArr
-			if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&lArr[i][2]==(getIndexByValue('tissue',typeObj.value)).toString()&&!Contains(arr,lArr[i][3]))
-			{
-				arr[idx++]=lArr[i][3];
-			}  
-		}
-		idx=0;
-		len = arr.length;
-		removeOptions("database");
-		for (var i=0; i < len; i++) {
-			// setting Database's option			
-			if( dArr[arr[i]].val==defaultValue){
-				options =options+"<option SELECTED value='"+dArr[arr[i]].val+"'>"+dArr[arr[i]].txt+"</option>";
-			}else{
-				options =options+"<option value='"+dArr[arr[i]].val+"'>"+dArr[arr[i]].txt+"</option>";
-			}
-		}
-	}	
-	return options;
-}
-/* 
-*  input: selectObjId (designated select menu, such as species, cross, etc... )
-*  function: setting options value for select menu dynamically based on linkage array(lArr)
-*  output: null
-*/
-function fillOptions(selectObjId)
-{	
-	if(selectObjId==null)
-	{
-
-		var speciesObj = document.getElementById('species');	
-		var len = sArr.length;
-		for (var i=1; i < len; i++) { 
-		    // setting Species' option
-			speciesObj.options[i-1] = new Option(sArr[i].txt, sArr[i].val);
-		}
-		updateChocie('species');
-	
-	}else if(selectObjId=='species')
-	{
-		var speciesObj = document.getElementById('species');
-		var groupObj = document.getElementById('cross');
-		var len = lArr.length;
-		var arr = [];
-		var idx = 0;
-		for (var i=1; i < len; i++) {
-			//get group(cross) info from lArr
-			if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&!Contains(arr,lArr[i][1]))
-			{
-				arr[idx++]=lArr[i][1];
-			}  
-		}
-		idx=0;
-		len = arr.length;
-		removeOptions("cross");
-		for (var i=0; i < len; i++) {
-			// setting Group's option
-			groupObj.options[idx++] = new Option(gArr[arr[i]].txt, gArr[arr[i]].val); 
-		}
-		updateChocie('cross');
-
-	}else if(selectObjId=='cross')
-	{
-		var speciesObj = document.getElementById('species');
-		var groupObj = document.getElementById('cross');
-		var typeObj = document.getElementById('tissue');
-		var len = lArr.length;
-		var arr = [];
-		var idx = 0;
-		for (var i=1; i < len; i++) {
-			//get type(tissue) info from lArr
-			if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&!Contains(arr,lArr[i][2]))
-			{
-				arr[idx++]=lArr[i][2];
-			}  
-		}
-		idx=0;
-		len = arr.length;
-		removeOptions("tissue");
-		for (var i=0; i < len; i++) {
-			// setting Type's option
-			typeObj.options[idx++] = new Option(tArr[arr[i]].txt, tArr[arr[i]].val); 
-		}
-		updateChocie('tissue');
-
-	}else if(selectObjId=='tissue')
-	{
-		var speciesObj = document.getElementById('species');
-		var groupObj = document.getElementById('cross');
-		var typeObj = document.getElementById('tissue');
-		var databaseObj = document.getElementById('database');
-
-		var len = lArr.length;
-		var arr = [];
-		var idx = 0;
-		for (var i=1; i < len; i++) {
-			//get dataset(database) info from lArr
-			if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&lArr[i][2]==(getIndexByValue('tissue',typeObj.value)).toString()&&!Contains(arr,lArr[i][3]))
-			{
-				arr[idx++]=lArr[i][3];
-			}  
-		}
-		idx=0;
-		len = arr.length;
-		removeOptions("database");
-		for (var i=0; i < len; i++) {
-			// setting Database's option
-			databaseObj.options[idx++] = new Option(dArr[arr[i]].txt, dArr[arr[i]].val); 
-		}
-		updateChocie('database');
-	}	
-}
-
-/* 
-*  input: arr (targeted array); obj (targeted value)
-*  function: check whether targeted array contains targeted value or not
-*  output: return true, if array contains targeted value, otherwise return false
-*/
-function Contains(arr,obj) { 
-	var i = arr.length; 
-	while (i--) { 
-		if (arr[i] == obj) { 
-			return true; 
-		}
-	} 
-	return false; 
-} 
-
-/* 
-* input: selectObj (designated select menu, such as species, cross, etc... )
-* function: clear designated select menu's option
-* output: null
-*/
-function removeOptions(selectObj) {     
-	if (typeof selectObj != 'object'){         
-		selectObj = document.getElementById(selectObj);
-	}        
-	var len = selectObj.options.length;      
-	for (var i=0; i < len; i++)     {         
-		// clear current selection       
-		selectObj.options[0] = null;    
-	} 
-} 
-
-/* 
-*  input: selectObjId (designated select menu, such as species, cross, etc... )
-*         Value: target value
-*  function: retrieve Index info of target value in designated array
-*  output: index info
-*/
-function getIndexByValue(selectObjId,val)
-{
-	if(selectObjId=='species')
-	{
-		for(var i=1;i<sArr.length;i++){
-			if(sArr[i].val==val)
-				return i;				
-		}
-	}else if(selectObjId=='cross')
-	{
-		for(var i=1;i<gArr.length;i++)
-			if(gArr[i].val==val)
-				return i;
-	}else if(selectObjId=='tissue')
-	{
-		for(var i=1;i<tArr.length;i++)
-			if(tArr[i].val==val)
-				return i;
-	}
-	else return;
-}
-
-/* 
-*  input: objId (designated select menu, such as species, cross, etc... )
-*  		  val(targeted value)
-*  function: setting option's selected status for designated select menu based on target value, also update the following select menu in the main search page 
-*  output: return true if selected status has been set, otherwise return false.
