diff options
Diffstat (limited to 'scripts/batch_assign_data_to_default_admin.py')
-rw-r--r-- | scripts/batch_assign_data_to_default_admin.py | 87 |
1 files changed, 87 insertions, 0 deletions
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] |