Renamed webqtlTrait.py to trait.py

Renamed webqtlTrait class to GeneralTrait

Began process of removing fd from show_trait.py

Created DatasetGroup object in data_set.py (this may end up becoming
its own file later if it becomes big enough)

1 files changed, 0 insertions, 695 deletions

diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
deleted file mode 100755
index 5367b41f..00000000
--- a/wqflask/base/webqtlTrait.py
+++ /dev/null
@@ -1,695 +0,0 @@
-from __future__ import division, print_function
-
-import string
-
-from htmlgen import HTMLgen2 as HT
-
-import webqtlConfig
-from webqtlCaseData import webqtlCaseData
-from data_set import create_dataset
-from dbFunction import webqtlDatabaseFunction
-from utility import webqtlUtil
-
-from MySQLdb import escape_string as escape
-from pprint import pformat as pf
-
-from flask import Flask, g
-
-class GeneralTrait:
-    """
-    Trait class defines a trait in webqtl, can be either Microarray,
-    Published phenotype, genotype, or user input trait
-
-    """
-
-    def __init__(self, **kw):
-        print("in GeneralTrait")
-        self.dataset = kw.get('dataset', None)                  # database object
-        self.name = kw.get('name', None)                 # Trait ID, ProbeSet ID, Published ID, etc.
-        self.cellid = kw.get('cellid', None)
-        self.identification = kw.get('identification', 'un-named trait')
-        self.group = kw.get('group', None)
-        self.haveinfo = kw.get('haveinfo', False)
-        self.sequence = kw.get('sequence', None)              # Blat sequence, available for ProbeSet
-        self.data = kw.get('data', {})
-        
-        if kw.get('fullname'):
-            name2 = value.split("::")
-            if len(name2) == 2:
-                self.dataset, self.name = name2
-            elif len(name2) == 3:
-                self.dataset, self.name, self.cellid = name2
-                
-        #if self.dataset and isinstance(self.dataset, basestring):
-        self.dataset = create_dataset(self.dataset.name)
-
-        print("self.dataset is:", self.dataset, type(self.dataset))
-        #if self.dataset:
-        
-        self.dataset.get_group()
-        
-        if self.dataset.type == "Temp":
-            self.cursor.execute('''
-                    SELECT
-                            InbredSet.Name
-                    FROM
-                            InbredSet, Temp
-                    WHERE
-                            Temp.InbredSetId = InbredSet.Id AND
-                            Temp.Name = "%s"
-            ''', self.name)
-            self.group = self.cursor.fetchone()[0]
-        else:
-            self.group = self.dataset.get_group()
-
-        print("trinity, self.group is:", self.group)
-
-        #
-        # 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.dataset:
-        if self.dataset.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.dataset.name)
-            print("query is:", query)
-            self.sequence = g.db.execute(*query).fetchone()[0]
-            #self.sequence = self.cursor.fetchone()[0]
-            print("self.sequence is:", self.sequence)
-
-
-    def getName(self):
-        str = ""
-        if self.dataset and self.name:
-            str = "%s::%s" % (self.dataset, 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.dataset and self.name:
-            if self.dataset.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.dataset and self.name:
-            if self.dataset.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.dataset, desc)
-            else:
-                str = "%s::%s" % (self.dataset, self.name)
-                if self.cellid:
-                    str += "::" + self.cellid
-        else:
-            str = self.description
-
-        return str
-
-
-    #def __str__(self):
-    #       #return "%s %s" % (self.getName(), self.group)
-    #       return self.getName()
-    #__str__ = getName
-    #__repr__ = __str__
-
-    def exportData(self, samplelist, type="val"):
-        """
-                export data according to samplelist
-                mostly used in calculating correlation
-        """
-        result = []
-        for sample in samplelist:
-            if self.data.has_key(sample):
-                if type=='val':
-                    result.append(self.data[sample].val)
-                elif type=='var':
-                    result.append(self.data[sample].var)
-                elif type=='N':
-                    result.append(self.data[sample].N)
-                else:
-                    raise KeyError, `type`+' type is incorrect.'
-            else:
-                result.append(None)
-        return result
-
-    def exportInformative(self, incVar=0):
-        """
-                export informative sample
-                mostly used in qtl regression
-        """
-        samples = []
-        vals = []
-        vars = []
-        for sample, value in self.data.items():
-            if value.val != None:
-                if not incVar or value.var != None:
-                    samples.append(sample)
-                    vals.append(value.val)
-                    vars.append(value.var)
-        return  samples, 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.dataset.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.dataset.name)
-            #self.cursor.execute(query)
