def test_replicated_ids():
replicator = ProtocolReplicator("replicator-a")
protocol_a = DummyProtocol("protocol-a")
protocol_a.input_value = 1
group_a = ProtocolGroup(f"group-a-{replicator.placeholder_id}")
group_a.add_protocols(protocol_a)
schema = WorkflowSchema()
schema.protocol_schemas = [group_a.schema]
schema.protocol_replicators = [replicator]
with pytest.raises(ValueError) as error_info:
schema.validate()
assert (
f"The children of replicated protocol {group_a.id} must also contain the "
"replicators placeholder" in str(error_info.value))
def build_protocols(prefix):
# .-------------------.
# | / i - j -|- b
# a - | g - h - | |
# | \ k - l -|- c
# .-------------------.
protocol_a = DummyInputOutputProtocol(prefix + "protocol_a")
protocol_a.input_value = 1
fork_protocols = build_fork(prefix)
fork_protocols[0].input_value = ProtocolPath("output_value",
protocol_a.id)
protocol_group = ProtocolGroup(prefix + "protocol_group")
protocol_group.add_protocols(*fork_protocols)
protocol_b = DummyInputOutputProtocol(prefix + "protocol_b")
protocol_b.input_value = ProtocolPath("output_value",
protocol_group.id, "protocol_j")
protocol_c = DummyInputOutputProtocol(prefix + "protocol_c")
protocol_c.input_value = ProtocolPath("output_value",
protocol_group.id, "protocol_l")
return [protocol_a, protocol_group, protocol_b, protocol_c]
def test_protocol_group_resume():
"""A test that protocol groups can recover after being killed
(e.g. by a worker being killed due to hitting a wallclock limit)
"""
compute_resources = ComputeResources()
# Fake a protocol group which executes the first
# two protocols and then 'gets killed'.
protocol_a = DummyInputOutputProtocol("protocol_a")
protocol_a.input_value = 1
protocol_b = DummyInputOutputProtocol("protocol_b")
protocol_b.input_value = ProtocolPath("output_value", protocol_a.id)
protocol_group_a = ProtocolGroup("group_a")
protocol_group_a.add_protocols(protocol_a, protocol_b)
protocol_graph = ProtocolGraph()
protocol_graph.add_protocols(protocol_group_a)
protocol_graph.execute("graph_a", compute_resources=compute_resources)
# Remove the output file so it appears the the protocol group had not
# completed.
os.unlink(
os.path.join("graph_a", protocol_group_a.id,
f"{protocol_group_a.id}_output.json"))
# Build the 'full' group with the last two protocols which
# 'had not been exited' after the group was 'killed'
protocol_a = DummyInputOutputProtocol("protocol_a")
protocol_a.input_value = 1
protocol_b = DummyInputOutputProtocol("protocol_b")
protocol_b.input_value = ProtocolPath("output_value", protocol_a.id)
protocol_c = DummyInputOutputProtocol("protocol_c")
protocol_c.input_value = ProtocolPath("output_value", protocol_b.id)
protocol_d = DummyInputOutputProtocol("protocol_d")
protocol_d.input_value = ProtocolPath("output_value", protocol_c.id)
protocol_group_a = ProtocolGroup("group_a")
protocol_group_a.add_protocols(protocol_a, protocol_b, protocol_c,
protocol_d)
protocol_graph = ProtocolGraph()
protocol_graph.add_protocols(protocol_group_a)
protocol_graph.execute("graph_a", compute_resources=compute_resources)
assert all(x != UNDEFINED for x in protocol_group_a.outputs.values())
def test_protocol_group_exceptions():
exception_protocol = ExceptionProtocol("exception_protocol")
protocol_group = ProtocolGroup("protocol_group")
protocol_group.add_protocols(exception_protocol)
with tempfile.TemporaryDirectory() as directory:
with pytest.raises(RuntimeError):
protocol_group.execute(directory, ComputeResources())
def test_unique_ids():
protocol_a = DummyProtocol("protocol-a")
protocol_a.input_value = 1
group_a = ProtocolGroup("group-a")
group_a.add_protocols(protocol_a)
group_b = ProtocolGroup("group-b")
group_b.add_protocols(protocol_a)
schema = WorkflowSchema()
schema.protocol_schemas = [group_a.schema, group_b.schema]
with pytest.raises(ValueError) as error_info:
schema.validate()
assert "Several protocols in the schema have the same id" in str(
error_info.value)
assert "protocol-a" in str(error_info.value)
def test_protocol_group_execution():
protocol_a = DummyInputOutputProtocol("protocol_a")
protocol_a.input_value = 1
protocol_b = DummyInputOutputProtocol("protocol_b")
protocol_b.input_value = ProtocolPath("output_value", protocol_a.id)
protocol_group = ProtocolGroup("protocol_group")
protocol_group.add_protocols(protocol_a, protocol_b)
with tempfile.TemporaryDirectory() as directory:
protocol_group.execute(directory, ComputeResources())
value_path = ProtocolPath("output_value", protocol_group.id, protocol_b.id)
final_value = protocol_group.get_value(value_path)
assert final_value == protocol_a.input_value