Adding meta-boxes to plugin settings page. (Doesn't work)

adding-metaboxes-settings-page.php

<?php
/**
 * WP Malware Removal
 *
 * @package     WP Malware Removal
 * @author      Shivanand Sharma
 * @copyright   2018 ConverticaCommerce.Com
 * @license     MIT
 *
 * @wordpress-plugin
 * Plugin Name: WP Malware Removal
 * Plugin URI:  https://www.converticacommerce.com/
 * Description: Malware scanner for your WP website.
 * Version:     0.1
 * Author:      Shivanand Sharma
 * Author URI:  https://www.converticacommerce.com/
 * Text Domain: wpmr
 * License:     MIT
 * License URI: https://opensource.org/licenses/MIT
 */

define( 'WPMR_PLUGIN_DIR', trailingslashit(plugin_dir_url( __FILE__ )));

class WPMR_Init {

    private $status = array(
        'start_time' => false,
        'end_time' => false,
        'altered'=>array(), // changed files
        'altered'=>array(), // changed files
        'skipped' => array(), // skipped files
        'matched' => array(), // good files
        'errors' => array(), // any errors
        'empty' => array(), // total number of empty directories
        'dirs' => array(), // total number of directories
        'files' => array(), // total number of files
        'notices' => array(), // any notices encountered like no files to scan etc.
        'state' => false
    );

    /* Get the engine going */
    public function __construct() {
        add_filter( 'plugin_action_links_' . plugin_basename( __FILE__ ), array( $this, 'plugin_action_links' ) );
        add_action( 'admin_enqueue_scripts', array( $this, 'plugin_styles' ) );
        add_action( 'admin_menu', array( $this, 'settings_menu' ) );

        add_action( 'wp_ajax_wpmr_clear_log', array( $this, 'wpmr_clear_log' ));
        add_action( 'wp_ajax_wpmr_init_scan', array( $this, 'wpmr_init_scan' ));
        add_action( 'wp_ajax_wpmr_get_progress', array( $this, 'wpmr_get_progress' ));
        
        add_action( 'wp_ajax_nopriv_wpmr_clear_log', '__return_false' );
        add_action( 'wp_ajax_nopriv_wpmr_init_scan', '__return_false' );
        add_action( 'wp_ajax_nopriv_wpmr_check_files', '__return_false' );
        
        add_action( 'admin_footer',  array( $this, 'scripts'));

        /* Load the results meta boxes. */
        add_action( "load-toplevel_page_wpmr", array($this, 'load_meta_boxes' ));
        /* Create a hook for adding meta boxes. */
        add_action( 'load-toplevel_page_wpmr', array($this, 'add_meta_boxes' ));
        
    }

    function load_meta_boxes(){
        add_action( 'add_meta_boxes', array($this, 'wpmr_add_results' ));

    }

    function wpmr_add_results(){
        add_meta_box( 'wpmr-results-box', 'Title', array($this, 'meta_box_results'), 'toplevel_page_wpmr', 'main', 'high' );
    }

    function add_meta_boxes(){
        do_action( 'add_meta_boxes', 'toplevel_page_wpmr' );
    }

    function meta_box_results(){ ?>
        meta_box_results
    <?php
    }

    /* Add links below the plugin name on the plugins page */
    function plugin_action_links($links){
        $links[] = '<a href="'. esc_url( get_admin_url(null, 'options-general.php?page=wpmr') ) .'">Run Site Scan</a>';
        return $links;
    }

    /* Enqueue the styles for admin page */
    function plugin_styles(){
        $screen = get_current_screen();
		if( $screen->id == 'toplevel_page_' . basename( __FILE__ , '.php') ) {
			wp_enqueue_style( 'wpmr-stylesheet', WPMR_PLUGIN_DIR . 'assets/admin-styles.css' );
		}
    }

    /* Outputs any variable / php objects / arrays in a clear visible frmat */
    function llog($str, $echo = true) {
        if($echo){
            echo '<pre>';
            print_r($str);
            echo '</pre>';
        }
        else {
            return print_r($str, 1);
        }
    }
    
    /* Add the settings menu to WP Admin */
    function settings_menu(){
        $hook_suffix = add_menu_page(
			'Malware Removal', 
			'Malware Removal', 
			'manage_options', 
			'wpmr', 
			array( $this, 'settings_page' )
        );
        //$this->llog($hook_suffix);
        //die();
        add_submenu_page( 'wpmr', 'Tools', 'Tools', 'manage_options' , 'wpmr-tools', array($this, 'wpmrtools'));
    }
    
