diff options
Diffstat (limited to 'wqflask/maintenance/set_resource_defaults.py')
| -rw-r--r-- | wqflask/maintenance/set_resource_defaults.py | 35 |
1 files changed, 17 insertions, 18 deletions
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index 0f472494..22d73ba3 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -30,10 +30,9 @@ from utility.tools import SQL_URI from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources, get_resource_info Redis = get_redis_conn() -import MySQLdb - import urllib.parse +from wqflask.database import database_connection from utility.logger import getLogger logger = getLogger(__name__) @@ -53,14 +52,14 @@ def parse_db_uri(): return db_conn_info -def insert_probeset_resources(default_owner_id): +def insert_probeset_resources(cursor, default_owner_id): current_resources = Redis.hgetall("resources") - Cursor.execute(""" SELECT + cursor.execute(""" SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.confidentiality, ProbeSetFreeze.public FROM ProbeSetFreeze""") - resource_results = Cursor.fetchall() + resource_results = cursor.fetchall() for i, resource in enumerate(resource_results): resource_ob = {} resource_ob['name'] = resource[1] @@ -80,9 +79,9 @@ def insert_probeset_resources(default_owner_id): add_resource(resource_ob, update=False) -def insert_publish_resources(default_owner_id): +def insert_publish_resources(cursor, default_owner_id): current_resources = Redis.hgetall("resources") - Cursor.execute(""" SELECT + cursor.execute(""" SELECT PublishXRef.Id, PublishFreeze.Id, InbredSet.InbredSetCode FROM PublishXRef, PublishFreeze, InbredSet, Publication @@ -91,7 +90,7 @@ def insert_publish_resources(default_owner_id): InbredSet.Id = PublishXRef.InbredSetId AND Publication.Id = PublishXRef.PublicationId""") - resource_results = Cursor.fetchall() + resource_results = cursor.fetchall() for resource in resource_results: if resource[2]: resource_ob = {} @@ -114,14 +113,14 @@ def insert_publish_resources(default_owner_id): continue -def insert_geno_resources(default_owner_id): +def insert_geno_resources(cursor, default_owner_id): current_resources = Redis.hgetall("resources") - Cursor.execute(""" SELECT + cursor.execute(""" SELECT GenoFreeze.Id, GenoFreeze.ShortName, GenoFreeze.confidentiality FROM GenoFreeze""") - resource_results = Cursor.fetchall() + resource_results = cursor.fetchall() for i, resource in enumerate(resource_results): resource_ob = {} resource_ob['name'] = resource[1] @@ -147,15 +146,15 @@ def insert_geno_resources(default_owner_id): def insert_resources(default_owner_id): current_resources = get_resources() print("START") - insert_publish_resources(default_owner_id) + insert_publish_resources(cursor, default_owner_id) print("AFTER PUBLISH") - insert_geno_resources(default_owner_id) + insert_geno_resources(cursor, default_owner_id) print("AFTER GENO") - insert_probeset_resources(default_owner_id) + insert_probeset_resources(cursor, default_owner_id) print("AFTER PROBESET") -def main(): +def main(cursor): """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" Redis.delete("resources") @@ -166,6 +165,6 @@ def main(): if __name__ == '__main__': - Conn = MySQLdb.Connect(**parse_db_uri()) - Cursor = Conn.cursor() - main() + with database_connection() as conn: + with conn.cursor() as cursor: + main(cursor) |