Add all the source codes into the github.

1 files changed, 536 insertions, 0 deletions

diff --git a/web/webqtl/search/TextSearchPage.py b/web/webqtl/search/TextSearchPage.py
new file mode 100755
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+++ b/web/webqtl/search/TextSearchPage.py
@@ -0,0 +1,536 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+import string
+import os
+import cPickle
+from math import *
+
+import reaper
+from htmlgen import HTMLgen2 as HT
+
+from base import admin
+from base import webqtlConfig
+from base.templatePage import templatePage
+from utility import webqtlUtil
+from base.webqtlDataset import webqtlDataset
+from base.webqtlTrait import webqtlTrait
+from utility.THCell import THCell
+from utility.TDCell import TDCell
+from utility import webqtlUtil
+
+
+
+class TextSearchPage(templatePage):
+	maxReturn = 200
+
+	def __init__(self, fd):
+
+		templatePage.__init__(self, fd)
+
+                if not self.openMysql():
+                        return
+
+		# updated by NL, deleted jquery here, move it to dhtml.js
+		self.dict['js1'] = ''
+
+		species_list = [] #List of species (mouse, rat, human), with the selected species listed first
+
+		input_species = string.strip(string.lower(fd.formdata.getfirst('species', "mouse"))) #XZ, Oct 28, 2009: I changed the default species to mouse.
+		species_list.append(input_species)
+		#Create list of species (mouse, rat, human) with the species the user selected first
+		for species in ["mouse","rat","human"]:
+			if species not in species_list:
+				species_list.append(species)
+
+		ADMIN_tissue_alias = admin.ADMIN_tissue_alias
+
+		tissue = string.strip(string.lower(fd.formdata.getfirst('tissue', "")))
+		if tissue:
+			try:
+				rev_ADMIN_tissue_alias = {}
+				for key in ADMIN_tissue_alias.keys():
+					rev_ADMIN_tissue_alias[key] = key
+					for alias in ADMIN_tissue_alias[key]:
+						rev_ADMIN_tissue_alias[alias.upper()] = key
+				tissue = rev_ADMIN_tissue_alias[tissue.upper()]
+			except:
+				tissue = "UNKNOWN"
+
+		#possibly text output
+		txtOutput = [] #ZS: if format=text
+		all_species_dataset_count = 0 #XZ: count of datasets across all species; used in the opening text of the page
+		all_species_trait_count = 0  #XZ: count of records across all species; used in opening text of the page and text file (if format = text)
+
+		#div containing the tabs (species_container), the tabs themselves (species_tab_list, which is inserted into species_tabs), and the table (species_table) containing both the tissue and results tables for each tab
+		species_container = HT.Div(id="species_tabs", Class="tab_container") #Div that will contain tabs for mouse/rat/human species; each tab contains a table with the result count for each tissue group
+		species_tab_list = [HT.Href(text="%s" % species_list[0].capitalize(), url="#species1"), HT.Href(text="%s" % species_list[1].capitalize(), url="#species2"), HT.Href(text="%s" % species_list[2].capitalize(), url="#species3")]
+		species_tabs = HT.List(species_tab_list, Class="tabs")
+		species_table = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left")
+
+		for i in range(len(species_list)):
+			species_container_table = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left") #ZS: Table containing both the tissue record count and trait record tables as cells; this fixes a display issue in some browsers that places the tables side by side instead of top/bottom
+
+			species = species_list[i]
+			ADMIN_search_dbs = admin.ADMIN_search_dbs[species]
+			this_species_dataset_count = 0 #XZ: count of the datasets containing results for this species
+			this_species_trait_count = 0  #XZ: count of the trait records for this species
+
+			div = HT.Div(id="species%s" % (i+1), Class="tab_content")
+			tab_container = HT.Span() #ZS: Contains species_container_table within the species' tab
+
+			tissuePageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left")				
+			tissue_tblobj = {} # object used to create the table listing the results for each tissue
+			tissue_tblobj['header'] = self.getTissueTableHeader() # creates header for table listing results for selected tissue
+
+			traitPageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left")
+			trait_tblobj = {} # object used to create the table listing the trait results for each tissue
