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 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_head(self):
kp = KQMLPerformative('tell')
self.assertEqual(kp.head(), 'tell')
kp = KQMLPerformative(
KQMLList(['tell', ':content',
KQMLList(['success'])]))
self.assertEqual(kp.head(), 'tell')
def test_init(self):
kl = KQMLList()
self.assertEqual(kl.data, [])
kl = KQMLList('head')
self.assertEqual(kl.data, ['head'])
self.assertTrue(isinstance(kl.data[0], KQMLToken))
kl = KQMLList(['a', 'b'])
self.assertEqual(kl.data, ['a', 'b'])
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 test_init():
kl = KQMLList()
assert(kl.data == [])
kl = KQMLList('head')
assert(kl.data == ['head'])
assert(type(kl.data[0] == KQMLToken))
kl = KQMLList(['a', 'b'])
assert(kl.data == ['a', 'b'])
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 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):
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 test_description_not_list_handling():
mm = MRA_Module(testing=True)
content = KQMLList.from_string(
'(BUILD-MODEL :DESCRIPTION ('
':TYPE "Inhibition" '
':SUBJ (:NAME "SB-525334" '
' :DB--REFS (:+TYPE+ "ONT::GENE-PROTEIN" '
' :+TEXT+ "SB525334"'
' :+PUBCHEM+ "9967941")) '
':OBJ (:NAME "TGFBR1"'
' :DB--REFS (:+TYPE+ "ONT::GENE-PROTEIN" '
' :+TEXT+ "TGFBR1" '
' :+HGNC+ "11772" '
' :+UP+ "P36897" '
' :+NCIT+ "C51730")) '
':OBJ--ACTIVITY "activity" '
':BELIEF 1 '
':EVIDENCE ((:SOURCE--API "trips" '
' :SOURCE--HASH -1613118243458052451)) '
':ID "ce486f46-3670-42e6-8f0e-d5f510525352" '
':MATCHES--HASH "-32031145755534420"))''')
try:
reply = mm.respond_build_model(content)
except InvalidModelDescriptionError:
return
assert False, "Model should have explicitly failed: " + reply.to_string()
def create_type_and_source(self):
filter_agents = KQMLList([map2k1, mapk1])
return self._get_content('FIND-RELATIONS-FROM-LITERATURE',
type='Phosphorylation',
source=braf,
target=NONE,
filter_agents=filter_agents)
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_undo_no_model_yet():
mm = MRA_Module(testing=True)
content = KQMLList.from_string('(MODEL-UNDO)')
reply = mm.respond_model_undo(content)
assert reply.gets('model-id') == 'NIL'
action = reply.get('action')
assert action.head() == 'remove_stmts', reply
stmts = action.get('statements')
assert not stmts
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 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 test_respond_model_undo():
mm = MRA_Module(testing=True)
_, content = _get_build_model_request('HRAS activates RAF')
reply = mm.respond_build_model(content)
_, content = _get_expand_model_request('NRAS activates RAF', '1')
expand_reply = mm.respond_expand_model(content)
expand_stmts = expand_reply.gets('model-new')
content = KQMLList.from_string('(MODEL-UNDO)')
reply = mm.respond_model_undo(content)
assert reply.gets('model-id') == '3'
action = reply.get('action')
assert action.head() == 'remove_stmts'
stmts = action.get('statements')
assert json.loads(stmts.string_value()) == json.loads(expand_stmts)
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_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_model_undo():
mm = MRA_Module(testing=True)
_, content = _get_build_model_request('HRAS activates RAF')
reply = mm.respond_build_model(content)
_, content = _get_expand_model_request('NRAS activates RAF', '1')
expand_reply = mm.respond_expand_model(content)
expand_stmts = mm.get_statement(expand_reply.get('model-new'))
assert len(expand_stmts) == 1
content = KQMLList.from_string('(MODEL-UNDO)')
reply = mm.respond_model_undo(content)
assert reply.gets('model-id') == '3'
action = reply.get('action')
assert action.head() == 'remove_stmts'
stmts = mm.get_statement(action.get('statements'))
assert len(stmts) == 1
assert stmts[0].equals(expand_stmts[0])
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 _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_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_undo(self):
content = KQMLList('MODEL-UNDO')
content.sets('model-id', '4')
msg = get_request(content)
return msg, content
def test_gets():
kl = KQMLList.from_string(b'(:hello "")')
hello = kl.gets('hello')
assert(hello == '')
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('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 create_message(self):
content = KQMLList('MODEL-UNDO')
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
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('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-PAPER-MODEL')
content.set('pmid', 'PMID-27906130')
return get_request(content), content
def create_get_json(self):
content = KQMLList('MODEL-GET-JSON')
content.sets('model-id', '1')
msg = get_request(content)
return msg, content
def test_from_string():
s = b'(FAILURE :reason INVALID_DESCRIPTION)'
kl = KQMLList.from_string(s)
for obj in kl.data:
assert(isinstance(obj, KQMLObject))
def create_get_json(self):
content = KQMLList('MODEL-GET-JSON')
msg = get_request(content)
return msg, 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_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
