def test_flush_nodes_changing_node():
# exact same test as non changing node except have to get different synonym map from flush_nodes
node = KNode('MESH:D000096', type=node_types.CHEMICAL_SUBSTANCE)
properties = {'a': 'some prop'}
node.properties = properties
bf = BufferedWriter(rosetta_mock)
bf.write_node(node)
def write_transaction_mock(export_func, nodes, types):
print(types)
# make sure this is the right function
assert export_func == export_node_chunk
# make sure we have out node id in there
assert node.id in nodes
# get the node and see if the properties are preserved
assert nodes[node.id].properties == properties
# see if the types are expected
assert nodes[node.id].export_labels == types == frozenset([
"chemical_substance", "named_thing", "biological_entity",
"molecular_entity"
])
session = Mock()
session.write_transaction = write_transaction_mock
# pass the mock tester to bf and let it rip
bf.flush_nodes(session)
# make sure the synonym map we get here to be used for edge correction is sane
assert 'MESH:D000096' in bf.synonym_map
assert bf.synonym_map['MESH:D000096'] == 'CHEBI:15347'
def test_flush_nodes_non_normilizable():
# exact same test as non changing node except have to get different synonym map from flush_nodes
node = KNode('SOME:curie', type=node_types.CHEMICAL_SUBSTANCE)
properties = {'a': 'some prop'}
node.properties = properties
bf = BufferedWriter(rosetta_mock)
bf.write_node(node)
def write_transaction_mock(export_func, nodes, types):
print(types)
# make sure this is the right function
assert export_func == export_node_chunk
# make sure we have out node id in there
assert node.id in nodes
# get the node and see if the properties are preserved
assert nodes[node.id].properties == properties
# see if the types are expected
assert nodes[node.id].export_labels == []
assert types == frozenset()
session = Mock()
session.write_transaction = write_transaction_mock
# pass the mock tester to bf and let it rip
bf.flush_nodes(session)
# make sure the synonym map we get here to be used for edge correction is sane
assert 'SOME:curie' in bf.synonym_map
assert bf.synonym_map['SOME:curie'] == 'SOME:curie'
def test_flush_nodes_non_changing_node():
# test if nodes are sent to export function if they are already assigned primary id
node = KNode('CHEBI:15347', type=node_types.CHEMICAL_SUBSTANCE)
properties = {'a': 'some prop'}
node.properties = properties
bf = BufferedWriter(rosetta_mock)
# label_by_export_graph = ['this_should_be_overridden']
# def mock_add_labels(node): node.add_export_labels(label_by_export_graph)
# # patch export_graph.add_type_labels and see if its called
# bf.export_graph.add_type_labels = mock_add_labels
# we add the node
bf.write_node(node)
def write_transaction_mock(export_func, nodes, types):
print(types)
# make sure this is the right function
assert export_func == export_node_chunk
# make sure we have out node id in there
assert node.id in nodes
# get the node and see if the properties are preserved
assert nodes[node.id].properties == properties
# see if the types are expected
assert nodes[node.id].export_labels == types == frozenset([
"chemical_substance", "named_thing", "biological_entity",
"molecular_entity"
])
session = Mock()
session.write_transaction = write_transaction_mock
# pass the mock tester to bf and let it rip
bf.flush_nodes(session)
# make sure the synonym map we get here to be used for edge correction is sane
assert 'CHEBI:15347' in bf.synonym_map
assert bf.synonym_map['CHEBI:15347'] == 'CHEBI:15347'