+			trait_tblobj['header'] = self.getTraitTableHeader() # creates header for table listing trait results for selected tissue
+
+			tissue_tblobj['body'], trait_tblobj['body'], this_species_dataset_count, this_species_trait_count, this_species_txtOutput = self.createTableBodies(fd, species, tissue, ADMIN_search_dbs)
+
+			if species == input_species:
+				txtOutput = this_species_txtOutput
+
+			filename1 = webqtlUtil.genRandStr("Search_") #filename for tissue table object
+			tissue_objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename1), 'wb')
+			cPickle.dump(tissue_tblobj, tissue_objfile)
+			tissue_objfile.close()
+
+			tissue_sortby = self.getTissueSortByValue() # sets how the tissue table should be sorted by default
+			tissue_div = HT.Div(webqtlUtil.genTableObj(tblobj=tissue_tblobj, file=filename1, sortby=tissue_sortby, tableID = "tissue_sort%s" % (i+1), addIndex = "1"), Id="tissue_sort%s" % (i+1))
+
+			tissuePageTable.append(HT.TR(HT.TD(" ")))
+			tissuePageTable.append(HT.TR(HT.TD(tissue_div)))
+			tissuePageTable.append(HT.TR(HT.TD(" ")))
+			species_container_table.append(HT.TR(HT.TD(tissuePageTable)), HT.TR(HT.TD(" ")))
+
+
+			filename2 = webqtlUtil.genRandStr("Search_") #filename for trait table object
+			trait_objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename2), 'wb')
+			cPickle.dump(trait_tblobj, trait_objfile)
+			trait_objfile.close()
+
+			trait_sortby = self.getTraitSortByValue() # sets how the trait table should be sorted by default
+			trait_div = HT.Div(webqtlUtil.genTableObj(tblobj=trait_tblobj, file=filename2, sortby=trait_sortby, tableID = "results_sort%s" % (i+1), addIndex = "0"), Id="results_sort%s" % (i+1))
+
+			traitPageTable.append(HT.TR(HT.TD(" ")))
+			traitPageTable.append(HT.TR(HT.TD(trait_div)))
+			traitPageTable.append(HT.TR(HT.TD(" ")))
+			species_container_table.append(HT.TR(HT.TD(traitPageTable)), HT.TR(HT.TD(" ")))
+
+			if this_species_trait_count == 0:
+				tab_container.append(HT.Div("No records retrieved for this species.", align="left", valign="top", style="font-size:42"))
+			else:
+				tab_container.append(species_container_table)
+
+			all_species_dataset_count += this_species_dataset_count
+			all_species_trait_count += this_species_trait_count
+
+			div.append(tab_container)
+			species_table.append(HT.TR(HT.TD(div)))
+
+		species_container.append(species_table)
+		
+
+
+
+		if fd.returnFmt != 'text': #if the format is not 'text'
+			self.dict['title'] = 'Search Results'
+			TD_LR = HT.TD(height=100,width="100%",bgColor='#fafafa',valign="top")
+			pageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%",border=0, align="Left") # Table containing all of the page's elements (opening text, form); in some browers the elements arrange themselves horizontally if you don't put them into a table, so this fixes that problem
+
+			formTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="100%",border=0) # Table containing all of the form's elements (tabs, option buttons); used to correct the same issue mentioned in pageTable's comment
+
+			mainForm = HT.Form( cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='showDatabase', submit=HT.Input(type='hidden'))
+			hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':fd.RISet}
+			hddn['incparentsf1']='ON'
+			for key in hddn.keys():
+				mainForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+
+			#Add to collection, select all, invert selection, and deselect all ("reset") buttons
+			addselect = HT.Href(url="#redirect", Class="add_traits")
+			addselect_img = HT.Image("/images/add_collection1_final.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;")
+			addselect.append(addselect_img)
+			selectall = HT.Href(url="#redirect", onClick="checkAll(document.getElementsByName('showDatabase')[0]);")
+			selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;")
+			selectall.append(selectall_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)
+			reset = HT.Href(url="#redirect", onClick="checkNone(document.getElementsByName('showDatabase')[0]); return false;")
+			reset_img = HT.Image("/images/select_none2_final.jpg", alt="Select None", title="Select None", style="border:none;")
+			reset.append(reset_img)
+
+			#Table with select, deselect, invert, etc. It is used for the results table.
