path: root/web/webqtl/search/SearchResultPage.py

import string
import os
import cPickle
import re
from math import *
import time
import pyXLWriter as xl
import pp
import math
import datetime

from htmlgen import HTMLgen2 as HT

from base import webqtlConfig
from utility.THCell import THCell
from utility.TDCell import TDCell
from base.data_set import DataSet
from base.webqtlTrait import webqtlTrait
from base.templatePage import templatePage
from utility import webqtlUtil
from dbFunction import webqtlDatabaseFunction

import PubmedSearch

import logging
logging.basicConfig(filename="/tmp/gn_log_leiyan", level=logging.INFO)
_log = logging.getLogger("search")

class SearchResultPage(templatePage):

	maxReturn = 3000
#	NPerPage = 100
	nkeywords = 0

	def __init__(self, fd):

		templatePage.__init__(self, fd)

		if not self.openMysql():
			return

		self.dict['title'] = 'Search Results'
		TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="top")
		self.database = fd.formdata.getfirst('database', '')
		if not self.database or self.database == 'spacer':
			#Error, No database selected
			heading = "Search Result"
			detail = ['''No database was selected for this search, please
				go back and SELECT at least one database.''']
			self.error(heading=heading,detail=detail,error="No Database Selected")
			return
		elif type(self.database) == type(""):
			#convert database into a database list
			#was used for multiple databases search, this
			#feature has been abandoned,
			self.database = string.split(self.database,',')
		else:
			pass

		###########################################
		#   Names and IDs of RISet / F2 set
		###########################################
		if self.database == ['_allPublish']:
			self.cursor.execute("""select PublishFreeze.Name, InbredSet.Name, InbredSet.Id from PublishFreeze,
				InbredSet where PublishFreeze.Name not like 'BXD300%' and InbredSet.Id =
				PublishFreeze.InbredSetId""")
			results = self.cursor.fetchall()
			self.database = map(lambda x: DataSet(x[0], self.cursor), results)
			self.databaseCrosses = map(lambda x: x[1], results)
			self.databaseCrossIds = map(lambda x: x[2], results)
			self.singleCross = False
		else:
			self.database = map(lambda x: DataSet(x, self.cursor), self.database)
			#currently, webqtl wouldn't allow multiple crosses
			#for other than multiple publish db search
			#so we can use the first database as example
			if self.database[0].type=="Publish":
				pass
			elif self.database[0].type in ("Geno", "ProbeSet"):

				#userExist = None

				for individualDB in self.database:
					self.cursor.execute('SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM %sFreeze WHERE Name = "%s"' %  (self.database[0].type, individualDB))
					indId, indName, indFullName, confidential, AuthorisedUsers = self.cursor.fetchall()[0]
				
					if confidential == 1:
						access_to_confidential_dataset = 0

						#for the dataset that confidentiality is 1
						#1. 'admin' and 'root' can see all of the dataset
						#2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
						if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']:
							access_to_confidential_dataset = 1
						else:
							AuthorisedUsersList=AuthorisedUsers.split(',')
							if AuthorisedUsersList.__contains__(self.userName):
								access_to_confidential_dataset = 1

						if not access_to_confidential_dataset:
							#Error, No database selected
							heading = "Search Result"
							detail = ["The %s database you selected is not open to the public at this time, please go back and SELECT other database." % indFullName]
							self.error(heading=heading,detail=detail,error="Confidential Database")
							return
			else:
				heading = "Search Result"
				detail = ['''The database has not been established yet, please
					go back and SELECT at least one database.''']
				self.error(heading=heading,detail=detail,error="No Database Selected")
				return

			self.database[0].getRISet()
			self.databaseCrosses = [self.database[0].riset]
			self.databaseCrossIds = [self.database[0].risetid]
			self.singleCross = True
			#XZ, August 24,2010: Since self.singleCross = True, it's safe to assign one species Id.
			self.speciesId = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.database[0].riset)

		###########################################
		#    make sure search from same type of databases
		###########################################
		dbTypes = map(lambda X: X.type, self.database)
		self.dbType = dbTypes[0]
		for item in dbTypes:
			if item != self.dbType:
				heading = "Search Result"
				detail = ["Search can only be performed among the same type of databases"]
				self.error(heading=heading,detail=detail,error="Error")
				return
		if self.dbType == "Publish":
			self.searchField = ['Phenotype.Post_publication_description', 'Phenotype.Pre_publication_description', 'Phenotype.Pre_publication_abbreviation', 'Phenotype.Post_publication_abbreviation', 'Phenotype.Lab_code', 'Publication.PubMed_ID', 'Publication.Abstract', 'Publication.Title', 'Publication.Authors', 'PublishXRef.Id']

		elif self.dbType == "ProbeSet":
			self.searchField = ['Name','Description','Probe_Target_Description','Symbol','Alias','GenbankId', 'UniGeneId','RefSeq_TranscriptId']
		elif self.dbType == "Geno":
			self.searchField = ['Name','Chr']

		###########################################
		#	Search Options
		###########################################
		self.matchwhole = fd.formdata.getfirst('matchwhole')
		#split result into pages
		self.pageNumber = fd.formdata.getfirst('pageno', '0')
		try:
			self.pageNumber = int(self.pageNumber)
		except:
			self.pageNumber = 0


		###########################################
		#       Generate Mysql Query
		###########################################
		geneIdListQuery = fd.formdata.getfirst('geneId', '')
		if geneIdListQuery:
			geneIdListQuery = string.replace(geneIdListQuery, ",", " ")
			geneIdListQuery = " geneId=%s" % string.join(string.split(geneIdListQuery), "-")

		self.ANDkeyword = fd.formdata.getfirst('ANDkeyword', "")
		_log.info("self.ANDkeyword[1]: " + self.ANDkeyword)
		pubmedSearchObject = PubmedSearch.PubmedSearch(self.ANDkeyword, self.database[0].id)
		self.ANDkeyword = pubmedSearchObject.getNewS()
		_log.info("self.ANDkeyword[2]: " + self.ANDkeyword)

		self.ORkeyword = fd.formdata.getfirst('ORkeyword', "")
		_log.info("self.ORkeyword[1]: " + self.ORkeyword)
		pubmedSearchObject = PubmedSearch.PubmedSearch(self.ORkeyword, self.database[0].id)
		self.ORkeyword = pubmedSearchObject.getNewS()
		_log.info("self.ORkeyword[2]: "+self.ORkeyword)

		self.ORkeyword += geneIdListQuery

		self.ANDkeyword = self.ANDkeyword.replace("\\", "").strip()
		self.ORkeyword = self.ORkeyword.replace("\\", "").strip()
		#user defined sort option
		self.orderByUserInput = fd.formdata.getfirst('orderByUserInput', "").strip()
		#default sort option if user have not defined
		self.orderByDefalut = ""

		#XZ, Dec/16/2010: I add examples to help understand this block of code. See details in function pattersearch.

