public static function run()
 {
     spl_autoload_register(['Bootstrap', 'autoload']);
     putenv('LANG=en_US.UTF-8');
     setlocale(LC_CTYPE, 'en_US.UTF-8');
     date_default_timezone_set(@date_default_timezone_get());
     session_start();
     $session = new Session($_SESSION);
     $request = new Request($_REQUEST);
     $setup = new Setup($request->query_boolean('refresh', false));
     $context = new Context($session, $request, $setup);
     if ($context->is_api_request()) {
         (new Api($context))->apply();
     } else {
         if ($context->is_info_request()) {
             $public_href = $setup->get('PUBLIC_HREF');
             $x_head_tags = $context->get_x_head_html();
             require __DIR__ . '/pages/info.php';
         } else {
             $public_href = $setup->get('PUBLIC_HREF');
             $x_head_tags = $context->get_x_head_html();
             $fallback_html = (new Fallback($context))->get_html();
             require __DIR__ . '/pages/index.php';
         }
     }
 }

 public function __construct(Setup $setup)
 {
     $this->setup = $setup;
     $this->storageMode = 'flat-file';
     $metadata_file = $this->setup->dir . '/.metadata';
     $update_metadata = false;
     // Read exist metadata file if one exists
     if (file_exists($metadata_file)) {
         $json_metadata = json_decode(file_get_contents($metadata_file), true);
         $this->setup->metadata = array_merge($this->setup->metadata, $json_metadata);
     }
     // Check if comment thread directory exists
     if ($setup->mode !== 'api') {
         if (file_exists(dirname($metadata_file)) and is_writable(dirname($metadata_file))) {
             // Check whether the page and metadata URLs differ
             if ($this->setup->metadata['title'] !== $setup->pageTitle) {
                 $this->setup->metadata['title'] = $setup->pageTitle;
                 $update_metadata = true;
             }
             // Check whether the page and metadata titles differ
             if ($this->setup->metadata['url'] !== $setup->pageURL) {
                 $this->setup->metadata['url'] = $setup->pageURL;
                 $update_metadata = true;
             }
             // Update metadata if the data has changed
             if ($update_metadata === true) {
                 if ($this->save_metadata($this->setup->metadata, $metadata_file) === false) {
                     exit($setup->escapeOutput('<b>HashOver</b>: Failed to create metadata file.', 'single'));
                 }
             }
         }
     }
 }

 /**
  * Given a valid servive URI and a valid string of JSON,
  * this method communcates with the SiCDS and returns a
  * list of all unique ID's
  *
  * @param string $uri
  * @param string $json
  * @return string
  */
 public function InterafceWithSiCDS($uri, $json)
 {
     include_once Setup::Modules_Directory() . "/SiSW/ServiceWrapper.php";
     $service = new \Swiftriver\Core\Modules\SiSW\ServiceWrapper($uri);
     $jsonFromService = $service->MakePOSTRequest(array("data" => $json), 5);
     return $jsonFromService;
 }

 private function __construct()
 {
     $settings = Setup::getSettings();
     $config = \Doctrine\ORM\Tools\Setup::createXMLMetadataConfiguration([__DIR__ . '/../Mapper', 'Bh/Mapper'], $settings['DevMode']);
     $conn = array('driver' => 'pdo_mysql', 'user' => $settings['DbUser'], 'password' => $settings['DbPass'], 'dbname' => $settings['DbName']);
     self::$entityManager = \Doctrine\ORM\EntityManager::create($conn, $config);
 }

 protected function setUp()
 {
     include_once dirname(__FILE__) . "/../Setup.php";
     $config = Setup::Configuration();
     include_once $config["SwiftriverCoreDirectory"] . "/ObjectModel/Content.php";
     include_once dirname(__FILE__) . "/../TextForUrlParser.php";
 }

 /**
  * If you made changes to config, you may call this to persist the changes
  * back to disk
  */
 protected function saveConfig()
 {
     if (!isset($this->config)) {
         return;
     }
     Setup::save();
 }

 protected function setUp()
 {
     include_once dirname(__FILE__) . "/../../../Modules/TagTheNetInterface/Setup.php";
     $config = Setup::Configuration();
     include_once $config["SwiftriverCoreDirectory"] . "/ObjectModel/Content.php";
     include_once $config["SwiftriverCoreDirectory"] . "/ObjectModel/Tag.php";
     include_once dirname(__FILE__) . "/../../../Modules/TagTheNetInterface/ContentFromJSONParser.php";
 }

