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<?php

/**
 * @file classes/install/Installer.inc.php
 *
 * Copyright (c) 2014-2021 Simon Fraser University
 * Copyright (c) 2000-2021 John Willinsky
 * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
 *
 * @class Installer
 * @ingroup install
 *
 * @brief Base class for install and upgrade scripts.
 */

// Database installation files
define('INSTALLER_DATA_DIR', 'dbscripts/xml');

// Installer error codes
define('INSTALLER_ERROR_GENERAL', 1);
define('INSTALLER_ERROR_DB', 2);

// Default data
define('INSTALLER_DEFAULT_LOCALE', 'en_US');

import('lib.pkp.classes.db.DBDataXMLParser');
import('lib.pkp.classes.site.Version');
import('lib.pkp.classes.site.VersionDAO');
import('lib.pkp.classes.config.ConfigParser');
import('lib.pkp.classes.xml.PKPXMLParser');

use Illuminate\Database\Capsule\Manager as Capsule;
use Illuminate\Database\Schema\Blueprint;

class Installer {

/** @var string descriptor path (relative to INSTALLER_DATA_DIR) */
	var $descriptor;

/** @var boolean indicates if a plugin is being installed (thus modifying the descriptor path) */
	var $isPlugin;

/** @var array installation parameters */
	var $params;

/** @var Version currently installed version */
	var $currentVersion;

/** @var Version version after installation */
	var $newVersion;

/** @var string default locale */
	var $locale;

/** @var string available locales */
	var $installedLocales;

/** @var DBDataXMLParser database data parser */
	var $dataXMLParser;

/** @var array installer actions to be performed */
	var $actions;

/** @var array SQL statements for database installation */
	var $sql;

/** @var array installation notes */
	var $notes;

/** @var string contents of the updated config file */
	var $configContents;

/** @var boolean indicating if config file was written or not */
	var $wroteConfig;

/** @var int error code (null | INSTALLER_ERROR_GENERAL | INSTALLER_ERROR_DB) */
	var $errorType;

/** @var string the error message, if an installation error has occurred */
	var $errorMsg;

/** @var Logger logging object */
	var $logger;

/** @var array List of migrations executed already */
	var $migrations = [];

/**
	 * Constructor.
	 * @param $descriptor string descriptor path
	 * @param $params array installer parameters
	 * @param $isPlugin boolean true iff a plugin is being installed
	 */
	function __construct($descriptor, $params = array(), $isPlugin = false) {
		// Load all plugins. If any of them use installer hooks,
		// they'll need to be loaded here.
		PluginRegistry::loadAllPlugins();
		$this->isPlugin = $isPlugin;

// Give the HookRegistry the opportunity to override this
		// method or alter its parameters.
		if (!HookRegistry::call('Installer::Installer', array($this, &$descriptor, &$params))) {
			$this->descriptor = $descriptor;
			$this->params = $params;
			$this->actions = array();
			$this->sql = array();
			$this->notes = array();
			$this->wroteConfig = true;
		}
	}

/**
	 * Returns true iff this is an upgrade process.
	 */
	function isUpgrade() {
		die ('ABSTRACT CLASS');
	}

/**
	 * Destroy / clean-up after the installer.
	 */
	function destroy() {
		HookRegistry::call('Installer::destroy', array($this));
	}

/**
	 * Pre-installation.
	 * @return boolean
	 */
	function preInstall() {
		$this->log('pre-install');
		if (!isset($this->currentVersion)) {
			// Retrieve the currently installed version
			$versionDao = DAORegistry::getDAO('VersionDAO'); /* @var $versionDao VersionDAO */
			$this->currentVersion = $versionDao->getCurrentVersion();
		}

if (!isset($this->locale)) {
			$this->locale = AppLocale::getLocale();
		}

if (!isset($this->installedLocales)) {
			$this->installedLocales = array_keys(AppLocale::getAllLocales());
		}

if (!isset($this->dataXMLParser)) {
			$this->dataXMLParser = new DBDataXMLParser();
		}

