def test_filter_concept_names():
stmts = [
Influence(Event(Concept('a')), Event(Concept('b'))),
Influence(Event(Concept('a')), Event(Concept('c'))),
Influence(Event(Concept('a')), Event(Concept('d'))),
Influence(Event(Concept('c')), Event(Concept('d')))
]
stmts_out = ac.filter_concept_names(stmts, ['a'], 'one')
assert len(stmts_out) == 3, stmts_out
stmts_out = ac.filter_concept_names(stmts, ['a', 'b', 'c'], 'all')
assert len(stmts_out) == 2, stmts_out
stmts_out = ac.filter_concept_names(stmts, ['a', 'd'], 'one')
assert len(stmts_out) == 4, stmts_out
stmts_out = ac.filter_concept_names(stmts, ['a', 'b'], 'one', invert=True)
assert len(stmts_out) == 1, stmts_out
def get_evidence_for_stmts():
if request.method == 'OPTIONS':
return {}
req = request.body.read().decode('utf-8')
body = json.loads(req)
stmt_json = body.get('statement')
stmt = Statement._from_json(stmt_json)
def _get_agent_ref(agent):
"""Get the preferred ref for an agent for db web api."""
if agent is None:
return None
ag_hgnc_id = hgnc_client.get_hgnc_id(agent.name)
if ag_hgnc_id is not None:
return ag_hgnc_id + "@HGNC"
db_refs = agent.db_refs
for namespace in ['HGNC', 'FPLX', 'CHEBI', 'TEXT']:
if namespace in db_refs.keys():
return '%s@%s' % (db_refs[namespace], namespace)
return '%s@%s' % (agent.name, 'TEXT')
def _get_matching_stmts(stmt_ref):
# Filter by statement type.
stmt_type = stmt_ref.__class__.__name__
agent_name_list = [_get_agent_ref(ag) for ag in stmt_ref.agent_list()]
non_binary_statements = (Complex, SelfModification, ActiveForm)
# TODO: We should look at more than just the agent name.
# Doing so efficiently may require changes to the web api.
if isinstance(stmt_ref, non_binary_statements):
agent_list = [
ag_name for ag_name in agent_name_list if ag_name is not None
]
kwargs = {}
else:
agent_list = []
kwargs = {
k: v
for k, v in zip(['subject', 'object'], agent_name_list)
}
if not any(kwargs.values()):
return []
print(agent_list)
stmts = get_statements(agents=agent_list,
stmt_type=stmt_type,
simple_response=True,
**kwargs)
return stmts
stmts_out = _get_matching_stmts(stmt)
agent_name_list = [ag.name for ag in stmt.agent_list()]
stmts_out = stmts = ac.filter_concept_names(stmts_out, agent_name_list,
'all')
return _return_stmts(stmts_out)
def get_evidence_for_stmts():
if request.method == 'OPTIONS':
return {}
req = request.body.read().decode('utf-8')
body = json.loads(req)
stmt_json = body.get('statement')
stmt = Statement._from_json(stmt_json)
def _get_agent_ref(agent):
"""Get the preferred ref for an agent for db web api."""
if agent is None:
return None
ag_hgnc_id = hgnc_client.get_hgnc_id(agent.name)
if ag_hgnc_id is not None:
return ag_hgnc_id + "@HGNC"
db_refs = agent.db_refs
for namespace in ['HGNC', 'FPLX', 'CHEBI', 'TEXT']:
if namespace in db_refs.keys():
return '%s@%s' % (db_refs[namespace], namespace)
return '%s@%s' % (agent.name, 'TEXT')
def _get_matching_stmts(stmt_ref):
# Filter by statement type.
stmt_type = stmt_ref.__class__.__name__
agent_name_list = [_get_agent_ref(ag) for ag in stmt_ref.agent_list()]
non_binary_statements = (Complex, SelfModification, ActiveForm)
# TODO: We should look at more than just the agent name.
# Doing so efficiently may require changes to the web api.
if isinstance(stmt_ref, non_binary_statements):
agent_list = [ag_name for ag_name in agent_name_list
if ag_name is not None]
kwargs = {}
else:
agent_list = []
kwargs = {k: v for k, v in zip(['subject', 'object'],
agent_name_list)}
if not any(kwargs.values()):
return []
print(agent_list)
stmts = get_statements(agents=agent_list, stmt_type=stmt_type,
simple_response=True, **kwargs)
return stmts
stmts_out = _get_matching_stmts(stmt)
agent_name_list = [ag.name for ag in stmt.agent_list()]
stmts_out = stmts = ac.filter_concept_names(stmts_out, agent_name_list, 'all')
return _return_stmts(stmts_out)