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authorFrederick Muriuki Muriithi2023-10-09 12:34:38 +0300
committerFrederick Muriuki Muriithi2023-10-09 12:49:04 +0300
commit14bd560cd8c4c7e6574f30a8d0bcab268d557b07 (patch)
treea944dbd6f546da3556c068ad681b6412ff295c69 /scripts
parentdd00a799a7f8b00c7f27460cb2be2b39b8a47c1c (diff)
downloadgn-auth-14bd560cd8c4c7e6574f30a8d0bcab268d557b07.tar.gz
scripts: Provide script to link InbredSets to auth system.
Diffstat (limited to 'scripts')
-rw-r--r--scripts/link_inbredsets.py108
1 files changed, 108 insertions, 0 deletions
diff --git a/scripts/link_inbredsets.py b/scripts/link_inbredsets.py
new file mode 100644
index 0000000..2647fd0
--- /dev/null
+++ b/scripts/link_inbredsets.py
@@ -0,0 +1,108 @@
+"""
+Link any unlinked InbredSet groups.
+"""
+import uuid
+from pathlib import Path
+
+import click
+
+import gn_auth.auth.db.sqlite3 as authdb
+
+from gn_auth.auth.db import mariadb as biodb
+
+from scripts.migrate_existing_data import sys_admins, admin_group, select_sys_admin
+
+def linked_inbredsets(conn):
+ """Fetch all inbredset groups that are linked to the auth system."""
+ with authdb.cursor(conn) as cursor:
+ cursor.execute(
+ "SELECT SpeciesId, InbredSetId FROM linked_inbredset_groups")
+ return tuple((row["SpeciesId"], row["InbredSetId"])
+ for row in cursor.fetchall())
+
+def unlinked_inbredsets(conn, linked):
+ """Fetch any inbredset groups that are not linked to the auth system."""
+ with conn.cursor() as cursor:
+ where_clause = ""
+ query = "SELECT SpeciesId, InbredSetId, InbredSetName, FullName FROM InbredSet"
+ if len(linked) > 0:
+ pholders = ["(%s, %s)"] * len(linked)
+ where_clause = (f" WHERE (SpeciesId, InbredSetId) "
+ f"NOT IN ({pholders})")
+ cursor.execute(query + where_clause,
+ tuple(arg for sublist in linked for arg in sublist))
+ return cursor.fetchall()
+
+ cursor.execute(query)
+ return cursor.fetchall()
+
+def link_unlinked(conn, unlinked):
+ """Link the unlinked inbredset groups to the auth system."""
+ params = tuple((str(uuid.uuid4()),) + row for row in unlinked)
+ with authdb.cursor(conn) as cursor:
+ cursor.executemany(
+ "INSERT INTO linked_inbredset_groups VALUES (?, ?, ?, ?, ?)",
+ params)
+
+ return params
+
+def build_resources(conn, new_linked):
+ """Build resources for newly linked inbredsets."""
+ with authdb.cursor(conn) as cursor:
+ cursor.execute(
+ "SELECT resource_category_id FROM resource_categories "
+ "WHERE resource_category_key='inbredset-group'")
+ category_id = cursor.fetchone()["resource_category_id"]
+ resources = tuple({
+ "resource_id": str(uuid.uuid4()),
+ "resource_name": f"InbredSet: {name}",
+ "resource_category_id": category_id,
+ "public": 1,
+ "data_link_id": datalinkid
+ } for datalinkid, _sid, _isetid, name, _name in new_linked)
+ cursor.executemany(
+ "INSERT INTO resources VALUES "
+ "(:resource_id, :resource_name, :resource_category_id, :public)",
+ resources)
+ cursor.executemany(
+ "INSERT INTO inbredset_group_resources VALUES "
+ "(:resource_id, :data_link_id)",
+ resources)
+ return resources
+
+def own_resources(conn, group, resources):
+ """Link new resources to admin group."""
+ with authdb.cursor(conn) as cursor:
+ 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
+
+@click.command()
+@click.argument("authdbpath") # "Path to the Auth(entic|oris)ation database"
+@click.argument("mysqldburi") # "URI to the MySQL database with the biology data"
+def run(authdbpath, mysqldburi):
+ """Setup command-line arguments."""
+ if not Path(authdbpath).exists():
+ print(
+ f"ERROR: Auth db file `{authdbpath}` does not exist.",
+ file=sys.stderr)
+ sys.exit(2)
+
+ with (authdb.connection(authdbpath) as authconn,
+ biodb.database_connection(mysqldburi) as bioconn):
+ admin = select_sys_admin(sys_admins(authconn))
+ unlinked = own_resources(
+ authconn,
+ admin_group(authconn, admin),
+ build_resources(
+ authconn, link_unlinked(
+ authconn,
+ unlinked_inbredsets(bioconn, linked_inbredsets(authconn)))))
+
+if __name__ == "__main__":
+ run() # pylint: disable=[no-value-for-parameter]