def workflow_run_config_to_request(trans, run_config, workflow):
param_types = model.WorkflowRequestInputParameter.types
workflow_invocation = model.WorkflowInvocation()
workflow_invocation.uuid = uuid.uuid1()
workflow_invocation.history = run_config.target_history
def add_parameter(name, value, type):
parameter = model.WorkflowRequestInputParameter(
name=name,
value=value,
type=type,
)
workflow_invocation.input_parameters.append(parameter)
replacement_dict = run_config.replacement_dict
for name, value in replacement_dict.iteritems():
add_parameter(
name=name,
value=value,
type=param_types.REPLACEMENT_PARAMETERS,
)
for step_id, content in run_config.inputs.iteritems():
if content.history_content_type == "dataset":
request_to_content = model.WorkflowRequestToInputDatasetAssociation(
)
request_to_content.dataset = content
request_to_content.workflow_step_id = step_id
workflow_invocation.input_datasets.append(request_to_content)
else:
request_to_content = model.WorkflowRequestToInputDatasetCollectionAssociation(
)
request_to_content.dataset_collection = content
request_to_content.workflow_step_id = step_id
workflow_invocation.input_dataset_collections.append(
request_to_content)
for step in workflow.steps:
state = step.state
serializable_runtime_state = step.module.normalize_runtime_state(state)
step_state = model.WorkflowRequestStepState()
step_state.workflow_step_id = step.id
step_state.value = serializable_runtime_state
workflow_invocation.step_states.append(step_state)
add_parameter("copy_inputs_to_history",
"true" if run_config.copy_inputs_to_history else "false",
param_types.META_PARAMETERS)
return workflow_invocation
def test_workflows(self):
model = self.model
user = model.User(
email="*****@*****.**",
password="******"
)
def workflow_from_steps(steps):
stored_workflow = model.StoredWorkflow()
stored_workflow.user = user
workflow = model.Workflow()
workflow.steps = steps
workflow.stored_workflow = stored_workflow
return workflow
child_workflow = workflow_from_steps([])
self.persist(child_workflow)
workflow_step_1 = model.WorkflowStep()
workflow_step_1.order_index = 0
workflow_step_1.type = "data_input"
workflow_step_2 = model.WorkflowStep()
workflow_step_2.order_index = 1
workflow_step_2.type = "subworkflow"
workflow_step_2.subworkflow = child_workflow
workflow_step_1.get_or_add_input("moo1")
workflow_step_1.get_or_add_input("moo2")
workflow_step_2.get_or_add_input("moo")
workflow_step_1.add_connection("foo", "cow", workflow_step_2)
workflow = workflow_from_steps([workflow_step_1, workflow_step_2])
self.persist(workflow)
workflow_id = workflow.id
annotation = model.WorkflowStepAnnotationAssociation()
annotation.annotation = "Test Step Annotation"
annotation.user = user
annotation.workflow_step = workflow_step_1
self.persist(annotation)
assert workflow_step_1.id is not None
h1 = model.History(name="WorkflowHistory1", user=user)
invocation_uuid = uuid.uuid1()
workflow_invocation = model.WorkflowInvocation()
workflow_invocation.uuid = invocation_uuid
workflow_invocation.history = h1
workflow_invocation_step1 = model.WorkflowInvocationStep()
workflow_invocation_step1.workflow_invocation = workflow_invocation
workflow_invocation_step1.workflow_step = workflow_step_1
subworkflow_invocation = model.WorkflowInvocation()
workflow_invocation.attach_subworkflow_invocation_for_step(workflow_step_2, subworkflow_invocation)
workflow_invocation_step2 = model.WorkflowInvocationStep()
workflow_invocation_step2.workflow_invocation = workflow_invocation
workflow_invocation_step2.workflow_step = workflow_step_2
workflow_invocation.workflow = workflow
d1 = self.new_hda(h1, name="1")
workflow_request_dataset = model.WorkflowRequestToInputDatasetAssociation()
workflow_request_dataset.workflow_invocation = workflow_invocation
workflow_request_dataset.workflow_step = workflow_step_1
workflow_request_dataset.dataset = d1
self.persist(workflow_invocation)
assert workflow_request_dataset is not None
assert workflow_invocation.id is not None
history_id = h1.id
self.expunge()
loaded_invocation = self.query(model.WorkflowInvocation).get(workflow_invocation.id)
assert loaded_invocation.uuid == invocation_uuid, "%s != %s" % (loaded_invocation.uuid, invocation_uuid)
assert loaded_invocation
assert loaded_invocation.history.id == history_id
step_1, step_2 = loaded_invocation.workflow.steps
assert not step_1.subworkflow
assert step_2.subworkflow
assert len(loaded_invocation.steps) == 2
subworkflow_invocation_assoc = loaded_invocation.get_subworkflow_invocation_association_for_step(step_2)
assert subworkflow_invocation_assoc is not None
assert isinstance(subworkflow_invocation_assoc.subworkflow_invocation, model.WorkflowInvocation)
assert isinstance(subworkflow_invocation_assoc.parent_workflow_invocation, model.WorkflowInvocation)
assert subworkflow_invocation_assoc.subworkflow_invocation.history.id == history_id
loaded_workflow = self.query(model.Workflow).get(workflow_id)
assert len(loaded_workflow.steps[0].annotations) == 1
copied_workflow = loaded_workflow.copy(user=user)
annotations = copied_workflow.steps[0].annotations
assert len(annotations) == 1
