diff options
Diffstat (limited to 'web/webqtl/cmdLine/webqtlCmdLine.py')
| -rwxr-xr-x | web/webqtl/cmdLine/webqtlCmdLine.py | 176 |
1 files changed, 0 insertions, 176 deletions
diff --git a/web/webqtl/cmdLine/webqtlCmdLine.py b/web/webqtl/cmdLine/webqtlCmdLine.py deleted file mode 100755 index ebc10e1c..00000000 --- a/web/webqtl/cmdLine/webqtlCmdLine.py +++ /dev/null @@ -1,176 +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 - - - -######################################################## -#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() |