Connections that use sqlalchemy are the only placen in GN2 where connections remain "open" indefinitely until a connection is closed. In the event that we have many users at the same time, say like during one of Rob's classes; and they do a search, we have N connections indefinitely open until their sessions are killed. And removing that is trivial, and to demonstrate that using a random example from GN2 (/wqflask/wqflask/search_results.py):
def get_GO_symbols(a_search):
query = """SELECT genes
FROM GORef
WHERE goterm='{0}:{1}'""".format(a_search['key'], a_search['search_term'][0])
gene_list = g.db.execute(query).fetchone()[0].strip().split()
new_terms = []
for gene in gene_list:
this_term = dict(key=None,
separator=None,
search_term=[gene])
new_terms.append(this_term)
return new_terms
could be replaced with:
def get_GO_symbols(a_search):
- query = """SELECT genes
- FROM GORef
- WHERE goterm='{0}:{1}'""".format(a_search['key'], a_search['search_term'][0])
-
- gene_list = g.db.execute(query).fetchone()[0].strip().split()
-
- new_terms = []
- for gene in gene_list:
- this_term = dict(key=None,
- separator=None,
- search_term=[gene])
-
- new_terms.append(this_term)
-
- return new_terms
+ genes = []
+ with database_connection() as conn:
+ with conn.cursor() as cursor:
+ cursor.execute("SELECT genes FROM GORef WHERE goterm=%s",
+ (a_search.get("key")))
+ genes = cursor.fetchone()[0].strip().split()
+ return [dict(key=None, separator=None, search_term=[gene])
+ for gene in genes]
This is has been merged in:
https://github.com/genenetwork/genenetwork2/pull/730
Should problems occur, a new issue will be created.