+			optionsTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="20%",border=0)
+			optionsRow = HT.TR(HT.TD(selectall, width="25%"), HT.TD(reset, width="25%"), HT.TD(selectinvert, width="25%"), HT.TD(addselect, width="25%"))
+			labelsRow = HT.TR(HT.TD(" "*2,"Select", width="25%"), HT.TD(" ","Deselect", width="25%"), HT.TD(" "*3,"Invert", width="25%"), HT.TD(" "*4,"Add", width="25%"))
+			optionsTable.append(HT.TR(HT.TD(" ")), optionsRow, labelsRow)
+			
+			if fd.geneName:
+				searchType = "gene name " + fd.geneName
+			elif fd.refseq:
+				searchType = "RefSeq accession number " + fd.refseq
+			elif fd.genbankid:
+				searchType = "Genbank ID " + fd.genbankid
+			elif fd.geneid:
+				searchType = "Gene ID " + fd.geneid
+			else:
+				searchType = ""
+
+			SearchText = HT.Span("You searched for the %s in GeneNetwork." % searchType, HT.BR(),
+						"We queried %s expression datasets across %s species and listed the results" % (all_species_dataset_count, len(species_list)), HT.BR(),
+						"below. A total of %s records that may be of interest to you were found. The" % all_species_trait_count, HT.BR(),
+						"top table lists the number of results found for each relevant tissue, and the", HT.BR(),
+						"bottom gives a basic summary of each result. To study one of the results, click", HT.BR(),
+						"its Record ID. More detailed information is also available for each result's group", HT.BR() ,
+						"and dataset. To switch between species, click the tab with the corresponding", HT.BR(),
+						"label.", HT.BR(), HT.BR(),
+						"Please visit the links to the right to learn more about the variety of features", HT.BR(),
+						"available within GeneNetwork.")	
+			
+			LinkText = HT.Span()
+			
+			mainLink = HT.Href(url="/webqtl/main.py", text = "Main Search Page", target="_blank")
+			homeLink = HT.Href(url="/home.html", text = "What is GeneNetwork?", target="_blank")
+			tourLink = HT.Href(url="/tutorial/WebQTLTour/", text = "Tour of GeneNetwork (20-40 min)", target="_blank")
+			faqLink = HT.Href(url="/faq.html", text = "Frequently Asked Questions", target="_blank")
+			glossaryLink = HT.Href(url="/glossary.html", text = "Glossary of terms used throughout GeneNetwork", target="_blank")
+			
+			LinkText.append(mainLink, HT.BR(), homeLink, HT.BR(), tourLink, HT.BR(), faqLink, HT.BR(), glossaryLink)
+			
+			formTable.append(HT.TR(HT.TD(species_tabs, species_container)), HT.TR(HT.TD(optionsTable)))
+			mainForm.append(formTable)
+			
+
+			if fd.geneName:
+				SearchHeading = HT.Paragraph('Search Results for gene name ', fd.geneName)
+			elif fd.refseq:
+				SearchHeading = HT.Paragraph('Search Results for RefSeq accession number ', fd.refseq)
+			elif fd.genbankid:
+				SearchHeading = HT.Paragraph('Search Results for Genbank ID ', fd.genbankid)
+			elif fd.geneid:
+				SearchHeading = HT.Paragraph('Search Results for Gene ID ', fd.geneid)
+			else:
+				SearchHeading = HT.Paragraph('')
+
+			SearchHeading.__setattr__("class","title")
+
+			pageTable.append(HT.TR(HT.TD(SearchText, width=600), HT.TD(LinkText, align="left", valign="top")), HT.TR(HT.TD(" ", colspan=2)), HT.TR(HT.TD(mainForm, colspan=2)))
+			TD_LR.append(SearchHeading, pageTable)
+			self.dict['body'] = TD_LR
+		else:
+		    if len(txtOutput) == 0:
+			self.output = "##No records were found for this species. \n"
+		    else:
+			self.output = "##A total of %d records were returned. \n" % all_species_trait_count
+			newOutput = []
+			strainLists = {}
+			for item in txtOutput:
+				tissueGrp, thisTrait = item
+				RISet = thisTrait.riset
+				if strainLists.has_key(RISet):
+					thisStrainlist = strainLists[RISet]
+				else:
+					thisGenotype = reaper.Dataset()
+					thisGenotype.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno'))
+					if thisGenotype.type == "riset": 
+						_f1, _f12, _mat, _pat = webqtlUtil.ParInfo[RISet]
+						thisGenotype = thisGenotype.add(Mat=_mat, Pat=_pat, F1=_f1)
+					thisStrainlist = list(thisGenotype.prgy)
+					strainLists[RISet] = thisStrainlist
+				thisTrait.retrieveData(strainlist=thisStrainlist)
+				thisData = []
+				for item in thisStrainlist:
+					if thisTrait.data.has_key(item): thisData.append(thisTrait.data[item].val)
+					else: thisData.append(None)
+				newOutput.append(["Structure", "Database", "ProbeSetID", "Cross"] + thisStrainlist)
+				newOutput.append([tissueGrp, '"%s"' % thisTrait.db.fullname, thisTrait.name, RISet]+map(str,thisData))
+			newOutput = webqtlUtil.asymTranspose(newOutput)
+			for item in newOutput:
+				 self.output += string.join(item, "\t") + "\n"		
+
+
+	def createTableBodies(self, fd, species, tissue, ADMIN_search_dbs):
+
+		this_species_txtOutput = []
+
+		#priority GeneName > refseq > genbankid
+		this_species_trait_count = 0 #count of all traits in this species
+		this_species_dataset_count = 0 #Number of datasets in this species
+		row_count = 0 #Index number used in the first row of the trait table
+		trait_tblobj_body = [] #body of table with the results themselves; 
+		tissue_tblobj_body = [] #body of table with the number of results for each tissue group
+		className = "fs12 fwn b1 c222"
+
+		for i, tissueGrp in enumerate(ADMIN_search_dbs.keys()):
+			if tissue and tissue.upper() != tissueGrp.upper():
+				continue
+			dbNames = ADMIN_search_dbs[tissueGrp]
+
+			tissue_tr = [] #Table row for tissue group
+			tissue_tr.append(TDCell(HT.TD('', Class=className)))
+			tissue_tr.append(TDCell(HT.TD(tissueGrp.capitalize(), Class=className), tissueGrp, tissueGrp)) #Append cell with tissue name to row
+
+			this_tissue_record_count = 0 #Count of the results for each tissue		
+			for dbName in dbNames:
+				this_species_dataset_count += 1
+				thisDB = webqtlDataset(dbName, self.cursor)
+
+				if fd.geneName:
+					if fd.searchAlias:
+						self.cursor.execute("""SELECT ProbeSet.Name
+											FROM
+										ProbeSet, ProbeSetFreeze, ProbeSetXRef
+											WHERE
+										ProbeSetFreeze.Name = "%s" AND
+										ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND
+										MATCH (ProbeSet.symbol, alias) AGAINST ("+%s" IN BOOLEAN MODE) AND
+										ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.geneName))
+					else:
+						self.cursor.execute("""SELECT ProbeSet.Name
+											FROM
+										ProbeSet, ProbeSetFreeze, ProbeSetXRef
+											WHERE
+										ProbeSetFreeze.Name = "%s" AND
+										ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND
+										ProbeSet.symbol = "%s" AND
+										ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.geneName))
+				elif fd.refseq:
+
+				# XZ, Oct/08/2009: Search for RefSeq ID is kind of tricky. One probeset can have multiple RefseqIDs that are delimited by ' /// ' (currently). 
+				# So I have to use 'like' instead of '=' in SQL query. But user search with one short string, for example 'NM_1', it will return thousands of results. 
+				# To prevent this, I set the restriction that the length of input Refseq ID must be at least 9 characters. Otherwise, do NOT start searching. 
