Changed a number of variables (riset to group, db to dataset)

Put most of the code for cisLRS and transLRS searches into the class
CisTransLrsSearch (might change this name to something else later)

Simplified escape code for searches in do_search.py

Got search_results working again after some changes

1 files changed, 74 insertions, 72 deletions

diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
index 29087721..cc0e2321 100755
--- a/wqflask/base/webqtlTrait.py
+++ b/wqflask/base/webqtlTrait.py
@@ -24,11 +24,11 @@ class webqtlTrait:
         print("in webqtlTrait")
         self.db_conn = db_conn
         self.cursor = self.db_conn.cursor()
-        self.db = None                  # database object
+        self.dataset = None                  # database object
         self.name = ''                  # Trait ID, ProbeSet ID, Published ID, etc.
         self.cellid = ''
         self.identification = 'un-named trait'
-        self.riset = ''
+        self.group = ''
         self.haveinfo = 0
         self.sequence = ''              # Blat sequence, available for ProbeSet
         self.data = {}
@@ -41,22 +41,22 @@ class webqtlTrait:
             elif name == 'fullname':
                 name2 = value.split("::")
                 if len(name2) == 2:
-                    self.db, self.name = name2
+                    self.dataset, self.name = name2
                 elif len(name2) == 3:
-                    self.db, self.name, self.cellid = name2
+                    self.dataset, self.name, self.cellid = name2
                 else:
                     raise KeyError, repr(value) + ' parameter format error.'
             else:
                 raise KeyError, repr(name) + ' not a valid parameter for this class.'
 
-        if self.db and isinstance(self.db, basestring):
+        if self.dataset and isinstance(self.dataset, basestring):
             assert self.cursor, "Don't have a cursor"
-            self.db = create_dataset(self.db_conn, self.db)
+            self.dataset = create_dataset(self.db_conn, self.dataset)
 
-        #if self.db == None, not from a database
-        print("self.db is:", self.db, type(self.db))
-        if self.db:
-            if self.db.type == "Temp":
+        #if self.dataset == None, not from a database
+        print("self.dataset is:", self.dataset, type(self.dataset))
+        if self.dataset:
+            if self.dataset.type == "Temp":
                 self.cursor.execute('''
                         SELECT
                                 InbredSet.Name
@@ -66,9 +66,11 @@ class webqtlTrait:
                                 Temp.InbredSetId = InbredSet.Id AND
                                 Temp.Name = "%s"
                 ''', self.name)
-                self.riset = self.cursor.fetchone()[0]
+                self.group = self.cursor.fetchone()[0]
             else:
-                self.riset = self.db.get_group()
+                self.group = self.dataset.get_group()
+
+            print("trinity, self.group is:", self.group)
 
         #
         # In ProbeSet, there are maybe several annotations match one sequence
@@ -82,8 +84,8 @@ class webqtlTrait:
         # The variable self.sequence should be changed to self.BlatSeq
         # It also should be changed in other places where it are used.
 
-        if self.db:
-            if self.db.type == 'ProbeSet':
+        if self.dataset:
+            if self.dataset.type == 'ProbeSet':
                 print("Doing ProbeSet Query")
                 query = '''
                         SELECT
@@ -95,7 +97,7 @@ class webqtlTrait:
                                 ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and
                                 ProbeSet.Name = %s and
                                 ProbeSetFreeze.Name = %s
-                ''', (self.name, self.db.name)
+                ''', (self.name, self.dataset.name)
                 print("query is:", query)
                 self.cursor.execute(*query)
                 self.sequence = self.cursor.fetchone()[0]
@@ -104,8 +106,8 @@ class webqtlTrait:
 
     def getName(self):
         str = ""
-        if self.db and self.name:
-            str = "%s::%s" % (self.db, self.name)
+        if self.dataset and self.name:
+            str = "%s::%s" % (self.dataset, self.name)
             if self.cellid:
                 str += "::" + self.cellid
         else:
@@ -124,8 +126,8 @@ class webqtlTrait:
     #
     def getGivenName(self):
         str = self.name
-        if self.db and self.name:
-            if self.db.type=='Temp':
+        if self.dataset and self.name:
+            if self.dataset.type=='Temp':
                 self.cursor.execute('SELECT description FROM Temp WHERE Name=%s', self.name)
                 desc = self.cursor.fetchone()[0]
                 if desc.__contains__('PCA'):
@@ -137,16 +139,16 @@ class webqtlTrait:
 
