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

    @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

    @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.db.id)
            probeDBName = self.cursor.fetchone()[0]
            return dict(name = probeDBName,
                        url = None)
        else:
            return dict(name = self.db.fullname,
                        url = webqtlConfig.INFOPAGEHREF % self.db.name)