Sensei_Lesson

Complexity

Total Complexity

551

Size/Duplication

Total Lines	3759
Duplicated Lines	8.01 %

Coupling/Cohesion

Components	1
Dependencies	11

69 Methods

Rating	Name	Duplication	Size	Complexity
B	__construct()	0	82	2
B	meta_box_setup()	0	30	1
B	lesson_info_meta_box_content()	0	28	2
B	lesson_prerequisite_meta_box_content()	10	29	3
A	lesson_preview_meta_box_content()	0	18	3
C	meta_box_save()	17	29	11
D	quiz_update()	0	109	20
B	get_submitted_setting_value()	0	23	6
B	save_post_meta()	5	34	6
D	lesson_course_meta_box_content()	12	134	15
F	quiz_panel()	21	117	10
C	quiz_panel_questions()	0	48	7
F	quiz_panel_question()	0	168	24
F	quiz_panel_add()	15	193	21
F	quiz_panel_get_existing_questions()	14	79	12
B	quiz_panel_add_existing_question()	0	29	3
C	quiz_panel_filter_existing_questions()	0	70	11
D	quiz_panel_question_field()	39	191	33
B	quiz_panel_question_feedback()	0	30	5
A	question_get_answer_id()	0	9	1
A	get_answer_id()	0	11	2
A	lesson_quiz_meta_box_content()	0	13	2
A	lesson_quiz_settings_meta_box_content()	0	21	3
A	quiz_settings_panel()	0	14	3
B	get_quiz_settings()	8	83	5
C	enqueue_scripts()	0	37	12
B	enqueue_styles()	3	13	7
A	add_column_headings()	10	10	2
B	add_column_data()	12	23	6
A	lesson_add_course()	0	21	3
C	lesson_update_question()	0	44	7
B	lesson_add_multiple_questions()	0	56	8
B	lesson_remove_multiple_questions()	0	23	4
A	get_question_category_limit()	0	21	4
C	lesson_add_existing_questions()	5	50	8
A	lesson_update_grade_type()	15	15	3
B	lesson_update_question_order()	0	23	5
A	lesson_update_question_order_random()	15	15	3
D	lesson_save_course()	3	65	14
F	lesson_save_question()	8	229	69
B	lesson_delete_question()	3	21	6
A	lesson_complexities()	0	11	1
B	lesson_count()	0	32	2
A	lesson_quizzes()	18	18	1
F	lesson_quiz_questions()	0	196	37
B	set_default_question_order()	0	33	4
C	lesson_image()	10	61	10
A	lesson_excerpt()	0	13	4
C	get_course_id()	0	22	8
B	all_lessons_edit_fields()	0	92	5
A	generate_all_lessons_edit_field()	0	13	1
C	save_all_lessons_edit_fields()	0	69	16
B	set_quick_edit_admin_defaults()	0	27	6
B	single_course_lessons_classes()	0	34	6
D	the_lesson_meta()	14	99	10
A	the_lesson_thumbnail()	0	14	3
A	alter_the_lesson_excerpt()	0	13	2
A	get_lesson_prerequisite_id()	0	16	4
C	is_prerequisite_complete()	7	23	7
B	user_not_taking_course_message()	0	25	5
A	prerequisite_complete_message()	0	12	3
A	deprecate_sensei_lesson_archive_header_hook()	0	5	1
A	the_archive_header()	0	9	1
A	the_title()	0	23	1
A	flush_rewrite_rules()	16	16	4
C	footer_quiz_call_to_action()	0	60	12
B	output_comments()	0	20	6
D	user_lesson_quiz_status_message()	0	27	9
C	course_signup_link()	21	82	10

<?php
if ( ! defined( 'ABSPATH' ) ) exit; // Exit if accessed directly

/**
 * Sensei Lessons Class
 *
 * All functionality pertaining to the lessons post type in Sensei.
 *
 * @package WordPress
 * @subpackage Sensei
 * @category Core
 * @author WooThemes
 * @since 1.0.0
 */
class Sensei_Lesson {
	public $token;
	public $meta_fields;

	/**
	 * Constructor.
	 * @since  1.0.0
	 */
	public function __construct () {

        $this->token = 'lesson';

		// Setup meta fields for this post type
		$this->meta_fields = array( 'lesson_prerequisite', 'lesson_course', 'lesson_preview', 'lesson_length', 'lesson_complexity', 'lesson_video_embed' );

        $this->question_order = '';

The property question_order does not exist. Did you maybe forget to declare it?

		// Admin actions
		if ( is_admin() ) {

			// Metabox functions
			add_action( 'admin_menu', array( $this, 'meta_box_setup' ), 20 );
			add_action( 'save_post', array( $this, 'meta_box_save' ) );
			add_action( 'save_post', array( $this, 'quiz_update' ) );

			// Custom Write Panel Columns
			add_filter( 'manage_edit-lesson_columns', array( $this, 'add_column_headings' ), 10, 1 );
			add_action( 'manage_posts_custom_column', array( $this, 'add_column_data' ), 10, 2 );

			// Add/Update question
			add_action( 'wp_ajax_lesson_update_question', array( $this, 'lesson_update_question' ) );
			add_action( 'wp_ajax_nopriv_lesson_update_question', array( $this, 'lesson_update_question' ) );

			// Add course
			add_action( 'wp_ajax_lesson_add_course', array( $this, 'lesson_add_course' ) );
			add_action( 'wp_ajax_nopriv_lesson_add_course', array( $this, 'lesson_add_course' ) );

			// Update grade type
			add_action( 'wp_ajax_lesson_update_grade_type', array( $this, 'lesson_update_grade_type' ) );
			add_action( 'wp_ajax_nopriv_lesson_update_grade_type', array( $this, 'lesson_update_grade_type' ) );

			// Update question order
			add_action( 'wp_ajax_lesson_update_question_order', array( $this, 'lesson_update_question_order' ) );
			add_action( 'wp_ajax_nopriv_lesson_update_question_order', array( $this, 'lesson_update_question_order' ) );

			//Update question order
			add_action( 'wp_ajax_lesson_update_question_order_random', array( $this, 'lesson_update_question_order_random' ) );
			add_action( 'wp_ajax_nopriv_lesson_update_question_order_random', array( $this, 'lesson_update_question_order_random' ) );

			// Get answer ID
			add_action( 'wp_ajax_question_get_answer_id', array( $this, 'question_get_answer_id' ) );
			add_action( 'wp_ajax_nopriv_question_get_answer_id', array( $this, 'question_get_answer_id' ) );

			// Add multiple questions
			add_action( 'wp_ajax_lesson_add_multiple_questions', array( $this, 'lesson_add_multiple_questions' ) );
			add_action( 'wp_ajax_nopriv_lesson_add_multiple_questions', array( $this, 'lesson_add_multiple_questions' ) );

			// Remove multiple questions
			add_action( 'wp_ajax_lesson_remove_multiple_questions', array( $this, 'lesson_remove_multiple_questions' ) );
			add_action( 'wp_ajax_nopriv_lesson_remove_multiple_questions', array( $this, 'lesson_remove_multiple_questions' ) );

			// Get question category limit
			add_action( 'wp_ajax_get_question_category_limit', array( $this, 'get_question_category_limit' ) );
			add_action( 'wp_ajax_nopriv_get_question_category_limit', array( $this, 'get_question_category_limit' ) );

			// Add existing questions
			add_action( 'wp_ajax_lesson_add_existing_questions', array( $this, 'lesson_add_existing_questions' ) );
			add_action( 'wp_ajax_nopriv_lesson_add_existing_questions', array( $this, 'lesson_add_existing_questions' ) );

			// Filter existing questions
			add_action( 'wp_ajax_filter_existing_questions', array( $this, 'quiz_panel_filter_existing_questions' ) );
			add_action( 'wp_ajax_nopriv_filter_existing_questions', array( $this, 'quiz_panel_filter_existing_questions' ) );

            // output bulk edit fields
            add_action( 'bulk_edit_custom_box', array( $this, 'all_lessons_edit_fields' ), 10, 2 );
            add_action( 'quick_edit_custom_box', array( $this, 'all_lessons_edit_fields' ), 10, 2 );

            // load quick edit default values
            add_action('manage_lesson_posts_custom_column', array( $this, 'set_quick_edit_admin_defaults'), 11, 2);

            // save bulk edit fields
            add_action( 'wp_ajax_save_bulk_edit_book', array( $this, 'save_all_lessons_edit_fields' ) );

            // flush rewrite rules when saving a lesson
            add_action('save_post', array( __CLASS__, 'flush_rewrite_rules' ) );

		} else {

This else statement is empty and can be removed.

			// Frontend actions
		} // End If Statement
	} // End __construct()

	/**
	 * meta_box_setup function.
	 *
	 * @access public
	 * @return void
	 */
	public function meta_box_setup () {

		// Add Meta Box for Prerequisite Lesson
		add_meta_box( 'lesson-prerequisite', __( 'Lesson Prerequisite', 'woothemes-sensei' ), array( $this, 'lesson_prerequisite_meta_box_content' ), $this->token, 'side', 'default' );

		// Add Meta Box for Lesson Course
		add_meta_box( 'lesson-course', __( 'Lesson Course', 'woothemes-sensei' ), array( $this, 'lesson_course_meta_box_content' ), $this->token, 'side', 'default' );

		// Add Meta Box for Lesson Preview
		add_meta_box( 'lesson-preview', __( 'Lesson Preview', 'woothemes-sensei' ), array( $this, 'lesson_preview_meta_box_content' ), $this->token, 'side', 'default' );

		// Add Meta Box for Lesson Information
		add_meta_box( 'lesson-info', __( 'Lesson Information', 'woothemes-sensei' ), array( $this, 'lesson_info_meta_box_content' ), $this->token, 'normal', 'default' );

		// Add Meta Box for Quiz Settings
		add_meta_box( 'lesson-quiz-settings', __( 'Quiz Settings', 'woothemes-sensei' ), array( $this, 'lesson_quiz_settings_meta_box_content' ), $this->token, 'normal', 'default' );

		// Add Meta Box for Lesson Quiz Questions
		add_meta_box( 'lesson-quiz', __( 'Quiz Questions', 'woothemes-sensei' ), array( $this, 'lesson_quiz_meta_box_content' ), $this->token, 'normal', 'default' );

		// Remove "Custom Settings" meta box.
		remove_meta_box( 'woothemes-settings', $this->token, 'normal' );

		// Add JS scripts
		add_action( 'admin_enqueue_scripts', array( $this, 'enqueue_scripts' ) );

		// Add CSS
		add_action( 'admin_enqueue_scripts', array( $this, 'enqueue_styles' ) );

	} // End meta_box_setup()


	/**
	 * lesson_info_meta_box_content function.
	 *
	 * @access public
	 * @return void
	 */
	public function lesson_info_meta_box_content () {
		global $post;

		$lesson_length = get_post_meta( $post->ID, '_lesson_length', true );
		$lesson_complexity = get_post_meta( $post->ID, '_lesson_complexity', true );
		$complexity_array = $this->lesson_complexities();
		$lesson_video_embed = get_post_meta( $post->ID, '_lesson_video_embed', true );

		$html = '';
		// Lesson Length
		$html .= '<p><label for="lesson_length">' . __( 'Lesson Length in minutes', 'woothemes-sensei' ) . ': </label>';
		$html .= '<input type="number" id="lesson-length" name="lesson_length" class="small-text" value="' . esc_attr( $lesson_length ) . '" /></p>' . "\n";
		// Lesson Complexity
		$html .= '<p><label for="lesson_complexity">' . __( 'Lesson Complexity', 'woothemes-sensei' ) . ': </label>';
		$html .= '<select id="lesson-complexity-options" name="lesson_complexity" class="chosen_select lesson-complexity-select">';
			$html .= '<option value="">' . __( 'None', 'woothemes-sensei' ) . '</option>';
			foreach ($complexity_array as $key => $value){
				$html .= '<option value="' . esc_attr( $key ) . '"' . selected( $key, $lesson_complexity, false ) . '>' . esc_html( $value ) . '</option>' . "\n";
			} // End For Loop
		$html .= '</select></p>' . "\n";

		$html .= '<p><label for="lesson_video_embed">' . __( 'Video Embed Code', 'woothemes-sensei' ) . ':</label><br/>' . "\n";
		$html .= '<textarea rows="5" cols="50" name="lesson_video_embed" tabindex="6" id="course-video-embed">' . $lesson_video_embed . '</textarea></p>' . "\n";
		$html .= '<p>' .  __( 'Paste the embed code for your video (e.g. YouTube, Vimeo etc.) in the box above.', 'woothemes-sensei' ) . '</p>';

		echo $html;

	} // End lesson_info_meta_box_content()

	/**
	 * lesson_prerequisite_meta_box_content function.
	 *
	 * @access public
	 * @return void
	 */
	public function lesson_prerequisite_meta_box_content () {
		global $post;
		// Get existing post meta
		$select_lesson_prerequisite = get_post_meta( $post->ID, '_lesson_prerequisite', true );
		// Get the Lesson Posts
		$post_args = array(	'post_type' 		=> 'lesson',
							'posts_per_page' 		=> -1,
							'orderby'         	=> 'title',
    						'order'           	=> 'ASC',
    						'exclude' 			=> $post->ID,
							'suppress_filters' 	=> 0
							);
		$posts_array = get_posts( $post_args );
		// Build the HTML to Output
		$html = '';
		$html .= wp_nonce_field( 'sensei-save-post-meta','woo_' . $this->token . '_nonce', true, false  );
		if ( count( $posts_array ) > 0 ) {

This code seems to be duplicated across your project.