 /**
  * @param \Saigon\Conpago\IDbConfig $dbConfig
  * @param \Saigon\Conpago\IDoctrineConfig $doctrineConfig
  */
 public function __construct(IDBConfig $dbConfig, IDoctrineConfig $doctrineConfig)
 {
     $this->dbConfig = $dbConfig;
     $this->doctrineConfig = $doctrineConfig;
     $paths = array($this->doctrineConfig->getModelPath());
     $this->setDbParams();
     $config = Setup::createAnnotationMetadataConfiguration($paths, $this->doctrineConfig->getDevMode());
     $this->entityManager = EntityManager::create($this->dbParams, $config);
 }

 /**
  * Check plugin requirements.
  *
  * @return bool True is fails requirements. False otherwise.
  */
 public function maybe_self_deactivate()
 {
     if (false === Setup::meets_requirements()) {
         add_action('admin_init', array('HM\\BackUpWordPress\\Setup', 'self_deactivate'));
         add_action('admin_notices', array('HM\\BackUpWordPress\\Setup', 'display_admin_notices'));
         return true;
     }
     return false;
 }

 public function database(\Base $f3)
 {
     $this->response->data['SUBPART'] = 'settings_database.html';
     $cfg = \Config::instance();
     if ($f3->get('VERB') == 'POST' && $f3->exists('POST.active_db')) {
         $type = $f3->get('POST.active_db');
         $cfg->{'DB_' . $type} = $f3->get('POST.DB_' . $type);
         $cfg->ACTIVE_DB = $type;
         $cfg->save();
         \Flash::instance()->addMessage('Config saved', 'success');
         $setup = new \Setup();
         $setup->install($type);
         // logout
         $f3->clear('SESSION.user_id');
     }
     $cfg->copyto('POST');
     $f3->set('JIG_format', array('JSON', 'Serialized'));
 }

 public function __construct(Setup $setup)
 {
     $this->setup = $setup;
     $this->storageMode = $setup->databaseType;
     try {
         if ($setup->databaseType === 'sqlite') {
             $this->database = new PDO('sqlite:' . $setup->rootDirectory . '/pages/' . $setup->databaseName . '.sqlite');
         } else {
             $sql_connection = 'host=' . $setup->databaseHost . ';' . 'dbname=' . $setup->databaseName . ';' . 'charset=' . $setup->databaseCharset;
             $this->database = new PDO($setup->databaseType . ':' . $sql_connection, $setup->databaseUser, $setup->databasePassword);
         }
     } catch (PDOException $error) {
         exit($setup->escapeOutput($error->getMessage(), 'single'));
     }
     // Create comment tread table
     $create = 'CREATE TABLE IF NOT EXISTS \'' . $setup->threadDirectory . '\' ' . '(id TEXT PRIMARY KEY,' . ' name TEXT,' . ' password TEXT,' . ' login_id TEXT,' . ' email TEXT,' . ' encryption TEXT,' . ' website TEXT,' . ' date TEXT,' . ' likes TEXT,' . ' dislikes TEXT,' . ' notifications TEXT,' . ' ipaddr TEXT,' . ' status TEXT,' . ' body TEXT)';
     $this->database->exec($create);
 }

 /**
  * Given a valid servive URI and a valid string of text
  * this service wraps the TagThe.Net taggin service
  *
  * @param string $uri
  * @param string $json
  * @return string
  */
 public function InterafceWithService($uri, $text)
 {
     $config = Setup::Configuration();
     require $config["SwiftriverModulesDirectory"] . "/SwiftriverServiceWrapper/ServiceWrapper.php";
     $uri = str_replace("?view=json", "", $uri);
     $uri = $uri . "?view=json&text=" . $text;
     $service = new \Swiftriver\Core\Modules\SiSW\ServiceWrapper($uri);
     $jsonFromService = $service->MakeGETRequest();
     return $jsonFromService;
 }

