""" Similar to the 'assign_data_to_default_admin' script but without user interaction. """ import sys import logging from pathlib import Path import click from gn_libs import mysqldb as biodb from pymonad.maybe import Just, Maybe, Nothing from pymonad.tools import monad_from_none_or_value 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]