def create_message2(self):
drug = agent_clj_from_text('Vemurafenib')
content = KQMLList('FIND-DRUG-TARGETS')
content.set('drug', drug)
kagents = KQMLList([agent_clj_from_text('RAF1')])
content.set('filter_agents', kagents)
return get_request(content), content
def create_message_failure(self):
content = KQMLList('FIND-MUTATION-SIGNIFICANCE')
gene = agent_clj_from_text('ACTN4')
disease = agent_clj_from_text('abc cancer')
content.set('gene', gene)
content.set('disease', disease)
msg = get_request(content)
return msg, content
def create_message_PAAD(self):
content = KQMLList('FIND-MUTATION-SIGNIFICANCE')
gene = agent_clj_from_text('ACTN4')
disease = agent_clj_from_text('pancreatic adenocarcinoma')
content.set('gene', gene)
content.set('disease', disease)
msg = get_request(content)
return msg, content
def create_message(self):
content = KQMLList('FIND-MUTEX')
gene = agent_clj_from_text('TP53')
disease = agent_clj_from_text('breast cancer')
content.set('gene', gene)
content.set('disease', disease)
msg = get_request(content)
return msg, content
def create_message_failure(self):
content = KQMLList('FIND-COMMON-UPSTREAMS')
genes = KQMLList(
[agent_clj_from_text('UGT2B10'),
agent_clj_from_text('PTEN')])
content.set('genes', genes)
msg = get_request(content)
return msg, content
def create_message_OV(self):
content = KQMLList('FIND-MUTATION-FREQUENCY')
gene = agent_clj_from_text('TP53')
disease = agent_clj_from_text('Ovarian serous cystadenocarcinoma')
content.set('gene', gene)
content.set('disease', disease)
msg = get_request(content)
return msg, content
def create_message_failure(self):
source = agent_clj_from_text('MAPK1')
target = agent_clj_from_text('RAS')
content = KQMLList('FIND-CAUSAL-PATH')
content.set('source', source)
content.set('target', target)
content.sets('direction', 'both')
msg = get_request(content)
return msg, content
def create_message_3(self):
content = KQMLList('FIND-CELLULAR-LOCATION')
genes = KQMLList(
[agent_clj_from_text('AKT1'),
agent_clj_from_text('MAPK1')])
content.set('genes', genes)
msg = get_request(content)
return msg, content
def create_message(self):
content = KQMLList('FIND-COMMON-UPSTREAMS')
genes = KQMLList([
agent_clj_from_text('AKT1'),
agent_clj_from_text('BRAF'),
agent_clj_from_text('MAPK1')
])
content.set('genes', genes)
msg = get_request(content)
return msg, content
def create_message(self):
target = agent_clj_from_text(self.target)
content = KQMLList('FIND-TARGET-DRUG')
content.set('target', target)
st = agent_clj_from_text('Staurosporine')
st.sets('NAME', 'Staurosporine')
print(st)
filter_agents = KQMLList([st])
content.set('filter_agents', filter_agents)
return get_request(content), content
def create_message_1(self):
content = KQMLList('FIND-VARIANTS-FOR-GENES')
genes = KQMLList(
[agent_clj_from_text('EGFR'),
agent_clj_from_text('PTEN')])
content.set('genes', genes)
disease = agent_clj_from_text('glioblastoma')
content.set('disease', disease)
content.sets('dataset', "tcga")
msg = get_request(content)
return msg, content
def create_message(self):
target = agent_clj_from_text('BRAF')
content = KQMLList('FIND-CAUSALITY-SOURCE')
content.set('target', target)
content.sets('type', 'phosphorylation')
msg = get_request(content)
return msg, content
def create_message_AKT1(self):
content = KQMLList('FIND-GENE-SUMMARY')
genes = agent_clj_from_text('AKT1')
content.set('gene', genes)
msg = get_request(content)
return msg, content
def create_message_05_explainable_again(self):
time.sleep(2)
source = agent_clj_from_text('AKT1')
content = KQMLList('DATASET-CORRELATED-ENTITY')
content.set('source', source)
msg = get_request(content)
return msg, content
def create_message_failure(self):
target = agent_clj_from_text('BRAF')
content = KQMLList('FIND-CAUSALITY-SOURCE')
content.set('target', target)
content.sets('type', 'activates')
msg = get_request(content)
return msg, content
def create_message_failure(self):
source = agent_clj_from_text('MAPK1')
content = KQMLList('FIND-CAUSALITY-TARGET')
content.set('source', source)
content.sets('type', 'activation')
msg = get_request(content)
return msg, content
def test_get_synonyms_chemical():
"""raises InvalidAgentError when the agent is not recognized or if the
input submitted is not valid XML or is not in the correct format
"""
synonyms = bs.get_synonyms(
Bioagent.get_agent(agent_clj_from_text('vemurafenib')))
assert synonyms
def create_message_1(self):
content = KQMLList('FIND-DRUGS-FOR-MUTATION-DATASET')
genes = agent_clj_from_text('TP53')
content.set('genes', genes)
content.set('dataset', "CTRP")
msg = get_request(content)
return msg, content
def _get_qca_content(task, source, target):
"""Get the KQMLList content to be sent to the QCA for given task.