		#XZ: self._1mPattern examples: WIKI=xxx, RIF=xxx, GO:0045202
		self._1mPattern = re.compile('\s*(\S+)\s*[:=]\s*([a-zA-Z-\+\d\.]+)\s*')

		#XZ: self._2mPattern examples: Mean=(15.0 16.0), Range=(10 100), LRS=(Low_LRS_limit, High_LRS_limit), pvalue=(Low_limit, High_limit), Range=(10 100) 
		self._2mPattern = re.compile('\s*(\S+)\s*[=in]{1,2}\s*\(\s*([-\d\.]+)[, \t]+([-\d\.]+)[, \t]*([-\d\.]*)\s*\)')

		#XZ: self._3mPattern examples: Position=(Chr1 98 104), Pos=(Chr1 98 104), Mb=(Chr1 98 104), CisLRS=(Low_LRS_limit, High_LRS_limit, Mb_buffer), TransLRS=(Low_LRS_limit, High_LRS_limit, Mb_buffer)
		self._3mPattern = re.compile('\s*(\S+)\s*[=in]{1,2}\s*\(\s*[Cc][Hh][Rr]([^, \t]+)[, \t]+([-\d\.]+)[, \t]+([-\d\.]+)\s*\)')

		#XZ: self._5mPattern examples: LRS=(Low_LRS_limit, High_LRS_limit, ChrNN, Mb_Low_Limit, Mb_High_Limit)
		self._5mPattern = re.compile('\s*(\S+)\s*[=in]{1,2}\s*\(\s*([-\d\.]+)[, \t]+([-\d\.]+)[, \t]+[Cc][Hh][Rr]([^, \t]+)[, \t]+([-\d\.]+)[, \t]+([-\d\.]+)\s*\)')

		#Error, No keyword input
		if not (self.ORkeyword or self.ANDkeyword):
			heading = "Search Result"
			detail = ["Please make sure to enter either your search terms (genes, traits, markers), or advanced search commands."]
			self.error(heading=heading,detail=detail,error="No search terms were entered")
			return

		#query clauses
		self.ANDQuery = []
		self.ORQuery = []
		#descriptions, one for OR search, one for AND search
		self.ANDDescriptionText = []
		self.ORDescriptionText = []

		if not self.normalSearch():
			return
		if not self.patternSearch():
			return
		if not self.assembleQuery():
			return
		self.nresults = self.executeQuery()

		if len(self.database) > 1:
			dbUrl =  "Multiple phenotype databases"
			dbUrlLink = " were"
		else:
			dbUrl =  self.database[0].genHTML()
			dbUrlLink = " was"

		SearchText = HT.Blockquote('GeneNetwork searched the ', dbUrl, ' for all records ')
		if self.ORkeyword2:
			NNN = len(self.ORkeyword2)
			if NNN > 1:
				SearchText.append(' that match the terms ')
			else:
				SearchText.append(' that match the term ')
			for j, term in enumerate(self.ORkeyword2):
				SearchText.append(HT.U(term))
				if NNN > 1 and j < NNN-2:
					SearchText.append(", ")
				elif j == NNN-2:
					SearchText.append(", or ")
				else:
					pass
		if self.ORDescriptionText:
			if self.ORkeyword2:
				SearchText.append("; ")
			else:
				SearchText.append(" ")
			for j, item in enumerate(self.ORDescriptionText):
				SearchText.append(item)
				if j < len(self.ORDescriptionText) -1:
					SearchText.append(";")

		if (self.ORkeyword2 or self.ORDescriptionText) and (self.ANDkeyword2 or self.ANDDescriptionText):
			SearchText.append("; ")
		if self.ANDkeyword2:
			if (self.ORkeyword2 or self.ORDescriptionText):
				SearchText.append(' records')
			NNN = len(self.ANDkeyword2)
			if NNN > 1:
				SearchText.append(' that match the terms ')
			else:
				SearchText.append(' that match the term ')
			for j, term in enumerate(self.ANDkeyword2):
				SearchText.append(HT.U(term))
				if NNN > 1 and j < NNN-2:
					SearchText.append(", ")
				elif j == NNN-2:
					SearchText.append(", and ")
				else:
					pass
		if self.ANDDescriptionText:
			if self.ANDkeyword2:
				SearchText.append(" and ")
			else:
				SearchText.append(" ")
			for j, item in enumerate(self.ANDDescriptionText):
				SearchText.append(item)
				if j < len(self.ANDDescriptionText) -1:
					SearchText.append(" and ")

		SearchText.append(". ")
		if self.nresults == 0:
			heading = "Search Result"
			detail = ["Sorry, GeneNetwork did not find any records matching your request. Please check the syntax or try the ANY rather than the ALL field."]
			self.error(heading=heading,intro = SearchText.contents,detail=detail,error="Not Found")
			return
		elif self.nresults == 1:
			SearchText.append(HT.P(), 'GeneNetwork found one record that matches your request. To study this record, click on its text below. To add this record to your Selection window, use the checkbox and then click the ', HT.Strong('Add to Collection'),' button. ')
		elif self.nresults >= 1 and self.nresults <= self.maxReturn:
			SearchText.append(HT.P(), 'GeneNetwork found a total of ', HT.Span(self.nresults, Class='fwb cr'), ' records. To study any one of these records, click on its ID below. To add one or more records to your Selection window, use the checkbox and then click the ' , HT.Strong('Add to Collection'),' button. ')
		else:
			SearchText.append(' A total of ',HT.Span(self.nresults, Class='fwb cr'), ' records were found.')
			heading = "Search Result"
			# Modified by Hongqiang Li
			# detail = ["The terms you entered match %d records. Please modify your search to generate %d or fewer matches, or review  " % (self.nresults, self.maxReturn), HT.Href(text='Search Help', target='_blank',  url='http://web2qtl.utmem.edu/searchHelp.html', Class='fs14'), " to learn more about syntax and the use of wildcard characters."]
			detail = ["The terms you entered match %d records. Please modify your search to generate %d or fewer matches, or review  " % (self.nresults, self.maxReturn), HT.Href(text='Search Help', target='_blank',  url='%s/searchHelp.html' % webqtlConfig.PORTADDR, Class='fs14'), " to learn more about syntax and the use of wildcard characters."]
			#
			self.error(heading=heading,intro = SearchText.contents,detail=detail,error="Over %d" % self.maxReturn)
			return