 /**
  * Get the shared instance for the logger
  * @return \Log
  */
 public static function GetLogger()
 {
     $log = new \Log("this message is ignored, however not supplying one throws an error :o/");
     $logger = $log->singleton('file', Setup::Configuration()->CachingDirectory . "/log.log", '   ');
     if (!self::Configuration()->EnableDebugLogging) {
         $mask = \Log::UPTO(\PEAR_LOG_INFO);
         $logger->setMask($mask);
     }
     return $logger;
 }

 /**
  * Get database config.
  * load it from setup, fall back to legacy config.php constants
  *
  * @return array
  */
 public static function getConfig()
 {
     $setup = Setup::get();
     if (isset($setup['database'])) {
         $config = $setup['database']->toArray();
     } else {
         // legacy: import from constants
         $config = array('driver' => APP_SQL_DBTYPE, 'hostname' => APP_SQL_DBHOST, 'database' => APP_SQL_DBNAME, 'username' => APP_SQL_DBUSER, 'password' => APP_SQL_DBPASS, 'port' => APP_SQL_DBPORT, 'table_prefix' => APP_TABLE_PREFIX);
         // save it back. this will effectively do the migration
         Setup::save(array('database' => $config));
     }
     return $config;
 }

 public function testParseToRequestJson()
 {
     include_once dirname(__FILE__) . "/../../../Setup.php";
     include_once dirname(__FILE__) . "/../../../Modules/SiCDSInterface/Parser.php";
     include_once dirname(__FILE__) . "/../../../Modules/SiCDSInterface/SiCDSPreProcessingStep.php";
     include_once dirname(__FILE__) . "/../../../Modules/SiCDSInterface/ServiceInterface.php";
     $item = new ObjectModel\Content();
     $item->id = "testId";
     $item->difs = array(new ObjectModel\DuplicationIdentificationFieldCollection("names", array(new ObjectModel\DuplicationIdentificationField("first", "homer"), new ObjectModel\DuplicationIdentificationField("second", "simpson"))));
     $configuration = new MockConfiguration();
     $SiCDS = new \Swiftriver\PreProcessingSteps\SiCDSPreProcessingStep();
     $SiCDS->Process(array($item), $configuration, Setup::GetLogger());
 }

 function &init()
 {
     static $instance;
     if (!isset($instance)) {
         require_once 'base_CLI.class.php';
         if (base_CLI::runningFromCLI()) {
             $interface = 'cli';
         } else {
             $interface = 'web';
         }
         $instance =& Setup::factory($interface);
     }
     return $instance;
 }

 /**
  * Notifies site administrators of the error condition
  *
  * @access private
  * @param  mixed $error_msg The error message
  * @param  string $script The script name where the error happened
  * @param  integer $line The line number where the error happened
  */
 function _notify($error_msg = "unknown", $script = "unknown", $line = "unknown")
 {
     global $HTTP_SERVER_VARS;
     $setup = Setup::load();
     $notify_list = trim($setup['email_error']['addresses']);
     if (empty($notify_list)) {
         return false;
     }
     $notify_list = str_replace(';', ',', $notify_list);
     $notify_list = explode(',', $notify_list);
     $subject = APP_SITE_NAME . " - Error found! - " . date("m/d/Y H:i:s");
     $msg = "Hello,\n\n";
     $msg .= "An error was found at " . date("m/d/Y H:i:s") . " (" . time() . ") on line '" . $line . "' of script " . "'{$script}'.\n\n";
     $msg .= "The error message passed to us was:\n\n";
     if (is_array($error_msg) && count($error_msg) > 1) {
         $msg .= "'" . $error_msg[0] . "'\n\n";
         $msg .= "A more detailed error message follows:\n\n";
         $msg .= "'" . $error_msg[1] . "'\n\n";
     } else {
         $msg .= "'{$error_msg}'\n\n";
     }
     @($msg .= "That happened on page '" . $HTTP_SERVER_VARS["PHP_SELF"] . "' from IP Address '" . getenv("REMOTE_ADDR") . "' coming from the page (referrer) '" . getenv("HTTP_REFERER") . "'.\n\n");
     @($msg .= "The user agent given was '" . $HTTP_SERVER_VARS['HTTP_USER_AGENT'] . "'.\n\n");
     $msg .= "Sincerely yours,\nAutomated Error_Handler Class";
     // only try to include the backtrace if we are on PHP 4.3.0 or later
     if (version_compare(phpversion(), "4.3.0", ">=")) {
         $msg .= "\n\nA backtrace is available:\n\n";
         ob_start();
         $backtrace = debug_backtrace();
         // remove the two entries related to the error handling stuff itself
         array_shift($backtrace);
         array_shift($backtrace);
         // now we can print it out
         print_r($backtrace);
         $contents = ob_get_contents();
         $msg .= $contents;
         ob_end_clean();
     }
     // avoid triggering an email notification about a query that
     // was bigger than max_allowed_packet (usually 16 megs on 3.23
     // client libraries)
     if (strlen($msg) > 16777216) {
         return false;
     }
     foreach ($notify_list as $notify_email) {
         $mail = new Mail_API();
         $mail->setTextBody($msg);
         $mail->send($setup['smtp']['from'], $notify_email, $subject);
     }
 }

