import urllib from copy import copy from datetime import datetime from typing import List import flask import requests from SpiffWorkflow import WorkflowException from SpiffWorkflow.bpmn.PythonScriptEngine import Box from SpiffWorkflow.exceptions import WorkflowTaskExecException from ldap3.core.exceptions import LDAPSocketOpenError from crc import db, session, app from crc.api.common import ApiError from crc.models.data_store import DataStoreModel from crc.models.email import EmailModel from crc.models.file import FileModel, File from crc.models.ldap import LdapSchema from crc.models.protocol_builder import ProtocolBuilderStudy from crc.models.study import StudyModel, Study, StudyStatus, Category, \ WorkflowMetadata, StudyEventType, StudyEvent, IrbStatus, StudyAssociated from crc.models.task_event import TaskEventModel from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \ WorkflowStatus, WorkflowSpecDependencyFile from crc.services.document_service import DocumentService from crc.services.file_service import FileService from crc.services.ldap_service import LdapService from crc.services.lookup_service import LookupService from crc.services.protocol_builder import ProtocolBuilderService from crc.services.workflow_processor import WorkflowProcessor class StudyService(object): """Provides common tools for working with a Study""" INVESTIGATOR_LIST = "investigators.xlsx" # A reference document containing details about what investigators to show, and when. @staticmethod def _is_valid_study(study_id): study_info = ProtocolBuilderService().get_study_details(study_id) if 'REVIEW_TYPE' in study_info.keys() and study_info['REVIEW_TYPE'] in [2, 3, 23, 24]: return True return False def get_studies_for_user(self, user): """Returns a list of all studies for the given user.""" associated = session.query(StudyAssociated).filter_by(uid=user.uid,access=True).all() associated_studies = [x.study_id for x in associated] db_studies = session.query(StudyModel).filter((StudyModel.user_uid==user.uid)| (StudyModel.id.in_(associated_studies))).all() studies = [] for study_model in db_studies: if self._is_valid_study(study_model.id): studies.append(StudyService.get_study(study_model.id, study_model,do_status=False)) return studies @staticmethod def get_all_studies_with_files(): """Returns a list of all studies""" db_studies = session.query(StudyModel).all() studies = [] for s in db_studies: study = Study.from_model(s) study.files = FileService.get_files_for_study(study.id) studies.append(study) return studies @staticmethod def get_study(study_id, study_model: StudyModel = None, do_status=False): """Returns a study model that contains all the workflows organized by category. IMPORTANT: This is intended to be a lightweight call, it should never involve loading up and executing all the workflows in a study to calculate information.""" if not study_model: study_model = session.query(StudyModel).filter_by(id=study_id).first() study = Study.from_model(study_model) study.create_user_display = LdapService.user_info(study.user_uid).display_name last_event: TaskEventModel = session.query(TaskEventModel)\ .filter_by(study_id=study_id,action='COMPLETE')\ .order_by(TaskEventModel.date.desc()).first() if last_event is None: study.last_activity_user = 'Not Started' study.last_activity_date = "" else: study.last_activity_user = LdapService.user_info(last_event.user_uid).display_name study.last_activity_date = last_event.date study.categories = StudyService.get_categories() workflow_metas = StudyService._get_workflow_metas(study_id) files = FileService.get_files_for_study(study.id) files = (File.from_models(model, FileService.get_file_data(model.id), DocumentService.get_dictionary()) for model in files) study.files = list(files) # Calling this line repeatedly is very very slow. It creates the # master spec and runs it. Don't execute this for Abandoned studies, as # we don't have the information to process them. if study.status != StudyStatus.abandoned: # this line is taking 99% of the time that is used in get_study. # see ticket #196 if do_status: # __get_study_status() runs the master workflow to generate the status dictionary status = StudyService._get_study_status(study_model) study.warnings = StudyService._update_status_of_workflow_meta(workflow_metas, status) # Group the workflows into their categories. for category in study.categories: category.workflows = {w for w in workflow_metas if w.category_id == category.id} return study @staticmethod def get_study_associate(study_id = None, uid=None): """ gets all associated people for a study from the database """ study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first() if study is None: raise ApiError('study_not_found', 'No study found with id = %d' % study_id) if uid is None: raise ApiError('uid not specified','A valid uva uid is required for this function') if uid == study.user_uid: return {'uid': ownerid, 'role': 'owner', 'send_email': True, 'access': True} person = db.session.query(StudyAssociated).filter((StudyAssociated.study_id == study_id)&( StudyAssociated.uid == uid)).first() if person: newAssociate = {'uid':person.uid} newAssociate['role'] = person.role newAssociate['send_email'] = person.send_email newAssociate['access'] = person.access return newAssociate raise ApiError('uid_not_associated_with_study',"user id %s was not associated with study number %d"%(uid, study_id)) @staticmethod def get_study_associates(study_id): """ gets all associated people for a study from the database """ study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first() if study is None: raise ApiError('study_not_found','No study found with id = %d'%study_id) ownerid = study.user_uid people_list = [{'uid':ownerid,'role':'owner','send_email':True,'access':True}] people = db.session.query(StudyAssociated).filter(StudyAssociated.study_id == study_id) for person in people: newAssociate = {'uid':person.uid} newAssociate['role'] = person.role newAssociate['send_email'] = person.send_email newAssociate['access'] = person.access people_list.append(newAssociate) return people_list @staticmethod def update_study_associates(study_id,associates): """ updates the list of associates in the database for a study_id and a list of dicts that contains associates """ if study_id is None: raise ApiError('study_id not specified', "This function requires the study_id parameter") for person in associates: if not LdapService.user_exists(person.get('uid','impossible_uid')): if person.get('uid','impossible_uid') == 'impossible_uid': raise ApiError('associate with no uid','One of the associates passed as a parameter doesnt have ' 'a uid specified') raise ApiError('trying_to_grant_access_to_user_not_found_in_ldap',"You are trying to grant access to " "%s, but that user was not found in " "ldap " "- please check to ensure it is a " "valid uva uid"%person.get('uid')) study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first() if study is None: raise ApiError('study_id not found', "A study with id# %d was not found"%study_id) db.session.query(StudyAssociated).filter(StudyAssociated.study_id == study_id).delete() for person in associates: newAssociate = StudyAssociated() newAssociate.study_id = study_id newAssociate.uid = person['uid'] newAssociate.role = person.get('role', None) newAssociate.send_email = person.get('send_email', False) newAssociate.access = person.get('access',False) session.add(newAssociate) session.commit() @staticmethod def update_study_associate(study_id=None,uid=None,role="",send_email=False,access=False): if study_id is None: raise ApiError('study_id not specified', "This function requires the study_id parameter") if uid is None: raise ApiError('uid not specified', "This function requires a uva uid parameter") if not LdapService.user_exists(uid): raise ApiError('trying_to_grant_access_to_user_not_found_in_ldap',"You are trying to grant access to " "%s but they were not found in ldap " "- please check to ensure it is a " "valid uva uid"%uid) study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first() if study is None: raise ApiError('study_id not found', "A study with id# %d was not found"%study_id) db.session.query(StudyAssociated).filter((StudyAssociated.study_id == study_id)&(StudyAssociated.uid == uid) ).delete() newAssociate = StudyAssociated() newAssociate.study_id = study_id newAssociate.uid = uid newAssociate.role = role newAssociate.send_email = send_email newAssociate.access = access session.add(newAssociate) session.commit() return True @staticmethod def delete_study(study_id): session.query(TaskEventModel).filter_by(study_id=study_id).delete() session.query(StudyAssociated).filter_by(study_id=study_id).delete() session.query(EmailModel).filter_by(study_id=study_id).delete() session.query(StudyEvent).filter_by(study_id=study_id).delete() for workflow in session.query(WorkflowModel).filter_by(study_id=study_id): StudyService.delete_workflow(workflow.id) study = session.query(StudyModel).filter_by(id=study_id).first() session.delete(study) session.commit() @staticmethod def delete_workflow(workflow_id): workflow = session.query(WorkflowModel).get(workflow_id) if not workflow: return session.query(TaskEventModel).filter_by(workflow_id=workflow.id).delete() session.query(WorkflowSpecDependencyFile).filter_by(workflow_id=workflow_id).delete(synchronize_session='fetch') session.query(FileModel).filter_by(workflow_id=workflow_id).update({'archived': True, 'workflow_id': None}) session.delete(workflow) session.commit() @staticmethod def get_categories(): """Returns a list of category objects, in the correct order.""" cat_models = db.session.query(WorkflowSpecCategoryModel) \ .order_by(WorkflowSpecCategoryModel.display_order).all() categories = [] for cat_model in cat_models: categories.append(Category(cat_model)) return