Changed the way trait data is retrieved for the global search page (it now gets the LRS location repr and other variables needed to display in table during the retrieve_info function in trait.py instead of retrieve_trait_info in dataset.py)

This change increases the speed by a bit (85 seconds to 66 seconds for example)

Made the column width for location a bit wider for global search page so it doesn't spill onto a second line

3 files changed, 147 insertions, 101 deletions

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index acff38d9..ce3a7608 100755..100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -256,10 +256,10 @@ class GeneralTrait(object):
                             PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
                             PublishFreeze.Id = %s
                     """ % (self.name, self.dataset.id)
-            
-            #print("query is:", 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':
@@ -294,7 +294,6 @@ class GeneralTrait(object):
                            escape(self.dataset.name),
                            escape(self.name))
             trait_info = g.db.execute(query).fetchone()
-            #print("trait_info is: ", pf(trait_info))
         else: #Temp type
             query = """SELECT %s FROM %s WHERE Name = %s"""
             trait_info = g.db.execute(query,
@@ -305,7 +304,6 @@ class GeneralTrait(object):
 
             #XZ: assign SQL query result to trait attributes.
             for i, field in enumerate(self.dataset.display_fields):
-                #print("  mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i]))
                 holder = trait_info[i]
                 if isinstance(trait_info[i], basestring):
                     holder = unicode(trait_info[i], "utf8", "ignore")
@@ -315,12 +313,37 @@ class GeneralTrait(object):
                 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 = ""
+                
+                    #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
+                    #        privilege=self.dataset.privilege,
+                    #        userName=self.dataset.userName,
+                    #        authorized_users=self.authorized_users):
+                    #        
+                    #    description = self.pre_publication_description
+                
+                if len(description) > 0:
+                    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
 
-            #print("self.geneid is:", self.geneid)
-            #print("  type:", type(self.geneid))
-            #print("self.dataset.group.name is:", self.dataset.group.name)
             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.
@@ -330,10 +353,7 @@ class GeneralTrait(object):
                 #    geneidIsNumber = True
                 #except ValueError:
                 #    geneidIsNumber = False
-
                 #if geneidIsNumber:
-
-
                 query = """
                         SELECT
                                 HomologeneId
@@ -353,6 +373,11 @@ class GeneralTrait(object):
                     self.homologeneid = result[0]
 
             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
@@ -365,12 +390,8 @@ class GeneralTrait(object):
                                     ProbeSetXRef.ProbeSetFreezeId ={}
                             """.format(self.name, self.dataset.id)
                     trait_qtl = g.db.execute(query).fetchone()
-                    #self.cursor.execute(query)
-                    #trait_qtl = self.cursor.fetchone()
                     if trait_qtl:
-                        #print("trait_qtl:", trait_qtl)
                         self.locus, self.lrs, self.pvalue, self.mean, self.additive= trait_qtl
-                        #print("self.locus:", self.locus)
                         if self.locus:
                             query = """
                                 select Geno.Chr, Geno.Mb from Geno, Species
@@ -403,8 +424,37 @@ class GeneralTrait(object):
                             """, (self.name, self.dataset.id)).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)
+                            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 = ""
+                        else:
+                            self.locus = self.locus_chr = self.locus_mb = ""
                     else:
                         self.locus = self.lrs = self.additive = ""
+                
+                if 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))                                        
+                    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.'
 
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 179f054e..4cd3874c 100755..100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -9,90 +9,86 @@ from utility.benchmark import Bench
 
 class GSearch(object):
 
-	def __init__(self, kw):
-		self.type = kw['type']
-		self.terms = kw['terms']
-		if self.type == "gene":
-			sql = """
-				SELECT
-				Species.`Name` AS species_name,
-				InbredSet.`Name` AS inbredset_name,
-				Tissue.`Name` AS tissue_name,
-				ProbeSetFreeze.Name AS probesetfreeze_name,
-				ProbeSet.Name AS probeset_name,
-				ProbeSet.Symbol AS probeset_symbol,
-				ProbeSet.`description` AS probeset_description,
-				ProbeSet.Chr AS chr,
-				ProbeSet.Mb AS mb,
-				ProbeSetXRef.Mean AS mean,
-				ProbeSetXRef.LRS AS lrs,
-				ProbeSetXRef.`Locus` AS locus,
-				ProbeSetXRef.`pValue` AS pvalue,
-				ProbeSetXRef.`additive` AS additive
-				FROM Species, InbredSet, ProbeSetXRef, ProbeSet, ProbeFreeze, ProbeSetFreeze, Tissue
-				WHERE InbredSet.`SpeciesId`=Species.`Id`
-				AND ProbeFreeze.InbredSetId=InbredSet.`Id`
-				AND ProbeFreeze.`TissueId`=Tissue.`Id`
-				AND ProbeSetFreeze.ProbeFreezeId=ProbeFreeze.Id
-				AND ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) )
-				AND ProbeSet.Id = ProbeSetXRef.ProbeSetId
-				AND ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id
-				AND ProbeSetFreeze.public > 0
-				ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
-				LIMIT 6000
-				""" % (self.terms)
-			with Bench("Running query"):
-			    re = g.db.execute(sql).fetchall()
-			self.trait_list = []
-			with Bench("Creating trait objects"):
-				for line in re:
-					dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
-					trait_id = line[4]
-					#with Bench("Building trait object"):
-					this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
-					self.trait_list.append(this_trait)
-					species = webqtlDatabaseFunction.retrieve_species(dataset.group.name)
-					#with Bench("Getting trait info"):
-					dataset.get_trait_info([this_trait], species)
+    def __init__(self, kw):
+        self.type = kw['type']
+        self.terms = kw['terms']
+        if self.type == "gene":
+            sql = """
+                SELECT
+                Species.`Name` AS species_name,
+                InbredSet.`Name` AS inbredset_name,
+                Tissue.`Name` AS tissue_name,
+                ProbeSetFreeze.Name AS probesetfreeze_name,
+                ProbeSet.Name AS probeset_name,
+                ProbeSet.Symbol AS probeset_symbol,
+                ProbeSet.`description` AS probeset_description,
+                ProbeSet.Chr AS chr,
+                ProbeSet.Mb AS mb,
+                ProbeSetXRef.Mean AS mean,
+                ProbeSetXRef.LRS AS lrs,
+                ProbeSetXRef.`Locus` AS locus,
+                ProbeSetXRef.`pValue` AS pvalue,
+                ProbeSetXRef.`additive` AS additive
+                FROM Species, InbredSet, ProbeSetXRef, ProbeSet, ProbeFreeze, ProbeSetFreeze, Tissue
+                WHERE InbredSet.`SpeciesId`=Species.`Id`
+                AND ProbeFreeze.InbredSetId=InbredSet.`Id`
+                AND ProbeFreeze.`TissueId`=Tissue.`Id`
+                AND ProbeSetFreeze.ProbeFreezeId=ProbeFreeze.Id
+                AND ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) )
+                AND ProbeSet.Id = ProbeSetXRef.ProbeSetId
+                AND ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id
+                AND ProbeSetFreeze.public > 0
+                ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
+                LIMIT 6000
+                """ % (self.terms)
+            with Bench("Running query"):
+                re = g.db.execute(sql).fetchall()
+            self.trait_list = []
+            with Bench("Creating trait objects"):
+                for line in re:
+                    dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
+                    trait_id = line[4]
+                    #with Bench("Building trait object"):
+                    this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+                    self.trait_list.append(this_trait)
 