-*/
-function setChoice(objId,val)
-{
-	var Obj = document.getElementById(objId);
-	var idx=-1;
-
-	for(i=0;i<Obj.options.length;i++){
-		if(Obj.options[i].value==val){
-			idx=i;
-			break;
-		}
-	}
-	
-	if(idx>=0){
-		//setting option's selected status 
-		Obj.options[idx].selected=true;
-		//update the following select menu 
-		fillOptions(objId);
-	}else{
-		Obj.options[0].selected=true;
-		fillOptions(objId);
-	}
-}
-
-// setting option's selected status based on default setting or cookie setting for Species, Group, Type and Database select menu in the main search page http://www.genenetwork.org/
-function updateChocie(selectObjId){
-
-	if (selectObjId =='species')
-	{
-		defaultSpecies= getDefaultValue('species'); 
-		//setting option's selected status
-		setChoice('species',defaultSpecies);
-	}else if (selectObjId =='cross')
-	{	
-		defaultSet= getDefaultValue('cross'); 
-		//setting option's selected status
-		setChoice('cross',defaultSet);
-	}else if (selectObjId =='tissue')
-	{
-		defaultType= getDefaultValue('tissue'); 
-		//setting option's selected status
-		setChoice('tissue',defaultType);
-	}else if (selectObjId =='database')
-	{
-		defaultDB= getDefaultValue('database'); 
-		//setting option's selected status
-		setChoice('database',defaultDB);
-	}
-}
-
-//get default value;if cookie exists, then use cookie value, otherwise use default value
-function getDefaultValue(selectObjId){	
-	//define default value
-	var defaultSpecies = 'mouse'
-	var defaultSet = 'BXD'
-	var defaultType = 'Hippocampus'
-	var defaultDB = 'HC_M2_0606_P'
-
-	if (selectObjId =='species')
-	{
-		//if cookie exists, then use cookie value, otherwise use default value
-		var cookieSpecies = getCookie('defaultSpecies');
-		if(cookieSpecies)
-		{
-			defaultSpecies= cookieSpecies; 
-		}
-		return defaultSpecies;
-	}else if (selectObjId =='cross'){
-		var cookieSet = getCookie('defaultSet');
-		if(cookieSet){
-			defaultSet= cookieSet; 
-		} 
-		return defaultSet;
-	}else if (selectObjId =='tissue'){
-		var cookieType = getCookie('defaultType');
-		if(cookieType){
-			defaultType= cookieType;
-		} 
-		return defaultType;
-	}else if (selectObjId =='database')
-	{
-		var cookieDB = getCookie('defaultDB');
-		if(cookieDB){
-			defaultDB= cookieDB;
-		}
-		return defaultDB;
-	}
-
-}
-
-//setting default value into cookies for the dropdown menus: Species,Group, Type, and Database 
-function setDefault(thisform){
-	
-	setCookie('cookieTest', 'cookieTest', 1);
-	var cookieTest = getCookie('cookieTest');
-	delCookie('cookieTest');
-	if (cookieTest){
-		var defaultSpecies = thisform.species.value;
-		setCookie('defaultSpecies', defaultSpecies, 10);
-		var defaultSet = thisform.cross.value;
-		setCookie('defaultSet', defaultSet, 10);
-		var defaultType = thisform.tissue.value;
-		setCookie('defaultType', defaultType, 10);
-		var defaultDB = thisform.database.value;
-		setCookie('defaultDB', defaultDB, 10);
-		updateChocie('species');
-		updateChocie('cross');
-		updateChocie('tissue');
-		updateChocie('database');		
-		alert("The current settings are now your default");
-	}
-	else{
-		alert("You need to enable Cookies in your browser.");
-	}
-}
-
-'''	
-# write all strings' info into selectDatasetMenu.js file
-fileHandler.write(outputStr)
-fileHandler.close()
diff --git a/web/webqtl/maintainance/updateMenuJS.py b/web/webqtl/maintainance/updateMenuJS.py
deleted file mode 100755
index 8b6e25d3..00000000
--- a/web/webqtl/maintainance/updateMenuJS.py
+++ /dev/null
@@ -1,127 +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
-#
-# created by Lei Yan 02/08/2011
-import sys, os
-import MySQLdb
-import string
-
-
-
-abs_path = os.path.abspath(os.path.dirname(__file__))
-path1 = abs_path + "/.."
