My boilerplate for functional tests of controllers in Symfony 3:

client = $this->createAuthorizedClient();
    }

    /**
     * @return Client
     */
    protected function createAuthorizedClient()
    {
        $client = static::createClient();
        $container = $client->getContainer();

        $session = $container->get('session');

        /** @var $userManager \FOS\UserBundle\Doctrine\UserManager */
        $userManager = $container->get('fos_user.user_manager');

        /** @var $loginManager \FOS\UserBundle\Security\LoginManager */
        $loginManager = $container->get('fos_user.security.login_manager');
        $firewallName = $container->getParameter('fos_user.firewall_name');

        $user = $userManager->findUserBy(array('username' => 'thomas'));
        $loginManager->loginUser($firewallName, $user);

        // save the login token into the session and put it in a cookie
        $container->get('session')->set(
            '_security_'.$firewallName,
            serialize($container->get('security.token_storage')->getToken())
        );

        $container->get('session')->save();
        $client->getCookieJar()->set(new Cookie($session->getName(), $session->getId()));

        return $client;
    }
}

Happy testing 🙂