def test_respond_choose_nonsense():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('CHOOSE-SENSE')
msg_content.sets('ekb-term', ekb_from_text('bagel'))
res = bs.respond_choose_sense(msg_content)
print(res)
assert res.head() == 'SUCCESS'
assert res.get('agents')[0].gets('ont-type') is None
def test_choose_nonsense():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('CHOOSE-SENSE')
msg_content.sets('ekb-term', ekb_from_text('bagel'))
res = bs.respond_choose_sense(msg_content)
print(res)
assert res.head() == 'SUCCESS'
assert res.get('agents')[0].gets('ont-type') == None
def test_respond_choose_sense():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('CHOOSE-SENSE')
msg_content.set('agent', mek1)
res = bs.respond_choose_sense(msg_content)
agent_clj = res.get('agent')
assert agent_clj
agent = Bioagent.get_agent(agent_clj)
assert agent.name == 'MAP2K1'
assert agent.db_refs['HGNC'] == '6840'
def test_choose_sense_what_member():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('CHOOSE-SENSE-WHAT-MEMBER')
msg_content.sets('collection', mek_ekb)
print(msg_content)
res = bs.respond_choose_sense_what_member(msg_content)
print(res)
print(res.head)
assert (res.head() == 'SUCCESS')
assert (len(res.get('members')) == 2)
def test_choose_sense_category():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('CHOOSE-SENSE-CATEGORY')
msg_content.sets('ekb-term', mek1_ekb)
msg_content.sets('category', 'kinase activity')
res = bs.respond_choose_sense_category(msg_content)
print(res)
print(res.head)
assert (res.head() == 'SUCCESS')
assert (res.get('in-category') == 'TRUE')
def test_respond_choose_nonsense():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('CHOOSE-SENSE')
msg_content.set('agent', agent_clj_from_text('bagel'))
res = bs.respond_choose_sense(msg_content)
print(res)
assert res.head() == 'SUCCESS'
agents_clj = res.get('agent')
agent = Bioagent.get_agent(agents_clj)
assert agent.name == 'BAGEL'
assert len(agent.db_refs) == 1
def test_respond_get_synonyms():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('GET-SYNONYMS')
msg_content.sets('entity', mek1_ekb)
res = bs.respond_get_synonyms(msg_content)
assert res.head() == 'SUCCESS'
syns = res.get('synonyms')
syn_strs = [s.gets(':name') for s in syns]
assert 'MAP2K1' in syn_strs
assert 'MEK1' in syn_strs
assert 'MKK1' in syn_strs
def test_respond_choose_sense_is_member():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('CHOOSE-SENSE-IS-MEMBER')
msg_content.set('ekb-term', mek1)
msg_content.set('collection', mek)
print(msg_content)
res = bs.respond_choose_sense_is_member(msg_content)
print(res)
print(res.head())
assert (res.head() == 'SUCCESS')
assert (res.get('is-member') == 'TRUE')
def test_respond_choose_sense_is_member():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('CHOOSE-SENSE-IS-MEMBER')
msg_content.sets('ekb-term', mek1_ekb)
msg_content.sets('collection', mek_ekb)
print(msg_content)
res = bs.respond_choose_sense_is_member(msg_content)
print(res)
print(res.head())
assert(res.head() == 'SUCCESS')
assert(res.get('is-member') == 'TRUE')
def test_respond_get_synonyms():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('GET-SYNONYMS')
msg_content.set('entity', mek1)
res = bs.respond_get_synonyms(msg_content)
assert res.head() == 'SUCCESS'
syns = res.get('synonyms')
syn_strs = [s.gets(':name') for s in syns]
assert 'MAP2K1' in syn_strs, syn_strs
assert 'MEK1' in syn_strs, syn_strs
assert 'MKK1' in syn_strs, syn_strs
assert res.get('num_synonyms') == '23', res
def test_choose_sense():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('CHOOSE-SENSE')
msg_content.sets('ekb-term', mek1_ekb)
res = bs.respond_choose_sense(msg_content)
print(res)
agents = res.get('agents')
assert agents and agents.data
agent = agents[0]
name = agent.gets('name')
assert name == 'MAP2K1'
