def test_connected_components():
test_graph_id = "Test Graph"
manager = ursa.Graph_manager()
manager.create_graph(test_graph_id)
manager.insert(test_graph_id, "Key1", "Value1")
manager.insert(test_graph_id, "Key2", "Value2")
manager.add_local_keys(test_graph_id, "Key2", "Key1")
# TODO remove this eventually
# In ray, we do not have the FIFO scheduling guarantee when tasks are
# submitted to actors from both remote tasks and the main thread.
# Therefore we can get transactions arriving out of order until the
# problem is fixed in ray. A sleep works here for now.
time.sleep(1)
manager.insert(test_graph_id, "Key3", "Value3", "Key2")
manager.insert(test_graph_id, "Key4", "Value4", "Key6")
# TODO See above
time.sleep(1)
manager.insert(test_graph_id, "Key5", "Value5", "Key1")
manager.insert(test_graph_id, "Key6", "Value6", "Key9")
manager.insert(test_graph_id, "Key7", "Value7")
manager.insert(test_graph_id, "Key8", "Value8")
manager.insert(test_graph_id, "Key9", "Value9")
manager.insert(test_graph_id, "Key10", "Value10", "Key11")
# TODO See above
time.sleep(1)
manager.insert(test_graph_id, "Key11", "Value11", "Key12")
# TODO See above
time.sleep(1)
manager.insert(test_graph_id, "Key12", "Value12", "Key10")
g = manager.get_graph(test_graph_id)
conn = g.connected_components.remote()
correct_output = [{'Key1', 'Key2', 'Key3', 'Key5'},
{'Key9', 'Key4', 'Key6'}, {'Key7'}, {'Key8'},
{'Key10', 'Key12', 'Key11'}]
test_output = ray.get(ray.get(ray.get(conn)[0]))
for s in test_output:
assert s in correct_output
assert len(test_output) == len(correct_output)
def test_connected_components():
test_graph_id = "Test Graph"
manager = ursa.Graph_manager()
manager.create_graph(test_graph_id)
manager.insert(test_graph_id, "Key1", "Value1")
manager.insert(test_graph_id, "Key2", "Value2")
manager.add_local_keys(test_graph_id, "Key2", "Key1")
manager.insert(test_graph_id, "Key3", "Value3", "Key2")
manager.insert(test_graph_id, "Key4", "Value4", "Key6")
manager.insert(test_graph_id, "Key5", "Value5", "Key1")
manager.insert(test_graph_id, "Key6", "Value6", "Key9")
manager.insert(test_graph_id, "Key7", "Value7")
manager.insert(test_graph_id, "Key8", "Value8")
manager.insert(test_graph_id, "Key9", "Value9")
manager.insert(test_graph_id, "Key10", "Value10", "Key11")
manager.insert(test_graph_id, "Key11", "Value11", "Key12")
manager.insert(test_graph_id, "Key12", "Value12", "Key10")
g = manager.get_graph(test_graph_id)
conn = g.connected_components.remote()
correct_output = [{'Key1', 'Key2', 'Key3', 'Key5'},
{'Key9', 'Key4', 'Key6'},
{'Key7'},
{'Key8'},
{'Key10', 'Key12', 'Key11'}]
test_output = ray.get(ray.get(ray.get(conn)[0]))
for s in test_output:
assert s in correct_output
assert len(test_output) == len(correct_output)
graph_collection.insert(graph_id, coordinate, node, neighbors)
graph_collection.add_foreign_edges(graph_id, coordinate,
"individuals",
indiv["individualID"])
edge_to_this_node = ursa.graph.Edge(coordinate, 0, "none")
for neighbor in neighbors:
graph_collection.add_local_edges(graph_id,
neighbor.destination,
edge_to_this_node)
ray.init()
graph_collection = ursa.Graph_manager()
reference_genome = "CAGTCCTAGCTACGCTCTATCCTCTCAGAGGACCGATCGATATACGCGT\
GAAACTAGTGCACTAGACTCGAACTGA"
dna_test_data = [{
"individualID":
0,
"dnaData": [{
"coordinateStart": 7.1,
"coordinateStop": 8.0,
"variantAllele": "C"
}, {
"coordinateStart": 12.2,
"coordinateStop": 13.0,
"variantAllele": "T"
def init_test():
manager = ursa.Graph_manager()
manager.create_graph(test_graph_id)
return manager