			$html .= '<select id="lesson-prerequisite-options" name="lesson_prerequisite" class="chosen_select widefat">' . "\n";
			$html .= '<option value="">' . __( 'None', 'woothemes-sensei' ) . '</option>';
				foreach ($posts_array as $post_item){
					$html .= '<option value="' . esc_attr( absint( $post_item->ID ) ) . '"' . selected( $post_item->ID, $select_lesson_prerequisite, false ) . '>' . esc_html( $post_item->post_title ) . '</option>' . "\n";
				} // End For Loop
			$html .= '</select>' . "\n";
		} else {
			$html .= '<p>' . esc_html( __( 'No lessons exist yet. Please add some first.', 'woothemes-sensei' ) ) . '</p>';
		} // End If Statement
		// Output the HTML
		echo $html;
	} // End lesson_prerequisite_meta_box_content()

	/**
	 * lesson_preview_meta_box_content function.
	 *
	 * @access public
	 * @return void
	 */
	public function lesson_preview_meta_box_content () {
		global $post;
		// Get existing post meta
		$lesson_preview = get_post_meta( $post->ID, '_lesson_preview', true );
		$html = '';
		$html .= wp_nonce_field( 'sensei-save-post-meta','woo_' . $this->token . '_nonce', true, false  );

		$checked = '';
		if ( isset( $lesson_preview ) && ( '' != $lesson_preview ) ) {
	 	    $checked = checked( 'preview', $lesson_preview, false );
	 	} // End If Statement

	 	$html .= '<label for="lesson_preview">';
	 	$html .= '<input type="checkbox" id="lesson_preview" name="lesson_preview" value="preview" ' . $checked . '>&nbsp;' . __( 'Allow this lesson to be viewed without purchase/login', 'woothemes-sensei' ) . '<br>';

		// Output the HTML
		echo $html;
	} // End lesson_preview_meta_box_content()

	/**
	 * meta_box_save function.
	 *
	 * @access public
	 * @param int $post_id
	 * @return void
	 */
	public function meta_box_save ( $post_id ) {

		// Verify the nonce before proceeding.
		if ( ( get_post_type( $post_id ) != $this->token ) || !isset(   $_POST[ 'woo_' . $this->token . '_nonce'] )  || ! wp_verify_nonce( $_POST[ 'woo_' . $this->token . '_nonce' ], 'sensei-save-post-meta' ) ) {

This code seems to be duplicated across your project.

			return $post_id;
		} // End If Statement
		// Get the post type object.
		$post_type = get_post_type_object( get_post_type( $post_id ) );
		// Check if the current user has permission to edit the post.
		if ( !current_user_can( $post_type->cap->edit_post, $post_id ) ) {
			return $post_id;
		} // End If Statement
		// Check if the current post type is a page
		if ( 'page' == $_POST[ 'post_type' ] ) {

This code seems to be duplicated across your project.

			if ( ! current_user_can( 'edit_page', $post_id ) ) {
				return $post_id;
			} // End If Statement
		} else {
			if ( ! current_user_can( 'edit_post', $post_id ) ) {
				return $post_id;
			} // End If Statement
		} // End If Statement
		// Save the post meta data fields
		if ( isset($this->meta_fields) && is_array($this->meta_fields) ) {

This code seems to be duplicated across your project.

			foreach ( $this->meta_fields as $meta_key ) {
				$this->save_post_meta( $meta_key, $post_id );
			} // End For Loop
		} // End If Statement
	} // End meta_box_save()


	/**
     * Update the lesson quiz and all the post meta
	 *
	 * @access public
	 * @return void
	 */
	public function quiz_update( $post_id ) {
		global $post;
		// Verify the nonce before proceeding.
		if ( ( 'lesson' != get_post_type( $post_id ) )|| !isset(   $_POST[ 'woo_' . $this->token . '_nonce'] )  || ! wp_verify_nonce( $_POST[ 'woo_' . $this->token . '_nonce' ], 'sensei-save-post-meta') ) {
			if ( isset($post->ID) ) {
				return $post->ID;
			} else {
				return false;
			} // End If Statement
		} // End If Statement

		if( wp_is_post_revision( $post_id ) || wp_is_post_autosave( $post_id ) ) {
			return;
		}

		// Temporarily disable the filter
        remove_action( 'save_post', array( $this, 'quiz_update' ) );
		// Save the Quiz
		$quiz_id = $this->lesson_quizzes( $post_id, 'any');

		 // Sanitize and setup the post data
		$_POST = stripslashes_deep( $_POST );
		if ( isset( $_POST[ 'quiz_id' ] ) && ( 0 < absint( $_POST[ 'quiz_id' ] ) ) ) {
			$quiz_id = absint( $_POST[ 'quiz_id' ] );
		} // End If Statement
		$post_title = esc_html( $_POST[ 'post_title' ] );
		$post_status = esc_html( $_POST[ 'post_status' ] );
		$post_content = '';

		// Setup Query Arguments
		$post_type_args = array(	'post_content' => $post_content,
  		    						'post_status' => $post_status,
  		    						'post_title' => $post_title,
  		    						'post_type' => 'quiz',
                                    'post_parent' => $post_id,
  		    						);

		$settings = $this->get_quiz_settings();

  		// Update or Insert the Lesson Quiz
		if ( 0 < $quiz_id ) {
			// Update the Quiz
			$post_type_args[ 'ID' ] = $quiz_id;
		    wp_update_post($post_type_args);

		    // Update the post meta data
		    update_post_meta( $quiz_id, '_quiz_lesson', $post_id );

		    foreach( $settings as $field ) {
		    	if( 'random_question_order' != $field['id'] ) {
			    	$value = $this->get_submitted_setting_value( $field );
			    	if( isset( $value ) ) {
			    		update_post_meta( $quiz_id, '_' . $field['id'], $value );
			    	}
			    }
		    }

		    // Set the post terms for quiz-type
		    wp_set_post_terms( $quiz_id, array( 'multiple-choice' ), 'quiz-type' );
		} else {
			// Create the Quiz
		    $quiz_id = wp_insert_post($post_type_args);

		    // Add the post meta data WP will add it if it doesn't exist
            update_post_meta( $quiz_id, '_quiz_lesson', $post_id );

		    foreach( $settings as $field ) {
		    	if( 'random_question_order' != $field['id'] ) {

                    //ignore values not posted to avoid
                    // overwriting with empty or default values
                    // when the values are posted from bulk edit or quick edit
                    if( !isset( $_POST[ $field['id'] ] ) ){
                        continue;
                    }

			    	$value = $this->get_submitted_setting_value( $field );
			    	if( isset( $value ) ) {
			    		add_post_meta( $quiz_id, '_' . $field['id'], $value );
			    	}
			    }
		    }

		    // Set the post terms for quiz-type
		    wp_set_post_terms( $quiz_id, array( 'multiple-choice' ), 'quiz-type' );
		} // End If Statement

		// Add default lesson order meta value
		$course_id = get_post_meta( $post_id, '_lesson_course', true );
		if( $course_id ) {
			if( ! get_post_meta( $post_id, '_order_' . $course_id, true ) ) {
				update_post_meta( $post_id, '_order_' . $course_id, 0 );
			}
		}
		// Add reference back to the Quiz
		update_post_meta( $post_id, '_lesson_quiz', $quiz_id );
		// Mark if the Lesson Quiz has questions
		$quiz_questions = Sensei()->lesson->lesson_quiz_questions( $quiz_id );
		if( 0 < count( $quiz_questions ) ) {
			update_post_meta( $post_id, '_quiz_has_questions', '1' );
		}
		else {
			delete_post_meta( $post_id, '_quiz_has_questions' );
		}

		// Restore the previously disabled filter
        add_action( 'save_post', array( $this, 'quiz_update' ) );

	} // End post_updated()

	public function get_submitted_setting_value( $field = false ) {

		if( ! $field ) return;

		$value = false;

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

		if( 'quiz_grade_type' == $field['id'] ) {
			if( isset( $_POST[ $field['id'] ] ) && 'on' == $_POST[ $field['id'] ] ) {
				$value = 'auto';
			} else {
				$value = 'manual';
			}
			return $value;
		}

		if ( isset( $_POST[ $field['id'] ] ) ) {
			$value = $_POST[ $field['id'] ];
		} else {
			$value = $field['default'];
		}

		return $value;
	}

	/**
	 * save_post_meta function.
	 * Saves lesson meta data
	 * @access private
	 * @param string $post_key (default: '')
	 * @param int $post_id (default: 0)
	 * @return int|bool meta id or saved status
	 */
	private function save_post_meta( $post_key = '', $post_id = 0 ) {
		// Get the meta key.
		$meta_key = '_' . $post_key;

        //ignore fields are not posted

        if( !isset( $_POST[ $post_key ] ) ){

            // except for lesson preview checkbox field
            if( 'lesson_preview' == $post_key ){

                $_POST[ $post_key ] = '';

            } else {

                return false;

            }

        }

		// Get the posted data and sanitize it for use as an HTML class.
		if ( 'lesson_video_embed' == $post_key) {

This code seems to be duplicated across your project.

			$new_meta_value = esc_html( $_POST[$post_key] );
		} else {
			$new_meta_value = ( isset( $_POST[$post_key] ) ? sanitize_html_class( $_POST[$post_key] ) : '' );
		} // End If Statement

        // update field with the new value
        if( -1 != $new_meta_value  ){
            return update_post_meta( $post_id, $meta_key, $new_meta_value );
        }

	} // End save_post_meta()

	/**
	 * lesson_course_meta_box_content function.
	 *
	 * @access public
	 * @return void
	 */
	public function lesson_course_meta_box_content () {
		global $post;
		// Setup Lesson Meta Data
		$selected_lesson_course = 0;
		if ( 0 < $post->ID ) {
			$selected_lesson_course = get_post_meta( $post->ID, '_lesson_course', true );
		} // End If Statement
		// Handle preselected course
		if ( isset( $_GET[ 'course_id' ] ) && ( 0 < absint( $_GET[ 'course_id' ] ) ) ) {

This code seems to be duplicated across your project.

			$selected_lesson_course = absint( $_GET[ 'course_id' ] );
		} // End If Statement
		// Get the Lesson Posts
		$post_args = array(	'post_type' 		=> 'course',
							'posts_per_page' 		=> -1,
							'orderby'         	=> 'title',
    						'order'           	=> 'ASC',
    						'post_status'      	=> 'any',
    						'suppress_filters' 	=> 0,
							);
		$posts_array = get_posts( $post_args );
		// Buid the HTML to Output
		$html = '';
		// Nonce
		$html .= wp_nonce_field( 'sensei-save-post-meta','woo_' . $this->token . '_nonce', true, false  );

        // Select the course for the lesson
        $drop_down_args = array(
            'name'=>'lesson_course',
            'id' => 'lesson-course-options'
        );

        $courses = WooThemes_Sensei_Course::get_all_courses();
        $courses_options = array();
        foreach( $courses as $course ){
            $courses_options[ $course->ID ] = get_the_title( $course ) ;
        }
        $html .= Sensei_Utils::generate_drop_down( $selected_lesson_course, $courses_options, $drop_down_args );

        // Course Actions Panel
		if ( current_user_can( 'publish_courses' )) {
				$html .= '<div id="lesson-course-actions">';
					$html .= '<p>';
						// Add a course action link
						$html .= '<a id="lesson-course-add" href="#course-add" class="lesson-add-course">+ ' . __('Add New Course', 'woothemes-sensei' ) . '</a>';
					$html .= '</p>';
				$html .= '</div>';
				// Add a course input fields
				$html .= '<div id="lesson-course-details" class="hidden">';
					$html .= '<p>';
						// Course Title input
						$html .= '<label>' . __( 'Course Title' , 'woothemes-sensei' ) . '</label> ';
	  					$html .= '<input type="text" id="course-title" name="course_title" value="" size="25" class="widefat" />';
	  					// Course Description input
	  					$html .= '<label>' . __( 'Description' , 'woothemes-sensei' ) . '</label> ';
	  					$html .= '<textarea rows="10" cols="40" id="course-content" name="course_content" value="" size="300" class="widefat"></textarea>';
	  					// Course Prerequisite
	  					$html .= '<label>' . __( 'Course Prerequisite' , 'woothemes-sensei' ) . '</label> ';
	  					$html .= '<select id="course-prerequisite-options" name="course_prerequisite" class="chosen_select widefat">' . "\n";
							$html .= '<option value="">' . __( 'None', 'woothemes-sensei' ) . '</option>';
							foreach ($posts_array as $post_item){
								$html .= '<option value="' . esc_attr( absint( $post_item->ID ) ) . '">' . esc_html( $post_item->post_title ) . '</option>' . "\n";
							} // End For Loop
						$html .= '</select>' . "\n";
						// Course Product
                        if ( Sensei_WC::is_woocommerce_active() ) {
	  						// Get the Products
							$select_course_woocommerce_product = get_post_meta( $post_item->ID, '_course_woocommerce_product', true );

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

The variable $post_item seems to be defined by a foreach iteration on line 526. Are you sure the iterator is never empty, otherwise this variable is not defined?

