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

1 files changed, 0 insertions, 695 deletions

diff --git a/web/webqtl/collection/AddToSelectionPage.py b/web/webqtl/collection/AddToSelectionPage.py
deleted file mode 100644
index 2a99e8c1..00000000
--- a/web/webqtl/collection/AddToSelectionPage.py
+++ /dev/null
@@ -1,695 +0,0 @@
-#AddToSelectionPage.py
-
-import string
-from htmlgen import HTMLgen2 as HT
-import os
-import cPickle
-import reaper
-
-from base import webqtlConfig
-from base.templatePage import templatePage
-from utility.THCell import THCell
-from utility.TDCell import TDCell
-from utility import webqtlUtil
-from showTrait import ShowProbeInfoPage
-# NL, 07/27/2010: add 'import webqtlDatabaseFunction' for retrieveSpecies function
-from dbFunction import webqtlDatabaseFunction
-from base.webqtlTrait import webqtlTrait
-
-	
-#########################################
-#      Add to Selection Page
-#########################################
-class AddToSelectionPage(templatePage):
-
-	def __init__(self,fd):
-
-		templatePage.__init__(self, fd)
-
-		if not self.openMysql():
-			return
-
-		if not fd.genotype:
-			fd.readGenotype()
-		
-		self.searchResult = fd.formdata.getvalue('searchResult', [])
-		if type("1") == type(self.searchResult):
-			self.searchResult = [self.searchResult]
-		if fd.formdata.getvalue('fromDataEditingPage'):
-			searchResult2 = fd.formdata.getvalue('fullname')
-			if searchResult2:
-				self.searchResult.append(searchResult2)
-		
-		if self.searchResult:
-			pass
-		else:
-			templatePage.__init__(self, fd)
-			heading = 'Add Collections'
-			detail = ['You need to select at least one trait to add to your selection.']
-			self.error(heading=heading,detail=detail)
-			return
-
-		if self.genSelection(fd=fd):
-			self.writeHTML(fd)
-
-
-		
-	def genSelection(self, fd=None, checkPreSelection = 1):
-		collectionName = '%s_Select' % fd.RISet
-
-		if checkPreSelection:
-			try:
-				preSelection = fd.input_session_data[collectionName]
-				preSelection = list(string.split(preSelection,','))
-			except:
-				preSelection = []
-		else:
-			preSelection = []
-
-		if preSelection:
-			for item in preSelection:
-				if item not in self.searchResult:
-					self.searchResult.append(item)
-
-		self.searchResult = map(self.transfer2NewName, self.searchResult)
-
-		for item in self.searchResult:
-			if not item:
-				self.searchResult.remove(item)
-
-		if len(self.searchResult) > 3000:
-                        heading = 'Add Collections'
-                        detail = ['You are adding over 3000 traits to selections, please reduce your number of traits.']
-                        self.error(heading=heading,detail=detail)
-                        return 0
-	
-		searchResult2 = []
-		self.theseTraits = []
-		for item in self.searchResult:
-			try:
-				thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
-				thisTrait.retrieveInfo(QTL=1)
-				self.theseTraits.append(thisTrait)
-				searchResult2.append(item)
-			except:
-				pass
-
-		allTraitStr = string.join(searchResult2,',')
-
-		self.session_data_changed[collectionName] = allTraitStr
-
-		return 1
-
-
-	
-	def writeHTML(self,fd):
-		TD_LR = HT.TD(height=100,width="100%",bgColor='#eeeeee',valign="top")
-		pageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left")
-		tbl = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0, align="Left")
-		seq = 1
-		SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title")
-		
-		mintmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'showIntMap');}")
-		mintmap_img = HT.Image("/images/multiple_interval_mapping1_final.jpg", name='mintmap', alt="Multiple Interval Mapping", title="Multiple Interval Mapping", style="border:none;")
-		mintmap.append(mintmap_img)
-		mcorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'compCorr');}")
-		mcorr_img = HT.Image("/images/compare_correlates2_final.jpg", name='comparecorr', alt="Compare Correlates", title="Compare Correlates", style="border:none;")
-		mcorr.append(mcorr_img)
-		cormatrix = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'corMatrix');}")
-		cormatrix_img = HT.Image("/images/correlation_matrix1_final.jpg", name='corrmatrix', alt="Correlation Matrix and PCA", title="Correlation Matrix and PCA", style="border:none;")
