Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

16 files changed, 0 insertions, 892 deletions

diff --git a/web/webqtl/cmdLine/__init__.py b/web/webqtl/cmdLine/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/web/webqtl/cmdLine/__init__.py
+++ /dev/null
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 = '</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()