Add all the source codes into the github.

1 files changed, 154 insertions, 0 deletions

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
+