Moved a bunch of functions out of the GeneralTrait class that didn't need to be there and changed the code that calls them accordingly

Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static)

Removed some unused code from show_trait.py

changed appearance of table headers some, though needs a little more work

Updated dataset_menu_structure.json

1 files changed, 443 insertions, 577 deletions

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 295502b3..ab0e6b82 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -57,6 +57,7 @@ class GeneralTrait(object):
         self.lrs = None
         self.pvalue = None
         self.mean = None
+        self.additive = None
         self.num_overlap = None
         self.strand_probe = None
         self.symbol = None
@@ -71,114 +72,11 @@ class GeneralTrait(object):
 
         # 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(get_qtl_info=get_qtl_info)
+        self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
         if get_sample_info != False:
-            self.retrieve_sample_data()
+            self = retrieve_sample_data(self, self.dataset)
 
 
-    def jsonable(self):
-        """Return a dict suitable for using as json
-
-        Actual turning into json doesn't happen here though"""
-
-        if self.dataset.type == "ProbeSet":
-            return dict(name=self.name,
-                        symbol=self.symbol,
-                        dataset=self.dataset.name,
-                        description=self.description_display,
-                        mean=self.mean,
-                        location=self.location_repr,
-                        lrs_score=self.LRS_score_repr,
-                        lrs_location=self.LRS_location_repr,
-                        additive=self.additive
-                        )
-        elif self.dataset.type == "Publish":
-            if self.pubmed_id:
-                return dict(name=self.name,
-                            dataset=self.dataset.name,
-                            description=self.description_display,
-                            authors=self.authors,
-                            pubmed_text=self.pubmed_text,
-                            pubmed_link=self.pubmed_link,
-                            lrs_score=self.LRS_score_repr,
-                            lrs_location=self.LRS_location_repr,
-                            additive=self.additive
-                            )
-            else:
-                return dict(name=self.name,
-                            dataset=self.dataset.name,
-                            description=self.description_display,
-                            authors=self.authors,
-                            pubmed_text=self.pubmed_text,
-                            lrs_score=self.LRS_score_repr,
-                            lrs_location=self.LRS_location_repr,
-                            additive=self.additive
-                            )
-        elif self.dataset.type == "Geno":
-            return dict(name=self.name,
-                        dataset=self.dataset.name,
-                        location=self.location_repr
-                        )
-        else:
-            return dict()
-
-    def jsonable_table_row(self, index):
-        """Return a list suitable for json and intended to be displayed in a table
-
-        Actual turning into json doesn't happen here though"""
-
-        if self.dataset.type == "ProbeSet":
-            if self.mean == "":
-                mean = "N/A"
-            else:
-                mean = "%.3f" % round(float(self.mean), 2)
-            if self.additive == "":
-                additive = "N/A"
-            else:
-                additive = "%.3f" % round(float(self.additive), 2)
-            return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(self.name), self.dataset.name)) + '">',
-                    index,
-                    '<a href="/show_trait?trait_id='+str(self.name)+'&dataset='+self.dataset.name+'">'+str(self.name)+'</a>',
-                    self.symbol,
-                    self.description_display,
-                    self.location_repr,
-                    mean, 
-                    self.LRS_score_repr,
-                    self.LRS_location_repr,
-                    additive]
-        elif self.dataset.type == "Publish":
-            if self.additive == "":
-                additive = "N/A"
-            else:
-                additive = "%.2f" % round(float(self.additive), 2)
-            if self.pubmed_id:
-                return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(self.name), self.dataset.name)) + '">',
-                        index,
-                        '<a href="/show_trait?trait_id='+str(self.name)+'&dataset='+self.dataset.name+'">'+str(self.name)+'</a>',
-                        self.description_display,
-                        self.authors,
-                        '<a href="' + self.pubmed_link + '">' + self.pubmed_text + '</href>',
-                        self.LRS_score_repr,
-                        self.LRS_location_repr,
-                        additive]
-            else:
-                return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(self.name), self.dataset.name)) + '">',
-                        index,
-                        '<a href="/show_trait?trait_id='+str(self.name)+'&dataset='+self.dataset.name+'">'+str(self.name)+'</a>',
-                        self.description_display,
-                        self.authors,
-                        self.pubmed_text,
-                        self.LRS_score_repr,
-                        self.LRS_location_repr,
-                        additive]
-        elif self.dataset.type == "Geno":
-            return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(self.name), self.dataset.name)) + '">',
-                    index,
