Source code for bio2bel.io.automate

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

"""Automation of installation and execution of Bio2BEL packages."""

import importlib
import logging
import os
import sys
import types
from contextlib import redirect_stdout
from typing import Any, Mapping, Optional, Tuple

from pybel import BELGraph, from_nodelink_gz, to_nodelink_gz, to_tsv
from ..manager.bel_manager import BELManagerMixin
from ..utils import get_data_dir

__all__ = [
    'ensure_tsv',
    'ensure_graph',
    'ensure_bio2bel_installation',
]

_SPECIAL_CASES = {
    'compath': 'compath_resources',
}

logger = logging.getLogger(__name__)


[docs]def ensure_tsv(name: str, *, manager_kwargs: Optional[Mapping[str, Any]] = None) -> str: """Generate/save a TSV from the Bio2BEL package using :func:`pybel.to_tsv` and return its path. The resulting file is cached within the bio2bel package's data directory. If it already exists, the path is directly returned with no other code being run. :param name: The name of the Bio2BEL package :param manager_kwargs: Optional mapping to give as keyword arguments to the manager upon instantiation. :return: The path to the TSV file generated (inside the Bio2BEL directory) or """ directory = get_data_dir(name) path = os.path.join(directory, f'{name}.bel.tsv') if os.path.exists(path): return path graph = ensure_graph(name, manager_kwargs=manager_kwargs) to_tsv(graph, path) return path
[docs]def ensure_graph(name: str, *, manager_kwargs: Optional[Mapping[str, Any]] = None) -> BELGraph: """Generate, cache, and return the BEL graph for a given Bio2BEL package. If it has already been cached, it is loaded directly. :param name: The name of the Bio2BEL package :param manager_kwargs: Optional mapping to give as keyword arguments to the manager upon instantiation. """ directory = get_data_dir(name) path = os.path.join(directory, f'{name}.bel.nodelink.json.gz') if os.path.exists(path): return from_nodelink_gz(path) _, module = ensure_bio2bel_installation(name) manager = module.Manager(**(manager_kwargs or {})) if not isinstance(manager, BELManagerMixin): raise ValueError(f'{module} is not enabled for BEL export') graph = manager.to_bel() to_nodelink_gz(graph, path) return graph
[docs]def ensure_bio2bel_installation(name: str) -> Tuple[bool, types.ModuleType]: """Import a Bio2BEL package, or install it. :return: If the package was already installed :return: A module object representing the Bio2BEL package """ package = _SPECIAL_CASES.get(name, f'bio2bel_{name}') try: return True, importlib.import_module(package) except ImportError: logger.info(f'pip install {package}') # Install this package using pip # https://stackoverflow.com/questions/12332975/installing-python-module-within-code with redirect_stdout(sys.stderr): pip_exit_code = os.system(f'python -m pip install -q {package}') # noqa:S605 if 0 != pip_exit_code: # command failed logger.warning(f'could not find {package} on PyPI. Try installing from GitHub with:') name = package.split("_")[-1] logger.warning(f'\n pip install git+https://github.com/bio2bel/{name}.git\n') sys.exit(1) try: return False, importlib.import_module(package) except ImportError: logger.exception(f'failed to import {package}') sys.exit(1)