		TD_LR.append(HT.Paragraph('Search Results', Class="title"), SearchText)
		self.genSearchResultTable(TD_LR)
		self.dict['body'] = str(TD_LR)
            	self.dict['js1'] = ''
            	self.dict['js2'] = 'onLoad="pageOffset()"'
		self.dict['layer'] = self.generateWarningLayer()

	def genSearchResultTable(self, TD_LR):
		
		pageTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="100%",border=0)
	
		lastone = False
		for i, item in enumerate(self.results):
			if not item:
				continue
			lastone = False

			traitList = []
			for k, item2 in enumerate(item):
				j, ProbeSetID = item2[:2]
				thisTrait = webqtlTrait(db=self.database[j], name=ProbeSetID, cursor=self.cursor)
				traitList.append(thisTrait)				
			
				##############
        		# Excel file #
        		##############	
        		filename= webqtlUtil.genRandStr("Search_")
        		xlsUrl = HT.Input(type='button', value = 'Download Table', onClick= "location.href='/tmp/%s.xls'" % filename, Class='button')
        		# Create a new Excel workbook
        		workbook = xl.Writer('%s.xls' % (webqtlConfig.TMPDIR+filename))
        		headingStyle = workbook.add_format(align = 'center', bold = 1, border = 1, size=13, fg_color = 0x1E, color="white")

        		#XZ, 3/18/2010: pay attention to the line number of header in this file. As of today, there are 7 lines.
        		worksheet = self.createExcelFileWithTitleAndFooter(workbook=workbook, db=thisTrait.db, returnNumber=len(traitList))
        		newrow = 7
		
			tbl = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0)
			#seq = self.pageNumber*self.NPerPage+1  //Edited out because we show all results in one page now - Zach 2/22/11
			seq = 1
			RISet = self.databaseCrosses[i]
			thisFormName = 'showDatabase'+RISet
			selectall = HT.Href(url="#", onClick="checkAll(document.getElementsByName('%s')[0]);" % thisFormName)
        		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="#", onClick="checkNone(document.getElementsByName('%s')[0]);" % thisFormName)
        		reset_img = HT.Image("/images/select_none2_final.jpg", alt="Select None", title="Select None", style="border:none;")
        		reset.append(reset_img)        		        					
        		selectinvert = HT.Href(url="#", onClick="checkInvert(document.getElementsByName('%s')[0]);" % thisFormName)
        		selectinvert_img = HT.Image("/images/invert_selection2_final.jpg", name="selectinvert", alt="Invert Selection", title="Invert Selection", style="border:none;")
        		selectinvert.append(selectinvert_img)
			addselect = HT.Href(url="#")
        		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)
			
			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("&nbsp;"*2,"Select", width="25%"), HT.TD("&nbsp;","Deselect", width="255"), HT.TD("&nbsp;"*3,"Invert", width="25%"), HT.TD("&nbsp;"*4,"Add", width="25%"))
			optionsTable.append(optionsRow, labelsRow)

			pageTable.append(HT.TR(HT.TD(optionsTable)), HT.TR(HT.TD(xlsUrl, height=40)))		

			tblobj = {}
			mainfmName = thisFormName
			species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=RISet)

			if thisTrait.db.type=="Geno":
				tblobj['header'] = self.getTableHeaderForGeno(worksheet=worksheet, newrow=newrow, headingStyle=headingStyle)
				
				newrow += 1

				sortby = self.getSortByValue(datasetType="Geno")

				tblobj['body'] = self.getTableBodyForGeno(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow)
				
				workbook.close()
            			objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
            			cPickle.dump(tblobj, objfile)
            			objfile.close()

				div = HT.Div(webqtlUtil.genTableObj(tblobj, filename, sortby), Id="sortable")
				
				pageTable.append(HT.TR(HT.TD(div)))

			elif thisTrait.db.type=="Publish":
				tblobj['header'] = self.getTableHeaderForPublish(worksheet=worksheet, newrow=newrow, headingStyle=headingStyle)
				
				newrow += 1

				sortby = self.getSortByValue(datasetType="Publish")

				tblobj['body'] = self.getTableBodyForPublish(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow, species=species)
				
				workbook.close()
            			objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
            			cPickle.dump(tblobj, objfile)
            			objfile.close()

				div = HT.Div(webqtlUtil.genTableObj(tblobj, filename, sortby), Id="sortable")
				
				pageTable.append(HT.TR(HT.TD(div)))

			elif thisTrait.db.type=="ProbeSet":
				tblobj['header'] = self.getTableHeaderForProbeSet(worksheet=worksheet, newrow=newrow, headingStyle=headingStyle)
				
				newrow += 1

				sortby = self.getSortByValue(datasetType="ProbeSet")

				tblobj['body'] = self.getTableBodyForProbeSet(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow, species=species)
				
				workbook.close()
            			objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
            			cPickle.dump(tblobj, objfile)
            			objfile.close()

				div = HT.Div(webqtlUtil.genTableObj(tblobj, filename, sortby), Id="sortable")
				
				pageTable.append(HT.TR(HT.TD(div)))

			
			traitForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=thisFormName, submit=HT.Input(type='hidden'))
			hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':RISet}
			hddn['incparentsf1']='ON'
			for key in hddn.keys():
				traitForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))

			traitForm.append(HT.P(),pageTable)

			TD_LR.append(traitForm)
			if len(self.results) > 1 and i < len(self.results) - 1:
				lastone = True
		if lastone:
			TD_LR.contents.pop()

	def executeQuery(self):

		##construct sorting
		if self.dbType == "Publish":
			sortQuery = " order by Publication_PubMed_ID desc, Phenotype_Name, thistable"
		elif self.dbType == "Geno":
			if not self.orderByUserInput:
				if self.orderByDefalut:
					self.orderByUserInput = self.orderByDefalut
				else:
					self.orderByUserInput = "POSITION"
				if self.orderByUserInput.upper() in ["POS", "POSITION", "MB"]:
					self.orderByUserInput = "POSITION"
				else:
					pass
			self.orderByUserInput = self.orderByUserInput.upper()
			self.orderByUserInputOrig = self.orderByUserInput[:]
			if self.orderByUserInput == "NAME":
				sortQuery = " order by Geno_Name, Geno_chr_num, Geno_Mb"
			elif self.orderByUserInput == "SOURCE":
				sortQuery = " order by Geno_Source2, Geno_chr_num, Geno_Mb"
			else:
				sortQuery = " order by Geno_chr_num, Geno_Mb"
		#ProbeSet
		else:
			if not self.orderByUserInput:
				if self.orderByDefalut:
					self.orderByUserInput = self.orderByDefalut
				else:
					self.orderByUserInput = "POSITION"