-		cormatrix.append(cormatrix_img)
-		networkGraph = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'networkGraph');}")
-		networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='networkgraph', alt="Network Graphs", title="Network Graphs", style="border:none;")
-		networkGraph.append(networkGraph_img)
-		heatmap = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'heatmap');}")
-		heatmap_img = HT.Image("/images/heatmap2_final.jpg", name='heatmap', alt="QTL Heat Map and Clustering", title="QTL Heatmap and Clustering", style="border:none;")
-		heatmap.append(heatmap_img)
-		partialCorr = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'partialCorrInput');}")
-		partialCorr_img = HT.Image("/images/partial_correlation_final.jpg", name='partialCorr', alt="Partial Correlation", title="Partial Correlation", style="border:none;")
-		partialCorr.append(partialCorr_img)
-
-		BN = HT.Href(url="#redirect", onClick="if(validateTraitNumber()){databaseFunc(document.getElementsByName('showDatabase')[0], 'BNInput');}")
-		networkGraph_img = HT.Image("/images/network_graph1_final.jpg", name='BayesianNetwork', alt="Bayesian Network", title="Bayesian Network", style="border:none;")
-		BN.append(networkGraph_img)
-
-		removeselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('showDatabase')[0], 'removeSelection');" % fd.RISet)
-		removeselect_img = HT.Image("/images/remove_selection1_final.jpg", name="removeselect", alt="Remove Selection", title="Remove Selection", style="border:none;")
-		removeselect.append(removeselect_img)	
-		selectall = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', true);")
-		selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;")
-		selectall.append(selectall_img)
-		reset = HT.Href(url="#redirect", onClick="$('.checkallbox').attr('checked', false);")
-		reset_img = HT.Image("/images/select_none2_final.jpg", alt="Select None", title="Select None", style="border:none;")
-		reset.append(reset_img)
-		exportSelect = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'exportSelectionDetailInfo');")
-		exportSelect_img = HT.Image("/images/export2_final.jpg", name="exportSelection", alt="Export Selection", title="Export Selection", style="border:none;")
-		exportSelect.append(exportSelect_img)
-		selectinvert = HT.Href(url="#redirect", onClick = "checkInvert(document.getElementsByName('showDatabase')[0]);")
-		selectinvert_img = HT.Image("/images/invert_selection2_final.jpg", name="selectinvert", alt="Invert Selection", title="Invert Selection", style="border:none;")
-		selectinvert.append(selectinvert_img)
-
-		chrMenu = HT.Input(type='hidden',name='chromosomes',value='all')
-		
-		importFile = HT.Input(type='file', name='importfile', size=15)
-		importButton = HT.Input(type='button',name='importSelection',value='Load Collection', onClick="addRmvSelection('%s', this.form, 'importSelect');" % fd.RISet,Class="button")
-		exportButton = HT.Input(type='button' ,name='exportSelection',value='Save Collection', onClick="databaseFunc(this.form,'exportSelect');", Class="button")
-		importMenu = HT.Select(name='importmethod')
-		importMenu.append(('append','append'))
-		importMenu.append(('replace','replace'))            
-	
-		ODE = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'ODE');")
-		ODE_img = HT.Image("/images/ODE_logo_final.jpg", name="ode", alt="ODE", title="ODE", style="border:none")
-		ODE.append(ODE_img)
-	        
-		GCATButton = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0], 'GCAT');")
-		GCATButton_img = HT.Image("/images/GCAT_logo_final.jpg", name="GCAT", alt="GCAT", title="GCAT", style="border:none")
-		GCATButton.append(GCATButton_img)
-		
-        	GeneSet = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('showDatabase')[0],'GOTree');")
-        	GeneSet_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none")        
-        	GeneSet.append(GeneSet_img)      
-
-		#need to be refined
-        	if fd.genotype.Mbmap:
-            	    scale = HT.Input(name="scale", value="physic", type="hidden")
-        	else:
-            	    scale = ""
- 
-        	formMain = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))
-
-		#XZ, July 22, 2011: I add parameters for interval mapping
