def test_load_sofia_hierarchy():
sofia_ont = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../sources/sofia/sofia_ontology.rdf')
hm = HierarchyManager(sofia_ont, True, True)
assert hm.isa_closure
sofia_isa = lambda a, b: hm.isa('SOFIA', a, 'SOFIA', b)
assert sofia_isa('Accessibility/Accessibility', 'Accessibility')
assert not sofia_isa('Movement/Transportation', 'Movement/Human_Migration')
assert sofia_isa('Movement/Human_Migration', 'Movement')
def test_load_hume_hierarchy():
hume_ont = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../sources/hume/hume_ontology.rdf')
hm = HierarchyManager(hume_ont, True, True)
assert hm.isa_closure
hume_isa = lambda a, b: hm.isa('HUME', a, 'HUME', b)
assert hume_isa('entity/academic_discipline', 'entity')
assert not hume_isa('entity', 'entity/academic_discipline')
assert hume_isa('event/healthcare/human_disease',
'event/healthcare')
def test_load_trips_hierarchy():
trips_ont = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../sources/cwms/trips_ontology.rdf')
hm = HierarchyManager(trips_ont, True, True)
assert hm.isa_closure
trips_isa = lambda a, b: hm.isa('CWMS', a, 'CWMS', b)
assert trips_isa('ONT::TRUCK', 'ONT::VEHICLE')
assert not trips_isa('ONT::VEHICLE', 'ONT::TRUCK')
assert trips_isa('ONT::MONEY', 'ONT::PHYS-OBJECT')
assert trips_isa('ONT::TABLE', 'ONT::MANUFACTURED-OBJECT')
def test_influence_duplicate():
gov = 'UN/entities/human/government/government_entity'
agr = 'UN/entities/natural/crop_technology'
cgov = Event(Concept('government', db_refs={'UN': [(gov, 1.0)]}))
cagr = Event(Concept('agriculture', db_refs={'UN': [(agr, 1.0)]}))
stmt1 = Influence(cgov, cagr, evidence=[Evidence(source_api='eidos1')])
stmt2 = Influence(cagr, cgov, evidence=[Evidence(source_api='eidos2')])
stmt3 = Influence(cgov, cagr, evidence=[Evidence(source_api='eidos3')])
eidos_ont = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../sources/eidos/eidos_ontology.rdf')
hm = HierarchyManager(eidos_ont, True, True)
hierarchies = {'entity': hm}
pa = Preassembler(hierarchies, [stmt1, stmt2, stmt3])
unique_stmts = pa.combine_duplicates()
assert len(unique_stmts) == 2
assert len(unique_stmts[0].evidence) == 2
assert len(unique_stmts[1].evidence) == 1
sources = [e.source_api for e in unique_stmts[0].evidence]
assert set(sources) == set(['eidos1', 'eidos3'])
def test_influence_refinement():
tran = 'UN/entities/human/infrastructure/transportation'
truck = 'UN/entities/human/infrastructure/transportation/' + \
'transportation_methods'
agr = 'UN/entities/human/livelihood'
ctran = Concept('transportation', db_refs={'UN': [(tran, 1.0)]})
ctruck = Concept('trucking', db_refs={'UN': [(truck, 1.0)]})
cagr = Concept('agriculture', db_refs={'UN': [(agr, 1.0)]})
stmt1 = Influence(ctran, cagr, evidence=[Evidence(source_api='eidos1')])
stmt2 = Influence(ctruck, cagr, evidence=[Evidence(source_api='eidos2')])
stmt3 = Influence(cagr, ctran, evidence=[Evidence(source_api='eidos3')])
eidos_ont = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../sources/eidos/eidos_ontology.rdf')
hm = HierarchyManager(eidos_ont, True, True)
hierarchies = {'entity': hm}
pa = Preassembler(hierarchies, [stmt1, stmt2, stmt3])
rel_stmts = pa.combine_related()
assert len(rel_stmts) == 2
truck_stmt = [st for st in rel_stmts if st.subj.name == 'trucking'][0]
assert len(truck_stmt.supported_by) == 1
assert truck_stmt.supported_by[0].subj.name == 'transportation'
def test_association_duplicate():
ev1 = Event(Concept('a'))
ev2 = Event(Concept('b'))
ev3 = Event(Concept('c'))
# Order of members does not matter
st1 = Association([ev1, ev2], evidence=[Evidence(source_api='eidos1')])
st2 = Association([ev1, ev3], evidence=[Evidence(source_api='eidos2')])
st3 = Association([ev2, ev1], evidence=[Evidence(source_api='eidos3')])
st4 = Association([ev2, ev3], evidence=[Evidence(source_api='eidos4')])
st5 = Association([ev2, ev3], evidence=[Evidence(source_api='eidos5')])
