Trimmed a large amount of code from search_results.py

Removed everything related to drawing html; finished code for getting
info for Phenotype and Genotype result tables

Did some more with CisLRS and TransLRS searches

Put something in parser about using square brackets as well as parentheses

Edited template for other table types (Geno and Pheno)

4 files changed, 126 insertions, 225 deletions

diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index ac6014e7..61bfbaba 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -7,19 +7,18 @@ from pprint import pformat as pf
 
 from dbFunction import webqtlDatabaseFunction
 
-
 class DoSearch(object):
     """Parent class containing parameters/functions used for all searches"""
-    
+
     # Used to translate search phrases into classes
     search_types = dict()
-    
+
     def __init__(self, search_term, dataset, cursor, db_conn):
         self.search_term = search_term
         self.dataset = dataset
         self.db_conn = db_conn
         self.cursor = cursor
-        
+
         #Get group information for dataset and the species id
         self.dataset.get_group()
         self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group)           
@@ -40,7 +39,7 @@ class DoSearch(object):
         """Strips out newlines/extra spaces and replaces them with just spaces"""
         step_one = " ".join(stringy.split())
         return step_one
-        
+
     @classmethod
     def get_search(cls, search_type):
         return cls.search_types[search_type]
@@ -48,9 +47,9 @@ class DoSearch(object):
 
 class ProbeSetSearch(DoSearch):
     """A search within an mRNA expression dataset"""
-    
+
     DoSearch.search_types['ProbeSet'] = "ProbeSetSearch"
-    
+
     base_query = """SELECT ProbeSet.Name as TNAME,
                 0 as thistable,
                 ProbeSetXRef.Mean as TMEAN,
@@ -63,9 +62,10 @@ class ProbeSetSearch(DoSearch):
                 FROM ProbeSetXRef, ProbeSet """
 
 
-    def compile_final_query(self, from_clause, where_clause):
+    def compile_final_query(self, from_clause = '', where_clause = ''):
         """Generates the final query string"""
         
+        from_clause = ''
         from_clause = self.normalize_spaces(from_clause)
 
         query = (self.base_query +
@@ -78,12 +78,12 @@ class ProbeSetSearch(DoSearch):
                                     self.escape(self.dataset.id)))        
 
         print("query is:", pf(query))
-        
+
         return query
 
     def run(self):
         """Generates and runs a simple search of an mRNA expression dataset"""
-        
+
         print("Running ProbeSetSearch")
         query = (self.base_query +
                 """WHERE (MATCH (ProbeSet.Name,
@@ -106,9 +106,9 @@ class ProbeSetSearch(DoSearch):
 
 class PhenotypeSearch(DoSearch):
     """A search within a phenotype dataset"""
-    
+
     DoSearch.search_types['Publish'] = "PhenotypeSearch"
-    
+
     base_query = """SELECT PublishXRef.Id,
                 PublishFreeze.createtime as thistable,
                 Publication.PubMed_ID as Publication_PubMed_ID,
@@ -125,7 +125,7 @@ class PhenotypeSearch(DoSearch):
                     'Publication.Title',
                     'Publication.Authors',
                     'PublishXRef.Id')
-    
+
     def get_where_clause(self):
         """Generate clause for WHERE portion of query"""
 
@@ -140,7 +140,7 @@ class PhenotypeSearch(DoSearch):
         for field in self.search_fields:
             where_clause.append('''%s REGEXP "%s"''' % (field, search_term))
         where_clause = "(%s)" % ' OR '.join(where_clause)
-        
+
         return where_clause
 
     def run(self):
@@ -164,7 +164,7 @@ class PhenotypeSearch(DoSearch):
 
 class GenotypeSearch(DoSearch):
     """A search within a genotype dataset"""
-    
+
     DoSearch.search_types['Geno'] = "GenotypeSearch"
 
     base_query = """SELECT Geno.Name,
@@ -185,7 +185,8 @@ class GenotypeSearch(DoSearch):
         where_clause = []
         for field in self.search_fields:
             where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % (self.dataset.type, field),
-                                                                self.search_term))
+                                                                self.escape(self.search_term)))
+        print("where_clause is:", pf(where_clause))
         where_clause = "(%s)" % ' OR '.join(where_clause)
 
         return where_clause
@@ -209,7 +210,7 @@ class GenotypeSearch(DoSearch):
 
 class RifSearch(ProbeSetSearch):
     """Searches for traits with a Gene RIF entry including the search term."""
-    
+
     DoSearch.search_types['RIF'] = "RifSearch"
 
     def run(self):
@@ -224,9 +225,9 @@ class RifSearch(ProbeSetSearch):
 
 class WikiSearch(ProbeSetSearch):
     """Searches GeneWiki for traits other people have annotated"""
-    
+
     DoSearch.search_types['WIKI'] =  "WikiSearch"
-    
+
     def run(self):
         where_clause = """%s.symbol = GeneRIF.symbol
             and GeneRIF.versionId=0 and GeneRIF.display>0
@@ -259,43 +260,44 @@ class GoSearch(ProbeSetSearch):
         from_clause = """ , db_GeneOntology.term as GOterm,
             db_GeneOntology.association as GOassociation,
             db_GeneOntology.gene_product as GOgene_product """
-            
+
         query = self.compile_final_query(from_clause, where_clause)
 
         return self.execute(query)
 
+#ZS: Not sure what the best way to deal with LRS searches is
 class LrsSearch(ProbeSetSearch):
     """Searches for genes with a QTL within the given LRS values
-    
+
     LRS searches can take 2 different forms:
     - LRS=(min_LRS max_LRS)
     - LRS=(min_LRS max_LRS chromosome start_Mb end_Mb)
     where min/max_LRS represent the range of LRS scores and start/end_Mb represent
     the range in megabases on the given chromosome
-    
+
     """
-    
+
     DoSearch.search_types['LRS'] = 'LrsSearch'
     
 class CisLrsSearch(LrsSearch):
     """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
-    
+
     A cisLRS search can take 2 forms:
     - cisLRS=(min_LRS max_LRS)
     - cisLRS=(min_LRS max_LRS mb_buffer)
     where min/max_LRS represent the range of LRS scores and the mb_buffer is the range around
     a particular QTL where its eQTL would be considered "cis". If there is no third parameter,
     mb_buffer will default to 5 megabases.
-    
+
     A QTL is a cis-eQTL if a gene's expression is regulated by a QTL in roughly the same area
     (where the area is determined by the mb_buffer that the user can choose).
-    
+
     """
-    
+
     # This is tentatively a child of LrsSearch; I'll need to check what code, if any, overlaps
     # between this and the LrsSearch code. In the original code, commands are divided by
     # the number of inputs they take, so these commands are completely separate
-    
+
     DoSearch.search_types['CISLRS'] = "CisLrsSearch"
 
     def run(self):
@@ -318,27 +320,28 @@ class CisLrsSearch(LrsSearch):
                     self.dataset.type,
                     min_threshold
                     )
-
         else:
-            NeedSomeErrorHere            
+            NeedSomeErrorHere     
 
-        return None
+        query = self.compile_final_query(where_clause)
+
+        return self.execute(query)
     
 class TransLrsSearch(LrsSearch):
     """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
-    
+
     A transLRS search can take 2 forms:
     - transLRS=(min_LRS max_LRS)
     - transLRS=(min_LRS max_LRS mb_buffer)
     where min/max_LRS represent the range of LRS scores and the mb_buffer is the range around
     a particular QTL where its eQTL would be considered "cis". If there is no third parameter,
     mb_buffer will default to 5 megabases.
-    
+
     A QTL is a trans-eQTL if a gene's expression is regulated by a QTL in a different location/area
     (where the area is determined by the mb_buffer that the user can choose). Opposite of cis-eQTL.
-    
+
     """
-    
+
     # This is tentatively a child of LrsSearch; I'll need to check what code, if any, overlaps
     # between this and the LrsSearch code. In the original code, commands are divided by
     # the number of inputs they take, so these commands are completely separate
@@ -370,8 +373,8 @@ class TransLrsSearch(LrsSearch):
             NeedSomeErrorHere            
 