-        	hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet,'incparentsf1':'ON','showHideOptions':'more','scale':'physic','additiveCheck':'ON', 'showSNP':'ON', 'showGenes':'ON', 'intervalAnalystCheck':'ON','bootCheck':None, 'permCheck':None, 'applyVarianceSE':None}
-        	for key in hddn.keys():
-            	    formMain.append(HT.Input(name=key, value=hddn[key], type='hidden'))
-
-        	if not self.searchResult:
-            	    SelectionHeading = HT.Paragraph('%s Trait Collection' % fd.RISet, Class="title")
-            	    formMain.append(HT.HR(width="70%", color = "blue"),importFile, ' ', importMenu, ' ', importButton)
-            	    TD_LR.append(SelectionHeading,HT.Blockquote('No trait has been added to this selection.'), HT.Center(HT.BR(), HT.BR(), HT.BR(), HT.BR(), formMain))
-            	    self.dict['body'] = str(TD_LR)
-            	    self.dict['title'] = "%s Trait Collection" % fd.RISet
-            	    return
-
-		#########################################
-		# Creating table object for AJAX table  #
-		#########################################
-		tblobj = {}
-		mainfmName = 'showDatabase'
-		# NL, 07/27/2010. retrieveSpecies function has been moved from webqtlTrait.py to webqtlDatabaseFunction.py;
-		species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
-		if species == 'human':
-			chrMenu = scale = mintmap = heatmap = ""
-
-		tblobj['header'] = self.getCollectionTableHeader()
-
-		sortby = self.getSortByValue()
-
-		thisRISet = fd.RISet
-		tblobj['body'] = self.getCollectionTableBody(RISet=thisRISet, traitList=self.theseTraits, formName=mainfmName, species=species)
-
-		filename= webqtlUtil.genRandStr("Search_")
-
-		objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
-		cPickle.dump(tblobj, objfile)
-		objfile.close()
-
-
-		div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "1"), Id="sortable")		
-
-
-        	containerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left")
-        	postContainerTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0,align="Left")
-
-        	optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="400", border=0, align="Left")
-        	optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(removeselect), HT.TD(exportSelect)))
-        	optionsTable.append(HT.TR(HT.TD(" "*1,"Select"), HT.TD("Deselect"), HT.TD(" "*1,"Invert"), HT.TD(" "*1,"Remove"), HT.TD(" "*1,"Export")))
-        	postContainerTable.append(HT.TR(HT.TD(optionsTable)))
-        	containerTable.append(HT.TR(HT.TD(optionsTable)))
-
-        	functionTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="480",border=0, align="Left")
-        	functionRow = HT.TR(HT.TD(networkGraph, width="16.7%"), HT.TD(cormatrix, width="16.7%"), HT.TD(partialCorr, width="16.7%"), HT.TD(mcorr, width="16.7%"), HT.TD(mintmap, width="16.7%"), HT.TD(heatmap))
-        	if species == "human":
-        	    labelRow = HT.TR(HT.TD(" "*2,HT.Text("Graph")), HT.TD(" "*2,HT.Text("Matrix")), HT.TD(" "*2, HT.Text("Partial")), HT.TD(HT.Text("Compare")))
-        	else:
-        		labelRow = HT.TR(HT.TD(" "*2,HT.Text("Graph")), HT.TD(" "*2,HT.Text("Matrix")), HT.TD(" "*2, HT.Text("Partial")), HT.TD(HT.Text("Compare")), HT.TD(HT.Text("QTL Map")), HT.TD(HT.Text(text="Heat Map")))
-        	functionTable.append(functionRow, labelRow)
-        	postContainerTable.append(HT.TR(HT.TD(functionTable)))
-        	containerTable.append(HT.TR(HT.TD(functionTable)))
-
-        	moreOptions = HT.Input(type='button',name='options',value='More Options', onClick="",Class="toggle")
-        	fewerOptions = HT.Input(type='button',name='options',value='Fewer Options', onClick="",Class="toggle")
-        	
-        	
-
-        	if (fd.formdata.getvalue('showHideOptions') == 'less'):		
-            	    postContainerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide"))))
-            	    containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide"))))
-        	else:	
-            	    postContainerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide"))))
-            	    containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide"))))	
-
-
-        	LinkOutTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="320",border=0, align="Left")