-                    '<a href="/show_trait?trait_id='+str(self.name)+'&dataset='+self.dataset.name+'">'+str(self.name)+'</a>',
-                    self.location_repr]
-        else:
-            return dict()
-
     def get_name(self):
         stringy = ""
         if self.dataset and self.name:
@@ -282,422 +180,6 @@ class GeneralTrait(object):
         return  samples, vals, the_vars, sample_aliases
 
 
-    #
-    # 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 = []
-
-        results = self.dataset.retrieve_sample_data(self.name)
-
-        # Todo: is this necessary? If not remove
-        self.data.clear()
-
-        all_samples_ordered = self.dataset.group.all_samples_ordered()
-
-        if results:
-            for item in results:
-                name, value, variance, num_cases, name2 = item
-                if not samplelist or (samplelist and name in samplelist):
-                    self.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
-
-    def retrieve_info(self, get_qtl_info=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)
-
-            logger.sql(query)
-            trait_info = 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(str(self.name)))
-            logger.sql(query)
-            trait_info = g.db.execute(query).fetchone()
-        #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))
-            logger.sql(query)
-            trait_info = g.db.execute(query).fetchone()
-        else: #Temp type
-            query = """SELECT %s FROM %s WHERE Name = %s"""
-            logger.sql(query)
-            trait_info = g.db.execute(query,
-                                      (string.join(self.dataset.display_fields,','),
-                                                   self.dataset.type, self.name)).fetchone()
-        if trait_info:
-            self.haveinfo = True
-
-            #XZ: assign SQL query result to trait attributes.
-            for i, field in enumerate(self.dataset.display_fields):
-                holder = trait_info[i]
-                if isinstance(trait_info[i], basestring):
-                    holder = unicode(trait_info[i], "utf8", "ignore")
-                setattr(self, field, holder)
-
-            if self.dataset.type == 'Publish':
-                self.confidential = 0
-                if self.pre_publication_description and not self.pubmed_id:
-                    self.confidential = 1
-
-                description = self.post_publication_description
-
-                #If the dataset is confidential and the user has access to confidential
-                #phenotype traits, then display the pre-publication description instead
-                #of the post-publication description
-                if self.confidential:
-                    self.description_display = self.pre_publication_description
-
-                    #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
-                    #        privilege=self.dataset.privilege,
-                    #        userName=self.dataset.userName,
-                    #        authorized_users=self.authorized_users):
-                    #
-                    #    description = self.pre_publication_description
-                else:
-                    if description:
-                        self.description_display = description.strip()
-                    else:
-                        self.description_display = ""
-
-                if not self.year.isdigit():
-                    self.pubmed_text = "N/A"
-                else:
-                    self.pubmed_text = self.year
-
-                if self.pubmed_id:
-                    self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id
-
-
-            self.homologeneid = None
-            if self.dataset.type == 'ProbeSet' and self.dataset.group:
-                if 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:
-                    #    float(self.geneid)
-                    #    geneidIsNumber = True
-                    #except ValueError:
-                    #    geneidIsNumber = False
-                    #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))
-                    logger.sql(query)
-                    result = g.db.execute(query).fetchone()
-                    #else:
-                    #    result = None
-
-                    if result:
-                        self.homologeneid = result[0]
-
-                description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8')
-                target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
-
-                if len(description_string) > 1 and description_string != 'None':
-                    description_display = description_string
-                else:
-                    description_display = self.symbol
-
-                if (len(description_display) > 1 and description_display != 'N/A' and
-                        len(target_string) > 1 and target_string != 'None'):
-                    description_display = description_display + '; ' + target_string.strip()
-
-                # Save it for the jinja2 template
-                self.description_display = description_display
-
-                #XZ: trait_location_value is used for sorting
-                self.location_repr = 'N/A'
-                self.location_value = 1000000
-
-                if self.chr and self.mb:
-                    #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
-                    #This is so we can convert the location to a number used for sorting
-                    trait_location_value = convert_location_to_value(self.chr, self.mb)
-                     #try:
-                    #    trait_location_value = int(self.chr)*1000 + self.mb
-                    #except ValueError:
-                    #    if self.chr.upper() == 'X':
