Cleaning up trait stuff in flask

2 files changed, 145 insertions, 125 deletions

diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
index f5051e45..c3c0cded 100755
--- a/wqflask/base/webqtlTrait.py
+++ b/wqflask/base/webqtlTrait.py
@@ -1,3 +1,5 @@
+from __future__ import division, print_function
+
 import string
 
 from htmlgen import HTMLgen2 as HT
@@ -8,14 +10,18 @@ from webqtlDataset import webqtlDataset
 from dbFunction import webqtlDatabaseFunction
 from utility import webqtlUtil
 
+from pprint import pformat as pf
+
 
 class webqtlTrait:
 	"""
-	Trait class defines a trait in webqtl, can be either Microarray, 	
+	Trait class defines a trait in webqtl, can be either Microarray,
 	Published phenotype, genotype, or user input trait
+
 	"""
 
 	def __init__(self, cursor = None, **kw):
+		print("in webqtlTrait")
 		self.cursor = cursor
 		self.db = None			# database object
 		self.name = ''			# Trait ID, ProbeSet ID, Published ID, etc.
@@ -25,6 +31,9 @@ class webqtlTrait:
 		self.haveinfo = 0
 		self.sequence = ''		# Blat sequence, available for ProbeSet
 		self.data = {}
+		print("foo")
+		print("kw in webqtlTrait are:", pf(kw))
+		print("printed\n\n")
 		for name, value in kw.items():
 			if self.__dict__.has_key(name):
 				setattr(self, name, value)
@@ -35,28 +44,29 @@ class webqtlTrait:
 				elif len(name2) == 3:
 					self.db, self.name, self.cellid = name2
 				else:
-					raise KeyError, `value` + ' parameter format error.'
+					raise KeyError, repr(value) + ' parameter format error.'
 			else:
-				raise KeyError, `name`+' not a valid parameter for this class.'
-		
-		if self.db and type(self.db) == type("1"):
-			assert self.cursor
+				raise KeyError, repr(name) + ' not a valid parameter for this class.'
+
+		if self.db and isinstance(self.db, basestring):
+			assert self.cursor, "Don't have a cursor"
 			self.db = webqtlDataset(self.db, self.cursor)
 
 		#if self.db == None, not from a database
+		print("self.db is:", self.db, type(self.db))
 		if self.db:
 			if self.db.type == "Temp":
 				self.cursor.execute('''
-					SELECT 
-						InbredSet.Name 
-					FROM 
-						InbredSet, Temp 
-					WHERE 
-						Temp.InbredSetId = InbredSet.Id AND 
+					SELECT
+						InbredSet.Name
+					FROM
+						InbredSet, Temp
+					WHERE
+						Temp.InbredSetId = InbredSet.Id AND
 						Temp.Name = "%s"
-				''' % self.name)
+				''', self.name)
 				self.riset = self.cursor.fetchone()[0]
-			else:	
+			else:
 				self.riset = self.db.getRISet()
 
 		#
@@ -73,8 +83,9 @@ class webqtlTrait:
 
 		if self.db:
 			if self.db.type == 'ProbeSet':
+				print("Doing ProbeSet Query")
 				query = '''
-					SELECT 
+					SELECT
 						ProbeSet.BlatSeq
 					FROM
 						ProbeSet, ProbeSetFreeze, ProbeSetXRef
@@ -84,10 +95,11 @@ class webqtlTrait:
 						ProbeSet.Name = "%s" and
 						ProbeSetFreeze.Name = "%s"
 				''' % (self.name, self.db.name)
+				print("query is:", query)
 				self.cursor.execute(query)
 				self.sequence = self.cursor.fetchone()[0]
 
-	
+
 	def getName(self):
 		str = ""
 		if self.db and self.name:
@@ -98,12 +110,12 @@ class webqtlTrait:
 			str = self.description
 		return str
 