+				# Even with the restriction of input RefSeqID, I'm still worried about the 'like' in SQL query. My concern is in future, there might be RefSeqIDs with 
+				# 10 characters whose first 9 characters are the same as the existing ones. So I decide to further check the result. We should also consider that the 
+				# RefSeqID in database may have version number such as "NM_177938.2". If the input RefSeqID is 'NM_177938', it should be matched. I think we should get rid of the version number in database.
+
+					if len(fd.refseq) < 9:
+						if fd.returnFmt != 'text':
+							heading = "Search Result"
+							detail = ["The RefSeq ID that you inputed is less than 9 characters. GeneNetwork thinks it is not a legitimate RefSeq ID and did not do the search. Please try to use a RefSeq ID with at least 9 characters."]
+							self.error(heading=heading,detail=detail,error="Not Found")
+						else:
+							self.output = "#The gene name or IDs you submitted did not match any record in the databases available. You may try different gene names or tissue type."
+						return
+					else:
+						sqlString = """SELECT ProbeSet.Id, ProbeSet.RefSeq_TranscriptId
+										FROM
+									ProbeSet, ProbeSetFreeze, ProbeSetXRef
+										WHERE
+									ProbeSetFreeze.Name = "%s" AND
+									ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND
+									MATCH(ProbeSet.RefSeq_TranscriptId) AGAINST ("+%s" IN BOOLEAN MODE) AND
+									ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.refseq)
+
+						self.cursor.execute(sqlString)
+
+						results = self.cursor.fetchall()
+						if results:
+							Id_of_really_matched_probeset = []
+
+							for one_result in results:
+								ProbeSet_Id, ProbeSet_RefSeq_TranscriptId = one_result
+								multiple_RefSeqId = string.split(string.strip(ProbeSet_RefSeq_TranscriptId), '///')
+								for one_RefSeqId in multiple_RefSeqId:
+									tokens = string.split( one_RefSeqId, '.' )
+									one_RefSeqId_without_versionNum = string.strip(tokens[0])
+									if one_RefSeqId_without_versionNum == fd.refseq:
+										Id_of_really_matched_probeset.append( ProbeSet_Id )
+										break
+
+							if Id_of_really_matched_probeset:
+								condition_string = " or ".join(["Id = %s" % one_ID for one_ID in Id_of_really_matched_probeset])
+								sqlString = """SELECT ProbeSet.Name from ProbeSet where (%s)""" % condition_string
+
+								self.cursor.execute(sqlString)
+						else:
+							pass
+
+				elif fd.genbankid:
+					self.cursor.execute("""SELECT ProbeSet.Name
+										FROM
+									ProbeSet, ProbeSetFreeze, ProbeSetXRef
+										WHERE
+									ProbeSetFreeze.Name = "%s" AND
+									ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND
+									ProbeSet.GenbankId = "%s" AND
+									ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.genbankid))
+				elif fd.geneid:
+					self.cursor.execute("""SELECT ProbeSet.Name
+										FROM
+									ProbeSet, ProbeSetFreeze, ProbeSetXRef
+										WHERE
+									ProbeSetFreeze.Name = "%s" AND
+									ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId AND
+									ProbeSet.GeneId = "%s" AND
+									ProbeSet.Id = ProbeSetXRef.ProbeSetId""" % (dbName, fd.geneid))
+				else:
+					continue
+
+				results = self.cursor.fetchall()			
+				if len(results) > 0:
+					this_tissue_record_count += len(results)
+					this_species_trait_count += this_tissue_record_count
+
+					for result in results:
+				 		_ProbeSetID = result[0]
+						thisTrait = webqtlTrait(db=thisDB, name=_ProbeSetID, cursor=self.cursor)
+						results_tr = []
+						trId = str(thisTrait)
+						_traitUrl = thisTrait.genHTML(dispFromDatabase=1)
+						_traitName = str(thisTrait)
+						
+						#ZS: check box column
+						results_tr.append(TDCell(HT.TD(str(row_count+1), HT.Input(type="checkbox", Class="checkallbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", align="right", Class=className), str(row_count+1), row_count+1))
