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 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)