Add all the source codes into the github.

1 files changed, 195 insertions, 0 deletions

diff --git a/web/webqtl/showTrait/ShowBestTrait.py b/web/webqtl/showTrait/ShowBestTrait.py
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+++ b/web/webqtl/showTrait/ShowBestTrait.py
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+# 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
+
+