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

1 files changed, 0 insertions, 590 deletions

diff --git a/web/webqtl/base/webqtlTrait.py b/web/webqtl/base/webqtlTrait.py
deleted file mode 100644
index 2469504f..00000000
--- a/web/webqtl/base/webqtlTrait.py
+++ /dev/null
@@ -1,590 +0,0 @@
-import string
-
-from htmlgen import HTMLgen2 as HT
-
-import webqtlConfig
-from webqtlCaseData import webqtlCaseData
-from webqtlDataset import webqtlDataset
-from dbFunction import webqtlDatabaseFunction
-from utility import webqtlUtil
-
-
-from __future__ import print_function, division
-
-from pprint import pformat as pf
-
-class webqtlTrait:
-	"""
-	Trait class defines a trait in webqtl, can be either Microarray, 	
-	Published phenotype, genotype, or user input trait
-	"""
-
-	def __init__(self, cursor = None, **kw):
-		self.cursor = cursor
-		self.db = None			# database object
-		self.name = ''			# Trait ID, ProbeSet ID, Published ID, etc.
-		self.cellid = ''
-		self.identification = 'un-named trait'
-		self.riset = ''
-		self.haveinfo = 0
-		self.sequence = ''		# Blat sequence, available for ProbeSet
-		self.data = {}
-		for name, value in kw.items():
-			if self.__dict__.has_key(name):
-				setattr(self, name, value)
-			elif name == 'fullname':
-				name2 = value.split("::")
-				if len(name2) == 2:
-					self.db, self.name = name2
-				elif len(name2) == 3:
-					self.db, self.name, self.cellid = name2
-				else:
-					raise KeyError, `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
-			self.db = webqtlDataset(self.db, self.cursor)
-
-		#if self.db == None, not from a database
-		if self.db:
-			if self.db.type == "Temp":
-				self.cursor.execute('''
-					SELECT 
-						InbredSet.Name 
-					FROM 
-						InbredSet, Temp 
-					WHERE 
-						Temp.InbredSetId = InbredSet.Id AND 
-						Temp.Name = "%s"
-				''' % self.name)
-				self.riset = self.cursor.fetchone()[0]
-			else:	
-				self.riset = self.db.getRISet()
-
-		#
-		# In ProbeSet, there are maybe several annotations match one sequence
-		# so we need use sequence(BlatSeq) as the identification, when we update
-		# one annotation, we update the others who match the sequence also.
-		#
-		# Hongqiang Li, 3/3/2008
-		#
-
-                #XZ, 05/08/2009: This block is not neccessary. We can add 'BlatSeq' into disfield.
-                # The variable self.sequence should be changed to self.BlatSeq
-                # It also should be changed in other places where it are used.
-
-		if self.db:
-			if self.db.type == 'ProbeSet':
-				query = '''
-					SELECT 
-						ProbeSet.BlatSeq
-					FROM
-						ProbeSet, ProbeSetFreeze, ProbeSetXRef
-					WHERE
-						ProbeSet.Id=ProbeSetXRef.ProbeSetId and
-						ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and
-						ProbeSet.Name = "%s" and
-						ProbeSetFreeze.Name = "%s"
-				''' % (self.name, self.db.name)
-				self.cursor.execute(query)
-				self.sequence = self.cursor.fetchone()[0]
-
-	
-	def getName(self):
-		str = ""
-		if self.db and self.name:
-			str = "%s::%s" % (self.db, self.name)
-			if self.cellid:
-				str += "::" + self.cellid
-		else:
-			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 
-	# same as self.name
-	#
-	# Hongqiang 11/29/07
-	#
-	def getGivenName(self):
-		str = self.name
-		if self.db and self.name:
-			if self.db.type=='Temp':
-				self.cursor.execute('SELECT description FROM Temp WHERE Name=%s',self.name)
-				desc = self.cursor.fetchone()[0]
-				if desc.__contains__('PCA'):
-					desc = desc[desc.rindex(':')+1:].strip()
-				else:
-					desc = desc[:desc.index('entered')].strip()
-				str = desc
-		return str
-
-	def displayName(self):
-		str = ""
-		if self.db and self.name:
-			if self.db.type=='Temp':
-				desc = self.description
-				if desc.__contains__('PCA'):
-					desc = desc[desc.rindex(':')+1:].strip()
-				else:
-					desc = desc[:desc.index('entered')].strip()
-				str = "%s::%s" % (self.db, desc)
-			else:
-				str = "%s::%s" % (self.db, self.name)
-				if self.cellid:
-					str += "::" + self.cellid
-		else:
-			str = self.description
-	
-		return str
-
-	
-	#def __str__(self):
-	#	#return "%s %s" % (self.getName(), self.riset)
-	#	return self.getName()
-	__str__ = getName
-	__repr__ = __str__
-
-	def exportData(self, strainlist, type="val"):
-		"""
-			export data according to strainlist
-			mostly used in calculating correlation
-		"""
-		result = []
-		for strain in strainlist:
-			if self.data.has_key(strain):
-				if type=='val':
-					result.append(self.data[strain].val)
-				elif type=='var':
-					result.append(self.data[strain].var)
-				elif type=='N':
-					result.append(self.data[strain].N)
-				else:
-					raise KeyError, `type`+' type is incorrect.'
