def test_yaml_hm(): yml = load_yaml_from_url(eidos_ont_url) hm = YamlHierarchyManager(yml, rdf_graph_from_yaml) entry = 'UN/events/natural_disaster/snowpocalypse' hm.add_entry(entry) assert hm.isa('UN', entry, 'UN', '/'.join(entry.split('/')[:-1])) entry = 'UN/events/galactic/alien_invasion' hm.add_entry(entry) assert hm.isa('UN', entry, 'UN', '/'.join(entry.split('/')[:-1])) assert hm.isa('UN', entry, 'UN', '/'.join(entry.split('/')[:-2]))
def _make_un_ontology(): return YamlHierarchyManager(load_yaml_from_url(eidos_ont_url), rdf_graph_from_yaml, True)
from indra.tools import assemble_corpus as ac from indra.sources.eidos import migration_table_processor as mtp from indra.preassembler.hierarchy_manager import YamlHierarchyManager from indra.preassembler.make_eidos_hume_ontologies import load_yaml_from_url, \ rdf_graph_from_yaml from indra.preassembler.custom_preassembly import location_time_delta_matches, \ location_time_delta_refinement from indra.belief.wm_scorer import get_eidos_scorer wm_ont_url = ('https://raw.githubusercontent.com/WorldModelers/'\ 'Ontologies/master/wm.yml') if __name__ == '__main__': fname = 'grounded CAG links - New Ontology.xlsx' stmts = mtp.process_workbook(fname) hm = YamlHierarchyManager(load_yaml_from_url(wm_ont_url), rdf_graph_from_yaml, True) stmts = ac.run_preassembly(stmts, return_toplevel=False, belief_score=get_eidos_scorer(), hierarchies={'entity': hm}, matches_fun=location_time_delta_matches, refinement_fun=location_time_delta_refinement) stmts = ac.standardize_names_groundings(stmts)