def create_concept_graphs(example_indices, typedb_session, infer=True):
"""
Builds an in-memory graph for each example, with an example_id as an anchor for each example subgraph.
Args:
example_indices: The values used to anchor the subgraph queries within the entire knowledge graph
typedb_session: TypeDB Session
Returns:
In-memory graphs of TypeDB subgraphs
"""
graphs = []
options = TypeDBOptions.core()
options.infer = infer
for example_id in example_indices:
print(f'Creating graph for example {example_id}')
graph_query_handles = get_query_handles(example_id)
with typedb_session.transaction(TransactionType.READ, options) as tx:
# Build a graph from the queries, samplers, and query graphs
graph = build_graph_from_queries(graph_query_handles, tx)
obfuscate_labels(graph, TYPES_AND_ROLES_TO_OBFUSCATE)
graph.name = example_id
graphs.append(graph)
return graphs
def test_exception_is_raised_when_there_are_no_results_for_any_query(self):
g1 = nx.MultiDiGraph()
g1.add_node('x')
query_sampler_variable_graph_tuples = [('match $x id V123;', mock_sampler, g1)]
class MockTransactionEmpty:
def query(self, query, infer=True):
return []
mock_tx = MockTransactionEmpty()
with self.assertRaises(RuntimeError) as context:
build_graph_from_queries(query_sampler_variable_graph_tuples, mock_tx)
self.assertEqual(f'The graph from queries: {[query_sampler_variable_graph_tuple[0] for query_sampler_variable_graph_tuple in query_sampler_variable_graph_tuples]}\n'
f'could not be created, since none of these queries returned results', str(context.exception))
def test_warning_given_when_one_query_gives_no_results(self):
g1 = nx.MultiDiGraph()
g1.add_node('x')
g2 = nx.MultiDiGraph()
g2.add_node('y')
query_sampler_variable_graph_tuples = [('match $x id V123;', mock_sampler, g1),
('match $y id V123;', mock_sampler, g2)]
class MockTransaction2:
def query(self, query, infer=True):
if query == 'match $x id V123;':
return [MockConceptMap({'x': MockThing('V123', MockType('V4123', 'person', 'ENTITY'))})]
elif query == 'match $y id V123;':
return []
mock_tx = MockTransaction2()
with self.assertWarns(UserWarning) as context:
build_graph_from_queries(query_sampler_variable_graph_tuples, mock_tx)
self.assertEqual(f'There were no results for query: \n\"match $y id V123;\"\nand so nothing will be added to the graph for this query', str(context.warning))
def test_graph_is_built_from_grakn_as_expected(self):
g1 = nx.MultiDiGraph()
g1.add_node('x')
g2 = nx.MultiDiGraph()
g2.add_node('x')
g2.add_node('n')
g2.add_edge('x', 'n', type='has')
g3 = nx.MultiDiGraph()
g3.add_node('x')
g3.add_node('r')
g3.add_node('y')
g3.add_edge('r', 'x', type='child')
g3.add_edge('r', 'y', type='parent')
query_sampler_variable_graph_tuples = [('match $x isa person;', mock_sampler, g1),
('match $x isa person, has name $n;', mock_sampler, g2),
('match $x isa person; $r(child: $x, parent: $y);', mock_sampler, g3),
# TODO Add functionality for loading schema at a later date
# ('match $x sub person; $x sub $type;', g4),
# ('match $x sub $y;', g5),
]
with self._client.session(self._database, SessionType.DATA) as session:
with session.transaction(TransactionType.WRITE) as tx:
tx.query(ITBuildGraphFromQueriesWithRealGrakn.SCHEMA)
tx.query(ITBuildGraphFromQueriesWithRealGrakn.DATA)
tx.commit()
with session.transaction(TransactionType.READ) as tx:
combined_graph = build_graph_from_queries(query_sampler_variable_graph_tuples, tx)
person_exp = build_thing(next(tx.query().match('match $x isa person;')).get('x'))
name_exp = build_thing(next(tx.query().match('match $x isa name;')).get('x'))
parentship_exp = build_thing(next(tx.query().match('match $x isa parentship;')).get('x'))
expected_combined_graph = nx.MultiDiGraph()
expected_combined_graph.add_node(person_exp, type='person')
expected_combined_graph.add_node(name_exp, type='name', value_type='string', value='Bob')
expected_combined_graph.add_node(parentship_exp, type='parentship')
expected_combined_graph.add_edge(parentship_exp, person_exp, type='child')
expected_combined_graph.add_edge(parentship_exp, person_exp, type='parent')
expected_combined_graph.add_edge(person_exp, name_exp, type='has')
self.assertGraphsEqual(expected_combined_graph, combined_graph)
def __getitem__(self, idx):
print(type(self._typedb_session))
example_id = self._example_indices[idx]