							$product_args = array(	'post_type' 		=> array( 'product', 'product_variation' ),
													'posts_per_page' 		=> -1,
													'orderby'         	=> 'title',
	    											'order'           	=> 'DESC',
	    											'post_status'		=> array( 'publish', 'private', 'draft' ),
	    											'tax_query'			=> array(
														array(
															'taxonomy'	=> 'product_type',
															'field'		=> 'slug',
															'terms'		=> array( 'variable', 'grouped' ),
															'operator'	=> 'NOT IN'
														)
													),
	    											'suppress_filters' 	=> 0
													);
							$products_array = get_posts( $product_args );
							$html .= '<label>' . __( 'WooCommerce Product' , 'woothemes-sensei' ) . '</label> ';
	  						$html .= '<select id="course-woocommerce-product-options" name="course_woocommerce_product" class="chosen_select widefat">' . "\n";
								$html .= '<option value="-">' . __( 'None', 'woothemes-sensei' ) . '</option>';
								$prev_parent_id = 0;
								foreach ($products_array as $products_item){

									if ( 'product_variation' == $products_item->post_type ) {
										$product_object = get_product( $products_item->ID );
										$parent_id = wp_get_post_parent_id( $products_item->ID );
										$product_name = ucwords( woocommerce_get_formatted_variation( $product_object->variation_data, true ) );

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

									} else {
										$parent_id = false;
										$prev_parent_id = 0;
										$product_name = $products_item->post_title;

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

									}

									// Show variations in groups
									if( $parent_id && $parent_id != $prev_parent_id ) {

This code seems to be duplicated across your project.

										if( 0 != $prev_parent_id ) {
											$html .= '</optgroup>';
										}
										$html .= '<optgroup label="' . get_the_title( $parent_id ) . '">';
										$prev_parent_id = $parent_id;
									} elseif( ! $parent_id && 0 == $prev_parent_id ) {
										$html .= '</optgroup>';
									}

									$html .= '<option value="' . esc_attr( absint( $products_item->ID ) ) . '">' . esc_html( $products_item->post_title ) . '</option>' . "\n";
								} // End For Loop
							$html .= '</select>' . "\n";
						} else {
							// Default
							$html .= '<input type="hidden" name="course_woocommerce_product" id="course-woocommerce-product-options" value="-" />';
						}
						// Course Category
	  					$html .= '<label>' . __( 'Course Category' , 'woothemes-sensei' ) . '</label> ';
	  					$cat_args = array( 'echo' => false, 'hierarchical' => true, 'show_option_none' => __( 'None', 'woothemes-sensei' ), 'taxonomy' => 'course-category', 'orderby' => 'name', 'id' => 'course-category-options', 'name' => 'course_category', 'class' => 'widefat' );
						$html .= wp_dropdown_categories(apply_filters('widget_course_categories_dropdown_args', $cat_args)) . "\n";
	  					// Save the course action button
	  					$html .= '<a title="' . esc_attr( __( 'Save Course', 'woothemes-sensei' ) ) . '" href="#add-course-metadata" class="lesson_course_save button button-highlighted">' . esc_html( __( 'Add Course', 'woothemes-sensei' ) ) . '</a>';
						$html .= '&nbsp;&nbsp;&nbsp;';
						// Cancel action link
						$html .= '<a href="#course-add-cancel" class="lesson_course_cancel">' . __( 'Cancel', 'woothemes-sensei' ) . '</a>';
					$html .= '</p>';
				$html .= '</div>';
			} // End If Statement

		// Output the HTML
		echo $html;
	} // End lesson_course_meta_box_content()

	public function quiz_panel( $quiz_id = 0 ) {

		$html = wp_nonce_field( 'sensei-save-post-meta','woo_' . $this->token . '_nonce', true, false  );
		$html .= '<div id="add-quiz-main">';
			if ( 0 == $quiz_id ) {

This code seems to be duplicated across your project.

				$html .= '<p>';
					// Default message and Add a Quiz button
					$html .= esc_html( __( 'Once you have saved your lesson you will be able to add questions.', 'woothemes-sensei' ) );
				$html .= '</p>';
			}

			// Quiz Panel CSS Class
			$quiz_class = '';
			if ( 0 == $quiz_id ) {
				$quiz_class = ' class="hidden"';
			} // End If Statement
			// Build the HTML to Output
			$message_class = '';

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

			// Setup Questions Query
			$questions = array();
			if ( 0 < $quiz_id ) {
				$questions = $this->lesson_quiz_questions( $quiz_id );
			} // End If Statement

			$question_count = 0;
			foreach( $questions as $question ) {

This code seems to be duplicated across your project.

				if( $question->post_type == 'multiple_question' ) {
					$question_number = get_post_meta( $question->ID, 'number', true );
					$question_count += $question_number;
				} else {
					++$question_count;
				}

			}

			// Inner DIV
			$html .= '<div id="add-quiz-metadata"' . $quiz_class . '>';

				// Quiz ID
				$html .= '<input type="hidden" name="quiz_id" id="quiz_id" value="' . esc_attr( $quiz_id ) . '" />';

				// Default Message
				if ( 0 == $quiz_id ) {

This code seems to be duplicated across your project.

					$html .= '<p class="save-note">';
						$html .= esc_html( __( 'Please save your lesson in order to add questions to your quiz.', 'woothemes-sensei' ) );
					$html .= '</p>';
				} // End If Statement

			$html .= '</div>';

			// Question Container DIV
			$html .= '<div id="add-question-main"' . $quiz_class . '>';
				// Inner DIV
				$html .= '<div id="add-question-metadata">';

					// Count of questions
					$html .= '<input type="hidden" name="question_counter" id="question_counter" value="' . esc_attr( $question_count ) . '" />';
					// Table headers
					$html .= '<table class="widefat" id="sortable-questions">
								<thead>
								    <tr>
								        <th class="question-count-column">#</th>
								        <th>' . __( 'Question', 'woothemes-sensei' ) . '</th>
								        <th style="width:45px;">' . __( 'Grade', 'woothemes-sensei' ) . '</th>
								        <th style="width:125px;">' . __( 'Type', 'woothemes-sensei' ) . '</th>
								        <th style="width:125px;">' . __( 'Action', 'woothemes-sensei' ) . '</th>
								    </tr>
								</thead>
								<tfoot>
								    <tr>
									    <th class="question-count-column">#</th>
									    <th>' . __( 'Question', 'woothemes-sensei' ) . '</th>
									    <th>' . __( 'Grade', 'woothemes-sensei' ) . '</th>
									    <th>' . __( 'Type', 'woothemes-sensei' ) . '</th>
									    <th>' . __( 'Action', 'woothemes-sensei' ) . '</th>
								    </tr>
								</tfoot>';

					$message_class = '';
					if ( 0 < $question_count ) { $message_class = 'hidden'; }

					$html .= '<tbody id="no-questions-message" class="' . esc_attr( $message_class ) . '">';
						$html .= '<tr>';
							$html .= '<td colspan="5">' . __( 'There are no Questions for this Quiz yet. Please add some below.', 'woothemes-sensei' ) . '</td>';
						$html .= '</tr>';
					$html .= '</tbody>';

					if( 0 < $question_count ) {
						$html .= $this->quiz_panel_questions( $questions );
					}

					$html .= '</table>';

					if( ! isset( $this->question_order ) ) {
						$this->question_order = '';
					}

					$html .= '<input type="hidden" id="question-order" name="question-order" value="' . $this->question_order . '" />';

				$html .= '</div>';

				// Question Action Container DIV
				$html .= '<div id="add-question-actions">';

					$html .= $this->quiz_panel_add();

				$html .= '</div>';

			$html .= '</div>';

		$html .= '</div>';

		return $html;

	}

	public function quiz_panel_questions( $questions = array() ) {
		global $quiz_questions;

		$quiz_questions = $questions;

		$html = '';

		if( count( $questions ) > 0 ) {

			$question_class = '';

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

			$question_counter = 1;

			foreach ( $questions as $question ) {

				$question_id = $question->ID;

				$question_type = Sensei()->question->get_question_type( $question_id );

				$multiple_data = array();
				$question_increment = 1;
				if( 'multiple_question' == $question->post_type ) {
					$question_type = 'category';

					$question_category = get_post_meta( $question->ID, 'category', true );
					$question_cat = get_term( $question_category, 'question-category' );

					$question_number = get_post_meta( $question->ID, 'number', true );
					$question_increment = $question_number;

					$multiple_data = array( $question_cat->name, $question_number );
				}

				if( ! $question_type ) {
					$question_type = 'multiple-choice';
				}

				// Row with question and actions
				$html .= $this->quiz_panel_question( $question_type, $question_counter, $question_id, 'quiz', $multiple_data );
				$question_counter += $question_increment;

				if( isset( $this->question_order ) && strlen( $this->question_order ) > 0 ) { $this->question_order .= ','; }
				$this->question_order .= $question_id;
			} // End For Loop
		}

		return $html;

	}

	public function quiz_panel_question( $question_type = '', $question_counter = 0, $question_id = 0, $context = 'quiz', $multiple_data = array() ) {
		global $row_counter,  $quiz_questions;

		$html = '';

		$question_class = '';
		if( 'quiz' == $context ) {
			if( ! $row_counter || ! isset( $row_counter ) ) {
				$row_counter = 1;
			}
			if( $row_counter % 2 ) { $question_class = 'alternate'; }
			++$row_counter;
		}

		if( $question_id ) {

			if( $question_type != 'category' ) {

				$question_grade = Sensei()->question->get_question_grade( $question_id );

				$question_media = get_post_meta( $question_id, '_question_media', true );
				$question_media_type = $question_media_thumb = $question_media_link = $question_media_title = '';

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

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

				$question_media_thumb_class = $question_media_link_class = $question_media_delete_class = 'hidden';
				$question_media_add_button = __( 'Add file', 'woothemes-sensei' );
				if( 0 < intval( $question_media ) ) {
					$mimetype = get_post_mime_type( $question_media );
					if( $mimetype ) {
						$mimetype_array = explode( '/', $mimetype);
						if( isset( $mimetype_array[0] ) && $mimetype_array[0] ) {
							$question_media_delete_class = '';
							$question_media_type = $mimetype_array[0];
							if( 'image' == $question_media_type ) {
								$question_media_thumb = wp_get_attachment_thumb_url( $question_media );
								if( $question_media_thumb ) {
									$question_media_thumb_class = '';
								}
							}
							$question_media_url = wp_get_attachment_url( $question_media );
							if( $question_media_url ) {
								$attachment = get_post( $question_media );
								$question_media_title = $attachment->post_title;

								if( ! $question_media_title ) {
									$question_media_filename = basename( $question_media_url );
									$question_media_title = $question_media_filename;
								}
								$question_media_link = '<a class="' . $question_media_type . '" href="' . esc_url( $question_media_url ) . '" target="_blank">' . $question_media_title . '</a>';
								$question_media_link_class = '';
							}

							$question_media_add_button = __( 'Change file', 'woothemes-sensei' );
						}
					}
				}

				$random_order = get_post_meta( $question_id, '_random_order', true );
				if( ! $random_order ) {
					$random_order = 'yes';
				}

				if( ! $question_type ) { $question_type = 'multiple-choice'; }
			}

			$html .= '<tbody class="' . $question_class . '">';

				if( 'quiz' == $context ) {
					$html .= '<tr>';
						if( $question_type != 'category' ) {
							$question = get_post( $question_id );
							$html .= '<td class="table-count question-number question-count-column"><span class="number">' . $question_counter . '</span></td>';
							$html .= '<td>' . esc_html( $question->post_title ) . '</td>';
							$html .= '<td class="question-grade-column">' . esc_html( $question_grade ) . '</td>';

The variable $question_grade does not seem to be defined for all execution paths leading up to this point.

							$question_types_filtered = ucwords( str_replace( array( '-', 'boolean' ), array( ' ', __( 'True/False', 'woothemes-sensei' ) ), $question_type ) );
							$html .= '<td>' . esc_html( $question_types_filtered ) . '</td>';
							$html .= '<td><a title="' . esc_attr( __( 'Edit Question', 'woothemes-sensei' ) ) . '" href="#question_' . $question_counter .'" class="question_table_edit">' . esc_html( __( 'Edit', 'woothemes-sensei' ) ) . '</a> <a title="' . esc_attr( __( 'Remove Question', 'woothemes-sensei' ) ) . '" href="#add-question-metadata" class="question_table_delete">' . esc_html( __( 'Remove', 'woothemes-sensei' ) ) . '</a></td>';

						} else {

							$end_number = intval( $question_counter ) + intval( $multiple_data[1] ) - 1;
							if( $question_counter == $end_number ) {
								$row_numbers = $question_counter;
							} else {
								$row_numbers = $question_counter . ' - ' . $end_number;
							}
							$row_title = sprintf( __( 'Selected from \'%1$s\' ', 'woothemes-sensei' ), $multiple_data[0] );

							$html .= '<td class="table-count question-number question-count-column"><span class="number hidden">' . $question_counter . '</span><span class="hidden total-number">' . $multiple_data[1] . '</span><span class="row-numbers">' . esc_html( $row_numbers ) . '</span></td>';
							$html .= '<td>' . esc_html( $row_title ) . '</td>';
							$html .= '<td class="question-grade-column"></td>';
							$html .= '<td><input type="hidden" name="question_id" class="row_question_id" id="question_' . $question_counter . '_id" value="' . $question_id . '" /></td>';
							$html .= '<td><a title="' . esc_attr( __( 'Edit Question', 'woothemes-sensei' ) ) . '" href="#question_' . $question_counter .'" class="question_table_edit" style="visibility:hidden;">' . esc_html( __( 'Edit', 'woothemes-sensei' ) ) . '</a> <a title="' . esc_attr( __( 'Remove Question(s)', 'woothemes-sensei' ) ) . '" href="#add-question-metadata" class="question_multiple_delete" rel="' . $question_id . '">' . esc_html( __( 'Remove', 'woothemes-sensei' ) ) . '</a></td>';

						}
					$html .= '</tr>';
				}

				if( $question_type != 'category' ) {

					$edit_class = '';
					if( 'quiz' == $context ) {
						$edit_class = 'hidden';
					}

					$question = get_post( $question_id );
					$html .= '<tr class="question-quick-edit ' . esc_attr( $edit_class ) . '">';
						$html .= '<td colspan="5">';
							$html .= '<span class="hidden question_original_counter">' . $question_counter . '</span>';
					    	$html .= '<div class="question_required_fields">';

						    	// Question title
						    	$html .= '<div>';
							    	$html .= '<label for="question_' . $question_counter . '">' . __( 'Question:', 'woothemes-sensei' ) . '</label> ';
							    	$html .= '<input type="text" id="question_' . $question_counter . '" name="question" value="' . esc_attr( htmlspecialchars( $question->post_title ) ) . '" size="25" class="widefat" />';
						    	$html .= '</div>';

						    	// Question description
						    	$html .= '<div>';
							    	$html .= '<label for="question_' . $question_counter . '_desc">' . __( 'Question Description (optional):', 'woothemes-sensei' ) . '</label> ';
						    	$html .= '</div>';
							    	$html .= '<textarea id="question_' . $question_counter . '_desc" name="question_description" class="widefat" rows="4">' . esc_textarea( $question->post_content ) . '</textarea>';

						    	// Question grade
						    	$html .= '<div>';
							    	$html .= '<label for="question_' . $question_counter . '_grade">' . __( 'Question grade:', 'woothemes-sensei' ) . '</label> ';
							    	$html .= '<input type="number" id="question_' . $question_counter . '_grade" class="question_grade small-text" name="question_grade" min="0" value="' . $question_grade . '" />';
						    	$html .= '</div>';

						    	// Random order
						    	if( $question_type == 'multiple-choice' ) {
						    		$html .= '<div>';
						    			$html .= '<label for="' . $question_counter . '_random_order"><input type="checkbox" name="random_order" class="random_order" id="' . $question_counter . '_random_order" value="yes" ' . checked( $random_order, 'yes', false ) . ' /> ' . __( 'Randomise answer order', 'woothemes-sensei' ) . '</label>';

The variable $random_order does not seem to be defined for all execution paths leading up to this point.

