def test_dynamic_property_to_english():
agent = Agent('EGFR', mods=[ModCondition('phosphorylation')],
db_refs={'HGNC': '3236'})
query = DynamicProperty(agent, 'always_value', 'low', 'qualitative')
assert query.to_english() == 'Phosphorylated EGFR is always low.'
query.pattern_type = 'eventual_value'
assert query.to_english() == 'Phosphorylated EGFR is eventually low.'
def test_dynamic_property_to_json():
agent = Agent('EGFR', mods=[ModCondition('phosphorylation')],
db_refs={'HGNC': '3236'})
query = DynamicProperty(agent, 'always_value', 'low', 'qualitative')
json = query.to_json()
assert json.get('type') == 'dynamic_property'
entity = json.get('entity')
assert entity.get('name') == 'EGFR'
assert entity.get('db_refs') == {"HGNC": "3236"}
assert json.get('pattern_type') == 'always_value'
quantity = json.get('quantity')
assert quantity.get('type') == 'qualitative'
assert quantity.get('value') == 'low'
def test_stringify_dynamic_property():
agent = Agent('EGFR', mods=[ModCondition('phosphorylation')],
db_refs={'HGNC': '3236'})
query = DynamicProperty(agent, 'always_value', 'low', 'qualitative')
query_str = str(query)
assert query_str == ("DynamicPropertyQuery(entity=EGFR(mods: "
"(phosphorylation)), pattern=always_value, "
"molecular quantity=('qualitative', 'low'))")
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
}
},
'obj': {
'type': 'Agent',
'name': 'MAPK1',
'db_refs': {
'HGNC': '6871'
}
},
'obj_activity': 'activity'
}
}
simple_query = 'BRAF activates MAPK1.'
query_object = Query._from_json(test_query)
dyn_ag = get_agent_from_trips('active MAP2K1')
dyn_query = DynamicProperty(dyn_ag, 'eventual_value', 'high')
open_qj = {
'type': 'open_search_query',
'entity': {
'type': 'Agent',
'name': 'BRAF',
'db_refs': {
'HGNC': '1097'
}
},
'entity_role': 'subject',
'stmt_type': 'Activation'
}
open_query = Query._from_json(open_qj)
interv_qj = {
'type': 'simple_intervention_property',