from typing import List, Optional, Union, Tuple, Dict from connexion import NoContent from flask import g from crc import session, auth from crc.api.common import ApiError, ApiErrorSchema from crc.api.workflow import __get_workflow_api_model from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy from crc.models.study import StudyModelSchema, StudyModel from crc.models.workflow import WorkflowModel, WorkflowApiSchema, WorkflowSpecModel, WorkflowApi from crc.services.workflow_processor import WorkflowProcessor from crc.services.protocol_builder import ProtocolBuilderService @auth.login_required def all_studies(): return update_from_protocol_builder() @auth.login_required 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) @auth.login_required 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 schema = StudyModelSchema() study = schema.load(body, session=session, instance=study, partial=True) session.add(study) session.commit() return schema.dump(study) @auth.login_required 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) @auth.login_required def update_from_protocol_builder(): """Updates the list of known studies for a given user based on data received from the protocol builder.""" user = g.user """:type: crc.models.user.UserModel""" # Get studies matching this user from Protocol Builder pb_studies: List[ProtocolBuilderStudy] = get_user_pb_studies() # Get studies from the database db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all() db_study_ids = list(map(lambda s: s.id, db_studies)) pb_study_ids = list(map(lambda s: s['STUDYID'], pb_studies)) for pb_study in pb_studies: # Update studies with latest data from Protocol Builder if pb_study['STUDYID'] in db_study_ids: update_study(pb_study['STUDYID'], map_pb_study_to_study(pb_study)) # Add studies from Protocol Builder that aren't in the database yet else: new_study = map_pb_study_to_study(pb_study) add_study(new_study) # Mark studies as inactive that are no longer in Protocol Builder for study_id in db_study_ids: if study_id not in pb_study_ids: update_study(study_id=study_id, body={'inactive': True}) # Return updated studies updated_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all() results = StudyModelSchema(many=True).dump(updated_studies) return results @auth.login_required def post_update_study_from_protocol_builder(study_id): """Update a single study based on data received from the protocol builder.""" pb_studies: List[ProtocolBuilderStudy] = get_user_pb_studies() for pb_study in pb_studies: if pb_study['STUDYID'] == study_id: return update_study(study_id, map_pb_study_to_study(pb_study)) return NoContent, 304 @auth.login_required 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) @auth.login_required 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)) @auth.login_required def get_user_pb_studies() -> List[ProtocolBuilderStudy]: """Get studies from Protocol Builder matching the given user""" user = g.user """:type: crc.models.user.UserModel""" return ProtocolBuilderService.get_studies(user.uid) def map_pb_study_to_study(pb_study): """Translates the given dict of ProtocolBuilderStudy properties to dict of StudyModel attributes""" prop_map = { 'STUDYID': 'id', 'HSRNUMBER': 'hsr_number', 'TITLE': 'title', 'NETBADGEID': 'user_uid', 'DATE_MODIFIED': 'last_updated', } study_info = {} # Translate Protocol Builder property names to Study attributes for k, v in pb_study.items(): if k in prop_map: study_info[prop_map[k]] = v if pb_study['Q_COMPLETE']: study_info['protocol_builder_status'] = ProtocolBuilderStatus.complete._value_ else: study_info['protocol_builder_status'] = ProtocolBuilderStatus.in_process._value_ return study_info