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authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/webqtl/showTrait/ShowTraitPage.py
parenta840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
downloadgenenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'
Diffstat (limited to 'web/webqtl/showTrait/ShowTraitPage.py')
-rw-r--r--web/webqtl/showTrait/ShowTraitPage.py170
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
-
-