path: root/wqflask/base/webqtlTrait.py

from __future__ import division, print_function

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 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):
		print("in webqtlTrait")
		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 = {}
		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)
			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, repr(value) + ' parameter format error.'
			else:
				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
						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':
				print("Doing ProbeSet Query")
				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)
				print("query is:", query)
				self.cursor.execute(*query)
				self.sequence = self.cursor.fetchone()[0]
				print("self.sequence is:", self.sequence)


	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':
			self.cursor.execute('''
					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

		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

	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