From d0911a04958a04042da02a334ccc528dae79cc17 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 27 Mar 2015 20:28:51 +0000 Subject: Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files' --- web/webqtl/cmdLine/__init__.py | 0 web/webqtl/cmdLine/cmdCompCorrPage.py | 49 ------ web/webqtl/cmdLine/cmdCorrelationPage.py | 53 ------- web/webqtl/cmdLine/cmdDirectPlotPage.py | 49 ------ web/webqtl/cmdLine/cmdHeatmapPage.py | 52 ------ web/webqtl/cmdLine/cmdIntervalMappingPage.py | 75 --------- web/webqtl/cmdLine/cmdMarkerRegressionPage.py | 47 ------ web/webqtl/cmdLine/cmdNetworkGraphPage.py | 49 ------ web/webqtl/cmdLine/cmdPartialCorrelationPage.py | 50 ------ web/webqtl/cmdLine/cmdQTLminerPage.py | 47 ------ web/webqtl/cmdLine/cmdShowAllPage.py | 50 ------ web/webqtl/cmdLine/cmdShowAllPage2.py | 55 ------- web/webqtl/cmdLine/cmdSnpBrowserResultPage.py | 47 ------ .../cmdLine/cmdTissueCorrelationResultPage.py | 47 ------ web/webqtl/cmdLine/procPage.py | 46 ------ web/webqtl/cmdLine/webqtlCmdLine.py | 176 --------------------- 16 files changed, 892 deletions(-) delete mode 100755 web/webqtl/cmdLine/__init__.py delete mode 100755 web/webqtl/cmdLine/cmdCompCorrPage.py delete mode 100755 web/webqtl/cmdLine/cmdCorrelationPage.py delete mode 100755 web/webqtl/cmdLine/cmdDirectPlotPage.py delete mode 100755 web/webqtl/cmdLine/cmdHeatmapPage.py delete mode 100755 web/webqtl/cmdLine/cmdIntervalMappingPage.py delete mode 100755 web/webqtl/cmdLine/cmdMarkerRegressionPage.py delete mode 100755 web/webqtl/cmdLine/cmdNetworkGraphPage.py delete mode 100755 web/webqtl/cmdLine/cmdPartialCorrelationPage.py delete mode 100755 web/webqtl/cmdLine/cmdQTLminerPage.py delete mode 100755 web/webqtl/cmdLine/cmdShowAllPage.py delete mode 100755 web/webqtl/cmdLine/cmdShowAllPage2.py delete mode 100755 web/webqtl/cmdLine/cmdSnpBrowserResultPage.py delete mode 100755 web/webqtl/cmdLine/cmdTissueCorrelationResultPage.py delete mode 100755 web/webqtl/cmdLine/procPage.py delete mode 100755 web/webqtl/cmdLine/webqtlCmdLine.py (limited to 'web/webqtl/cmdLine') diff --git a/web/webqtl/cmdLine/__init__.py b/web/webqtl/cmdLine/__init__.py deleted file mode 100755 index e69de29b..00000000 diff --git a/web/webqtl/cmdLine/cmdCompCorrPage.py b/web/webqtl/cmdLine/cmdCompCorrPage.py deleted file mode 100755 index f53e1bce..00000000 --- a/web/webqtl/cmdLine/cmdCompCorrPage.py +++ /dev/null @@ -1,49 +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 - -import os - -from base import webqtlConfig -from base.templatePage import templatePage -from utility import webqtlUtil - - - -class cmdCompCorrPage(templatePage): - - def __init__(self,fd): - - templatePage.__init__(self, fd) - - filename = self.session("Correlation Comparison", "Correlation Comparison in progress") - - webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session')) - - url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename) - - os.system("%s %swebqtlCmdLine.py correlationComparison %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename)) - - self.redirection = url diff --git a/web/webqtl/cmdLine/cmdCorrelationPage.py b/web/webqtl/cmdLine/cmdCorrelationPage.py deleted file mode 100755 index 4c76dc0b..00000000 --- a/web/webqtl/cmdLine/cmdCorrelationPage.py +++ /dev/null @@ -1,53 +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 - -import os - - -from base import webqtlConfig -from base.templatePage import templatePage -from utility import webqtlUtil - - -######################################### -# Correlation Page -######################################### -class cmdCorrelationPage(templatePage): - - def __init__(self,fd): - - templatePage.