$result = true;
		HookRegistry::call('Installer::preInstall', [$this, &$result]);

return $result;
	}

/**
	 * Installation.
	 * @return boolean
	 */
	function execute() {
		// Ensure that the installation will not get interrupted if it takes
		// longer than max_execution_time (php.ini). Note that this does not
		// work under safe mode.
		@set_time_limit (0);

if (!$this->preInstall()) {
			return false;
		}

if (!$this->parseInstaller()) {
			return false;
		}

if (!$this->executeInstaller()) {
			return false;
		}

if (!$this->postInstall()) {
			return false;
		}

return $this->updateVersion();
	}

/**
	 * Post-installation.
	 * @return boolean
	 */
	function postInstall() {
		$this->log('post-install');
		$result = true;
		HookRegistry::call('Installer::postInstall', array($this, &$result));
		return $result;
	}

/**
	 * Record message to installation log.
	 * @param $message string
	 */
	function log($message) {
		if (isset($this->logger)) {
			call_user_func(array($this->logger, 'log'), $message);
		}
	}

//
	// Main actions
	//

/**
	 * Parse the installation descriptor XML file.
	 * @return boolean
	 */
	function parseInstaller() {
		// Read installation descriptor file
		$this->log(sprintf('load: %s', $this->descriptor));
		$xmlParser = new PKPXMLParser();
		$installPath = $this->isPlugin ? $this->descriptor : INSTALLER_DATA_DIR . DIRECTORY_SEPARATOR . $this->descriptor;
		$installTree = $xmlParser->parse($installPath);
		if (!$installTree) {
			// Error reading installation file
			$this->setError(INSTALLER_ERROR_GENERAL, 'installer.installFileError');
			return false;
		}

$versionString = $installTree->getAttribute('version');
		if (isset($versionString)) {
			$this->newVersion = Version::fromString($versionString);
		} else {
			$this->newVersion = $this->currentVersion;
		}

// Parse descriptor
		$this->parseInstallNodes($installTree);

$result = $this->getErrorType() == 0;

HookRegistry::call('Installer::parseInstaller', array($this, &$result));
		return $result;
	}

/**
	 * Execute the installer actions.
	 * @return boolean
	 */
	function executeInstaller() {
		$this->log(sprintf('version: %s', $this->newVersion->getVersionString(false)));
		foreach ($this->actions as $action) {
			if (!$this->executeAction($action)) {
				return false;
			}
		}

$result = true;
		HookRegistry::call('Installer::executeInstaller', array($this, &$result));

return $result;
	}

/**
	 * Update the version number.
	 * @return boolean
	 */
	function updateVersion() {
		if ($this->newVersion->compare($this->currentVersion) > 0) {
			$versionDao = DAORegistry::getDAO('VersionDAO'); /* @var $versionDao VersionDAO */
			if (!$versionDao->insertVersion($this->newVersion)) {
				return false;
			}
		}

$result = true;
		HookRegistry::call('Installer::updateVersion', array($this, &$result));

return $result;
	}

//
	// Installer Parsing
	//

/**
	 * Parse children nodes in the install descriptor.
	 * @param $installTree XMLNode
	 */
	function parseInstallNodes($installTree) {
		foreach ($installTree->getChildren() as $node) {
			switch ($node->getName()) {
				case 'schema':
				case 'data':
				case 'code':
				case 'migration':
				case 'note':
					$this->addInstallAction($node);
					break;
				case 'upgrade':
					$minVersion = $node->getAttribute('minversion');
					$maxVersion = $node->getAttribute('maxversion');
					if ((!isset($minVersion) || $this->currentVersion->compare($minVersion) >= 0) && (!isset($maxVersion) || $this->currentVersion->compare($maxVersion) <= 0)) {
						$this->parseInstallNodes($node);
					}
					break;
			}
		}
	}

/**
	 * Add an installer action from the descriptor.
	 * @param $node XMLNode
	 */
	function addInstallAction($node) {
		$fileName = $node->getAttribute('file');

if (!isset($fileName)) {
			$this->actions[] = array('type' => $node->getName(), 'file' => null, 'attr' => $node->getAttributes());

} else if (strstr($fileName, '{$installedLocale}')) {
			// Filename substitution for locales
			foreach ($this->installedLocales as $thisLocale) {
				$newFileName = str_replace('{$installedLocale}', $thisLocale, $fileName);
				$this->actions[] = array('type' => $node->getName(), 'file' => $newFileName, 'attr' => $node->getAttributes());
			}

} else {
			$newFileName = str_replace('{$locale}', $this->locale, $fileName);
			if (!file_exists($newFileName)) {
				// Use version from default locale if data file is not available in the selected locale
				$newFileName = str_replace('{$locale}', INSTALLER_DEFAULT_LOCALE, $fileName);
			}

$this->actions[] = array('type' => $node->getName(), 'file' => $newFileName, 'attr' => $node->getAttributes());
		}
	}

//
	// Installer Execution
	//

/**
	 * Execute a single installer action.
	 * @param $action array
	 * @return boolean
	 */
	function executeAction($action) {
		switch ($action['type']) {
			case 'schema':
				$fileName = $action['file'];
				$this->log(sprintf('schema: %s', $action['file']));

require_once('lib/pkp/lib/vendor/adodb/adodb-php/adodb.inc.php');
				require_once('./lib/pkp/lib/vendor/adodb/adodb-php/adodb-xmlschema.inc.php');
				$dbconn = ADONewConnection(Config::getVar('database', 'driver'));
				$port = Config::getVar('database', 'port');
				$dbconn->Connect(
					Config::getVar('database', 'host') . ($port ? ':' . $port : ''),
					Config::getVar('database', 'username'),
					Config::getVar('database', 'password'),
					Config::getVar('database', 'name')
				);
				$schemaXMLParser = new adoSchema($dbconn);
				$dict = $schemaXMLParser->dict;
				$sql = $schemaXMLParser->parseSchema($fileName);
				$schemaXMLParser->destroy();

if ($sql) {
					return $this->executeSQL($sql);
				} else {
					$this->setError(INSTALLER_ERROR_DB, str_replace('{$file}', $fileName, __('installer.installParseDBFileError')));
					return false;
				}
				break;
			case 'data':
				$fileName = $action['file'];
				$condition = isset($action['attr']['condition'])?$action['attr']['condition']:null;
				$includeAction = true;
				if ($condition) {
					// Create a new scope to evaluate the condition
					$evalFunction = function($installer, $action) use ($condition) {
						return eval($condition);
					};
					$includeAction = $evalFunction($this, $action);
				}
				$this->log('data: ' . $action['file'] . ($includeAction?'':' (skipped)'));
				if (!$includeAction) break;

$sql = $this->dataXMLParser->parseData($fileName);
				// We might get an empty SQL if the upgrade script has
				// been executed before.
				if ($sql) {
					return $this->executeSQL($sql);
				}
				break;
			case 'migration':
				assert(isset($action['attr']['class']));
				$fullClassName = $action['attr']['class'];
				import($fullClassName);
				$shortClassName = substr($fullClassName, strrpos($fullClassName, '.')+1);
				$this->log(sprintf('migration: %s', $shortClassName));
				$migration = new $shortClassName();
				try {
					$migration->up();
					$this->migrations[] = $migration;
				} catch (Exception $e) {
					// Log an error message
					$this->setError(
						INSTALLER_ERROR_DB,
						Config::getVar('debug', 'show_stacktrace') ? (string) $e : $e->getMessage()
					);

// Back out already-executed migrations.
					while ($previousMigration = array_pop($this->migrations)) {
						try {
							$previousMigration->down();
						} catch (PKP\install\DowngradeNotSupportedException $e) {
							break;
						}
					}
					return false;
				}
				return true;
			case 'code':
				$condition = isset($action['attr']['condition'])?$action['attr']['condition']:null;
				$includeAction = true;
				if ($condition) {
					// Create a new scope to evaluate the condition
					$evalFunction = function($installer, $action) use ($condition) {
						return eval($condition);
					};
					$includeAction = $evalFunction($this, $action);
				}
				$this->log(sprintf('code: %s %s::%s' . ($includeAction?'':' (skipped)'), isset($action['file']) ? $action['file'] : 'Installer', isset($action['attr']['class']) ? $action['attr']['class'] : 'Installer', $action['attr']['function']));
				if (!$includeAction) return true; // Condition not met; skip the action.

