def create_message(self):
content = KQMLList('GET-COMMON')
ekb = ekb_from_text('MEK')
content.sets('genes', ekb)
content.sets('up-down', 'ONT::SUCCESSOR')
msg = get_request(content)
return msg, content
def test_msa_paper_retrieval_failure():
content = KQMLList('GET-PAPER-MODEL')
content.sets('pmid', 'PMID-00000123')
msa = msa_module.MSA_Module(testing=True)
resp = msa.respond_get_paper_model(content)
assert resp.head() == 'SUCCESS', str(resp)
assert resp.get('relations-found') == 0, resp
def _get_message(heading, target=None, residue=None, position=None):
msa = msa_module.MSA_Module(testing=True)
content = KQMLList(heading)
if target is not None:
content.sets('target', target)
if residue and position:
content.sets('site', '%s-%s' % (residue, position))
return msa.respond_phosphorylation_activating(content)
def test_msa_paper_retrieval_failure():
raise SkipTest("This feature is currently not available.")
content = KQMLList('GET-PAPER-MODEL')
content.sets('pmid', 'PMID-00000123')
msa = msa_module.MSA_Module(testing=True)
resp = msa.respond_get_paper_model(content)
assert resp.head() == 'FAILURE', str(resp)
assert resp.get('reason') == 'MISSING_MECHANISM'
def create_message(self):
content = KQMLList('PHOSPHORYLATION-ACTIVATING')
content.sets('target', ekb_from_text('MAPK1'))
for name, value in [('residue', 'T'), ('position', '185')]:
if value is not None:
content.sets(name, value)
msg = get_request(content)
return (msg, content)
def create_message(self):
content = KQMLList('PHOSPHORYLATION-ACTIVATING')
content.sets('target', ekb_from_text('MAPK1'))
for name, value in [('residue', 'T'), ('position', '185')]:
if value is not None:
content.sets(name, value)
msg = get_request(content)
return msg, content
def _get_message(heading, target=None, residue=None, position=None):
msa = msa_module.MSA_Module(testing=True)
content = KQMLList(heading)
if target is not None:
content.sets('target', ekb_from_text(target))
if residue and position:
content.sets('site', '%s-%s' % (residue, position))
return msa.respond_phosphorylation_activating(content)
def _get_message(heading, target=None, residue=None, position=None):
msa = msa_module.MSA_Module(testing=True)
content = KQMLList(heading)
if target is not None:
content.sets('target', ekb_from_text(target))
for name, value in [('residue', residue), ('position', position)]:
if value is not None:
content.sets(name, value)
return msa.respond_phosphorylation_activating(content)
def test_respond_build_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')
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 = 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_message(self):
content = KQMLList('PHOSPHORYLATION-ACTIVATING')
content.sets('target', mapk1)
content.sets('site', 'T-185')
msg = get_request(content)
return msg, content
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_undo(self):
content = KQMLList('MODEL-UNDO')
content.sets('model-id', '4')
msg = get_request(content)
return msg, content
def create_get_json(self):
content = KQMLList('MODEL-GET-JSON')
content.sets('model-id', '1')
msg = get_request(content)
return msg, content
def create_message(self):
content = KQMLList('BUILD-MODEL')
content.sets('description', '')
content.sets('format', 'ekb')
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-COMMON')
content.set('genes', KQMLList([mek]))
content.sets('up-down', 'ONT::SUCCESSOR')
msg = get_request(content)
return msg, content