ont_type = agent.get('ont-type')
assert ont_type == 'ONT::GENE'
def test_respond_choose_sense():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('CHOOSE-SENSE')
msg_content.sets('ekb-term', mek1_ekb)
res = bs.respond_choose_sense(msg_content)
print(res)
agents = res.get('agents')
assert agents and agents.data
agent = agents[0]
name = agent.gets('name')
assert name == 'MAP2K1'
ont_type = agent.get('ont-type')
assert ont_type == 'ONT::GENE'
def test_respond_choose_sense_what_member():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('CHOOSE-SENSE-WHAT-MEMBER')
msg_content.sets('collection', mek_ekb)
print(msg_content)
res = bs.respond_choose_sense_what_member(msg_content)
print(res)
print(res.head())
assert(res.head() == 'SUCCESS')
assert(len(res.get('members')) == 2)
m1 = res.get('members')[0]
m2 = res.get('members')[1]
assert m1.gets('name') == 'MAP2K1', m1.gets('name')
assert m2.gets('name') == 'MAP2K2', m2.gets('name')
def test_respond_choose_sense_what_member():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('CHOOSE-SENSE-WHAT-MEMBER')
msg_content.set('collection', mek)
print(msg_content)
res = bs.respond_choose_sense_what_member(msg_content)
print(res)
print(res.head())
assert (res.head() == 'SUCCESS')
assert (len(res.get('members')) == 2)
m1 = res.get('members')[0]
m2 = res.get('members')[1]
a1 = Bioagent.get_agent(m1)
a2 = Bioagent.get_agent(m2)
assert a1.name == 'MAP2K1'
assert a2.name == 'MAP2K2'
assert a2.db_refs['HGNC'] == '6842'
assert a1.db_refs['UP'] == 'Q02750'
def test_respond_choose_sense_category():
bs = BioSense_Module(testing=True)
cases = [(mek1, [('kinase activity', 'TRUE'), ('enzyme', 'TRUE'),
('kinase', 'TRUE'), ('transcription-factor', 'FALSE'),
('W::KINASE', 'TRUE'), ('phosphatase', 'FALSE')]),
(dusp6, [('phosphatase', 'TRUE'), ('enzyme', 'TRUE')]),
(braf, [('kinase', 'TRUE')])]
for agent_clj, result_tuples in cases:
msg_content = KQMLList('CHOOSE-SENSE-CATEGORY')
msg_content.set('ekb-term', agent_clj)
for cat, result in result_tuples:
print('Testing: %s. Excpet result %s.' % (cat, result))
msg_content.sets('category', cat)
res = bs.respond_choose_sense_category(msg_content)
print(res)
print(res.head())
assert (res.head() == 'SUCCESS')
assert (res.get('in-category') == result)
def test_choose_sense_category():
bs = BioSense_Module(testing=True)
msg_content = KQMLList('CHOOSE-SENSE-CATEGORY')
msg_content.sets('ekb-term', mek1_ekb)
for cat, result in [('kinase activity', 'TRUE'), ('enzyme', 'TRUE'),
('kinase', 'TRUE'), ('transcription-factor', 'FALSE'),
('W::KINASE', 'TRUE'), ('phosphatase', 'FALSE')]:
print('Testing: %s. Excpet result %s.' % (cat, result))
msg_content.sets('category', cat)
res = bs.respond_choose_sense_category(msg_content)
print(res)
print(res.head())
assert (res.head() == 'SUCCESS')
assert (res.get('in-category') == result)
msg_content = KQMLList('CHOOSE-SENSE-CATEGORY')
msg_content.sets('ekb-term', ekb_from_text('BRAF'))
msg_content.sets('category', 'kinase')
res = bs.respond_choose_sense_category(msg_content)
print(res)
assert res.head() == 'SUCCESS'
def test_respond_choose_sense_category():
bs = BioSense_Module(testing=True)
cases = [(mek1_ekb, [('kinase activity', 'TRUE'),
('enzyme', 'TRUE'),
('kinase', 'TRUE'),
('transcription-factor', 'FALSE'),
('W::KINASE', 'TRUE'),
('phosphatase', 'FALSE')]),
(dusp_ekb, [('phosphatase', 'TRUE'), ('enzyme', 'TRUE')]),
(ekb_from_text('BRAF'), [('kinase', 'TRUE')])]
for ekb, result_tuples in cases:
msg_content = KQMLList('CHOOSE-SENSE-CATEGORY')
msg_content.sets('ekb-term', ekb)
for cat, result in result_tuples:
print('Testing: %s. Excpet result %s.' % (cat, result))
msg_content.sets('category', cat)
res = bs.respond_choose_sense_category(msg_content)
print(res)
print(res.head())
assert(res.head() == 'SUCCESS')
assert(res.get('in-category') == result)