			self.orderByUserInput = self.orderByUserInput.upper()
			self.orderByUserInputOrig = self.orderByUserInput[:]
			#XZ: 8/18/2009: "POSITION-"
			if self.orderByUserInput[-1] == '-':
				self.orderByUserInput = self.orderByUserInput[:-1]
				sortDesc = 'desc'
			else:
				sortDesc = ''

			if self.orderByUserInput in  ["MEAN", "LRS", "PVALUE"]:
				#sortQuery = " order by T%s %s, TNAME, thistable desc" % (self.orderByUserInput, sortDesc)
				sortQuery = " order by T%s desc, TNAME, thistable desc" % self.orderByUserInput
			elif self.orderByUserInput in ["POS", "POSITION", "MB"]:
				sortQuery = " order by TCHR_NUM %s, TMB %s, TNAME, thistable desc" % (sortDesc, sortDesc)
			elif self.orderByUserInput == 'SYMBOL':
				sortQuery = " order by TSYMBOL, thistable desc"
			else:
				sortQuery = " order by TNAME_NUM, thistable desc"

		if self.singleCross:
			if len(self.query) > 1:
				searchQuery = map(lambda X:'(%s)' % X, self.query)
				searchQuery = string.join(searchQuery, '  UNION ALL ')
			else:
				searchQuery = self.query[0]
			searchQuery += sortQuery
			#searchCountQuery retrieve all the results
			searchCountQuery = [searchQuery]
			#searchQuery = searchQuery + " limit %d,%d" % (self.pageNumber*self.NPerPage, self.NPerPage) // We removed the page limit - Zach 2/22/11
			searchQuery = [searchQuery]
		else:
			searchCountQuery = searchQuery = map(lambda X: X+sortQuery, self.query)

		allResults = []
		self.results = []
		for item in searchCountQuery:
		    start_time = datetime.datetime.now()
		    _log.info("111 Executing query: %s"%(item))
		    self.cursor.execute(item)
		    allResults.append(self.cursor.fetchall())
		    end_time = datetime.datetime.now()
		    _log.info("Total time: %s"%(end_time-start_time))

		_log.info("Done executing queries")


		#searchCountQuery retrieve all the results, for counting use only
		if searchCountQuery != searchQuery:
			for item in searchQuery:
				_log.info("222 Executing query: %s"%(item))
				self.cursor.execute(item)
				self.results.append(self.cursor.fetchall())
		else:
			self.results = allResults

		nresults = reduce(lambda Y,X:len(X)+Y, allResults, 0)
		return nresults



	def assembleQuery(self):
		self.query = []
		if self.ANDQuery or self.ORQuery:
			clause = self.ORQuery[:]

			for j, database in enumerate(self.database):
				if self.ANDQuery:
					clause.append(" (%s) " % string.join(self.ANDQuery, " AND "))

				newclause = []

				for item in clause:
					##need to retrieve additional field which won't be used
					##in the future, for sorting purpose only
					if self.dbType == "Publish":
						if item.find("Geno.name") < 0:
							incGenoTbl = ""
						else:
							incGenoTbl = " Geno, "
						newclause.append("SELECT %d, PublishXRef.Id, PublishFreeze.createtime as thistable, Publication.PubMed_ID as Publication_PubMed_ID, Phenotype.Post_publication_description as Phenotype_Name FROM %s PublishFreeze, Publication, PublishXRef, Phenotype WHERE PublishXRef.InbredSetId = %d and %s and PublishXRef.PhenotypeId = Phenotype.Id and PublishXRef.PublicationId = Publication.Id and PublishFreeze.Id = %d" % (j, incGenoTbl, self.databaseCrossIds[j], item, database.id))
					elif self.dbType == "ProbeSet":
						if item.find("GOgene") < 0:
							incGoTbl = ""
						else:
							incGoTbl = " ,db_GeneOntology.term as GOterm, db_GeneOntology.association as GOassociation, db_GeneOntology.gene_product as GOgene_product "
						if item.find("Geno.name") < 0:
							incGenoTbl = ""
						else:
							incGenoTbl = " Geno, "
						if item.find("GeneRIF_BASIC.") < 0:
							incGeneRIFTbl = ""
						else:
							incGeneRIFTbl = " GeneRIF_BASIC, "
						if item.find("GeneRIF.") < 0:
							incGeneRIFTbl += ""
						else:
							incGeneRIFTbl += " GeneRIF, "
						newclause.append("""SELECT distinct %d, ProbeSet.Name as TNAME, 0 as thistable,
						ProbeSetXRef.Mean as TMEAN, ProbeSetXRef.LRS as TLRS, ProbeSetXRef.PVALUE as TPVALUE,
						ProbeSet.Chr_num as TCHR_NUM, ProbeSet.Mb as TMB,  ProbeSet.Symbol as TSYMBOL,
						ProbeSet.name_num as TNAME_NUM  FROM %s%s ProbeSetXRef, ProbeSet %s
						WHERE %s and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = %d
						""" % (j, incGeneRIFTbl, incGenoTbl, incGoTbl, item, database.id))
					elif self.dbType == "Geno":
						newclause.append("SELECT %d, Geno.Name, GenoFreeze.createtime as thistable, Geno.Name as Geno_Name, Geno.Source2 as Geno_Source2, Geno.chr_num as Geno_chr_num, Geno.Mb as Geno_Mb FROM GenoXRef, GenoFreeze, Geno WHERE %s and Geno.Id = GenoXRef.GenoId and GenoXRef.GenoFreezeId = GenoFreeze.Id and GenoFreeze.Id = %d"% (j, item, database.id))
					else:
						pass

				searchQuery = map(lambda X:'(%s)' % X, newclause)
				searchQuery = string.join(searchQuery, '  UNION ')
				self.query.append(searchQuery)
			return 1
		else:
			heading = "Search Result"
			detail = ["No keyword was entered for this search, please go back and enter your keyword."]
			self.error(heading=heading,detail=detail,error="No Keyword")
			return 0



	def normalSearch(self):
		self.ANDkeyword2 = re.sub(self._1mPattern, '', self.ANDkeyword)
		self.ANDkeyword2 = re.sub(self._2mPattern, '', self.ANDkeyword2)
		self.ANDkeyword2 = re.sub(self._3mPattern, '', self.ANDkeyword2)
		self.ANDkeyword2 = re.sub(self._5mPattern, '', self.ANDkeyword2)
		##remove remain parethesis, could be input with  syntax error
		self.ANDkeyword2 = re.sub(re.compile('\s*\([\s\S]*\)'), '', self.ANDkeyword2)
		self.ANDkeyword2 = self.encregexp(self.ANDkeyword2)