						    		$html .= '</div>';
						    	}

						    	// Question media
						    	$html .= '<div>';
							    	$html .= '<label for="question_' . $question_counter . '_media_button">' . __( 'Question media:', 'woothemes-sensei' ) . '</label><br/>';
							    	$html .= '<button id="question_' . $question_counter . '_media_button" class="upload_media_file_button button-secondary" data-uploader_title="' . __( 'Add file to question', 'woothemes-sensei' ) . '" data-uploader_button_text="' . __( 'Add to question', 'woothemes-sensei' ) . '">' . $question_media_add_button . '</button>';

The variable $question_media_add_button does not seem to be defined for all execution paths leading up to this point.

							    	$html .= '<button id="question_' . $question_counter . '_media_button_delete" class="delete_media_file_button button-secondary ' . $question_media_delete_class . '">' . __( 'Delete file', 'woothemes-sensei' ) . '</button><br/>';

The variable $question_media_delete_class does not seem to be defined for all execution paths leading up to this point.

							    	$html .= '<span id="question_' . $question_counter . '_media_link" class="question_media_link ' . $question_media_link_class . '">' . $question_media_link . '</span>';

The variable $question_media_link_class does not seem to be defined for all execution paths leading up to this point.

The variable $question_media_link does not seem to be defined for all execution paths leading up to this point.

							    	$html .= '<br/><img id="question_' . $question_counter . '_media_preview" class="question_media_preview ' . $question_media_thumb_class . '" src="' . $question_media_thumb . '" /><br/>';

The variable $question_media_thumb_class does not seem to be defined for all execution paths leading up to this point.

The variable $question_media_thumb does not seem to be defined for all execution paths leading up to this point.

							    	$html .= '<input type="hidden" id="question_' . $question_counter . '_media" class="question_media" name="question_media" value="' . $question_media . '" />';

The variable $question_media does not seem to be defined for all execution paths leading up to this point.

						    	$html .= '</div>';

						    $html .= '</div>';

						    $html .= $this->quiz_panel_question_field( $question_type, $question_id, $question_counter );

						    $html .= '<input type="hidden" id="question_' . $question_counter . '_question_type" class="question_type" name="question_type" value="' . $question_type . '" />';
							$html .= '<input type="hidden" name="question_id" class="row_question_id" id="question_' . $question_counter . '_id" value="' . $question_id . '" />';

							if( 'quiz' == $context ) {
					    		$html .= '<div class="update-question">';
						    		$html .= '<a href="#question-edit-cancel" class="lesson_question_cancel" title="' . esc_attr( __( 'Cancel', 'woothemes-sensei' ) ) . '">' . __( 'Cancel', 'woothemes-sensei' ) . '</a> ';
						    		$html .= '<a title="' . esc_attr( __( 'Update Question', 'woothemes-sensei' ) ) . '" href="#add-question-metadata" class="question_table_save button button-highlighted">' . esc_html( __( 'Update', 'woothemes-sensei' ) ) . '</a>';
					    		$html .= '</div>';
					    	}

			    		$html .= '</td>';
					$html .= '</tr>';
				}

			$html .= '</tbody>';

		}

		return $html;
	}

	public function quiz_panel_add( $context = 'quiz' ) {


		$html = '<div id="add-new-question">';

			$question_types = Sensei()->question->question_types();

			$question_cats = get_terms( 'question-category', array( 'hide_empty' => false ) );

			if( 'quiz' == $context ) {
	    		$html .= '<h2 class="nav-tab-wrapper add-question-tabs">';
	    			$html .= '<a id="tab-new" class="nav-tab nav-tab-active">' . __( 'New Question'  , 'woothemes-sensei' ) . '</a>';
	    			$html .= '<a id="tab-existing" class="nav-tab">' . __( 'Existing Questions'  , 'woothemes-sensei' ) . '</a>';
                    if ( ! empty( $question_cats ) && ! is_wp_error( $question_cats )  && ! Sensei()->teacher->is_admin_teacher() ) {
	    				$html .= '<a id="tab-multiple" class="nav-tab">' . __( 'Category Questions'  , 'woothemes-sensei' ) . '</a>';
	    			}
	    		$html .= '</h2>';
	    	}

	    	$html .= '<div class="tab-content" id="tab-new-content">';

	    		if( 'quiz' == $context ) {
	    			$html .= '<p><em>' . sprintf( __( 'Add a new question to this quiz - your question will also be added to the %1$squestion bank%2$s.', 'woothemes-sensei' ), '<a href="' . admin_url( 'edit.php?post_type=question' ) . '">', '</a>' ) . '</em></p>';
	    		}

				$html .= '<div class="question">';
					$html .= '<div class="question_required_fields">';

						// Question title
						$html .= '<p><label>' . __( 'Question:'  , 'woothemes-sensei' ) . '</label> ';
	  					$html .= '<input type="text" id="add_question" name="question" value="" size="25" class="widefat" /></p>';

						// Question description
						$html .= '<p>';
							$html .= '<label for="question_desc">' . __( 'Question Description (optional):', 'woothemes-sensei' ) . '</label> ';
						$html .= '</p>';
						$html .= '<textarea id="question_desc" name="question_description" class="widefat" rows="4"></textarea>';

	  					// Question type
						$html .= '<p><label>' . __( 'Question Type:' , 'woothemes-sensei' ) . '</label> ';
						$html .= '<select id="add-question-type-options" name="question_type" class="chosen_select widefat question-type-select">' . "\n";
							foreach ( $question_types as $type => $label ) {

This code seems to be duplicated across your project.

								$html .= '<option value="' . esc_attr( $type ) . '">' . esc_html( $label ) . '</option>' . "\n";
							} // End For Loop
						$html .= '</select></p>' . "\n";

						// Question category
						if( 'quiz' == $context ) {
							if ( ! empty( $question_cats ) && ! is_wp_error( $question_cats ) ) {
								$html .= '<p><label>' . __( 'Question Category:' , 'woothemes-sensei' ) . '</label> ';
								$html .= '<select id="add-question-category-options" name="question_category" class="chosen_select widefat question-category-select">' . "\n";
								$html .= '<option value="">' . __( 'None', 'woothemes-sensei' ) . '</option>' . "\n";
								foreach( $question_cats as $cat ) {

This code seems to be duplicated across your project.

									$html .= '<option value="' . esc_attr( $cat->term_id ) . '">' . esc_html( $cat->name ) . '</option>';
								} // End For Loop
								$html .= '</select></p>' . "\n";
							}
						}

	  					// Question grade
						$html .= '<p><label>' . __( 'Question Grade:'  , 'woothemes-sensei' ) . '</label> ';
						$html .= '<input type="number" id="add-question-grade" name="question_grade" class="small-text" min="0" value="1" /></p>' . "\n";

						// Random order
						$html .= '<p class="add_question_random_order">';
			    			$html .= '<label for="add_random_order"><input type="checkbox" name="random_order" class="random_order" id="add_random_order" value="yes" checked="checked" /> ' . __( 'Randomise answer order', 'woothemes-sensei' ) . '</label>';
			    		$html .= '</p>';

			    		// Question media
						$html .= '<p>';
					    	$html .= '<label for="question_add_new_media_button">' . __( 'Question media:', 'woothemes-sensei' ) . '</label><br/>';
					    	$html .= '<button id="question_add_new_media_button" class="upload_media_file_button button-secondary" data-uploader_title="' . __( 'Add file to question', 'woothemes-sensei' ) . '" data-uploader_button_text="' . __( 'Add to question', 'woothemes-sensei' ) . '">' . __( 'Add file', 'woothemes-sensei' ) . '</button>';
					    	$html .= '<button id="question_add_new_media_button_delete" class="delete_media_file_button button-secondary hidden">' . __( 'Delete file', 'woothemes-sensei' ) . '</button><br/>';
					    	$html .= '<span id="question_add_new_media_link" class="question_media_link hidden"></span>';
					    	$html .= '<br/><img id="question_add_new_media_preview" class="question_media_preview hidden" src="" /><br/>';
					    	$html .= '<input type="hidden" id="question_add_new_media" class="question_media" name="question_media" value="" />';
				    	$html .= '</p>';

					$html .= '</div>';
				$html .= '</div>';

				foreach ( $question_types as $type => $label ) {
					$html .= $this->quiz_panel_question_field( $type );
				}

				if( 'quiz' == $context ) {
					$html .= '<div class="add-question">';
			    		$html .= '<a title="' . esc_attr( __( 'Add Question', 'woothemes-sensei' ) ) . '" href="#add-question-metadata" class="add_question_save button button-primary button-highlighted">' . esc_html( __( 'Add Question', 'woothemes-sensei' ) ) . '</a>';
		    		$html .= '</div>';
		    	}

		    $html .= '</div>';

		    if( 'quiz' == $context ) {

			    $html .= '<div class="tab-content hidden" id="tab-existing-content">';

			    	$html .= '<p><em>' . sprintf( __( 'Add an existing question to this quiz from the %1$squestion bank%2$s.', 'woothemes-sensei' ), '<a href="' . admin_url( 'edit.php?post_type=question' ) . '">', '</a>' ) . '</em></p>';

			    	$html .= '<div id="existing-filters" class="alignleft actions">
			    				<select id="existing-status">
			    					<option value="all">' . __( 'All', 'woothemes-sensei' ) . '</option>
			    					<option value="unused">' . __( 'Unused', 'woothemes-sensei' ) . '</option>
			    					<option value="used">' . __( 'Used', 'woothemes-sensei' ) . '</option>
			    				</select>
			    				<select id="existing-type">
			    					<option value="">' . __( 'All Types', 'woothemes-sensei' ) . '</option>';
							    	foreach ( $question_types as $type => $label ) {

This code seems to be duplicated across your project.

										$html .= '<option value="' . esc_attr( $type ) . '">' . esc_html( $label ) . '</option>';
									}
    				$html .= '</select>
    							<select id="existing-category">
			    					<option value="">' . __( 'All Categories', 'woothemes-sensei' ) . '</option>';
				    				foreach( $question_cats as $cat ) {

This code seems to be duplicated across your project.

										$html .= '<option value="' . esc_attr( $cat->slug ) . '">' . esc_html( $cat->name ) . '</option>';
									}
    				$html .= '</select>
    							<input type="text" id="existing-search" placeholder="' . __( 'Search', 'woothemes-sensei' ) . '" />
    							<a class="button" id="existing-filter-button">' . __( 'Filter', 'woothemes-sensei' ) . '</a>
			    			</div>';

			    	$html .= '<table id="existing-table" class="widefat">';

			    		$html .= '<thead>
									    <tr>
									        <th scope="col" class="column-cb check-column"><input type="checkbox" /></th>
									        <th scope="col">' . __( 'Question', 'woothemes-sensei' ) . '</th>
									        <th scope="col">' . __( 'Type', 'woothemes-sensei' ) . '</th>
									        <th scope="col">' . __( 'Category', 'woothemes-sensei' ) . '</th>
									    </tr>
									</thead>
									<tfoot>
									    <tr>
										    <th scope="col" class="check-column"><input type="checkbox" /></th>
									        <th scope="col">' . __( 'Question', 'woothemes-sensei' ) . '</th>
									        <th scope="col">' . __( 'Type', 'woothemes-sensei' ) . '</th>
									        <th scope="col">' . __( 'Category', 'woothemes-sensei' ) . '</th>
									    </tr>
									</tfoot>';
						$html .= '<tbody id="existing-questions">';

						$questions = $this->quiz_panel_get_existing_questions();

						$row = 1;
						foreach( $questions['questions'] as $question ) {
							$html .= $this->quiz_panel_add_existing_question( $question->ID, $row );
							++$row;
						}

						$html .= '</tbody>';

			    	$html .= '</table>';

			    	$next_class = '';
			    	if( $questions['count'] <= 10 ) {
			    		$next_class = 'hidden';
			    	}

			    	$html .= '<div id="existing-pagination">';
			    		$html .= '<input type="hidden" id="existing-page" value="1" />';
			    		$html .= '<a class="prev no-paging">&larr; ' . __( 'Previous', 'woothemes-sensei') . '</a> <a class="next ' . esc_attr( $next_class ) . '">' . __( 'Next', 'woothemes-sensei') . ' &rarr;</a>';
			    	$html .= '</div>';

			    	$html .= '<div class="existing-actions">';
			    		$html .= '<a title="' . esc_attr( __( 'Add Selected Question(s)', 'woothemes-sensei' ) ) . '" class="add_existing_save button button-primary button-highlighted">' . esc_html( __( 'Add Selected Question(s)', 'woothemes-sensei' ) ) . '</a></p>';
			    	$html .= '</div>';

			    $html .= '</div>';

			    if ( ! empty( $question_cats ) && ! is_wp_error( $question_cats ) ) {
				    $html .= '<div class="tab-content hidden" id="tab-multiple-content">';

				    	$html .= '<p><em>' . sprintf( __( 'Add any number of questions from a specified category. Edit your question categories %1$shere%2$s.', 'woothemes-sensei' ), '<a href="' . admin_url( 'edit-tags.php?taxonomy=question-category&post_type=question' ) . '">', '</a>' ) . '</em></p>';

						$html .= '<p><select id="add-multiple-question-category-options" name="multiple_category" class="chosen_select widefat question-category-select">' . "\n";
						$html .= '<option value="">' . __( 'Select a Question Category', 'woothemes-sensei' ) . '</option>' . "\n";
						foreach( $question_cats as $cat ) {

This code seems to be duplicated across your project.