    /* Render the settings page */
    function settings_page(){
        ?>
        <div class="wrap">
            <h1>WP Malware Removal</h1>
            <div class="container-wrap">
                <div class="container">
                    <div class="gauge-a"></div>
                    <div class="gauge-c"></div>
                    <div class="gauge-data">
                        <h1 id="percent"></h1>
                    </div>
                </div>
                <div id="lcd"></div>
            </div>
            <div id="ux">
                <input type="submit" value="Start Scan" id="scan-control" data-state="0" class="button-primary"/>
            </div>
            <div class="scan-results">
                <h3>Results:</h3>
                <p>Core WordPress files will be checked for integrity. Core themes &amp; plugins may show altered after updating. Non-WordPress files will be skipped.</p>
                <div id="scan-results"></div>
                </div>
                <div id="postbox-container-1" class="postbox-container">
                    <?php do_meta_boxes( 'toplevel_page_wpmr', 'main', null ); ?>
                </div><!-- #postbox-container-1 -->
        </div>
    <?php
    }

     /* Ajax request handler for triggering scan */
     function wpmr_init_scan(){
        $this->status['state'] = 'initializing';
        $this->status['start_time'] = microtime(true);
        $this->run_tests();
        wp_die();
    }

    function save_progress($progress){
        update_option("WPMR_scan_log", $progress);
    }

    function wpmr_get_progress(){
        wp_die(json_encode(get_option('WPMR_scan_log')));
    }

    function wpmr_clear_log(){
        wp_die(delete_option("WPMR_scan_log"));
    }
    
    function file_integrity_check($local_file){
        $checksums = $this->get_checksums();
        $install_path = get_home_path();
        $file = array();
       
        //foreach($local_files as $local) {
            $match_path = str_replace($install_path,'', $local_file );
            if(array_key_exists($match_path, $checksums)) {
                if($checksums[$match_path] != md5_file($local_file)){
                    //$this->status['altered'][] = $file;
                    //$this->status['files'][$file]['altered'];
                    return 'altered';
                }
                else{
                    //$this->status['matched'][] = $file;
                    //$this->status['files'][$file]['matched'];
                    return  'matched';
                }
            }
            else{
                //$this->status['skipped'][] = $file;
                //$this->status['files'][$file]['skipped'];
                return 'skipped';
            }
           
        //}
        
    }

    /* Collect all files to scan */
    function get_all_files($path = false) {
        if(!$path) {
            $path = untrailingslashit( get_home_path() );
        }
        $this->get_checksums();
        
        if(is_dir($path)) {
            $children = @scandir($path);
            
            if(is_array($children)) {
                if($path == '/var/www/html/dev/wp-sandbox/wp-content/plugins/advanced-wp-reset') {
                    //$this->llog(is_array($children)); 
                }
                $children = array_diff($children, array('..', '.'));
                $dirs = array();
                $files = array();
                foreach( $children  as $child ) {
                    $target = trailingslashit($path) . $child;
                    if(is_dir($target)) {
                        $elements = $this->get_all_files($target);
                        
                        if($elements) { // check for read/write errors

                            foreach($elements as $element) {
                                $files[] = $element;
                            }
                        }
                    }
                    if(is_file($target)) {
                        $files[] = $target;
                    }
                }
                return $files;
            }
        }
    }

    function run_tests() {
        $files = $this->get_all_files();

        $tests = array();
        $i = 0;
        $current = 0;
        $percent = 0;
        $total = count($files);
        $start = microtime(true);
       
        foreach($files as $file) {
            $i++;
            $current++;
            $percent = round(( $current / $total ) * 100, 2);
            
            $tests[$file]['md5'] = $this->file_integrity_check($file);
            //if($i = 8) {
            //    break;
            //}
            if( ($current % 5) == 0 || $percent == 100) {
                $time_lapse = (microtime(TRUE) - $start );
                $this->save_progress(array('percent' => $percent, 'scanned' => $current, 'total' => $total, 'time' => $time_lapse, 'memory' => (memory_get_peak_usage(true)/1024/1024),  'math' => "$current:$total", 'result' => $tests));
                usleep(10000);
            }
        }
    }

    /* Update hashes for all WP core files */
    function get_checksums(){
        $checksums = get_transient( 'WPMR_checksums' );
        if(! $checksums) {
            global $wp_version;
            $checksums = get_core_checksums( $wp_version, get_locale() );
            if($checksums) {
                set_transient( 'WPMR_checksums',$checksums, 12 * HOUR_IN_SECONDS );
                return $checksums;
            }
            return;
        }
        else {
            return $checksums;
        }
    }

    function read_error($path) {
        if (!file_exists($path)) {
            return 'are you sure this file exists?: '. $path;
        }
        if (!is_readable($path) ) {
            return 'are you sure this file is readable?:' . $path;
        }
        return (is_array($error) && isset($error["message"])?preg_replace('/[\r\n]/', ' ', print_r($error["message"],1)):"readable?");
    }