 /**
  * Creates a lock file for the given name.
  * Returns FALSE if lock couldn't be created (lock already exists)
  *
  * @param int $issue_id Issue Id what is being locked
  * @param string $usr_id User Id who locked the issue
  * @return bool
  */
 public static function acquire($issue_id, $usr_id)
 {
     $setup = Setup::load();
     $lock_ttl = $setup['issue_lock'];
     $expires = time() + $lock_ttl;
     if (self::isLocked($issue_id)) {
         $info = self::getInfo($issue_id);
         // allow lock, if locked by user himself
         if ($info['usr_id'] != $usr_id) {
             return false;
         }
     }
     $lockfile = self::getLockFilename($issue_id);
     $info = array('usr_id' => $usr_id, 'expires' => $expires);
     $fp = fopen($lockfile, 'w');
     flock($fp, LOCK_EX);
     fwrite($fp, serialize($info));
     flock($fp, LOCK_UN);
     fclose($fp);
     return true;
 }

 /**
  * Logs the error condition to a specific file and if asked and possible
  * queue error in mail queue for reporting.
  *
  * @param  mixed $error_msg The error message
  * @param  string $script The script name where the error happened
  * @param  integer $line The line number where the error happened
  * @param  boolean $notify_error Whether error should be notified by email.
  */
 public static function logError($error_msg = 'unknown', $script = 'unknown', $line = 0, $notify_error = true)
 {
     $msg =& self::_createErrorReport($error_msg, $script, $line);
     if (is_resource(APP_ERROR_LOG)) {
         fwrite(APP_ERROR_LOG, date('[D M d H:i:s Y] '));
         fwrite(APP_ERROR_LOG, $msg);
     } else {
         file_put_contents(APP_ERROR_LOG, array(date('[D M d H:i:s Y] '), $msg), FILE_APPEND);
     }
     // if there's no database connection, then we cannot possibly queue up the error emails
     $dbh = DB_Helper::getInstance();
     if ($notify_error === false || !$dbh) {
         return;
     }
     $setup = Setup::get();
     if (isset($setup['email_error']['status']) && $setup['email_error']['status'] == 'enabled') {
         $notify_list = trim($setup['email_error']['addresses']);
         if (empty($notify_list)) {
             return;
         }
         self::_notify($msg, $setup['smtp']['from'], $notify_list);
     }
 }

function write_config()
{
    $setup = new Setup();
    if ($setup->mysqlConfigExists()) {
        return 'config already exist';
    }
    $mysql_data['host'] = $_POST['mysql_server'];
    $mysql_data['user'] = $_POST['user_name'];
    $mysql_data['passwd'] = $_POST['user_passwd'];
    $mysql_data['db'] = $_POST['db'];
    if (!$setup->mysqlConfigIsValid($mysql_data)) {
        $mysql_admin['user'] = $_POST['admin_name'];
        $mysql_admin['passwd'] = $_POST['admin_passwd'];
        $setup->createUser($mysql_data, $mysql_admin);
    }
    if ($setup->mysqlConfigIsValid($mysql_data)) {
        $setup->writeMysqlConfig($mysql_data);
    } else {
        return 'invalid config';
    }
}