+						row_count += 1
+
+						#ZS: Tissue column
+						results_tr.append(TDCell(HT.TD(tissueGrp.capitalize(), Class=className), tissueGrp, tissueGrp))
+
+						#ZS: Group column
+						risetUrl = HT.Href(text=thisTrait.riset, url="http://www.genenetwork.org/%sCross.html#%s" % (species, thisTrait.riset), target="_blank", Class=className)
+						results_tr.append(TDCell(HT.TD(risetUrl, Class=className), thisTrait.riset, thisTrait.riset))
+
+						#ZS: Dataset column
+						results_tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name,
+								target='_blank', Class="fs13 fwn non_bold"), Class=className), thisTrait.db.name.upper(), thisTrait.db.name.upper()))
+
+						#ZS: Trait ID column
+						results_tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.getGivenName(),url="javascript:showDatabase3('%s','%s','%s','')" % ('showDatabase', thisTrait.db.name, thisTrait.name), Class="fs12 fwn"), nowrap="yes",align="left", Class=className),str(thisTrait.name), thisTrait.name))
+
+						#ZS: Symbol column and Description column
+						description_string = str(thisTrait.description).strip()
+						if (thisTrait.db.type == "ProbeSet"):
+							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:
+							results_tr.append(TDCell(HT.TD("--", align="left", Class=className), "--", "Zz"))
+							
+            					results_tr.append(TDCell(HT.TD(description_string, Class=className), description_string, description_string))
+
+						#XZ: 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) )
+				
+						results_tr.append(TDCell(HT.TD(trait_location_repr, nowrap='ON', Class=className), trait_location_repr, trait_location_value))
+	
+						#ZS: Mean column
+	           	 			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
+	
+	            				repr = "%2.3f" % mean
+	            				results_tr.append(TDCell(HT.TD(repr, Class=className, align='right', nowrap='ON'),repr, mean))
+						trait_tblobj_body.append(results_tr)
+
+						this_species_txtOutput.append([tissueGrp, thisTrait])
+
+
+			tissue_tr.append(TDCell(HT.TD(str(this_tissue_record_count), Class=className), str(this_tissue_record_count), this_tissue_record_count))
+			tissue_tblobj_body.append(tissue_tr)
+	
+		self.output = "self.output"
+
+		return tissue_tblobj_body, trait_tblobj_body, this_species_dataset_count, this_species_trait_count, this_species_txtOutput
+
+
+	def getTissueSortByValue(self):
+	
+		sortby = ("tissue_group", "up")
+
+		return sortby
+
+
+	def getTraitSortByValue(self):
+	
+		sortby = ("tissue", "up")
+
+		return sortby
+
+
+	def getTissueTableHeader(self):
+
+		tblobj_header = []
+
+		className = "fs13 fwb ffl b1 cw cbrb"
+
+		tblobj_header = [[THCell(HT.TD(' ', Class=className, nowrap="on"), sort=0),
+			THCell(HT.TD('Tissue',HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="tissue_group", idx=1),	
+			THCell(HT.TD('Results', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="results", idx=2)]]
+
+		return tblobj_header
+
+	def getTraitTableHeader(self):
+
+		tblobj_header = []
+
+		className = "fs13 fwb ffl b1 cw cbrb"
+
+		tblobj_header = [[THCell(HT.TD('Index',HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="index", idx=0),
+			THCell(HT.TD('Tissue',HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="tissue", idx=1),	
+			THCell(HT.TD('Group',HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="group", idx=2),	
+			THCell(HT.TD('Dataset', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="dataset", idx=3),
+			THCell(HT.TD('Record ID', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="name", idx=4),
+			THCell(HT.TD('Description', HT.BR(), HT.BR(), valign="top", Class=className, nowrap="on"), text="desc", idx=5),
+			THCell(HT.TD('Location', HT.BR(), 'Chr and Mb', HT.BR(), valign="top", Class=className, nowrap="on"), text="location", idx=6),
+			THCell(HT.TD('Mean', HT.BR(), 'Expr', HT.BR(), valign="top", Class=className, nowrap="on"), text="mean", idx=7)]]
+
+		return tblobj_header