		self.ORkeyword2 = re.sub(self._1mPattern, '', self.ORkeyword)
		self.ORkeyword2 = re.sub(self._2mPattern, '', self.ORkeyword2)
		self.ORkeyword2 = re.sub(self._3mPattern, '', self.ORkeyword2)
		self.ORkeyword2 = re.sub(self._5mPattern, '', self.ORkeyword2)
		##remove remain parethesis, could be input with  syntax error
		self.ORkeyword2 = re.sub(re.compile('\s*\([\s\S]*\)'), '', self.ORkeyword2)
		self.ORkeyword2 = self.encregexp(self.ORkeyword2)

		if self.ORkeyword2 or self.ANDkeyword2:
			ANDFulltext = []
			ORFulltext = []
			for k, item in enumerate(self.ORkeyword2 + self.ANDkeyword2):
				self.nkeywords += 1
				if k >=len(self.ORkeyword2):
					query = self.ANDQuery
					DescriptionText = self.ANDDescriptionText
					clausejoin = ' OR '
					fulltext = ANDFulltext
				else:
					query = self.ORQuery
					DescriptionText = self.ORDescriptionText
					clausejoin = ' OR '
					fulltext = ORFulltext

				if self.dbType == "ProbeSet" and item.find('.') < 0 and item.find('\'') < 0:
					fulltext.append(item)
				else:
					if self.matchwhole and item.find("'") < 0:
						item = "[[:<:]]"+ item+"[[:>:]]"
					clause2 = []
					for field in self.searchField:
						if self.dbType == "Publish":
							clause2.append("%s REGEXP \"%s\"" % (field,item))
						else:
							clause2.append("%s REGEXP \"%s\"" % ("%s.%s" % (self.dbType,field),item))
					clauseItem = "(%s)" % string.join(clause2, clausejoin)
					query.append(" (%s) " % clauseItem)
			if ANDFulltext:
				clauseItem = " MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('+%s' IN BOOLEAN MODE) " % string.join(ANDFulltext, " +")
				self.ANDQuery.append(" (%s) " % clauseItem)
			if ORFulltext:
				clauseItem = " MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) " % string.join(ORFulltext, " ")
				self.ORQuery.append(" (%s) " % clauseItem)
		else:
			pass
		return 1



	def encregexp(self,str):
		if not str:
			return []
		else:
			wildcardkeyword = str.strip()
			wildcardkeyword = string.replace(wildcardkeyword,',',' ')
			wildcardkeyword = string.replace(wildcardkeyword,';',' ')
			wildcardkeyword = wildcardkeyword.split()
		NNN = len(wildcardkeyword)
		for i in range(NNN):
			keyword = wildcardkeyword[i]
			keyword = string.replace(keyword,"*",".*")
			keyword = string.replace(keyword,"?",".")
			wildcardkeyword[i] = keyword#'[[:<:]]'+ keyword+'[[:>:]]'
		return wildcardkeyword



	def patternSearch(self):
		# Lei Yan
		##Process Inputs
		m1_AND = self._1mPattern.findall(self.ANDkeyword)
		m2_AND = self._2mPattern.findall(self.ANDkeyword)
		m3_AND = self._3mPattern.findall(self.ANDkeyword)
		m5_AND = self._5mPattern.findall(self.ANDkeyword)
		m1_OR = self._1mPattern.findall(self.ORkeyword)
		m2_OR = self._2mPattern.findall(self.ORkeyword)
		m3_OR = self._3mPattern.findall(self.ORkeyword)
		m5_OR = self._5mPattern.findall(self.ORkeyword)

		#pattern search
		if m1_AND or m1_OR or m2_AND or m2_OR or m3_AND or m3_OR or m5_AND or m5_OR:

			self.orderByDefalut = 'PROBESETID'

			_1Cmds = map(string.upper, map(lambda x:x[0], m1_AND + m1_OR))
			_2Cmds = map(string.upper, map(lambda x:x[0], m2_AND + m2_OR))
			_3Cmds = map(string.upper, map(lambda x:x[0], m3_AND + m3_OR))
			_5Cmds = map(string.upper, map(lambda x:x[0], m5_AND + m5_OR))

			self.nkeywords += len(_1Cmds) + len(_2Cmds) + len(_3Cmds)

			if self.dbType == "Publish" and \
				( (_2Cmds and reduce(lambda x, y: (y not in ["LRS"]) or x, _2Cmds, False))\
				or (_5Cmds and reduce(lambda x, y: (y not in ["LRS"]) or x, _5Cmds, False)) ):
				heading = "Search Result"
				detail = ["Pattern search is not available for phenotype databases at this time."]
				self.error(heading=heading,detail=detail,error="Error")
				return 0
			elif self.dbType == "ProbeSet" and \
				((_2Cmds and reduce(lambda x, y: (y not in ["MEAN", "LRS", "PVALUE", "TRANSLRS", "CISLRS", "RANGE", "H2"]) or x, _2Cmds, False))\
				or (_3Cmds and reduce(lambda x, y: (y not in ["POS", "POSITION", "MB"]) or x, _3Cmds, False))\
				or (_5Cmds and reduce(lambda x, y: (y not in ["LRS"]) or x, _5Cmds, False))\
				or (_1Cmds and reduce(lambda x, y: (y not in ["FLAG", "STRAND_PROBE", "STRAND_GENE", "GO", "WIKI", "RIF", "GENEID"]) or x, _1Cmds, False))):
				heading = "Search Result"
				detail = ["You entered at least one incorrect search command."]
				self.error(heading=heading,detail=detail,error="Error")
				return 0
			elif self.dbType == "Geno" and (_1Cmds or _2Cmds or _5Cmds or (_3Cmds and reduce(lambda x, y: (y not in ["POS", "POSITION", "MB"]) or x, _3Cmds, False)) ):
				heading = "Search Result"
				detail = ["You entered at least one incorrect search command."]
				self.error(heading=heading,detail=detail,error="Error")
				return 0
			else:
				for k, item in enumerate(m1_OR+m1_AND):
					if k >=len(m1_OR):
						query = self.ANDQuery
						DescriptionText = self.ANDDescriptionText
					else:
						query = self.ORQuery
						DescriptionText = self.ORDescriptionText

					if item[1] == '-':
						strandName = 'minus'
					elif item[1] == '+':
						strandName = 'plus'
					else:
						strandName = item[1]

