Add all the source codes into the github.

4 files changed, 398 insertions, 0 deletions

diff --git a/web/webqtl/externalResource/GCATPage.py b/web/webqtl/externalResource/GCATPage.py
new file mode 100755
index 00000000..7e22f168
--- /dev/null
+++ b/web/webqtl/externalResource/GCATPage.py
@@ -0,0 +1,101 @@
+# 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
+
+#GCATPage.py
+
+from htmlgen import HTMLgen2 as HT
+
+from base.webqtlTrait import webqtlTrait
+from base.templatePage import templatePage
+    
+
+#Implemented by Xiaodong
+class GCATPage(templatePage):
+
+    def __init__(self,fd):
+
+        self.theseTraits = []
+        TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")
+
+        templatePage.__init__(self, fd)
+
+        if not self.openMysql():
+            return
+
+        self.searchResult = fd.formdata.getvalue('searchResult', [])
+        if type("1") == type(self.searchResult):
+            self.searchResult = [self.searchResult]
+
+        for item in self.searchResult:
+            try:
+                thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
+                thisTrait.retrieveInfo(QTL=1)
+                if thisTrait.db.type == "ProbeSet":
+                    self.theseTraits.append(thisTrait)
+            except:
+                pass
+
+        if self.theseTraits:
+            pass
+        else:
+            templatePage.__init__(self, fd)
+            heading = 'GCAT'
+            detail = ['You need to select at least one microarray trait to submit to GCAT.']
+            self.error(heading=heading,detail=detail)
+            return
+
+        geneSymbolList = self.getGeneSymbolList()
+
+        geneSymbolSet = set(geneSymbolList)
+
+        if ( len(geneSymbolSet) < 500 ):
+            temp = '+'.join(geneSymbolSet)
+            GCATurl = "http://binf1.memphis.edu/gcat/?organism=mouse&subset=all&year=2010&geneInput=%s" % temp
+
+            self.dict['js1'] = """
+                <SCRIPT LANGUAGE="JavaScript">
+                setTimeout( 'window.location = "%s"', 2000 );
+                </SCRIPT>
+            """ % GCATurl
+
+            TD_LR.append(HT.Paragraph("Your selection of %d genes is being submitted to GCAT" % len(geneSymbolSet), Class="cr fs16 fwb", align="Center"))
+        else:
+            TD_LR.append(HT.Paragraph("Your selection of %d genes exceeds the limit of 500. Please reduce your gene number to below the limit." % len(geneSymbolSet), Class="cr fs16 fwb", align="Center"))
+
+
+        self.dict['body'] = TD_LR
+
+
+    def getGeneSymbolList(self):
+        geneList = []
+
+        for item in self.theseTraits:
+            item.retrieveInfo()
+            geneList.append(str(item.symbol))
+		
+        return geneList
+
+                 
diff --git a/web/webqtl/externalResource/GoTreePage.py b/web/webqtl/externalResource/GoTreePage.py
new file mode 100755
index 00000000..07144a23
--- /dev/null
+++ b/web/webqtl/externalResource/GoTreePage.py
@@ -0,0 +1,154 @@
+#GoTreePage.py
+
+import string
+from htmlgen import HTMLgen2 as HT
+
+from base import webqtlConfig
+from base.webqtlTrait import webqtlTrait
+from base.templatePage import templatePage
+from dbFunction import webqtlDatabaseFunction
+	
+			
+#########################################
+#     GoTree Page
+#########################################
+class GoTreePage(templatePage):
+
+	def __init__(self,fd):
+
+		self.theseTraits = []
+		TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")
+		
+		templatePage.__init__(self, fd)
+
+		if not self.openMysql():
+			return
+
+		self.searchResult = fd.formdata.getvalue('searchResult', [])
+		if type("1") == type(self.searchResult):
+			self.searchResult = [self.searchResult]
+
+		#XZ, self.theseTraits holds the "ProbeSet" traits.
+
+		for item in self.searchResult:
+			try:
+				thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
+				thisTrait.retrieveInfo(QTL=1)
+				if thisTrait.db.type == "ProbeSet":
+					self.theseTraits.append(thisTrait)
+			except:
+				pass
+				
+		if self.theseTraits:
+			pass
+		else:
+			templatePage.__init__(self, fd)
+			heading = 'WebGestalt'
+			detail = ['You need to select at least one microarray trait to submit.']