-        	LinkOutRow = HT.TR(HT.TD(GeneSet, width="33%"), HT.TD(GCATButton, width="33%"), HT.TD(ODE, width="33%"), style="display:none;", Class="extra_options")
-        	LinkOutLabels = HT.TR(HT.TD(HT.Text("Gene Set")), HT.TD(" "*2, HT.Text("GCAT")), HT.TD(" "*3, HT.Text("ODE")), style="display:none;", Class="extra_options")
-        	LinkOutTable.append(LinkOutRow,LinkOutLabels)
-        	postContainerTable.append(HT.TR(HT.TD(" "), height=10), HT.TR(HT.TD(LinkOutTable)))
-        	containerTable.append(HT.TR(HT.TD(" "), height=10), HT.TR(HT.TD(LinkOutTable)))      
-                
-        	pageTable.append(HT.TR(HT.TD(containerTable)))
-        	chrMenu = scale = ""
-
-        	pageTable.append(HT.TR(HT.TD(div)))
-        	pageTable.append(HT.TR(HT.TD(" ")))
-        	if len(self.theseTraits) > 20:
-            	    pageTable.append(HT.TR(HT.TD(postContainerTable)))
-        	pageTable.append(HT.TR(HT.TD(importFile, ' ', importMenu, ' ', importButton, ' '*10, exportButton)))
-		    #Took out scaleMenu since it will be replaced with a jquery popup in the future - Zach 5/10/2010
-        	formMain.append(chrMenu,scale,pageTable)
-		    
-		#Updated by NL, deleted showHideJS, moved jquery to jqueryFunction.js 
-		self.dict['js1'] = ''
-            	TD_LR.append(SelectionHeading,formMain)
-
-        	self.dict['body'] = str(TD_LR)
-        	self.dict['js2'] = 'onLoad="pageOffset()"'
-        	self.dict['layer'] = self.generateWarningLayer()       	
-        	self.dict['title'] = "%s Trait Collection" % thisRISet
-
-	def transfer2NewName(self, str):
-		"this is temporary"
-		if str.find("::") < 0:
-			return str.replace(":", "::")
-		else:
-			return str
-		
-	def generateWarningLayer(self):
-
-		layerString = """
-			<!-- BEGIN FLOATING LAYER CODE //-->
-			<div id="warningLayer" style="padding:3px; border: 1px solid #222;
-  			background-color: #fff; position:absolute;width:250px;left:100;top:100;visibility:hidden">			
-				<table border="0" width="250" class="cbrb" cellspacing="0" cellpadding="5">
-					<tr>
-						<td width="100%">
-  							<table border="0" width="100%" cellspacing="0" cellpadding="0" height="36">
-  								<tr>
-  									<td class="cbrb cw ff15 fwb" align="Center" width="100%" style="padding:4px">
-        									Sort Table
-  									</td>
-  								</tr>
-  								<tr>
-  									<td width="100%" bgcolor="#eeeeee" align="Center" style="padding:4px">
-										<!-- PLACE YOUR CONTENT HERE //-->
-										Resorting this table <br>
-										<!-- END OF CONTENT AREA //-->
-  									</td>
-  								</tr>
-  							</table>
-						</td>
-					</tr>
-				</table>
-			</div>
-			<!-- END FLOATING LAYER CODE //-->
-
-            		"""
-
-		return layerString		
-		
-	def getCollectionTableHeader(self):
-
-		tblobj_header = []
-
-		className = "fs13 fwb ffl b1 cw cbrb"
-
-		tblobj_header = [[THCell(HT.TD(' ', Class=className, nowrap="on"), sort=0), 
-			THCell(HT.TD('Dataset', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="dataset", idx=1),
-			THCell(HT.TD('Trait', HT.BR(), 'ID', HT.BR(), valign="top", Class=className, nowrap="on"), text="name", idx=2),
-			THCell(HT.TD('Symbol', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="symbol", idx=3),
-			THCell(HT.TD('Description', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="desc", idx=4),
-			THCell(HT.TD('Location', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="location", idx=5),
-			THCell(HT.TD('Mean', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="mean", idx=6),
-			THCell(HT.TD('N', HT.BR(), 'Cases', HT.BR(), valign="top", Class=className, nowrap="on"), text="samples", idx=7),
-			THCell(HT.TD('Max LRS', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="lrs", idx=8),
-			THCell(HT.TD('Max LRS Location',HT.BR(),'Chr and Mb', HT.BR(), valign="top", Class=className, nowrap="on"), text="lrs_location", idx=9)]]
-
-		return tblobj_header
-
-	def getCollectionTableBody(self, RISet=None, traitList=None, formName=None, species=''):
-
-		tblobj_body = []
-
-		className = "fs12 fwn b1 c222"
-
-		for thisTrait in traitList:
-			tr = []
-
-			if not thisTrait.haveinfo:
-				thisTrait.retrieveInfo(QTL=1)
-
-			if thisTrait.riset != RISet:
-				continue	
-
-			trId = str(thisTrait)
