def test_from_source_entity_filter():
# Kinases
finder = msa.FromSource(Agent('MEK', db_refs={'FPLX': 'MEK'}),
ent_type='kinase',
persist=False)
oa = finder.get_other_agents(block=True)
oa_names = [a.name for a in oa]
# RAF1 as a kinase is in the list
assert 'MAPK1' in oa_names
# RAS, which normally is in the list should not be since it's not a kinase
assert 'apoptosis' not in oa_names
assert 'RAS' not in oa_names
# Transcription factors
finder = msa.FromSource(Agent('MEK', db_refs={'FPLX': 'MEK'}),
ent_type='transcription factor',
persist=False)
oa = finder.get_other_agents(block=True)
oa_names = [a.name for a in oa]
assert 'ESR1' in oa_names
assert 'RAF1' not in oa_names
# Proteins
finder = msa.FromSource(Agent('MEK', db_refs={'FPLX': 'MEK'}),
ent_type='protein',
persist=False)
oa = finder.get_other_agents(block=True)
oa_names = [a.name for a in oa]
assert 'ERK' in oa_names
assert 'MAPK1' in oa_names
assert 'apoptosis' not in oa_names
assert 'proliferation' not in oa_names
def test_from_source_agent_filter():
cdk12 = Agent('CDK12', db_refs={'HGNC': '24224'})
samhd1 = Agent('SAMHD1', db_refs={'HGNC': '15925'})
ezh2 = Agent('EZH2', db_refs={'HGNC': '3527'})
finder = msa.FromSource(cdk12, filter_agents=[samhd1, ezh2])
stmts = finder.get_statements()
assert len(stmts)
exp_ags = {'SAMHD1', 'EZH2'}
for stmt in stmts:
ag_names = {ag.name for ag in stmt.agent_list() if ag is not None}
assert ag_names & exp_ags, ag_names - exp_ags
summ = finder.summarize()
assert 'EZH2' in {a.name for a in summ['other_agents']}, summ
desc = finder.describe()
assert re.match(r'Overall, I found that CDK12 can affect '
r'EZH2. Here are the statements.*', desc), desc