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-rw-r--r--scripts/link_inbredsets.py32
1 files changed, 23 insertions, 9 deletions
diff --git a/scripts/link_inbredsets.py b/scripts/link_inbredsets.py
index 2647fd0..49cb47c 100644
--- a/scripts/link_inbredsets.py
+++ b/scripts/link_inbredsets.py
@@ -1,6 +1,7 @@
"""
Link any unlinked InbredSet groups.
"""
+import sys
import uuid
from pathlib import Path
@@ -73,14 +74,27 @@ def build_resources(conn, new_linked):
def own_resources(conn, group, resources):
"""Link new resources to admin group."""
with authdb.cursor(conn) as cursor:
+ params = tuple({
+ "group_id": str(group.group_id),
+ **resource
+ } for resource in resources)
cursor.executemany(
"INSERT INTO resource_ownership VALUES "
"(:group_id, :resource_id)",
- tuple({
- "group_id": str(group.group_id),
- **resource
- } for resource in resources))
- return resources
+ params)
+ return params
+
+def assign_role_for_admin(conn, user, resources):
+ """Assign basic role to admin on the inbredset-group resources."""
+ with authdb.cursor(conn) as cursor:
+ cursor.execute(
+ "SELECT * FROM roles WHERE role_name='inbredset-group-owner'")
+ role_id = cursor.fetchone()["role_id"]
+ cursor.executemany(
+ "INSERT INTO user_roles(user_id, role_id, resource_id) "
+ "VALUES (:user_id, :role_id, :resource_id)",
+ tuple({**rsc, "user_id": str(user.user_id), "role_id": role_id}
+ for rsc in resources))
@click.command()
@click.argument("authdbpath") # "Path to the Auth(entic|oris)ation database"
@@ -96,13 +110,13 @@ def run(authdbpath, mysqldburi):
with (authdb.connection(authdbpath) as authconn,
biodb.database_connection(mysqldburi) as bioconn):
admin = select_sys_admin(sys_admins(authconn))
- unlinked = own_resources(
+ unlinked = assign_role_for_admin(authconn, admin, own_resources(
authconn,
admin_group(authconn, admin),
build_resources(
- authconn, link_unlinked(
- authconn,
- unlinked_inbredsets(bioconn, linked_inbredsets(authconn)))))
+ authconn, link_unlinked(
+ authconn,
+ unlinked_inbredsets(bioconn, linked_inbredsets(authconn))))))
if __name__ == "__main__":
run() # pylint: disable=[no-value-for-parameter]