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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
########################################################
#XZ, Aug 10, 2010
#This part is the temporary solution to make python be able to find other subpackages.
#We can't set global environment because there are many branches on the development machine.
import sys, os
current_file_name = __file__
pathname = os.path.dirname( current_file_name )
abs_path = os.path.abspath(pathname)
sys.path.insert(0, abs_path + '/..')
########################################################
import traceback
import string
import cPickle
from base import webqtlConfig
from base.templatePage import templatePage
from utility import webqtlUtil
if __name__ == "__main__":
try:
if len(sys.argv) > 2:
getID = string.lower(sys.argv[1])
else:
raise ValueError
cmdtype = sys.argv[1]
sessionfile = sys.argv[2]
fd = None
fp = open(os.path.join(webqtlConfig.TMPDIR, sessionfile + '.session'), 'rb')
fd = cPickle.load(fp)
fp.close()
if cmdtype == "heatmap":
from heatmap import heatmapPage
reload(heatmapPage)
page = heatmapPage.heatmapPage(fd)
page.writeFile(sessionfile+'.html')
elif cmdtype == "directplot":
from pairScan import DirectPlotPage
reload(DirectPlotPage)
page = DirectPlotPage.DirectPlotPage(fd)
page.writeFile(sessionfile+'.html')
elif cmdtype == "networkGraph":
from networkGraph import networkGraphPage
reload(networkGraphPage)
page = networkGraphPage.networkGraphPage(fd)
page.writeFile(sessionfile+'.html')
elif cmdtype == "interval":
from intervalMapping import IntervalMappingPage
reload(IntervalMappingPage)
page = IntervalMappingPage.IntervalMappingPage(fd)
page.writeFile(sessionfile+'.html')
elif cmdtype == "correlation":
from correlation import CorrelationPage
reload (CorrelationPage)
page = CorrelationPage.CorrelationPage(fd)
page.writeFile(sessionfile+'.html')
elif cmdtype == "partialCorrelation":
from correlation import PartialCorrDBPage
reload(PartialCorrDBPage)
page = PartialCorrDBPage.PartialCorrDBPage(fd)
page.writeFile(sessionfile+'.html')
elif cmdtype == "correlationComparison":
from compareCorrelates import multitrait
reload(multitrait)
page = multitrait.compCorrPage(fd)
page.writeFile(sessionfile+'.html')
elif cmdtype == "genreport": # Generate Report Page
spacer = '</TR></Table><Table width=900 cellSpacing=0 cellPadding=5><TR>'
from basicStatistics import BasicStatisticsPage
reload(BasicStatisticsPage)
page1 = BasicStatisticsPage.BasicStatisticsPage(fd)
if not fd.formdata.getvalue('bsCheck'):
page1.dict['body'] = ""
if fd.formdata.getvalue('tcCheck'):
from correlation import CorrelationPage
reload(CorrelationPage)
page2 = CorrelationPage.CorrelationPage(fd)
page1.dict['body'] += spacer + str(page2.dict['body'])
page1.dict['js1'] += page2.dict['js1']
if fd.formdata.getvalue('imCheck'):
from intervalMapping import IntervalMappingPage
reload(IntervalMappingPage)
page3 = IntervalMappingPage.IntervalMappingPage(fd)
page1.dict['body'] += spacer + str(page3.dict['body'])
if fd.formdata.getvalue('mrCheck'):
from markerRegression import MarkerRegressionPage
reload(MarkerRegressionPage)
page4 = MarkerRegressionPage.MarkerRegressionPage(fd)
page1.dict['body'] += spacer + str(page4.dict['body'])
if fd.formdata.getvalue('psCheck'):
from pairScan import DirectPlotPage
reload(DirectPlotPage)
page5 = DirectPlotPage.DirectPlotPage(fd)
page1.dict['body'] += spacer + str(page5.dict['body'])
page1.writeFile(sessionfile+'.html')
elif cmdtype == "genreport2": # Generate Report Page v2
spacer = '</TR></Table><Table width=900 cellSpacing=0 cellPadding=5><TR>'
from basicStatistics import BasicStatisticsPage_alpha
reload(BasicStatisticsPage_alpha)
page1 = BasicStatisticsPage_alpha.BasicStatisticsPage_alpha(fd)
page1.writeFile(sessionfile+'.html')
elif cmdtype == "snpbrowser":
from snpBrowser import snpBrowserPage
reload(snpBrowserPage)
page = snpBrowserPage.snpBrowserPage(fd)
page.writeFile(sessionfile+'.html')
elif cmdtype == "QTLminer":
from qtlminer import QTLminer
reload(QTLminer)
page = QTLminer.QTLminer(fd)
page.writeFile(sessionfile+'.html')
elif cmdtype == "tissueCorrelation":
from correlationMatrix import TissueCorrelationPage
reload(TissueCorrelationPage)
page = TissueCorrelationPage.TissueCorrelationPage(fd)
page.writeFile(sessionfile+'.html')
elif cmdtype == "markerRegression":
from markerRegression import MarkerRegressionPage
reload(MarkerRegressionPage)
page = MarkerRegressionPage.MarkerRegressionPage(fd)
page.writeFile(sessionfile+'.html')
else:
raise ValueError
except:
fp = open(os.path.join(webqtlConfig.TMPDIR, sessionfile +'.html'), 'wb')
fp.write('\n\n<pre>')
traceback.print_exc(file=fp)
fp.write('\n</pre>')
fp.close()
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