categories @staticmethod def get_documents_status(study_id): """Returns a list of documents related to the study, and any file information that is available..""" # Get PB required docs, if Protocol Builder Service is enabled. if ProtocolBuilderService.is_enabled() and study_id is not None: try: pb_docs = ProtocolBuilderService.get_required_docs(study_id=study_id) except requests.exceptions.ConnectionError as ce: app.logger.error(f'Failed to connect to the Protocol Builder - {str(ce)}', exc_info=True) pb_docs = [] else: pb_docs = [] # Loop through all known document types, get the counts for those files, # and use pb_docs to mark those as required. doc_dictionary = DocumentService.get_dictionary() documents = {} for code, doc in doc_dictionary.items(): doc['required'] = False if ProtocolBuilderService.is_enabled() and doc['id']: pb_data = next((item for item in pb_docs if int(item['AUXDOCID']) == int(doc['id'])), None) if pb_data: doc['required'] = True doc['study_id'] = study_id doc['code'] = code # Make a display name out of categories name_list = [] for cat_key in ['category1', 'category2', 'category3']: if doc[cat_key] not in ['', 'NULL', None]: name_list.append(doc[cat_key]) doc['display_name'] = ' / '.join(name_list) # For each file, get associated workflow status doc_files = FileService.get_files_for_study(study_id=study_id, irb_doc_code=code) doc['count'] = len(doc_files) doc['files'] = [] # when we run tests - it doesn't look like the user is available # so we return a bogus token token = 'not_available' if hasattr(flask.g,'user'): token = flask.g.user.encode_auth_token() for file in doc_files: file_data = {'file_id': file.id, 'name': file.name, 'url': app.config['APPLICATION_ROOT']+ 'file/' + str(file.id) + '/download?auth_token='+ urllib.parse.quote_plus(token), 'workflow_id': file.workflow_id } data = db.session.query(DataStoreModel).filter(DataStoreModel.file_id==file.id).all() data_store_data = {} for d in data: data_store_data[d.key] = d.value file_data["data_store"] = data_store_data doc['files'].append(Box(file_data)) # update the document status to match the status of the workflow it is in. if 'status' not in doc or doc['status'] is None: workflow: WorkflowModel = session.query(WorkflowModel).filter_by(id=file.workflow_id).first() doc['status'] = workflow.status.value documents[code] = doc return Box(documents) @staticmethod def get_investigator_dictionary(): """Returns a dictionary of document details keyed on the doc_code.""" file_data = FileService.get_reference_file_data(StudyService.INVESTIGATOR_LIST) lookup_model = LookupService.get_lookup_model_for_file_data(file_data, 'code', 'label') doc_dict = {} for lookup_data in lookup_model.dependencies: doc_dict[lookup_data.value] = lookup_data.data return doc_dict @staticmethod def get_investigators(study_id, all=False): """Convert array of investigators from protocol builder into a dictionary keyed on the type. """ # Loop through all known investigator types as set in the reference file inv_dictionary = StudyService.get_investigator_dictionary() # Get PB required docs pb_investigators = ProtocolBuilderService.get_investigators(study_id=study_id) # It is possible for the same type to show up more than once in some circumstances, in those events # append a counter to the name. investigators = {} for i_type in inv_dictionary: pb_data_entries = list(item for item in pb_investigators if item['INVESTIGATORTYPE'] == i_type) entry_count = 0 investigators[i_type] = copy(inv_dictionary[i_type]) investigators[i_type]['user_id'] = None for pb_data in pb_data_entries: entry_count += 1 if entry_count == 1: t = i_type else: t = i_type + "_" + str(entry_count) investigators[t] = copy(inv_dictionary[i_type]) investigators[t]['user_id'] = pb_data["NETBADGEID"] investigators[t].update(StudyService.get_ldap_dict_if_available(pb_data["NETBADGEID"])) if not all: investigators = dict(filter(lambda elem: elem[1]['user_id'] is not None, investigators.items())) return investigators @staticmethod def get_ldap_dict_if_available(user_id): try: return LdapSchema().dump(LdapService().user_info(user_id)) except ApiError as ae: app.logger.info(str(ae)) return {"error": str(ae)} except LDAPSocketOpenError: app.logger.info("Failed to connect to LDAP Server.") return {} @staticmethod def synch_with_protocol_builder_if_enabled(user): """Assures that the studies we have locally for the given user are in sync with the studies available in protocol builder. """ if ProtocolBuilderService.is_enabled(): app.logger.info("The Protocol Builder is enabled. app.config['PB_ENABLED'] = " + str(app.config['PB_ENABLED'])) # Get studies matching this user from Protocol Builder pb_studies: List[ProtocolBuilderStudy] = ProtocolBuilderService.get_studies(user.uid) # Get studies from the database db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all() # Update all studies from the protocol