Below is the code I use to solve this problem, by breaking up a single large query into multiple small ones. I use the google.appengine.ext.ndb
library -- I don't know if that is required for the code below to work.
(If you are not using ndb, consider switching to it. It is an improved version of the db library and migrating to it is easy. For more information, see https://developers.google.com/appengine/docs/python/ndb.)
from google.appengine.datastore.datastore_query import Cursor
def ProcessAll():
curs = Cursor()
while True:
records, curs, more = MyEntity.query().fetch_page(5000, start_cursor=curs)
for record in records:
# Run your custom business logic on record.
RunMyBusinessLogic(record)
if more and curs:
# There are more records; do nothing here so we enter the
# loop again above and run the query one more time.
pass
else:
# No more records to fetch; break out of the loop and finish.
break