Sylius/app/migrations/Version20151015181310.php

<?php

namespace Sylius\Migrations;

use Doctrine\DBAL\Migrations\AbstractMigration;
use Doctrine\DBAL\Schema\Schema;

class Version20151015181310 extends AbstractMigration
{
    public function up(Schema $schema)
    {
        // this up() migration is auto-generated, please modify it to your needs
        $this->abortIf($this->connection->getDatabasePlatform()->getName() != 'mysql', 'Migration can only be executed safely on \'mysql\'.');

        $paymentMethods = $this->connection->fetchAll('SELECT * FROM sylius_payment_method WHERE fee_calculator_configuration=""');;
        foreach ($paymentMethods as $paymentMethod) {
            $this->connection->update(
                'sylius_payment_method',
                array('fee_calculator' => 'fixed','fee_calculator_configuration' => serialize(array('amount' => 0))),
                array('name' => $paymentMethod['name'])
            );
        }
    }

    public function down(Schema $schema)
    {

    }
}