def test_msa_custom_corpus_stmt_type():
# Create a pickle with a test statement
test_corpus = 'test_corpus2.pkl'
kras = Agent('KRAS', db_refs={'HGNC': '6407'})
st1 = Phosphorylation(Agent('x'), kras)
st2 = Inhibition(Agent('y'), kras)
st3 = Activation(Agent('z'), kras)
with open(test_corpus, 'wb') as fh:
pickle.dump([st1, st2, st3], fh)
# Instantiate MSA with that pickle as the corpus
msa = MSA(corpus_config='pickle:%s' % test_corpus)
# Query the MSA
finder = msa.find_mechanisms('to_target',
target=kras,
verb='activate')
# Make sure we got the original statement back
res_stmts = finder.get_statements()
assert res_stmts[0].__class__.__name__ == 'Activation'
assert res_stmts[0].subj.name == 'z'
finder = msa.find_mechanisms('to_target',
target=kras,
verb='phosphorylate')
# Make sure we got the original statement back
res_stmts = finder.get_statements()
assert res_stmts[0].__class__.__name__ == "Phosphorylation"
assert res_stmts[0].enz.name == 'x'
def test_statements_from_neo4j():
user = os.environ.get('INDRA_NEO4J_USER')
pw = os.environ.get('INDRA_NEO4J_PASSWORD')
url = os.environ.get('INDRA_NEO4J_URL')
config = 'neo4j:bolt://%s:%s@%s' % (user, pw, url)
msa = MSA(corpus_config=config)
kras = Agent('KRAS', db_refs={'HGNC': '6407'})
finder = msa.find_mechanisms('to_target', target=kras, verb='activate')
res_stmts = finder.get_statements()
assert len(res_stmts) > 1000
assert isinstance(res_stmts[0], Activation)
finder = msa.find_mechanisms('from_source', source=kras, verb='activate')
res_stmts = finder.get_statements()
assert len(res_stmts) > 1000
assert isinstance(res_stmts[0], Activation)
def test_valid_keys_no_text():
# We test that an agent with just a PUBCHEM ID can still be queried
msa = MSA()
ag = Agent('vemurafenib', db_refs={'PUBCHEM': '42611257'})
finder = msa.find_mechanisms('from_source', ag)
stmts = finder.get_statements(block=True)
assert stmts
def test_get_finder_agents():
msa = MSA()
ag = Agent('SOCS1', db_refs={'HGNC': '19383'})
finder = msa.find_mechanisms('to_target', ag, verb='phosphorylate')
other_agents = finder.get_other_agents()
assert all(isinstance(a, Agent) for a in other_agents)
# The other names should be sorted with PIM1 first (most evidence)
assert other_agents[0].name == 'PIM1'
fixed_agents = finder.get_fixed_agents()
assert 'object' in fixed_agents, fixed_agents
assert fixed_agents['object'][0].name == 'SOCS1', fixed_agents['target']
def test_msa_custom_corpus():
# Create a pickle with a test statement
test_corpus = 'test_corpus.pkl'
stmt = Phosphorylation(Agent('XXXX'),
Agent('YYYY', db_refs={'HGNC': '1'}))
with open(test_corpus, 'wb') as fh:
pickle.dump([stmt], fh)
# Instantiate MSA with that pickle as the corpus
msa = MSA(corpus_config='pickle:%s' % test_corpus)
# Query the MSA
finder = msa.find_mechanisms('to_target',
target=Agent('YYYY', db_refs={'HGNC': '1'}))
# Make sure we got the original statement back
res_stmts = finder.get_statements()
assert res_stmts[0].matches(stmt)
# Now try a modified query
finder = msa.find_mechanisms('to_target',
target=Agent('ERK', db_refs={'FPLX': 'ERK'}))
# Make sure we don't get anything
res_stmts = finder.get_statements()
assert not res_stmts