-		elif self.type == "phenotype":
-			sql = """
-				SELECT
-				Species.`Name`,
-				InbredSet.`Name`,
-				PublishFreeze.`Name`,
-				PublishXRef.`Id`,
-				Phenotype.`Post_publication_description`,
-				Publication.`Authors`,
-				Publication.`Year`,
-				PublishXRef.`LRS`,
-				PublishXRef.`Locus`,
-				PublishXRef.`additive`
-				FROM Species,InbredSet,PublishFreeze,PublishXRef,Phenotype,Publication
-				WHERE PublishXRef.`InbredSetId`=InbredSet.`Id`
-				AND PublishFreeze.`InbredSetId`=InbredSet.`Id`
-				AND InbredSet.`SpeciesId`=Species.`Id`
-				AND PublishXRef.`PhenotypeId`=Phenotype.`Id` 
-				AND PublishXRef.`PublicationId`=Publication.`Id`
-				AND	  (Phenotype.Post_publication_description REGEXP "[[:<:]]%s[[:>:]]" 
-					OR Phenotype.Pre_publication_description REGEXP "[[:<:]]%s[[:>:]]" 
-					OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]" 
-					OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]" 
-					OR Phenotype.Lab_code REGEXP "[[:<:]]%s[[:>:]]" 
-					OR Publication.PubMed_ID REGEXP "[[:<:]]%s[[:>:]]" 
-					OR Publication.Abstract REGEXP "[[:<:]]%s[[:>:]]" 
-					OR Publication.Title REGEXP "[[:<:]]%s[[:>:]]" 
-					OR Publication.Authors REGEXP "[[:<:]]%s[[:>:]]" 
-					OR PublishXRef.Id REGEXP "[[:<:]]%s[[:>:]]")
-				ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
-				LIMIT 6000
-				""" % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms)
-			re = g.db.execute(sql).fetchall()
-			self.trait_list = []
-			for line in re:
-				dataset = create_dataset(line[2], "Publish")
-				trait_id = line[3]
-				this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
-				self.trait_list.append(this_trait)
-				species = webqtlDatabaseFunction.retrieve_species(dataset.group.name)
-				dataset.get_trait_info([this_trait], species)
+        elif self.type == "phenotype":
+            sql = """
+                SELECT
+                Species.`Name`,
+                InbredSet.`Name`,
+                PublishFreeze.`Name`,
+                PublishXRef.`Id`,
+                Phenotype.`Post_publication_description`,
+                Publication.`Authors`,
+                Publication.`Year`,
+                PublishXRef.`LRS`,
+                PublishXRef.`Locus`,
+                PublishXRef.`additive`
+                FROM Species,InbredSet,PublishFreeze,PublishXRef,Phenotype,Publication
+                WHERE PublishXRef.`InbredSetId`=InbredSet.`Id`
+                AND PublishFreeze.`InbredSetId`=InbredSet.`Id`
+                AND InbredSet.`SpeciesId`=Species.`Id`
+                AND PublishXRef.`PhenotypeId`=Phenotype.`Id` 
+                AND PublishXRef.`PublicationId`=Publication.`Id`
+                AND	  (Phenotype.Post_publication_description REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Phenotype.Pre_publication_description REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Phenotype.Lab_code REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Publication.PubMed_ID REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Publication.Abstract REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Publication.Title REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR Publication.Authors REGEXP "[[:<:]]%s[[:>:]]" 
+                    OR PublishXRef.Id REGEXP "[[:<:]]%s[[:>:]]")
+                ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id`
+                LIMIT 6000
+                """ % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms)
+            re = g.db.execute(sql).fetchall()
+            self.trait_list = []
+            with Bench("Creating trait objects"):
+                for line in re:
+                    dataset = create_dataset(line[2], "Publish")
+                    trait_id = line[3]
+                    this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+                    self.trait_list.append(this_trait)
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 0bdc4f4e..3c9f6841 100755
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -137,7 +137,7 @@
                     { "type": "natural" },
                     { "type": "natural" },
                     { "type": "natural" },
-                    { "type": "natural" },
+                    { "type": "natural", "width": "12%"},
                     { "type": "natural" }
                 ],
                 "order": [[ 1, "asc" ]],