-	# 
+	#
 	# when user enter a trait or GN generate a trait, user want show the name
 	# not the name that generated by GN randomly, the two follow function are
-	# used to give the real name and the database. displayName() will show the 
-	# database also, getGivenName() just show the name. 
-	# For other trait, displayName() as same as getName(), getGivenName() as 
+	# used to give the real name and the database. displayName() will show the
+	# database also, getGivenName() just show the name.
+	# For other trait, displayName() as same as getName(), getGivenName() as
 	# same as self.name
 	#
 	# Hongqiang 11/29/07
@@ -137,10 +149,10 @@ class webqtlTrait:
 					str += "::" + self.cellid
 		else:
 			str = self.description
-	
+
 		return str
 
-	
+
 	#def __str__(self):
 	#	#return "%s %s" % (self.getName(), self.riset)
 	#	return self.getName()
@@ -166,7 +178,7 @@ class webqtlTrait:
 			else:
 				result.append(None)
 		return result
-		
+
 	def exportInformative(self, incVar=0):
 		"""
 			export informative strain
@@ -195,7 +207,7 @@ class webqtlTrait:
 		assert self.cursor
 		if self.db.type == 'ProbeSet':
 			query = '''
-					SELECT 
+					SELECT
 						ProbeSet.BlatSeq
 					FROM
 						ProbeSet, ProbeSetFreeze, ProbeSetXRef
@@ -209,40 +221,40 @@ class webqtlTrait:
 			results = self.fetchone()
 
 			return results[0]
-			
-			
-		
+
+
+
 	def retrieveData(self, strainlist=[]):
 		assert self.db and self.cursor
 
 		if self.db.type == 'Temp':
 			query = '''
-				SELECT 
-					Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id 
-				FROM 
-					TempData, Temp, Strain 
-				WHERE 
-					TempData.StrainId = Strain.Id AND 
-					TempData.Id = Temp.DataId AND 
+				SELECT
+					Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id
+				FROM
+					TempData, Temp, Strain
+				WHERE
+					TempData.StrainId = Strain.Id AND
+					TempData.Id = Temp.DataId AND
 					Temp.name = '%s'
 				Order BY
 					Strain.Name
 				''' % self.name
 		#XZ, 03/02/2009: Xiaodong changed Data to PublishData, SE to PublishSE
-		elif self.db.type == 'Publish': 
+		elif self.db.type == 'Publish':
 			query = '''
-				SELECT 
-					Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id 
-				FROM 
+				SELECT
+					Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id
+				FROM
 					(PublishData, Strain, PublishXRef, PublishFreeze)
-				left join PublishSE on 
+				left join PublishSE on
 					(PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId)
-				left join NStrain on 
-					(NStrain.DataId = PublishData.Id AND 
-					NStrain.StrainId = PublishData.StrainId) 
-				WHERE 
-					PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND 
-					PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND 
+				left join NStrain on
+					(NStrain.DataId = PublishData.Id AND
+					NStrain.StrainId = PublishData.StrainId)
+				WHERE
+					PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+					PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND
 					PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id
 				Order BY
 					Strain.Name
@@ -252,21 +264,21 @@ class webqtlTrait:
 		elif self.cellid:
 			#Probe Data
 			query = '''
-				SELECT 
-					Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id 
-				FROM 
-					(ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, 
+				SELECT
+					Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id
+				FROM
+					(ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef,
 					Strain, Probe, ProbeSet)
-				left join ProbeSE on 
+				left join ProbeSE on
 					(ProbeSE.DataId = ProbeData.Id AND ProbeSE.StrainId = ProbeData.StrainId)
-				WHERE 
-					Probe.Name = '%s' AND ProbeSet.Name = '%s' AND 
-					Probe.ProbeSetId = ProbeSet.Id AND 
-					ProbeXRef.ProbeId = Probe.Id AND 
-					ProbeXRef.ProbeFreezeId = ProbeFreeze.Id AND 
-					ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND 
-					ProbeSetFreeze.Name = '%s' AND 
-					ProbeXRef.DataId = ProbeData.Id AND 
+				WHERE
+					Probe.Name = '%s' AND ProbeSet.Name = '%s' AND
+					Probe.ProbeSetId = ProbeSet.Id AND
+					ProbeXRef.ProbeId = Probe.Id AND
+					ProbeXRef.ProbeFreezeId = ProbeFreeze.Id AND
+					ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
+					ProbeSetFreeze.Name = '%s' AND
+					ProbeXRef.DataId = ProbeData.Id AND
 					ProbeData.StrainId = Strain.Id
 				Order BY
 					Strain.Name
@@ -295,23 +307,23 @@ class webqtlTrait:
 			#Geno Data
 			#XZ: The SpeciesId is not necessary, but it's nice to keep it to speed up database search.
 			query = '''
-				SELECT 
-					Strain.Name, GenoData.value, GenoSE.error, GenoData.Id 
-				FROM 
+				SELECT
+					Strain.Name, GenoData.value, GenoSE.error, GenoData.Id
+				FROM
 					(GenoData, GenoFreeze, Strain, Geno, GenoXRef)
 				left join GenoSE on
 					(GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
-				WHERE 
+				WHERE
 					Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND
-					GenoXRef.GenoFreezeId = GenoFreeze.Id AND 
-					GenoFreeze.Name = '%s' AND 
-					GenoXRef.DataId = GenoData.Id AND 
+					GenoXRef.GenoFreezeId = GenoFreeze.Id AND
+					GenoFreeze.Name = '%s' AND
+					GenoXRef.DataId = GenoData.Id AND
 					GenoData.StrainId = Strain.Id
 				Order BY
 					Strain.Name
 				''' % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.db.riset), self.name, self.db.name)
 