__init__(self, fd) - - filename = self.session("Correlation", "Correlation Computation in Progress") - - webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session')) - - url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename) - - os.system("%s %swebqtlCmdLine.py correlation %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename)) - - self.redirection = url - diff --git a/web/webqtl/cmdLine/cmdDirectPlotPage.py b/web/webqtl/cmdLine/cmdDirectPlotPage.py deleted file mode 100755 index 21e936dc..00000000 --- a/web/webqtl/cmdLine/cmdDirectPlotPage.py +++ /dev/null @@ -1,49 +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 - -import os - -from base import webqtlConfig -from base.templatePage import templatePage -from utility import webqtlUtil - - - -class cmdDirectPlotPage(templatePage): - - def __init__(self,fd): - - templatePage.__init__(self, fd) - - filename = self.session("Pair Scan", "Pair Scan Computation in Progress") - - webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session')) - - url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename) - - os.system("%s %swebqtlCmdLine.py directplot %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename)) - - self.redirection = url diff --git a/web/webqtl/cmdLine/cmdHeatmapPage.py b/web/webqtl/cmdLine/cmdHeatmapPage.py deleted file mode 100755 index e96f3449..00000000 --- a/web/webqtl/cmdLine/cmdHeatmapPage.py +++ /dev/null @@ -1,52 +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 - -import os - -from base import webqtlConfig -from base.templatePage import templatePage -from utility import webqtlUtil - - -######################################### -# QTL Heatmap Page -######################################### - -class cmdHeatmapPage(templatePage): - - def __init__(self,fd): - - templatePage.__init__(self, fd) - - filename = self.session("QTL Heatmap", "Computing QTL Heatmap") - - webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session')) - - url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename) - - os.system("%s %swebqtlCmdLine.py heatmap %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename)) - - self.redirection = url diff --git a/web/webqtl/cmdLine/cmdIntervalMappingPage.py b/web/webqtl/cmdLine/cmdIntervalMappingPage.py deleted file mode 100755 index 8e0a3d92..00000000 --- a/web/webqtl/cmdLine/cmdIntervalMappingPage.py +++ /dev/null @@ -1,75 +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 - -import os - -from base import webqtlConfig -from base.templatePage import templatePage -from utility import webqtlUtil - -######################################### -# Interval Mapping Page -######################################### - -class cmdIntervalMappingPage(templatePage): - - def __init__(self,fd): - - templatePage.__init__(self, fd) - - wtext = "Mapping " - try: - selectedChr = int(fd.formdata.getvalue('chromosomes')) + 1 - if selectedChr < 1: - raise "ValueError" - if selectedChr == 21 or (selectedChr == 20 and fd.RISet != 'HXBBXH'): - selectedChr = 'X' - wtext += 'chromosome %s ' % selectedChr - except: - wtext += 'whole genome ' - - perm = 0 - if fd.formdata.getvalue('permCheck'): - perm = 1 - wtext += 'with %d permutation tests ' % fd.nperm - - boot = 0 - if fd.formdata.getvalue('bootCheck'): - boot = 1 - if perm: - wtext += 'and %d bootstrap tests ' % fd.nboot - else: - wtext += 'with %d bootstrap tests ' % fd.nboot - - if boot == 0 and perm == 0: - wtext += "without permutation or bootstrap tests" - - filename = self.session("Interval Mapping", wtext) - webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session')) - url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename) - os.system("%s %swebqtlCmdLine.py interval %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename)) - self.redirection = url - diff --git a/web/webqtl/cmdLine/cmdMarkerRegressionPage.py b/web/webqtl/cmdLine/cmdMarkerRegressionPage.py deleted file mode 100755 index fb974e33..00000000 --- a/web/webqtl/cmdLine/cmdMarkerRegressionPage.py +++ /dev/null @@ -1,47 +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 NL 2011/03/15 -# -# Last updated by NL 2011/03/15 - -import os - -from base import webqtlConfig -from base.templatePage import templatePage -from utility import webqtlUtil - - -######################################### -# Marker RegressionPage Page -######################################### - -class cmdMarkerRegressionPage(templatePage): - - def __init__(self,fd): - templatePage.