-            results = self.fetchone()
-
-            return results[0]
-
-
-
-    def retrieveData(self, samplelist=None):
-
-        if samplelist == None:
-            samplelist = []
-        assert self.dataset and self.cursor
-
-        if self.dataset.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.dataset.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.dataset.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.dataset.name)
-        #XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE
-        elif self.dataset.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.dataset.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.dataset.group), self.name, self.dataset.name)
-
-
-        self.cursor.execute(query)
-        results = self.cursor.fetchall()
-        self.data.clear()
-
-        if results:
-            self.mysqlid = results[0][-1]
-            #if samplelist:
-            for item in results:
-                #name, value, variance, num_cases = item
-                if not samplelist or (samplelist and name in samplelist):
-                    #if value != None:
-                    #    num_cases = None
-                    #    if self.dataset.type in ('Publish', 'Temp'):
-                    #        ndata = item[3]
-                    name = item[0]
-                    self.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
-                #end for
-        #    else:
-        #        for item in results:
-        #            val = item[1]
-        #            if val != None:
-        #                var = item[2]
-        #                ndata = None
-        #                if self.dataset.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 retrieve_info(self, QTL=False):
-        assert self.dataset, "Dataset doesn't exist"
-        if self.dataset.type == 'Publish':
-            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.dataset.id)
-            traitInfo = g.db.execute(query).fetchone()
-        #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.dataset.type == 'ProbeSet':
-            display_fields_string = ', ProbeSet.'.join(self.dataset.display_fields)
-            display_fields_string = 'ProbeSet.' + display_fields_string
-            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'
-                    """ % (display_fields_string, self.dataset.name, self.name)
-            traitInfo = g.db.execute(query).fetchone()
-            print("traitInfo is: ", pf(traitInfo))
-        #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.dataset.type == 'Geno':
-            display_fields_string = string.join(self.dataset.display_fields,',Geno.')
-            display_fields_string = 'Geno.' + display_fields_string
-            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'
-                    """ % (display_fields_string, self.dataset.name, self.name)
-            traitInfo = g.db.execute(query).fetchone()
-            print("traitInfo is: ", pf(traitInfo))
-        else: #Temp type
-            query = """SELECT %s FROM %s WHERE Name = %s
-                                     """ % (string.join(self.dataset.display_fields,','),
-                                            self.dataset.type, self.name)
-            traitInfo = g.db.execute(query).fetchone()
-
-
-        #self.cursor.execute(query)
-        #traitInfo = self.cursor.fetchone()
-        if traitInfo:
-            self.haveinfo = True
-
-            #XZ: assign SQL query result to trait attributes.
-            for i, field in enumerate(self.dataset.display_fields):
-                setattr(self, field, traitInfo[i])
-
-            if self.dataset.type == 'Publish':
-                self.confidential = 0
-                if self.pre_publication_description and not self.pubmed_id:
-                    self.confidential = 1
-
-            self.homologeneid = None
-            if self.dataset.type == 'ProbeSet' and self.group 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:
-                    result = g.db.execute("""
-                            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.group)).fetchone()
-                    #self.cursor.execute(query)
-                    #result = self.cursor.fetchone()
-                else:
-                    result = None
-
-                if result:
-                    self.homologeneid = result[0]
-
-            if QTL:
-                if self.dataset.type == 'ProbeSet' and not self.cellid:
-                    traitQTL = g.db.execute("""
-                            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.dataset.id)).fetchone()
-                    #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.dataset.type == 'Publish':
-                    traitQTL = g.db.execute("""
-                            SELECT
-                                    PublishXRef.Locus, PublishXRef.LRS
-                            FROM
-                                    PublishXRef, PublishFreeze
-                            WHERE
-                                    PublishXRef.Id = %s AND
-                                    PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
-                                    PublishFreeze.Id =%s
-                            """, (self.name, self.dataset.id)).fetchone()