-path2 = abs_path + "/../../javascript"
-sys.path.insert(0, path1)
-
-#must import GN python files after add path
-from base import webqtlConfig
-
-# build MySql database connection
-con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD)
-cursor = con.cursor()
-cursor.execute("SELECT id,menuname FROM Species ORDER BY OrderId")
-results = list(cursor.fetchall())
-collectionsText = ""
-for result in results:
-	specieid = result[0]
-	speciename = result[1]
-	collectionsText += ("['" + speciename + "', ")
-	collectionsText += ("null, ")
-	collectionsText += ("null, ")
-	collectionsText += "\n"
-	cursor.execute("select name from InbredSet where speciesid=" + str(specieid))
-	results2 = list(cursor.fetchall())
-	for result2 in results2:
-		inbredsetName = result2[0]
-		if not cmp(inbredsetName, "BXD300"):
-			continue
-		collectionsText += "\t"
-		collectionsText += ("['" + inbredsetName + "', ")
-		collectionsText += ("'/webqtl/main.py?FormID=dispSelection&RISet=" + inbredsetName + "'], ")
-		collectionsText += "\n"
-	collectionsText += "],"
-	collectionsText += "\n"
-collectionsText = collectionsText.strip()
-
-jstext = """/*
-  --- menu items --- 
-  note that this structure has changed its format since previous version.
-  additional third parameter is added for item scope settings.
-  Now this structure is compatible with Tigra Menu GOLD.
-  Format description can be found in product documentation.
-*/
-var MENU_ITEMS = [
-	['menu_grp1', null, null,
-		['GeneNetwork Intro', '/home.html'],
-		['Enter Trait Data', '/webqtl/main.py?FormID=submitSingleTrait'],
-		['Batch Submission', '/webqtl/main.py?FormID=batSubmit'],
-	],
-	['menu_grp2', null, null,
-		['Search Databases', '/'],
-		['Tissue Correlation', '/webqtl/main.py?FormID=tissueCorrelation'],
-		['SNP Browser', '/webqtl/main.py?FormID=snpBrowser'],
-		['Gene Wiki', '/webqtl/main.py?FormID=geneWiki'],
-		['Interval Analyst', '/webqtl/main.py?FormID=intervalAnalyst'],
-		['QTLminer', '/webqtl/main.py?FormID=qtlminer'],
-		['GenomeGraph', '/dbResults.html'],
-		['Trait Collections',null,null,
-%s
-		],
-		['Scriptable Interface', '/CGIDoc.html'],
-		/* ['Simple Query Interface', '/GUI.html'], */
-		['Database Information',null,null,
-			['Database Schema', '/webqtl/main.py?FormID=schemaShowPage'],
-		],
-		['Data Sharing', '/webqtl/main.py?FormID=sharing'],
-		['Microarray Annotations', '/webqtl/main.py?FormID=annotation'],
-	],
-	['menu_grp3', null, null,
-		['Movies','http://www.genenetwork.org/tutorial/movies'],
-		['Tutorials', null, null, 
-                ['GN Barley Tutorial','/tutorial/pdf/GN_Barley_Tutorial.pdf'],
-                ['GN Powerpoint', '/tutorial/ppt/index.html']],
-		['HTML Tour','/tutorial/WebQTLTour/'],
-		['FAQ','/faq.html'],
-		['Glossary of Terms','/glossary.html'],
-		['GN MediaWiki','http://wiki.genenetwork.org/'],
-	],
-	['menu_grp4', '/whats_new.html'
-	],
-	['menu_grp5', '/reference.html'
-	],
-	['menu_grp6', null, null,
-		['Conditions and Limitation', '/conditionsofUse.html'],
-		['Data Sharing Policy', '/dataSharing.html'],
-		['Status and Contacts', '/statusandContact.html'],
-		['Privacy Policy', '/privacy.html'],
-	],
-	['menu_grp8', '/links.html'
-	],
-];
-"""
-
-# create menu_items.js file
-fileHandler = open(path2 + '/menu_items.js', 'w')
-fileHandler.write(jstext % collectionsText)
-fileHandler.close()