-                    #        trait_location_value = 20*1000 + self.mb
-                    #    else:
-                    #        trait_location_value = (ord(str(self.chr).upper()[0])*1000 +
-                    #                               self.mb)
-
-                    #ZS: Put this in function currently called "convert_location_to_value"
-                    self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb))
-                    self.location_value = trait_location_value
-
-            elif self.dataset.type == "Geno":
-                self.location_repr = 'N/A'
-                self.location_value = 1000000
-
-                if self.chr and self.mb:
-                    #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
-                    #This is so we can convert the location to a number used for sorting
-                    trait_location_value = convert_location_to_value(self.chr, self.mb)
-
-                    #ZS: Put this in function currently called "convert_location_to_value"
-                    self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb))
-                    self.location_value = trait_location_value
-
-            if get_qtl_info:
-                #LRS and its location
-                self.LRS_score_repr = "N/A"
-                self.LRS_score_value = 0
-                self.LRS_location_repr = "N/A"
-                self.LRS_location_value = 1000000
-                if self.dataset.type == 'ProbeSet' and not self.cellid:
-                    query = """
-                            SELECT
-                                    ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive
-                            FROM
-                                    ProbeSetXRef, ProbeSet
-                            WHERE
-                                    ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-                                    ProbeSet.Name = "{}" AND
-                                    ProbeSetXRef.ProbeSetFreezeId ={}
-                            """.format(self.name, self.dataset.id)
-                    logger.sql(query)
-                    trait_qtl = g.db.execute(query).fetchone()
-                    if trait_qtl:
-                        self.locus, self.lrs, self.pvalue, self.mean, self.additive = trait_qtl
-                        if self.locus:
-                            query = """
-                                select Geno.Chr, Geno.Mb from Geno, Species
-                                where Species.Name = '{}' and
-                                Geno.Name = '{}' and
-                                Geno.SpeciesId = Species.Id
-                                """.format(self.dataset.group.species, self.locus)
-                            logger.sql(query)
-                            result = g.db.execute(query).fetchone()
-                            if result:
-                                self.locus_chr = result[0]
-                                self.locus_mb = result[1]
-                            else:
-                                self.locus = self.locus_chr = self.locus_mb = self.additive = ""
-                        else:
-                            self.locus = self.locus_chr = self.locus_mb = self.additive = ""
-                    else:
-                        self.locus = self.locus_chr = self.locus_mb = self.lrs = self.pvalue = self.mean = self.additive = ""
-
-
-                if self.dataset.type == 'Publish':
-                    query = """
-                            SELECT
-                                    PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive
-                            FROM
-                                    PublishXRef, PublishFreeze
-                            WHERE
-                                    PublishXRef.Id = %s AND
-                                    PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
-                                    PublishFreeze.Id =%s
-                    """ % (self.name, self.dataset.id)
-                    logger.sql(query)
-                    trait_qtl = g.db.execute(query).fetchone()
-                    if trait_qtl:
-                        self.locus, self.lrs, self.additive = trait_qtl
-                        if self.locus:
-                            query = """
-                                select Geno.Chr, Geno.Mb from Geno, Species
-                                where Species.Name = '{}' and
-                                Geno.Name = '{}' and
-                                Geno.SpeciesId = Species.Id
-                                """.format(self.dataset.group.species, self.locus)
-                            logger.sql(query)
-                            result = g.db.execute(query).fetchone()
-                            if result:
-                                self.locus_chr = result[0]
-                                self.locus_mb = result[1]
-                            else:
-                                self.locus = self.locus_chr = self.locus_mb = self.additive = ""
-                        else:
-                            self.locus = self.locus_chr = self.locus_mb = self.additive = ""
-                    else:
-                        self.locus = self.lrs = self.additive = ""
-
-                if (self.dataset.type == 'Publish' or self.dataset.type == "ProbeSet") and self.locus_chr != "" and self.locus_mb != "":
-                    #XZ: LRS_location_value is used for sorting
-                    try:
-                        LRS_location_value = int(self.locus_chr)*1000 + float(self.locus_mb)
-                    except:
-                        if self.locus_chr.upper() == 'X':
-                            LRS_location_value = 20*1000 + float(self.locus_mb)
-                        else:
-                            LRS_location_value = ord(str(self.locus_chr).upper()[0])*1000 + float(self.locus_mb)
-
-                    self.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (self.locus_chr, float(self.locus_mb))
-                    if self.lrs != "":
-                        self.LRS_score_repr = LRS_score_repr = '%3.1f' % self.lrs
-                        self.LRS_score_value = LRS_score_value = 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 name_header_fmt(self):
         '''Return a human-readable name for use in page header'''
@@ -763,62 +245,51 @@ class GeneralTrait(object):
 
         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:
-            query = """ select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze where
-                            ProbeFreeze.Id =
-                            ProbeSetFreeze.ProbeFreezeId AND
-                            ProbeSetFreeze.Id = %d""" % thisTrait.dataset.id
-            logger.sql(query)
-            probeDBName = g.db.execute(query).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)))
-
+# 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(trait, dataset_name):
+    dataset = create_dataset(dataset_name)
+     
+    if dataset.type == 'ProbeSet':
+        results = g.db.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
+               ''', trait.name, dataset.name).fetchone()
+
+        return results[0]        
+        
+def retrieve_sample_data(trait, dataset_name, samplelist=None):
+
+    dataset = create_dataset(dataset_name)
+
+    if samplelist == None:
+        samplelist = []
+
+    results = dataset.retrieve_sample_data(trait.name)
+
+    # Todo: is this necessary? If not remove
+    trait.data.clear()
+
+    all_samples_ordered = dataset.group.all_samples_ordered()
+
+    if results:
+        for item in results:
+            name, value, variance, num_cases, name2 = item
+            if not samplelist or (samplelist and name in samplelist):
+                trait.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
+                
+    return trait
+        
 def convert_location_to_value(chromosome, mb):
     try:
         location_value = int(chromosome)*1000 + float(mb)
@@ -846,3 +317,398 @@ def get_sample_data():
     #    jsonable_sample_data[sample] = trait_ob.data[sample].value
     #
     #return jsonable_sample_data
+    
+def jsonable(trait, dataset_name):
+    """Return a dict suitable for using as json
+
+    Actual turning into json doesn't happen here though"""
+
+    dataset = create_dataset(dataset_name)
+    
+    if dataset.type == "ProbeSet":
+        return dict(name=trait.name,
+                    symbol=trait.symbol,
+                    dataset=dataset.name,
+                    description=trait.description_display,
+                    mean=trait.mean,
+                    location=trait.location_repr,
+                    lrs_score=trait.LRS_score_repr,
+                    lrs_location=trait.LRS_location_repr,
+                    additive=trait.additive
+                    )
+    elif dataset.type == "Publish":
+        if trait.pubmed_id:
+            return dict(name=trait.name,
+                        dataset=dataset.name,
+                        description=trait.description_display,
+                        authors=trait.authors,
+                        pubmed_text=trait.pubmed_text,
+                        pubmed_link=trait.pubmed_link,
+                        lrs_score=trait.LRS_score_repr,
+                        lrs_location=trait.LRS_location_repr,
+                        additive=trait.additive
+                        )
+        else:
+            return dict(name=trait.name,
+                        dataset=dataset.name,
+                        description=trait.description_display,
+                        authors=trait.authors,
+                        pubmed_text=trait.pubmed_text,
+                        lrs_score=trait.LRS_score_repr,
+                        lrs_location=trait.LRS_location_repr,
+                        additive=trait.additive
+                        )
+    elif dataset.type == "Geno":
+        return dict(name=trait.name,
+                    dataset=dataset.name,
+                    location=trait.location_repr
+                    )
+    else:
+        return dict()
+
+def jsonable_table_row(trait, dataset_name, index):
+    """Return a list suitable for json and intended to be displayed in a table
+
+    Actual turning into json doesn't happen here though"""
+
+    dataset = create_dataset(dataset_name)
+    
+    if dataset.type == "ProbeSet":
+        if trait.mean == "":
+            mean = "N/A"
+        else:
+            mean = "%.3f" % round(float(trait.mean), 2)
+        if trait.additive == "":
+            additive = "N/A"
+        else:
+            additive = "%.3f" % round(float(trait.additive), 2)
+        return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+                index,
+                '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+                trait.symbol,
+                trait.description_display,
+                trait.location_repr,
+                mean, 
+                trait.LRS_score_repr,
+                trait.LRS_location_repr,
+                additive]
+    elif dataset.type == "Publish":
+        if trait.additive == "":
+            additive = "N/A"
+        else:
+            additive = "%.2f" % round(float(trait.additive), 2)
+        if trait.pubmed_id:
+            return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+                    index,
+                    '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+                    trait.description_display,
+                    trait.authors,
+                    '<a href="' + trait.pubmed_link + '">' + trait.pubmed_text + '</href>',
