scout/adapter/mongo/clinvar.py
def update_clinvar_id(self, clinvar_id, submission_id ):
        """saves an official clinvar submission ID in a clinvar submission object

            Args:
                clinvar_id(str): a string with a format: SUB[0-9]. It is obtained from clinvar portal when starting a new submission
                submission_id(str): submission_id(str) : id of the submission to be updated

            Returns:
                updated_submission(obj): a clinvar submission object, updated
        """
        updated_submission = self.clinvar_submission_collection.find_one_and_update( {'_id': ObjectId(submission_id)}, { '$set' : {'clinvar_subm_id' : clinvar_id, 'updated_at': datetime.now()} }, upsert=True, return_document=pymongo.ReturnDocument.AFTER )
        return updated_submission
def update_clinvar_id(self, clinvar_id, submission_id ):
        updated_submission = self.clinvar_submission_collection.find_one_and_update( {'_id': ObjectId(submission_id)}, { '$set' : {'clinvar_subm_id' : clinvar_id, 'updated_at': datetime.now()} }, upsert=True, return_document=pymongo.ReturnDocument.AFTER )
        return updated_submission
def update_clinvar_id ( self , clinvar_id , submission_id ) : updated_submission = self . clinvar_submission_collection . find_one_and_update ( { '_id' : ObjectId ( submission_id ) } , { '$set' : { 'clinvar_subm_id' : clinvar_id , 'updated_at' : datetime . now ( ) } } , upsert = True , return_document = pymongo . ReturnDocument . AFTER ) return updated_submission
saves an official clinvar submission ID in a clinvar submission object

            Args:
                clinvar_id(str): a string with a format: SUB[0-9]. It is obtained from clinvar portal when starting a new submission
                submission_id(str): submission_id(str) : id of the submission to be updated

            Returns:
                updated_submission(obj): a clinvar submission object, updated
saves an official clinvar submission ID in a clinvar submission object