def get_bel(repo: Repo, branch: str, manager: Optional[Manager] = None, use_tqdm: bool = False) -> BELGraph:
"""Get the BEL graph for the first BEL document found."""
line_groups = list(get_bel_lines(repo, branch))
file_name, lines = line_groups[0]
graph = BELGraph(path=file_name)
parse_lines(graph=graph, lines=lines, manager=manager, use_tqdm=use_tqdm)
return graph
def test_thorough_upgrade(self):
lines = to_bel_script_lines(self.thorough_graph, use_identifiers=True)
reconstituted = BELGraph()
parse_lines(reconstituted, lines, manager=self.manager)
self.bel_thorough_reconstituted(reconstituted,
check_citation_name=False,
check_path=False)
def test_isolated_upgrade(self):
lines = to_bel_script_lines(self.isolated_graph)
with mock_bel_resources:
reconstituted = BELGraph()
parse_lines(graph=reconstituted, lines=lines, manager=self.manager)
self.bel_isolated_reconstituted(reconstituted)
def parse_graph(report: Report, manager: Manager, task: Task) -> BELGraph:
"""Parse a graph from a report while keeping a celery :class:`Task` informed of progress."""
lines = iterate_report_lines_in_task(report, task)
graph = BELGraph()
parse_lines(
graph=graph,
lines=lines,
manager=manager,
citation_clearing=report.citation_clearing,
no_identifier_validation=not report.identifier_validation,
)
return graph