    /* JS routine to handle user-events and reporting */
    function scripts(){
    ?>
    <script type="text/javascript" >
    jQuery(document).ready(function ($) { //wrapper
        $("#scan-control").click(function () { //event
            $('.container .gauge-c').css('transform', 'rotate( 0turn)');
            $('#scan-results').html('');

            switch ($("#scan-control").attr('data-state')) {
                case '1':
                    $("#scan-control").attr('data-state', '0');
                    break;
                default:
                    total_files = 0;
                    $("#scan-control").attr('disabled', 'disabled');
                    wpmr_clear_log = {
                        _ajax_nonce: '<?php echo wp_create_nonce( 'wpmr' ); ?>',
                        action: "wpmr_clear_log",
                    };
                    $.post(ajaxurl, wpmr_clear_log, function (response) { //initialize and setup everything
                        console.log()
                        wpmr_init_scan = {
                            _ajax_nonce: '<?php echo wp_create_nonce( 'wpmr' ); ?>',
                            action: "wpmr_init_scan",
                        };
                        $.post(ajaxurl, wpmr_init_scan, function (response) { //initialize and setup everything
                        }); // ajax post
                        //interval = setInterval(get_progress, 1000); // get recurring progress
                        get_progress();

                        function get_progress() {
                            wpmr_get_progress = {
                                _ajax_nonce: '<?php echo wp_create_nonce( 'wpmr' ); ?>',
                                action: "wpmr_get_progress", //action
                            };

                            $.post(ajaxurl, wpmr_get_progress, function (progress) {
                                result = JSON.parse(progress);
                                if(result == false) {
                                    return get_progress();
                                }
                                //console.log(result)
                                progress = result.percent;
                                
                                scan_output = result.result;
                                //console.log(scan_output.length);
                                html = '';
                                Object.keys(scan_output).forEach(function(key) {
                                    if(scan_output[key].md5 == 'altered'){
                                        html += '<p class="record"><span class="result md5 altered">altered</span>' + key +  '</p>';
                                    }
                                    if(scan_output[key].md5 == 'skipped'){
                                        //html += '<p class="record"><span class="result md5 non-wp">non-wp</span>' + key +  '</p>';
                                    }
                                    
                                });
                                $('#scan-results').html(html);

                                $('#percent').html('<span class="percentage">' + parseFloat(progress).toFixed(0) + '%</span><br /><span class="time">' + Math.round(result.time) + ' sec</span>' );
                                $('#lcd').html('<span class="stats"><span class="speed"><span class="digits">' + parseFloat((result.scanned) / result.time).toFixed(1)  + '</span><span class="rate">&nbsp;files / sec</span></span><span class="ram">'+result.memory+'mb ram</span>' ).fadeIn(2000);
                                $('.container .gauge-c').css('transform', 'rotate( ' + (.005 * progress) + 'turn)');

                                if (progress < 100) {
                                    return get_progress();
                                } else {
                                    console.log(progress);
                                    $("#scan-control").val('Re-Scan');
                                    $("#scan-control").removeAttr('disabled');
                                }
                            });
                        }
                    });
            } // switch
        }); //click
    }); //ready
    </script>
    <?php
    }

    function wpmrtools() { ?>
        <div class="wrap">
        <h1>Diagnostic Tools</h1>
        <?php
        
        $this->status['state'] = 'initializing';
        $start = microtime(true);
        $this->status['start_time'] = $start;
        //$this->llog($this->get_all_files());
        $this->wpmr_init_scan();
        $this->llog( "Mem peak usage: " . (memory_get_peak_usage(true)/1024/1024)." MiB" );
        $time = (microtime(true) - $start);
        $this->llog( "Completed in: $time micro-seconds" );
        $this->llog($this->status);
        //$this->get_all_files();
        echo '
        <h2>Test these first</h2>
        <b>Click on any of the links below to run your site through the tool.</b><br>
        <div id="toolscol1">
        <a id="tool" target="_blank" href="https://www.google.com/transparencyreport/safebrowsing/diagnostic/index.html#url='.get_site_url().'">Google Safe Browsing Tool</a><br>
        <a id="tool" target="_blank" href="https://sitecheck.sucuri.net/results/'.get_site_url().'">Sucuri Website Malware Scanner</a><br>
        </div>
        <div id="toolscol2">
        <a id="tool" target="_blank" href="https://www.virustotal.com/#/domain/'.get_site_url().'">VirusTotal Analyzer</a><br>
        <a id="tool" target="_blank" href="https://tools.geekflare.com/report/screenshot/'.get_site_url().'">Geek Flare Screenshot Checker</a>
        <a id="tool" target="_blank" href="https://tools.geekflare.com/report/screenshot/'.get_site_url().'">Geek Flare Blacklist Test</a>
        </div>
        <div id="toolscol3">
        <a id="tool" target="_blank" href="https://geopeeker.com/fetch/?url='.get_site_url().'">GeoPeeker Peek Results</a><br>
        <a id="tool" target="_blank" href="https://tools.geekflare.com/report/https-test/'.get_site_url().'">Geek Flare DNSSEC Test</a>
        <a id="tool" target="_blank" href="https://tools.geekflare.com/report/https-test/'.get_site_url().'">Geek Flare HTTP/2 Test</a>
        </div>
        '; ?>
        </div>
        <?php
    }
}

$wpmr_init = new WPMR_Init();