-		
+
 		self.cursor.execute(query)
 		results = self.cursor.fetchall()
 		self.data.clear()
@@ -328,7 +340,7 @@ class webqtlTrait:
 								ndata = item[3]
 							self.data[item[0]] = webqtlCaseData(val, var, ndata)
 				#end for
-			else:	
+			else:
 				for item in results:
 					val = item[1]
 					if val != None:
@@ -341,16 +353,16 @@ class webqtlTrait:
 			#end if
 		else:
 			pass
-			
+
 	def keys(self):
 		return self.__dict__.keys()
-	
+
 	def has_key(self, key):
 		return self.__dict__.has_key(key)
-	
+
 	def items(self):
 		return self.__dict__.items()
-	
+
 	def retrieveInfo(self, QTL = None):
 		assert self.db and self.cursor
 		if self.db.type == 'Publish':
@@ -358,22 +370,22 @@ class webqtlTrait:
 			#	'Abstract', 'Journal','Volume','Pages','Month','Year','Sequence',\
 			#	'Units', 'comments']
 			query = '''
-				SELECT 
-					PublishXRef.Id, Publication.PubMed_ID, 
-					Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description, 
-					Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, 
+				SELECT
+					PublishXRef.Id, Publication.PubMed_ID,
+					Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
+					Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
 					Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
-					Publication.Authors, Publication.Title, Publication.Abstract, 
-					Publication.Journal, Publication.Volume, Publication.Pages, 
-					Publication.Month, Publication.Year, PublishXRef.Sequence, 
-					Phenotype.Units, PublishXRef.comments 
-				FROM 
-					PublishXRef, Publication, Phenotype, PublishFreeze 
-				WHERE 
-					PublishXRef.Id = %s AND 
-					Phenotype.Id = PublishXRef.PhenotypeId AND 
-					Publication.Id = PublishXRef.PublicationId AND 
-					PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND 
+					Publication.Authors, Publication.Title, Publication.Abstract,
+					Publication.Journal, Publication.Volume, Publication.Pages,
+					Publication.Month, Publication.Year, PublishXRef.Sequence,
+					Phenotype.Units, PublishXRef.comments
+				FROM
+					PublishXRef, Publication, Phenotype, PublishFreeze
+				WHERE
+					PublishXRef.Id = %s AND
+					Phenotype.Id = PublishXRef.PhenotypeId AND
+					Publication.Id = PublishXRef.PublicationId AND
+					PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
 					PublishFreeze.Id =%s
 				''' % (self.name, self.db.id)
 		#XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
@@ -382,7 +394,7 @@ class webqtlTrait:
 			disfieldString = string.join(self.db.disfield,',ProbeSet.')
 			disfieldString = 'ProbeSet.' + disfieldString
 			query = """
-				SELECT %s 
+				SELECT %s
 				FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef
 				WHERE
 					ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
@@ -396,7 +408,7 @@ class webqtlTrait:
 			disfieldString = string.join(self.db.disfield,',Geno.')
 			disfieldString = 'Geno.' + disfieldString
 			query = """
-				SELECT %s 
+				SELECT %s
 				FROM Geno, GenoFreeze, GenoXRef
 				WHERE
 					GenoXRef.GenoFreezeId = GenoFreeze.Id AND
@@ -408,7 +420,7 @@ class webqtlTrait:
 			query = 'SELECT %s FROM %s WHERE Name = "%s"' % \
 				(string.join(self.db.disfield,','), self.db.type, self.name)
 
