woothemes / sensei

includes/class-sensei-modules.php

<?php

For compatibility and reusability of your code, PSR1 recommends that a file should introduce either new symbols (like classes, functions, etc.) or have side-effects (like outputting something, or including other files), but not both at the same time. The first symbol is defined on line 15 and the first side effect is on line 3.

if ( ! defined( 'ABSPATH' ) ) exit;

/**
 * Sensei Modules Class
 *
 * Sensei Module Functionality
 *
 * @package Content
 * @author Automattic
 *
 * @since 1.8.0
 */
class Sensei_Core_Modules
{
    private $dir;
    private $file;
    private $assets_dir;
    private $assets_url;
    private $order_page_slug;
    public $taxonomy;

    public function __construct( $file )
    {
        $this->file = $file;
        $this->dir = dirname($this->file);
        $this->assets_dir = trailingslashit($this->dir) . 'assets';
        $this->assets_url = esc_url(trailingslashit(plugins_url('/assets/', $this->file)));
        $this->taxonomy = 'module';
        $this->order_page_slug = 'module-order';

        // setup taxonomy
        add_action( 'init', array( $this, 'setup_modules_taxonomy' ), 10 );

        // Manage lesson meta boxes for taxonomy
        add_action('add_meta_boxes', array($this, 'modules_metaboxes'), 20, 2 );

        // Save lesson meta box
        add_action('save_post', array($this, 'save_lesson_module'), 10, 1);

        //Reset the none modules lessons transient
        add_action( 'save_post', array( 'Sensei_Core_Modules', 'reset_none_modules_transient' ) );

        // Frontend styling
        add_action('wp_enqueue_scripts', array($this, 'enqueue_styles'));

        // Admin styling
        add_action('admin_enqueue_scripts', array($this, 'admin_enqueue_styles'));
        add_action('admin_enqueue_scripts', array($this, 'admin_enqueue_scripts'),  20 , 2 );

        // Handle module completion record
        add_action('sensei_lesson_status_updated', array($this, 'update_lesson_status_module_progress'), 10, 3);
        add_action('sensei_user_lesson_reset', array($this, 'save_lesson_module_progress'), 10, 2);
        add_action('wp', array($this, 'save_module_progress'), 10);

        // Handle module ordering
        add_action('admin_menu', array($this, 'register_modules_admin_menu_items'), 30 );
        add_filter('manage_edit-course_columns', array($this, 'course_columns'), 11, 1);
        add_action('manage_posts_custom_column', array($this, 'course_column_content'), 11, 2);

        // Ensure modules always show under courses
        add_action( 'admin_menu', array( $this, 'remove_lessons_menu_model_taxonomy' ) , 10 );
        add_action( 'admin_menu', array( $this, 'remove_courses_menu_model_taxonomy' ) , 10 );
        add_action( 'admin_menu', array( $this, 'redirect_to_lesson_module_taxonomy_to_course' ) , 20 );

        // Add course field to taxonomy
        add_action($this->taxonomy . '_add_form_fields', array($this, 'add_module_fields'), 50, 1);
        add_action($this->taxonomy . '_edit_form_fields', array($this, 'edit_module_fields'), 1, 1);
        add_action('edited_' . $this->taxonomy, array($this, 'save_module_course'), 10, 2);
        add_action('created_' . $this->taxonomy, array($this, 'save_module_course'), 10, 2);
        add_action('wp_ajax_sensei_json_search_courses', array($this, 'search_courses_json'));

        // Manage module taxonomy archive page
        add_filter('template_include', array($this, 'module_archive_template'), 10);
        add_action('pre_get_posts', array($this, 'module_archive_filter'), 10, 1);
        add_filter('sensei_lessons_archive_text', array($this, 'module_archive_title'));
        add_action('sensei_content_lesson_inside_before', array($this, 'module_archive_description'), 11);
        add_action('sensei_pagination', array($this, 'module_navigation_links'), 11);
        add_filter('body_class', array($this, 'module_archive_body_class'));

        // add modules to the single course template
        add_action( 'sensei_single_course_content_inside_after', array($this, 'load_course_module_content_template') , 8 );

        //Single Course modules actions. Add to single-course/course-modules.php
        add_action('sensei_single_course_modules_before',array( $this,'course_modules_title' ), 20);

        // Set up display on single lesson page
        add_filter('sensei_breadcrumb_output', array($this, 'module_breadcrumb_link'), 10, 2);

        // Add 'Modules' columns to Analysis tables
        add_filter('sensei_analysis_overview_columns', array($this, 'analysis_overview_column_title'), 10, 2);
        add_filter('sensei_analysis_overview_column_data', array($this, 'analysis_overview_column_data'), 10, 3);
        add_filter('sensei_analysis_course_columns', array($this, 'analysis_course_column_title'), 10, 2);
        add_filter('sensei_analysis_course_column_data', array($this, 'analysis_course_column_data'), 10, 3);

        // Manage module taxonomy columns
        add_filter('manage_edit-' . $this->taxonomy . '_columns', array($this, 'taxonomy_column_headings'), 1, 1);
        add_filter('manage_' . $this->taxonomy . '_custom_column', array($this, 'taxonomy_column_content'), 1, 3);
        add_filter('sensei_module_lesson_list_title', array($this, 'sensei_course_preview_titles'), 10, 2);

        //store new modules created on the course edit screen
        add_action( 'wp_ajax_sensei_add_new_module_term', array( 'Sensei_Core_Modules','add_new_module_term' ) );

        // for non admin users, only show taxonomies that belong to them
        add_filter('get_terms', array( $this, 'filter_module_terms' ), 20, 3 );
        add_filter('get_object_terms', array( $this, 'filter_course_selected_terms' ), 20, 3 );

        // add the teacher name next to the module term in for admin users
        add_filter('get_terms', array( $this, 'append_teacher_name_to_module' ), 70, 3 );

        // remove the default modules  metabox
        add_action('admin_init',array( 'Sensei_Core_Modules' , 'remove_default_modules_box' ));

    } // end constructor

    /**
     * Alter a module term slug when a new taxonomy term is created
     * This will add the creators user name to the slug for uniqueness.
     *
     * @since 1.8.0
     *
     * @param $term_id
     * @param $tt_id
     * @param $taxonomy
     *
     * @return void
     * @deprecated since 1.9.0
     */
    public function change_module_term_slug( $term_id, $tt_id, $taxonomy ){

The parameter $term_id is not used and could be removed.

The parameter $tt_id is not used and could be removed.

The parameter $taxonomy is not used and could be removed.

        _deprecated_function('change_module_term_slug', '1.9.0' );

    }// end add_module_term_group

    /**
     * Hook in all meta boxes related tot he modules taxonomy
     *
     * @since 1.8.0
     *
     * @param string $post_type
     * @param WP_Post $post
     *
     * @return void
     */
    public function modules_metaboxes( $post_type, $post )

The parameter $post is not used and could be removed.

    {
        if ('lesson' == $post_type ) {

            // Remove default taxonomy meta box from Lesson edit screen
            remove_meta_box($this->taxonomy . 'div', 'lesson', 'side');

            // Add custom meta box to limit module selection to one per lesson
            add_meta_box($this->taxonomy . '_select', __('Lesson Module', 'woothemes-sensei'), array($this, 'lesson_module_metabox'), 'lesson', 'side', 'default');
        }

        if( 'course' == $post_type ){
            // Course modules selection metabox
            add_meta_box( $this->taxonomy . '_course_mb', __('Course Modules', 'woothemes-sensei'), array( $this, 'course_module_metabox'), 'course', 'side', 'core');
        }
    }

    /**
     * Build content for custom module meta box
     *
     * @since 1.8.0
     * @param  object $post Current post object
     * @return void
     */
    public function lesson_module_metabox($post)
    {

        // Get lesson course
        $lesson_course = get_post_meta($post->ID, '_lesson_course', true);

        $html = '';

        // Only show module selection if this lesson is part of a course
        if ($lesson_course && $lesson_course > 0) {

            // Get existing lesson module
            $lesson_module = 0;
            $lesson_module_list = wp_get_post_terms($post->ID, $this->taxonomy);
            if (is_array($lesson_module_list) && count($lesson_module_list) > 0) {
                foreach ($lesson_module_list as $single_module) {
                    $lesson_module = $single_module->term_id;
                    break;
                }
            }

