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 remove_unused_annotation_metadata(graph) -> None:
used_annotations = get_annotations(graph)
unused_patterns = set(graph.annotation_pattern) - used_annotations
for annotation in unused_patterns:
logger.warning('deleting unused annotation pattern: %s', annotation)
del graph.annotation_pattern[annotation]
unused_urls = set(graph.annotation_pattern) - used_annotations
for annotation in unused_urls:
logger.warning('deleting unused annotation URL: %s', annotation)
del graph.annotation_url[annotation]
unused_lists = set(graph.annotation_list) - used_annotations
for annotation in unused_lists:
logger.warning('deleting unused annotation list: %s', annotation)
del graph.annotation_list[annotation]