					if item[0].upper() in ("FLAG"):
						clauseItem = " %s.%s = %s " % (self.dbType, item[0], item[1])
						DescriptionText.append(HT.Span(' with ', HT.U('FLAG'), ' equal to ', item[1]))
					elif item[0].upper() in ("WIKI"):
						clauseItem = " %s.symbol = GeneRIF.symbol and GeneRIF.versionId=0 and GeneRIF.display>0 and (GeneRIF.comment REGEXP \"%s\" or GeneRIF.initial = \"%s\") " % (self.dbType, "[[:<:]]"+ item[1]+"[[:>:]]", item[1])
						DescriptionText.append(HT.Span(' with GeneWiki contains ', HT.U(item[1])))
					elif item[0].upper() in ("RIF"):
						clauseItem = " %s.symbol = GeneRIF_BASIC.symbol and MATCH (GeneRIF_BASIC.comment) AGAINST ('+%s' IN BOOLEAN MODE) " % (self.dbType, item[1])
						DescriptionText.append(HT.Span(' with GeneRIF contains ', HT.U(item[1])))
					elif item[0].upper() in ("GENEID"):
						clauseItem = " %s.GeneId in ( %s ) " % (self.dbType, string.replace(item[1], '-', ', '))
						DescriptionText.append(HT.Span(' with Entrez Gene ID in  ', HT.U(string.replace(item[1], '-', ', '))))
					elif item[0].upper() in ("GO"):
						Field = 'GOterm.acc'
						Id = 'GO:'+('0000000'+item[1])[-7:]
						Statements = '%s.symbol=GOgene_product.symbol and GOassociation.gene_product_id=GOgene_product.id and GOterm.id=GOassociation.term_id' % (self.dbType);
						clauseItem = " %s = '%s' and %s " % (Field, Id, Statements)
						#self.incGoTbl = " ,db_GeneOntology.term as GOterm, db_GeneOntology.association as GOassociation, db_GeneOntology.gene_product as GOgene_product "
						DescriptionText.append(HT.Span(' with ', HT.U('GO'), ' ID equal to ', Id))
					else:
						clauseItem = " %s.%s = '%s' " % (self.dbType, item[0], item[1])
						if item[0].upper() in ["STRAND_PROBE"]:
							DescriptionText.append(' with probe on the %s strand' % strandName)
						elif item[0].upper() in ["STRAND_GENE"]:
							DescriptionText.append(' with gene on the %s strand' % strandName)
						else:
							pass
					query.append(" (%s) " % clauseItem)

				for k, item in enumerate(m2_OR+m2_AND):
					if k >=len(m2_OR):
						query = self.ANDQuery
						DescriptionText = self.ANDDescriptionText
					else:
						query = self.ORQuery
						DescriptionText = self.ORDescriptionText

					itemCmd = item[0]
					lowerLimit = float(item[1])
					upperLimit = float(item[2])

					if itemCmd.upper() in ("TRANSLRS", "CISLRS"):
						if item[3]:
							mthresh = float(item[3])
							clauseItem = " %sXRef.LRS > %2.7f and %sXRef.LRS < %2.7f " % \
								(self.dbType, min(lowerLimit, upperLimit), self.dbType, max(lowerLimit, upperLimit))
							if itemCmd.upper() == "CISLRS":
								clauseItem += """ and  %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) < %2.7f """ % (self.dbType, self.speciesId, self.dbType, self.dbType, mthresh)
								DescriptionText.append(HT.Span(' with a ', HT.U('cis-QTL'), ' having an LRS between %g and %g using a %g Mb exclusion buffer'  % (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit),  mthresh)))
							else:
								clauseItem += """ and  %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and (%s.Chr != Geno.Chr or (%s.Chr != Geno.Chr and ABS(%s.Mb-Geno.Mb) > %2.7f)) """ % (self.dbType, self.speciesId, self.dbType, self.dbType, self.dbType, mthresh)
								DescriptionText.append(HT.Span(' with a ', HT.U('trans-QTL'), ' having an LRS between %g and %g using a %g Mb exclusion buffer'  % (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit),  mthresh)))
							query.append(" (%s) " % clauseItem)
							self.orderByDefalut = "LRS"
						else:
							pass
					elif itemCmd.upper() in ("RANGE"):
						#XZ, 03/05/2009: Xiaodong changed Data to ProbeSetData
						clauseItem = " (select Pow(2, max(value) -min(value)) from ProbeSetData where Id = ProbeSetXRef.dataId) > %2.7f and (select Pow(2, max(value) -min(value)) from ProbeSetData where Id = ProbeSetXRef.dataId) < %2.7f " % (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit))
						query.append(" (%s) " % clauseItem)
						DescriptionText.append(HT.Span(' with a range of expression that varied between %g and %g' % (min(lowerLimit, upperLimit),  max(lowerLimit, upperLimit)), "  (fold difference)"))
					else:
						clauseItem = " %sXRef.%s > %2.7f and %sXRef.%s < %2.7f " % \
							(self.dbType, itemCmd, min(lowerLimit, upperLimit), self.dbType, itemCmd, max(lowerLimit, upperLimit))
						query.append(" (%s) " % clauseItem)
						self.orderByDefalut = itemCmd
						DescriptionText.append(HT.Span(' with ', HT.U(itemCmd), ' between %g and %g' % (min(lowerLimit, upperLimit),  max(lowerLimit, upperLimit))))

				for k, item in enumerate(m3_OR+m3_AND):
					if k >=len(m3_OR):
						query = self.ANDQuery
						DescriptionText = self.ANDDescriptionText
					else:
						query = self.ORQuery
						DescriptionText = self.ORDescriptionText
					itemCmd = item[0]
					chrsch = item[1]
					lowerLimit = float(item[2])
					upperLimit = float(item[3])
					fname = 'target genes'
					if self.dbType == "ProbeSet":
						clauseItem = " %s.Chr = '%s' and %s.Mb > %2.7f and %s.Mb < %2.7f " % \
							(self.dbType, chrsch, self.dbType, min(lowerLimit, upperLimit), self.dbType, max(lowerLimit, upperLimit))
					elif self.dbType == "Geno":
						fname = 'loci'
						clauseItem = " %s.Chr = '%s' and %s.Mb > %2.7f and %s.Mb < %2.7f " % \
							(self.dbType, chrsch, self.dbType, min(lowerLimit, upperLimit), self.dbType, max(lowerLimit, upperLimit))
					else:
						continue
					query.append(" (%s) " % clauseItem)
					self.orderByDefalut = itemCmd
					DescriptionText.append(HT.Span(' with ', HT.U('target genes'), ' on chromosome %s between %g and %g Mb' % \
						(chrsch, min(lowerLimit, upperLimit), max(lowerLimit, upperLimit))))