-
-			#XZ: check box column
-			tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkallbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class=className)))
-
-			#XZ: Dataset column
-			tr.append(TDCell(HT.TD(thisTrait.db.name, Class="fs12 fwn b1 c222"), thisTrait.db.name, thisTrait.db.name.upper()))
-
-			#XZ: Trait ID column
-			if thisTrait.cellid:
-				tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.cellid,url="javascript:showDatabase3('%s','%s','%s','%s')" % (formName, thisTrait.db.name, thisTrait.name, thisTrait.cellid), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.cellid), thisTrait.cellid))
-			else:
-				tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.getGivenName(),url="javascript:showDatabase3('%s','%s','%s','')" % (formName, thisTrait.db.name, thisTrait.name), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.name), thisTrait.name))
-
-			#XZ: Symbol column and Description column
-			if (thisTrait.db.type == "Publish"):
-				AbbreviationString = "--"
-				if (thisTrait.post_publication_abbreviation != None):
-					AbbreviationString = thisTrait.post_publication_abbreviation
-				PhenotypeString = thisTrait.post_publication_description
-				if thisTrait.confidential:
-					if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users):
-						if thisTrait.pre_publication_abbreviation:
-							AbbreviationString = thisTrait.pre_publication_abbreviation
-						else:
-							AbbreviationString = "--"
-						PhenotypeString = thisTrait.pre_publication_description
-
-				if AbbreviationString == "--":
-					tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
-				else:
-					tr.append(TDCell(HT.TD(AbbreviationString, Class=className), AbbreviationString, AbbreviationString.upper()))
-
-				tr.append(TDCell(HT.TD(PhenotypeString, Class=className), PhenotypeString, PhenotypeString.upper()))
-
-
-			elif (thisTrait.db.type == "ProbeSet" or thisTrait.db.type == "Temp"):
-				description_string = str(thisTrait.description).strip()
-				if (thisTrait.db.type == "ProbeSet"):
-					if (thisTrait.symbol != None):
-           					if thisTrait.geneid:
-                        				symbolurl = HT.Href(text=thisTrait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % thisTrait.geneid, Class="font_black fs12 fwn")
-            					else:
-                        				symbolurl = HT.Href(text=thisTrait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene&term=%s" % thisTrait.symbol, Class="font_black fs12 fwn")
-						tr.append(TDCell(HT.TD(symbolurl, align="left", Class="fs12 fwn b1 c222 fsI"), thisTrait.symbol, thisTrait.symbol))
-            				else:
-						tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
-					target_string = str(thisTrait.probe_target_description).strip()
-
-            				description_display = ''
-
-					if len(description_string) > 1 and description_string != 'None':
-						description_display = description_string
-					else:
-           		    			description_display = thisTrait.symbol
-
-            				if len(description_display) > 1 and description_display != 'N/A' and len(target_string) > 1 and target_string != 'None':
-                				description_display = description_display + '; ' + target_string.strip()
-					
-					description_string = description_display
-				else:
-					tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
-            			tr.append(TDCell(HT.TD(description_string, Class=className), description_string, description_string))
-			else:
-				if (thisTrait.name != None):
-					tr.append(TDCell(HT.TD(thisTrait.name, Class="fs12 fwn b1 c222"), thisTrait.name, thisTrait.name))
-				else:
-					tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
-				tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
-
-			#XZ: Location column
-			if (thisTrait.db.type == "Publish"):
-				tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
-			else:
-				if thisTrait.db.type == "ProbeSet" and thisTrait.cellid:
-					EnsemblProbeSetID = thisTrait.name
-					if '_at' in thisTrait.name:
-						EnsemblProbeSetID = thisTrait.name[0:thisTrait.name.index('_at')+3]	
-
-					#These tables (Ensembl) were created by Xusheng Wang in 2010 and are mm9 (so they'll need to be changed at some point to be mm10.
