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authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/webqtl/collection/BatchSubmitSelectionPage.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/collection/BatchSubmitSelectionPage.py')
-rwxr-xr-xweb/webqtl/collection/BatchSubmitSelectionPage.py225
1 files changed, 0 insertions, 225 deletions
diff --git a/web/webqtl/collection/BatchSubmitSelectionPage.py b/web/webqtl/collection/BatchSubmitSelectionPage.py
deleted file mode 100755
index 743606b2..00000000
--- a/web/webqtl/collection/BatchSubmitSelectionPage.py
+++ /dev/null
@@ -1,225 +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
-
-#BatchSubmitSelectionPage.py
-
-import string
-import time
-
-from base import webqtlConfig
-from base.templatePage import templatePage
-from utility import webqtlUtil
-from AddToSelectionPage import AddToSelectionPage
-
-
-#########################################
-# batch submission result Page
-#########################################
-class BatchSubmitSelectionPage(AddToSelectionPage):
-
- def __init__(self, fd):
-
- templatePage.__init__(self, fd)
-
- if not self.openMysql():
- return
- if not fd.genotype:
- fd.readGenotype()
-
- heading = 'Batch Submission'
-
- self.batchDataFile = fd.formdata.getvalue('batchdatafile')
- if not self.batchDataFile:
- templatePage.__init__(self, fd)
- detail = ['The file you choose to import from doesn\'t exist.']
- self.error(heading=heading,detail=detail)
- return
- self.batchDataFile = string.replace(self.batchDataFile, '\r', '\n')
- self.batchDataFile = string.replace(self.batchDataFile, '\n\n', '\n')
- self.batchDataFile = string.split(self.batchDataFile, '\n')
- self.batchDataFile = map(string.strip, self.batchDataFile)
-
- traitNames, strainNames, traitValues, SE, NStrain = self.parseDataFile()
- strainIds = []
-
- #print 'Content-type: text/html\n'
- #print len(traitNames), len(strainNames) , len(strainIds), len(traitValues) , len(SE), "<BR><BR>", len(NStrain)
- #return
-
- try:
-
- if not traitNames or not strainNames or not traitValues or len(traitNames) != len(traitValues) or len(traitNames) != len(SE) or len(traitNames) != len(NStrain):
- raise 'ValueError'
- for item in traitValues:
- if len(strainNames) != len(item):
- raise 'ValueError'
- for item in SE:
- if len(strainNames) != len(item):
- raise 'ValueError'
- for item in NStrain:
- if len(strainNames) != len(item):
- raise 'ValueError'
- for item in strainNames:
- self.cursor.execute('''Select
- Strain.Id
- from Strain, StrainXRef,InbredSet
- where
- Strain.Name = "%s" AND
- StrainXRef.StrainId = Strain.Id AND
- StrainXRef.InbredSetId = InbredSet.Id AND
- InbredSet.Name = "%s"
- ''' % (item, fd.RISet))
- strainId = self.cursor.fetchone()[0]
- strainIds.append(strainId)
- except:
- templatePage.__init__(self, fd)
- detail = ['The format of the file is incorrect, or it contains unknown strains.']
- self.error(heading=heading,detail=detail)
- return
-
- self.searchResult = []
- self.addToTable(traitNames, strainNames,strainIds, traitValues,SE, NStrain, fd)
-
- if self.genSelection(fd=fd):
- self.writeHTML(fd)
-
- def parseDataFile(self):
- rchSartPos = 0
- header = []
- traits = []
- data = []
- se = []
- nstrain = []
- strains = []
-
- if 1:
- for line in self.batchDataFile:
- line = line.strip()
- if line == '' or line[0] == '#':
- continue
-
- columns = string.split(line, '\t')
- columns = map(string.strip, columns)
-
- if rchSartPos == 'column':
- strains.append(columns[0])
- tdata = map(webqtlUtil.StringAsFloat,columns[1:])
- for j, item in enumerate(tdata):
- if posIdx[j][0] == 'data':
- data[posIdx[j][1]].append(item)
- elif posIdx[j][0] == 'n':
- if item != None:
- nstrain[posIdx[j][1]].append(int(item))
- else:
- nstrain[posIdx[j][1]].append(item)
- else:
- se[posIdx[j][1]].append(item)
-
- elif rchSartPos == 'row':
- if columns[0].lower() == 'se':
- se.append(map(webqtlUtil.StringAsFloat,columns[1:]))
- elif columns[0].lower() == 'n':
- nstrain.append(map(webqtlUtil.IntAsFloat,columns[1:]))
- else:
- while (len(data) > len(se)):
- se.append([None] * len(data[-1]))
- while (len(data) > len(nstrain)):
- nstrain.append([None] * len(data[-1]))
- header.append(columns[0])
- data.append(map(webqtlUtil.StringAsFloat,columns[1:]))
- elif columns[0] == '@format=column':
- rchSartPos = 'column'
- posIdx = []
- j = 0
- for item in columns[1:]:
- #assign column type
- if string.lower(item) == 'se':
- posIdx.append(('se',j-1))
- elif string.lower(item) == 'n':
- posIdx.append(('n',j-1))
- else:
- header.append(item)
- posIdx.append(('data',j))
- j += 1
-
- for i in range(len(header)):
- data.append([])
- se.append([])
- nstrain.append([])
- elif columns[0] == '@format=row':
- rchSartPos = 'row'
- strains = columns[1:]
- else:
- pass
- #modify
- for i in range(len(se)):
- if se[i] == []:
- se[i] = [None] * len(data[-1])
- for i in range(len(nstrain)):
- if nstrain[i] == []:
- nstrain[i] = [None] * len(data[-1])
- if len(data) > len(se):
- se.append([None] * len(data[-1]))
- if len(data) > len(nstrain):
- nstrain.append([None] * len(data[-1]))
-
- return header,strains,data,se, nstrain
- else:
- return [],[],[],[], []
-
-
- #XZ, add items to self.searchResult
- def addToTable(self, traitNames, strainNames,strainIds, traitValues, SE, NStrain, fd):
- self.cursor.execute('delete Temp, TempData from Temp, TempData where Temp.DataId = TempData.Id and UNIX_TIMESTAMP()-UNIX_TIMESTAMP(CreateTime)>%d;' % webqtlConfig.MAXLIFE)
-
- i = 0
- for trait in traitNames:
- ct0 = time.localtime(time.time())
- ct = time.strftime("%B/%d %H:%M:%S",ct0)
- if trait == '':
- trait = "Unnamed Trait"
- user_ip = fd.remote_ip
- newDescription = '%s entered at %s from IP %s' % (trait,ct,user_ip)
- newProbeSetID = webqtlUtil.genRandStr('Usr_TMP_')
-
- self.cursor.execute('SelecT max(id) from TempData')
- try:
- DataId = self.cursor.fetchall()[0][0] + 1
- except:
- DataId = 1
-
- self.cursor.execute('Select Id from InbredSet where Name = "%s"' % fd.RISet)
- InbredSetId = self.cursor.fetchall()[0][0]
-
- self.cursor.execute('insert into Temp(Name,description, createtime,DataId,InbredSetId,IP) values(%s,%s,Now(),%s,%s,%s)' ,(newProbeSetID, newDescription, DataId,InbredSetId,user_ip))
-
- for k in range(len(traitValues[i])):
- if traitValues[i][k] != None:
- self.cursor.execute('insert into TempData(Id, StrainId, value, SE, NStrain) values(%s, %s, %s, %s, %s)' , (DataId, strainIds[k], traitValues[i][k],SE[i][k],NStrain[i][k]))
-
- self.searchResult.append('Temp::%s' % newProbeSetID)
- i += 1
-