							$html .= '<option value="' . esc_attr( $cat->term_id ) . '">' . esc_html( $cat->name ) . '</option>';
						} // End For Loop
						$html .= '</select></p>' . "\n";

						$html .= '<p>' . __( 'Number of questions:', 'woothemes-sensei' ) . ' <input type="number" min="1" value="1" max="1" id="add-multiple-question-count" class="small-text"/>';

						$html .= '<a title="' . esc_attr( __( 'Add Question(s)', 'woothemes-sensei' ) ) . '" class="add_multiple_save button button-primary button-highlighted">' . esc_html( __( 'Add Question(s)', 'woothemes-sensei' ) ) . '</a></p>';

				    $html .= '</div>';
				}
			}

		$html .= '</div>';

		return $html;
	}

	public function quiz_panel_get_existing_questions( $question_status = 'all', $question_type = '', $question_category = '', $question_search = '', $page = 1 ) {

		$args = array(
			'post_type' => 'question',
			'posts_per_page' => 10,
			'post_status' => 'publish',
			'suppress_filters' => 0,
		);

		switch( $question_status ) {
			case 'unused': $quiz_status = 'NOT EXISTS'; break;
			case 'used': $quiz_status = 'EXISTS'; break;
			default: $quiz_status = ''; break;
		}

		if( $quiz_status ) {
			switch( $quiz_status ) {
				case 'EXISTS':
					$args['meta_query'][] = array(
						'key' => '_quiz_id',
						'compare' => $quiz_status,
					);
				break;

				case 'NOT EXISTS':
					$args['meta_query'][] = array(
						'key' => '_quiz_id',
						'value' => 'bug #23268',
						'compare' => $quiz_status,
					);
				break;
			}
		}

		if( $question_type ) {

This code seems to be duplicated across your project.

			$args['tax_query'][] = array(
				'taxonomy' => 'question-type',
				'field' => 'slug',
				'terms' => $question_type,
			);
		}

		if( $question_category ) {

This code seems to be duplicated across your project.

			$args['tax_query'][] = array(
				'taxonomy' => 'question-category',
				'field' => 'slug',
				'terms' => $question_category,
			);
		}

		if( $question_type && $question_category ) {
			$args['tax_query']['relation'] = 'AND';
		}

		if( $question_search ) {
			$args['s'] = $question_search;
		}

		if( $page ) {
			$args['paged'] = $page;
		}

		$qry = new WP_Query( $args );

        /**
         * Filter existing questions query
         *
         * @since 1.8.0
         *
         * @param WP_Query $wp_query
         */
        $qry = apply_filters( 'sensei_existing_questions_query_results', $qry );

		$questions['questions'] = $qry->posts;

$questions was never initialized. Although not strictly required by PHP, it is generally a good practice to add $questions = array(); before regardless.

		$questions['count'] = intval( $qry->found_posts );
		$questions['page'] = $page;

		return $questions;
	}

	public function quiz_panel_add_existing_question( $question_id = 0, $row = 1 ) {

		$html = '';

		if( ! $question_id ) {

            return;

        }

		$existing_class = '';
		if( $row % 2 ) {
            $existing_class = 'alternate';
        }

		$question_type = Sensei()->question->get_question_type( $question_id );

		$question_cat_list = strip_tags( get_the_term_list( $question_id, 'question-category', '', ', ', '' ) );

		$html .= '<tr class="' . esc_attr( $existing_class ) . '">
					<td class="cb"><input type="checkbox" value="' . $question_id . '" class="existing-item" /></td>
					<td>' . get_the_title( $question_id ) . '</td>
					<td>' . esc_html( $question_type ) . '</td>
					<td>' . esc_html( $question_cat_list ) . '</td>
				  </tr>';

		return $html;

	}

	public function quiz_panel_filter_existing_questions() {

		$return = '';

		//Add nonce security to the request
		$nonce = '';
		if( isset( $_POST['filter_existing_questions_nonce'] ) ) {
			$nonce = esc_html( $_POST['filter_existing_questions_nonce'] );
		} // End If Statement

		if( ! wp_verify_nonce( $nonce, 'filter_existing_questions_nonce' ) ) {
			die( $return );
		} // End If Statement

		// Parse POST data
		$data = $_POST['data'];
		$question_data = array();
		parse_str( $data, $question_data );

		if( 0 < count( $question_data ) ) {

			$question_status = '';
			if( isset( $question_data['question_status'] ) ) {
				$question_status = $question_data['question_status'];
			}

			$question_type = '';
			if( isset( $question_data['question_type'] ) ) {
				$question_type = $question_data['question_type'];
			}

			$question_category = '';
			if( isset( $question_data['question_category'] ) ) {
				$question_category = $question_data['question_category'];
			}

			$question_search = '';
			if( isset( $question_data['question_search'] ) ) {
				$question_search = $question_data['question_search'];
			}

			$question_page = 1;
			if( isset( $question_data['question_page'] ) ) {
				$question_page = intval( $question_data['question_page'] );
			}

			$questions = $this->quiz_panel_get_existing_questions( $question_status, $question_type, $question_category, $question_search, $question_page );

			$row = 1;
			$html = '';
			foreach( $questions['questions'] as $question ) {
				$html .= $this->quiz_panel_add_existing_question( $question->ID, $row );
				++$row;
			}

			if( ! $html ) {
				$html = '<tr class="alternate">
								<td class="no-results" colspan="4"><em>' . __( 'There are no questions matching your search.', 'woothemes-sensei' ) . '</em></td>
							  </tr>';
			}

			$return['html'] = $html;
			$return['count'] = $questions['count'];
			$return['page'] = $questions['page'];

			wp_send_json( $return );
		}

		die( $return );
	}

	public function quiz_panel_question_field( $question_type = '', $question_id = 0, $question_counter = 0 ) {

		$html = '';

		if( $question_type ) {

			$right_answer = '';
			$wrong_answers = array();
			$answer_order_string = '';
			$answer_order = array();
			if( $question_id ) {
				$right_answer = get_post_meta( $question_id, '_question_right_answer', true);
				$wrong_answers = get_post_meta( $question_id, '_question_wrong_answers', true);
				$answer_order_string = get_post_meta( $question_id, '_answer_order', true );
				$answer_order = array_filter( explode( ',', $answer_order_string ) );
				$question_class = '';
			} else {
				$question_id = '';
				$question_class = 'answer-fields question_required_fields hidden';
			}

			switch ( $question_type ) {
				case 'multiple-choice':
					$html .= '<div class="question_default_fields multiple-choice-answers ' . str_replace( ' hidden', '', $question_class ) . '">';

						$right_answers = (array) $right_answer;
						// Calculate total right answers available (defaults to 1)
						$total_right = 0;
						if( $question_id ) {
							$total_right = get_post_meta( $question_id, '_right_answer_count', true );
						}
						if( 0 == intval( $total_right ) ) {
							$total_right = 1;
						}
						for ( $i = 0; $i < $total_right; $i++ ) {
							if ( !isset( $right_answers[ $i ] ) ) { $right_answers[ $i ] = ''; }
							$right_answer_id = $this->get_answer_id( $right_answers[ $i ] );
							// Right Answer
							$right_answer = '<label class="answer" for="question_' . $question_counter . '_right_answer_' . $i . '"><span>' . __( 'Right:' , 'woothemes-sensei' ) . '</span> <input rel="' . esc_attr( $right_answer_id ) . '" type="text" id="question_' . $question_counter . '_right_answer_' . $i . '" name="question_right_answers[]" value="' . esc_attr( $right_answers[ $i ] ) . '" size="25" class="question_answer widefat" /> <a class="remove_answer_option"></a></label>';
							if( $question_id ) {
								$answers[ $right_answer_id ] = $right_answer;

$answers was never initialized. Although not strictly required by PHP, it is generally a good practice to add $answers = array(); before regardless.

							} else {
								$answers[] = $right_answer;

The variable $answers does not seem to be defined for all execution paths leading up to this point.

							}
						}

				    	// Calculate total wrong answers available (defaults to 4)
				    	$total_wrong = 0;
				    	if( $question_id ) {
				    		$total_wrong = get_post_meta( $question_id, '_wrong_answer_count', true );
				    	}
				    	if( 0 == intval( $total_wrong ) ) {
				    		$total_wrong = 1;
				    	}

                        // Setup Wrong Answer HTML
                        foreach ( $wrong_answers as $i => $answer ){

                            $answer_id = $this->get_answer_id( $answer );
                            $wrong_answer = '<label class="answer" for="question_' . $question_counter . '_wrong_answer_' . $i . '"><span>' . __( 'Wrong:' , 'woothemes-sensei' ) ;
                            $wrong_answer .= '</span> <input rel="' . esc_attr( $answer_id ) . '" type="text" id="question_' . $question_counter . '_wrong_answer_' . $i ;
                            $wrong_answer .= '" name="question_wrong_answers[]" value="' . esc_attr( $answer ) . '" size="25" class="question_answer widefat" /> <a class="remove_answer_option"></a></label>';
                            if( $question_id ) {

                                $answers[ $answer_id ] = $wrong_answer;

                            } else {

                                $answers[] = $wrong_answer;

                            }

                        } // end for each

				    	$answers_sorted = $answers;
				    	if( $question_id && count( $answer_order ) > 0 ) {

This code seems to be duplicated across your project.

				    		$answers_sorted = array();
				    		foreach( $answer_order as $answer_id ) {
				    			if( isset( $answers[ $answer_id ] ) ) {
				    				$answers_sorted[ $answer_id ] = $answers[ $answer_id ];
				    				unset( $answers[ $answer_id ] );
				    			}
				    		}

				    		if( count( $answers ) > 0 ) {
						    	foreach( $answers as $id => $answer ) {
						    		$answers_sorted[ $id ] = $answer;
						    	}
						    }
				    	}

						foreach( $answers_sorted as $id => $answer ) {
				    		$html .= $answer;
				    	}

				    	$html .= '<input type="hidden" class="answer_order" name="answer_order" value="' . $answer_order_string . '" />';
				    	$html .= '<span class="hidden right_answer_count">' . $total_right . '</span>';
				    	$html .= '<span class="hidden wrong_answer_count">' . $total_wrong . '</span>';

				    	$html .= '<div class="add_answer_options">';
					    	$html .= '<a class="add_right_answer_option add_answer_option button" rel="' . $question_counter . '">' . __( 'Add right answer', 'woothemes-sensei' ) . '</a>';
					    	$html .= '<a class="add_wrong_answer_option add_answer_option button" rel="' . $question_counter . '">' . __( 'Add wrong answer', 'woothemes-sensei' ) . '</a>';
				    	$html .= '</div>';

                        $html .= $this->quiz_panel_question_feedback( $question_counter, $question_id , 'multiple-choice' );

			    	$html .= '</div>';
				break;
				case 'boolean':
					$html .= '<div class="question_boolean_fields ' . $question_class . '">';
						if( $question_id ) {
							$field_name = 'question_' . $question_id . '_right_answer_boolean';
						} else {
							$field_name = 'question_right_answer_boolean';
							$right_answer = 'true';
						}
						$html .= '<label for="question_' . $question_id . '_boolean_true"><input id="question_' . $question_id . '_boolean_true" type="radio" name="' . $field_name . '" value="true" '. checked( $right_answer, 'true', false ) . ' /> ' . __( 'True', 'woothemes-sensei' ) . '</label>';
						$html .= '<label for="question_' . $question_id . '_boolean_false"><input id="question_' . $question_id . '_boolean_false" type="radio" name="' . $field_name . '" value="false" '. checked( $right_answer, 'false', false ) . ' /> ' . __( 'False', 'woothemes-sensei' ) . '</label>';

                    $html .= $this->quiz_panel_question_feedback( $question_counter, $question_id, 'boolean' );

					$html .= '</div>';
				break;
				case 'gap-fill':
					$gapfill_array = explode( '||', $right_answer );
					if ( isset( $gapfill_array[0] ) ) { $gapfill_pre = $gapfill_array[0]; } else { $gapfill_pre = ''; }
					if ( isset( $gapfill_array[1] ) ) { $gapfill_gap = $gapfill_array[1]; } else { $gapfill_gap = ''; }
					if ( isset( $gapfill_array[2] ) ) { $gapfill_post = $gapfill_array[2]; } else { $gapfill_post = ''; }
					$html .= '<div class="question_gapfill_fields ' . $question_class . '">';
						// Fill in the Gaps
						$html .= '<label>' . __( 'Text before the Gap:' , 'woothemes-sensei' ) . '</label> ';
						$html .= '<input type="text" id="question_' . $question_counter . '_add_question_right_answer_gapfill_pre" name="add_question_right_answer_gapfill_pre" value="' . $gapfill_pre . '" size="25" class="widefat gapfill-field" />';
	  					$html .= '<label>' . __( 'The Gap:' , 'woothemes-sensei' ) . '</label> ';
	  					$html .= '<input type="text" id="question_' . $question_counter . '_add_question_right_answer_gapfill_gap" name="add_question_right_answer_gapfill_gap" value="' . $gapfill_gap . '" size="25" class="widefat gapfill-field" />';
	  					$html .= '<label>' . __( 'Text after the Gap:' , 'woothemes-sensei' ) . '</label> ';
	  					$html .= '<input type="text" id="question_' . $question_counter . '_add_question_right_answer_gapfill_post" name="add_question_right_answer_gapfill_post" value="' . $gapfill_post . '" size="25" class="widefat gapfill-field" />';
	  					$html .= '<label>' . __( 'Preview:' , 'woothemes-sensei' ) . '</label> ';
	  					$html .= '<p class="gapfill-preview">' . $gapfill_pre . '&nbsp;<u>' . $gapfill_gap . '</u>&nbsp;' . $gapfill_post . '</p>';
	  				$html .= '</div>';
				break;
				case 'multi-line':

This code seems to be duplicated across your project.

					$html .= '<div class="question_multiline_fields ' . $question_class . '">';
						// Guides for grading
						if( $question_counter ) {
							$field_id = 'question_' . $question_counter . '_add_question_right_answer_multiline';
						} else {
							$field_id = 'add_question_right_answer_multiline';
						}
						$html .= '<label>' . __( 'Guide/Teacher Notes for grading the answer' , 'woothemes-sensei' ) . '</label> ';
						$html .= '<textarea id="' . $field_id . '" name="add_question_right_answer_multiline" rows="4" cols="40" class="widefat">' . $right_answer . '</textarea>';
					$html .= '</div>';
				break;
				case 'single-line':

This code seems to be duplicated across your project.

					$html .= '<div class="question_singleline_fields ' . $question_class . '">';
						// Recommended Answer
						if( $question_counter ) {
							$field_id = 'question_' . $question_counter . '_add_question_right_answer_singleline';
						} else {
							$field_id = 'add_question_right_answer_singleline';
						}
						$html .= '<label>' . __( 'Recommended Answer' , 'woothemes-sensei' ) . '</label> ';
						$html .= '<input type="text" id="' . $field_id . '" name="add_question_right_answer_singleline" value="' . $right_answer . '" size="25" class="widefat" />';
					$html .= '</div>';
				break;
				case 'file-upload':
					$html .= '<div class="question_fileupload_fields ' . $question_class . '">';
						if( $question_counter ) {
							$right_field_id = 'question_' . $question_counter . '_add_question_right_answer_fileupload';
							$wrong_field_id = 'question_' . $question_counter . '_add_question_wrong_answer_fileupload';
						} else {
							$right_field_id = 'add_question_right_answer_fileupload';
							$wrong_field_id = 'add_question_wrong_answer_fileupload';
						}

						$wrong_answer = '';
						if( isset( $wrong_answers[0] ) ) {
							$wrong_answer = $wrong_answers[0];
						}
						$html .= '<label>' . __( 'Description for student explaining what needs to be uploaded' , 'woothemes-sensei' ) . '</label> ';
						$html .= '<textarea id="' . $wrong_field_id . '" name="add_question_wrong_answer_fileupload" rows="4" cols="40" class="widefat">' . $wrong_answer . '</textarea>';

						// Guides for grading
						$html .= '<label>' . __( 'Guide/Teacher Notes for grading the upload' , 'woothemes-sensei' ) . '</label> ';
						$html .= '<textarea id="' . $right_field_id . '" name="add_question_right_answer_fileupload" rows="4" cols="40" class="widefat">' . $right_answer . '</textarea>';
					$html .= '</div>';
				break;
			}
		}

		return $html;
	}

	public function quiz_panel_question_feedback( $question_counter = 0, $question_id = 0, $question_type = '' ) {

        // default field name
        $field_name = 'answer_feedback';
        if( 'boolean' == $question_type ){

            $field_name = 'answer_feedback_boolean';

        }elseif( 'multiple-choice' == $question_type ){

            $field_name = 'answer_feedback_multiple_choice';

        }// end if

		if( $question_counter ) {
			$field_name = 'answer_' . $question_counter . '_feedback';
		}

		$feedback = '';
		if( $question_id ) {
			$feedback = get_post_meta( $question_id, '_answer_feedback', true );
		}

		$html = '<p title="' . __( 'This feedback will be automatically displayed to the student once they have completed the quiz.', 'woothemes-sensei' ) . '">';
		$html .= '<label for="' . $field_name . '">' . __( 'Answer Feedback' , 'woothemes-sensei' ) . ':</label>';
		$html .= '<textarea id="' . $field_name . '" name="' . $field_name . '" rows="4" cols="40" class="answer_feedback widefat">' . $feedback . '</textarea>';
		$html .= '</p>';

		return $html;
	}

	public function question_get_answer_id() {
		$data = $_POST['data'];
		$answer_data = array();
		parse_str( $data, $answer_data );
		$answer = $answer_data['answer_value'];
		$answer_id = $this->get_answer_id( $answer );
		echo $answer_id;
		die();
	}

	public function get_answer_id( $answer = '' ) {

		$answer_id = '';

		if( $answer ) {
			$answer_id = md5( $answer );
		}

		return $answer_id;

	}

	/**
	 * lesson_quiz_meta_box_content function.
	 *
	 * @access public
	 * @return void
	 */
	public function lesson_quiz_meta_box_content () {
		global $post;

		// Get quiz panel
		$quiz_id = 0;
		$quizzes = array();

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

		if ( 0 < $post->ID ) {
			$quiz_id = $this->lesson_quizzes( $post->ID, 'any' );
		}

		echo $this->quiz_panel( $quiz_id );

	} // End lesson_quiz_meta_box_content()

	/**
	 * Quiz settings metabox
	 * @return void
	 */
	public function lesson_quiz_settings_meta_box_content() {
		global $post;

		$html = '';

		// Get quiz panel
		$quiz_id = 0;
		$lesson_id = $post->ID;
		$quizzes = array();

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

		if ( 0 < $lesson_id ) {
			$quiz_id = $this->lesson_quizzes( $lesson_id, 'any' );
		}

		if( $quiz_id ) {
			$html .= $this->quiz_settings_panel( $lesson_id, $quiz_id );
		} else {
			$html .= '<p><em>' . __( 'There is no quiz for this lesson yet - please add one in the \'Quiz Questions\' box.', 'woothemes-sensei' ) . '</em></p>';
		}

		echo $html;
	}

	public function quiz_settings_panel( $lesson_id = 0, $quiz_id = 0 ) {


		$html = '';

		if( ! $lesson_id && ! $quiz_id ) return $html;

		$settings = $this->get_quiz_settings( $quiz_id );

		$html = Sensei()->admin->render_settings( $settings, $quiz_id, 'quiz-settings' );

		return $html;

	}

	public function get_quiz_settings( $quiz_id = 0 ) {

		$disable_passmark = '';
		$pass_required = get_post_meta( $quiz_id, '_pass_required', true );
		if( ! $pass_required ) {
			$disable_passmark = 'hidden';
		}

		// Setup Questions Query
		$questions = array();
		if ( 0 < $quiz_id ) {
			$questions = $this->lesson_quiz_questions( $quiz_id );
		}

		// Count questions
		$question_count = 0;
		foreach( $questions as $question ) {

This code seems to be duplicated across your project.

			if( $question->post_type == 'multiple_question' ) {
				$question_number = get_post_meta( $question->ID, 'number', true );
				$question_count += $question_number;
			} else {
				++$question_count;
			}
		}

		$settings = array(
			array(
				'id' 			=> 'pass_required',
				'label'			=> __( 'Pass required to complete lesson', 'woothemes-sensei' ),
				'description'	=> __( 'The passmark must be achieved before the lesson is complete.', 'woothemes-sensei' ),
				'type'			=> 'checkbox',
				'default'		=> '',
				'checked'		=> 'on',
			),
			array(
				'id' 			=> 'quiz_passmark',
				'label'			=> __( 'Quiz passmark percentage', 'woothemes-sensei' ),
				'description'	=> '',
				'type'			=> 'number',
				'default'		=> 0,
				'placeholder'	=> 0,
				'min'			=> 0,
				'max'			=> 100,
				'class'			=> $disable_passmark,
			),
			array(
				'id' 			=> 'show_questions',
				'label'			=> __( 'Number of questions to show', 'woothemes-sensei' ),
				'description'	=> __( 'Show a random selection of questions from this quiz each time a student views it.', 'woothemes-sensei' ),
				'type'			=> 'number',
				'default'		=> '',
				'placeholder'	=> __( 'All', 'woothemes-sensei' ),
				'min'			=> 1,
				'max'			=> $question_count,
			),
			array(
				'id' 			=> 'random_question_order',
				'label'			=> __( 'Randomise question order', 'woothemes-sensei' ),
				'description'	=> '',
				'type'			=> 'checkbox',
				'default'		=> 'no',
				'checked'		=> 'yes',
			),
			array(
				'id' 			=> 'quiz_grade_type',
				'label'			=> __( 'Grade quiz automatically', 'woothemes-sensei' ),
				'description'	=> __( 'Grades quiz and displays answer explanation immediately after completion. Only applicable if quiz is limited to Multiple Choice, True/False and Gap Fill questions. Questions that have a grade of zero are skipped during autograding.', 'woothemes-sensei' ),
				'type'			=> 'checkbox',
				'default'		=> 'auto',
				'checked'		=> 'auto',
			),
			array(
				'id' 			=> 'enable_quiz_reset',
				'label'			=> __( 'Allow user to retake the quiz', 'woothemes-sensei' ),
				'description'	=> __( 'Enables the quiz reset button.', 'woothemes-sensei' ),
				'type'			=> 'checkbox',
				'default'		=> '',
				'checked'		=> 'on',
			),
		);

		return apply_filters( 'sensei_quiz_settings', $settings );
	}

	/**
	 * enqueue_scripts function.
	 *
	 * @access public
	 * @return void
	 */
	public function enqueue_scripts( $hook ) {
		global  $post_type;

		$allowed_post_types = apply_filters( 'sensei_scripts_allowed_post_types', array( 'lesson', 'course', 'question' ) );
		$allowed_post_type_pages = apply_filters( 'sensei_scripts_allowed_post_type_pages', array( 'edit.php', 'post-new.php', 'post.php', 'edit-tags.php' ) );
		$allowed_pages = apply_filters( 'sensei_scripts_allowed_pages', array( 'sensei_grading', 'sensei_analysis', 'sensei_learners', 'sensei_updates', 'woothemes-sensei-settings', 'lesson-order' ) );

		// Test for Write Panel Pages
		if ( ( ( isset( $post_type ) && in_array( $post_type, $allowed_post_types ) ) && ( isset( $hook ) && in_array( $hook, $allowed_post_type_pages ) ) ) || ( isset( $_GET['page'] ) && in_array( $_GET['page'], $allowed_pages ) ) ) {

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

			// Load the lessons script
            wp_enqueue_media();
			wp_enqueue_script( 'sensei-lesson-metadata', Sensei()->plugin_url . 'assets/js/lesson-metadata' . $suffix . '.js', array( 'jquery', 'select2' ,'jquery-ui-sortable' ), Sensei()->version, true );
			wp_enqueue_script( 'sensei-lesson-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-lesson-chosen' ), Sensei()->version, true );

            // Load the bulk edit screen script
            if( 'edit.php' == $hook && 'lesson'==$_GET['post_type'] ) {
                wp_enqueue_script( 'sensei-lessons-bulk-edit', Sensei()->plugin_url . 'assets/js/admin/lesson-bulk-edit' . $suffix . '.js', array( 'jquery' ), Sensei()->version , true);
            }

			// Localise script
			$translation_strings = array( 'right_colon' => __( 'Right:', 'woothemes-sensei' ), 'wrong_colon' => __( 'Wrong:', 'woothemes-sensei' ), 'add_file' => __( 'Add file', 'woothemes-sensei' ), 'change_file' => __( 'Change file', 'woothemes-sensei' ), 'confirm_remove' => __( 'Are you sure you want to remove this question?', 'woothemes-sensei' ), 'confirm_remove_multiple' => __( 'Are you sure you want to remove these questions?', 'woothemes-sensei' ), 'too_many_for_cat' => __( 'You have selected more questions than this category contains - please reduce the number of questions that you are adding.', 'woothemes-sensei' ) );
			$ajax_vars = array( 'lesson_update_question_nonce' => wp_create_nonce( 'lesson_update_question_nonce' ), 'lesson_add_course_nonce' => wp_create_nonce( 'lesson_add_course_nonce' ), 'lesson_update_grade_type_nonce' => wp_create_nonce( 'lesson_update_grade_type_nonce' ), 'lesson_update_question_order_nonce' => wp_create_nonce( 'lesson_update_question_order_nonce' ), 'lesson_update_question_order_random_nonce' => wp_create_nonce( 'lesson_update_question_order_random_nonce' ), 'lesson_add_multiple_questions_nonce' => wp_create_nonce( 'lesson_add_multiple_questions_nonce' ), 'lesson_remove_multiple_questions_nonce' => wp_create_nonce( 'lesson_remove_multiple_questions_nonce' ), 'lesson_add_existing_questions_nonce' => wp_create_nonce( 'lesson_add_existing_questions_nonce' ), 'filter_existing_questions_nonce' => wp_create_nonce( 'filter_existing_questions_nonce' ) );
			$data = array_merge( $translation_strings, $ajax_vars );
			wp_localize_script( 'sensei-lesson-metadata', 'woo_localized_data', $data );

			// Chosen RTL
			if ( is_rtl() ) {
				wp_enqueue_script( 'sensei-chosen-rtl', Sensei()->plugin_url . 'assets/chosen/chosen-rtl' . $suffix . '.js', array( 'jquery' ), Sensei()->version, true );
			}

		}

	} // End enqueue_scripts()

	/**
	 * Load in CSS styles where necessary.
	 *
	 * @access public
	 * @since  1.4.0
	 * @return void
	 */
	public function enqueue_styles ( $hook ) {
		global  $post_type;

		$allowed_post_types = apply_filters( 'sensei_scripts_allowed_post_types', array( 'lesson', 'course', 'question', 'sensei_message' ) );
		$allowed_post_type_pages = apply_filters( 'sensei_scripts_allowed_post_type_pages', array( 'edit.php', 'post-new.php', 'post.php', 'edit-tags.php' ) );
		$allowed_pages = apply_filters( 'sensei_scripts_allowed_pages', array( 'sensei_grading', 'sensei_analysis', 'sensei_learners', 'sensei_updates', 'woothemes-sensei-settings' ) );

		// Test for Write Panel Pages
		if ( ( ( isset( $post_type ) && in_array( $post_type, $allowed_post_types ) ) && ( isset( $hook ) && in_array( $hook, $allowed_post_type_pages ) ) ) || ( isset( $_GET['page'] ) && in_array( $_GET['page'], $allowed_pages ) ) ) {

This code seems to be duplicated across your project.

			wp_enqueue_style( 'woothemes-sensei-settings-api', esc_url( Sensei()->plugin_url . 'assets/css/settings.css' ), '', Sensei()->version );
		}

	} // End enqueue_styles()

	/**
	 * Add column headings to the "lesson" post list screen.
	 * @access public
	 * @since  1.0.0
	 * @param  array $defaults
	 * @return array $new_columns
	 */
	public function add_column_headings ( $defaults ) {

This method seems to be duplicated in your project.

		$new_columns['cb'] = '<input type="checkbox" />';

$new_columns was never initialized. Although not strictly required by PHP, it is generally a good practice to add $new_columns = array(); before regardless.

		$new_columns['title'] = _x( 'Lesson Title', 'column name', 'woothemes-sensei' );
		$new_columns['lesson-course'] = _x( 'Course', 'column name', 'woothemes-sensei' );
		$new_columns['lesson-prerequisite'] = _x( 'Pre-requisite Lesson', 'column name', 'woothemes-sensei' );
		if ( isset( $defaults['date'] ) ) {
			$new_columns['date'] = $defaults['date'];
		}
		return $new_columns;
	} // End add_column_headings()

	/**
	 * Add data for our newly-added custom columns.
	 * @access public
	 * @since  1.0.0
	 * @param  string $column_name
	 * @param  int $id
	 * @return void
	 */
	public function add_column_data ( $column_name, $id ) {
		global $wpdb, $post;

		switch ( $column_name ) {
			case 'id':
				echo $id;
			break;
			case 'lesson-course':

This code seems to be duplicated across your project.