            // Get the available modules for this lesson's course
            $modules = $this->get_course_modules($lesson_course);

            // Build the HTML to output
            $html .= '<input type="hidden" name="' . esc_attr('woo_lesson_' . $this->taxonomy . '_nonce') . '" id="' . esc_attr('woo_lesson_' . $this->taxonomy . '_nonce') . '" value="' . esc_attr(wp_create_nonce(plugin_basename($this->file))) . '" />';
            if (is_array($modules) && count($modules) > 0) {
                $html .= '<select id="lesson-module-options" name="lesson_module" class="widefat">' . "\n";
                $html .= '<option value="">' . __('None', 'woothemes-sensei') . '</option>';
                foreach ($modules as $module) {
                    $html .= '<option value="' . esc_attr(absint($module->term_id)) . '"' . selected($module->term_id, $lesson_module, false) . '>' . esc_html($module->name) . '</option>' . "\n";
                }
                $html .= '</select>' . "\n";
            } else {
                $course_url = admin_url('post.php?post=' . urlencode($lesson_course) . '&action=edit');
                $html .= '<p>' . sprintf(__('No modules are available for this lesson yet. %1$sPlease add some to %3$sthe course%4$s.%2$s', 'woothemes-sensei'), '<em>', '</em>', '<a href="' . esc_url($course_url) . '">', '</a>') . '</p>';
            } // End If Statement

        } else {
            $html .= '<p>' . sprintf(__('No modules are available for this lesson yet. %1$sPlease select a course first.%2$s', 'woothemes-sensei'), '<em>', '</em>') . '</p>';
        } // End If Statement

        // Output the HTML
        echo $html;
    }

    /**
     * Save module to lesson
     *
     * @since 1.8.0
     * @param  integer $post_id ID of post
     * @return mixed            Post ID on permissions failure, boolean true on success
     */
    public function save_lesson_module($post_id)
    {
        global $post;

        // Verify post type and nonce
        if ((get_post_type() != 'lesson') || !isset($_POST['woo_lesson_' . $this->taxonomy . '_nonce'] )

This code seems to be duplicated across your project.

            ||!wp_verify_nonce($_POST['woo_lesson_' . $this->taxonomy . '_nonce'], plugin_basename($this->file))) {
            return $post_id;
        }

        // Check if user has permissions to edit lessons
        $post_type = get_post_type_object($post->post_type);
        if (!current_user_can($post_type->cap->edit_post, $post_id)) {
            return $post_id;
        }

        // Check if user has permissions to edit this specific post
        if (!current_user_can('edit_post', $post_id)) {
            return $post_id;
        }

        // Cast module ID as an integer if selected, otherwise leave as empty string
        if ( isset( $_POST['lesson_module'] ) ) {

            if( empty ( $_POST['lesson_module'] ) ){
                wp_delete_object_term_relationships($post_id, $this->taxonomy  );
                return true;
            }

            $module_id = intval( $_POST['lesson_module'] );

            // Assign lesson to selected module
            wp_set_object_terms($post_id, $module_id, $this->taxonomy, false);

            // Set default order for lesson inside module
            if (!get_post_meta($post_id, '_order_module_' . $module_id, true)) {
                update_post_meta($post_id, '_order_module_' . $module_id, 0);
            }
        }

        return true;
    }

    /**
     * Display course field on new module screen
     *
     * @since 1.8.0
     * @param object $taxonomy Taxonomy object
     * @return void
     */
    public function add_module_fields($taxonomy)

The parameter $taxonomy is not used and could be removed.

    {
        ?>
        <div class="form-field">
            <label for="module_courses"><?php _e('Course(s)', 'woothemes-sensei'); ?></label>
            <input type="hidden" id="module_courses" name="module_courses" class="ajax_chosen_select_courses"
                    placeholder="<?php esc_attr_e('Search for courses', 'woothemes-sensei'); ?>" />
            <span
                class="description"><?php _e('Search for and select the courses that this module will belong to.', 'woothemes-sensei'); ?></span>
        </div>
    <?php
    }

    /**
     * Display course field on module edit screen
     *
     * @since 1.8.0
     * @param  object $module Module term object
     * @return void
     */
    public function edit_module_fields($module)
    {

        $module_id = $module->term_id;

        // Get module's existing courses
        $args = array(
            'post_type' => 'course',
            'post_status' => array('publish', 'draft', 'future', 'private'),
            'posts_per_page' => -1,
            'tax_query' => array(
                array(
                    'taxonomy' => $this->taxonomy,
                    'field' => 'id',
                    'terms' => $module_id
                )
            )
        );
        $courses = get_posts($args);

        //build the defaults array
        $module_courses = array();
        if (isset($courses) && is_array($courses)) {
            foreach ($courses as $course) {
                $module_courses[] =   array( 'id' =>$course->ID, 'details'=>$course->post_title );
            }
        }

        ?>
        <tr class="form-field">
            <th scope="row" valign="top"><label
                    for="module_courses"><?php _e('Course(s)', 'woothemes-sensei'); ?></label></th>
            <td>
                <input type="hidden"
                       data-defaults="<?php echo esc_attr( json_encode($module_courses)); ?>"
                       value="<?php echo esc_attr( json_encode($module_courses) ); ?>"
                       id="module_courses" name="module_courses"
                       class="ajax_chosen_select_courses"
                       placeholder="<?php esc_attr_e('Search for courses...', 'woothemes-sensei'); ?>"
                    />
                <span
                    class="description"><?php _e('Search for and select the courses that this module will belong to.', 'woothemes-sensei'); ?></span>
            </td>
        </tr>
    <?php
    }

    /**
     * Save module course on add/edit
     *
     * @since 1.8.0
     * @param  integer $module_id ID of module
     * @return void
     */
    public function save_module_course($module_id)
    {

        // Get module's existing courses
        $args = array(
            'post_type' => 'course',
            'post_status' => array('publish', 'draft', 'future', 'private'),
            'posts_per_page' => -1,
            'tax_query' => array(
                array(
                    'taxonomy' => $this->taxonomy,
                    'field' => 'id',
                    'terms' => $module_id
                )
            )
        );
        $courses = get_posts($args);

        // Remove module from existing courses
        if (isset($courses) && is_array($courses)) {
            foreach ($courses as $course) {
                wp_remove_object_terms($course->ID, $module_id, $this->taxonomy);
            }
        }

        // Add module to selected courses
        if ( isset( $_POST['module_courses'] ) && ! empty( $_POST['module_courses'] ) ) {

            $course_ids = explode( ",", $_POST['module_courses'] );

            foreach ( $course_ids as $course_id ) {

                wp_set_object_terms($course_id, $module_id, $this->taxonomy, true);

            }
        }
    }

    /**
     * Ajax function to search for courses matching term
     *
     * @since 1.8.0
     * @return void
     */
    public function search_courses_json()
    {

        // Security check
        check_ajax_referer('search-courses', 'security');

        // Set content type
        header('Content-Type: application/json; charset=utf-8');

        // Get user input
        $term = urldecode(stripslashes($_GET['term']));

        // Return nothing if term is empty
        if (empty($term))
            die();

        // Set a default if none is given
        $default = isset($_GET['default']) ? $_GET['default'] : __('No course', 'woothemes-sensei');

        // Set up array of results
        $found_courses = array('' => $default);

        // Fetch results
        $args = array(
            'post_type' => 'course',
            'post_status' => array('publish', 'draft', 'future', 'private'),
            'posts_per_page' => -1,
            'orderby' => 'title',
            's' => $term
        );
        $courses = get_posts($args);

        // Add results to array
        if ($courses) {
            foreach ($courses as $course) {
                $found_courses[$course->ID] = $course->post_title;
            }
        }

        // Encode and return results for processing & selection
        echo json_encode($found_courses);
        die();
    }

    /**
     * display modules on single course pages
     *
     * @since 1.8.0
     * @return void
     */
    public function single_course_modules(){

        _deprecated_function('Sensei_Modules->single_course_modules','Sensei 1.9.0', 'Sensei()->modules->load_course_module_content_template');
        // only show modules on the course that has modules
        if( is_singular( 'course' ) && has_term( '', 'module' )  )  {

            $this->load_course_module_content_template();

        }

    } // end single_course_modules

    public function sensei_course_preview_titles($title, $lesson_id)
    {
        global $post, $current_user;

