3 files changed, 91 insertions, 3 deletions
diff --git a/scripts/migrate_existing_data.py b/scripts/assign_data_to_default_admin.py
index 198d37d..0ae209a 100644
--- a/scripts/migrate_existing_data.py
+++ b/scripts/assign_data_to_default_admin.py
@@ -1,6 +1,6 @@
 """
-Migrate existing data that is not assigned to any group to the default sys-admin
-group for accessibility purposes.
+Assign any existing data (that is not currently assigned to any group) to the
+default sys-admin group for accessibility purposes.
 """
 import sys
 import json
diff --git a/scripts/batch_assign_data_to_default_admin.py b/scripts/batch_assign_data_to_default_admin.py
new file mode 100644
index 0000000..3df123d
--- /dev/null
+++ b/scripts/batch_assign_data_to_default_admin.py
@@ -0,0 +1,87 @@
+"""
+Similar to the 'assign_data_to_default_admin' script but without user
+interaction.
+"""
+import sys
+import logging
+from pathlib import Path
+
+import click
+from pymonad.maybe import Just, Maybe, Nothing
+from pymonad.tools import monad_from_none_or_value
+
+from gn_auth.auth.db import mariadb as biodb
+from gn_auth.auth.db import sqlite3 as authdb
+from gn_auth.auth.authentication.users import User
+from gn_auth.auth.authorisation.resources.groups.models import (
+    Group, db_row_to_group)
+
+from scripts.assign_data_to_default_admin import (
+    default_resources, assign_data_to_resource)
+
+
+def resources_group(conn: authdb.DbConnection) -> Maybe:
+    """Retrieve resources' group"""
+    with authdb.cursor(conn) as cursor:
+        cursor.execute(
+            "SELECT g.* FROM resources AS r "
+            "INNER JOIN resource_ownership AS ro "
+            "ON r.resource_id=ro.resource_id "
+            "INNER JOIN groups AS g ON ro.group_id=g.group_id "
+            "WHERE resource_name='mRNA-euhrin'")
+        return monad_from_none_or_value(
+            Nothing, Just, cursor.fetchone()).then(
+                db_row_to_group)
+
+
+def resource_owner(conn: authdb.DbConnection) -> Maybe:
+    """Retrieve the resource owner."""
+    with authdb.cursor(conn) as cursor:
+        cursor.execute(
+            "SELECT u.* FROM users AS u WHERE u.user_id IN "
+            "(SELECT ur.user_id FROM resources AS rsc "
+            "INNER JOIN user_roles AS ur ON rsc.resource_id=ur.resource_id "
+            "INNER JOIN roles AS r on ur.role_id=r.role_id "
+            "WHERE resource_name='mRNA-euhrin' "
+            "AND r.role_name='resource-owner')")
+        return monad_from_none_or_value(
+            Nothing, Just, cursor.fetchone()).then(
+                User.from_sqlite3_row)
+
+
+def assign_data(authconn: authdb.DbConnection, bioconn, group: Group):
+    """Do actual data assignments."""
+    try:
+        for resource in default_resources(authconn, group):
+            assign_data_to_resource(authconn, bioconn, resource, group)
+
+        return 1
+    except Exception as _exc:# pylint: disable=[broad-except]
+        logging.error("Failed to assign some data!", exc_info=True)
+        return 1
+
+
+if __name__ == "__main__":
+    @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"
+    @click.option("--loglevel",
+                  default="WARNING",
+                  show_default=True,
+                  type=click.Choice([
+                      "CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"]))
+    def run(authdbpath, mysqldburi, loglevel):
+        """Script entry point."""
+        _logger = logging.getLogger()
+        _logger.setLevel(loglevel)
+        if Path(authdbpath).exists():
+            with (authdb.connection(authdbpath) as authconn,
+                  biodb.database_connection(mysqldburi) as bioconn):
+                return resources_group(authconn).maybe(
+                    1,
+                    lambda group: assign_data(authconn, bioconn, group))
+
+        logging.error("There is no such SQLite3 database file.")
+        return 1
+
+    sys.exit(run()) # pylint: disable=[no-value-for-parameter]
diff --git a/scripts/link_inbredsets.py b/scripts/link_inbredsets.py
index ac9fa2b..5db7ea8 100644
--- a/scripts/link_inbredsets.py
+++ b/scripts/link_inbredsets.py
@@ -11,7 +11,8 @@ 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
+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."""