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

1 files changed, 0 insertions, 195 deletions

diff --git a/web/webqtl/showTrait/ShowBestTrait.py b/web/webqtl/showTrait/ShowBestTrait.py
deleted file mode 100755
index 9eb42923..00000000
--- a/web/webqtl/showTrait/ShowBestTrait.py
+++ /dev/null
@@ -1,195 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import string
-
-#from base.templatePage import templatePage
-#from basicStatistics.BasicStatisticsPage import BasicStatisticsPage
-from htmlgen import HTMLgen2 as HT
-
-from base import webqtlConfig
-from utility import webqtlUtil
-from base.webqtlTrait import webqtlTrait
-from base.templatePage import templatePage
-from DataEditingPage import DataEditingPage
-
-
-#class ShowBestTrait(BasicStatisticsPage, templatePage):
-
-class ShowBestTrait(DataEditingPage):
-	def __init__(self,fd):
-
-		########## geneName means symbol ##########
-		geneName = fd.formdata.getvalue('gene')
-		if geneName:
-			geneName = string.strip(geneName)
-
-		refseq = fd.formdata.getvalue('refseq')
-		if refseq:
-			refseq = string.strip(refseq)
-
-		genbankid = fd.formdata.getvalue('genbankid')
-		if genbankid:
-			genbankid = string.strip(genbankid)
-
-		geneid = fd.formdata.getvalue('geneid')
-		if geneid:
-			geneid = string.strip(geneid)
-
-		species = fd.formdata.getvalue('species')
-		tissue = fd.formdata.getvalue('tissue')
-		database = fd.formdata.getvalue('database')
-
-		########## searchAlias is just a singal, so it doesn't need be stripped ##########
-		searchAlias = fd.formdata.getvalue('searchAlias')
-
-		if not self.openMysql():
-			return
-
-		if database:
-			if geneName:
-				if searchAlias:
-					self.cursor.execute(""" SELECT ProbeSetXRef.*
-								FROM
-									ProbeSet, ProbeSetXRef, DBList
-								WHERE
-									ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
-									ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-									(DBList.Name=%s or DBList.Code=%s) AND
-									MATCH (ProbeSet.symbol, alias) AGAINST ("+%s" IN BOOLEAN MODE)
-								ORDER BY ProbeSetXRef.mean DESC
-							    """ , (database, database, geneName))
-				else:
-					self.cursor.execute(""" SELECT ProbeSetXRef.*
-								FROM    
-									ProbeSet, ProbeSetXRef, DBList
-								WHERE   
-									ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
-									ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-									(DBList.Name=%s or DBList.Code=%s) AND
-									ProbeSet.symbol = %s
-								ORDER BY ProbeSetXRef.mean DESC
-							    """ , (database, database, geneName))
-			elif refseq:
-				self.cursor.execute(""" SELECT ProbeSetXRef.*
-							FROM
-								ProbeSet, ProbeSetXRef, DBList
-							WHERE
-								ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
-								ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-								(DBList.Name=%s or DBList.Code=%s) AND
-								ProbeSet.RefSeq_TranscriptId = %s
-							ORDER BY ProbeSetXRef.mean DESC
-						    """ , (database, database, refseq))
-			elif genbankid:
-				self.cursor.execute(""" SELECT ProbeSetXRef.*
-							FROM
-								ProbeSet, ProbeSetXRef, DBList
-							WHERE
-								ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
-								ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-								(DBList.Name=%s or DBList.Code=%s) AND
-								ProbeSet.GenbankId = %s
-							ORDER BY ProbeSetXRef.mean DESC
-						    """ , (database, database, genbankid))
-			elif geneid:
-				self.cursor.execute(""" SELECT ProbeSetXRef.*
-							FROM
-								ProbeSet, ProbeSetXRef, DBList
-							WHERE
-								ProbeSetXRef.ProbeSetFreezeId = DBList.FreezeId AND
-								ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-								(DBList.Name=%s or DBList.Code=%s) AND
-								ProbeSet.GeneId = %s
-							ORDER BY ProbeSetXRef.mean DESC
-						    """ , (database, database, geneid))
-
-			Results = self.cursor.fetchone()
-
-
-
-			########## select the Data that match the selection(currently, only max mean available) ##########
-			if Results:
-				ProbeSetFreezeId = Results[0]
-				ProbeSetId = Results[1]
-				DataId = Results[2]
-
-				self.cursor.execute("""
-					select
-						InbredSet.Name
-					from
-						InbredSet, ProbeFreeze, ProbeSetFreeze
-					where
-						InbredSet.Id=ProbeFreeze.InbredSetId and
-						ProbeFreeze.Id=ProbeSetFreeze.ProbeFreezeId and
-						ProbeSetFreeze.Id=%s
-					""", ProbeSetFreezeId)
-				fd.RISet = self.cursor.fetchone()[0]
-				#fd.RISet = Results[0]
-
-				self.cursor.execute("select Name, FullName from ProbeSetFreeze where Id=%s", ProbeSetFreezeId)
-				fd.database, fd.identification = self.cursor.fetchone()
-
-				self.cursor.execute("select Name, symbol, description from ProbeSet where Id=%s", ProbeSetId)
-				fd.ProbeSetID, fd.symbol, fd.description = self.cursor.fetchone()
-
-				fd.identification += ' : '+fd.ProbeSetID
-				fd.formdata['fullname'] = fd.database+'::'+fd.ProbeSetID
-
-				#XZ, 03/03/2009: Xiaodong changed Data to ProbeSetData	
-				self.cursor.execute("select Strain.Name, ProbeSetData.Value from Strain, ProbeSetData where Strain.Id=ProbeSetData.StrainId and ProbeSetData.Id=%s", DataId)
-				Results = self.cursor.fetchall()
-
-				fd.allstrainlist = []
-				for item in Results:
-					fd.formdata[item[0]] = item[1]
-					fd.allstrainlist.append(item[0])
-
-				#XZ, 03/12/2009: Xiaodong changed SE to ProbeSetSE
-				self.cursor.execute("select Strain.Name, ProbeSetSE.error from Strain, ProbeSetSE where Strain.Id = ProbeSetSE.StrainId and ProbeSetSE.DataId=%s", DataId)
-				Results = self.cursor.fetchall()
-				for item in Results:
-					fd.formdata['V'+item[0]] = item[1]
-			else:
-				fd.RISet = 'BXD'
-				fd.database = 'KI_2A_0405_Rz'
-				fd.ProbeSetID = '1367452_at'
-		else:
-			fd.RISet = 'BXD'
-			fd.database = 'KI_2A_0405_Rz'
-			fd.ProbeSetID = '1367452_at'
-
-
-		#BasicStatisticsPage.__init__(self, fd)
-
-
-		thisTrait = webqtlTrait(db=fd.database, name=fd.ProbeSetID, cursor=self.cursor)
-		thisTrait.retrieveInfo()
-		thisTrait.retrieveData()
-		DataEditingPage.__init__(self, fd, thisTrait)
-		self.dict['title'] = '%s: Display Trait' % fd.identification
-
-