-			else:
-				result.append(None)
-		return result
-		
-	def exportInformative(self, incVar=0):
-		"""
-			export informative strain
-			mostly used in qtl regression
-		"""
-		strains = []
-		vals = []
-		vars = []
-		for strain, value in self.data.items():
-			if value.val != None:
-				if not incVar or value.var != None:
-					strains.append(strain)
-					vals.append(value.val)
-					vars.append(value.var)
-		return 	strains, vals, vars
-
-
-	#
-	# In ProbeSet, there are maybe several annotations match one sequence
-	# so we need use sequence(BlatSeq) as the identification, when we update
-	# one annotation, we update the others who match the sequence also.
-	#
-	# Hongqiang Li, 3/3/2008
-	#
-	def getSequence(self):
-		assert self.cursor
-		if self.db.type == 'ProbeSet':
-			query = '''
-					SELECT 
-						ProbeSet.BlatSeq
-					FROM
-						ProbeSet, ProbeSetFreeze, ProbeSetXRef
-					WHERE
-						ProbeSet.Id=ProbeSetXRef.ProbeSetId and
-						ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and
-						ProbeSet.Name = %s
-						ProbeSetFreeze.Name = %s
-				''' , (self.name, self.db.name)
-			self.cursor.execute(query)
-			results = self.fetchone()
-
-			return results[0]
-			
-			
-		
-	def retrieveData(self, strainlist=[]):
-		assert self.db and self.cursor
-
-		debug_file = open("/home/zas1024/gn/web/traitlist_debug.txt", "w")
-		debug_file.write("strianlist is:" + strainlist + "\n")
-
-		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 
-					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': 
-			query = '''
-				SELECT 
-					Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id 
-				FROM 
-					(PublishData, Strain, PublishXRef, PublishFreeze)
-				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 
-					PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id
-				Order BY
-					Strain.Name
-				''' % (self.name, self.db.id)
-
-                #XZ, 03/02/2009: Xiaodong changed Data to ProbeData, SE to ProbeSE
-		elif self.cellid:
-			#Probe Data
-			query = '''
-				SELECT 
-					Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id 
-				FROM 
-					(ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, 
-					Strain, Probe, ProbeSet)
-				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 
-					ProbeData.StrainId = Strain.Id
-				Order BY
-					Strain.Name
-				''' % (self.cellid, self.name, self.db.name)
-                #XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE
-		elif self.db.type == 'ProbeSet':
-			#ProbeSet Data
-                        query = '''
-                                SELECT
-                                        Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id
-                                FROM
-                                        (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
-                                left join ProbeSetSE on
-                                        (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
-                                WHERE
-                                        ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-                                        ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
-                                        ProbeSetFreeze.Name = '%s' AND
-                                        ProbeSetXRef.DataId = ProbeSetData.Id AND
-                                        ProbeSetData.StrainId = Strain.Id
-                                Order BY
-                                        Strain.Name
-                                ''' % (self.name, self.db.name)
-                #XZ, 03/02/2009: Xiaodong changeded Data to GenoData, SE to GenoSE
-		else:
-			#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 
-					(GenoData, GenoFreeze, Strain, Geno, GenoXRef)
-				left join GenoSE on
-					(GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
-				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 
-					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()
-		if results:
-			self.mysqlid = results[0][-1]
-			if strainlist:
-				for item in results:
-					if item[0] in strainlist:
-						val = item[1]
-						if val != None:
-							var = item[2]
-							ndata = None
-							if self.db.type in ('Publish', 'Temp'):
-								ndata = item[3]
-							self.data[item[0]] = webqtlCaseData(val, var, ndata)
-				#end for
-			else:	
-				for item in results:
-					val = item[1]
-					if val != None:
-						var = item[2]
-						ndata = None
-						if self.db.type in ('Publish', 'Temp'):
-							ndata = item[3]
-						self.data[item[0]] = webqtlCaseData(val, var, ndata)
-				#end for
-			#end if
-		else:
-			pass
-
-		debug_file.write("self.data is:", pf(self.data) + "\n")
-			
-	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':
-			#self.db.DisField = ['Name','PubMed_ID','Phenotype','Abbreviation','Authors','Title',\
-			#	'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, 
-					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 
-					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
-		#XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
-		elif self.db.type == 'ProbeSet':
-			disfieldString = string.join(self.db.disfield,',ProbeSet.')
-			disfieldString = 'ProbeSet.' + disfieldString
-			query = """
-				SELECT %s 
-				FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef
-				WHERE
-					ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
-					ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-					ProbeSetFreeze.Name = '%s' AND
-					ProbeSet.Name = '%s'
-				""" % (disfieldString, self.db.name, self.name)
-		#XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
-		# to avoid the problem of same marker name from different species.
