from crc import session from crc.api.common import ApiError from crc.models.study import StudyModel, StudySchema from crc.scripts.script import Script from crc.services.protocol_builder import ProtocolBuilderService from crc.services.workflow_processor import WorkflowProcessor class StudyInfo(Script): """Just your basic class that can pull in data from a few api endpoints and do a basic task.""" pb = ProtocolBuilderService() type_options = ['info', 'investigators', 'details'] def get_description(self): return """StudyInfo [TYPE], where TYPE is one of 'info', 'investigators', or 'details' Adds details about the current study to the Task Data. The type of information required should be provided as an argument. Basic returns the basic information such as the title. Investigators provides detailed information about each investigator in th study. Details provides a large number of details about the study, as gathered within the protocol builder, and 'required_docs', lists all the documents the Protocol Builder has determined will be required as a part of this study. """ def do_task_validate_only(self, task, study_id, *args, **kwargs): """For validation only, pretend no results come back from pb""" self.check_args(args) data = { "study":{ "info": { "id": 12, "title": "test", "primary_investigator_id":21, "user_uid": "dif84", "sponsor": "sponsor", "ind_number": "1234", "inactive": False }, "investigators": { "INVESTIGATORTYPE": "PI", "INVESTIGATORTYPEFULL": "Primary Investigator", "NETBADGEID": "dhf8r" }, "details": {} } } self.add_data_to_task(task=task, data=data["study"]) def do_task(self, task, study_id, *args, **kwargs): self.check_args(args) cmd = args[0] study_info = {} if self.__class__.__name__ in task.data: study_info = task.data[self.__class__.__name__] if cmd == 'info': study = session.query(StudyModel).filter_by(id=study_id).first() schema = StudySchema() study_info["info"] = schema.dump(study) if cmd == 'investigators': study_info["investigators"] = self.pb.get_investigators(study_id) if cmd == 'details': study_info["details"] = self.pb.get_study_details(study_id) task.data["study"] = study_info def check_args(self, args): if len(args) != 1 or (args[0] not in StudyInfo.type_options): raise ApiError(code="missing_argument", message="The StudyInfo script requires a single argument which must be " "one of %s" % ",".join(StudyInfo.type_options))