diff options
Diffstat (limited to 'web/webqtl/showTrait/ShowTraitPage.py')
| -rwxr-xr-x | web/webqtl/showTrait/ShowTraitPage.py | 170 |
1 files changed, 170 insertions, 0 deletions
diff --git a/web/webqtl/showTrait/ShowTraitPage.py b/web/webqtl/showTrait/ShowTraitPage.py new file mode 100755 index 00000000..82511228 --- /dev/null +++ b/web/webqtl/showTrait/ShowTraitPage.py @@ -0,0 +1,170 @@ +# 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 + + |