        $course_id = $post->ID;
        $title_text = '';

        if (method_exists('Sensei_Utils', 'is_preview_lesson') && Sensei_Utils::is_preview_lesson($lesson_id)) {
            $is_user_taking_course = Sensei_Utils::sensei_check_for_activity(array('post_id' => $course_id, 'user_id' => $current_user->ID, 'type' => 'sensei_course_status'));
            if (!$is_user_taking_course) {
                if (method_exists('WooThemes_Sensei_Frontend', 'sensei_lesson_preview_title_text')) {
                    $title_text = Sensei()->frontend->sensei_lesson_preview_title_text($course_id);
                    // Remove brackets for display here
                    $title_text = str_replace('(', '', $title_text);
                    $title_text = str_replace(')', '', $title_text);
                    $title_text = '<span class="preview-label">' . $title_text . '</span>';
                }
                $title .= ' ' . $title_text;
            }
        }

        return $title;
    }

    public function module_breadcrumb_link($html, $separator)
    {
        global $post;
        // Lesson
        if (is_singular('lesson')) {
            if (has_term('', $this->taxonomy, $post->ID)) {
                $module = $this->get_lesson_module($post->ID);
                if( $module ) {
                    $html .= ' ' . $separator . ' <a href="' . esc_url($module->url) . '" title="' .  __('Back to the module', 'woothemes-sensei') . '">' . $module->name . '</a>';
                }
            }
        }
        // Module
        if (is_tax($this->taxonomy)) {
            if (isset($_GET['course_id']) && 0 < intval($_GET['course_id'])) {
                $course_id = intval($_GET['course_id']);
                $html .= '<a href="' . esc_url(get_permalink($course_id)) . '" title="' .  __('Back to the course', 'woothemes-sensei') . '">' . get_the_title($course_id) . '</a>';
            }
        }
        return $html;
    }

    /**
     * Set lesson archive template to display on module taxonomy archive page
     *
     * @since 1.8.0
     * @param  string $template Default template
     * @return string           Modified template
     */
    public function module_archive_template($template) {

        if ( ! is_tax($this->taxonomy) ) {
            return $template;
        }

        $file = 'archive-lesson.php';
        $find = array( $file, Sensei()->template_url . $file );

        // locate the template file
        $template = locate_template($find);
        if (!$template) {

            $template = Sensei()->plugin_path() . 'templates/' . $file;

        }


        return $template;
    }

    /**
     * Modify module taxonomy archive query
     *
     * @since 1.8.0
     * @param  object $query The query object passed by reference
     * @return void
     */
    public function module_archive_filter($query)
    {
        if (is_tax($this->taxonomy) && $query->is_main_query()) {


            // Limit to lessons only
            $query->set('post_type', 'lesson');

            // Set order of lessons
            if (version_compare(Sensei()->version, '1.6.0', '>=')) {
                $module_id = $query->queried_object_id;
                $query->set('meta_key', '_order_module_' . $module_id);
                $query->set('orderby', 'meta_value_num date');
            } else {
                $query->set('orderby', 'menu_order');
            }
            $query->set('order', 'ASC');

            // Limit to specific course if specified
            if (isset($_GET['course_id']) && 0 < intval($_GET['course_id'])) {
                $course_id = intval($_GET['course_id']);
                $meta_query[] = array(
                    'key' => '_lesson_course',
                    'value' => intval($course_id)
                );
                $query->set('meta_query', $meta_query);
            }

        }
    }

    /**
     * Modify archive page title
     *
     * @since 1.8.0
     * @param  string $title Default title
     * @return string        Modified title
     */
    public function module_archive_title($title)
    {
        if (is_tax($this->taxonomy)) {
            $title = apply_filters('sensei_module_archive_title', get_queried_object()->name);
        }
        return $title;
    }

    /**
     * Display module description on taxonomy archive page
     *
     * @since 1.8.0
     * @return void
     */
    public function module_archive_description()
    {
        if (is_tax($this->taxonomy)) {

            $module = get_queried_object();

            $module_progress = false;
            if (is_user_logged_in() && isset($_GET['course_id']) && intval($_GET['course_id']) > 0) {
                global $current_user;
                wp_get_current_user();
                $module_progress = $this->get_user_module_progress($module->term_id, $_GET['course_id'], $current_user->ID);
            }

            if ($module_progress && $module_progress > 0) {
                $status = __('Completed', 'woothemes-sensei');
                $class = 'completed';
                if ($module_progress < 100) {
                    $status = __('In progress', 'woothemes-sensei');
                    $class = 'in-progress';
                }
                echo '<p class="status ' . esc_attr($class) . '">' . $status . '</p>';
            }

            echo '<p class="archive-description module-description">' . apply_filters('sensei_module_archive_description', nl2br($module->description), $module->term_id) . '</p>';
        }
    }

    public function module_archive_body_class($classes)
    {
        if (is_tax($this->taxonomy)) {
            $classes[] = 'module-archive';
        }
        return $classes;
    }

    /**
     * Display module navigation links on module taxonomy archive page
     *
     * @since 1.8.0
     * @return void
     */
    public function module_navigation_links()
    {
        if (is_tax($this->taxonomy) && isset($_GET['course_id'])) {

            $queried_module = get_queried_object();
            $course_modules = $this->get_course_modules($_GET['course_id']);

            $prev_module = false;
            $next_module = false;
            $on_current = false;
            foreach ($course_modules as $module) {
                $this_module = $module;
                if ($on_current) {
                    $next_module = $this_module;
                    break;
                }
                if ($this_module == $queried_module) {
                    $on_current = true;
                } else {
                    $prev_module = $module;
                }
            }

            ?>
            <div id="post-entries" class="post-entries module-navigation fix">
                <?php if ($next_module) {

This code seems to be duplicated across your project.

                    $module_link = add_query_arg('course_id', intval($_GET['course_id']), get_term_link($next_module, $this->taxonomy));
                    ?>
                    <div class="nav-next fr"><a href="<?php echo esc_url($module_link); ?>"
                                                title="<?php esc_attr_e('Next module', 'woothemes-sensei'); ?>"><?php echo $next_module->name; ?>
                            <span class="meta-nav"></span></a></div>
                <?php } ?>
                <?php if ($prev_module) {

This code seems to be duplicated across your project.

                    $module_link = add_query_arg('course_id', intval($_GET['course_id']), get_term_link($prev_module, $this->taxonomy));
                    ?>
                    <div class="nav-prev fl"><a href="<?php echo esc_url($module_link); ?>"
                                                title="<?php _e('Previous module', 'woothemes-sensei'); ?>"><span
                                class="meta-nav"></span> <?php echo $prev_module->name; ?></a></div>
                <?php } ?>
            </div>
        <?php
        }
    }

    /**
     * Trigger save_lesson_module_progress() when a lesson status is updated for a specific user
     *
     * @since 1.8.0
     * @param  string $status Status of the lesson for the user
     * @param  integer $user_id ID of user
     * @param  integer $lesson_id ID of lesson
     * @return void
     */
    public function update_lesson_status_module_progress($status = '', $user_id = 0, $lesson_id = 0)
    {
        $this->save_lesson_module_progress($user_id, $lesson_id);
    }

    /**
     * Save lesson's module progress for a specific user
     *
     * @since 1.8.0
     * @param  integer $user_id ID of user
     * @param  integer $lesson_id ID of lesson
     * @return void
     */
    public function save_lesson_module_progress($user_id = 0, $lesson_id = 0)
    {
        $module = $this->get_lesson_module($lesson_id);
        $course_id = get_post_meta($lesson_id, '_lesson_course', true);
        if ($module && $course_id) {
            $this->save_user_module_progress(intval($module->term_id), intval($course_id), intval($user_id));
        }
    }

    /**
     * Save progress of module for user
     *
     * @since 1.8.0
     * @return void
     */
    public function save_module_progress()
    {
        if (is_tax($this->taxonomy) && is_user_logged_in() && isset($_GET['course_id']) && 0 < intval($_GET['course_id'])) {
            global $current_user;
            wp_get_current_user();
            $user_id = $current_user->ID;

            $module = get_queried_object();

            $this->save_user_module_progress(intval($module->term_id), intval($_GET['course_id']), intval($user_id));
        }
    }