-		elif self.db.type == 'Geno':
-			disfieldString = string.join(self.db.disfield,',Geno.')
-			disfieldString = 'Geno.' + disfieldString
-			query = """
-				SELECT %s 
-				FROM Geno, GenoFreeze, GenoXRef
-				WHERE
-					GenoXRef.GenoFreezeId = GenoFreeze.Id AND
-					GenoXRef.GenoId = Geno.Id AND
-					GenoFreeze.Name = '%s' AND
-					Geno.Name = '%s'
-				""" % (disfieldString, self.db.name, self.name)
-		else: #Temp type
-			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:
-			self.haveinfo = 1
-
-			#XZ: assign SQL query result to trait attributes.
-			for i, field in enumerate(self.db.disfield):
-				setattr(self, field, traitInfo[i])
-
-			if self.db.type == 'Publish':
-				self.confidential = 0
-				if self.pre_publication_description and not self.pubmed_id:
-					self.confidential = 1
-
-			self.homologeneid = None
-			if self.db.type == 'ProbeSet' and self.riset and self.geneid:
-				#XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number.
-				#XZ: So I have to test if geneid is number before execute the query.
-				#XZ: The geneid values in database should be cleaned up.
-				try:
-					junk = float(self.geneid)
-					geneidIsNumber = 1
-				except:
-					geneidIsNumber = 0
-
-				if geneidIsNumber:
-					query = """
-						SELECT
-							HomologeneId
-						FROM
-							Homologene, Species, InbredSet
-						WHERE
-							Homologene.GeneId =%s AND
-							InbredSet.Name = '%s' AND
-							InbredSet.SpeciesId = Species.Id AND
-							Species.TaxonomyId = Homologene.TaxonomyId
-						""" % (self.geneid, self.riset)
-					self.cursor.execute(query)
-					result = self.cursor.fetchone()
-				else:
-					result = None
-
-				if result:
-					self.homologeneid = result[0]
-
-			if QTL:
-				if self.db.type == 'ProbeSet' and not self.cellid:
-					query = '''
-						SELECT 
-							ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean 
-						FROM 
-							ProbeSetXRef, ProbeSet
-						WHERE 
-							ProbeSetXRef.ProbeSetId = ProbeSet.Id AND 
-							ProbeSet.Name = "%s" AND
-							ProbeSetXRef.ProbeSetFreezeId =%s
-						''' % (self.name, self.db.id)
-					self.cursor.execute(query)
-					traitQTL = self.cursor.fetchone()
-					if traitQTL:
-						self.locus, self.lrs, self.pvalue, self.mean = traitQTL
-					else:
-						self.locus = self.lrs = self.pvalue = self.mean = ""
-				if self.db.type == 'Publish':
-					query = '''
-						SELECT
-							PublishXRef.Locus, PublishXRef.LRS
-						FROM
-							PublishXRef, PublishFreeze
-						WHERE
-							PublishXRef.Id = %s AND
-							PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
-							PublishFreeze.Id =%s
-						''' % (self.name, self.db.id)
-					self.cursor.execute(query)
-					traitQTL = self.cursor.fetchone()
-					if traitQTL:
-						self.locus, self.lrs = traitQTL
-					else:
-						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:
-	 			PubMedLink = HT.Href(text="PubMed %d : " % self.pubmed_id,
-	 			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','')" % 
-				(formName, self.db.name, self.name), Class = "fs14")
-			else:
-				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:
-				setDescription2.append('RecordID/%s - %s' % (self.name, self.post_publication_description))
-
-			#XZ 03/26/2011: Xiaodong comment out the following two lins as Rob asked. Need to check with Rob why in PublishXRef table, there are few row whose Sequence > 1.
-			#if self.sequence > 1:
-			#	setDescription2.append(' btach %d' % self.sequence)
-			if self.authors:
-				a1 = string.split(self.authors,',')[0]
-				while a1[0] == '"' or a1[0] == "'" :
-					a1 = a1[1:]
-				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,\
-			'%2.3f' % self.mb),url="javascript:showDatabase3('%s','%s','%s','')" % \
-			(formName, self.db.name, self.name), Class = "fs14")
-			else:
-				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:	
-					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:	
-					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")
-			else:
-				if formName:
-					setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\
-				"javascript:showDatabase3('%s','%s','%s','')" % (formName, self.db.name,self.name), \
-				Class = "fs14")
-				else:
-					setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\
-				"javascript:showDatabase2('%s','%s','')" % (self.db.name,self.name), \
-				Class = "fs14")
-			if self.symbol and self.chr and self.mb:
-				setDescription.append(' [')
-				setDescription.append(HT.Italic('%s' % self.symbol,Class="cdg fwb"))
-				setDescription.append(' on Chr %s @ %s Mb]' % (self.chr,self.mb))
-			if self.description:
-				setDescription.append(': %s' % self.description)
-			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
-	
-