     def displayName(self):
         str = ""
-        if self.db and self.name:
-            if self.db.type=='Temp':
+        if self.dataset and self.name:
+            if self.dataset.type=='Temp':
                 desc = self.description
                 if desc.__contains__('PCA'):
                     desc = desc[desc.rindex(':')+1:].strip()
                 else:
                     desc = desc[:desc.index('entered')].strip()
-                str = "%s::%s" % (self.db, desc)
+                str = "%s::%s" % (self.dataset, desc)
             else:
-                str = "%s::%s" % (self.db, self.name)
+                str = "%s::%s" % (self.dataset, self.name)
                 if self.cellid:
                     str += "::" + self.cellid
         else:
@@ -156,7 +158,7 @@ class webqtlTrait:
 
 
     #def __str__(self):
-    #       #return "%s %s" % (self.getName(), self.riset)
+    #       #return "%s %s" % (self.getName(), self.group)
     #       return self.getName()
     #__str__ = getName
     #__repr__ = __str__
@@ -207,7 +209,7 @@ class webqtlTrait:
     #
     def getSequence(self):
         assert self.cursor
-        if self.db.type == 'ProbeSet':
+        if self.dataset.type == 'ProbeSet':
             self.cursor.execute('''
                             SELECT
                                     ProbeSet.BlatSeq
@@ -218,7 +220,7 @@ class webqtlTrait:
                                     ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and
                                     ProbeSet.Name = %s
                                     ProbeSetFreeze.Name = %s
-                    ''', self.name, self.db.name)
+                    ''', self.name, self.dataset.name)
             #self.cursor.execute(query)
             results = self.fetchone()
 
@@ -230,9 +232,9 @@ class webqtlTrait:
 
         if samplelist == None:
             samplelist = []
-        assert self.db and self.cursor
+        assert self.dataset and self.cursor
 
-        if self.db.type == 'Temp':
+        if self.dataset.type == 'Temp':
             query = '''
                     SELECT
                             Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id
@@ -246,7 +248,7 @@ class webqtlTrait:
                             Strain.Name
                     ''' % self.name
         #XZ, 03/02/2009: Xiaodong changed Data to PublishData, SE to PublishSE
-        elif self.db.type == 'Publish':
+        elif self.dataset.type == 'Publish':
             query = '''
                     SELECT
                             Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id
@@ -263,7 +265,7 @@ class webqtlTrait:
                             PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id
                     Order BY
                             Strain.Name
-                    ''' % (self.name, self.db.id)
+                    ''' % (self.name, self.dataset.id)
 
         #XZ, 03/02/2009: Xiaodong changed Data to ProbeData, SE to ProbeSE
         elif self.cellid:
@@ -287,9 +289,9 @@ class webqtlTrait:
                             ProbeData.StrainId = Strain.Id
                     Order BY
                             Strain.Name
-                    ''' % (self.cellid, self.name, self.db.name)
+                    ''' % (self.cellid, self.name, self.dataset.name)
         #XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE
-        elif self.db.type == 'ProbeSet':
+        elif self.dataset.type == 'ProbeSet':
             #ProbeSet Data
             query = '''
                     SELECT
@@ -306,7 +308,7 @@ class webqtlTrait:
                             ProbeSetData.StrainId = Strain.Id
                     Order BY
                             Strain.Name
-                    ''' % (self.name, self.db.name)
+                    ''' % (self.name, self.dataset.name)
         #XZ, 03/02/2009: Xiaodong changeded Data to GenoData, SE to GenoSE
         else:
             #Geno Data
@@ -326,7 +328,7 @@ class webqtlTrait:
                             GenoData.StrainId = Strain.Id
                     Order BY
                             Strain.Name
-                    ''' % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.db.riset), self.name, self.db.name)
+                    ''' % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group), self.name, self.dataset.name)
 
 
         self.cursor.execute(query)
@@ -341,7 +343,7 @@ class webqtlTrait:
                 if not samplelist or (samplelist and name in samplelist):
                     #if value != None:
                     #    num_cases = None
-                    #    if self.db.type in ('Publish', 'Temp'):
+                    #    if self.dataset.type in ('Publish', 'Temp'):
                     #        ndata = item[3]
                     name = item[0]
                     self.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
@@ -352,7 +354,7 @@ class webqtlTrait:
         #            if val != None:
         #                var = item[2]
         #                ndata = None
-        #                if self.db.type in ('Publish', 'Temp'):
+        #                if self.dataset.type in ('Publish', 'Temp'):
         #                    ndata = item[3]
         #                self.data[item[0]] = webqtlCaseData(val, var, ndata)
         #        #end for
@@ -370,9 +372,9 @@ class webqtlTrait:
     #    return self.__dict__.items()
 