         return None
-    
-    
+
+
 #itemCmd = item[0]
 #lowerLimit = float(item[1])
 #upperLimit = float(item[2])
@@ -402,15 +405,15 @@ class TransLrsSearch(LrsSearch):
 #    query.append(" (%s) " % clauseItem)
 #    self.orderByDefalut = itemCmd
 #    DescriptionText.append(HT.Span(' with ', HT.U(itemCmd), ' between %g and %g' % (min(lowerLimit, upperLimit),  max(lowerLimit, upperLimit))))    
-    
-    
+
+
 class MeanSearch(ProbeSetSearch):
     """Searches for genes expressed within an interval (log2 units) determined by the user"""
-    
+
     DoSearch.search_types['MEAN'] = "MeanSearch"
-    
+
     def run(self):
-        
+
         return None
 
 
@@ -443,8 +446,9 @@ if __name__ == "__main__":
     #results = RifSearch("diabetes", dataset, cursor, db_conn).run()
     #results = WikiSearch("nicotine", dataset, cursor, db_conn).run()
     results = CisLrsSearch(['9','99','10'], dataset, cursor, db_conn).run()
+    #results = TransLrsSearch(['9', '999', '10'], dataset, cursor, db_conn).run()
     #results = PhenotypeSearch("brain", dataset, cursor, db_conn).run()
     #results = GenotypeSearch("rs13475699", dataset, cursor, db_conn).run()
     #results = GoSearch("0045202", dataset, cursor, db_conn).run()
-    
+
     print("results are:", pf(results))
\ No newline at end of file
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index b220f837..74343b8a 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -9,9 +9,9 @@ def parse(pstring):
     pstring = re.split(r"""(?:(\w+\s*=\s*\([^)]*\))|(\w+\s*[=:]\w+)|(\w+))""", pstring)
     pstring = [item.strip() for item in pstring if item and item.strip()]
     print(pstring)
-    
+
     items = []
-    
+
     for item in pstring:
         if ":" in item:
             key, seperator, value = item.partition(':')
@@ -19,7 +19,7 @@ def parse(pstring):
             key, seperator, value = item.partition('=')
         else:
             seperator = None
-        
+
         if seperator:
             if '(' in value:
                 assert value.startswith("("), "Invalid token"
@@ -41,11 +41,11 @@ def parse(pstring):
             term = dict(key=None,
                         seperator=None,
                         search_term = item)
-            
+
         items.append(term)
     print(pf(items))
     return(items)
-    
+
 if __name__ == '__main__':
     parse("foo=(3 2 1)")
     parse("shh")
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 4aa1f2bc..dc3c72fc 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -45,7 +45,6 @@ from utility import formatting
 class SearchResultPage(templatePage):
 
     maxReturn = 3000
-    #NPerPage = 100
     nkeywords = 0
 
     def __init__(self, fd):
@@ -155,6 +154,13 @@ class SearchResultPage(templatePage):
                                 'Publication.Title',
                                 'Publication.Authors',
                                 'PublishXRef.Id']
+            self.header_fields = ['',
+                                'ID',
+                                'Description',
+                                'Authors',
+                                'Year',
+                                'Max LRS',
+                                'Max LRS Location']            
 
         elif self.dataset.type == "ProbeSet":
             self.search_fields = ['Name',
@@ -175,13 +181,19 @@ class SearchResultPage(templatePage):
                                 'Max LRS Location']
         elif self.dataset.type == "Geno":
             self.search_fields = ['Name','Chr']
+            self.header_fields = ['',
+                                'ID',
+                                'Location']
 
         self.search()
         self.gen_search_result()
 
 
     def gen_search_result(self):
-
+        """Get the info displayed in the search result table from the set of results computed in
+        the "search" function
+        
+        """
         self.trait_list = []
         # result_set represents the results for each search term; a search of 
         # "shh grin2b" would have two sets of results, one for each term
@@ -192,52 +204,27 @@ class SearchResultPage(templatePage):
 
             seq = 1
             group = self.dataset.group
-            self.form_name = form_name = 'show_dataset_'+group
 
-            tblobj = {}
             species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=group)
 
-            #### Excel file 
-
-            # Todo: Replace this with official Python temp file naming functions?
-            filename= webqtlUtil.genRandStr("Search_")
-            #xlsUrl = HT.Input(type='button', value = 'Download Table', onClick= "location.href='/tmp/%s.xls'" % filename, Class='button')
-            # Create a new Excel workbook
-            #workbook = xl.Writer('%s.xls' % (webqtlConfig.TMPDIR+filename))
-            #headingStyle = workbook.add_format(align = 'center', bold = 1, border = 1, size=13, fg_color = 0x1E, color="white")
-
-            #XZ, 3/18/2010: pay attention to the line number of header in this file. As of today, there are 7 lines.
-            #worksheet = self.createExcelFileWithTitleAndFooter(workbook=workbook, db=this_trait.db, returnNumber=len(self.trait_list))
-            newrow = 7
-
-            #### Excel file stuff stops
-
-            if self.dataset.type == "ProbeSet":
-                print("foo locals are:", locals())
-                probe_set_id = result[0]
-                this_trait = webqtlTrait(db=self.dataset, name=probe_set_id, cursor=self.cursor)
-                this_trait.retrieveInfo(QTL=True)
-                print("this_trait is:", pf(this_trait))
-                self.trait_list.append(this_trait)
-            #elif self.dataset.type == "Publish":
-            #    tblobj['body'] = self.getTableBodyForPublish(trait_list=self.trait_list, formName=mainfmName, worksheet=worksheet, species=species)
-            #elif self.dataset.type == "Geno":
-            #    tblobj['body'] = self.getTableBodyForGeno(trait_list=self.trait_list, form_name=form_name, worksheet=worksheet)
-
-            #traitForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=thisFormName, submit=HT.Input(type='hidden'))
-            hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','group':group}
-            hddn['incparentsf1']='ON'
+            #### Excel file needs to be generated ####
+
+            print("foo locals are:", locals())
+            trait_id = result[0]
+            this_trait = webqtlTrait(db=self.dataset, name=trait_id, cursor=self.cursor)
+            this_trait.retrieveInfo(QTL=True)
+            print("this_trait is:", pf(this_trait))
+            self.trait_list.append(this_trait)
 
         if self.dataset.type == "ProbeSet":
-            tblobj['body'] = self.getTableBodyForProbeSet(trait_list=self.trait_list, formName=self.form_name, species=species)            
+            self.getTraitInfoForProbeSet(trait_list=self.trait_list, species=species)            
         elif self.dataset.type == "Publish":
-            tblobj['body'] = self.getTableBodyForPublish(trait_list=self.trait_list, formName=self.form_name, species=species)
+            self.getTraitInfoForPublish(trait_list=self.trait_list, species=species)
         elif self.dataset.type == "Geno":
-            tblobj['body'] = self.getTableBodyForGeno(trait_list=self.trait_list, form_name=self.form_name)
+            self.getTraitInfoForGeno(trait_list=self.trait_list)
 
 
     def search(self):
-        print("fd.search_terms:", self.fd['search_terms'])
         self.search_terms = parser.parse(self.fd['search_terms'])
         print("After parsing:", self.search_terms)
 
@@ -267,6 +254,7 @@ class SearchResultPage(templatePage):
             print("in the search results are:", self.results)
 
 
+    #ZS: This should be handled in the parser
     def encregexp(self,str):
         if not str:
             return []
@@ -284,24 +272,12 @@ class SearchResultPage(templatePage):
         return wildcardkeyword
     
 
-    def getTableBodyForGeno(self, trait_list, formName=None):
-
-        tblobj_body = []
-
-        className = "fs12 fwn ffl b1 c222"
+    def getTraitInfoForGeno(self, trait_list):
 
         for this_trait in trait_list:
-            tr = []
-
             if not this_trait.haveinfo:
                 this_trait.retrieveInfo()
 
-            trId = str(this_trait)
-
-            tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class=className), text=trId))
-
-            tr.append(TDCell(HT.TD(HT.Href(text=this_trait.name,url="javascript:showDatabase3('%s','%s','%s','')" % (formName, this_trait.db.name, this_trait.name), Class="fs12 fwn ffl"),align="left", Class=className), text=this_trait.name, val=this_trait.name.upper()))
-
             #XZ: trait_location_value is used for sorting
             trait_location_repr = 'N/A'
             trait_location_value = 1000000
@@ -315,70 +291,37 @@ class SearchResultPage(templatePage):
                     else:
                         trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb
 
-                trait_location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) )
+                this_trait.location_repr = 'Chr%s: %.4f' % (this_trait.chr, float(this_trait.mb) )
+                this_trait.location_value = trait_location_value
 
-            tr.append(TDCell(HT.TD(trait_location_repr, Class="fs12 fwn b1 c222", nowrap="on"), trait_location_repr, trait_location_value))
 
-            tblobj_body.append(tr)
-
-            #for ncol, item in enumerate([this_trait.name, trait_location_repr]):
-            #    worksheet.write([newrow, ncol], item)
-
-        return tblobj_body
-
-
-    def getTableBodyForPublish(self, trait_list, formName=None, species=''):
-
-        tblobj_body = []
-
-        className = "fs12 fwn b1 c222"
+    def getTraitInfoForPublish(self, trait_list, species=''):
 
         for this_trait in trait_list:
-            tr = []
-
             if not this_trait.haveinfo:
                 this_trait.retrieveInfo(QTL=1)
 
-            trId = str(this_trait)
-
-            tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class=className), text=trId))
-
-            tr.append(TDCell(HT.TD(HT.Href(text=this_trait.name,url="javascript:showDatabase3('%s','%s','%s','')" % (formName, this_trait.db.name, this_trait.name), Class="fs12 fwn"), nowrap="yes",align="center", Class=className),str(this_trait.name), this_trait.name))
-
-            PhenotypeString = this_trait.post_publication_description
+            description = this_trait.post_publication_description
             if this_trait.confidential:
                 if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users):
-                    PhenotypeString = this_trait.pre_publication_description
-            tr.append(TDCell(HT.TD(PhenotypeString, Class=className), PhenotypeString, PhenotypeString.upper()))
-
-            tr.append(TDCell(HT.TD(this_trait.authors, Class="fs12 fwn b1 c222 fsI"),this_trait.authors, this_trait.authors.strip().upper()))
+                    description = this_trait.pre_publication_description
+            this_trait.description_display = description
 
             try:
-                PubMedLinkText = myear = repr = int(this_trait.year)
+                this_trait.pubmed_text =  int(this_trait.year)
             except:
-                PubMedLinkText = repr = "N/A"
-                myear = 0
+                this_trait.pubmed_text = "N/A"
 
             if this_trait.pubmed_id:
-                PubMedLink = HT.Href(text= repr,url= webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id,target='_blank', Class="fs12 fwn")
-            else:
-                PubMedLink = repr
-
-            tr.append(TDCell(HT.TD(PubMedLink, Class=className, align='center'), repr, myear))
+                this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
 
             #LRS and its location
-            LRS_score_repr = 'N/A'
-            LRS_score_value = 0
-            LRS_location_repr = 'N/A'
-            LRS_location_value = 1000000
-            LRS_flag = 1
-
+            this_trait.LRS_score_repr = 'N/A'
+            this_trait.LRS_score_value = 0
+            this_trait.LRS_location_repr = 'N/A'
+            this_trait.LRS_location_value = 1000000
 
             if this_trait.lrs:
-                LRS_score_repr = '%3.1f' % this_trait.lrs
-                LRS_score_value = this_trait.lrs
-                tr.append(TDCell(HT.TD(LRS_score_repr, Class=className), LRS_score_repr, LRS_score_value))
-
                 self.cursor.execute("""
                     select Geno.Chr, Geno.Mb from Geno, Species
                     where Species.Name = '%s' and
@@ -401,27 +344,14 @@ class SearchResultPage(templatePage):
                             else:
                                 LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb)
 
-                        LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb) )
-                        LRS_flag = 0
-
-                tr.append(TDCell(HT.TD(LRS_location_repr, Class=className, nowrap="on"), LRS_location_repr, LRS_location_value))
-
-            else:
-                tr.append(TDCell(HT.TD("N/A", Class=className), "N/A", "N/A"))
-                tr.append(TDCell(HT.TD("N/A", Class=className), "N/A", "N/A"))
-
-            tblobj_body.append(tr)
-
-            #for ncol, item in enumerate([this_trait.name, PhenotypeString, this_trait.authors, this_trait.year, this_trait.pubmed_id, LRS_score_repr, LRS_location_repr]):
-            #    worksheet.write([newrow, ncol], item)
+                        this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
+                        this_trait.LRS_score_value = LRS_score_value = this_trait.lrs
+                        this_trait.LRS_location_repr = LRS_location_repr = 'Chr %s: %.4f Mb' % (LRS_Chr, float(LRS_Mb) )
 
-        return tblobj_body
 
+    def getTraitInfoForProbeSet(self, trait_list=None, species=''):
 
-    def getTableBodyForProbeSet(self, trait_list=None, primaryTrait=None, formName=None, species=''):
         #  Note: setting trait_list to [] is probably not a great idea.
-        tblobj_body = []
-
         if not trait_list:
             trait_list = []
 
@@ -435,27 +365,6 @@ class SearchResultPage(templatePage):
             else:
                 this_trait.symbol = "N/A"
 
-            tr = []
-
-            trId = str(this_trait)
-
-            #XZ, 12/08/2008: checkbox
-            #tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class="fs12 fwn ffl b1 c222"), text=trId))
-
-            #XZ, 12/08/2008: probeset name
-            #if this_trait.cellid:
-            #    tr.append(TDCell(HT.TD(HT.Href(text=this_trait.name, url="javascript:showDatabase3('%s','%s','%s','%s')" % (formName, this_trait.db.name,this_trait.name,this_trait.cellid), Class="fs12 fwn"), Class=className), this_trait.name, this_trait.name.upper()))
-            #else:
-            #    tr.append(TDCell(HT.TD(HT.Href(text=this_trait.name, url="javascript:showDatabase3('%s','%s','%s','')" % (formName, this_trait.db.name,this_trait.name), Class="fs12 fwn"), Class=className), this_trait.name, this_trait.name.upper()))
-            #
-            #if this_trait.geneid:
-            #    symbolurl = HT.Href(text=this_trait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % this_trait.geneid, Class="font_black fs12 fwn")
-            #else:
-            #    symbolurl = HT.Href(text=this_trait.symbol,target='_blank',url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene&term=%s" % this_trait.symbol, Class="font_black fs12 fwn")
-            #
-            ##XZ, 12/08/2008: gene symbol
-            #tr.append(TDCell(HT.TD(symbolurl, Class="fs12 fwn b1 c222 fsI"),this_trait.symbol, this_trait.symbol.upper()))
-
             #XZ, 12/08/2008: description
             #XZ, 06/05/2009: Rob asked to add probe target description
             description_string = str(this_trait.description).strip()
@@ -487,8 +396,8 @@ class SearchResultPage(templatePage):
                     else:
                         trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb
 
-                trait_location_repr = 'Chr %s: %.4f Mb' % (this_trait.chr, float(this_trait.mb) )
-                this_trait.trait_location_repr = trait_location_repr
+                this_trait.location_repr = 'Chr %s: %.4f Mb' % (this_trait.chr, float(this_trait.mb) )
+                this_trait.location_value = trait_location_value
                 #this_trait.trait_location_value = trait_location_value
 
             #XZ, 01/12/08: This SQL query is much faster.
@@ -517,11 +426,10 @@ class SearchResultPage(templatePage):
             this_trait.mean = repr = "%2.3f" % mean
 
             #LRS and its location
-            LRS_score_repr = 'N/A'
-            LRS_score_value = 0
-            LRS_location_repr = 'N/A'
-            LRS_location_value = 1000000
-            LRS_flag = 1
+            this_trait.LRS_score_repr = 'N/A'
+            this_trait.LRS_score_value = 0
+            this_trait.LRS_location_repr = 'N/A'
+            this_trait.LRS_location_value = 1000000
 
             #Max LRS and its Locus location
             if this_trait.lrs and this_trait.locus:
@@ -550,28 +458,3 @@ class SearchResultPage(templatePage):
                         this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
                         this_trait.LRS_score_value = LRS_score_value = this_trait.lrs
                         this_trait.LRS_location_repr = LRS_location_repr = 'Chr %s: %.4f Mb' % (LRS_Chr, float(LRS_Mb) )
-                        LRS_flag = 0
-
-                #if LRS_flag:
-                    #tr.append(TDCell(HT.TD(LRS_score_repr, Class=className), LRS_score_repr, LRS_score_value))
-                    #tr.append(TDCell(HT.TD(LRS_location_repr, Class=className), LRS_location_repr, LRS_location_value))
-
-            #else:
-                #tr.append(TDCell(HT.TD("N/A", Class=className), "N/A", "N/A"))
-                #tr.append(TDCell(HT.TD("N/A", Class=className), "N/A", "N/A"))
-
-            tblobj_body.append(tr)
-
-        return tblobj_body
-
-
-    def getSortByValue(self, datasetType=''):
-
-        if datasetType == 'Geno':
-            sortby = ("location", "up")
-        elif datasetType == 'ProbeSet':
-            sortby = ("symbol", "up")
-        else: #Phenotype
-            sortby = ("record_id", "down")
-
-        return sortby
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 65182e1f..e393ced6 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -50,18 +50,32 @@
                         </TD>
                         <TD>
                             <a href="{{ url_for('show_trait_page',
-                                    database=this_trait.db.name,
-                                    ProbeSetID=this_trait.name, incparentsf1='ON',
-                                    RISet='BXD')}}">
-                                {{ this_trait.name.upper() }}
+                                    dataset = dataset.name,
+                                    trait_id = this_trait.name,
+                                    group = dataset.group)}}">
+                                {{ this_trait.name }}
                             </a>
                         </TD>
-                        <TD>{{ this_trait.symbol }}</TD>
-                        <TD>{{ this_trait.description_display }}</TD>
-                        <TD>{{ this_trait.trait_location_repr }}</TD>
-                        <TD>{{ this_trait.mean }}</TD>
-                        <TD>{{ this_trait.LRS_score_repr }}</TD>
-                        <TD>{{ this_trait.LRS_location_repr }}</TD>
+                        {% if dataset.type == 'ProbeSet' %}
+                            <TD>{{ this_trait.symbol }}</TD>
+                            <TD>{{ this_trait.description_display }}</TD>
+                            <TD>{{ this_trait.location_repr }}</TD>
+                            <TD>{{ this_trait.mean }}</TD>
+                            <TD>{{ this_trait.LRS_score_repr }}</TD>
+                            <TD>{{ this_trait.LRS_location_repr }}</TD>
+                        {% elif dataset.type == 'Publish' %}
+                            <TD>{{ this_trait.description_display }}</TD>
+                            <TD>{{ this_trait.authors }}</TD>
+                            <TD>
+                                <a href="{{ this_trait.pubmed_link }}">
+                                    {{ this_trait.pubmed_text }}
+                                </a>
+                            </TD>
+                            <TD>{{ this_trait.LRS_score_repr }}</TD>
+                            <TD>{{ this_trait.LRS_location_repr }}</TD>
+                        {% elif dataset.type == 'Geno' %}
+                            <TD>{{ this_trait.location_repr }}</TD>
+                        {% endif %}
                     </TR>
                 {% endfor %}
                 </tbody>