+			self.error(heading=heading,detail=detail)
+			return
+			
+		chipName = self.testChip(fd)
+
+		#XZ, 8/24/2009: the name of arraylist is misleading. It holds the name of traits.
+		arraylist, geneIdList = self.genGeneIdList(fd)
+		
+		target_url = "http://bioinfo.vanderbilt.edu/webgestalt/webgestalt.php"
+		
+		formWebGestalt = HT.Form(cgi=target_url, enctype='multipart/form-data', name='WebGestalt', submit = HT.Input(type='hidden'))
+
+		id_type = chipName
+
+		hddnWebGestalt = {'id_list':string.join(arraylist, ","),
+				  'id_type':id_type}
+		
+		hddnWebGestalt['ref_type'] = hddnWebGestalt['id_type']
+		hddnWebGestalt['analysis_type'] = 'GO'
+		hddnWebGestalt['significancelevel'] = 'Top10'
+		hddnWebGestalt['stat'] = 'Hypergeometric'
+		hddnWebGestalt['mtc'] = 'BH'
+		hddnWebGestalt['min'] = '2'
+		hddnWebGestalt['id_value'] = fd.formdata.getvalue('correlation') 
+			
+                species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
+
+                if species == 'rat':
+                    hddnWebGestalt['org'] = 'Rattus norvegicus'
+                elif species == 'human':
+                    hddnWebGestalt['org'] = 'Homo sapiens'
+                elif species == 'mouse':
+                    hddnWebGestalt['org'] = 'Mus musculus'
+                else:
+                    hddnWebGestalt['org'] = ''
+
+		hddnWebGestalt['org'] = hddnWebGestalt['org'].replace(' ','_')
+		
+		for key in hddnWebGestalt.keys():
+				formWebGestalt.append(HT.Input(name=key, value=hddnWebGestalt[key], type='hidden'))
+	
+		TD_LR.append(formWebGestalt)
+
+		TD_LR.append(HT.Paragraph("Your selection of %d traits is being submitted to GO Tree" % len(self.theseTraits), Class="cr fs16 fwb", align="Center"))
+		
+		# updated by NL, moved mixedChipError() to webqtl.js and change it to mixedChipError(methodName)
+		#                moved unknownChipError() to webqtl.js and change it to unknownChipError(chipName)
+		if chipName == 'mixed':
+			methodName = "WebGestalt"
+			self.dict['js1'] = """
+				<SCRIPT LANGUAGE="JavaScript">		
+					setTimeout("mixedChipError('%s')" ,1000);
+				</SCRIPT>
+			""" % methodName 
+		elif chipName.find('_NA') > 0:
+			chipName = chipName[0:-3]
+			self.dict['js1'] = """
+                <SCRIPT LANGUAGE="JavaScript">
+                setTimeout("unknownChipError('%s')",1000);
+                </SCRIPT>
+            """ % chipName
+		else:
+			self.dict['js1'] = """
+				<SCRIPT LANGUAGE="JavaScript">
+					setTimeout('document.WebGestalt.submit()',1000);
+				</SCRIPT>
+			"""
+			
+		self.dict['body'] = TD_LR
+	
+	def testChip(self, fd):
+		chipName0 = ""
+
+		for item in self.theseTraits:
+			self.cursor.execute('SELECT GeneChip.GO_tree_value FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Name = "%s"' % item.db.name)
+			result = self.cursor.fetchone()
+			if result:
+				chipName = result[0]
+				if chipName:
+					if chipName != chipName0:
+						if chipName0:
+							return 'mixed'
+						else:
+							chipName0 = chipName
+					else:
+						pass
+				else:
+					self.cursor.execute('SELECT GeneChip.Name FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Name = "%s"' % item.db.name)
+					result = self.cursor.fetchone()
+					chipName = '%s_NA' % result[0]
+					return chipName
+			else:
+				self.cursor.execute('SELECT GeneChip.Name FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Name = "%s"' % item.db.name)
+				result = self.cursor.fetchone()
+				chipName = '%s_NA' % result[0]
+				return chipName
+		return chipName
+
+	def genGeneIdList(self, fd):
+		arrayList = []
+		geneList = []
+		for item in self.theseTraits:
+			arrayList.append(item.name)
+			item.retrieveInfo()
+			geneList.append(str(item.geneid))
+		return arrayList, geneList
+	
diff --git a/web/webqtl/externalResource/ODEPage.py b/web/webqtl/externalResource/ODEPage.py
new file mode 100755
index 00000000..f02fe5aa
--- /dev/null
+++ b/web/webqtl/externalResource/ODEPage.py
@@ -0,0 +1,143 @@
+# 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
+
+#ODEPage.py
+
+import string
+from htmlgen import HTMLgen2 as HT
+
+from base import webqtlConfig
+from base.webqtlTrait import webqtlTrait
+from base.templatePage import templatePage
+from dbFunction import webqtlDatabaseFunction
+		
+class ODEPage(templatePage):
+
+    def __init__(self,fd):
+
+        templatePage.__init__(self, fd)
+
+        if not self.openMysql():
+            return
+
+        #XZ, self.theseTraits holds the "ProbeSet" traits.
