def test_model_extend():
ev1 = Evidence(pmid='1234', text='abcd', source_api='x')
ev2 = Evidence(pmid='1234', text='abcde', source_api='x')
ev3 = Evidence(pmid='1234', text='abcd', source_api='x')
indra_sts = [Phosphorylation(None, Agent('a'), evidence=ev) for ev in
[ev1, ev2, ev3]]
emmaa_sts = [EmmaaStatement(st, datetime.datetime.now(), []) for st in
indra_sts]
em = EmmaaModel('x', {'search_terms': [], 'ndex': {'network': None}})
em.add_statements([emmaa_sts[0]])
em.extend_unique(emmaa_sts[1:])
assert len(em.stmts) == 2
stmt = EmmaaStatement(Phosphorylation(None, Agent('b'), evidence=ev1),
datetime.datetime.now(), [])
em.extend_unique([stmt])
assert len(em.stmts) == 3
def test_filter_relevance():
config_dict = {
'ndex': {
'network': 'a08479d1-24ce-11e9-bb6a-0ac135e8bacf'
},
'search_terms': [{
'db_refs': {
'HGNC': '20974'
},
'name': 'MAPK1',
'search_term': 'MAPK1',
'type': 'gene'
}]
}
indra_stmts = \
[Activation(Agent('BRAF', db_refs={'HGNC': '20974'}),
Agent('MAP2K1'),
evidence=[Evidence(text='BRAF activates MAP2K1.',
source_api='assertion')]),
Activation(Agent('MAP2K1',
activity=ActivityCondition('activity', True)),
Agent('MAPK1'),
evidence=[Evidence(text='Active MAP2K1 activates '
'MAPK1.',
source_api='assertion')])
]
st = SearchTerm('gene', 'MAP2K1', db_refs={}, search_term='MAP2K1')
emmaa_stmts = [
EmmaaStatement(stmt, datetime.datetime.now(), [st])
for stmt in indra_stmts
]
# Try no filter first
emmaa_model = EmmaaModel('test', config_dict)
emmaa_model.extend_unique(emmaa_stmts)
emmaa_model.run_assembly()
assert len(emmaa_model.assembled_stmts) == 2, emmaa_model.assembled_stmts
# Next do a prior_one filter
config_dict['assembly'] = {'filter_relevance': 'prior_one'}
emmaa_model = EmmaaModel('test', config_dict)
emmaa_model.extend_unique(emmaa_stmts)
emmaa_model.run_assembly()
assert len(emmaa_model.assembled_stmts) == 1, emmaa_model.assembled_stmts
assert emmaa_model.assembled_stmts[0].obj.name == 'MAPK1'
# Next do a prior_all filter
config_dict['assembly'] = {'filter_relevance': 'prior_all'}
emmaa_model = EmmaaModel('test', config_dict)
emmaa_model.extend_unique(emmaa_stmts)
emmaa_model.run_assembly()
assert len(emmaa_model.assembled_stmts) == 0