+                    trait.LRS_score_repr,
+                    trait.LRS_location_repr,
+                    additive]
+        else:
+            return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+                    index,
+                    '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+                    trait.description_display,
+                    trait.authors,
+                    trait.pubmed_text,
+                    trait.LRS_score_repr,
+                    trait.LRS_location_repr,
+                    additive]
+    elif dataset.type == "Geno":
+        return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+                index,
+                '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+                trait.location_repr]
+    else:
+        return dict()
+
+def retrieve_trait_info(trait, dataset, get_qtl_info=False):
+    assert dataset, "Dataset doesn't exist"
+    
+    if 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
+                """ % (trait.name, dataset.id)
+
+        logger.sql(query)
+        trait_info = 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 dataset.type == 'ProbeSet':
+        display_fields_string = ', ProbeSet.'.join(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(dataset.name),
+                       escape(str(trait.name)))
+        logger.sql(query)
+        trait_info = g.db.execute(query).fetchone()
+    #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 dataset.type == 'Geno':
+        display_fields_string = string.join(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(dataset.name),
+                       escape(trait.name))
+        logger.sql(query)
+        trait_info = g.db.execute(query).fetchone()
+    else: #Temp type
+        query = """SELECT %s FROM %s WHERE Name = %s"""
+        logger.sql(query)
+        trait_info = g.db.execute(query,
+                                  (string.join(dataset.display_fields,','),
+                                               dataset.type, trait.name)).fetchone()
+    if trait_info:
+        trait.haveinfo = True
+
+        #XZ: assign SQL query result to trait attributes.
+        for i, field in enumerate(dataset.display_fields):
+            holder = trait_info[i]
+            if isinstance(trait_info[i], basestring):
+                holder = unicode(trait_info[i], "utf8", "ignore")
+            setattr(trait, field, holder)
+
+        if dataset.type == 'Publish':
+            trait.confidential = 0
+            if trait.pre_publication_description and not trait.pubmed_id:
+                trait.confidential = 1
+
+            description = trait.post_publication_description
+
+            #If the dataset is confidential and the user has access to confidential
+            #phenotype traits, then display the pre-publication description instead
+            #of the post-publication description
+            if trait.confidential:
+                trait.description_display = trait.pre_publication_description
+
+                #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
+                #        privilege=self.dataset.privilege,
+                #        userName=self.dataset.userName,
+                #        authorized_users=self.authorized_users):
+                #
+                #    description = self.pre_publication_description
+            else:
+                if description:
+                    trait.description_display = description.strip()
+                else:
+                    trait.description_display = ""
+
+            if not trait.year.isdigit():
+                trait.pubmed_text = "N/A"
+            else:
+                trait.pubmed_text = trait.year
+
+            if trait.pubmed_id:
+                trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id
+
+
+        trait.homologeneid = None
+        if dataset.type == 'ProbeSet' and dataset.group:
+            if trait.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:
+                #    float(self.geneid)
+                #    geneidIsNumber = True
+                #except ValueError:
+                #    geneidIsNumber = False
+                #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(trait.geneid)), escape(dataset.group.name))
+                logger.sql(query)
+                result = g.db.execute(query).fetchone()
+                #else:
+                #    result = None
+
+                if result:
+                    trait.homologeneid = result[0]
+
+            description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
+            target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
+
+            if len(description_string) > 1 and description_string != 'None':
+                description_display = description_string
+            else:
+                description_display = trait.symbol
+
+            if (len(description_display) > 1 and description_display != 'N/A' and
+                    len(target_string) > 1 and target_string != 'None'):
+                description_display = description_display + '; ' + target_string.strip()
+
+            # Save it for the jinja2 template
+            trait.description_display = description_display
+
+            #XZ: trait_location_value is used for sorting
+            trait.location_repr = 'N/A'
+            trait.location_value = 1000000
+
+            if trait.chr and trait.mb:
+                #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
+                #This is so we can convert the location to a number used for sorting
+                trait_location_value = convert_location_to_value(trait.chr, trait.mb)
+                 #try:
+                #    trait_location_value = int(self.chr)*1000 + self.mb
+                #except ValueError:
+                #    if self.chr.upper() == 'X':
