Source code for

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

"""Conversion functions for BEL graphs with INDRA.

After assembling a model with `INDRA <>`_, a list of
:class:`indra.statements.Statement` can be converted to a :class:`pybel.BELGraph` with

.. code-block:: python

    from indra.assemblers.pybel import PybelAssembler
    import pybel

    stmts = [
        # A list of INDRA statements

    pba = PybelAssembler(
        name='Graph Name',
        description='Graph Description'
    graph = pba.make_model()

    # Write to BEL file
    pybel.to_bel_path(belgraph, 'simple_pybel.bel')

.. warning::

    These functions are hard to unit test because they rely on a whole set of java dependencies and will likely
    not be for a while.

import json
from typing import Any, List, Mapping, Optional, TextIO, Union

from networkx.utils import open_file

    from pickle5 import load
except ImportError:
    from pickle import load

__all__ = [

[docs]def from_indra_statements( stmts, name: Optional[str] = None, version: Optional[str] = None, description: Optional[str] = None, authors: Optional[str] = None, contact: Optional[str] = None, license: Optional[str] = None, copyright: Optional[str] = None, disclaimer: Optional[str] = None, ): """Import a model from :mod:`indra`. :param List[indra.statements.Statement] stmts: A list of statements :param name: The graph's name :param version: The graph's version. Recommended to use `semantic versioning <>`_ or ``YYYYMMDD`` format. :param description: The description of the graph :param authors: The authors of this graph :param contact: The contact email for this graph :param license: The license for this graph :param copyright: The copyright for this graph :param disclaimer: The disclaimer for this graph :rtype: pybel.BELGraph """ from indra.assemblers.pybel import PybelAssembler if authors is None: authors = 'INDRA' pba = PybelAssembler( stmts=stmts, name=name, version=version, description=description, authors=authors, contact=contact, license=license, copyright=copyright, disclaimer=disclaimer, ) graph = pba.make_model() return graph
[docs]def from_indra_statements_json(stmts_json: List[Mapping[str, Any]], **kwargs): """Get a BEL graph from INDRA statements JSON. :rtype: BELGraph Other kwargs are passed to :func:`from_indra_statements`. """ from indra.statements import stmts_from_json statements = stmts_from_json(stmts_json) return from_indra_statements(statements, **kwargs)
[docs]@open_file(0, mode='r') def from_indra_statements_json_file(file, **kwargs): """Get a BEL graph from INDRA statements JSON file. :rtype: BELGraph Other kwargs are passed to :func:`from_indra_statements`. """ return from_indra_statements_json(json.load(file), **kwargs)
def from_indra_pickle(path: str, **kwargs): """Import a model from :mod:`indra`. :param path: Path to pickled list of :class:`indra.statements.Statement` :rtype: pybel.BELGraph Other kwargs are passed to :func:`from_indra_statements`. """ with open(path, 'rb') as f: statements = load(f) return from_indra_statements(stmts=statements, **kwargs)
[docs]def to_indra_statements(graph): """Export this graph as a list of INDRA statements using the :py:class:`indra.sources.pybel.PybelProcessor`. :param pybel.BELGraph graph: A BEL graph :rtype: list[indra.statements.Statement] """ from indra.sources.bel import process_pybel_graph pbp = process_pybel_graph(graph) return pbp.statements
[docs]def to_indra_statements_json(graph) -> List[Mapping[str, Any]]: """Export this graph as INDRA JSON list. :param pybel.BELGraph graph: A BEL graph """ return [ statement.to_json() for statement in to_indra_statements(graph) ]
[docs]@open_file(1, mode='w') def to_indra_statements_json_file(graph, path: Union[str, TextIO], indent: Optional[int] = 2, **kwargs): """Export this graph as INDRA statement JSON. :param pybel.BELGraph graph: A BEL graph :param path: A writable file or file-like Other kwargs are passed to :func:`json.dump`. """ json.dump(to_indra_statements_json(graph), path, indent=indent, **kwargs)
[docs]def from_biopax(path: str, encoding: Optional[str] = None, **kwargs): """Import a model encoded in Pathway Commons `BioPAX <>`_ via :mod:`indra`. :param path: Path to a BioPAX OWL file :param encoding: The encoding passed to :func:`indra.sources.biopax.process_owl`. See :rtype: pybel.BELGraph Other kwargs are passed to :func:`from_indra_statements`. .. warning:: Not compatible with all BioPAX! See INDRA documentation. """ from indra.sources.biopax import process_owl model = process_owl(path, encoding=encoding) return from_indra_statements(stmts=model.statements, **kwargs)