def ground(
graph: BELGraph,
remove_ungrounded: bool = True,
skip_namespaces: Optional[Collection[str]] = None,
) -> BELGraph:
"""Ground all entities in a BEL graph."""
j = to_nodelink(graph)
ground_nodelink(j, skip_namespaces=skip_namespaces)
graph = from_nodelink(j)
remove_unused_annotation_metadata(graph)
if remove_ungrounded:
ungrounded_nodes = {
node
for node in get_ungrounded_nodes(graph) if
not isinstance(node, BaseConcept) or node.namespace not in NO_NAMES
}
graph.remove_nodes_from(ungrounded_nodes)
graph.namespace_url.clear()
graph.namespace_pattern.clear()
graph.namespace_pattern.update(
{namespace: '.*'
for namespace in get_namespaces(graph)})
graph.annotation_url.clear()
graph.annotation_pattern.clear()
graph.annotation_list.clear()
graph.annotation_pattern.update(
{annotation: '.*'
for annotation in get_annotations(graph)})
return graph
def test_convert_json(self, mock_get):
with self.runner.isolated_filesystem():
test_json = os.path.abspath('test.json')
args = [
'convert', '--path', test_bel_thorough, '--json', test_json,
'--connection', self.connection, '--allow-nested'
]
result = self.runner.invoke(cli.main, args)
self.assertEqual(0, result.exit_code, msg=result.exc_info)
with open(test_json) as f:
self.bel_thorough_reconstituted(from_nodelink(json.load(f)))