     def retrieveInfo(self, QTL = None):
-        assert self.db and self.cursor
-        if self.db.type == 'Publish':
-            #self.db.DisField = ['Name','PubMed_ID','Phenotype','Abbreviation','Authors','Title',\
+        assert self.dataset and self.cursor
+        if self.dataset.type == 'Publish':
+            #self.dataset.DisField = ['Name','PubMed_ID','Phenotype','Abbreviation','Authors','Title',\
             #       'Abstract', 'Journal','Volume','Pages','Month','Year','Sequence',\
             #       'Units', 'comments']
             query = '''
@@ -393,11 +395,11 @@ class webqtlTrait:
                             Publication.Id = PublishXRef.PublicationId AND
                             PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
                             PublishFreeze.Id =%s
-                    ''' % (self.name, self.db.id)
+                    ''' % (self.name, self.dataset.id)
         #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
         #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
-        elif self.db.type == 'ProbeSet':
-            display_fields_string = ',ProbeSet.'.join(self.db.display_fields)
+        elif self.dataset.type == 'ProbeSet':
+            display_fields_string = ',ProbeSet.'.join(self.dataset.display_fields)
             display_fields_string = 'ProbeSet.' + display_fields_string
             query = """
                     SELECT %s
@@ -407,11 +409,11 @@ class webqtlTrait:
                             ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
                             ProbeSetFreeze.Name = '%s' AND
                             ProbeSet.Name = '%s'
-                    """ % (display_fields_string, self.db.name, self.name)
+                    """ % (display_fields_string, self.dataset.name, self.name)
         #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
         # to avoid the problem of same marker name from different species.
-        elif self.db.type == 'Geno':
-            display_fields_string = string.join(self.db.display_fields,',Geno.')
+        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
@@ -421,10 +423,10 @@ class webqtlTrait:
                             GenoXRef.GenoId = Geno.Id AND
                             GenoFreeze.Name = '%s' AND
                             Geno.Name = '%s'
-                    """ % (display_fields_string, self.db.name, self.name)
+                    """ % (display_fields_string, self.dataset.name, self.name)
         else: #Temp type
             query = 'SELECT %s FROM %s WHERE Name = "%s"' % \
-                    (string.join(self.db.display_fields,','), self.db.type, self.name)
+                    (string.join(self.dataset.display_fields,','), self.dataset.type, self.name)
 
 
         self.cursor.execute(query)
@@ -433,16 +435,16 @@ class webqtlTrait:
             self.haveinfo = 1
 
             #XZ: assign SQL query result to trait attributes.
-            for i, field in enumerate(self.db.display_fields):
+            for i, field in enumerate(self.dataset.display_fields):
                 setattr(self, field, traitInfo[i])
 
-            if self.db.type == 'Publish':
+            if self.dataset.type == 'Publish':
                 self.confidential = 0
                 if self.pre_publication_description and not self.pubmed_id:
                     self.confidential = 1
 
             self.homologeneid = None
-            if self.db.type == 'ProbeSet' and self.riset and self.geneid:
+            if self.dataset.type == 'ProbeSet' and self.group and self.geneid:
                 #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number.
                 #XZ: So I have to test if geneid is number before execute the query.
                 #XZ: The geneid values in database should be cleaned up.
@@ -463,7 +465,7 @@ class webqtlTrait:
                                     InbredSet.Name = '%s' AND
                                     InbredSet.SpeciesId = Species.Id AND
                                     Species.TaxonomyId = Homologene.TaxonomyId
-                            """ % (self.geneid, self.riset)
+                            """ % (self.geneid, self.group)
                     self.cursor.execute(query)
                     result = self.cursor.fetchone()
                 else:
@@ -473,7 +475,7 @@ class webqtlTrait:
                     self.homologeneid = result[0]
 