    /**
     * Save module progess for user
     *
     * @since 1.8.0
     *
     * @param  integer $module_id ID of module
     * @param  integer $course_id ID of course
     * @param  integer $user_id ID of user
     * @return void
     */
    public function save_user_module_progress($module_id = 0, $course_id = 0, $user_id = 0)
    {
        $module_progress = $this->calculate_user_module_progress($user_id, $module_id, $course_id);
        update_user_meta(intval($user_id), '_module_progress_' . intval($course_id) . '_' . intval($module_id), intval($module_progress));

        do_action('sensei_module_save_user_progress', $course_id, $module_id, $user_id, $module_progress);
    }

    /**
     * Get module progress for a user
     *
     * @since 1.8.0
     *
     * @param  integer $module_id ID of module
     * @param  integer $course_id ID of course
     * @param  integer $user_id ID of user
     * @return mixed              Module progress percentage on success, false on failure
     */
    public function get_user_module_progress($module_id = 0, $course_id = 0, $user_id = 0)
    {
        $module_progress = get_user_meta(intval($user_id), '_module_progress_' . intval($course_id) . '_' . intval($module_id), true);
        if ($module_progress) {
            return (float)$module_progress;
        }
        return false;
    }

    /**
     * Calculate module progess for user
     *
     * @since 1.8.0
     *
     * @param  integer $user_id ID of user
     * @param  integer $module_id ID of module
     * @param  integer $course_id ID of course
     * @return integer            Module progress percentage
     */
    public function calculate_user_module_progress($user_id = 0, $module_id = 0, $course_id = 0)
    {

        $args = array(
            'post_type' => 'lesson',
            'post_status' => 'publish',
            'posts_per_page' => -1,
            'tax_query' => array(
                array(
                    'taxonomy' => $this->taxonomy,
                    'field' => 'id',
                    'terms' => $module_id
                )
            ),
            'meta_query' => array(
                array(
                    'key' => '_lesson_course',
                    'value' => $course_id
                )
            ),
            'fields' => 'ids'
        );
        $lessons = get_posts($args);

        if (is_wp_error($lessons) || 0 >= count($lessons)) return 0;

        $completed = false;

$completed is not used, you could remove the assignment.

        $lesson_count = 0;
        $completed_count = 0;
        foreach ($lessons as $lesson_id) {
            $completed = Sensei_Utils::user_completed_lesson($lesson_id, $user_id);
            ++$lesson_count;
            if ($completed) {
                ++$completed_count;
            }
        }
        $module_progress = ($completed_count / $lesson_count) * 100;

        return (float)$module_progress;
    }

    /**
     * Register admin screen for ordering modules
     *
     * @since 1.8.0
     *
     * @return void
     */
    public function register_modules_admin_menu_items()
    {
        //add the modules link under the Course main menu
        add_submenu_page('edit.php?post_type=course', __('Modules', 'woothemes-sensei'), __('Modules', 'woothemes-sensei'), 'manage_categories', 'edit-tags.php?taxonomy=module','' );

        // Regsiter new admin page for module ordering
        $hook = add_submenu_page('edit.php?post_type=course', __('Order Modules', 'woothemes-sensei'), __('Order Modules', 'woothemes-sensei'), 'edit_lessons', $this->order_page_slug, array($this, 'module_order_screen'));

$hook is not used, you could remove the assignment.

    }

    /**
     * Display Module Order screen
     *
     * @since 1.8.0
     *
     * @return void
     */
    public function module_order_screen()
    {
        ?>
        <div id="<?php echo esc_attr($this->order_page_slug); ?>"
             class="wrap <?php echo esc_attr($this->order_page_slug); ?>">
        <h2><?php _e('Order Modules', 'woothemes-sensei'); ?></h2><?php

        $html = '';

        if (isset($_POST['module-order']) && 0 < strlen($_POST['module-order'])) {

This code seems to be duplicated across your project.

            $ordered = $this->save_course_module_order(esc_attr($_POST['module-order']), esc_attr($_POST['course_id']));

            if ($ordered) {
                $html .= '<div class="updated fade">' . "\n";
                $html .= '<p>' . __('The module order has been saved for this course.', 'woothemes-sensei') . '</p>' . "\n";
                $html .= '</div>' . "\n";
            }
        }

        $courses = Sensei()->course->get_all_courses();

        $html .= '<form action="' . admin_url('edit.php') . '" method="get">' . "\n";
        $html .= '<input type="hidden" name="post_type" value="course" />' . "\n";
        $html .= '<input type="hidden" name="page" value="' . esc_attr($this->order_page_slug) . '" />' . "\n";
        $html .= '<select id="module-order-course" name="course_id">' . "\n";
        $html .= '<option value="">' . __('Select a course', 'woothemes-sensei') . '</option>' . "\n";

        foreach ($courses as $course) {
            if (has_term('', $this->taxonomy, $course->ID)) {
                $course_id = '';
                if (isset($_GET['course_id'])) {
                    $course_id = intval($_GET['course_id']);
                }
                $html .= '<option value="' . esc_attr(intval($course->ID)) . '" ' . selected($course->ID, $course_id, false) . '>' . get_the_title($course->ID) . '</option>' . "\n";
            }
        }

        $html .= '</select>' . "\n";
        $html .= '<input type="submit" class="button-primary module-order-select-course-submit" value="' . __('Select', 'woothemes-sensei') . '" />' . "\n";
        $html .= '</form>' . "\n";

        if (isset($_GET['course_id'])) {
            $course_id = intval($_GET['course_id']);
            if ($course_id > 0) {
                $modules = $this->get_course_modules($course_id);
                $modules = $this->append_teacher_name_to_module( $modules, array( 'module' ), array() );
                if ($modules) {

                    $order = $this->get_course_module_order($course_id);

                    $order_string='';
                    if ($order) {
                        $order_string = implode(',', $order);
                    }

                    $html .= '<form id="editgrouping" method="post" action="" class="validate">' . "\n";
                    $html .= '<ul class="sortable-module-list">' . "\n";
                    $count = 0;
                    foreach ($modules as $module) {

This code seems to be duplicated across your project.

                        $count++;
                        $class = $this->taxonomy;
                        if ($count == 1) {
                            $class .= ' first';
                        }
                        if ($count == count($module)) {
                            $class .= ' last';
                        }
                        if ($count % 2 != 0) {
                            $class .= ' alternate';
                        }
                        $html .= '<li class="' . esc_attr($class) . '"><span rel="' . esc_attr($module->term_id) . '" style="width: 100%;"> ' . $module->name . '</span></li>' . "\n";
                    }
                    $html .= '</ul>' . "\n";

                    $html .= '<input type="hidden" name="module-order" value="' . $order_string . '" />' . "\n";
                    $html .= '<input type="hidden" name="course_id" value="' . $course_id . '" />' . "\n";
                    $html .= '<input type="submit" class="button-primary" value="' . __('Save module order', 'woothemes-sensei') . '" />' . "\n";
                    $html .= '<a href="' . admin_url('post.php?post=' . $course_id . '&action=edit') . '" class="button-secondary">' . __('Edit course', 'woothemes-sensei') . '</a>' . "\n";
                }
            }
        }

        echo $html;

        ?></div><?php
    }

    /**
     * Add 'Module order' column to courses list table
     *
     * @since 1.8.0
     *
     * @param  array $columns Existing columns
     * @return array           Modifed columns
     */
    public function course_columns($columns = array())
    {
        $columns['module_order'] = __('Module order', 'woothemes-sensei');
        return $columns;
    }

    /**
     * Load content in 'Module order' column
     *
     * @since 1.8.0
     *
     * @param  string $column Current column name
     * @param  integer $course_id ID of course
     * @return void
     */
    public function course_column_content($column = '', $course_id = 0)
    {
        if ($column == 'module_order') {
            if (has_term('', $this->taxonomy, $course_id)) {
                echo '<a class="button-secondary" href="' . admin_url('edit.php?post_type=course&page=module-order&course_id=' . urlencode(intval($course_id))) . '">' . __('Order modules', 'woothemes-sensei') . '</a>';
            }
        }
    }

    /**
     * Save module order for course
     *
     * @since 1.8.0
     *
     * @param  string $order_string Comma-separated string of module IDs
     * @param  integer $course_id ID of course
     * @return boolean                 True on success, false on failure
     */
    private function save_course_module_order($order_string = '', $course_id = 0)
    {
        if ($order_string && $course_id) {
            $order = explode(',', $order_string);
            update_post_meta(intval($course_id), '_module_order', $order);
            return true;
        }
        return false;
    }

    /**
     * Get module order for course
     *
     * @since 1.8.0
     *
     * @param  integer $course_id ID of course
     * @return mixed              Module order on success, false if no module order has been saved
     */
    public function get_course_module_order($course_id = 0)
    {
        if ($course_id) {
            $order = get_post_meta(intval($course_id), '_module_order', true);
            return $order;
        }
        return false;
    }

    /**
     * Modify module taxonomy columns
     *
     * @since 1.8.0
     *
     * @param  array $columns Default columns
     * @return array          Modified columns
     */
    public function taxonomy_column_headings($columns)
    {

        unset($columns['posts']);

        $columns['lessons'] = __('Lessons', 'woothemes-sensei');

        return $columns;
    }

    /**
     * Manage content in custom module taxonomy columns
     *
     * @since 1.8.0
     *
     * @param  string $column_data Default data for column
     * @param  string $column_name Name of current column
     * @param  integer $term_id ID of current term
     * @return string               Modified column data
     */
    public function taxonomy_column_content($column_data, $column_name, $term_id)
    {

        $args = array(
            'post_status' => 'publish',
            'posts_per_page' => -1,
            'tax_query' => array(
                array(
                    'taxonomy' => $this->taxonomy,
                    'field' => 'id',
                    'terms' => intval($term_id)
                )
            )
        );

        $module = get_term($term_id, $this->taxonomy);

        switch ($column_name) {

            case 'lessons':
                $args['post_type'] = 'lesson';
                $lessons = get_posts($args);
                $total_lessons = count($lessons);
                $column_data = '<a href="' . admin_url('edit.php?module=' . urlencode($module->slug) . '&post_type=lesson') . '">' . intval($total_lessons) . '</a>';
                break;
        }

        return $column_data;
    }

    /**
     * Add 'Module' columns to Analysis Lesson Overview table
     *
     * @since 1.8.0
     *
     * @param  array $columns Default columns
     * @return array          Modified columns
     */
    public function analysis_overview_column_title($columns)
    {

        if ( isset( $_GET['view'] ) && 'lessons' == $_GET['view'] ) {
            $new_columns = array();
            if (is_array($columns) && 0 < count($columns)) {
                foreach ($columns as $column => $title) {
                    $new_columns[$column] = $title;
                    if ($column == 'title') {
                        $new_columns['lesson_module'] = __('Module', 'woothemes-sensei');
                    }
                }
            }

            if (0 < count($new_columns)) {
                return $new_columns;
            }
        }

        return $columns;
    }

    /**
     * Data for 'Module' column Analysis Lesson Overview table
     *
     * @since 1.8.0
     *
     * @param  array $columns Table column data
     * @param  WP_Post $lesson
     * @return array              Updated column data
     */
    public function analysis_overview_column_data($columns, $lesson )

This method seems to be duplicated in your project.

    {

        if ( isset( $_GET['view'] ) && 'lessons' == $_GET['view'] ) {
            $lesson_module = '';
            $lesson_module_list = wp_get_post_terms($lesson->ID, $this->taxonomy);
            if (is_array($lesson_module_list) && count($lesson_module_list) > 0) {
                foreach ($lesson_module_list as $single_module) {
                    $lesson_module = '<a href="' . esc_url(admin_url('edit-tags.php?action=edit&taxonomy=' . urlencode($this->taxonomy) . '&tag_ID=' . urlencode($single_module->term_id))) . '">' . $single_module->name . '</a>';
                    break;
                }
            }

            $columns['lesson_module'] = $lesson_module;
        }

        return $columns;
    }

    /**
     * Add 'Module' columns to Analysis Course table
     *
     * @since 1.8.0
     *
     * @param  array $columns Default columns
     * @return array          Modified columns
     */
    public function analysis_course_column_title($columns)
    {
        if ( isset( $_GET['view'] ) && 'lessons' == $_GET['view'] ) {
            $columns['lesson_module'] = __('Module', 'woothemes-sensei');
        }
        return $columns;
    }

    /**
     * Data for 'Module' column in Analysis Course table
     *
     * @since 1.8.0
     *
     * @param  array $columns Table column data
     * @param  WP_Post $lesson
     * @return array              Updated columns data
     */
    public function analysis_course_column_data($columns, $lesson )

This method seems to be duplicated in your project.

    {

        if ( isset( $_GET['course_id'] ) ) {
            $lesson_module = '';
            $lesson_module_list = wp_get_post_terms($lesson->ID, $this->taxonomy);
            if (is_array($lesson_module_list) && count($lesson_module_list) > 0) {
                foreach ($lesson_module_list as $single_module) {
                    $lesson_module = '<a href="' . esc_url(admin_url('edit-tags.php?action=edit&taxonomy=' . urlencode($this->taxonomy) . '&tag_ID=' . urlencode($single_module->term_id))) . '">' . $single_module->name . '</a>';
                    break;
                }
            }

            $columns['lesson_module'] = $lesson_module;
        }

        return $columns;
    }

    /**
     * Get module for lesson
     *
     * This function also checks if the module still
     * exists on the course before returning it. Although
     * the lesson has a module the same module must exist on the
     * course for it to be valid.
     *
     * @since 1.8.0
     *
     * @param  integer $lesson_id ID of lesson
     * @return object             Module taxonomy term object
     */
    public function get_lesson_module($lesson_id = 0)
    {
        $lesson_id = intval($lesson_id);
        if ( ! ( intval( $lesson_id > 0) ) ) {
            return false;
        }

        // get taxonomy terms on this lesson
        $modules = wp_get_post_terms($lesson_id, $this->taxonomy);

        //check if error returned
        if(    empty( $modules )
            || is_wp_error( $modules )
            || isset( $modules['errors'] ) ){

            return false;

        }

       // get the last item in the array there should be only be 1 really.
       // this method works for all php versions.
       foreach( $modules as $module ){
           break;
       }

        if ( ! isset($module) || ! is_object($module) || is_wp_error($module)) {
            return false;
        }

        $module->url = get_term_link($module, $this->taxonomy);
        $course_id = intval(get_post_meta(intval($lesson_id), '_lesson_course', true));
        if (isset($course_id) && 0 < $course_id) {

            // the course should contain the same module taxonomy term for this to be valid
            if( ! has_term( $module, $this->taxonomy, $course_id)){
                return false;
            }

            $module->url = esc_url(add_query_arg('course_id', intval($course_id), $module->url));
        }
        return $module;

    }

	/**
	 * Get ordered array of all modules in course
	 *
	 * @since 1.8.0
	 *
	 * @param  integer $course_id ID of course
	 * @return array              Ordered array of module taxonomy term objects
	 */
	public function get_course_modules($course_id = 0) {

		$course_id = intval($course_id);
		if ( empty(  $course_id ) ) {
			return array();
		}

		// Get modules for course
		$modules = wp_get_post_terms( $course_id, $this->taxonomy );

		// Get custom module order for course
		$order = $this->get_course_module_order($course_id);

		if ( ! $order) {
			return $modules;
		}

		// Sort by custom order
		$ordered_modules = array();
		$unordered_modules = array();
		foreach ( $modules as $module ) {
			$order_key = array_search($module->term_id, $order);
			if ($order_key !== false) {
				$ordered_modules[$order_key] = $module;
			} else {
				$unordered_modules[] = $module;
			}
		}

		// Order modules correctly
		ksort( $ordered_modules );

		// Append modules that have not yet been ordered
		if ( count($unordered_modules) > 0 ) {
			$ordered_modules = array_merge($ordered_modules, $unordered_modules);
		}

		// remove order key but maintain order
		$ordered_modules_with_keys_in_sequence = array();
		foreach ( $ordered_modules as $key => $module ) {

			$ordered_modules_with_keys_in_sequence[] = $module;

		}

		return $ordered_modules_with_keys_in_sequence;

	}

    /**
     * Load frontend CSS
     *
     * @since 1.8.0
     *
     * @return void
     */
    public function enqueue_styles() {

        wp_register_style($this->taxonomy . '-frontend', esc_url($this->assets_url) . 'css/modules-frontend.css', Sensei()->version );
        wp_enqueue_style($this->taxonomy . '-frontend');

    }

    /**
     * Load admin Javascript
     *
     * @since 1.8.0
     *
     * @return void
     */
    public function admin_enqueue_scripts( $hook ) {