if (isset($action['file'])) {
					require_once($action['file']);
				}
				if (isset($action['attr']['class'])) {
					return call_user_func(array($action['attr']['class'], $action['attr']['function']), $this, $action['attr']);
				} else {
					return call_user_func(array($this, $action['attr']['function']), $this, $action['attr']);
				}
				break;
			case 'note':
				$this->log(sprintf('note: %s', $action['file']));
				$this->notes[] = join('', file($action['file']));
				break;
		}

return true;
	}

/**
	 * Execute an SQL statement.
	 * @param $sql mixed
	 * @return boolean
	 */
	function executeSQL($sql) {
		if (is_array($sql)) {
			foreach($sql as $stmt) {
				if (!$this->executeSQL($stmt)) {
					return false;
				}
			}
		} else {
			try {
				Capsule::affectingStatement($sql);
			} catch (Exception $e) {
				$this->setError(INSTALLER_ERROR_DB, $e->getMessage());
				return false;
			}
		}

return true;
	}

/**
	 * Update the specified configuration parameters.
	 * @param $configParams arrays
	 * @return boolean
	 */
	function updateConfig($configParams) {
		// Update config file
		$configParser = new ConfigParser();
		if (!$configParser->updateConfig(Config::getConfigFileName(), $configParams)) {
			// Error reading config file
			$this->setError(INSTALLER_ERROR_GENERAL, 'installer.configFileError');
			return false;
		}

$this->configContents = $configParser->getFileContents();
		if (!$configParser->writeConfig(Config::getConfigFileName())) {
			$this->wroteConfig = false;
		}

return true;
	}

//
	// Accessors
	//

/**
	 * Get the value of an installation parameter.
	 * @param $name
	 * @return mixed
	 */
	function getParam($name) {
		return isset($this->params[$name]) ? $this->params[$name] : null;
	}

/**
	 * Return currently installed version.
	 * @return Version
	 */
	function getCurrentVersion() {
		return $this->currentVersion;
	}

/**
	 * Return new version after installation.
	 * @return Version
	 */
	function getNewVersion() {
		return $this->newVersion;
	}

/**
	 * Get the set of SQL statements required to perform the install.
	 * @return array
	 */
	function getSQL() {
		return $this->sql;
	}

/**
	 * Get the set of installation notes.
	 * @return array
	 */
	function getNotes() {
		return $this->notes;
	}

/**
	 * Get the contents of the updated configuration file.
	 * @return string
	 */
	function getConfigContents() {
		return $this->configContents;
	}

/**
	 * Check if installer was able to write out new config file.
	 * @return boolean
	 */
	function wroteConfig() {
		return $this->wroteConfig;
	}

/**
	 * Return the error code.
	 * Valid return values are:
	 *   - 0 = no error
	 *   - INSTALLER_ERROR_GENERAL = general installation error.
	 *   - INSTALLER_ERROR_DB = database installation error
	 * @return int
	 */
	function getErrorType() {
		return isset($this->errorType) ? $this->errorType : 0;
	}

/**
	 * The error message, if an error has occurred.
	 * In the case of a database error, an unlocalized string containing the error message is returned.
	 * For any other error, a localization key for the error message is returned.
	 * @return string
	 */
	function getErrorMsg() {
		return $this->errorMsg;
	}

/**
	 * Return the error message as a localized string.
	 * @return string.
	 */
	function getErrorString() {
		switch ($this->getErrorType()) {
			case INSTALLER_ERROR_DB:
				return 'DB: ' . $this->getErrorMsg();
			default:
				return __($this->getErrorMsg());
		}
	}

