def _make_queries_in_results(result_iter):
# Each element of result_iter: (model_id, query_json, result_json, date)
# Replace query_json with Query object
results = []
for res in result_iter:
query = QueryObject._from_json(res[1])
results.append((res[0], query, res[2], res[3], res[4]))
return results
def test_intervention_query_from_json():
query_file = join(dirname(abspath(__file__)), 'intervention_query.json')
with open(query_file, 'r') as f:
json_dict = json.load(f)
query = Query._from_json(json_dict)
assert query
assert isinstance(query, SimpleInterventionProperty)
assert isinstance(query.condition_entity, Agent)
assert query.condition_entity.name == 'EGF'
assert isinstance(query.target_entity, Agent)
assert query.target_entity.name == 'ERK'
assert query.direction == 'up'
def test_open_query_to_json():
ag = Agent('EGFR', db_refs={'HGNC': '3236'})
query = OpenSearchQuery(ag, 'Inhibition', 'object', ['chebi'])
assert query
json = query.to_json()
assert json.get('type') == 'open_search_query'
assert json.get('stmt_type') == 'Inhibition'
assert json.get('entity_role') == 'object'
assert json.get('terminal_ns') == ['chebi']
deserialize_query = Query._from_json(json)
json2 = deserialize_query.to_json()
assert json == json2, {'json': json, 'json2': json2}
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_open_query_from_json():
query_file = join(dirname(abspath(__file__)), 'open_query.json')
with open(query_file, 'r') as f:
json_dict = json.load(f)
query = Query._from_json(json_dict)
assert query
assert isinstance(query, OpenSearchQuery)
assert isinstance(query.entity, Agent)
assert query.entity.name == 'EGFR'
assert query.entity_role == 'object'
assert query.stmt_type == 'Inhibition'
assert isinstance(query.path_stmt, Inhibition)
assert query.path_stmt.subj is None
assert query.terminal_ns == ['chebi']
def test_path_property_from_json():
query_file = join(dirname(abspath(__file__)), 'path_property_query.json')
with open(query_file, 'r') as f:
json_dict = json.load(f)
query = Query._from_json(json_dict)
assert query
assert isinstance(query, PathProperty)
assert isinstance(query.path_stmt, Phosphorylation), query.path_stmt
assert query.path_stmt.enz.name == 'EGFR', query.path_stmt
assert query.path_stmt.sub.name == 'ERK', query.path_stmt
assert isinstance(query.exclude_entities[0], Agent)
assert query.exclude_entities[0].name == 'PI3K'
assert isinstance(query.include_entities[0], Agent)
assert query.include_entities[0].name == 'MAPK1'
assert set(query.exclude_rels) == set(['IncreaseAmount', 'DecreaseAmount'])
assert query.include_rels[0] == 'Inhibition'
def test_dynamic_property_from_json():
query_file = join(dirname(abspath(__file__)),
'dynamic_property_query.json')
with open(query_file, 'r') as f:
json_dict = json.load(f)
query = Query._from_json(json_dict)
assert query
assert isinstance(query, DynamicProperty)
assert isinstance(query.entity, Agent)
assert query.entity.name == 'EGFR'
assert isinstance(query.pattern_type, str)
assert query.pattern_type == 'always_value'
assert isinstance(query.quant_value, str)
assert query.quant_value == 'low'
assert isinstance(query.quant_type, str)
assert query.quant_type == 'qualitative'
def get_queries(self, model_id):
"""Get queries that refer to the given model_id.
Parameters
----------
model_id : str
The short, standard model ID.
Returns
-------
queries : list[emmaa.queries.Query]
A list of queries retrieved from the database.
"""
# TODO: check whether a query is registered or not.
with self.get_session() as sess:
q = sess.query(Query.json).filter(Query.model_id == model_id)
queries = [QueryObject._from_json(q) for q, in q.all()]
return queries
def get_queries(self, model_id):
"""Get queries that refer to the given model_id.
Parameters
----------
model_id : str
The short, standard model ID.
Returns
-------
queries : list[emmaa.queries.Query]
A list of queries retrieved from the database.
"""
with self.get_session() as sess:
q = sess.query(Query.json).filter(
Query.model_id == model_id, Query.hash == UserQuery.query_hash,
UserQuery.subscription).distinct()
queries = [QueryObject._from_json(q) for q, in q.all()]
return queries
def get_subscribed_queries(self, email):
"""Get a list of (query object, model id, query hash) for a user
Parameters
----------
email : str
The email address to check subscribed queries for
Returns
-------
list(tuple(emmaa.queries.Query, str, query_hash))
"""
logger.info(f"Got request to list user queries for {email}")
# Get the query json for which email is subscribed
with self.get_session() as sess:
q = sess.query(Query.json, Query.model_id, Query.hash).filter(
Query.hash == UserQuery.query_hash,
UserQuery.user_id == User.id, User.email == email,
UserQuery.subscription)
# Returns list of (query json, query hash) tuples
return [(QueryObject._from_json(qj), mid, qh)
for qj, mid, qh in q.all()]
'db_refs': {
'HGNC': '1097'
}
},
'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)
},
'obj': {
'type': 'Agent',
'name': 'MAPK1',
'db_refs': {
'HGNC': '6871'
}
}
}
}
simple_query = {
'typeSelection': 'Activation',
'subjectSelection': 'BRAF',
'objectSelection': 'MAPK1'
}
query_object = Query._from_json(test_query)
test_response = {
3801854542:
[('BRAF activates MAP2K1.',
'https://db.indra.bio/statements/from_agents?subject=1097@HGNC&object='
'6840@HGNC&type=Activation&format=html'),
('Active MAP2K1 activates MAPK1.',
'https://db.indra.bio/statements/from_agents?subject=6840@HGNC&object='
'6871@HGNC&type=Activation&format=html')]
}
processed_link = '<a href="https://db.indra.bio/statements/from_agents?'\
'subject=1097@HGNC&object=6840@HGNC&type=Activation&format=html" '\
'target="_blank" class="status-link">'\
'BRAF activates MAP2K1.</a>'
query_not_appl = {
}, {
'type': 'path_property',
'path': {
'type': 'Phosphorylation',
'enz': {
'type': 'Agent',
'name': 'ERK'
},
'sub': {
'type': 'Agent',
'name': 'MEK'
}
}
}]
test_queries = [QueryObject._from_json(qj) for qj in test_query_jsons]
@with_setup(setup_query_db, teardown_query_db)
@attr('nonpublic')
def test_instantiation():
db = _get_test_db()
assert db
return
@with_setup(setup_query_db, teardown_query_db)
@attr('nonpublic')
def test_put_queries():
db = _get_test_db()
db.put_queries('joshua', 1, test_queries[0], ['aml', 'luad'])