Removed a little more code in webqtlDatabaseFunction.py and do_search

3 files changed, 1 insertions, 36 deletions

diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index ba998e91..8a9dc79d 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -30,14 +30,6 @@ logger = getLogger(__name__ )
 #output: cursor instance
 #function: connect to database and return cursor instance
 ###########################################################################
-def getCursor():
-    try:
-        logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)")
-        con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD)
-        cursor = con.cursor()
-        return cursor
-    except:
-        return None
 
 def retrieve_species(group):
     """Get the species of a group (e.g. returns string "mouse" on "BXD"
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index e2a0a479..c7dbc972 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -872,32 +872,6 @@ if __name__ == "__main__":
     dataset_name = "HC_M2_0606_P"
     dataset = create_dataset(db_conn, dataset_name)
 
-    #cursor.execute("""
-    #            SELECT ProbeSet.Name as TNAME, 0 as thistable,
-    #            ProbeSetXRef.Mean as TMEAN, ProbeSetXRef.LRS as TLRS,
-    #            ProbeSetXRef.PVALUE as TPVALUE, ProbeSet.Chr_num as TCHR_NUM,
-    #            ProbeSet.Mb as TMB, ProbeSet.Symbol as TSYMBOL,
-    #            ProbeSet.name_num as TNAME_NUM
-    #            FROM ProbeSetXRef, ProbeSet, Geno
-    #            WHERE ProbeSetXRef.LRS > 99.0 and
-    #            ABS(ProbeSet.Mb-Geno.Mb) < 5 and
-    #            ProbeSetXRef.Locus = Geno.name and
-    #            Geno.SpeciesId = 1 and
-    #            ProbeSet.Chr = Geno.Chr and
-    #            ProbeSet.Id = ProbeSetXRef.ProbeSetId and
-    #            ProbeSetXRef.ProbeSetFreezeId = 112""")
-
-    #logger.debug(pf(cursor.fetchall()))
-    #results = ProbeSetSearch("shh", None, dataset, cursor, db_conn).run()
     results = PvalueSearch(['0.005'], '<', dataset, cursor, db_conn).run()
-    #results = RifSearch("diabetes", dataset, cursor, db_conn).run()
-    #results = WikiSearch("nicotine", dataset, cursor, db_conn).run()
-    #results = CisLrsSearch(['99'], '>', dataset, cursor, db_conn).run() # cisLRS > 99
-    #results = LrsSearch('99', '>', 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()
-
-    logger.debug("results are:", pf(results))
+
     db_conn.close()
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 49b47123..2089f9de 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -72,7 +72,6 @@ import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
 
-
 @app.before_request
 def connect_db():
     db = getattr(g, '_database', None)