Replace fetchall, fetchone, fetch1 with database_connection

* wqflask/base/data_set.py: Replace "db.call" import with
"database_connection".
(create_datasets_list): Use "database_connection" to fetch data.
(DatasetGroup.__init__): Ditto.
(DataSet.retrieve_other_names): Ditto.
(PhenotypeDataSet.setup): Remove query escaping in string and format
the string.
(GenotypeDataSet.setup): Ditto.
(MrnaAssayDataSet.setup): Ditto.
* wqflask/db/webqtlDatabaseFunction.py: Remove db.call import.
(retrieve_species): Use database_connection() to fetch data.
(retrieve_species_id): Ditto.

1 files changed, 10 insertions, 6 deletions

diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 9ec650a4..122c546f 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -20,19 +20,23 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from db.call import fetch1
+from wqflask.database import database_connection
 
 
 def retrieve_species(group):
     """Get the species of a group (e.g. returns string "mouse" on "BXD"
 
     """
-    result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (
-        group), "/cross/" + group + ".json", lambda r: (r["species"],))[0]
+    with database_connection() as conn, conn.cursor() as cursor:
+        cursor.execute(
+            "SELECT Species.Name FROM Species, InbredSet WHERE InbredSet.Name = %s AND InbredSet.SpeciesId = Species.Id",
+            (group,))
+        return cursor.fetchone()[0]
     return result
 
 
 def retrieve_species_id(group):
-    result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (
-        group), "/cross/" + group + ".json", lambda r: (r["species_id"],))[0]
-    return result
+    with database_connection() as conn, conn.cursor() as cursor:
+        cursor.execute("SELECT SpeciesId FROM InbredSet WHERE Name = %s",
+                       (group,))
+        return cursor.fetchone()[0]