-		
+
 		self.cursor.execute(query)
 		traitInfo = self.cursor.fetchone()
 		if traitInfo:
@@ -457,12 +469,12 @@ class webqtlTrait:
 			if QTL:
 				if self.db.type == 'ProbeSet' and not self.cellid:
 					query = '''
-						SELECT 
-							ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean 
-						FROM 
+						SELECT
+							ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean
+						FROM
 							ProbeSetXRef, ProbeSet
-						WHERE 
-							ProbeSetXRef.ProbeSetId = ProbeSet.Id AND 
+						WHERE
+							ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
 							ProbeSet.Name = "%s" AND
 							ProbeSetXRef.ProbeSetFreezeId =%s
 						''' % (self.name, self.db.id)
@@ -491,11 +503,11 @@ class webqtlTrait:
 						self.locus = self.lrs = ""
 		else:
 			raise KeyError, `self.name`+' information is not found in the database.'
-	
+
 	def genHTML(self, formName = "", dispFromDatabase=0, privilege="guest", userName="Guest", authorized_users=""):
 		if not self.haveinfo:
 			self.retrieveInfo()
-		
+
 		if self.db.type == 'Publish':
 			PubMedLink = ""
 	 		if self.pubmed_id:
@@ -503,14 +515,14 @@ class webqtlTrait:
 	 			target = "_blank", url = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id)
 			else:
 				PubMedLink = HT.Span("Unpublished : ", Class="fs15")
-			
+
 			if formName:
-				setDescription2 = HT.Href(url="javascript:showDatabase3('%s','%s','%s','')" % 
+				setDescription2 = HT.Href(url="javascript:showDatabase3('%s','%s','%s','')" %
 				(formName, self.db.name, self.name), Class = "fs14")
 			else:
-				setDescription2 = HT.Href(url="javascript:showDatabase2('%s','%s','')" % 
+				setDescription2 = HT.Href(url="javascript:showDatabase2('%s','%s','')" %
 				(self.db.name,self.name), Class = "fs14")
-	
+
 			if self.confidential and not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=privilege, userName=userName, authorized_users=authorized_users):
 					setDescription2.append('RecordID/%s - %s' % (self.name, self.pre_publication_description))
 			else:
@@ -526,12 +538,12 @@ class webqtlTrait:
 				setDescription2.append(' by ')
 				setDescription2.append(HT.Italic('%s, and colleagues' % a1))
 			setDescription = HT.Span(PubMedLink, setDescription2)
-			
+
 		elif self.db.type == 'Temp':
 			setDescription = HT.Href(text="%s" % (self.description),url="javascript:showDatabase2\
 			('%s','%s','')" % (self.db.name,self.name), Class = "fs14")
 			setDescription = HT.Span(setDescription)
-			
+
 		elif self.db.type == 'Geno': # Genome DB only available for single search
 			if formName:
 				setDescription = HT.Href(text="Locus %s [Chr %s @ %s Mb]" % (self.name,self.chr,\
@@ -541,16 +553,16 @@ class webqtlTrait:
 				setDescription = HT.Href(text="Locus %s [Chr %s @ %s Mb]" % (self.name,self.chr,\
 			'%2.3f' % self.mb),url="javascript:showDatabase2('%s','%s','')" % \
 			(self.db.name,self.name), Class = "fs14")
-				
+
 			setDescription = HT.Span(setDescription)
-			
+
 		else:
 			if self.cellid:
-				if formName:	
+				if formName:
 					setDescription = HT.Href(text="ProbeSet/%s/%s" % (self.name, self.cellid),url=\
 				"javascript:showDatabase3('%s','%s','%s','%s')" % (formName, self.db.name,self.name,self.cellid), \
 				Class = "fs14")
-				else:	
+				else:
 					setDescription = HT.Href(text="ProbeSet/%s/%s" % (self.name,self.cellid),url=\
 				"javascript:showDatabase2('%s','%s','%s')" % (self.db.name,self.name,self.cellid), \
 				Class = "fs14")
@@ -572,10 +584,8 @@ class webqtlTrait:
 			if self.probe_target_description:
 				setDescription.append('; %s' % self.probe_target_description)
 			setDescription = HT.Span(setDescription)
-			
+
 		if self.db.type != 'Temp' and dispFromDatabase:
 			setDescription.append( ' --- FROM : ')
 			setDescription.append(self.db.genHTML(Class='cori'))
 		return setDescription
-	
-	
diff --git a/wqflask/wqflask/show_trait/show_trait_page.py b/wqflask/wqflask/show_trait/show_trait_page.py
index 03f8b9b3..c7d6618e 100644
--- a/wqflask/wqflask/show_trait/show_trait_page.py
+++ b/wqflask/wqflask/show_trait/show_trait_page.py
@@ -36,29 +36,39 @@ from DataEditingPage import DataEditingPage
 
