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-rwxr-xr-xweb/webqtl/cmdLine/__init__.py0
-rwxr-xr-xweb/webqtl/cmdLine/cmdCompCorrPage.py49
-rwxr-xr-xweb/webqtl/cmdLine/cmdCorrelationPage.py53
-rwxr-xr-xweb/webqtl/cmdLine/cmdDirectPlotPage.py49
-rwxr-xr-xweb/webqtl/cmdLine/cmdHeatmapPage.py52
-rwxr-xr-xweb/webqtl/cmdLine/cmdIntervalMappingPage.py75
-rwxr-xr-xweb/webqtl/cmdLine/cmdMarkerRegressionPage.py47
-rwxr-xr-xweb/webqtl/cmdLine/cmdNetworkGraphPage.py49
-rwxr-xr-xweb/webqtl/cmdLine/cmdPartialCorrelationPage.py50
-rwxr-xr-xweb/webqtl/cmdLine/cmdQTLminerPage.py47
-rwxr-xr-xweb/webqtl/cmdLine/cmdShowAllPage.py50
-rwxr-xr-xweb/webqtl/cmdLine/cmdShowAllPage2.py55
-rwxr-xr-xweb/webqtl/cmdLine/cmdSnpBrowserResultPage.py47
-rwxr-xr-xweb/webqtl/cmdLine/cmdTissueCorrelationResultPage.py47
-rwxr-xr-xweb/webqtl/cmdLine/procPage.py46
-rwxr-xr-xweb/webqtl/cmdLine/webqtlCmdLine.py176
16 files changed, 892 insertions, 0 deletions
diff --git a/web/webqtl/cmdLine/__init__.py b/web/webqtl/cmdLine/__init__.py
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/web/webqtl/cmdLine/__init__.py
diff --git a/web/webqtl/cmdLine/cmdCompCorrPage.py b/web/webqtl/cmdLine/cmdCompCorrPage.py
new file mode 100755
index 00000000..f53e1bce
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdCompCorrPage.py
@@ -0,0 +1,49 @@
+# 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
new file mode 100755
index 00000000..4c76dc0b
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdCorrelationPage.py
@@ -0,0 +1,53 @@
+# 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
new file mode 100755
index 00000000..21e936dc
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdDirectPlotPage.py
@@ -0,0 +1,49 @@
+# 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
new file mode 100755
index 00000000..e96f3449
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdHeatmapPage.py
@@ -0,0 +1,52 @@
+# 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
new file mode 100755
index 00000000..8e0a3d92
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdIntervalMappingPage.py
@@ -0,0 +1,75 @@
+# 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
new file mode 100755
index 00000000..fb974e33
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdMarkerRegressionPage.py
@@ -0,0 +1,47 @@
+# 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
new file mode 100755
index 00000000..a16fcbaf
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdNetworkGraphPage.py
@@ -0,0 +1,49 @@
+# 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
new file mode 100755
index 00000000..fb5324c6
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdPartialCorrelationPage.py
@@ -0,0 +1,50 @@
+# 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
new file mode 100755
index 00000000..2197d3ce
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdQTLminerPage.py
@@ -0,0 +1,47 @@
+# 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
new file mode 100755
index 00000000..37e159e9
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdShowAllPage.py
@@ -0,0 +1,50 @@
+# 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
new file mode 100755
index 00000000..a1ac172f
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdShowAllPage2.py
@@ -0,0 +1,55 @@
+# 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
new file mode 100755
index 00000000..54cb1181
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdSnpBrowserResultPage.py
@@ -0,0 +1,47 @@
+# 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
new file mode 100755
index 00000000..1f28953c
--- /dev/null
+++ b/web/webqtl/cmdLine/cmdTissueCorrelationResultPage.py
@@ -0,0 +1,47 @@
+# 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
new file mode 100755
index 00000000..03ce242c
--- /dev/null
+++ b/web/webqtl/cmdLine/procPage.py
@@ -0,0 +1,46 @@
+# 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
new file mode 100755
index 00000000..ebc10e1c
--- /dev/null
+++ b/web/webqtl/cmdLine/webqtlCmdLine.py
@@ -0,0 +1,176 @@
+# 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()