scout/adapter/mongo/variant.py
def delete_variants(self, case_id, variant_type, category=None):
        """Delete variants of one type for a case

            This is used when a case is reanalyzed

            Args:
                case_id(str): The case id
                variant_type(str): 'research' or 'clinical'
                category(str): 'snv', 'sv' or 'cancer'
        """
        category = category or ''
        LOG.info("Deleting old {0} {1} variants for case {2}".format(
                    variant_type, category, case_id))
        query = {'case_id': case_id, 'variant_type': variant_type}
        if category:
            query['category'] = category
        result = self.variant_collection.delete_many(query)
        LOG.info("{0} variants deleted".format(result.deleted_count))
def delete_variants(self, case_id, variant_type, category=None):
        category = category or ''
        LOG.info("Deleting old {0} {1} variants for case {2}".format(
                    variant_type, category, case_id))
        query = {'case_id': case_id, 'variant_type': variant_type}
        if category:
            query['category'] = category
        result = self.variant_collection.delete_many(query)
        LOG.info("{0} variants deleted".format(result.deleted_count))
def delete_variants ( self , case_id , variant_type , category = None ) : category = category or '' LOG . info ( "Deleting old {0} {1} variants for case {2}" . format ( variant_type , category , case_id ) ) query = { 'case_id' : case_id , 'variant_type' : variant_type } if category : query [ 'category' ] = category result = self . variant_collection . delete_many ( query ) LOG . info ( "{0} variants deleted" . format ( result . deleted_count ) )
Delete variants of one type for a case

            This is used when a case is reanalyzed

            Args:
                case_id(str): The case id
                variant_type(str): 'research' or 'clinical'
                category(str): 'snv', 'sv' or 'cancer'
Delete variants of one type for a case