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

1 files changed, 0 insertions, 170 deletions

diff --git a/web/webqtl/showTrait/ShowTraitPage.py b/web/webqtl/showTrait/ShowTraitPage.py
deleted file mode 100644
index 82511228..00000000
--- a/web/webqtl/showTrait/ShowTraitPage.py
+++ /dev/null
@@ -1,170 +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
-
-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
-
-