/**
	 * Set the error type and messgae.
	 * @param $type int
	 * @param $msg string Text message (INSTALLER_ERROR_DB) or locale key (otherwise)
	 */
	function setError($type, $msg) {
		$this->errorType = $type;
		$this->errorMsg = $msg;
	}

/**
	 * Set the logger for this installer.
	 * @param $logger Logger
	 */
	function setLogger($logger) {
		$this->logger = $logger;
	}

/**
	 * Clear the data cache files (needed because of direct tinkering
	 * with settings tables)
	 * @return boolean
	 */
	function clearDataCache() {
		$cacheManager = CacheManager::getManager();
		$cacheManager->flush(null, CACHE_TYPE_FILE);
		$cacheManager->flush(null, CACHE_TYPE_OBJECT);
		return true;
	}

/**
	 * Set the current version for this installer.
	 * @param $version Version
	 */
	function setCurrentVersion($version) {
		$this->currentVersion = $version;
	}

/**
	 * For upgrade: install email templates and data
	 * @param $installer object
	 * @param $attr array Attributes: array containing
	 * 		'key' => 'EMAIL_KEY_HERE',
	 * 		'locales' => 'en_US,fr_CA,...'
	 */
	function installEmailTemplate($installer, $attr) {
		$locales = explode(',', $attr['locales']);
		foreach ($locales as $locale) AppLocale::requireComponents(LOCALE_COMPONENT_APP_EMAIL, $locale);
		$emailTemplateDao = DAORegistry::getDAO('EmailTemplateDAO'); /* @var $emailTemplateDao EmailTemplateDAO */
		// FIXME pkp/pkp-lib#6284 Remove after drop of support for upgrades from 3.2.0
		if (!Capsule::schema()->hasColumn('email_templates_default', 'stage_id')) {
			Capsule::schema()->table('email_templates_default', function (Blueprint $table) {
				$table->bigInteger('stage_id')->nullable();
			});
		}
		$emailTemplateDao->installEmailTemplates($emailTemplateDao->getMainEmailTemplatesFilename(), $locales, false, $attr['key']);
		return true;
	}

/**
	 * Install the given filter configuration file.
	 * @param $filterConfigFile string
	 * @return boolean true when successful, otherwise false
	 */
	function installFilterConfig($filterConfigFile) {
		static $filterHelper = false;

// Parse the filter configuration.
		$xmlParser = new PKPXMLParser();
		$tree = $xmlParser->parse($filterConfigFile);

// Validate the filter configuration.
		if (!$tree) return false;

// Get the filter helper.
		if ($filterHelper === false) {
			import('lib.pkp.classes.filter.FilterHelper');
			$filterHelper = new FilterHelper();
		}

// Are there any filter groups to be installed?
		$filterGroupsNode = $tree->getChildByName('filterGroups');
		if (is_a($filterGroupsNode, 'XMLNode')) {
			$filterHelper->installFilterGroups($filterGroupsNode);
		}

// Are there any filters to be installed?
		$filtersNode = $tree->getChildByName('filters');
		if (is_a($filtersNode, 'XMLNode')) {
			foreach ($filtersNode->getChildren() as $filterNode) { /* @var $filterNode XMLNode */
				$filterHelper->configureFilter($filterNode);
			}
		}

return true;
	}

/**
	 * Check to see whether a column exists.
	 * Used in installer XML in conditional checks on <data> nodes.
	 * @param $tableName string
	 * @param $columnName string
	 * @return boolean
	 */
	function columnExists($tableName, $columnName) {
		$schema = Capsule::connection()->getDoctrineSchemaManager();
		// Make sure the table exists
		$tables = $schema->listTableNames();
		if (!in_array($tableName, $tables)) return false;

return Capsule::schema()->hasColumn($tableName, $columnName);
	}

/**
	 * Check to see whether a table exists.
	 * Used in installer XML in conditional checks on <data> nodes.
	 * @param $tableName string
	 * @return boolean
	 */
	function tableExists($tableName) {
		$tables = Capsule::connection()->getDoctrineSchemaManager()->listTableNames();
		return in_array($tableName, $tables);
	}

