Source code for pybel.manager.database_io

# -*- coding: utf-8 -*-

"""Conversion functions for BEL graphs with a SQL database."""

import logging
from typing import Optional

from sqlalchemy.exc import IntegrityError, OperationalError

from .cache_manager import Manager

__all__ = [

logger = logging.getLogger(__name__)

[docs]def to_database( graph, manager: Optional[Manager] = None, use_tqdm: bool = True, ): """Store a graph in a database. :param BELGraph graph: A BEL graph :return: If successful, returns the network object from the database. :rtype: Optional[Network] """ if manager is None: manager = Manager() try: return manager.insert_graph(graph, use_tqdm=use_tqdm) except (IntegrityError, OperationalError): manager.session.rollback() logger.exception('Error storing graph') except Exception as e: manager.session.rollback() raise e
[docs]def from_database( name: str, version: Optional[str] = None, manager: Optional[Manager] = None, ): """Load a BEL graph from a database. If name and version are given, finds it exactly with :meth:`pybel.manager.Manager.get_network_by_name_version`. If just the name is given, finds most recent with :meth:`pybel.manager.Manager.get_network_by_name_version` :param name: The name of the graph :param version: The version string of the graph. If not specified, loads most recent graph added with this name :return: A BEL graph loaded from the database :rtype: Optional[BELGraph] """ if manager is None: manager = Manager() if version is None: return manager.get_graph_by_most_recent(name) return manager.get_graph_by_name_version(name, version)