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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
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