Apply payment

gistfile1.php

    /**
     * Apply payment against order.
     *
     * @param string $order_uuid
     *   The order UUID.
     * @param string $payment_method
     *   The pipe-delimited string representing the payment method.
     * @param integer $amount
     *   The amount to apply to the order, without the decimal.
     */
    public function payment($order_uuid, $payment_method, $amount)
    {
        // Bootstrap store.
        $this->drupalWithUser->bootstrapStore();

        // Load order.
        $order = reset(entity_uuid_load('commerce_order', array($order_uuid)));
        $order->status = "checkout_checkout";

        commerce_checkout_complete($order);

        // Load chosen payment method.
        $payment_method = commerce_payment_method_instance_load($payment_method);
        $method_id = $payment_method['method_id'];
        $instance_id = $payment_method['instance_id'];

        // Add pointer to charge.
        $charge =& $order->commerce_order_total['und'][0];

        // Create a new transaction.
        $transaction = commerce_payment_transaction_new($method_id, $order->order_id);
        $transaction->instance_id = $instance_id;
        $transaction->amount = $amount;
        $transaction->currency_code = $charge['currency_code'];
        $transaction->status = COMMERCE_PAYMENT_STATUS_SUCCESS;
        $transaction->message = 'Method: @method';
        $transaction->message_variables = array('@method' => 'Members 2.0');

        commerce_payment_transaction_save($transaction);

        commerce_payment_commerce_payment_transaction_insert($transaction);
    }