 class ShowTraitPage(DataEditingPage):
 
-	def __init__(self, fd, traitInfos = []):
+	def __init__(self, fd, traitInfos = None):
 
-		templatePage.__init__(self, fd)
+		#templatePage.__init__(self, fd)
 
 		if not self.openMysql():
 			return
 
-		TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
-
+		#TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
+		print("j2")
+		# When is traitInfos used?
 		if traitInfos:
-			database,ProbeSetID,CellID = traitInfos
+			print("j2.2")
+			database, ProbeSetID, CellID = traitInfos
 		else:
-			database = fd.formdata.getfirst('database')
-			ProbeSetID = fd.formdata.getfirst('ProbeSetID')
-			CellID = fd.formdata.getfirst('CellID')
-		try:
-			thisTrait = webqtlTrait(db=database, name=ProbeSetID, cellid= CellID, cursor=self.cursor)
-		except:
-			heading = "Trait Data and Analysis Form"
-			detail = ["The trait isn't available currently."]
-			self.error(heading=heading,detail=detail,error="Error")
-			return
-
+			print("j2.3")
+			print("fd is:", fd)
+			database = fd['database']
+			ProbeSetID = fd['ProbeSetID']
+			print("j2.4")
+			CellID = fd.get('CellID')
+			print("j2.6")
+
+		# We're no longer wrapping this in an exception. If we fail, let's fail hard
+		# Log it and fix it
+		#try:
+		print("j3")
+		thisTrait = webqtlTrait(db=database, name=ProbeSetID, cellid= CellID, cursor=self.cursor)
+		#except:
+		#	heading = "Trait Data and Analysis Form"
+		#	detail = ["The trait isn't available currently."]
+		#	self.error(heading=heading,detail=detail,error="Error")
+		#	return
+		print("j4")
 		if thisTrait.db.type == "ProbeSet":
 
 			self.cursor.execute('''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers