from connexion import NoContent from crc import session from crc.api.common import ApiError, ApiErrorSchema from crc.api.workflow import __get_workflow_api_model from crc.models.study import StudyModelSchema, StudyModel from crc.models.workflow import WorkflowModel, WorkflowApiSchema, WorkflowSpecModel from crc.services.workflow_processor import WorkflowProcessor def all_studies(): # todo: Limit returned studies to a user schema = StudyModelSchema(many=True) return schema.dump(session.query(StudyModel).all()) def add_study(body): study = StudyModelSchema().load(body, session=session) session.add(study) session.commit() # FIXME: We need to ask the protocol builder what workflows to add to the study, not just add them all. for spec in session.query(WorkflowSpecModel).all(): WorkflowProcessor.create(study.id, spec.id) return StudyModelSchema().dump(study) def update_study(study_id, body): if study_id is None: error = ApiError('unknown_study', 'Please provide a valid Study ID.') return ApiErrorSchema.dump(error), 404 study = session.query(StudyModel).filter_by(id=study_id).first() if study is None: error = ApiError('unknown_study', 'The study "' + study_id + '" is not recognized.') return ApiErrorSchema.dump(error), 404 study = StudyModelSchema().load(body, session=session) session.add(study) session.commit() return StudyModelSchema().dump(study) def get_study(study_id): study = session.query(StudyModel).filter_by(id=study_id).first() schema = StudyModelSchema() if study is None: return NoContent, 404 return schema.dump(study) def update_from_protocol_builder(): """Call the """ def post_update_study_from_protocol_builder(study_id): """This will update the list of known studies based on data received from the protocol builder.""" # todo: Actually get data from an external service here return NoContent, 304 def get_study_workflows(study_id): workflow_models = session.query(WorkflowModel).filter_by(study_id=study_id).all() api_models = [] for workflow_model in workflow_models: processor = WorkflowProcessor(workflow_model.workflow_spec_id, workflow_model.bpmn_workflow_json) api_models.append( __get_workflow_api_model(processor)) schema = WorkflowApiSchema(many=True) return schema.dump(api_models) def add_workflow_to_study(study_id, body): workflow_spec_model = session.query(WorkflowSpecModel).filter_by(id=body["id"]).first() if workflow_spec_model is None: error = ApiError('unknown_spec', 'The specification "' + body['id'] + '" is not recognized.') return ApiErrorSchema.dump(error), 404 processor = WorkflowProcessor.create(study_id, workflow_spec_model.id) return WorkflowApiSchema().dump(__get_workflow_api_model(processor))