def _agent_from_ns_id(ag_ns, ag_id):
# Add the ID as a placeholder name
agent = Agent(ag_id)
# If we have a proper grounding, add to db_refs
if ag_id is not None:
agent.db_refs[ag_ns] = ag_id
# Now standardize db_refs and set standardized name
GroundingMapper.standardize_agent_name(agent, standardize_refs=True)
agent.db_refs['TEXT'] = agent.name
return agent
def get_agent(name):
opts = {'text': name}
indra_url = read_from_config('INDRA_GROUND_URL')
res = requests.post(indra_url, json=opts)
if res.status_code != 200 and not res.json():
return Agent(name, db_refs={'TEXT': name})
js = res.json()
top_term = js[0]['term']
agent = Agent(name, db_refs={'TEXT': name, top_term['db']: top_term['id']})
GroundingMapper.standardize_agent_name(agent, standardize_refs=True)
return agent
def test_name_standardize_hgnc_up():
a1 = Agent('x', db_refs={'HGNC': '9387'})
GroundingMapper.standardize_agent_name(a1, True)
assert a1.name == 'PRKAG3'
a1 = Agent('x', db_refs={'UP': 'Q9UGI9'})
GroundingMapper.standardize_agent_name(a1, True)
assert a1.name == 'PRKAG3'
a1 = Agent('x', db_refs={'UP': 'Q8BGM7'})
GroundingMapper.standardize_agent_name(a1, True)
assert a1.name == 'Prkag3'
def get_channel_agent(channel):
ag = Agent(channel, db_refs={'HGNC': hgnc_client.get_hgnc_id(channel)})
GroundingMapper.standardize_agent_name(ag, standardize_refs=True)
return ag
def test_name_standardize_mesh():
a1 = Agent('x', db_refs={'MESH': 'D008545'})
GroundingMapper.standardize_agent_name(a1, False)
assert a1.name == 'Melanoma', a1.name
def test_name_standardize_go():
a1 = Agent('x', db_refs={'GO': 'GO:0006915'})
GroundingMapper.standardize_agent_name(a1, False)
assert a1.name == 'apoptotic process'
def test_name_standardize_chebi():
a1 = Agent('x', db_refs={'CHEBI': '15996'})
GroundingMapper.standardize_agent_name(a1, False)
assert a1.name == 'GTP'
