Add all the source codes into the github.

1 files changed, 170 insertions, 0 deletions

diff --git a/web/webqtl/showTrait/ShowTraitPage.py b/web/webqtl/showTrait/ShowTraitPage.py
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+++ b/web/webqtl/showTrait/ShowTraitPage.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
+
+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 ShowTraitPage(DataEditingPage):
+
+	def __init__(self, fd, traitInfos = []):
+
+		templatePage.__init__(self, fd)
+
+		if not self.openMysql():
+			return
+			
+		TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
+		
+		if traitInfos:
+			database,ProbeSetID,CellID = traitInfos
+		else:
+			database = fd.formdata.getfirst('database')
+			ProbeSetID = fd.formdata.getfirst('ProbeSetID')
+			CellID = fd.formdata.getfirst('CellID')
+		try:
+			thisTrait = webqtlTrait(db=database, name=ProbeSetID, cellid= CellID, cursor=self.cursor)
+		except:
+			heading = "Trait Data and Analysis Form"
+			detail = ["The trait isn't available currently."]
+			self.error(heading=heading,detail=detail,error="Error")
+			return
+
+		if thisTrait.db.type == "ProbeSet":
+
+			self.cursor.execute('''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers 
+						FROM ProbeSetFreeze WHERE Name = "%s"''' %  database)
+
+			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, Confidential Database
+					heading = "Show Database"
+					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
+					
+		user_ip = fd.remote_ip
+		query = "SELECT count(id) FROM AccessLog WHERE ip_address = %s and \
+				UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400"
+		self.cursor.execute(query,user_ip)
+		daycount = self.cursor.fetchall()
+		if daycount:
+			daycount = daycount[0][0]
+			if daycount > webqtlConfig.DAILYMAXIMUM:
+				heading = "Retrieve Data"
+				detail = ['For security reasons, the maximum access to a database is \
+				%d times per day per ip address. You have reached the limit, please \
+				try it again tomorrow.' % webqtlConfig.DAILYMAXIMUM]
+				self.error(heading=heading,detail=detail)
+				return
+			else:
+				pass
+		else:
+			pass
+		
+		if thisTrait.db.type != 'ProbeSet' and thisTrait.cellid:
+				heading = "Retrieve Data"
+				detail = ['The Record you requested doesn\'t exist!']
+				self.error(heading=heading,detail=detail)
+				return
+
+		#XZ: Aug 23, 2010: I commented out this block because this feature is not used anymore		
+		# check if animal information are available
+		"""
+		self.cursor.execute('''
+						SELECT 
+							SampleXRef.ProbeFreezeId 
+						FROM 
+							SampleXRef, ProbeSetFreeze 
+						WHERE 
+							SampleXRef.ProbeFreezeId = ProbeSetFreeze.ProbeFreezeId AND
+							ProbeSetFreeze.Name = "%s"
+					 ''' % thisTrait.db.name)
+		
+		sampleId = self.cursor.fetchall()
+		if sampleId:
+			thisTrait.strainInfo = 1
+		else:
+			thisTrait.strainInfo = None
+		"""
+
+		##identification, etc.
+		fd.identification = '%s : %s'%(thisTrait.db.shortname,ProbeSetID)
+		thisTrait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\
+			&ProbeSetID=%s&RISet=%s&parentsf1=on' %(database,ProbeSetID,fd.RISet)
+		
+		if CellID:
+			fd.identification = '%s/%s'%(fd.identification, CellID)
+			thisTrait.returnURL = '%s&CellID=%s' % (thisTrait.returnURL, CellID)
+		
+		#retrieve trait information		
+		try:
+			thisTrait.retrieveInfo()
+			thisTrait.retrieveData()
+			self.updMysql()
+			self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)" ,user_ip)
+			self.openMysql()
+		except:
+			heading = "Retrieve Data"
+			detail = ["The information you requested is not avaiable at this time."]
+			self.error(heading=heading,detail=detail)
+			return
+			
+		##read genotype file
+		fd.RISet = thisTrait.riset
+		fd.readGenotype()
+		
+		if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())):
+			fd.displayVariance = 1
+			fd.varianceDispName = 'SE'
+			fd.formID = 'varianceChoice'
+		
+		self.dict['body']= thisTrait
+		DataEditingPage.__init__(self, fd, thisTrait)
+		self.dict['title'] = '%s: Display Trait' % fd.identification
+
+