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-rw-r--r--scripts/batch_assign_data_to_default_admin.py89
1 files changed, 89 insertions, 0 deletions
diff --git a/scripts/batch_assign_data_to_default_admin.py b/scripts/batch_assign_data_to_default_admin.py
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+++ b/scripts/batch_assign_data_to_default_admin.py
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+"""
+Similar to the 'assign_data_to_default_admin' script but without user
+interaction.
+"""
+import sys
+import logging
+from pathlib import Path
+
+import click
+from MySQLdb.cursors import DictCursor
+from pymonad.maybe import Just, Maybe, Nothing
+from pymonad.tools import curry, 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:
+ 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())