-                    #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.dataset.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.dataset.name, self.name), Class = "fs14")
-            else:
-                setDescription2 = HT.Href(url="javascript:showDatabase2('%s','%s','')" %
-                (self.dataset.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.dataset.type == 'Temp':
-            setDescription = HT.Href(text="%s" % (self.description),url="javascript:showDatabase2\
-            ('%s','%s','')" % (self.dataset.name,self.name), Class = "fs14")
-            setDescription = HT.Span(setDescription)
-
-        elif self.dataset.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.dataset.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.dataset.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.dataset.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.dataset.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.dataset.name,self.name), \
-            Class = "fs14")
-                else:
-                    setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\
-            "javascript:showDatabase2('%s','%s','')" % (self.dataset.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.dataset.type != 'Temp' and dispFromDatabase:
-            setDescription.append( ' --- FROM : ')
-            setDescription.append(self.dataset.genHTML(Class='cori'))
-        return setDescription
-
-    @property
-    def description_fmt(self):
-        '''Return a text formated description'''
-        if self.description:
-            formatted = self.description
-            if self.probe_target_description:
-                formatted += "; " + self.probe_target_description
-        else:
-            formatted = "Not available"
-        return formatted.capitalize()
-
-    @property
-    def alias_fmt(self):
-        '''Return a text formatted alias'''
-        if self.alias:
-            alias = string.replace(self.alias, ";", " ")
-            alias = string.join(string.split(alias), ", ")
-        return alias
-
-
-    @property
-    def location_fmt(self):
-        '''Return a text formatted location
-
-        While we're at it we set self.location in case we need it later (do we?)
-
-        '''
-
-        if self.chr and self.mb:
-            self.location = 'Chr %s @ %s Mb'  % (self.chr,self.mb)
-        elif self.chr:
-            self.location = 'Chr %s @ Unknown position' % (self.chr)
-        else:
-            self.location = 'Not available'
-
-        fmt = self.location
-        ##XZ: deal with direction
-        if self.strand_probe == '+':
-            fmt += (' on the plus strand ')
-        elif self.strand_probe == '-':
-            fmt += (' on the minus strand ')
-
-        return fmt
-
-
-    def get_database(self):
-        """
-        Returns the database, and the url referring to the database if it exists
-
-        We're going to to return two values here, and we don't want to have to call this twice from
-        the template. So it's not a property called from the template, but instead is called from the view
-
-        """
-        if self.cellid:
-            self.cursor.execute("""
-                            select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze
-                                    where
-                            ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
-                            ProbeSetFreeze.Id = %d""" % thisTrait.dataset.id)
-            probeDBName = self.cursor.fetchone()[0]
-            return dict(name = probeDBName,
-                        url = None)
-        else:
-            return dict(name = self.dataset.fullname,
-                        url = webqtlConfig.INFOPAGEHREF % self.dataset.name)
-
-    def calculate_correlation(self, values, method):
-        """Calculate the correlation value and p value according to the method specified"""
-
-        #ZS: This takes the list of values of the trait our selected trait is being correlated against and removes the values of the samples our trait has no value for
-        #There's probably a better way of dealing with this, but I'll have to ask Christian
-        updated_raw_values = []
-        updated_values = []
-        for i in range(len(values)):
-            if values[i] != "None":
-                updated_raw_values.append(self.raw_values[i])
-                updated_values.append(values[i])
-
-        self.raw_values = updated_raw_values
-        values = updated_values
-
-        if method == METHOD_SAMPLE_PEARSON or method == METHOD_LIT or method == METHOD_TISSUE_PEARSON:
-            corr, nOverlap = webqtlUtil.calCorrelation(self.raw_values, values, len(values))
-        else:
-            corr, nOverlap = webqtlUtil.calCorrelationRank(self.raw_values, values, len(values))
-
-        self.correlation = corr
-        self.overlap = nOverlap
-
-        if self.overlap < 3:
-            self.p_value = 1.0
-        else:
-            #ZS - This is probably the wrong way to deal with this. Correlation values of 1.0 definitely exist (the trait correlated against itself), so zero division needs to br prevented.
-            if abs(self.correlation) >= 1.0:
-                self.p_value = 0.0
-            else:
-                ZValue = 0.5*log((1.0+self.correlation)/(1.0-self.correlation))
-                ZValue = ZValue*sqrt(self.overlap-3)
-                self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue)))