def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
step = invocation_step.workflow_step
if invocation_step.output_value:
outputs[invocation_step.output_value.workflow_output.output_name] = invocation_step.output_value.value
self.outputs[step.id] = outputs
if not already_persisted:
workflow_outputs_by_name = {wo.output_name: wo for wo in step.workflow_outputs}
for output_name, output_object in outputs.items():
if hasattr(output_object, "history_content_type"):
invocation_step.add_output(output_name, output_object)
else:
# Add this non-data, non workflow-output output to the workflow outputs.
# This is required for recovering the output in the next scheduling iteration,
# and should be replaced with a WorkflowInvocationStepOutputValue ASAP.
if not workflow_outputs_by_name.get(output_name) and not output_object == modules.NO_REPLACEMENT:
workflow_output = model.WorkflowOutput(step, output_name=output_name)
step.workflow_outputs.append(workflow_output)
for workflow_output in step.workflow_outputs:
output_name = workflow_output.output_name
if output_name not in outputs:
message = f"Failed to find expected workflow output [{output_name}] in step outputs [{outputs}]"
# raise KeyError(message)
# Pre-18.01 we would have never even detected this output wasn't configured
# and even in 18.01 we don't have a way to tell the user something bad is
# happening so I guess we just log a debug message and continue sadly for now.
# Once https://github.com/galaxyproject/galaxy/issues/5142 is complete we could
# at least tell the user what happened, give them a warning.
log.debug(message)
continue
output = outputs[output_name]
self._record_workflow_output(
step,
workflow_output,
output=output,
)
def update_workflow_from_dict(self, trans, stored_workflow, workflow_data, from_editor=False):
# Put parameters in workflow mode
trans.workflow_building_mode = True
# Convert incoming workflow data from json if coming from editor
data = json.loads(workflow_data) if from_editor else workflow_data
# Create new workflow from incoming data
workflow = model.Workflow()
# Just keep the last name (user can rename later)
workflow.name = stored_workflow.name
# Assume no errors until we find a step that has some
workflow.has_errors = False
# Create each step
steps = []
# The editor will provide ids for each step that we don't need to save,
# but do need to use to make connections
steps_by_external_id = {}
errors = []
for key, step_dict in data['steps'].iteritems():
is_tool = is_tool_module_type( step_dict[ 'type' ] )
if is_tool and not trans.app.toolbox.has_tool( step_dict['tool_id'], exact=True ):
errors.append("Step %s requires tool '%s'." % (step_dict['id'], step_dict['tool_id']))
if errors:
raise MissingToolsException(workflow, errors)
# First pass to build step objects and populate basic values
for step_dict in self.__walk_step_dicts( data ):
module, step = self.__module_from_dict( trans, step_dict, secure=from_editor )
# Create the model class for the step
steps.append( step )
steps_by_external_id[ step_dict['id' ] ] = step
if 'workflow_outputs' in step_dict:
for output_name in step_dict['workflow_outputs']:
m = model.WorkflowOutput(workflow_step=step, output_name=output_name)
trans.sa_session.add(m)
if step.tool_errors:
# DBTODO Check for conditional inputs here.
workflow.has_errors = True
# Second pass to deal with connections between steps
self.__connect_workflow_steps( steps, steps_by_external_id )
# Order the steps if possible
attach_ordered_steps( workflow, steps )
# Connect up
workflow.stored_workflow = stored_workflow
stored_workflow.latest_workflow = workflow
# Persist
trans.sa_session.flush()
# Return something informative
errors = []
if workflow.has_errors:
errors.append( "Some steps in this workflow have validation errors" )
if workflow.has_cycles:
errors.append( "This workflow contains cycles" )
return workflow, errors
def example_invocation(trans):
invocation = model.WorkflowInvocation()
workflow = yaml_to_model(TEST_WORKFLOW_YAML)
workflow.id = 342
invocation.id = 44
invocation.workflow = workflow
# TODO: fix this to use workflow id and eliminate hack.
stored_workflow = model.StoredWorkflow()
stored_workflow.id = 342
invocation.workflow.stored_workflow = stored_workflow
hda = model.HistoryDatasetAssociation(create_dataset=True, sa_session=trans.sa_session)
hda.id = 567
invocation.add_input(hda, step=workflow.steps[0])
out_hda = model.HistoryDatasetAssociation(create_dataset=True, sa_session=trans.sa_session)
out_hda.id = 563
wf_output = model.WorkflowOutput(workflow.steps[2], label="output_label")
invocation.add_output(wf_output, workflow.steps[2], out_hda)
return invocation
def _dict_to_workflow_output(workflow_step, as_dict):
output = model.WorkflowOutput(workflow_step)
for key, value in as_dict.items():
setattr(output, key, value)
return output
def tag_outputs(self, trans, id, **kwargs):
stored = self.get_stored_workflow(trans, id, check_ownership=False)
user = trans.get_user()
if stored.user != user:
if trans.sa_session.query(model.StoredWorkflowUserShareAssociation) \
.filter_by(user=user, stored_workflow=stored).count() == 0:
error("Workflow is not owned by or shared with current user")
# Get the latest revision
workflow = stored.latest_workflow
# It is possible for a workflow to have 0 steps
if len(workflow.steps) == 0:
error(
"Workflow cannot be tagged for outputs because it does not have any steps"
)
if workflow.has_cycles:
error(
"Workflow cannot be tagged for outputs because it contains cycles"
)
if workflow.has_errors:
error(
"Workflow cannot be tagged for outputs because of validation errors in some steps"
)
# Build the state for each step
errors = {}
has_upgrade_messages = False
# has_errors is never used
# has_errors = False
if kwargs:
# If kwargs were provided, the states for each step should have
# been POSTed
for step in workflow.steps:
if step.type == 'tool':
# Extract just the output flags for this step.
p = "%s|otag|" % step.id
l = len(p)
outputs = [
k[l:] for (k, v) in kwargs.items() if k.startswith(p)
]
if step.workflow_outputs:
for existing_output in step.workflow_outputs:
if existing_output.output_name not in outputs:
trans.sa_session.delete(existing_output)
else:
outputs.remove(existing_output.output_name)
for outputname in outputs:
m = model.WorkflowOutput(workflow_step_id=int(step.id),
output_name=outputname)
trans.sa_session.add(m)
# Prepare each step
trans.sa_session.flush()
module_injector = WorkflowModuleInjector(trans)
for step in workflow.steps:
step.upgrade_messages = {}
# Contruct modules
module_injector.inject(step)
if step.upgrade_messages:
has_upgrade_messages = True
if step.type == 'tool' or step.type is None:
# Error dict
if step.tool_errors:
errors[step.id] = step.tool_errors
# Render the form
return trans.fill_template("workflow/tag_outputs.mako",
steps=workflow.steps,
workflow=stored,
has_upgrade_messages=has_upgrade_messages,
errors=errors,
incoming=kwargs)
