def create_event(self, institute, case, user, link, category, verb, subject, level='specific', variant_id="", content=""): """Create an Event with the parameters given. Arguments: institute (Institute): A Institute object case (Case): A Case object user (User): A User object link (str): The url to be used in the event category (str): Case or Variant verb (str): What type of event subject (str): What is operated on level (str): 'specific' or 'global'. Default is 'specific' variant (Variant): A variant object content (str): The content of the comment """ event = Event( institute=institute, case=case, author=user.to_dbref(), link=link, category=category, verb=verb, subject=subject, level=level, variant_id=variant_id, content=content ) logger.debug("Saving Event") event.save() logger.debug("Event Saved")
def delete_event(self, event_id): """Delete a event Arguments: event_id (str): The database key for the event """ logger.info("Deleting event{0}".format(event_id)) Event.objects(id=event_id).delete() logger.debug("Event {0} deleted".format(event_id))
def delete_event(self, event_id): """ Delete a event Arguments: event_id (str): The database key for the event """ self.logger.info("Deleting event{0}".format( event_id )) Event.objects(id=event_id).delete() self.logger.debug("Event {0} deleted".format( event_id ))
def has_comments(self): """ Return True is there are any comments for this variant in the database """ if Event.objects(verb='comment', variant_id=self.variant_id, institute=self.institute): return True return False
def test_add_mim(setup_database, get_institute, get_user, get_case): logger.info("Add OMIM term for a case") # Non existing mim phenotype mim_term = "MIM:614300" setup_database.add_phenotype( institute=get_institute, case=get_case, user=get_user, link="mimlink", omim_term=mim_term ) # Assert that the synopsis has been added to the case updated_case = Case.objects.get(case_id="acase") assert len(updated_case.phenotype_terms) != 0 # Check that the event not exists for event in Event.objects(verb="add_phenotype"): assert event.link == "mimlink" event.delete()
Arguments: institute (Institute): A Institute object case (Case): A Case object user (User): A User object link (str): The url to be used in the event category (str): Case or Variant verb (str): What type of event subject (str): What is operated on level (str): 'specific' or 'global'. Default is 'specific' variant (Variant): A variant object content (str): The content of the comment """ event = Event( institute=institute, case=case, author=user.to_dbref(), link=link, category=category, verb=verb, subject=subject, level=level, variant_id=variant_id, content=content ) self.logger.debug("Saving Event") event.save() self.logger.debug("Event Saved")