				for k, item in enumerate(m5_OR+m5_AND):
					if k >=len(m5_OR):
						query = self.ANDQuery
						DescriptionText = self.ANDDescriptionText
					else:
						query = self.ORQuery
						DescriptionText = self.ORDescriptionText
					itemCmd = item[0]
					lowerLimit = float(item[1])
					upperLimit = float(item[2])
					chrsch = item[3]
					MblowerLimit = float(item[4])
					MbupperLimit = float(item[5])
					if self.dbType == "ProbeSet" or self.dbType == "Publish":
						clauseItem = " %sXRef.LRS > %2.7f and %sXRef.LRS < %2.7f " % \
							(self.dbType, min(lowerLimit, upperLimit), self.dbType, max(lowerLimit, upperLimit))
						clauseItem += " and  %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and Geno.Chr = '%s' and Geno.Mb > %2.7f and Geno.Mb < %2.7f" \
							% (self.dbType, self.speciesId, chrsch, min(MblowerLimit, MbupperLimit),  max(MblowerLimit, MbupperLimit))
						query.append(" (%s) " % clauseItem)
						self.orderByDefalut = "MB"
						DescriptionText.append(HT.Span(' with ', HT.U('LRS'), ' between %g and %g' % \
							(min(lowerLimit, upperLimit),  max(lowerLimit, upperLimit)), \
							' on chromosome %s between %g and %g Mb' % \
							(chrsch, min(MblowerLimit, MbupperLimit),  max(MblowerLimit, MbupperLimit))))
			pass

		return 1

    	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 getTableHeaderForGeno(self, worksheet=None, newrow=None, headingStyle=None):

		tblobj_header = []

		className = "fs13 fwb ffl b1 cw cbrb"

		tblobj_header = [[THCell(HT.TD(' ', Class=className), sort=0),
			THCell(HT.TD('Record', HT.BR(), 'ID', HT.BR(), Class=className), text='record_id', idx=1),
			THCell(HT.TD('Location', HT.BR(), 'Chr and Mb', HT.BR(), Class=className), text='location', idx=2)]]

		for ncol, item in enumerate(['Record ID', 'Location (Chr, Mb)']):
			worksheet.write([newrow, ncol], item, headingStyle)
			worksheet.set_column([ncol, ncol], 2*len(item))

		return tblobj_header


	def getTableBodyForGeno(self, traitList, formName=None, worksheet=None, newrow=None):

		tblobj_body = []

		className = "fs12 fwn ffl b1 c222"

		for thisTrait in traitList:
			tr = []

			if not thisTrait.haveinfo:
				thisTrait.retrieveInfo()

			trId = str(thisTrait)
                
			tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class=className), text=trId))

			tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.name,url="javascript:showDatabase3('%s','%s','%s','')" % (formName, thisTrait.db.name, thisTrait.name), Class="fs12 fwn ffl"),align="left", Class=className), text=thisTrait.name, val=thisTrait.name.upper()))

			#XZ: trait_location_value is used for sorting
			trait_location_repr = 'N/A'
			trait_location_value = 1000000

			if 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, Class="fs12 fwn b1 c222", nowrap="on"), trait_location_repr, trait_location_value))

			tblobj_body.append(tr)

			for ncol, item in enumerate([thisTrait.name, trait_location_repr]):
				worksheet.write([newrow, ncol], item)

			newrow += 1

		return tblobj_body

	def getTableHeaderForPublish(self, worksheet=None, newrow=None, headingStyle=None):

		tblobj_header = []

		className = "fs13 fwb ffl b1 cw cbrb"

		tblobj_header = [[THCell(HT.TD(' ', Class=className, nowrap="on"), sort=0), 
			THCell(HT.TD('Record',HT.BR(), 'ID',HT.BR(), Class=className, nowrap="on"), text="recond_id", idx=1),
			THCell(HT.TD('Phenotype',HT.BR(),HT.BR(), Class=className, nowrap="on"), text="pheno", idx=2),
			THCell(HT.TD('Authors',HT.BR(),HT.BR(), Class=className, nowrap="on"), text="auth", idx=3),
			THCell(HT.TD('Year',HT.BR(),HT.BR(), Class=className, nowrap="on"), text="year", idx=4),
			THCell(HT.TD('Max',HT.BR(), 'LRS', HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="lrs", idx=5),
			THCell(HT.TD('Max LRS Location',HT.BR(),'Chr and Mb',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="lrs_location", idx=6)]]

		for ncol, item in enumerate(["Record", "Phenotype", "Authors", "Year", "Pubmed Id", "Max LRS", "Max LRS Location (Chr: Mb)"]):
			worksheet.write([newrow, ncol], item, headingStyle)
			worksheet.set_column([ncol, ncol], 2*len(item))

		return tblobj_header

	def getTableBodyForPublish(self, traitList, formName=None, worksheet=None, newrow=None, species=''):

		tblobj_body = []

		className = "fs12 fwn b1 c222"

		for thisTrait in traitList:
			tr = []

			if not thisTrait.haveinfo:
				thisTrait.retrieveInfo(QTL=1)

			trId = str(thisTrait)

			tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class=className), text=trId))

			tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.name,url="javascript:showDatabase3('%s','%s','%s','')" % (formName, thisTrait.db.name, thisTrait.name), Class="fs12 fwn"), nowrap="yes",align="center", Class=className),str(thisTrait.name), thisTrait.name))

			PhenotypeString = thisTrait.post_publication_description
			if thisTrait.confidential:
				if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users):
					PhenotypeString = thisTrait.pre_publication_description
			tr.append(TDCell(HT.TD(PhenotypeString, Class=className), PhenotypeString, PhenotypeString.upper()))

			tr.append(TDCell(HT.TD(thisTrait.authors, Class="fs12 fwn b1 c222 fsI"),thisTrait.authors, thisTrait.authors.strip().upper()))

			try:
				PubMedLinkText = myear = repr = int(thisTrait.year)
			except:
                		PubMedLinkText = repr = "N/A"
				myear = 0

			if thisTrait.pubmed_id:
				PubMedLink = HT.Href(text= repr,url= webqtlConfig.PUBMEDLINK_URL % thisTrait.pubmed_id,target='_blank', Class="fs12 fwn")
			else:
				PubMedLink = repr

			tr.append(TDCell(HT.TD(PubMedLink, Class=className, align='center'), repr, myear))

