Add all the source codes into the github.

5 files changed, 973 insertions, 0 deletions

diff --git a/web/webqtl/maintainance/__init__.py b/web/webqtl/maintainance/__init__.py
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/web/webqtl/maintainance/__init__.py
diff --git a/web/webqtl/maintainance/addRif.py b/web/webqtl/maintainance/addRif.py
new file mode 100755
index 00000000..c7cdde7a
--- /dev/null
+++ b/web/webqtl/maintainance/addRif.py
@@ -0,0 +1,107 @@
+# 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
new file mode 100755
index 00000000..6aa0d771
--- /dev/null
+++ b/web/webqtl/maintainance/checkInfoFile.py
@@ -0,0 +1,102 @@
+# 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
new file mode 100755
index 00000000..bc88beec
--- /dev/null
+++ b/web/webqtl/maintainance/genSelectDatasetJS.py
@@ -0,0 +1,637 @@
+# 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 .
+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
new file mode 100755
index 00000000..8b6e25d3
--- /dev/null
+++ b/web/webqtl/maintainance/updateMenuJS.py
@@ -0,0 +1,127 @@
+# 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()