				$lesson_course_id = get_post_meta( $id, '_lesson_course', true);
				if ( 0 < absint( $lesson_course_id ) ) {
					echo '<a href="' . esc_url( get_edit_post_link( absint( $lesson_course_id ) ) ) . '" title="' . esc_attr( sprintf( __( 'Edit %s', 'woothemes-sensei' ), get_the_title( absint( $lesson_course_id ) ) ) ) . '">' . get_the_title( absint( $lesson_course_id ) ) . '</a>';
				} // End If Statement
			break;
			case 'lesson-prerequisite':

This code seems to be duplicated across your project.

				$lesson_prerequisite_id = get_post_meta( $id, '_lesson_prerequisite', true);
				if ( 0 < absint( $lesson_prerequisite_id ) ) {
					echo '<a href="' . esc_url( get_edit_post_link( absint( $lesson_prerequisite_id ) ) ) . '" title="' . esc_attr( sprintf( __( 'Edit %s', 'woothemes-sensei' ), get_the_title( absint( $lesson_prerequisite_id ) ) ) ) . '">' . get_the_title( absint( $lesson_prerequisite_id ) ) . '</a>';
				} // End If Statement
			break;
			default:
			break;
		} // End Switch Statement
	} // End add_column_data()

	/**
	 * lesson_add_course function.
	 *
	 * @access public
	 * @return void
	 */
	public function lesson_add_course () {
		global $current_user;
		//Add nonce security to the request
		if ( isset($_POST['lesson_add_course_nonce']) ) {
			$nonce = esc_html( $_POST['lesson_add_course_nonce'] );
		} // End If Statement
		if ( ! wp_verify_nonce( $nonce, 'lesson_add_course_nonce' ) ) {

The variable $nonce does not seem to be defined for all execution paths leading up to this point.

			die('');
		} // End If Statement
		// Parse POST data
		$data = $_POST['data'];
		$course_data = array();
		parse_str($data, $course_data);
		// Save the Course
		$updated = false;

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

		$current_user = wp_get_current_user();
		$question_data['post_author'] = $current_user->ID;

$question_data was never initialized. Although not strictly required by PHP, it is generally a good practice to add $question_data = array(); before regardless.

		$updated = $this->lesson_save_course($course_data);

It seems like $course_data can also be of type null; however, Sensei_Lesson::lesson_save_course() does only seem to accept array, maybe add an additional type check?

Are you sure the assignment to $updated is correct as $this->lesson_save_course($course_data) (which targets Sensei_Lesson::lesson_save_course()) seems to always return null.

		echo $updated;
		die(); // WordPress may print out a spurious zero without this can be particularly bad if using JSON
	} // End lesson_add_course()

	/**
	 * lesson_update_question function.
	 *
	 * @access public
	 * @return void
	 */
	public function lesson_update_question () {
		global $current_user;
		//Add nonce security to the request
		if ( isset($_POST['lesson_update_question_nonce']) ) {
			$nonce = esc_html( $_POST['lesson_update_question_nonce'] );
		} // End If Statement
		if ( ! wp_verify_nonce( $nonce, 'lesson_update_question_nonce' ) ) {

The variable $nonce does not seem to be defined for all execution paths leading up to this point.

			die('');
		} // End If Statement
		// Parse POST data
		// WP slashes all incoming data regardless of Magic Quotes setting (see wp_magic_quotes()), which means that
		// even the $_POST['data'] encoded with encodeURIComponent has it's apostrophes slashed.
		// So first restore the original unslashed apostrophes by removing those slashes
		$data = wp_unslash( $_POST['data'] );
		// Then parse the string to an array (note that parse_str automatically urldecodes all the variables)
		$question_data = array();
		parse_str($data, $question_data);
		// Finally re-slash all elements to ensure consistancy for lesson_save_question()
		$question_data = wp_slash( $question_data );
		// Save the question
		$return = false;
		// Question Save and Delete logic
		if ( isset( $question_data['action'] ) && ( $question_data['action'] == 'delete' ) ) {
			// Delete the Question
			$return = $this->lesson_delete_question($question_data);
		} else {
			// Save the Question
			if ( isset( $question_data['quiz_id'] ) && ( 0 < absint( $question_data['quiz_id'] ) ) ) {
				$current_user = wp_get_current_user();
				$question_data['post_author'] = $current_user->ID;
				$question_id = $this->lesson_save_question( $question_data );

Are you sure the assignment to $question_id is correct as $this->lesson_save_question($question_data) (which targets Sensei_Lesson::lesson_save_question()) seems to always return null.

				$question_type = Sensei()->question->get_question_type( $question_id );

				$question_count = intval( $question_data['question_count'] );
				++$question_count;

				$return = $this->quiz_panel_question( $question_type, $question_count, $question_id );
			} // End If Statement
		} // End If Statement

		echo $return;

		die();
	} // End lesson_update_question()

	public function lesson_add_multiple_questions() {

		$return = '';

		//Add nonce security to the request
		$nonce = '';
		if( isset( $_POST['lesson_add_multiple_questions_nonce'] ) ) {
			$nonce = esc_html( $_POST['lesson_add_multiple_questions_nonce'] );
		} // End If Statement

		if( ! wp_verify_nonce( $nonce, 'lesson_add_multiple_questions_nonce' ) ) {
			die( $return );
		} // End If Statement

		// Parse POST data
		$data = $_POST['data'];
		$question_data = array();
		parse_str( $data, $question_data );

		if( is_array( $question_data ) ) {
			if( isset( $question_data['quiz_id'] ) && ( 0 < absint( $question_data['quiz_id'] ) ) ) {

				$quiz_id = intval( $question_data['quiz_id'] );
				$question_number = intval( $question_data['question_number'] );
				$question_category = intval( $question_data['question_category'] );

				$question_counter = intval( $question_data['question_count'] );
				++$question_counter;

				$cat = get_term( $question_category, 'question-category' );

				$post_data = array(
					'post_content' => '',
					'post_status' => 'publish',
					'post_title' => sprintf( __( '%1$s Question(s) from %2$s', 'woothemes-sensei' ), $question_number, $cat->name ),
					'post_type' => 'multiple_question'
				);

				$multiple_id = wp_insert_post( $post_data );

				if( $multiple_id && ! is_wp_error( $multiple_id ) ) {
					add_post_meta( $multiple_id, 'category', $question_category );
					add_post_meta( $multiple_id, 'number', $question_number );
					add_post_meta( $multiple_id, '_quiz_id', $quiz_id, false );
					add_post_meta( $multiple_id, '_quiz_question_order' . $quiz_id, $quiz_id . '000' . $question_counter );
					$lesson_id = get_post_meta( $quiz_id, '_quiz_lesson', true );
					update_post_meta( $lesson_id, '_quiz_has_questions', '1' );
					$return = $this->quiz_panel_question( 'category', $question_counter, $multiple_id, 'quiz', array( $cat->name, $question_number ) );
				}
			}
		}

		echo $return;

		die();
	}

	public function lesson_remove_multiple_questions() {

		//Add nonce security to the request
		$nonce = '';
		if( isset( $_POST['lesson_remove_multiple_questions_nonce'] ) ) {
			$nonce = esc_html( $_POST['lesson_remove_multiple_questions_nonce'] );
		} // End If Statement

		if( ! wp_verify_nonce( $nonce, 'lesson_remove_multiple_questions_nonce' ) ) {
			die('');
		} // End If Statement

		// Parse POST data
		$data = $_POST['data'];
		$question_data = array();
		parse_str( $data, $question_data );

		if( is_array( $question_data ) ) {
			wp_delete_post( $question_data['question_id'], true );
		}

		die( 'Deleted' );
	}

	public function get_question_category_limit() {

		// Set default
		$return = 1;

		// Parse POST data
		$data = $_POST['data'];
		$cat_data = array();
		parse_str( $data, $cat_data );

		if( isset( $cat_data['cat'] ) && '' != $cat_data['cat'] ) {
			$cat = get_term( $cat_data['cat'], 'question-category' );
			if( isset( $cat->count ) ) {
				$return = $cat->count;
			}
		}

		echo $return;

		die('');
	}

	public function lesson_add_existing_questions() {

		//Add nonce security to the request
		$nonce = '';
		if( isset( $_POST['lesson_add_existing_questions_nonce'] ) ) {
			$nonce = esc_html( $_POST['lesson_add_existing_questions_nonce'] );
		} // End If Statement

		if( ! wp_verify_nonce( $nonce, 'lesson_add_existing_questions_nonce' ) ) {
			die('');
		} // End If Statement

		// Parse POST data
		$data = $_POST['data'];
		$question_data = array();
		parse_str( $data, $question_data );

		$return = '';

		if( is_array( $question_data ) ) {

			if( isset( $question_data['questions'] ) && '' != $question_data['questions'] ) {

				$questions = explode( ',', trim( $question_data['questions'], ',' ) );
				$quiz_id = $question_data['quiz_id'];
				$question_count = intval( $question_data['question_count'] );

				foreach( $questions as $question_id ) {

					++$question_count;

					$quizzes = get_post_meta( $question_id, '_quiz_id', false );
					if( ! in_array( $quiz_id, $quizzes ) ) {

This code seems to be duplicated across your project.

			    		add_post_meta( $question_id, '_quiz_id', $quiz_id, false );
						$lesson_id = get_post_meta( $quiz_id, '_quiz_lesson', true );
						update_post_meta( $lesson_id, '_quiz_has_questions', '1' );
			    	}

			    	add_post_meta( $question_id, '_quiz_question_order' . $quiz_id, $quiz_id . '000' . $question_count );
					$question_type = Sensei()->question->get_question_type( $question_id );

					$return .= $this->quiz_panel_question( $question_type, $question_count, $question_id );
				}
			}
		}

		echo $return;

		die('');
	}

	public function lesson_update_grade_type() {

This method seems to be duplicated in your project.

		//Add nonce security to the request
		if ( isset($_POST['lesson_update_grade_type_nonce']) ) {
			$nonce = esc_html( $_POST['lesson_update_grade_type_nonce'] );
		} // End If Statement
		if ( ! wp_verify_nonce( $nonce, 'lesson_update_grade_type_nonce' ) ) {

The variable $nonce does not seem to be defined for all execution paths leading up to this point.

			die('');
		} // End If Statement
		// Parse POST data
		$data = $_POST['data'];
		$quiz_data = array();
		parse_str($data, $quiz_data);
		update_post_meta( $quiz_data['quiz_id'], '_quiz_grade_type', $quiz_data['quiz_grade_type'] );
		die();
	}

	public function lesson_update_question_order() {
		// Add nonce security to the request
		if ( isset($_POST['lesson_update_question_order_nonce']) ) {
			$nonce = esc_html( $_POST['lesson_update_question_order_nonce'] );
		} // End If Statement
		if ( ! wp_verify_nonce( $nonce, 'lesson_update_question_order_nonce' ) ) {

The variable $nonce does not seem to be defined for all execution paths leading up to this point.

			die('');
		} // End If Statement
		// Parse POST data
		$data = $_POST['data'];
		$quiz_data = array();
		parse_str($data, $quiz_data);
		if( strlen( $quiz_data['question_order'] ) > 0 ) {
			$questions = explode( ',', $quiz_data['question_order'] );
			$o = 1;
			foreach( $questions as $question_id ) {
				update_post_meta( $question_id, '_quiz_question_order' . $quiz_data['quiz_id'], $quiz_data['quiz_id'] . '000' . $o );
				++$o;
			}
			update_post_meta( $quiz_data['quiz_id'], '_question_order', $questions );
		}
		die();
	}

	public function lesson_update_question_order_random() {

This method seems to be duplicated in your project.

		//Add nonce security to the request
		if ( isset($_POST['lesson_update_question_order_random_nonce']) ) {
			$nonce = esc_html( $_POST['lesson_update_question_order_random_nonce'] );
		} // End If Statement
		if ( ! wp_verify_nonce( $nonce, 'lesson_update_question_order_random_nonce' ) ) {

The variable $nonce does not seem to be defined for all execution paths leading up to this point.

			die('');
		} // End If Statement
		// Parse POST data
		$data = $_POST['data'];
		$quiz_data = array();
		parse_str($data, $quiz_data);
		update_post_meta( $quiz_data['quiz_id'], '_random_question_order', $quiz_data['random_question_order'] );
		die();
	}

	/**
	 * lesson_save_course function.
	 *
	 * @access private
	 * @param array $data (default: array())
	 * @return void
	 */
	private function lesson_save_course( $data = array() ) {
		global $current_user;
		$return = false;
		// Setup the course data
		$course_id = 0;
		$course_content = '';
		$course_title = '';
		$course_prerequisite = 0;

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

		$course_category = 0;

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

		if ( isset( $data[ 'course_id' ] ) && ( 0 < absint( $data[ 'course_id' ] ) ) ) {

This code seems to be duplicated across your project.

