Importer.php

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<?php
namespace Magento\Store\Model\Config;

use Magento\Framework\App\CacheInterface;
use Magento\Framework\App\DeploymentConfig\ImporterInterface;
use Magento\Framework\Exception\State\InvalidTransitionException;
use Magento\Store\Model\Config\Importer\DataDifferenceCalculator;
use Magento\Store\Model\Config\Importer\Processor\ProcessorFactory;
use Magento\Store\Model\ScopeInterface;
use Magento\Store\Model\StoreManagerInterface;
use Magento\Store\Model\ResourceModel\Website;

class Importer implements ImporterInterface
{
    private $dataDifferenceCalculator;

    private $processFactory;

    private $storeManager;

    private $resource;

    private $cacheManager;

    public function __construct(
        DataDifferenceCalculator $dataDifferenceCalculator,
        ProcessorFactory $processFactory,
        StoreManagerInterface $storeManager,
        CacheInterface $cacheManager,
        Website $resource
    ) {
        $this->dataDifferenceCalculator = $dataDifferenceCalculator;
        $this->processFactory = $processFactory;
        $this->storeManager = $storeManager;
        $this->cacheManager = $cacheManager;
        $this->resource = $resource;
    }

    public function import(array $data)
    {
        $actions = [
            ProcessorFactory::TYPE_CREATE,
            ProcessorFactory::TYPE_DELETE,
            ProcessorFactory::TYPE_UPDATE
        ];
        $messages = ['Stores were processed'];

        try {
            $newGroups = $this->getGroupsToCreate($data);

            if ($newGroups) {
                $messages[] = sprintf(
                    $this->getStoreGroupAssignMessage(),
                    implode(', ', array_column($newGroups, 'name'))
                );
            }
            // during import websites/stores database already has new entities
            // but cache is outdated which can cause to error in some cases
            $this->reinitStores();

            $this->resource->beginTransaction();

            foreach ($actions as $action) {
                $this->processFactory->create($action)->run($data);
            }
        } catch (\Exception $exception) {
            $this->resource->rollBack();
            $this->reinitStores();

            throw new InvalidTransitionException(__('%1', $exception->getMessage()), $exception);
        }

        $this->resource->commit();
        $this->reinitStores();

        return $messages;
    }

    private function reinitStores()
    {
        $this->storeManager->reinitStores();
        $this->cacheManager->clean();
    }

    private function getStoreGroupAssignMessage()
    {
        return 'The following new store groups must be associated with a root category: %s. '
            . PHP_EOL
            . 'Associate a store group with a root category in the Admin Panel: Stores > Settings > All Stores.';
    }

    private function getGroupsToCreate(array $data)
    {
        if (!isset($data[ScopeInterface::SCOPE_GROUPS])) {
            return [];
        }

        $groups = $this->dataDifferenceCalculator->getItemsToCreate(
            ScopeInterface::SCOPE_GROUPS,
            $data[ScopeInterface::SCOPE_GROUPS]
        );

        return $groups;
    }

    public function getWarningMessages(array $data)
    {
        $messages = [];

        foreach ($data as $scope => $scopeData) {
            $messageMap = [
                'These %s will be deleted: %s' => $this->dataDifferenceCalculator->getItemsToDelete($scope, $scopeData),
                'These %s will be updated: %s' => $this->dataDifferenceCalculator->getItemsToUpdate($scope, $scopeData),
                'These %s will be created: %s' => $this->dataDifferenceCalculator->getItemsToCreate($scope, $scopeData),
            ];

            foreach ($messageMap as $message => $items) {
                if (!$items) {
                    continue;
                }

                $messages[] = $this->formatMessage($message, $items, $scope);
            }
        }

        return $messages;
    }

    private function formatMessage($message, array $items, $scope)
    {
        return sprintf(
            $message,
            ucfirst($scope),
            implode(', ', array_column($items, 'name'))
        );
    }
}