def test_parts(self):
"""Test splitting file into annotations and definitions."""
lines = simple.splitlines()
docs, definitions, statements = split_file_to_annotations_and_definitions(lines)
self.assertEqual(8, len(list(docs)))
self.assertEqual(4, len(list(definitions)))
self.assertEqual(14, len(list(statements)))
def parse_lines(
graph: BELGraph,
lines: Iterable[str],
manager: Optional[Manager] = None,
disallow_nested: bool = False,
citation_clearing: bool = True,
use_tqdm: bool = False,
tqdm_kwargs: Optional[Mapping[str, Any]] = None,
no_identifier_validation: bool = False,
disallow_unqualified_translocations: bool = False,
allow_redefinition: bool = False,
allow_definition_failures: bool = False,
allow_naked_names: bool = False,
required_annotations: Optional[List[str]] = None,
upgrade_urls: bool = False,
) -> None:
"""Parse an iterable of lines into this graph.
Delegates to :func:`parse_document`, :func:`parse_definitions`, and :func:`parse_statements`.
:param graph: A BEL graph
:param lines: An iterable over lines of BEL script
:param manager: A PyBEL database manager
:param disallow_nested: If true, turns on nested statement failures
:param citation_clearing: Should :code:`SET Citation` statements clear evidence and all annotations?
Delegated to :class:`pybel.parser.ControlParser`
:param use_tqdm: Use :mod:`tqdm` to show a progress bar?
:param tqdm_kwargs: Keywords to pass to ``tqdm``
:param disallow_unqualified_translocations: If true, allow translocations without TO and FROM clauses.
:param required_annotations: Annotations that are required for all statements
:param upgrade_urls: Automatically upgrade old namespace URLs. Defaults to false.
.. warning::
These options allow concessions for parsing BEL that is either **WRONG** or **UNSCIENTIFIC**. Use them at
risk to reproducibility and validity of your results.
:param no_identifier_validation: If true, turns off namespace validation
:param allow_naked_names: If true, turns off naked namespace failures
:param allow_redefinition: If true, doesn't fail on second definition of same name or annotation
:param allow_definition_failures: If true, allows parsing to continue if a terminology file download/parse fails
"""
docs, definitions, statements = split_file_to_annotations_and_definitions(lines)
if manager is None:
manager = Manager()
metadata_parser = MetadataParser(
manager,
allow_redefinition=allow_redefinition,
skip_validation=no_identifier_validation,
upgrade_urls=upgrade_urls,
)
parse_document(
graph,
docs,
metadata_parser,
)
parse_definitions(
graph,
definitions,
metadata_parser,
allow_failures=allow_definition_failures,
use_tqdm=use_tqdm,
tqdm_kwargs=tqdm_kwargs,
)
bel_parser = BELParser(
graph=graph,
# terminologies
namespace_to_term_to_encoding=metadata_parser.namespace_to_term_to_encoding,
namespace_to_pattern=metadata_parser.namespace_to_pattern,
annotation_to_term=metadata_parser.annotation_to_term,
annotation_to_pattern=metadata_parser.annotation_to_pattern,
annotation_to_local=metadata_parser.annotation_to_local,
# language settings
disallow_nested=disallow_nested,
citation_clearing=citation_clearing,
skip_validation=no_identifier_validation,
allow_naked_names=allow_naked_names,
disallow_unqualified_translocations=disallow_unqualified_translocations,
required_annotations=required_annotations,
)
parse_statements(
graph,
statements,
bel_parser,
use_tqdm=use_tqdm,
tqdm_kwargs=tqdm_kwargs,
)
logger.info('Network has %d nodes and %d edges', graph.number_of_nodes(), graph.number_of_edges())