eidos_ont = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../sources/eidos/eidos_ontology.rdf')
hm = HierarchyManager(eidos_ont, True, True)
hierarchies = {'entity': hm}
pa = Preassembler(hierarchies, [st1, st2, st3, st4, st5])
unique_stmts = pa.combine_duplicates()
assert len(unique_stmts) == 3
assert len(unique_stmts[0].evidence) == 2
assert len(unique_stmts[1].evidence) == 1
assert len(unique_stmts[2].evidence) == 2
sources = [e.source_api for e in unique_stmts[0].evidence]
assert set(sources) == set(['eidos1', 'eidos3'])
def _agent_from_uri(uri):
ag_ns, ag_id = HierarchyManager.ns_id_from_uri(uri)
agent = _agent_from_ns_id(ag_ns, ag_id)
return agent
def test_load_eid_hierarchy():
eidos_ont = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../sources/eidos/eidos_ontology.rdf')
eidos_ns = 'https://github.com/clulab/eidos/wiki/JSON-LD/Grounding#'
hm = HierarchyManager(eidos_ont, True, True)
assert hm.isa_closure
eidos_isa = lambda a, b: hm.isa('UN', a, 'UN', b)
assert eidos_isa('UN/events/human/conflict',
'UN/events/human')
assert not eidos_isa('UN/events/human/conflict',
'UN/events/human/human_migration')
assert eidos_isa('UN/entities/human/infrastructure',
'UN/entities')
assert eidos_isa('UN/events/natural_disaster/storm',
'UN/events')
assert not eidos_isa('UN/events',
'UN/events/natural/weather/storm')
# Test case where graph is not given
hm = HierarchyManager(None, True, True)
hm.load_from_rdf_file(eidos_ont)
assert eidos_isa('UN/events/natural_disaster/storm',
'UN/events')
# Test loading from string
with open(eidos_ont, 'r') as fh:
hm = HierarchyManager(None, True, True)
hm.load_from_rdf_string(fh.read())
assert eidos_isa('UN/events/natural_disaster/storm',
'UN/events')
# Test loading from Graph
import rdflib
g = rdflib.Graph()
g.parse(eidos_ont, format='nt')
hm = HierarchyManager(None, True, True)
hm.load_from_rdf_graph(g)
assert eidos_isa('UN/events/natural_disaster/storm',
'UN/events')
import os
from indra.preassembler.hierarchy_manager import HierarchyManager
# Make a TRIPS ontology
_fname = os.path.join(os.path.dirname(__file__), 'trips_ontology.rdf')
trips_ontology = HierarchyManager(_fname,
uri_as_name=False,
build_closure=True)
trips_ontology.relations_prefix = 'http://trips.ihmc.us/relations/'
trips_ontology.initialize()
def trips_isa(concept1, concept2):
# Preprocess to make this more general
concept1 = concept1.lower().replace('ont::', '')
concept2 = concept2.lower().replace('ont::', '')
if concept1 == concept2:
return True
isa = trips_ontology.isa('http://trips.ihmc.us/concepts/', concept1,
'http://trips.ihmc.us/concepts/', concept2)
return isa
def test_load_eid_hierarchy():
eidos_ont = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../sources/eidos/eidos_ontology.rdf')
eidos_ns = 'https://github.com/clulab/eidos/wiki/JSON-LD/Grounding#'
hm = HierarchyManager(eidos_ont, True, True)
assert hm.isa_closure
eidos_isa = lambda a, b: hm.isa('UN', a, 'UN', b)
assert eidos_isa('UN/events/human/conflict', 'UN/events/human')
assert not eidos_isa('UN/events/human/conflict',
'UN/events/human/human_migration')
assert eidos_isa('UN/entities/human/infrastructure', 'UN/entities')
assert eidos_isa('UN/events/natural_disaster/storm', 'UN/events')
assert not eidos_isa('UN/events', 'UN/events/natural/weather/storm')
# Test case where graph is not given
hm = HierarchyManager(None, True, True)
hm.load_from_rdf_file(eidos_ont)
assert eidos_isa('UN/events/natural_disaster/storm', 'UN/events')
# Test loading from string
with open(eidos_ont, 'r') as fh:
hm = HierarchyManager(None, True, True)
hm.load_from_rdf_string(fh.read())
assert eidos_isa('UN/events/natural_disaster/storm', 'UN/events')
# Test loading from Graph
import rdflib
g = rdflib.Graph()
g.parse(eidos_ont, format='nt')
hm = HierarchyManager(None, True, True)
hm.load_from_rdf_graph(g)
assert eidos_isa('UN/events/natural_disaster/storm', 'UN/events')