Paramters
---------
source, target : str
The strings representing the proteins for source and target,
respectively, for example 'BRAF'.
Returns
-------
content : KQMLList
The KQML content to be sent to the QCA module as part of the request.
"""
content = KQMLList(task)
content.set('source', agent_clj_from_text(source))
content.set('target', agent_clj_from_text(target))
return content
def create_message_1(self):
content = KQMLList('GET-VARIANT-INFO')
gene = agent_clj_from_text('TP53')
content.set('gene', gene)
mutation = 'p.S241F'
content.sets('mutation', mutation)
msg = get_request(content)
return msg, content
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 create_message(self):
content = KQMLList('CHOOSE-SENSE')
agent = agent_clj_from_text('BRAF')
content.set('agent', agent)
print(content)
return get_request(content), content
class TestGetIndraRepInactiveRAFActivatesMEK(_GetIndraRepTemplate):
kqml_file = 'Inactive_RAF_activates_MEK.kqml'
def check_result(self, res):
stmts = self.bioagent.get_statement(res)
assert len(stmts) == 1, stmts
stmt = stmts[0]
assert isinstance(stmt, Activation), type(stmt)
assert stmt.subj.name == 'RAF', stmt
assert stmt.subj.activity, stmt
assert not stmt.subj.activity.is_active, stmt
assert stmt.obj.name == 'MEK', stmt
mek1 = agent_clj_from_text('MEK1')
mek1a = Bioagent.get_agent(mek1)
mek = agent_clj_from_text('MEK')
meka = Bioagent.get_agent(mek)
dusp6 = agent_clj_from_text('DUSP6')
dusp6a = Bioagent.get_agent(dusp6)
braf = agent_clj_from_text('BRAF')
brafa = Bioagent.get_agent(braf)
bs = BioSense()
def test_choose_sense_category():
cases = [(mek1a, [('kinase activity', 'TRUE'), ('enzyme', 'TRUE'),
('kinase', 'TRUE'), ('transcription-factor', 'FALSE'),
('W::KINASE', 'TRUE'), ('phosphatase', 'FALSE')]),
def create_message_failure(self):
content = KQMLList('FIND-MUTEX')
gene = agent_clj_from_text('BRAF')
content.set('gene', gene)
msg = get_request(content)
return msg, content
def create_message(self):
target = agent_clj_from_text(self.target)
content = KQMLList('FIND-TARGET-DRUG')
content.set('target', target)
return get_request(content), content
def create_message(self):
disease = agent_clj_from_text('common cold')
content = KQMLList('FIND-TREATMENT')
content.set('disease', disease)
return get_request(content), content
def create_message(self):
disease = agent_clj_from_text('prostate cancer')
content = KQMLList('FIND-DISEASE-TARGETS')
content.set('disease', disease)
return get_request(content), content
def create_message(self):
drug = agent_clj_from_text('SB525334')
content = KQMLList('FIND-DRUG-TARGETS')
content.set('drug', drug)
return get_request(content), content
