def test_path_property_to_json():
stmt = Phosphorylation(enz=Agent('EGFR', db_refs={'HGNC': '3236'}),
sub=Agent('ERK', db_refs={'FPLX': 'ERK'}))
entity_constraints = {'exclude': [Agent('PI3K', db_refs={'FPLX': 'PI3K'})]}
relationship_contraints = {'exclude': ['IncreaseAmount', 'DecreaseAmount']}
query = PathProperty(stmt, entity_constraints, relationship_contraints)
assert query
json = query.to_json()
assert json.get('type') == 'path_property'
path = json.get('path')
assert path.get('type') == 'Phosphorylation'
deserialize_query = Query._from_json(json)
json2 = deserialize_query.to_json()
assert json == json2, {'json': json, 'json2': json2}
def test_stringify_path_property():
stmt = Phosphorylation(enz=Agent('EGFR', db_refs={'HGNC': '3236'}),
sub=Agent('ERK', db_refs={'FPLX': 'ERK'}))
entity_constraints = {'exclude': [Agent('PI3K', db_refs={'FPLX': 'PI3K'})]}
relationship_contraints = {'exclude': ['IncreaseAmount', 'DecreaseAmount']}
query = PathProperty(stmt, entity_constraints, relationship_contraints)
query_str = str(query)
assert query_str == 'PathPropertyQuery(stmt=Phosphorylation(EGFR(), ERK()). Exclude entities: PI3K(). Exclude relations: IncreaseAmount, DecreaseAmount.'
def _make_query(query_dict, use_grouding_service=True):
stmt_type = query_dict['typeSelection']
stmt_class = get_statement_by_name(stmt_type)
subj = get_agent_from_text(query_dict['subjectSelection'],
use_grouding_service)
obj = get_agent_from_text(query_dict['objectSelection'],
use_grouding_service)
stmt = stmt_class(subj, obj)
query = PathProperty(path_stmt=stmt)
return query
def _make_query(query_dict):
if 'typeSelection' in query_dict.keys():
stmt_type = query_dict['typeSelection']
stmt_class = get_statement_by_name(stmt_type)
subj = get_agent_from_text(query_dict['subjectSelection'])
obj = get_agent_from_text(query_dict['objectSelection'])
stmt = stmt_class(subj, obj)
query = PathProperty(path_stmt=stmt)
tab = 'static'
elif 'agentSelection' in query_dict.keys():
agent = get_agent_from_trips(query_dict['agentSelection'])
value = query_dict['valueSelection']
if not value:
value = None
pattern = query_dict['patternSelection']
query = DynamicProperty(agent, pattern, value)
tab = 'dynamic'
return query, tab
def test_path_property_to_english():
stmt = Phosphorylation(enz=Agent('EGFR', db_refs={'HGNC': '3236'}),
sub=Agent('ERK', db_refs={'FPLX': 'ERK'}))
query = PathProperty(stmt)
engl = query.to_english()
assert engl == 'EGFR phosphorylates ERK.'