1 files changed, 0 insertions, 122 deletions
diff --git a/scripts/link_inbredsets.py b/scripts/link_inbredsets.py
deleted file mode 100644
index c78a050..0000000
--- a/scripts/link_inbredsets.py
+++ /dev/null
@@ -1,122 +0,0 @@
-"""
-Link any unlinked InbredSet groups.
-"""
-import sys
-import uuid
-from pathlib import Path
-
-import click
-from gn_libs import mysqldb as biodb
-
-import gn_auth.auth.db.sqlite3 as authdb
-
-from scripts.assign_data_to_default_admin 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:
-        params = tuple({
-            "group_id": str(group.group_id),
-            **resource
-        } for resource in resources)
-        cursor.executemany(
-            "INSERT INTO resource_ownership VALUES "
-            "(:group_id, :resource_id)",
-            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"
-@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))
-        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))))))
-
-if __name__ == "__main__":
-    run() # pylint: disable=[no-value-for-parameter]