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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
#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
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