+                #        trait_location_value = 20*1000 + self.mb
+                #    else:
+                #        trait_location_value = (ord(str(self.chr).upper()[0])*1000 +
+                #                               self.mb)
+
+                #ZS: Put this in function currently called "convert_location_to_value"
+                trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
+                trait.location_value = trait_location_value
+
+        elif dataset.type == "Geno":
+            trait.location_repr = 'N/A'
+            trait.location_value = 1000000
+
+            if trait.chr and trait.mb:
+                #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
+                #This is so we can convert the location to a number used for sorting
+                trait_location_value = convert_location_to_value(trait.chr, trait.mb)
+
+                #ZS: Put this in function currently called "convert_location_to_value"
+                trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
+                trait.location_value = trait_location_value
+
+        if get_qtl_info:
+            #LRS and its location
+            trait.LRS_score_repr = "N/A"
+            trait.LRS_score_value = 0
+            trait.LRS_location_repr = "N/A"
+            trait.LRS_location_value = 1000000
+            if dataset.type == 'ProbeSet' and not trait.cellid:
+                query = """
+                        SELECT
+                                ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive
+                        FROM
+                                ProbeSetXRef, ProbeSet
+                        WHERE
+                                ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+                                ProbeSet.Name = "{}" AND
+                                ProbeSetXRef.ProbeSetFreezeId ={}
+                        """.format(trait.name, dataset.id)
+                logger.sql(query)
+                trait_qtl = g.db.execute(query).fetchone()
+                if trait_qtl:
+                    trait.locus, trait.lrs, trait.pvalue, trait.mean, trait.additive = trait_qtl
+                    if trait.locus:
+                        query = """
+                            select Geno.Chr, Geno.Mb from Geno, Species
+                            where Species.Name = '{}' and
+                            Geno.Name = '{}' and
+                            Geno.SpeciesId = Species.Id
+                            """.format(dataset.group.species, trait.locus)
+                        logger.sql(query)
+                        result = g.db.execute(query).fetchone()
+                        if result:
+                            trait.locus_chr = result[0]
+                            trait.locus_mb = result[1]
+                        else:
+                            trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
+                    else:
+                        trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
+                else:
+                    trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.mean = trait.additive = ""
+
+
+            if dataset.type == 'Publish':
+                query = """
+                        SELECT
+                                PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive
+                        FROM
+                                PublishXRef, PublishFreeze
+                        WHERE
+                                PublishXRef.Id = %s AND
+                                PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+                                PublishFreeze.Id =%s
+                """ % (trait.name, dataset.id)
+                logger.sql(query)
+                trait_qtl = g.db.execute(query).fetchone()
+                if trait_qtl:
+                    trait.locus, trait.lrs, trait.additive = trait_qtl
+                    if trait.locus:
+                        query = """
+                            select Geno.Chr, Geno.Mb from Geno, Species
+                            where Species.Name = '{}' and
+                            Geno.Name = '{}' and
+                            Geno.SpeciesId = Species.Id
+                            """.format(dataset.group.species, trait.locus)
+                        logger.sql(query)
+                        result = g.db.execute(query).fetchone()
+                        if result:
+                            trait.locus_chr = result[0]
+                            trait.locus_mb = result[1]
+                        else:
+                            trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
+                    else:
+                        trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
+                else:
+                    trait.locus = trait.lrs = trait.additive = ""
+
+            if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "":
+                #XZ: LRS_location_value is used for sorting
+                try:
+                    LRS_location_value = int(trait.locus_chr)*1000 + float(trait.locus_mb)
+                except:
+                    if trait.locus_chr.upper() == 'X':
+                        LRS_location_value = 20*1000 + float(trait.locus_mb)
+                    else:
+                        LRS_location_value = ord(str(trait.locus_chr).upper()[0])*1000 + float(trait.locus_mb)
+
+                trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb))
+                if trait.lrs != "":
+                    trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
+                    trait.LRS_score_value = LRS_score_value = trait.lrs
+    else:
+        raise KeyError, `trait.name`+' information is not found in the database.'
+        
+    return trait
\ No newline at end of file