def create_message(self):
txt = 'Selumetinib decreases FOS in BT20 cells'
explain = stmts_clj_from_text(txt)
explain_stmt = self.bioagent.get_statement(explain)[0]
assert explain_stmt.evidence[0].context, explain_stmt.evidence[0]
content = KQMLList('USER-GOAL')
content.set('explain', explain)
msg = get_request(content)
return msg, content
def _get_build_model_request(text, format=None):
content = KQMLList('BUILD-MODEL')
if format == 'ekb':
descr = ekb_kstring_from_text(text)
content.sets('description', descr)
content.sets('format', 'ekb')
else:
descr = stmts_clj_from_text(text)
content.set('description', descr)
return get_request(content), content
def test_respond_model_get_upstream():
mm = MRA_Module(testing=True)
egfr = sts.Agent('EGFR', db_refs={'HGNC': '3236', 'TEXT': 'EGFR'})
kras = sts.Agent('KRAS', db_refs={'HGNC': '6407', 'TEXT': 'KRAS'})
stmts = [sts.Activation(egfr, kras)]
model_id = mm.mra.new_model(stmts)
kras_term = ekb_from_agent(kras)
msg = KQMLList('MODEL-GET-UPSTREAM')
msg.sets('target', kras_term)
msg.set('model-id', str(model_id))
reply = mm.respond_model_get_upstream(msg)
ups = reply.get('upstream')
assert(len(ups) == 1)
def test_respond_expand_model_from_json():
mm = MRA_Module(testing=True)
st = sts.Phosphorylation(sts.Agent('MEK'), sts.Agent('ERK'))
msg = KQMLList('BUILD-MODEL')
msg.sets('description', json.dumps(sts.stmts_to_json([st])))
msg.sets('format', 'indra_json')
reply = mm.respond_build_model(msg)
assert (reply.get('model'))
assert (reply.get('model-id') == '1')
st = sts.Phosphorylation(sts.Agent('RAF'), sts.Agent('MEK'))
msg = KQMLList('EXPAND-MODEL')
msg.sets('description', json.dumps(sts.stmts_to_json([st])))
msg.sets('format', 'indra_json')
msg.set('model-id', '1')
reply = mm.respond_expand_model(msg)
assert (reply.get('model'))
assert (reply.get('model-id') == '2')
def test_respond_expand_model_from_json():
mm = MRA_Module(testing=True)
st = stmts_json_from_text('MEK phosphorylates ERK')
msg = KQMLList('BUILD-MODEL')
msg.sets('description', json.dumps(st))
msg.sets('format', 'indra_json')
reply = mm.respond_build_model(msg)
assert(reply.get('model'))
assert(reply.get('model-id') == '1')
st = stmts_json_from_text('Active BRAF inhibits MEK.')
msg = KQMLList('EXPAND-MODEL')
msg.sets('description', json.dumps(st))
msg.sets('format', 'indra_json')
msg.set('model-id', '1')
reply = mm.respond_expand_model(msg)
assert(reply.get('model'))
assert(reply.get('model-id') == '2')
def create_hasmech2(self):
content = KQMLList('MODEL-HAS-MECHANISM')
content.set('model-id', '1')
content.sets('description', stmts_clj_from_text('NRAS activates BRAF'))
msg = get_request(content)
return msg, content
def create_remove(self):
content = KQMLList('MODEL-REMOVE-MECHANISM')
content.set('model-id', '1')
content.set('description', stmts_clj_from_text('Unphosphorylated ERK'))
msg = get_request(content)
return msg, content
def create_remove2(self):
content = KQMLList('MODEL-REMOVE-MECHANISM')
content.set('model-id', '3')
content.set('description', stmts_clj_from_text('NRAS activates BRAF'))
msg = get_request(content)
return msg, content
def create_message(self):
content = KQMLList('DESCRIBE-MODEL')
content.set('model-id', str(self.bioagent.mra.id_counter))
msg = get_request(content)
return msg, content
def create_message(self):
content = KQMLList('DESCRIBE-MODEL')
content.set('model-id', '1')
msg = get_request(content)
return msg, content
def _get_build_model_request(text):
content = KQMLList('BUILD-MODEL')
descr = ekb_kstring_from_text(text)
content.set('description', descr)
return get_request(content), content
def _get_content(self, task, **contents):
content = KQMLList(task)
for key, value in contents.items():
content.set(key, value)
msg = get_request(content)
return msg, content
def create_message(self):
content = KQMLList('GET-COMMON')
content.set('genes', KQMLList([mek]))
content.sets('up-down', 'ONT::SUCCESSOR')
msg = get_request(content)
return msg, content
def create_message(self):
content = KQMLList('GET-COMMON')
content.set('genes', KQMLList(self.inp_genes))
content.sets('up-down', self.param_dict[self.updown])
msg = get_request(content)
return msg, content
def create_message(self):
content = KQMLList('GET-PAPER-MODEL')
content.set('pmid', 'PMID-27906130')
return get_request(content), content
def _get_content(self, task, **contents):
content = KQMLList(task)
for key, value in contents.items():
content.set(key, value)
msg = get_request(content)
return msg, content
def _get_expand_model_request(text, model_id):
content = KQMLList('EXPAND-MODEL')
descr = stmts_clj_from_text(text)
content.set('description', descr)
content.set('model-id', model_id)
return get_request(content), content
