scout/adapter/mongo/variant_events.py
def update_acmg(self, institute_obj, case_obj, user_obj, link, variant_obj, acmg_str):
        """Create an event for updating the ACMG classification of a variant.

        Arguments:
            institute_obj (dict): A Institute object
            case_obj (dict): Case object
            user_obj (dict): A User object
            link (str): The url to be used in the event
            variant_obj (dict): A variant object
            acmg_str (str): The new ACMG classification string

        Returns:
            updated_variant
        """
        self.create_event(
            institute=institute_obj,
            case=case_obj,
            user=user_obj,
            link=link,
            category='variant',
            verb='acmg',
            variant=variant_obj,
            subject=variant_obj['display_name'],
        )
        LOG.info("Setting ACMG to {} for: {}".format(acmg_str, variant_obj['display_name']))

        if acmg_str is None:
            updated_variant = self.variant_collection.find_one_and_update(
                {'_id': variant_obj['_id']},
                {'$unset': {'acmg_classification': 1}},
                return_document=pymongo.ReturnDocument.AFTER
            )
        else:
            updated_variant = self.variant_collection.find_one_and_update(
                {'_id': variant_obj['_id']},
                {'$set': {'acmg_classification': REV_ACMG_MAP[acmg_str]}},
                return_document=pymongo.ReturnDocument.AFTER
            )

        LOG.debug("Variant updated")
        return updated_variant
def update_acmg(self, institute_obj, case_obj, user_obj, link, variant_obj, acmg_str):
        self.create_event(
            institute=institute_obj,
            case=case_obj,
            user=user_obj,
            link=link,
            category='variant',
            verb='acmg',
            variant=variant_obj,
            subject=variant_obj['display_name'],
        )
        LOG.info("Setting ACMG to {} for: {}".format(acmg_str, variant_obj['display_name']))

        if acmg_str is None:
            updated_variant = self.variant_collection.find_one_and_update(
                {'_id': variant_obj['_id']},
                {'$unset': {'acmg_classification': 1}},
                return_document=pymongo.ReturnDocument.AFTER
            )
        else:
            updated_variant = self.variant_collection.find_one_and_update(
                {'_id': variant_obj['_id']},
                {'$set': {'acmg_classification': REV_ACMG_MAP[acmg_str]}},
                return_document=pymongo.ReturnDocument.AFTER
            )

        LOG.debug("Variant updated")
        return updated_variant
def update_acmg ( self , institute_obj , case_obj , user_obj , link , variant_obj , acmg_str ) : self . create_event ( institute = institute_obj , case = case_obj , user = user_obj , link = link , category = 'variant' , verb = 'acmg' , variant = variant_obj , subject = variant_obj [ 'display_name' ] , ) LOG . info ( "Setting ACMG to {} for: {}" . format ( acmg_str , variant_obj [ 'display_name' ] ) ) if acmg_str is None : updated_variant = self . variant_collection . find_one_and_update ( { '_id' : variant_obj [ '_id' ] } , { '$unset' : { 'acmg_classification' : 1 } } , return_document = pymongo . ReturnDocument . AFTER ) else : updated_variant = self . variant_collection . find_one_and_update ( { '_id' : variant_obj [ '_id' ] } , { '$set' : { 'acmg_classification' : REV_ACMG_MAP [ acmg_str ] } } , return_document = pymongo . ReturnDocument . AFTER ) LOG . debug ( "Variant updated" ) return updated_variant
Create an event for updating the ACMG classification of a variant.

        Arguments:
            institute_obj (dict): A Institute object
            case_obj (dict): Case object
            user_obj (dict): A User object
            link (str): The url to be used in the event
            variant_obj (dict): A variant object
            acmg_str (str): The new ACMG classification string

        Returns:
            updated_variant
Create an event for updating the ACMG classification of a variant .