__init__(self, fd) - - filename = self.session("Genome Association Result", "Computing Genome Association Results") - webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session')) - url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename) - os.system("%s %swebqtlCmdLine.py markerRegression %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename)) - self.redirection = url diff --git a/web/webqtl/cmdLine/cmdNetworkGraphPage.py b/web/webqtl/cmdLine/cmdNetworkGraphPage.py deleted file mode 100755 index a16fcbaf..00000000 --- a/web/webqtl/cmdLine/cmdNetworkGraphPage.py +++ /dev/null @@ -1,49 +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 - -import os - -from base import webqtlConfig -from base.templatePage import templatePage -from utility import webqtlUtil - - - -class cmdNetworkGraphPage(templatePage): - - def __init__(self, fd): - - templatePage.__init__(self, fd) - - filename = self.session("Network Graph", "Computing Network Graph") - - webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename + '.session')) - - url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename) - - os.system("%s %swebqtlCmdLine.py networkGraph %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename)) - - self.redirection = url diff --git a/web/webqtl/cmdLine/cmdPartialCorrelationPage.py b/web/webqtl/cmdLine/cmdPartialCorrelationPage.py deleted file mode 100755 index fb5324c6..00000000 --- a/web/webqtl/cmdLine/cmdPartialCorrelationPage.py +++ /dev/null @@ -1,50 +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 - -import os - -from base import webqtlConfig -from base.templatePage import templatePage -from utility import webqtlUtil - -######################################## -# Partial Correlation Page -######################################## -class cmdPartialCorrelationPage(templatePage): - - def __init__(self,fd): - - templatePage.__init__(self, fd) - - filename = self.session("Partial Correlation", "Partial Correlation in Progress") - - webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session')) - - url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename) - - os.system("%s %swebqtlCmdLine.py partialCorrelation %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename)) - - self.redirection = url diff --git a/web/webqtl/cmdLine/cmdQTLminerPage.py b/web/webqtl/cmdLine/cmdQTLminerPage.py deleted file mode 100755 index 2197d3ce..00000000 --- a/web/webqtl/cmdLine/cmdQTLminerPage.py +++ /dev/null @@ -1,47 +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 NL 2011/03/15 -# -# Last updated by NL 2011/03/15 - -import os - -from base import webqtlConfig -from base.templatePage import templatePage -from utility import webqtlUtil - - -######################################### -# QTLminer Page -######################################### - -class cmdQTLminerPage(templatePage): - - def __init__(self,fd): - templatePage.__init__(self, fd) - - filename = self.session("QTLminer Result", "Computing QTLminer Results") - webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session')) - url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename) - os.system("%s %swebqtlCmdLine.py QTLminer %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename)) - self.redirection = url diff --git a/web/webqtl/cmdLine/cmdShowAllPage.py b/web/webqtl/cmdLine/cmdShowAllPage.py deleted file mode 100755 index 37e159e9..00000000 --- a/web/webqtl/cmdLine/cmdShowAllPage.py +++ /dev/null @@ -1,50 +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 - -import os - -from base import webqtlConfig -from base.templatePage import templatePage -from utility import webqtlUtil - - - -class cmdShowAllPage(templatePage): - - def __init__(self,fd): - - templatePage.