/**
	 * Insert or update plugin data in versions
	 * and plugin_settings tables.
	 * @return boolean
	 */
	function addPluginVersions() {
		$versionDao = DAORegistry::getDAO('VersionDAO'); /* @var $versionDao VersionDAO */
		import('lib.pkp.classes.site.VersionCheck');
		$fileManager = new FileManager();
		$categories = PluginRegistry::getCategories();
		foreach ($categories as $category) {
			PluginRegistry::loadCategory($category);
			$plugins = PluginRegistry::getPlugins($category);
			if (!empty($plugins)) {
				foreach ($plugins as $plugin) {
					$versionFile = $plugin->getPluginPath() . '/version.xml';

if ($fileManager->fileExists($versionFile)) {
						$versionInfo = VersionCheck::parseVersionXML($versionFile);
						$pluginVersion = $versionInfo['version'];
					} else {
						$pluginVersion = new Version(
							1, 0, 0, 0, // Major, minor, revision, build
							Core::getCurrentDate(), // Date installed
							1,	// Current
							'plugins.'.$category, // Type
							basename($plugin->getPluginPath()), // Product
							'',	// Class name
							0,	// Lazy load
							$plugin->isSitePlugin()	// Site wide
						);
					}
					$versionDao->insertVersion($pluginVersion, true);
				}
			}
		}

return true;
	}

/**
	 * Fail the upgrade.
	 * @param $installer Installer
	 * @param $attr array Attributes
	 * @return boolean
	 */
	function abort($installer, $attr) {
		$installer->setError(INSTALLER_ERROR_GENERAL, $attr['message']);
		return false;
	}

/**
	 * For 3.1.0 upgrade.  DefaultMenus Defaults
	 * @return boolean Success/failure
	 */
	function installDefaultNavigationMenus() {
		$contextDao = Application::getContextDAO();
		$navigationMenuDao = DAORegistry::getDAO('NavigationMenuDAO'); /* @var $navigationMenuDao NavigationMenuDAO */

$contexts = $contextDao->getAll();
		while ($context = $contexts->next()) {
			$navigationMenuDao->installSettings($context->getId(), 'registry/navigationMenus.xml');
		}

$navigationMenuDao->installSettings(CONTEXT_ID_NONE, 'registry/navigationMenus.xml');

return true;
	}

/**
	 * Check that the environment meets minimum PHP requirements.
	 * @return boolean Success/failure
	 */
	function checkPhpVersion() {
		if (version_compare(PHP_REQUIRED_VERSION, PHP_VERSION) != 1) return true;

$this->setError(INSTALLER_ERROR_GENERAL, 'installer.unsupportedPhpError');
		return false;
	}

/*
	 * Migrate site locale settings to a serialized array in the database
	 */
	function migrateSiteLocales() {
		$siteDao = DAORegistry::getDAO('SiteDAO'); /* @var $siteDao SiteDAO */

$result = $siteDao->retrieve('SELECT installed_locales, supported_locales FROM site');

$set = $params = [];
		$row = (array) $result->current();
		$type = 'array';
		foreach ($row as $column => $value) {
			if (!empty($value)) {
				$set[] = $column . ' = ?';
				$params[] = $siteDao->convertToDB(explode(':', $value), $type);
			}
		}
		$siteDao->update('UPDATE site SET ' . join(',', $set), $params);

return true;
	}

/**
	 * Migrate active sidebar blocks from plugin_settings to journal_settings
	 *
	 * @return boolean
	 */
	function migrateSidebarBlocks() {

$siteDao = DAORegistry::getDAO('SiteDAO'); /* @var $siteDao SiteDAO */
		$site = $siteDao->getSite();

$plugins = PluginRegistry::loadCategory('blocks');
		if (empty($plugins)) {
			return true;
		}

// Sanitize plugin names for use in sql IN().
		$sanitizedPluginNames = array_map(function($name) {
			return "'" . preg_replace("/[^A-Za-z0-9]/", '', $name) . "'";
		}, array_keys($plugins));