-					self.cursor.execute('''
-							SELECT EnsemblProbeLocation.* 
-							FROM EnsemblProbeLocation, EnsemblProbe, EnsemblChip, GeneChipEnsemblXRef, ProbeFreeze, ProbeSetFreeze
-							WHERE EnsemblProbeLocation.ProbeId=EnsemblProbe.Id and EnsemblProbe.ChipId=GeneChipEnsemblXRef.EnsemblChipId and
-								GeneChipEnsemblXRef.GeneChipId=ProbeFreeze.ChipId and EnsemblProbe.Name=%s and EnsemblProbe.ProbeSet=%s and
-								ProbeSetFreeze.Id=%s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id group by Chr, Start, End'''
-							,(thisTrait.cellid, EnsemblProbeSetID, thisTrait.db.id))
-					LocationFields = self.cursor.fetchall()
-
-					Chr=''
-					Mb=''
-					Start=''
-					End=''
-					if (len(LocationFields)>=1):
-						Chr,Start,End,Strand,MisMatch,ProbeId = map(self.nullRecord,LocationFields[0])
-						Start /= 1000000.0
-						End /= 1000000.0
-						Mb = Start
-					if (len(LocationFields)>1):
-						self.cursor.execute('''
-								SELECT ProbeSet.Chr, ProbeSet.Mb FROM ProbeSet, ProbeFreeze, ProbeSetFreeze 
-								WHERE ProbeSet.ChipId=ProbeFreeze.ChipId and ProbeSet.Name=%s and ProbeSetFreeze.Id=%s and
-									ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id'''
-								,(thisTrait.name, thisTrait.db.id))
-						ProbeSetChr, ProbeSetMb = map(self.nullRecord,self.cursor.fetchall()[0])
-					
-						self.cursor.execute('''
-								SELECT EnsemblProbeLocation.*, ABS(EnsemblProbeLocation.Start/1000000-%s) as Mb 
-								FROM EnsemblProbeLocation, EnsemblProbe, EnsemblChip, GeneChipEnsemblXRef, ProbeFreeze
-								WHERE EnsemblProbeLocation.ProbeId=EnsemblProbe.Id and EnsemblProbe.ChipId=GeneChipEnsemblXRef.EnsemblChipId and
-									GeneChipEnsemblXRef.GeneChipId=ProbeFreeze.ChipId and EnsemblProbe.Name=%s and EnsemblProbe.ProbeSet=%s and
-									EnsemblProbeLocation.Chr=%s and ProbeSetFreezeId=%s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id order by Mb limit 1'''
-								,(ProbeSetMb, thisTrait.cellid, EnsemblProbeSetID, ProbeSetChr, thisTrait.db.id))
-						NewLocationFields = self.cursor.fetchall()
-						if (len(NewLocationFields)>0):
-							Chr,Start,End,Strand,MisMatch,ProbeId,Mb = map(self.nullRecord,NewLocationFields[0])
-							Start /= 1000000.0
-							End /= 1000000.0
-							Mb = Start
-
-					#ZS: trait_location_value is used for sorting
-					trait_location_repr = "--"
-					trait_location_value = 1000000
-
-					if Chr and Mb:
-						try:
-							trait_location_value = int(Chr)*1000 + Mb
-						except:
-							if Chr.upper() == "X":
-								trait_location_value = 20*1000 + Mb
-							else:
-								trait_location_value = ord(str(Chr).upper()[0])*1000 + Mb
-					
-						trait_location_repr = "Chr%s: %.6f" % (Chr, float(Mb) )
-			
-					tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value))
-				
-				else:
-
-					#ZS: trait_location_value is used for sorting
-					trait_location_repr = "--"
-					trait_location_value = 1000000
-
-					if hasattr(thisTrait, 'chr') and hasattr(thisTrait, 'mb') and thisTrait.chr and thisTrait.mb:
-						try:
-							trait_location_value = int(thisTrait.chr)*1000 + thisTrait.mb
-						except:
-							if thisTrait.chr.upper() == "X":
-								trait_location_value = 20*1000 + thisTrait.mb
-							else:
-								trait_location_value = ord(str(thisTrait.chr).upper()[0])*1000 + thisTrait.mb
-					
-						trait_location_repr = "Chr%s: %.6f" % (thisTrait.chr, float(thisTrait.mb) )
-			
-					tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value))
-
-			#XZ: Mean column