__init__(self, fd) - - filename = self.session("Generate Report", "Generating Report. Please be Patient") - - webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session')) - - url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename) - - os.system("%s %swebqtlCmdLine.py genreport %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename)) - - self.redirection = url - diff --git a/web/webqtl/cmdLine/cmdShowAllPage2.py b/web/webqtl/cmdLine/cmdShowAllPage2.py deleted file mode 100755 index a1ac172f..00000000 --- a/web/webqtl/cmdLine/cmdShowAllPage2.py +++ /dev/null @@ -1,55 +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 - -import os - -from base import webqtlConfig -from base.templatePage import templatePage -from utility import webqtlUtil - - - -######################################### -# Generate Report Page -######################################### - -class cmdShowAllPage2(templatePage): - - def __init__(self,fd): - - templatePage.__init__(self, fd) - - filename = self.session("Generate Report v2", "Generating Report v2. Please be Patient") - - webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session')) - - url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename) - - os.system("%s %swebqtlCmdLine.py genreport2 %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename)) - - self.redirection = url - - diff --git a/web/webqtl/cmdLine/cmdSnpBrowserResultPage.py b/web/webqtl/cmdLine/cmdSnpBrowserResultPage.py deleted file mode 100755 index 54cb1181..00000000 --- a/web/webqtl/cmdLine/cmdSnpBrowserResultPage.py +++ /dev/null @@ -1,47 +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 NL 2011/03/15 -# -# Last updated by NL 2011/03/15 - -import os - -from base import webqtlConfig -from base.templatePage import templatePage -from utility import webqtlUtil - - -######################################### -# SnpBrowser Page -######################################### - -class cmdSnpBrowserResultPage(templatePage): - - def __init__(self,fd): - templatePage.__init__(self, fd) - - filename = self.session("Variant Browser Result", "Computing Variant Browser Results") - webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session')) - url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename) - os.system("%s %swebqtlCmdLine.py snpbrowser %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename)) - self.redirection = url diff --git a/web/webqtl/cmdLine/cmdTissueCorrelationResultPage.py b/web/webqtl/cmdLine/cmdTissueCorrelationResultPage.py deleted file mode 100755 index 1f28953c..00000000 --- a/web/webqtl/cmdLine/cmdTissueCorrelationResultPage.py +++ /dev/null @@ -1,47 +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 NL 2011/03/15 -# -# Last updated by NL 2011/03/15 - -import os - -from base import webqtlConfig -from base.templatePage import templatePage -from utility import webqtlUtil - - -######################################### -# SnpBrowser Page -######################################### - -class cmdTissueCorrelationResultPage(templatePage): - - def __init__(self,fd): - templatePage.__init__(self, fd) - - filename = self.session("Tissue Correlation Result Page", "Computing Tissue Correlation Result") - webqtlUtil.dump_session(fd, os.path.join(webqtlConfig.TMPDIR, filename +'.session')) - url = webqtlConfig.REFRESHDIR % (webqtlConfig.CGIDIR, self.filename) - os.system("%s %swebqtlCmdLine.py tissueCorrelation %s >/dev/null 2>&1 &" % (webqtlConfig.PythonPath, webqtlConfig.CMDLINEDIR, filename)) - self.redirection = url diff --git a/web/webqtl/cmdLine/procPage.py b/web/webqtl/cmdLine/procPage.py deleted file mode 100755 index 03ce242c..00000000 --- a/web/webqtl/cmdLine/procPage.py +++ /dev/null @@ -1,46 +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 - -#--Only imported by WebQTL.py -KA - -#Xiaodong changed the dependancy structure - -import os - -from base import webqtlConfig - - -class procPage: - def __init__(self, myID, req): - try: - fp = open(os.path.join(webqtlConfig.TMPDIR, myID + '.html'), 'rb') - except: - fp = open(os.path.join(webqtlConfig.ChangableHtmlPath, 'missing.html'), 'rb') - - content = fp.read() - fp.close() - req.write(content) - 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 = '' - - 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 = '
' - - 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
')
-		traceback.print_exc(file=fp)							
-		fp.write('\n
') - fp.close() -- cgit v1.2.3