        /**
         * Filter the page hooks where modules admin script can be loaded on.
         *
         * @param array $white_listed_pages
         */
        $script_on_pages_white_list = apply_filters( 'sensei_module_admin_script_page_white_lists', array(
            'edit-tags.php',
            'course_page_module-order',
            'post-new.php',
            'post.php'
        ) );

        if ( ! in_array( $hook, $script_on_pages_white_list ) ) {
            return;
        }

        $suffix = defined( 'SCRIPT_DEBUG' ) && SCRIPT_DEBUG ? '' : '.min';

        wp_enqueue_script( 'sensei-chosen', Sensei()->plugin_url . 'assets/chosen/chosen.jquery' . $suffix . '.js', array( 'jquery' ), Sensei()->version , true);
        wp_enqueue_script( 'sensei-chosen-ajax', Sensei()->plugin_url . 'assets/chosen/ajax-chosen.jquery' . $suffix . '.js', array( 'jquery', 'sensei-chosen' ), Sensei()->version , true );
        wp_enqueue_script( $this->taxonomy . '-admin', esc_url( $this->assets_url ) . 'js/modules-admin' . $suffix . '.js', array( 'jquery', 'sensei-chosen', 'sensei-chosen-ajax', 'jquery-ui-sortable', 'sensei-core-select2' ), Sensei()->version, true );

        // localized module data
        $localize_modulesAdmin = array(
            'search_courses_nonce' => wp_create_nonce( 'search-courses' ),
            'selectPlaceholder'    => __( 'Search for courses', 'woothemes-sensei' )
        );

        wp_localize_script( $this->taxonomy . '-admin' ,'modulesAdmin', $localize_modulesAdmin );
    }

    /**
     * Load admin CSS
     *
     * @since 1.8.0
     *
     * @return void
     */
    public function admin_enqueue_styles() {

        wp_register_style($this->taxonomy . '-sortable', esc_url($this->assets_url) . 'css/modules-admin.css','',Sensei()->version );
        wp_enqueue_style($this->taxonomy . '-sortable');

    }

    /**
     * Show the title modules on the single course template.
     *
     * Function is hooked into sensei_single_course_modules_before.
     *
     * @since 1.8.0
     * @return void
     */
    public function course_modules_title( ) {

       if( sensei_module_has_lessons() ){

            echo '<header><h2>' . __('Modules', 'woothemes-sensei') . '</h2></header>';

        }

    }

    /**
     * Display the single course modules content this will only show
     * if the course has modules.
     *
     * @since 1.8.0
     * @return void
     */
    public function load_course_module_content_template(){

This method seems to be duplicated in your project.

	    if ( ! is_singular( 'course' )  ) {
		    return;
	    }

        // load backwards compatible template name if it exists in the users theme
        $located_template= locate_template( Sensei()->template_url . 'single-course/course-modules.php' );
        if( $located_template ){

            Sensei_Templates::get_template( 'single-course/course-modules.php' );
            return;

        }

        Sensei_Templates::get_template( 'single-course/modules.php' );

    } // end course_module_content

    /**
     * Returns all lessons for the given module ID
     *
     * @since 1.8.0
     *
     * @param $course_id
     * @param $term_id
     * @return array $lessons
     */
    public function get_lessons( $course_id , $term_id ){

        $lesson_query = $this->get_lessons_query( $course_id, $term_id );

        if( isset( $lesson_query->posts ) ){

            return $lesson_query->posts;

        }else{

            return array();

        }

    } // end get lessons

    /**
     * Returns all lessons for the given module ID
     *
     * @since 1.8.0
     *
     * @param $course_id
     * @param $term_id
     * @return WP_Query $lessons_query
     */
    public function get_lessons_query( $course_id , $term_id ){

        if( empty( $term_id ) || empty( $course_id ) ){

            return array();

        }

        $args = array(
            'post_type' => 'lesson',
            'post_status' => 'publish',
            'posts_per_page' => -1,
            'meta_query' => array(
                array(
                    'key' => '_lesson_course',
                    'value' => intval($course_id),
                    'compare' => '='
                )
            ),
            'tax_query' => array(
                array(
                    'taxonomy' => 'module',
                    'field' => 'id',
                    'terms' => intval( $term_id )
                )
            ),
            'orderby' => 'menu_order',
            'order' => 'ASC',
            'suppress_filters' => 0
        );

        if (version_compare( Sensei()->version, '1.6.0', '>=')) {
            $args['meta_key'] = '_order_module_' . intval( $term_id );
            $args['orderby'] = 'meta_value_num date';
        }

        $lessons_query = new WP_Query( $args );

        return $lessons_query;

    } // end get lessons

    /**
     * Find the lesson in the given course that doesn't belong
     * to any of the courses modules
     *
     *
     * @param $course_id
     *
     * @return array $non_module_lessons
     */
    public function get_none_module_lessons( $course_id ){

        $non_module_lessons = array();

        //exit if there is no course id passed in
        if( empty( $course_id ) || 'course' != get_post_type( $course_id ) ) {

            return $non_module_lessons;
        }

        //save some time and check if we already have the saved
        if( get_transient( 'sensei_'. $course_id .'_none_module_lessons') ){

            return get_transient( 'sensei_'. $course_id .'_none_module_lessons');

        }

        // create terms array which must be excluded from other arrays
        $course_modules = $this->get_course_modules( $course_id );

        //exit if there are no module on this course
        if( empty( $course_modules ) || ! is_array( $course_modules ) ){

            return  Sensei()->course->course_lessons( $course_id );

        }

        $terms = array();
        foreach( $course_modules as $module ){

            array_push( $terms ,  $module->term_id );

        }

        $args = array(
            'post_type' => 'lesson',
            'post_status' => 'publish',
            'posts_per_page' => -1,
            'meta_query' => array(
                array(
                    'key' => '_lesson_course',
                    'value' => intval( $course_id ),
                    'compare' => '='
                )
            ),
            'tax_query' => array(
                array(
                    'taxonomy' => 'module',
                    'field' => 'id',
                    'terms' =>  $terms,
                    'operator' => 'NOT IN'
                )
            ),
            'orderby' => 'menu_order',
            'order' => 'ASC',
            'suppress_filters' => 0
        );

        $wp_lessons_query = new WP_Query( $args );

        if( isset( $wp_lessons_query->posts) && count( $wp_lessons_query->posts ) > 0  ){
            $non_module_lessons = $wp_lessons_query->get_posts();
            set_transient( 'sensei_'. $course_id .'_none_module_lessons', $non_module_lessons, 10 * DAY_IN_SECONDS );
        }

        return $non_module_lessons;
    } // end get_none_module_lessons

    /**
     * Register the modules taxonomy
     *
     * @since 1.8.0
     */
    public function setup_modules_taxonomy(){

        $labels = array(
            'name' => __('Modules', 'woothemes-sensei'),
            'singular_name' => __('Module', 'woothemes-sensei'),
            'search_items' => __('Search Modules', 'woothemes-sensei'),
            'all_items' => __('All Modules', 'woothemes-sensei'),
            'parent_item' => __('Parent Module', 'woothemes-sensei'),
            'parent_item_colon' => __('Parent Module:', 'woothemes-sensei'),
            'edit_item' => __('Edit Module', 'woothemes-sensei'),
            'update_item' => __('Update Module', 'woothemes-sensei'),
            'add_new_item' => __('Add New Module', 'woothemes-sensei'),
            'new_item_name' => __('New Module Name', 'woothemes-sensei'),
            'menu_name' => __('Modules', 'woothemes-sensei'),
        );

        /**
         * Filter to alter the Sensei Modules rewrite slug
         *
         * @since 1.8.0
         * @param string default 'modules'
         */
        $modules_rewrite_slug = apply_filters('sensei_module_slug', 'modules');

        $args = array(
            'public' => true,
            'hierarchical' => true,
            'show_admin_column' => true,
            'capabilities' => array(
                'manage_terms' => 'manage_categories',
                'edit_terms'   => 'edit_courses',
                'delete_terms' => 'manage_categories',
                'assign_terms' => 'edit_courses'
            ),
            'show_in_nav_menus' => false,
            'show_in_quick_edit' => false,
            'show_ui' => true,
            'rewrite' => array('slug' => $modules_rewrite_slug ),
            'labels' => $labels
        );

        register_taxonomy( 'module' , array('course', 'lesson'), $args);

