Began changing references to cursor/db_conn to use sqlalchemy

Wrote function for phenotype author searches

2 files changed, 26 insertions, 23 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 34e5eaa1..cd9e810e 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -90,9 +90,7 @@ class DataSet(object):
 
 
     def get_group(self):
-        assert self.cursor
-        self.cursor.execute(self.query)
-        self.group, self.group_id = self.cursor.fetchone()
+        self.group, self.group_id = g.db.execute(self.query).fetchone()
         if self.group == 'BXD300':
             self.group = "BXD"
         #return group
@@ -107,7 +105,7 @@ class DataSet(object):
 
         """
 
-        query_args = tuple(self.db_conn.escape_string(x) for x in (
+        query_args = tuple(escape(x) for x in (
             (self.type + "Freeze"),
             str(webqtlConfig.PUBLICTHRESH),
             self.name,
@@ -115,18 +113,22 @@ class DataSet(object):
             self.name))
         print("query_args are:", query_args)
 
-        query = '''
-                SELECT
-                        Id, Name, FullName, ShortName
-                FROM
-                        %s
-                WHERE
-                        public > %s AND
-                        (Name = "%s" OR FullName = "%s" OR ShortName = "%s")
-          ''' % (query_args)
+        print("""
+                SELECT Id, Name, FullName, ShortName
+                FROM %s
+                WHERE public > %s AND
+                     (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+          """ % (query_args))
+
+        self.id, self.name, self.fullname, self.shortname = g.db.execute("""
+                SELECT Id, Name, FullName, ShortName
+                FROM %s
+                WHERE public > %s AND
+                     (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+          """ % (query_args)).fetchone()
 
-        self.cursor.execute(query)
-        self.id, self.name, self.fullname, self.shortname = self.cursor.fetchone()
+        #self.cursor.execute(query)
+        #self.id, self.name, self.fullname, self.shortname = self.cursor.fetchone()
 
 
     #def genHTML(self, Class='c0dd'):
@@ -185,7 +187,7 @@ class PhenotypeDataSet(DataSet):
                             WHERE
                                     PublishFreeze.InbredSetId = InbredSet.Id AND
                                     PublishFreeze.Name = "%s"
-                    ''' % self.db_conn.escape_string(self.name)
+                    ''' % escape(self.name)
 
     def check_confidentiality(self):
         # (Urgently?) Need to write this
diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
index 1dceba08..9763e441 100755
--- a/wqflask/base/webqtlTrait.py
+++ b/wqflask/base/webqtlTrait.py
@@ -30,9 +30,9 @@ class webqtlTrait:
         self.cellid = kw.get('cellid', None)
         self.identification = kw.get('identification', 'un-named trait')
         self.group = kw.get('group', None)
-        self.haveinfo = kw.get(haveinfo, False)
-        self.sequence = kw.get(sequence, None)              # Blat sequence, available for ProbeSet
-        self.data = kw.get(data, {})
+        self.haveinfo = kw.get('haveinfo', False)
+        self.sequence = kw.get('sequence', None)              # Blat sequence, available for ProbeSet
+        self.data = kw.get('data', {})
         
         if kw.get('fullname'):
             name2 = value.split("::")
@@ -381,7 +381,7 @@ class webqtlTrait:
     #    return self.__dict__.items()
 
     def retrieveInfo(self, QTL = None):
-        assert self.dataset and self.cursor
+        assert self.dataset
         if self.dataset.type == 'Publish':
             #self.dataset.DisField = ['Name','PubMed_ID','Phenotype','Abbreviation','Authors','Title',\
             #       'Abstract', 'Journal','Volume','Pages','Month','Year','Sequence',\
@@ -434,10 +434,11 @@ class webqtlTrait:
                             Geno.Name = '%s'
                     """ % (display_fields_string, self.dataset.name, self.name)
         else: #Temp type
-            query = 'SELECT %s FROM %s WHERE Name = "%s"' % \
-                    (string.join(self.dataset.display_fields,','), self.dataset.type, self.name)
-
+            traitInfo = g.db.execute("""SELECT %s FROM %s WHERE Name = '%s'
+                                     """, (string.join(self.dataset.display_fields,','),
+                                             self.dataset.type, self.name)).fetchone()
 
+        
         self.cursor.execute(query)
         traitInfo = self.cursor.fetchone()
         if traitInfo: