def test_replace_agent_one(): m = MRA() m.build_model_from_text('BRAF binds MEK1.') m.replace_agent('BRAF', ['RAF1'], 1) assert(len(m.statements) == 1) assert(len(m.statements[0]) == 1) assert((m.statements[0][0].members[0].name == 'RAF1') or\ (m.statements[0][0].members[1].name == 'RAF1'))
def test_build_model_from_text(): m = MRA() model = m.build_model_from_text('MEK1 phosphorylates ERK2.') assert (model is not None) assert (len(m.statements) == 1) assert (len(m.statements[0]) == 1) assert (isinstance(m.statements[0][0], indra.statements.Phosphorylation)) assert (m.statements[0][0].enz.name == 'MAP2K1') assert (m.statements[0][0].sub.name == 'MAPK1')
def test_build_model_from_text(): m = MRA() model = m.build_model_from_text('MEK1 phosphorylates ERK2.') assert(model is not None) assert(len(m.statements) == 1) assert(len(m.statements[0]) == 1) assert(isinstance(m.statements[0][0], indra.statements.Phosphorylation)) assert(m.statements[0][0].enz.name == 'MAP2K1') assert(m.statements[0][0].sub.name == 'MAPK1')
def test_build_model_from_ekb(): m = MRA() html = trips_client.send_query('MEK1 phosphorylates ERK2.') ekb_xml = trips_client.get_xml(html) model = m.build_model_from_ekb(ekb_xml) assert (model is not None) assert (len(m.statements[0]) == 1) assert (isinstance(m.statements[0][0], indra.statements.Phosphorylation)) assert (m.statements[0][0].enz.name == 'MAP2K1') assert (m.statements[0][0].sub.name == 'MAPK1')
def test_build_model_from_ekb(): m = MRA() html = trips_client.send_query('MEK1 phosphorylates ERK2.') ekb_xml = trips_client.get_xml(html) model = m.build_model_from_ekb(ekb_xml) assert(model is not None) assert(len(m.statements[0]) == 1) assert(isinstance(m.statements[0][0], indra.statements.Phosphorylation)) assert(m.statements[0][0].enz.name == 'MAP2K1') assert(m.statements[0][0].sub.name == 'MAPK1')
def test_build_model_from_ekb(): m = MRA() html = trips_client.send_query('MAP2K1 phosphorylates ERK2.') ekb_xml = trips_client.get_xml(html) res = m.build_model_from_ekb(ekb_xml) assert (res.get('model')) assert (res.get('model_id') == 1) assert (res.get('model_exec')) assert (len(m.models[1]) == 1) assert (isinstance(m.models[1][0], Phosphorylation)) assert (m.models[1][0].enz.name == 'MAP2K1') assert (m.models[1][0].sub.name == 'MAPK1')
def test_get_upstream(): m = MRA() egfr = Agent('EGFR', db_refs={'HGNC': '3236', 'TEXT': 'EGFR'}) kras = Agent('KRAS', db_refs={'HGNC': '6407', 'TEXT': 'KRAS'}) stmts = [Activation(egfr, kras)] model_id = m.new_model(stmts) upstream = m.get_upstream(kras, model_id) assert (len(upstream) == 1) assert (upstream[0].name == 'EGFR') mm = MRA_Module(testing=True) mm.mra = m kras_term = ekb_from_agent(kras) msg = KQMLList('MODEL-GET-UPSTREAM') msg.sets('target', kras_term) msg.set('model-id', str(model_id)) print(msg) reply = mm.respond_model_get_upstream(msg) ups = reply.get('upstream') assert (len(ups) == 1) print(reply)
def test_replace_agent_one(): m = MRA() m.build_model_from_text('BRAF binds MEK1.') m.replace_agent('BRAF', ['RAF1'], 1) assert (len(m.statements) == 1) assert (len(m.statements[0]) == 1) assert((m.statements[0][0].members[0].name == 'RAF1') or\ (m.statements[0][0].members[1].name == 'RAF1'))
def test_has_mechanism(): m = MRA() ekb = '<ekb><EVENT id="V33716"><type>ONT::BIND</type><arg1 id="V33712" role=":AGENT" /><arg2 id="V33734" role=":AFFECTED" /></EVENT><TERM id="V33712" dbid="HGNC:1097|NCIT:C51194|NCIT:C17476"><features></features><type>ONT::GENE-PROTEIN</type><name>BRAF</name></TERM><TERM id="V33734" dbid="NCIT:C52823|NCIT:C105947|NCIT:C17808|HGNC:6840|UP:Q91447|UP:Q05116"><features></features><type>ONT::GENE-PROTEIN</type><name>MEK-1</name></TERM></ekb>' m.build_model_from_ekb(ekb) has_mechanism = m.has_mechanism(ekb, 1) assert (has_mechanism)
def test_find_family_members_id(): m = MRA() family_members = m.find_family_members('', family_id='FA:03114') assert (family_members is not None) assert (len(family_members) == 3) assert ('BRAF' in family_members)
def test_find_family_members_name(): m = MRA() family_members = m.find_family_members('Raf') assert (family_members is not None) assert (len(family_members) == 3) assert ('BRAF' in family_members)
def test_has_mechanism(): m = MRA() ekb = '<ekb><EVENT id="V33716"><type>ONT::BIND</type><arg1 id="V33712" role=":AGENT" /><arg2 id="V33734" role=":AFFECTED" /></EVENT><TERM id="V33712" dbid="HGNC:1097|NCIT:C51194|NCIT:C17476"><features></features><type>ONT::GENE-PROTEIN</type><name>BRAF</name></TERM><TERM id="V33734" dbid="NCIT:C52823|NCIT:C105947|NCIT:C17808|HGNC:6840|UP:Q91447|UP:Q05116"><features></features><type>ONT::GENE-PROTEIN</type><name>MEK-1</name></TERM></ekb>' m.build_model_from_ekb(ekb) has_mechanism = m.has_mechanism(ekb, 1) assert(has_mechanism)
def test_find_family_members_id(): m = MRA() family_members = m.find_family_members('', family_id='FA:03114') assert(family_members is not None) assert(len(family_members) == 3) assert('BRAF' in family_members)
def test_find_family_members_name(): m = MRA() family_members = m.find_family_members('Raf') assert(family_members is not None) assert(len(family_members) == 3) assert('BRAF' in family_members)