$pluginSettingsDao = DAORegistry::getDAO('PluginSettingsDAO'); /* @var $pluginSettingsDao PluginSettingsDAO */
		$result = $pluginSettingsDao->retrieve(
			'SELECT plugin_name, context_id, setting_value FROM plugin_settings WHERE plugin_name IN (' . join(',', $sanitizedPluginNames) . ') AND setting_name=\'context\';'
		);

$sidebarSettings = [];
		foreach ($result as $row) {
			if ($row->setting_value != 1) continue; // BLOCK_CONTEXT_SIDEBAR

$seq = $pluginSettingsDao->getSetting($row->context_id, $row->plugin_name, 'seq');
			if (!isset($sidebarSettings[$row->context_id])) {
				$sidebarSettings[$row->context_id] = [];
			}
			$sidebarSettings[$row->context_id][(int) $seq] = $row->plugin_name;
		}

foreach ($sidebarSettings as $contextId => $contextSetting) {
			// Order by sequence
			ksort($contextSetting);
			$contextSetting = array_values($contextSetting);
			if ($contextId) {
				$contextDao = Application::getContextDAO();
				$context = $contextDao->getById($contextId);
				$context->setData('sidebar', $contextSetting);
				$contextDao->updateObject($context);
			} else {
				$siteDao = DAORegistry::getDAO('SiteDAO'); /* @var $siteDao SiteDAO */
				$site = $siteDao->getSite();
				$site->setData('sidebar', $contextSetting);
				$siteDao->updateObject($site);
			}
		}

$pluginSettingsDao->update('DELETE FROM plugin_settings WHERE plugin_name IN (' . join(',', $sanitizedPluginNames ) . ') AND (setting_name=\'context\' OR setting_name=\'seq\');');

return true;
	}

/**
	 * Migrate the metadata settings in the database to use a single row with one
	 * of the new constants
	 */
	function migrateMetadataSettings() {
		$contextDao = Application::getContextDao();

$metadataSettings = [
			'coverage',
			'languages',
			'rights',
			'source',
			'subjects',
			'type',
			'disciplines',
			'keywords',
			'agencies',
			'citations',
		];

$result = $contextDao->retrieve('SELECT ' . $contextDao->primaryKeyColumn . ' from ' . $contextDao->tableName);
		$contextIds = [];
		foreach ($result as $row) {
			$row = (array) $row;
			$contextIds[] = $row[$contextDao->primaryKeyColumn];
		}

foreach ($metadataSettings as $metadataSetting) {
			foreach ($contextIds as $contextId) {
				$result = $contextDao->retrieve('
					SELECT * FROM ' . $contextDao->settingsTableName . ' WHERE
						' . $contextDao->primaryKeyColumn . ' = ?
						AND (
							setting_name = ?
							OR setting_name = ?
							OR setting_name = ?
						)
					',
					[
						$contextId,
						$metadataSetting . 'EnabledWorkflow',
						$metadataSetting . 'EnabledSubmission',
						$metadataSetting . 'Required',
					]
				);
				$value = METADATA_DISABLE;
				foreach ($result as $row) {
					if ($row->setting_name === $metadataSetting . 'Required' && $row->setting_value) {
						$value = METADATA_REQUIRE;
					} elseif ($row->setting_name === $metadataSetting . 'EnabledSubmission' && $row->setting_value && $value !== METADATA_REQUIRE) {
						$value = METADATA_REQUEST;
					} elseif ($row->setting_name === $metadataSetting . 'EnabledWorkflow' && $row->setting_value && $value !== METADATA_REQUEST && $value !== METADATA_REQUIRE) {
						$value = METADATA_ENABLE;
					}
				}

if ($value !== METADATA_DISABLE) {
					$contextDao->update('
						INSERT INTO ' . $contextDao->settingsTableName . ' (
							' . $contextDao->primaryKeyColumn . ',
							locale,
							setting_name,
							setting_value
						) VALUES (?, ?, ?, ?)',
						[
							$contextId,
							'',
							$metadataSetting,
							$value,
						]
					);
				}