builder, create new studies as needed. # Further assures that every active study (that does exist in the protocol builder) # has a reference to every available workflow (though some may not have started yet) for pb_study in pb_studies: new_status = None db_study = next((s for s in db_studies if s.id == pb_study.STUDYID), None) if not db_study: db_study = StudyModel(id=pb_study.STUDYID) db_study.status = None # Force a new sa new_status = StudyStatus.in_progress session.add(db_study) db_studies.append(db_study) if pb_study.HSRNUMBER: db_study.irb_status = IrbStatus.hsr_assigned if db_study.status != StudyStatus.open_for_enrollment: new_status = StudyStatus.open_for_enrollment db_study.update_from_protocol_builder(pb_study) StudyService._add_all_workflow_specs_to_study(db_study) # If there is a new automatic status change and there isn't a manual change in place, record it. if new_status and db_study.status != StudyStatus.hold: db_study.status = new_status StudyService.add_study_update_event(db_study, status=new_status, event_type=StudyEventType.automatic) # Mark studies as inactive that are no longer in Protocol Builder for study in db_studies: pb_study = next((pbs for pbs in pb_studies if pbs.STUDYID == study.id), None) if not pb_study and study.status != StudyStatus.abandoned: study.status = StudyStatus.abandoned StudyService.add_study_update_event(study, status=StudyStatus.abandoned, event_type=StudyEventType.automatic) db.session.commit() @staticmethod def add_study_update_event(study, status, event_type, user_uid=None, comment=''): study_event = StudyEvent(study=study, status=status, event_type=event_type, user_uid=user_uid, comment=comment) db.session.add(study_event) db.session.commit() @staticmethod def _update_status_of_workflow_meta(workflow_metas, status): # Update the status on each workflow warnings = [] for wfm in workflow_metas: wfm.state_message = '' # do we have a status for you if wfm.name not in status.keys(): warnings.append(ApiError("missing_status", "No status specified for workflow %s" % wfm.name)) continue if not isinstance(status[wfm.name], dict): warnings.append(ApiError(code='invalid_status', message=f'Status must be a dictionary with "status" and "message" keys. Name is {wfm.name}. Status is {status[wfm.name]}')) continue if 'status' not in status[wfm.name].keys(): warnings.append(ApiError("missing_status", "Workflow '%s' does not have a status setting" % wfm.name)) continue if not WorkflowState.has_value(status[wfm.name]['status']): warnings.append(ApiError("invalid_state", "Workflow '%s' can not be set to '%s', should be one of %s" % ( wfm.name, status[wfm.name]['status'], ",".join(WorkflowState.list()) ))) continue wfm.state = WorkflowState[status[wfm.name]['status']] if 'message' in status[wfm.name].keys(): wfm.state_message = status[wfm.name]['message'] return warnings @staticmethod def _get_workflow_metas(study_id): # Add in the Workflows for each category workflow_models = db.session.query(WorkflowModel). \ join(WorkflowSpecModel). \ filter(WorkflowSpecModel.is_master_spec == False). \ filter(WorkflowModel.study_id == study_id). \ all() workflow_metas = [] for workflow in workflow_models: workflow_metas.append(WorkflowMetadata.from_workflow(workflow)) return workflow_metas @staticmethod def _get_study_status(study_model): """Uses the Top Level Workflow to calculate the status of the study, and it's workflow models.""" master_specs = db.session.query(WorkflowSpecModel). \ filter_by(is_master_spec=True).all() if len(master_specs) < 1: raise ApiError("missing_master_spec", "No specifications are currently marked as the master spec.") if len(master_specs) > 1: raise ApiError("multiple_master_specs", "There is more than one master specification, and I don't know what to do.") return WorkflowProcessor.run_master_spec(master_specs[0], study_model) @staticmethod def _add_all_workflow_specs_to_study(study_model: StudyModel): existing_models = session.query(WorkflowModel).filter(WorkflowModel.study == study_model).all() existing_specs = list(m.workflow_spec_id for m in existing_models) new_specs = session.query(WorkflowSpecModel). \ filter(WorkflowSpecModel.is_master_spec == False). \ filter(WorkflowSpecModel.id.notin_(existing_specs)). \ all() errors = [] for workflow_spec in new_specs: try: StudyService._create_workflow_model(study_model, workflow_spec) except WorkflowTaskExecException as wtee: errors.append(ApiError.from_task("workflow_startup_exception", str(wtee), wtee.task)) except WorkflowException as we: errors.append(ApiError.from_task_spec("workflow_startup_exception", str(we), we.sender)) return errors @staticmethod def _create_workflow_model(study: StudyModel, spec): workflow_model = WorkflowModel(status=WorkflowStatus.not_started, study=study, user_id=None, workflow_spec_id=spec.id, last_updated=datetime.utcnow()) session.add(workflow_model) session.commit() return workflow_model