-			if (thisTrait.db.type == "ProbeSet"):
-				if thisTrait.cellid:
-					mean = -10000.0
-					try:
-						thisTrait.retrieveData()
-						mean, median, var, stdev, sem, N = reaper.anova(thisTrait.exportInformative()[1])
-					except:
-						pass
-					repr = '%2.3f' % mean
-					mean = '%2.2f' % mean
-            				tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))	
-				else:
-           	 			self.cursor.execute("""
-                   	 			select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
-                   	 			where ProbeSetXRef.ProbeSetFreezeId = %d and
-                        	  			ProbeSet.Id = ProbeSetXRef.ProbeSetId and
-                        	  			ProbeSet.Name = '%s'
-            				""" % (thisTrait.db.id, thisTrait.name))
-            				result = self.cursor.fetchone()
-            				if result:
-                				if result[0]:
-                    					mean = result[0]
-                				else:
-                    					mean=0
-            				else:
-                				mean = 0
-
-					#XZ, 06/05/2009: It is neccessary to turn on nowrap
-            				repr = "%2.3f" % mean
-            				tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))	
-
-			elif (thisTrait.db.type == "Publish"):
-				self.cursor.execute("""
-				select count(PublishData.value), sum(PublishData.value) from PublishData, PublishXRef, PublishFreeze
-				where PublishData.Id = PublishXRef.DataId and 
-					PublishXRef.Id = %s and
-					PublishXRef.InbredSetId = PublishFreeze.InbredSetId and
-					PublishFreeze.Id = %d
-				""" % (thisTrait.name, thisTrait.db.id))
-				result = self.cursor.fetchone()
-
-				if result:
-					if result[0] and result[1]:
-						mean = result[1]/result[0]
-					else:	
-						mean = 0
-				else:
-					mean = 0
-
-				repr = "%2.3f" % mean
-				tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))		
-			else:
-				tr.append(TDCell(HT.TD("--", Class=className, align='left', nowrap='ON'),"--", 0))			
-			
-			#Number of cases
-			n_cases_value = 0
-			n_cases_repr = "--"
-			if (thisTrait.db.type == "Publish"):
-				self.cursor.execute("""
-				select count(PublishData.value) from PublishData, PublishXRef, PublishFreeze
-				where PublishData.Id = PublishXRef.DataId and 
-					PublishXRef.Id = %s and
-					PublishXRef.InbredSetId = PublishFreeze.InbredSetId and
-					PublishFreeze.Id = %d
-				""" % (thisTrait.name, thisTrait.db.id))
-				result = self.cursor.fetchone()
-
-				if result:
-					if result[0]:
-						n_cases_value = result[0]
-						n_cases_repr = result[0]
-
-				if (n_cases_value == "--"):
-					tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
-				else:
-					tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value))	
-			
-			elif (thisTrait.db.type == "ProbeSet"):
-				self.cursor.execute("""
-				select count(ProbeSetData.value) from ProbeSet, ProbeSetXRef, ProbeSetData, ProbeSetFreeze
-				where ProbeSet.Name='%s' and
-					ProbeSetXRef.ProbeSetId = ProbeSet.Id and
-					ProbeSetXRef.DataId = ProbeSetData.Id and
-					ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and
-					ProbeSetFreeze.Name = '%s'
-				""" % (thisTrait.name, thisTrait.db.name))
-				result = self.cursor.fetchone()
-
-				if result:
-					if result[0]:
-						n_cases_value = result[0]
-						n_cases_repr = result[0]
-				if (n_cases_value == "--"):
-					tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
-				else:
-					tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value))
-			
-			elif (thisTrait.db.type == "Geno"):