             if QTL:
-                if self.db.type == 'ProbeSet' and not self.cellid:
+                if self.dataset.type == 'ProbeSet' and not self.cellid:
                     query = '''
                             SELECT
                                     ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean
@@ -483,14 +485,14 @@ class webqtlTrait:
                                     ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
                                     ProbeSet.Name = "%s" AND
                                     ProbeSetXRef.ProbeSetFreezeId =%s
-                            ''' % (self.name, self.db.id)
+                            ''' % (self.name, self.dataset.id)
                     self.cursor.execute(query)
                     traitQTL = self.cursor.fetchone()
                     if traitQTL:
                         self.locus, self.lrs, self.pvalue, self.mean = traitQTL
                     else:
                         self.locus = self.lrs = self.pvalue = self.mean = ""
-                if self.db.type == 'Publish':
+                if self.dataset.type == 'Publish':
                     query = '''
                             SELECT
                                     PublishXRef.Locus, PublishXRef.LRS
@@ -500,7 +502,7 @@ class webqtlTrait:
                                     PublishXRef.Id = %s AND
                                     PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
                                     PublishFreeze.Id =%s
-                            ''' % (self.name, self.db.id)
+                            ''' % (self.name, self.dataset.id)
                     self.cursor.execute(query)
                     traitQTL = self.cursor.fetchone()
                     if traitQTL:
@@ -514,7 +516,7 @@ class webqtlTrait:
         if not self.haveinfo:
             self.retrieveInfo()
 
-        if self.db.type == 'Publish':
+        if self.dataset.type == 'Publish':
             PubMedLink = ""
             if self.pubmed_id:
                 PubMedLink = HT.Href(text="PubMed %d : " % self.pubmed_id,
@@ -524,10 +526,10 @@ class webqtlTrait:
 
             if formName:
                 setDescription2 = HT.Href(url="javascript:showDatabase3('%s','%s','%s','')" %
-                (formName, self.db.name, self.name), Class = "fs14")
+                (formName, self.dataset.name, self.name), Class = "fs14")
             else:
                 setDescription2 = HT.Href(url="javascript:showDatabase2('%s','%s','')" %
-                (self.db.name,self.name), Class = "fs14")
+                (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))
@@ -545,20 +547,20 @@ class webqtlTrait:
                 setDescription2.append(HT.Italic('%s, and colleagues' % a1))
             setDescription = HT.Span(PubMedLink, setDescription2)
 
-        elif self.db.type == 'Temp':
+        elif self.dataset.type == 'Temp':
             setDescription = HT.Href(text="%s" % (self.description),url="javascript:showDatabase2\
-            ('%s','%s','')" % (self.db.name,self.name), Class = "fs14")
+            ('%s','%s','')" % (self.dataset.name,self.name), Class = "fs14")
             setDescription = HT.Span(setDescription)
 
-        elif self.db.type == 'Geno': # Genome DB only available for single search
+        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.db.name, self.name), Class = "fs14")
+        (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.db.name,self.name), Class = "fs14")
+        (self.dataset.name,self.name), Class = "fs14")
 
             setDescription = HT.Span(setDescription)
 
@@ -566,20 +568,20 @@ class webqtlTrait:
             if self.cellid:
                 if formName:
                     setDescription = HT.Href(text="ProbeSet/%s/%s" % (self.name, self.cellid),url=\
-            "javascript:showDatabase3('%s','%s','%s','%s')" % (formName, self.db.name,self.name,self.cellid), \
+            "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.db.name,self.name,self.cellid), \
+            "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.db.name,self.name), \
+            "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.db.name,self.name), \
+            "javascript:showDatabase2('%s','%s','')" % (self.dataset.name,self.name), \
             Class = "fs14")
             if self.symbol and self.chr and self.mb:
                 setDescription.append(' [')
@@ -591,9 +593,9 @@ class webqtlTrait:
                 setDescription.append('; %s' % self.probe_target_description)
             setDescription = HT.Span(setDescription)
 
-        if self.db.type != 'Temp' and dispFromDatabase:
+        if self.dataset.type != 'Temp' and dispFromDatabase:
             setDescription.append( ' --- FROM : ')
-            setDescription.append(self.db.genHTML(Class='cori'))
+            setDescription.append(self.dataset.genHTML(Class='cori'))
         return setDescription
 
     @property
@@ -654,13 +656,13 @@ class webqtlTrait:
                             select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze
                                     where
                             ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
-                            ProbeSetFreeze.Id = %d""" % thisTrait.db.id)
+                            ProbeSetFreeze.Id = %d""" % thisTrait.dataset.id)
             probeDBName = self.cursor.fetchone()[0]
             return dict(name = probeDBName,
                         url = None)
         else:
-            return dict(name = self.db.fullname,
-                        url = webqtlConfig.INFOPAGEHREF % self.db.name)
+            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"""