    }// end setup_modules_taxonomy

    /**
     * When the wants to edit the lesson modules redirect them to the course modules.
     *
     * This function is hooked into the admin_menu
     *
     * @since 1.8.0
     * @return void
     */
    function redirect_to_lesson_module_taxonomy_to_course( ){

It is generally recommended to explicitly declare the visibility for methods.

        global $typenow , $taxnow;

        if( 'lesson'== $typenow && 'module'==$taxnow ){
            wp_safe_redirect( esc_url_raw( 'edit-tags.php?taxonomy=module&post_type=course'  ) );
        }

    }// end redirect to course taxonomy

    /**
     * Completely remove the module menu item under lessons.
     *
     * This function is hooked into the admin_menu
     *
     * @since 1.8.0
     * @return void
     */
    public function remove_lessons_menu_model_taxonomy(){

This method seems to be duplicated in your project.

        global $submenu;

        if( ! isset( $submenu['edit.php?post_type=lesson'] ) || !is_array( $submenu['edit.php?post_type=lesson'] ) ){
            return; // exit
        }

        $lesson_main_menu = $submenu['edit.php?post_type=lesson'];
        foreach( $lesson_main_menu as $index => $sub_item ){

            if( 'edit-tags.php?taxonomy=module&post_type=lesson' == $sub_item[2] ){
                unset( $submenu['edit.php?post_type=lesson'][ $index ]);
            }
        }

    }// end remove lesson module tax

    /**
     * Completely remove the second modules under courses
     *
     * This function is hooked into the admin_menu
     *
     * @since 1.8.0
     * @return void
     */
    public function remove_courses_menu_model_taxonomy(){

This method seems to be duplicated in your project.

        global $submenu;

        if( ! isset( $submenu['edit.php?post_type=course'] ) || !is_array( $submenu['edit.php?post_type=course'] ) ){
            return; // exit
        }

        $course_main_menu = $submenu['edit.php?post_type=course'];
        foreach( $course_main_menu as $index => $sub_item ){

            if( 'edit-tags.php?taxonomy=module&post_type=course' == $sub_item[2] ){
                unset( $submenu['edit.php?post_type=course'][ $index ]);
            }
        }

    }// end remove courses module tax

    /**
     * Determine the author of a module term term by looking at
     * the prefixed author id. This function will query the full term object.
     * Will return the admin user author could not be determined.
     *
     * @since 1.8.0
     *
     * @param string $term_name
     * @return array $owners { type WP_User }. Empty array if none if found.
     */
    public static function get_term_authors( $term_name ){

        $terms = get_terms( array( 'module') , array( 'name__like'=>$term_name, 'hide_empty' => false )  );

        $owners = array();
        if( empty( $terms ) ){

            return $owners;

        }

        // setup the admin user


        //if there are more handle them appropriately and get the ones we really need that matches the desired name exactly
        foreach( $terms as $term){
            if( $term->name == $term_name ){

                // look for the author in the slug
                $owners[] = Sensei_Core_Modules::get_term_author( $term->slug  );

            }// end if term name

        } // end for each

        return $owners;

    }// end get_term_author

    /**
     * Looks at a term slug and figures out
     * which author created the slug. The author was
     * appended when the user saved the module term in the course edit
     * screen.
     *
     * @since 1.8.0
     *
     * @param $slug
     * @return WP_User $author if no author is found or invalid term is passed the admin user will be returned.
     */
    public static function get_term_author( $slug='' ){

        $term_owner = get_user_by( 'email', get_bloginfo( 'admin_email' ) );

        if( empty( $slug ) ){

            return $term_owner;

        }

        // look for the author in the slug
        $slug_parts = explode( '-', $slug );

        if( count( $slug_parts ) > 1 ){

            // get the user data
            $possible_user_id = $slug_parts[0];
            $author = get_userdata( $possible_user_id );

            // if the user doesnt exist for the first part of the slug
            // then this slug was also created by admin
            if( is_a( $author, 'WP_User' ) ){

                $term_owner =  $author;

            }
        }

        return $term_owner;
    }

    /**
     * Display the Sensei modules taxonomy terms metabox
     *
     * @since 1.8.0
     *
     * @hooked into add_meta_box
     *
     * @param WP_Post $post Post object.
     */
    public function course_module_metabox( $post ) {

        $tax_name = 'module';
        $taxonomy = get_taxonomy( 'module' );

        ?>
        <div id="taxonomy-<?php echo $tax_name; ?>" class="categorydiv">
            <ul id="<?php echo $tax_name; ?>-tabs" class="category-tabs">
                <li class="tabs"><a href="#<?php echo $tax_name; ?>-all"><?php echo $taxonomy->labels->all_items; ?></a></li>
                <li class="hide-if-no-js"><a href="#<?php echo $tax_name; ?>-pop"><?php _e( 'Most Used' ); ?></a></li>
            </ul>

            <div id="<?php echo $tax_name; ?>-pop" class="tabs-panel" style="display: none;">
                <ul id="<?php echo $tax_name; ?>checklist-pop" class="categorychecklist form-no-clear" >
                    <?php $popular_ids = wp_popular_terms_checklist( $tax_name ); ?>
                </ul>
            </div>

            <div id="<?php echo $tax_name; ?>-all" class="tabs-panel">
                <?php
                $name = ( $tax_name == 'category' ) ? 'post_category' : 'tax_input[' . $tax_name . ']';
                echo "<input type='hidden' name='{$name}[]' value='0' />"; // Allows for an empty term set to be sent. 0 is an invalid Term ID and will be ignored by empty() checks.
                ?>
                <ul id="<?php echo $tax_name; ?>checklist" data-wp-lists="list:<?php echo $tax_name; ?>" class="categorychecklist form-no-clear">
                    <?php wp_terms_checklist( $post->ID, array( 'taxonomy'=>$tax_name , 'popular_cats' => $popular_ids ) ); ?>
                </ul>
            </div>
            <?php if ( current_user_can( $taxonomy->cap->edit_terms ) ) : ?>
                <div id="<?php echo $tax_name; ?>-adder" class="wp-hidden-children">
                    <h4>
                        <a id="sensei-<?php echo $tax_name; ?>-add-toggle" href="#<?php echo $tax_name; ?>-add" class="hide-if-no-js">
                            <?php
                            /* translators: %s: add new taxonomy label */
                            printf( __( '+ %s' ), $taxonomy->labels->add_new_item );
                            ?>
                        </a>
                    </h4>
                    <p id="sensei-<?php echo $tax_name; ?>-add" class="category-add wp-hidden-child">
                        <label class="screen-reader-text" for="new<?php echo $tax_name; ?>"><?php echo $taxonomy->labels->add_new_item; ?></label>
                        <input type="text" name="new<?php echo $tax_name; ?>" id="new<?php echo $tax_name; ?>" class="form-required form-input-tip" value="<?php echo esc_attr( $taxonomy->labels->new_item_name ); ?>" aria-required="true"/>
                        <a class="button" id="sensei-<?php echo $tax_name; ?>-add-submit" class="button category-add-submit"><?php echo esc_attr( $taxonomy->labels->add_new_item ); ?></a>
                        <?php wp_nonce_field( '_ajax_nonce-add-' . $tax_name, 'add_module_nonce' ); ?>
                        <span id="<?php echo $tax_name; ?>-ajax-response"></span>
                    </p>
                </div>
            <?php endif; ?>
        </div>
    <?php

    } // end course_module_metabox


    /**
     * Submits a new module term prefixed with the
     * the current author id.
     *
     * @since 1.8.0
     */
    public static function add_new_module_term( ) {


        if( ! isset( $_POST[ 'security' ] ) || ! wp_verify_nonce( $_POST[ 'security' ], '_ajax_nonce-add-module'  ) ){
            wp_send_json_error( array('error'=> 'wrong security nonce') );
        }

        // get the term an create the new term storing infomration
        $term_name = sanitize_text_field( $_POST['newTerm'] );

        if( current_user_can('manage_options' ) ) {

            $term_slug = str_ireplace(' ', '-', trim( $term_name ) );

        } else {

            $term_slug =  get_current_user_id() . '-' . str_ireplace(' ', '-', trim( $term_name ) );

        }

        $course_id = sanitize_text_field( $_POST['course_id'] );