$contextDao->update('
					DELETE FROM ' . $contextDao->settingsTableName . ' WHERE
						' . $contextDao->primaryKeyColumn . ' = ?
						AND (
							setting_name = ?
							OR setting_name = ?
							OR setting_name = ?
						)
					',
					[
						$contextId,
						$metadataSetting . 'EnabledWorkflow',
						$metadataSetting . 'EnabledSubmission',
						$metadataSetting . 'Required',
					]
				);
			}
		}

return true;
	}

/**
	 * Set the notification settings for journal managers and subeditors so
	 * that they are opted out of the monthly stats email.
	 */
	public function setStatsEmailSettings() {
		import('lib.pkp.classes.notification.PKPNotification'); // NOTIFICATION_TYPE_EDITORIAL_REPORT
		$roleIds = [ROLE_ID_MANAGER, ROLE_ID_SUB_EDITOR];

$userGroupDao = DAORegistry::getDAO('UserGroupDAO'); /* @var $userGroupDao UserGroupDAO */
		$notificationSubscriptionSettingsDao = DAORegistry::getDAO('NotificationSubscriptionSettingsDAO'); /* @var $notificationSubscriptionSettingsDao NotificationSubscriptionSettingsDAO */
		for ($contexts = Application::get()->getContextDAO()->getAll(true); $context = $contexts->next(); ) {
			foreach ($roleIds as $roleId) {
				for ($userGroups = $userGroupDao->getByRoleId($context->getId(), $roleId); $userGroup = $userGroups->next(); ) {
					for ($users = $userGroupDao->getUsersById($userGroup->getId(), $context->getId()); $user = $users->next(); ) {
						$notificationSubscriptionSettingsDao->update(
							'INSERT INTO notification_subscription_settings
								(setting_name, setting_value, user_id, context, setting_type)
								VALUES
								(?, ?, ?, ?, ?)',
							array(
								'blocked_emailed_notification',
								NOTIFICATION_TYPE_EDITORIAL_REPORT,
								$user->getId(),
								$context->getId(),
								'int'
							)
						);
					}
				}
			}
		}

return true;
	}

/**
	 * Fix library files, which were mistakenly named server-side using source filenames.
	 * See https://github.com/pkp/pkp-lib/issues/5471
	 * @return boolean
	 */
	public function fixLibraryFiles() {
		import('classes.file.LibraryFileManager');
		// Fetch all library files (no method currently in LibraryFileDAO for this)
		$libraryFileDao = DAORegistry::getDAO('LibraryFileDAO'); /* @var $libraryFileDao LibraryFileDAO */
		$result = $libraryFileDao->retrieve('SELECT * FROM library_files');
		$libraryFiles = new DAOResultFactory($result, $libraryFileDao, '_fromRow', array('id'));
		$wrongFiles = array();
		while ($libraryFile = $libraryFiles->next()) {
			$libraryFileManager = new LibraryFileManager($libraryFile->getContextId());
			$wrongFilePath = $libraryFileManager->getBasePath() .  $libraryFile->getOriginalFileName();
			$rightFilePath = $libraryFile->getFilePath();

if (isset($wrongFiles[$wrongFilePath])) {
				error_log('A potential collision was found between library files ' . $libraryFile->getId() . ' and ' . $wrongFiles[$wrongFilePath]->getId() . '. Please review the database entries and ensure that the associated files are correct.');
			} else {
				$wrongFiles[$wrongFilePath] = $libraryFile;
			}

// For all files for which the "wrong" filename exists and the "right" filename doesn't,
			// copy the "wrong" file over to the "right" one. This will leave the "wrong" file in
			// place, and won't disambiguate cases for which files were clobbered.
			if (file_exists($wrongFilePath) && !file_exists($rightFilePath)) {
				$libraryFileManager->copyFile($wrongFilePath, $rightFilePath);
			}
		}
		return true;
	}
}