def test_nested_input():
dict_protocol = DummyInputOutputProtocol("dict_protocol")
dict_protocol.input_value = {"a": ThermodynamicState(1.0 * unit.kelvin)}
quantity_protocol = DummyInputOutputProtocol("quantity_protocol")
quantity_protocol.input_value = ProtocolPath("output_value[a].temperature",
dict_protocol.id)
schema = WorkflowSchema()
schema.protocol_schemas = [dict_protocol.schema, quantity_protocol.schema]
schema.validate()
workflow = Workflow({})
workflow.schema = schema
workflow_graph = workflow.to_graph()
with tempfile.TemporaryDirectory() as temporary_directory:
with DaskLocalCluster() as calculation_backend:
results_futures = workflow_graph.execute(temporary_directory,
calculation_backend)
assert len(results_futures) == 1
result = results_futures[0].result()
assert isinstance(result, WorkflowResult)
def test_index_replicated_protocol():
replicator = ProtocolReplicator("replicator")
replicator.template_values = ["a", "b", "c", "d"]
replicated_protocol = DummyInputOutputProtocol(
f"protocol_{replicator.placeholder_id}")
replicated_protocol.input_value = ReplicatorValue(replicator.id)
schema = WorkflowSchema()
schema.protocol_replicators = [replicator]
schema.protocol_schemas = [replicated_protocol.schema]
for index in range(len(replicator.template_values)):
indexing_protocol = DummyInputOutputProtocol(
f"indexing_protocol_{index}")
indexing_protocol.input_value = ProtocolPath("output_value",
f"protocol_{index}")
schema.protocol_schemas.append(indexing_protocol.schema)
schema.validate()
workflow = Workflow({})
workflow.schema = schema
def test_simple_workflow_graph(calculation_backend, compute_resources,
exception):
expected_value = (1 * unit.kelvin).plus_minus(0.1 * unit.kelvin)
protocol_a = DummyInputOutputProtocol("protocol_a")
protocol_a.input_value = expected_value
protocol_b = DummyInputOutputProtocol("protocol_b")
protocol_b.input_value = ProtocolPath("output_value", protocol_a.id)
schema = WorkflowSchema()
schema.protocol_schemas = [protocol_a.schema, protocol_b.schema]
schema.final_value_source = ProtocolPath("output_value", protocol_b.id)
schema.validate()
workflow = Workflow({})
workflow.schema = schema
workflow_graph = workflow.to_graph()
with tempfile.TemporaryDirectory() as directory:
if calculation_backend is not None:
with DaskLocalCluster() as calculation_backend:
if exception:
with pytest.raises(AssertionError):
workflow_graph.execute(directory, calculation_backend,
compute_resources)
return
else:
results_futures = workflow_graph.execute(
directory, calculation_backend, compute_resources)
assert len(results_futures) == 1
result = results_futures[0].result()
else:
result = workflow_graph.execute(directory, calculation_backend,
compute_resources)[0]
if exception:
with pytest.raises(AssertionError):
workflow_graph.execute(directory, calculation_backend,
compute_resources)
return
assert isinstance(result, WorkflowResult)
assert result.value.value == expected_value.value
def test_workflow_with_groups():
expected_value = (1 * unit.kelvin).plus_minus(0.1 * unit.kelvin)
protocol_a = DummyInputOutputProtocol("protocol_a")
protocol_a.input_value = expected_value
protocol_b = DummyInputOutputProtocol("protocol_b")
protocol_b.input_value = ProtocolPath("output_value", protocol_a.id)
conditional_group = ConditionalGroup("conditional_group")
conditional_group.add_protocols(protocol_a, protocol_b)
condition = ConditionalGroup.Condition()
condition.right_hand_value = 2 * unit.kelvin
condition.type = ConditionalGroup.Condition.Type.LessThan
condition.left_hand_value = ProtocolPath("output_value.value",
conditional_group.id,
protocol_b.id)
conditional_group.add_condition(condition)
schema = WorkflowSchema()
schema.protocol_schemas = [conditional_group.schema]
schema.final_value_source = ProtocolPath("output_value",
conditional_group.id,
protocol_b.id)
schema.validate()
workflow = Workflow({})
workflow.schema = schema
workflow_graph = workflow.to_graph()
with tempfile.TemporaryDirectory() as directory:
with DaskLocalCluster() as calculation_backend:
results_futures = workflow_graph.execute(directory,
calculation_backend)
assert len(results_futures) == 1
result = results_futures[0].result()
assert isinstance(result, WorkflowResult)
assert result.value.value == expected_value.value
def test_nested_replicators():
dummy_schema = WorkflowSchema()
dummy_protocol = DummyReplicableProtocol("dummy_$(rep_a)_$(rep_b)")
dummy_protocol.replicated_value_a = ReplicatorValue("rep_a")
dummy_protocol.replicated_value_b = ReplicatorValue("rep_b")
dummy_schema.protocol_schemas = [dummy_protocol.schema]
replicator_a = ProtocolReplicator(replicator_id="rep_a")
replicator_a.template_values = ["a", "b"]