        // save the term
        $slug = wp_insert_term( $term_name,'module', array('slug'=> $term_slug)  );

        // send error for all errors except term exits
        if( is_wp_error( $slug ) ){

            // prepare for possible term name and id to be passed down if term exists
            $term_data = array();

            // if term exists also send back the term name and id
            if( isset( $slug->errors['term_exists'] ) ){

                $term = get_term_by( 'slug', $term_slug, 'module');
                $term_data['name'] = $term_name;
                $term_data['id'] = $term->term_id;

                // set the object terms
                wp_set_object_terms( $course_id, $term->term_id, 'module', true );
            }

            wp_send_json_error(array( 'errors'=>$slug->errors , 'term'=> $term_data ) );

        }

        //make sure the new term is checked for this course

        wp_set_object_terms( $course_id, $slug['term_id'], 'module', true );

        // Handle request then generate response using WP_Ajax_Response
        wp_send_json_success( array( 'termId' => $slug['term_id'], 'termName' => $term_name ) );

    }

    /**
     * Limit the course module metabox
     * term list to only those on courses belonging to current teacher.
     *
     * Hooked into 'get_terms'
     *
     * @since 1.8.0
     */
    public function filter_module_terms( $terms, $taxonomies, $args ){

        //dont limit for admins and other taxonomies. This should also only apply to admin
        if( current_user_can( 'manage_options' ) || !in_array( 'module', $taxonomies ) || ! is_admin()  ){
            return $terms;
        }

        // avoid infinite call loop
        remove_filter('get_terms', array( $this, 'filter_module_terms' ), 20, 3 );

        // in certain cases the array is passed in as reference to the parent term_id => parent_id
        if( isset( $args['fields'] ) && 'id=>parent' == $args['fields'] ){
            // change only scrub the terms ids form the array keys
            $terms = array_keys( $terms );
        }

        $teachers_terms =  $this->filter_terms_by_owner( $terms, get_current_user_id() );

        // add filter again as removed above
        add_filter('get_terms', array( $this, 'filter_module_terms' ), 20, 3 );

        return $teachers_terms;
    }// end filter_module_terms

    /**
     * For the selected items on a course module only return those
     * for the current user. This does not apply to admin and super admin users.
     *
     * hooked into get_object_terms
     *
     * @since 1.8.0
     */
    public function filter_course_selected_terms( $terms, $course_ids_array, $taxonomies ){

        //dont limit for admins and other taxonomies. This should also only apply to admin
        if( current_user_can( 'manage_options' ) || ! is_admin() || empty( $terms )

This code seems to be duplicated across your project.

            // only apply this to module only taxonomy queries so 1 taxonomy only:
            ||  count( $taxonomies ) > 1 || !in_array( 'module', $taxonomies )  ){
            return $terms;
        }

        $term_objects = $this->filter_terms_by_owner( $terms, get_current_user_id() );

        // if term objects were passed in send back objects
        // if term id were passed in send that back
        if( is_object( $terms[0] ) ){
            return $term_objects;
        }

        $terms = array();
        foreach( $term_objects as $term_object ){
            $terms[] = $term_object->term_id;
        }

        return $terms;


    }// end filter_course_selected_terms

    /**
     * Filter the given terms and only return the
     * terms that belong to the given user id.
     *
     * @since 1.8.0
     * @param $terms
     * @param $user_id
     * @return array
     */
    public function filter_terms_by_owner( $terms, $user_id ){

        $users_terms = array();

        foreach( $terms as $index => $term ){

            if( is_numeric( $term ) ){
                // the term id was given, get the term object
                $term = get_term( $term, 'module' );
            }

            $author = Sensei_Core_Modules::get_term_author( $term->slug );

            if ( $user_id == $author->ID ) {
                // add the term to the teachers terms
                $users_terms[] = $term;
            }

        }

        return $users_terms;

    } // end filter terms by owner

    /**
     * Add the teacher name next to modules. Only works in Admin for Admin users.
     * This will not add name to terms belonging to admin user.
     *
     * Hooked into 'get_terms'
     *
     * @since 1.8.0
     */
    public function append_teacher_name_to_module( $terms, $taxonomies, $args )
    {

        // only for admin users ont he module taxonomy
        if ( empty( $terms ) || !current_user_can('manage_options') || !in_array('module', $taxonomies) || !is_admin()) {

This code seems to be duplicated across your project.

            return $terms;
        }

        // in certain cases the array is passed in as reference to the parent term_id => parent_id
        // simply return this as wp doesn't need an array of stdObject Term
        if (isset( $args['fields'] ) && 'id=>parent' == $args['fields']) {

            return $terms;

        }

        // loop through and update all terms adding the author name
        foreach( $terms as $index => $term ){

            if( is_numeric( $term ) ){
                // the term id was given, get the term object
                $term = get_term( $term, 'module' );
            }

            $author = Sensei_Core_Modules::get_term_author( $term->slug );

            if( ! user_can( $author, 'manage_options' ) && isset( $term->name ) ) {
                $term->name = $term->name . ' (' . $author->display_name . ') ';
            }

            // add the term to the teachers terms
            $users_terms[] = $term;

        }

        return $users_terms;
    }

    /**
     * Remove modules metabox that come by default
     * with the modules taxonomy. We are removing this as
     * we have created our own custom meta box.
     */
    public static function remove_default_modules_box() {

        remove_meta_box('modulediv', 'course', 'side');

    }

    /**
     * When a course is save make sure to reset the transient set
     * for it when determining the none module lessons.
     *
     * @sine 1.9.0
     * @param $post_id
     */
    public static function reset_none_modules_transient ( $post_id ){

        // this should only apply to course and lesson post types
        if( in_array( get_post_type( $post_id ), array( 'course', 'lesson' ) ) ){

            $course_id = '';

            if( 'lesson' == get_post_type( $post_id ) ){

                $course_id = Sensei()->lesson->get_course_id( $post_id );

            }


            if( !empty( $course_id ) ){

                delete_transient( 'sensei_'. $course_id .'_none_module_lessons' );

            }

        } // end if is a course or a lesson

    } // end reset_none_modules_transient

    /**
     * This function calls the deprecated hook 'sensei_single_course_modules_content' to fire
     *
     * @since 1.9.0
     * @deprecated since 1.9.0
     *
     */
    public static function deprecate_sensei_single_course_modules_content(){

        sensei_do_deprecated_action( 'sensei_single_course_modules_content','1.9.0','sensei_single_course_modules_before or sensei_single_course_modules_after' );

    }

    /**
     * Setup the single course module loop.
     *
     * Setup the global $sensei_modules_loop
     *
     * @since 1.9.0
     */
    public static function setup_single_course_module_loop(){

        global $sensei_modules_loop, $post;
        $course_id = $post->ID;

        $modules = Sensei()->modules->get_course_modules( $course_id );

        //initial setup
        $sensei_modules_loop['total'] = 0;
        $sensei_modules_loop['modules'] = array();
        $sensei_modules_loop['current'] = -1;

        // exit if this course doesn't have modules
        if( !$modules || empty( $modules )  ){

The expression $modules of type array is implicitly converted to a boolean; are you sure this is intended? If so, consider using empty($expr) instead to make it clear that you intend to check for an array without elements.

            return;
        }


        $lessons_in_all_modules = array();
        foreach( $modules as $term ){

            $lessons_in_this_module = Sensei()->modules->get_lessons( $course_id , $term->term_id);
            $lessons_in_all_modules = array_merge(  $lessons_in_all_modules, $lessons_in_this_module  );

        }


        //setup all of the modules loop variables
        $sensei_modules_loop['total'] = count( $modules );
        $sensei_modules_loop['modules'] = $modules;
        $sensei_modules_loop['current'] = -1;
        $sensei_modules_loop['course_id'] = $course_id;

    }// end setup_single_course_module_loop

    /**
     * Tear down the course module loop.
     *
     * @since 1.9.0
     *
     */
    public static function teardown_single_course_module_loop(){

        global $sensei_modules_loop, $wp_query, $post;

        //reset all of the modules loop variables
        $sensei_modules_loop['total'] = 0;
        $sensei_modules_loop['modules'] = array();
        $sensei_modules_loop['current'] = -1;

        // set the current course to be the global post again
        wp_reset_query();
        $post = $wp_query->post;
    }// end teardown_single_course_module_loop

} // end modules class