def update(self, trans, id, payload, **kwds):
"""
* PUT /api/workflows/{id}
updates the workflow stored with ``id``
:type id: str
:param id: the encoded id of the workflow to update
:type payload: dict
:param payload: a dictionary containing any or all the
* workflow the json description of the workflow as would be
produced by GET workflows/<id>/download or
given to `POST workflows`
The workflow contents will be updated to target
this.
:rtype: dict
:returns: serialized version of the workflow
"""
stored_workflow = self.__get_stored_workflow(trans, id)
if 'workflow' in payload:
workflow_contents_manager = workflows.WorkflowContentsManager()
workflow, errors = workflow_contents_manager.update_workflow_from_dict(
trans,
stored_workflow,
payload['workflow'],
)
else:
message = "Updating workflow requires dictionary containing 'workflow' attribute with new JSON description."
raise exceptions.RequestParameterInvalidException(message)
return self.workflow_contents_manager.workflow_to_dict(
trans, stored_workflow, style="instance")
def load_workflow(self, trans, id, version=None):
"""
Get the latest Workflow for the StoredWorkflow identified by `id` and
encode it as a json string that can be read by the workflow editor
web interface.
"""
trans.workflow_building_mode = workflow_building_modes.ENABLED
stored = self.get_stored_workflow(trans, id, check_ownership=True, check_accessible=False)
workflow_contents_manager = workflows.WorkflowContentsManager(trans.app)
return workflow_contents_manager.workflow_to_dict(trans, stored, style="editor", version=version)
def save_workflow_as(self,
trans,
workflow_name,
workflow_data,
workflow_annotation=""):
"""
Creates a new workflow based on Save As command. It is a new workflow, but
is created with workflow_data already present.
"""
user = trans.get_user()
if workflow_name is not None:
workflow_contents_manager = workflows.WorkflowContentsManager(
trans.app)
stored_workflow = model.StoredWorkflow()
stored_workflow.name = workflow_name
stored_workflow.user = user
self.create_item_slug(trans.sa_session, stored_workflow)
workflow = model.Workflow()
workflow.name = workflow_name
workflow.stored_workflow = stored_workflow
stored_workflow.latest_workflow = workflow
# Add annotation.
workflow_annotation = sanitize_html(workflow_annotation)
self.add_item_annotation(trans.sa_session, trans.get_user(),
stored_workflow, workflow_annotation)
# Persist
session = trans.sa_session
session.add(stored_workflow)
session.flush()
try:
workflow, errors = workflow_contents_manager.update_workflow_from_raw_description(
trans,
stored_workflow,
workflow_data,
)
except workflows.MissingToolsException as e:
return dict(
name=e.workflow.name,
message=
("This workflow includes missing or invalid tools. "
"It cannot be saved until the following steps are removed or the missing tools are enabled."
),
errors=e.errors,
)
return (trans.security.encode_id(stored_workflow.id))
else:
# This is an error state, 'save as' must have a workflow_name
log.exception("Error in Save As workflow: no name.")
def __init__(self, app):
super(WorkflowsAPIController, self).__init__(app)
self.history_manager = histories.HistoryManager(app)
self.workflow_manager = workflows.WorkflowsManager(app)
self.workflow_contents_manager = workflows.WorkflowContentsManager()
