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

1 files changed, 0 insertions, 154 deletions

diff --git a/web/webqtl/externalResource/GoTreePage.py b/web/webqtl/externalResource/GoTreePage.py
deleted file mode 100755
index 07144a23..00000000
--- a/web/webqtl/externalResource/GoTreePage.py
+++ /dev/null
@@ -1,154 +0,0 @@
-#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
-