Merge branch 'flask' of http://github.com/zsloan/genenetwork

1 files changed, 564 insertions, 0 deletions

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
new file mode 100755
index 00000000..241bf2ab
--- /dev/null
+++ b/wqflask/base/trait.py
@@ -0,0 +1,564 @@
+from __future__ import absolute_import, division, print_function
+
+import string
+
+from htmlgen import HTMLgen2 as HT
+
+from base import webqtlConfig
+from base.webqtlCaseData import webqtlCaseData
+from base.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')           # database name
+        self.name = kw.get('name')                 # Trait ID, ProbeSet ID, Published ID, etc.
+        self.cellid = kw.get('cellid')
+        self.identification = kw.get('identification', 'un-named trait')
+        self.haveinfo = kw.get('haveinfo', False)
+        self.sequence = kw.get('sequence')         # 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
+                # self.cellid is set to None above
+            elif len(name2) == 3:
+                self.dataset, self.name, self.cellid = name2
+
+        self.dataset = create_dataset(self.dataset)
+        
+        # Todo: These two lines are necessary most of the time, but perhaps not all of the time
+        # So we could add a simple if statement to short-circuit this if necessary
+        self.retrieve_info()
+        self.retrieve_sample_data()
+
+
+    def get_name(self):
+        stringy = ""
+        if self.dataset and self.name:
+            stringy = "%s::%s" % (self.dataset, self.name)
+            if self.cellid:
+                stringy += "::" + self.cellid
+        else:
+            stringy = self.description
+        return stringy
+
+
+    def get_given_name(self):
+        """    
+         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
+         
+        """
+        stringy = self.name
+        if self.dataset and self.name:
+            desc = self.dataset.get_desc()  
+            if desc:
+                #desc = self.handle_pca(desc)
+                stringy = desc
+        return stringy
+    
+
+
+    def display_name(self):
+        stringy = ""
+        if self.dataset and self.name:
+            desc = self.dataset.get_desc()
+            #desc = self.handle_pca(desc)
+            if desc:
+                #desc = self.handle_pca(desc)
+                #stringy = desc
+                #if desc.__contains__('PCA'):
+                #    desc = desc[desc.rindex(':')+1:].strip()
+                #else:
+                #    desc = desc[:desc.index('entered')].strip()
+                #desc = self.handle_pca(desc)
+                stringy = "%s::%s" % (self.dataset, desc)
+            else:
+                stringy = "%s::%s" % (self.dataset, self.name)
+                if self.cellid:
+                    stringy += "::" + self.cellid
+        else:
+            stringy = self.description
+
+        return stringy
+
+
+    #def __str__(self):
+    #       #return "%s %s" % (self.getName(), self.group)
+    #       return self.getName()
+    #__str__ = getName
+    #__repr__ = __str__
+
+    def export_data(self, samplelist, the_type="val"):
+        """
+        export data according to samplelist
+        mostly used in calculating correlation
+        
+        """
+        result = []
+        for sample in samplelist:
+            if self.data.has_key(sample):
+                if the_type=='val':
+                    result.append(self.data[sample].val)
+                elif the_type=='var':
+                    result.append(self.data[sample].var)
+                elif the_type=='N':
+                    result.append(self.data[sample].N)
+                else:
+                    raise KeyError, `the_type`+' the_type is incorrect.'
+            else:
+                result.append(None)
+        return result
+
+    def export_informative(self, incVar=0):
+        """
+        export informative sample
+        mostly used in qtl regression
+        
+        """
+        samples = []
+        vals = []
+        the_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)
+                    the_vars.append(value.var)
+        return  samples, vals, the_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 retrieve_sample_data(self, samplelist=None):
+        if samplelist == None:
+            samplelist = []
+            
+        #assert self.dataset
+        
+        #if 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)
+        #            
+        #else:
+        results = self.dataset.retrieve_sample_data(self)
+
+        # Todo: is this necessary? If not remove
+        self.data.clear()
+
+        if results:
+            for item in results:
+                #name, value, variance, num_cases = item
+                if not samplelist or (samplelist and name in samplelist):
+                    name = item[0]
+                    self.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
+
+    #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'
+                    """ % (escape(display_fields_string),
+                           escape(self.dataset.name),
+                           escape(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'
+                    """ % (escape(display_fields_string),
+                           escape(self.dataset.name),
+                           escape(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.dataset.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:
+                    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
+                            """ % (escape(str(self.geneid)), escape(self.dataset.group.name))
+                    result = g.db.execute(query).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)))