# -*- coding: utf-8 -*-
"""Conversion functions for BEL graphs with INDRA.
After assembling a model with `INDRA <https://github.com/sorgerlab/indra>`_, a list of
:class:`indra.statements.Statement` can be converted to a :class:`pybel.BELGraph` with
:class:`indra.assemblers.pybel.PybelAssembler`.
.. code-block:: python
from indra.assemblers.pybel import PybelAssembler
import pybel
stmts = [
# A list of INDRA statements
]
pba = PybelAssembler(
stmts,
name='Graph Name',
version='0.0.1',
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
try:
from pickle5 import load
except ImportError:
from pickle import load
__all__ = [
"from_indra_statements",
"from_indra_statements_json",
"from_indra_statements_json_file",
"from_indra_pickle",
"to_indra_statements",
"to_indra_statements_json",
"to_indra_statements_json_file",
"from_biopax",
]
[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 <http://semver.org/>`_ 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 <http://www.biopax.org/>`_ via :mod:`indra`.
:param path: Path to a BioPAX OWL file
:param encoding: The encoding passed to :func:`indra.sources.biopax.process_owl`.
See https://github.com/sorgerlab/indra/pull/1199.
: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)