print(f"Fetching subgraph for example {example_id}")
graph_query_handles = self.get_query_handles_for_id(example_id)
options = TypeDBOptions.core()
options.infer = self._infer
with self.typedb_session.transaction(TransactionType.READ, options=options) as tx:
# Build a graph from the queries, samplers, and query graphs
graph = build_graph_from_queries(graph_query_handles, tx)
graph.name = example_id
if self._transform:
graph = self._transform(graph)
return graph
def test_graph_is_built_as_expected(self):
g1 = nx.MultiDiGraph()
g1.add_node('x')
g2 = nx.MultiDiGraph()
g2.add_node('x')
g2.add_node('n')
g2.add_edge('x', 'n', type='has')
g3 = nx.MultiDiGraph()
g3.add_node('x')
g3.add_node('r')
g3.add_node('y')
g3.add_edge('r', 'x', type='child')
g3.add_edge('r', 'y', type='parent')
query_sampler_variable_graph_tuples = [('match $x id V123;', mock_sampler, g1),
('match $x id V123, has name $n;', mock_sampler, g2),
('match $x id V123; $r(child: $x, parent: $y);', mock_sampler, g3),
# TODO Add functionality for loading schema at a later date
# ('match $x sub person; $x sub $type;', g4),
# ('match $x sub $y;', g5),
]
mock_tx = MockTransaction()
combined_graph = build_graph_from_queries(query_sampler_variable_graph_tuples, mock_tx)
person_exp = Thing('V123', 'person', 'entity')
parentship_exp = Thing('V567', 'parentship', 'relation')
name_exp = Thing('V987', 'name', 'attribute', value_type='string', value='Bob')
expected_combined_graph = nx.MultiDiGraph()
expected_combined_graph.add_node(person_exp, type='person')
expected_combined_graph.add_node(name_exp, type='name', value_type='string', value='Bob')
expected_combined_graph.add_node(parentship_exp, type='parentship')
expected_combined_graph.add_edge(parentship_exp, person_exp, type='child')
expected_combined_graph.add_edge(parentship_exp, person_exp, type='parent')
expected_combined_graph.add_edge(person_exp, name_exp, type='has')
self.assertGraphsEqual(expected_combined_graph, combined_graph)
def test_graph_is_built_as_expected(self):
g1 = nx.MultiDiGraph()
g1.add_node('x')
g2 = nx.MultiDiGraph()
g2.add_node('x')
g2.add_node('n')
g2.add_edge('x', 'n', type='has')
g3 = nx.MultiDiGraph()
g3.add_node('x')
g3.add_node('r')
g3.add_node('y')
g3.add_edge('r', 'x', type='child')
g3.add_edge('r', 'y', type='parent')
query_sampler_variable_graph_tuples = [
('match $x iid V123;', mock_sampler, g1),
('match $x iid V123, has name $n;', mock_sampler, g2),
('match $x iid V123; $r(child: $x, parent: $y);', mock_sampler,
g3),
# TODO Add functionality for loading schema at a later date
# ('match $x sub person; $x sub $type;', g4),
# ('match $x sub $y;', g5),
]
class MockTransaction:
def query(self):
return MockQueryManager()
class MockQueryManager:
def match(self, query):
if query == 'match $x iid V123;':
return [
MockConceptMap({
'x':
MockThing('V123',
MockType('V4123', 'person', 'ENTITY'))
})
]
elif query == 'match $x iid V123, has name $n;':
return [
MockConceptMap({
'x':
MockThing('V123',
MockType('V4123', 'person', 'ENTITY')),
'n':
MockAttribute(
'V987', 'Bob',
MockAttributeType(
'V555', 'name', 'ATTRIBUTE',
AttributeType.ValueType.STRING))
})
]
elif query == 'match $x iid V123; $r(child: $x, parent: $y);':
return [
MockConceptMap({
'x':
MockThing('V123',
MockType('V4123', 'person', 'ENTITY')),
'y':
MockThing('V123',
MockType('V4123', 'person', 'ENTITY')),
'r':
MockThing(
'V567',
MockType('V9876', 'parentship', 'RELATION'))
})
]
else:
raise NotImplementedError
mock_tx = MockTransaction()
combined_graph = build_graph_from_queries(
query_sampler_variable_graph_tuples, mock_tx)
person_exp = Thing('V123', 'person', 'entity')
parentship_exp = Thing('V567', 'parentship', 'relation')
name_exp = Thing('V987',
'name',
'attribute',
value_type=AttributeType.ValueType.STRING,
value='Bob')
expected_combined_graph = nx.MultiDiGraph()
expected_combined_graph.add_node(person_exp, type='person')
expected_combined_graph.add_node(
name_exp,
type='name',
value_type=AttributeType.ValueType.STRING,
value='Bob')
expected_combined_graph.add_node(parentship_exp, type='parentship')
expected_combined_graph.add_edge(parentship_exp,
person_exp,
type='child')
expected_combined_graph.add_edge(parentship_exp,
person_exp,
type='parent')
expected_combined_graph.add_edge(person_exp, name_exp, type='has')
self.assertGraphsEqual(expected_combined_graph, combined_graph)