-				self.cursor.execute("""
-				select count(GenoData.value) from GenoData, GenoXRef, GenoFreeze, Geno, Strain
-				where Geno.SpeciesId = %s and Geno.Name='%s' and
-					GenoXRef.GenoId = Geno.Id and
-					GenoXRef.DataId = GenoData.Id and
-					GenoXRef.GenoFreezeId = GenoFreeze.Id and
-					GenoData.StrainId = Strain.Id and
-					GenoFreeze.Name = '%s'
-				""" % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, thisTrait.db.riset), thisTrait.name, thisTrait.db.name))
-				result = self.cursor.fetchone()
-
-				if result:
-					if result[0]:
-						n_cases_value = result[0]
-						n_cases_repr = result[0]
-				if (n_cases_value == "--"):
-					tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
-				else:
-					tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='right', nowrap="on"), n_cases_repr, n_cases_value))
-
-			else:
-				tr.append(TDCell(HT.TD(n_cases_repr, Class=className, align='left', nowrap="on"), n_cases_repr, n_cases_value))
-
-			#XZ: Max LRS column and Max LRS Location column
-			if (thisTrait.db.type != "Geno"):
-            			#LRS and its location
-            			LRS_score_repr = '--'
-            			LRS_score_value = 0
-            			LRS_location_repr = '--'
-            			LRS_location_value = 1000000
-            			LRS_flag = 1
-
-            			#Max LRS and its Locus location
-            			if hasattr(thisTrait, 'lrs') and hasattr(thisTrait, 'locus') and thisTrait.lrs and thisTrait.locus:
-                			self.cursor.execute("""
-                    			select Geno.Chr, Geno.Mb from Geno, Species
-                    			where Species.Name = '%s' and
-                          			Geno.Name = '%s' and
-                          			Geno.SpeciesId = Species.Id
-                			""" % (species, thisTrait.locus))
-                			result = self.cursor.fetchone()
-
-                			if result:
-                    				if result[0] and result[1]:
-                        				LRS_Chr = result[0]
-                        				LRS_Mb = result[1]
-
-                        				#XZ: LRS_location_value is used for sorting
-                        				try:
-								LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb)
-							except:
-								if LRS_Chr.upper() == 'X':
-									LRS_location_value = 20*1000 + float(LRS_Mb)
-								else:
-									LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb)
-
-
-                        				LRS_score_repr = '%3.1f' % thisTrait.lrs
-                        				LRS_score_value = thisTrait.lrs
-                        				LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb) )
-                        				LRS_flag = 0
-
-                        				tr.append(TDCell(HT.TD(LRS_score_repr, Class=className, align='right', nowrap="on"), LRS_score_repr, LRS_score_value))
-                        				tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value))
-
-            			if LRS_flag:
-                			tr.append(TDCell(HT.TD(LRS_score_repr, Class=className), LRS_score_repr, LRS_score_value))
-                			tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value))
-			else:
-                		tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 0))
-                		tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", 1000000))							
-
-			tblobj_body.append(tr)
-
-		return tblobj_body		
-		
-	def getSortByValue(self):
-
-		sortby = ("pv", "up")
-
-		return sortby
-
-	def nullRecord(self,x):
-		if x or x == 0:
-			return x
-		else:
-			return ""
-