           	 	#LRS and its location
           	 	LRS_score_repr = 'N/A'
           	 	LRS_score_value = 0
           	 	LRS_location_repr = 'N/A'
           	 	LRS_location_value = 1000000
            		LRS_flag = 1


			if thisTrait.lrs:
                        	LRS_score_repr = '%3.1f' % thisTrait.lrs
                        	LRS_score_value = thisTrait.lrs
                		tr.append(TDCell(HT.TD(LRS_score_repr, Class=className), LRS_score_repr, LRS_score_value))

				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_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb) )
                        			LRS_flag = 0

                		tr.append(TDCell(HT.TD(LRS_location_repr, Class=className, nowrap="on"), LRS_location_repr, LRS_location_value))

			else:
				tr.append(TDCell(HT.TD("N/A", Class=className), "N/A", "N/A"))
            			tr.append(TDCell(HT.TD("N/A", Class=className), "N/A", "N/A"))

			tblobj_body.append(tr)

			for ncol, item in enumerate([thisTrait.name, PhenotypeString, thisTrait.authors, thisTrait.year, thisTrait.pubmed_id, LRS_score_repr, LRS_location_repr]):
				worksheet.write([newrow, ncol], item)

			newrow += 1

		return tblobj_body

	def getTableHeaderForProbeSet(self, worksheet=None, newrow=None, headingStyle=None):

		tblobj_header = []

		className = "fs13 fwb ffl b1 cw cbrb"
	
		tblobj_header = [[THCell(HT.TD(' ', Class="fs13 fwb ffl b1 cw cbrb",nowrap='ON'), sort=0),
					  	THCell(HT.TD('Record',HT.BR(), 'ID',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="record_id", idx=1),
					 	 THCell(HT.TD('Symbol',HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="symbol", idx=2),
					 	 THCell(HT.TD('Description',HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="desc", idx=3),
					 	 THCell(HT.TD('Location',HT.BR(), 'Chr and Mb', HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="location", idx=4),
					 	 THCell(HT.TD('Mean',HT.BR(),'Expr',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="mean", idx=5),
					 	 THCell(HT.TD('Max',HT.BR(),'LRS',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="lrs", idx=6),
					  	THCell(HT.TD('Max LRS Location',HT.BR(),'Chr and Mb',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="lrs_location", idx=7)]]

		for ncol, item in enumerate(['Record', 'Gene ID', 'Homologene ID', 'Symbol', 'Description', 'Location (Chr, Mb)', 'Mean Expr', 'Max LRS', 'Max LRS Location (Chr: Mb)']):
			worksheet.write([newrow, ncol], item, headingStyle)
			worksheet.set_column([ncol, ncol], 2*len(item))

		return tblobj_header

	def getTableBodyForProbeSet(self, traitList=[], primaryTrait=None, formName=None, worksheet=None, newrow=None, species=''):

		tblobj_body = []

		className = "fs12 fwn b1 c222"

		for thisTrait in traitList:

			if not thisTrait.haveinfo:
				thisTrait.retrieveInfo(QTL=1)

			if thisTrait.symbol:
                		pass
            		else:
                		thisTrait.symbol = "N/A"

            		tr = []

            		trId = str(thisTrait)

            		#XZ, 12/08/2008: checkbox
            		tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class="fs12 fwn ffl b1 c222"), text=trId))

            		#XZ, 12/08/2008: probeset name
			if thisTrait.cellid:
            			tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.name, url="javascript:showDatabase3('%s','%s','%s','%s')" % (formName, thisTrait.db.name,thisTrait.name,thisTrait.cellid), Class="fs12 fwn"), Class=className), thisTrait.name, thisTrait.name.upper()))
			else:
				tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.name, url="javascript:showDatabase3('%s','%s','%s','')" % (formName, thisTrait.db.name,thisTrait.name), Class="fs12 fwn"), Class=className), thisTrait.name, thisTrait.name.upper()))            	

           		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")

            		#XZ, 12/08/2008: gene symbol
            		tr.append(TDCell(HT.TD(symbolurl, Class="fs12 fwn b1 c222 fsI"),thisTrait.symbol, thisTrait.symbol.upper()))

            		#XZ, 12/08/2008: description
            		#XZ, 06/05/2009: Rob asked to add probe target description
           	 	description_string = str(thisTrait.description).strip()
            		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()

            		tr.append(TDCell(HT.TD(description_display, Class=className), description_display, description_display))

			#XZ: trait_location_value is used for sorting
            		trait_location_repr = 'N/A'
            		trait_location_value = 1000000

            		if 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, Class=className, nowrap="on"), trait_location_repr, trait_location_value))

            		#XZ, 01/12/08: This SQL query is much faster.
           	 	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))

            		#LRS and its location
            		LRS_score_repr = 'N/A'
            		LRS_score_value = 0
            		LRS_location_repr = 'N/A'
            		LRS_location_value = 1000000
            		LRS_flag = 1

			#Max LRS and its Locus location
			if 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(HT.Href(text=LRS_score_repr,url="javascript:showIntervalMapping('%s', '%s : %s')" % (formName, thisTrait.db.shortname, thisTrait.name), Class="fs12 fwn"), Class=className, align='right', nowrap="on"),LRS_score_repr, LRS_score_value))
                        			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, nowrap="on"), 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("N/A", Class=className), "N/A", "N/A"))
				tr.append(TDCell(HT.TD("N/A", Class=className), "N/A", "N/A"))

			tblobj_body.append(tr)

			for ncol, item in enumerate([thisTrait.name, thisTrait.geneid, thisTrait.homologeneid, thisTrait.symbol, description_display, trait_location_repr, mean, LRS_score_repr, LRS_location_repr]):
      				worksheet.write([newrow, ncol], item)
				

            		newrow += 1

		return tblobj_body

	def createExcelFileWithTitleAndFooter(self, workbook=None, identification=None, db=None, returnNumber=None):

		worksheet = workbook.add_worksheet()

		titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray")

		##Write title Info
		# Modified by Hongqiang Li 
		worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
		worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
		worksheet.write([2, 0], "Trait : %s" % identification, titleStyle)
		worksheet.write([3, 0], "Database : %s" % db.fullname, titleStyle)
		worksheet.write([4, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle)
		worksheet.write([5, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle)
		worksheet.write([6, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle)
		#Write footer info
		worksheet.write([9 + returnNumber, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)", titleStyle)
		worksheet.write([10 + returnNumber, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle)

		return worksheet

	def getSortByValue(self, datasetType=''):

		if datasetType == 'Geno':
			sortby = ("location", "up")
		elif datasetType == 'ProbeSet':
			sortby = ("symbol", "up")
		else: #Phenotype
			sortby = ("record_id", "down")

		return sortby