replicator_b = ProtocolReplicator(replicator_id="rep_b")
replicator_b.template_values = [1, 2]
dummy_schema.protocol_replicators = [replicator_a, replicator_b]
dummy_schema.validate()
dummy_property = create_dummy_property(Density)
dummy_metadata = Workflow.generate_default_metadata(
dummy_property, "smirnoff99Frosst-1.1.0.offxml", [])
dummy_workflow = Workflow(dummy_metadata, "")
dummy_workflow.schema = dummy_schema
assert len(dummy_workflow.protocols) == 4
assert dummy_workflow.protocols["dummy_0_0"].replicated_value_a == "a"
assert dummy_workflow.protocols["dummy_0_1"].replicated_value_a == "a"
assert dummy_workflow.protocols["dummy_1_0"].replicated_value_a == "b"
assert dummy_workflow.protocols["dummy_1_1"].replicated_value_a == "b"
assert dummy_workflow.protocols["dummy_0_0"].replicated_value_b == 1
assert dummy_workflow.protocols["dummy_0_1"].replicated_value_b == 2
assert dummy_workflow.protocols["dummy_1_0"].replicated_value_b == 1
assert dummy_workflow.protocols["dummy_1_1"].replicated_value_b == 2
print(dummy_workflow.schema)
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 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_advanced_nested_replicators():
dummy_schema = WorkflowSchema()
replicator_a = ProtocolReplicator(replicator_id="replicator_a")
replicator_a.template_values = ["a", "b"]
replicator_b = ProtocolReplicator(
replicator_id=f"replicator_b_{replicator_a.placeholder_id}")
replicator_b.template_values = ProtocolPath(
f"dummy_list[{replicator_a.placeholder_id}]", "global")
dummy_protocol = DummyReplicableProtocol(f"dummy_"
f"{replicator_a.placeholder_id}_"
f"{replicator_b.placeholder_id}")
dummy_protocol.replicated_value_a = ReplicatorValue(replicator_a.id)
dummy_protocol.replicated_value_b = ReplicatorValue(replicator_b.id)
dummy_schema.protocol_schemas = [dummy_protocol.schema]
dummy_schema.protocol_replicators = [replicator_a, replicator_b]
dummy_schema.validate()
dummy_property = create_dummy_property(Density)
dummy_metadata = Workflow.generate_default_metadata(
dummy_property, "smirnoff99Frosst-1.1.0.offxml", [])
dummy_metadata["dummy_list"] = [[1], [2]]
dummy_workflow = Workflow(dummy_metadata, "")
dummy_workflow.schema = dummy_schema
assert len(dummy_workflow.protocols) == 2
assert dummy_workflow.protocols["dummy_0_0"].replicated_value_a == "a"
assert dummy_workflow.protocols["dummy_0_0"].replicated_value_b == 1
assert dummy_workflow.protocols["dummy_1_0"].replicated_value_a == "b"
assert dummy_workflow.protocols["dummy_1_0"].replicated_value_b == 2
def test_group_replicators():
dummy_schema = WorkflowSchema()
replicator_id = "replicator"
dummy_replicated_protocol = DummyInputOutputProtocol(
f"dummy_$({replicator_id})")
dummy_replicated_protocol.input_value = ReplicatorValue(replicator_id)
dummy_group = ProtocolGroup("dummy_group")
dummy_group.add_protocols(dummy_replicated_protocol)
dummy_protocol_single_value = DummyInputOutputProtocol(
f"dummy_single_$({replicator_id})")
dummy_protocol_single_value.input_value = ProtocolPath(
"output_value", dummy_group.id, dummy_replicated_protocol.id)
dummy_protocol_list_value = AddValues("dummy_list")
dummy_protocol_list_value.values = ProtocolPath(
"output_value", dummy_group.id, dummy_replicated_protocol.id)
dummy_schema.protocol_schemas = [
dummy_group.schema,
dummy_protocol_single_value.schema,
dummy_protocol_list_value.schema,
]
replicator = ProtocolReplicator(replicator_id)
replicator.template_values = [
(1.0 * unit.kelvin).plus_minus(1.0 * unit.kelvin),
(2.0 * unit.kelvin).plus_minus(2.0 * unit.kelvin),
]
dummy_schema.protocol_replicators = [replicator]
dummy_schema.validate()
dummy_property = create_dummy_property(Density)
dummy_metadata = Workflow.generate_default_metadata(
dummy_property, "smirnoff99Frosst-1.1.0.offxml", [])
dummy_workflow = Workflow(dummy_metadata, "")
dummy_workflow.schema = dummy_schema
assert len(dummy_workflow.protocols) == 4
assert (dummy_workflow.protocols[dummy_group.id].protocols["dummy_0"].
input_value.value == replicator.template_values[0].value)
assert (dummy_workflow.protocols[dummy_group.id].protocols["dummy_1"].
input_value.value == replicator.template_values[1].value)
assert dummy_workflow.protocols[
"dummy_single_0"].input_value == ProtocolPath("output_value",
dummy_group.id,
"dummy_0")
assert dummy_workflow.protocols[
"dummy_single_1"].input_value == ProtocolPath("output_value",
dummy_group.id,
"dummy_1")
assert len(dummy_workflow.protocols["dummy_list"].values) == 2
assert dummy_workflow.protocols["dummy_list"].values[0] == ProtocolPath(
"output_value", dummy_group.id, "dummy_0")
assert dummy_workflow.protocols["dummy_list"].values[1] == ProtocolPath(
"output_value", dummy_group.id, "dummy_1")