+        self.theseTraits = []
+
+        self.searchResult = fd.formdata.getvalue('searchResult', [])
+        if type("1") == type(self.searchResult):
+            self.searchResult = [self.searchResult]
+
+        for item in self.searchResult:
+            try:
+                thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
+                thisTrait.retrieveInfo(QTL=1)
+                if thisTrait.db.type == "ProbeSet":
+                    self.theseTraits.append(thisTrait)
+            except:
+                pass
+
+        if self.theseTraits:
+            pass
+        else:
+            heading = 'ODE'
+            detail = ['You need to select at least one microarray trait to submit.']
+            self.error(heading=heading,detail=detail)
+            return
+
+        chipName = self.getChipName(fd)
+        species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
+
+        if species == 'rat':
+            species = 'Rattus norvegicus'
+        elif species == 'human':
+            species = 'Homo sapiens'
+        elif species == 'mouse':
+            species = 'Mus musculus'
+        else:
+            species = ''
+
+        probesetNameList = self.getProbesetNameList(fd)
+
+        TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")
+
+        formODE = HT.Form(cgi="http://ontologicaldiscovery.org/index.php?action=manage&cmd=importGeneSet", enctype='multipart/form-data', name='formODE', submit = HT.Input(type='hidden'))
+
+        hddnODE = {}
+
+        hddnODE['client'] = 'genenetwork'
+        hddnODE['species'] = species
+        hddnODE['idtype'] = chipName
+        hddnODE['list'] = string.join(probesetNameList, ",")
+
+        for key in hddnODE.keys():
+            formODE.append(HT.Input(name=key, value=hddnODE[key], type='hidden'))
+
+        TD_LR.append(formODE)
+
+        TD_LR.append(HT.Paragraph("Your selections of %d traits is being exported to the ODE" % len(self.theseTraits), Class="cr fs16 fwb", align="Center"))
+        # updated by NL, moved mixedChipError() to webqtl.js and change it to mixedChipError(methodName)		
+        if chipName == 'mixed':
+            methodName = "ODE" 	
+            self.dict['js1'] = """
+                <SCRIPT LANGUAGE="JavaScript">
+                    setTimeout("mixedChipError('%s')",1000);
+                </SCRIPT>
+                        """ % methodName 
+        else:
+            self.dict['js1'] = """
+                <SCRIPT LANGUAGE="JavaScript">
+                    setTimeout('document.formODE.submit()',1000);
+                </SCRIPT>
+                """
+
+        self.dict['body'] = TD_LR
+
+
+
+    def getProbesetNameList(self, fd):
+        probesetNameList = []
+
+        for item in self.theseTraits:
+            probesetNameList.append(item.name)
+
+        return probesetNameList
+
+
+
+    def getChipName(self, fd):
+        chipName0 = ""
+        for item in self.theseTraits:
+            self.cursor.execute('SELECT GeneChip.Name FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Name = "%s"' % item.db.name)
+            chipName = self.cursor.fetchone()[0]
+            if chipName != chipName0:
+                if chipName0:
+                    return 'mixed'
+                else:
+                    chipName0 = chipName
+            else:
+                pass
+
+        return chipName
diff --git a/web/webqtl/externalResource/__init__.py b/web/webqtl/externalResource/__init__.py
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/web/webqtl/externalResource/__init__.py