			$course_id = absint( $data[ 'course_id' ] );
		} // End If Statement
		if ( isset( $data[ 'course_title' ] ) && ( '' != $data[ 'course_title' ] ) ) {
			$course_title = $data[ 'course_title' ];
		} // End If Statement
		$post_title = $course_title;
		if ( isset($data[ 'post_author' ]) ) {
			$post_author = $data[ 'post_author' ];

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

		} else {
			$current_user = wp_get_current_user();
			$post_author = $current_user->ID;

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

		} // End If Statement
		$post_status = 'publish';
		$post_type = 'course';
		if ( isset( $data[ 'course_content' ] ) && ( '' != $data[ 'course_content' ] ) ) {
			$course_content = $data[ 'course_content' ];
		} // End If Statement
		$post_content = $course_content;
		// Course Query Arguments
		$post_type_args = array(	'post_content' => $post_content,
  		    						'post_status' => $post_status,
  		    						'post_title' => $post_title,
  		    						'post_type' => $post_type
  		    						);
  		// Only save if there is a valid title
  		if ( $post_title != '' ) {
  		    // Check for prerequisite courses & product id
  		    $course_prerequisite_id = absint( $data[ 'course_prerequisite' ] );
  		    $course_woocommerce_product_id = absint( $data[ 'course_woocommerce_product' ] );
  		    $course_category_id = absint( $data[ 'course_category' ] );
  		    if ( 0 == $course_woocommerce_product_id ) { $course_woocommerce_product_id = '-'; }
  		    // Insert or Update the Lesson Quiz
		    if ( 0 < $course_id ) {
		    	$post_type_args[ 'ID' ] = $course_id;
		    	$course_id = wp_update_post($post_type_args);
		    	update_post_meta( $course_id, '_course_prerequisite', $course_prerequisite_id );
		    	update_post_meta( $course_id, '_course_woocommerce_product', $course_woocommerce_product_id );
		    	if ( 0 < $course_category_id ) {
		    		wp_set_object_terms( $course_id, $course_category_id, 'course-category' );
		    	} // End If Statement
		    } else {
		    	$course_id = wp_insert_post($post_type_args);
		    	add_post_meta( $course_id, '_course_prerequisite', $course_prerequisite_id );
		    	add_post_meta( $course_id, '_course_woocommerce_product', $course_woocommerce_product_id );
		    	if ( 0 < $course_category_id ) {
		    		wp_set_object_terms( $course_id, $course_category_id, 'course-category' );
		    	} // End If Statement
		    } // End If Statement
		} // End If Statement
  		// Check that the insert or update saved by testing the post id
  		if ( 0 < $course_id ) {
  			$return = $course_id;
  		} // End If Statement
  		return $return;
  	} // End lesson_save_course()


	/**
	 * lesson_save_question function.
	 *
	 * @access private
	 * @param array $data (default: array())
	 * @return void
	 */
	public function lesson_save_question( $data = array(), $context = 'quiz' ) {
		$return = false;
		// Save the Questions
		// Setup the Question data
		$question_id = 0;
		$question_text = '';
		$question_right_answer = '';
		$question_wrong_answers = $question_right_answers = array();
		$question_type = 'multiple-choice';
		$question_category = '';

		// Handle Question Type
		if ( isset( $data[ 'question_type' ] ) && ( '' != $data[ 'question_type' ] ) ) {
			$question_type = $data[ 'question_type' ];
		} // End If Statement

		if ( isset( $data[ 'question_category' ] ) && ( '' != $data[ 'question_category' ] ) ) {
			$question_category = $data[ 'question_category' ];
		} // End If Statement

		if ( isset( $data[ 'question_id' ] ) && ( 0 < absint( $data[ 'question_id' ] ) ) ) {

This code seems to be duplicated across your project.

			$question_id = absint( $data[ 'question_id' ] );
		} // End If Statement
		if ( isset( $data[ 'question' ] ) && ( '' != $data[ 'question' ] ) ) {
			$question_text = $data[ 'question' ];
		} // End If Statement
		$post_title = $question_text;

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

		// Handle Default Fields (multiple choice)
		if ( 'multiple-choice' == $question_type && isset( $data[ 'question_right_answers' ] ) && ( '' != $data[ 'question_right_answers' ] ) ) {
			$question_right_answers = $data[ 'question_right_answers' ];
		} // End If Statement
		elseif ( 'multiple-choice' == $question_type && isset( $data[ 'question_right_answer' ] ) && ( '' != $data[ 'question_right_answer' ] ) ) {
			$question_right_answer = $data[ 'question_right_answer' ];
		} // End If Statement
		if ( 'multiple-choice' == $question_type && isset( $data[ 'question_wrong_answers' ] ) && ( '' != $data[ 'question_wrong_answers' ] ) ) {
			$question_wrong_answers = $data[ 'question_wrong_answers' ];
		} // End If Statement
		// Handle Boolean Fields - Edit
		if ( 'boolean' == $question_type && isset( $data[ 'question_' . $question_id . '_right_answer_boolean' ] ) && ( '' != $data[ 'question_' . $question_id . '_right_answer_boolean' ] ) ) {
			$question_right_answer = $data[ 'question_' . $question_id . '_right_answer_boolean' ];
		} // End If Statement
		// Handle Boolean Fields - Add
		if ( 'boolean' == $question_type && isset( $data[ 'question_right_answer_boolean' ] ) && ( '' != $data[ 'question_right_answer_boolean' ] ) ) {
			$question_right_answer = $data[ 'question_right_answer_boolean' ];
		} // End If Statement
		// Handle Gap Fill Fields
		if ( 'gap-fill' == $question_type && isset( $data[ 'add_question_right_answer_gapfill_gap' ] ) && '' != $data[ 'add_question_right_answer_gapfill_gap' ] ) {
			$question_right_answer = $data[ 'add_question_right_answer_gapfill_pre' ] . '||' . $data[ 'add_question_right_answer_gapfill_gap' ] . '||' . $data[ 'add_question_right_answer_gapfill_post' ];
		} // End If Statement
		// Handle Multi Line Fields
		if ( 'multi-line' == $question_type && isset( $data[ 'add_question_right_answer_multiline' ] ) && ( '' != $data[ 'add_question_right_answer_multiline' ] ) ) {
			$question_right_answer = $data[ 'add_question_right_answer_multiline' ];
		} // End If Statement
		// Handle Single Line Fields
		if ( 'single-line' == $question_type && isset( $data[ 'add_question_right_answer_singleline' ] ) && ( '' != $data[ 'add_question_right_answer_singleline' ] ) ) {
			$question_right_answer = $data[ 'add_question_right_answer_singleline' ];
		} // End If Statement
		// Handle File Upload Fields
		if ( 'file-upload' == $question_type && isset( $data[ 'add_question_right_answer_fileupload' ] ) && ( '' != $data[ 'add_question_right_answer_fileupload' ] ) ) {
			$question_right_answer = $data[ 'add_question_right_answer_fileupload' ];
		} // End If Statement
		if ( 'file-upload' == $question_type && isset( $data[ 'add_question_wrong_answer_fileupload' ] ) && ( '' != $data[ 'add_question_wrong_answer_fileupload' ] ) ) {
			$question_wrong_answers = array( $data[ 'add_question_wrong_answer_fileupload' ] );
		} // End If Statement

		// Handle Question Grade
		if ( isset( $data[ 'question_grade' ] ) && ( '' != $data[ 'question_grade' ] ) ) {
			$question_grade = $data[ 'question_grade' ];
		} // End If Statement

		// Handle Answer Feedback
		$answer_feedback = '';
		if ( isset( $data[ 'answer_feedback_boolean' ] ) && !empty( $data[ 'answer_feedback_boolean' ] ) ) {

            $answer_feedback = $data[ 'answer_feedback_boolean' ];

		}elseif( isset( $data[ 'answer_feedback_multiple_choice' ] ) && !empty( $data[ 'answer_feedback_multiple_choice' ] ) ){

            $answer_feedback = $data[ 'answer_feedback_multiple_choice' ];

        }elseif( isset( $data[ 'answer_feedback' ] )  ){

            $answer_feedback = $data[ 'answer_feedback' ];

        } // End If Statement

		$post_title = $question_text;
		$post_author = $data[ 'post_author' ];

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

		$post_status = 'publish';
		$post_type = 'question';
		// Handle the extended question text
		if ( isset( $data[ 'question_description' ] ) && ( '' != $data[ 'question_description' ] ) ) {
			$post_content = $data[ 'question_description' ];
		}
		else {
			$post_content = '';
		}
		// Question Query Arguments
		$post_type_args = array(	'post_content' => $post_content,
  		    						'post_status' => $post_status,
  		    						'post_title' => $post_title,
  		    						'post_type' => $post_type
  		    						);

  		// Remove empty values and reindex the array
  		if ( is_array( $question_right_answers ) && 0 < count($question_right_answers) ) {
  			$question_right_answers_array = array_values( array_filter( $question_right_answers, 'strlen' ) );
  			$question_right_answers = array();

  			foreach( $question_right_answers_array as $answer ) {
  				if( ! in_array( $answer, $question_right_answers ) ) {
  					$question_right_answers[] = $answer;
  				}
  			}
  			if ( 0 < count($question_right_answers) ) {
  				$question_right_answer = $question_right_answers;
  			}
  		} // End If Statement
  		$right_answer_count = count( $question_right_answer );

		// Remove empty values and reindex the array
  		if ( is_array( $question_wrong_answers ) ) {
  			$question_wrong_answers_array = array_values( array_filter( $question_wrong_answers, 'strlen' ) );
  			$question_wrong_answers = array();
  		} // End If Statement

  		foreach( $question_wrong_answers_array as $answer ) {

The variable $question_wrong_answers_array does not seem to be defined for all execution paths leading up to this point.

  			if( ! in_array( $answer, $question_wrong_answers ) ) {
  				$question_wrong_answers[] = $answer;
  			}
  		}

  		$wrong_answer_count = count( $question_wrong_answers );

  		// Only save if there is a valid title
  		if ( $post_title != '' ) {

  			// Get Quiz ID for the question
  		    $quiz_id = $data['quiz_id'];

  		    // Get question media
			$question_media = $data['question_media'];

  		    // Get answer order
  		    $answer_order = '';
  		    if( isset( $data['answer_order'] ) ) {
				$answer_order = $data['answer_order'];
			}

			// Get random order selection
			$random_order = 'no';
			if( isset( $data['random_order'] ) ) {
				$random_order = $data['random_order'];
			}

  		    // Insert or Update the question
  		    if ( 0 < $question_id ) {

  		    	$post_type_args[ 'ID' ] = $question_id;
		    	$question_id = wp_update_post( $post_type_args );

		    	// Update poast meta
		    	if( 'quiz' == $context ) {
		    		$quizzes = get_post_meta( $question_id, '_quiz_id', false );
		    		if( ! in_array( $quiz_id, $quizzes ) ) {
			    		add_post_meta( $question_id, '_quiz_id', $quiz_id, false );
			    	}
		    	}

		    	update_post_meta( $question_id, '_question_grade', $question_grade );

The variable $question_grade does not seem to be defined for all execution paths leading up to this point.

		    	update_post_meta( $question_id, '_question_right_answer', $question_right_answer );
		    	update_post_meta( $question_id, '_right_answer_count', $right_answer_count );
		    	update_post_meta( $question_id, '_question_wrong_answers', $question_wrong_answers );
		    	update_post_meta( $question_id, '_wrong_answer_count', $wrong_answer_count );
		    	update_post_meta( $question_id, '_question_media', $question_media );
		    	update_post_meta( $question_id, '_answer_order', $answer_order );
		    	update_post_meta( $question_id, '_random_order', $random_order );

		    	if( 'quiz' != $context ) {
		    		wp_set_post_terms( $question_id, array( $question_type ), 'question-type', false );
		    	}
				// Don't store empty value, no point
				if ( !empty($answer_feedback) ) {
					update_post_meta( $question_id, '_answer_feedback', $answer_feedback );
				}

		    } else {
				$question_id = wp_insert_post( $post_type_args );
				$question_count = intval( $data['question_count'] );
				++$question_count;

				// Set post meta
				if( 'quiz' == $context ) {

This code seems to be duplicated across your project.

					add_post_meta( $question_id, '_quiz_id', $quiz_id, false );
					$lesson_id = get_post_meta( $quiz_id, '_quiz_lesson', true );
					update_post_meta( $lesson_id, '_quiz_has_questions', '1' );
				}

				if( isset( $question_grade ) ) {
		    		add_post_meta( $question_id, '_question_grade', $question_grade );
		    	}
		    	add_post_meta( $question_id, '_question_right_answer', $question_right_answer );
		    	add_post_meta( $question_id, '_right_answer_count', $right_answer_count );
		    	add_post_meta( $question_id, '_question_wrong_answers', $question_wrong_answers );
		    	add_post_meta( $question_id, '_wrong_answer_count', $wrong_answer_count );
		    	add_post_meta( $question_id, '_quiz_question_order' . $quiz_id, $quiz_id . '000' . $question_count );
		    	add_post_meta( $question_id, '_question_media', $question_media );
		    	add_post_meta( $question_id, '_answer_order', $answer_order );
		    	add_post_meta( $question_id, '_random_order', $random_order );
				// Don't store empty value, no point
				if ( !empty($answer_feedback) ) {
					add_post_meta( $question_id, '_answer_feedback', $answer_feedback );
				}

		    	// Set the post terms for question-type
			    wp_set_post_terms( $question_id, array( $question_type ), 'question-type' );

			    if( $question_category ) {
	    			wp_set_post_terms( $question_id, array( $question_category ), 'question-category' );
	    		}

		    } // End If Statement
		} // End If Statement
  		// Check that the insert or update saved by testing the post id
  		if ( 0 < $question_id ) {
  			$return = $question_id;
  		} // End If Statement
  		return $return;
  	} // End lesson_question_save()


	/**
	 * lesson_delete_question function.
	 *
	 * @access private
	 * @param array $data (default: array())
	 * @return void
	 */
	private function lesson_delete_question( $data = array() ) {

		// Get which question to delete
		$question_id = 0;
		if ( isset( $data[ 'question_id' ] ) && ( 0 < absint( $data[ 'question_id' ] ) ) ) {

This code seems to be duplicated across your project.

			$question_id = absint( $data[ 'question_id' ] );
		} // End If Statement
		// Delete the question
		if ( 0 < $question_id ) {
			$quizzes = get_post_meta( $question_id, '_quiz_id', false );

			foreach( $quizzes as $quiz_id ) {
				if( $quiz_id == $data['quiz_id'] ) {
					delete_post_meta( $question_id, '_quiz_id', $quiz_id );
				}
			}

			return true;
		} // End If Statement
		return false;
	} // End lesson_delete_question()


	/**
	 * lesson_complexities function.
	 *
	 * @access public
	 * @return array $lesson_complexities
	 */
	public function lesson_complexities() {

		// V2 - make filter for this array
        $lesson_complexities = array( 	'easy' => __( 'Easy', 'woothemes-sensei' ),
									'std' => __( 'Standard', 'woothemes-sensei' ),
									'hard' => __( 'Hard', 'woothemes-sensei' )
									);

		return $lesson_complexities;

	} // End lesson_complexities


	/**
	 * lesson_count function.
	 *
	 * @access public
	 * @param string $post_status (default: 'publish')
	 * @return int
	 */
	public function lesson_count( $post_status = 'publish', $course_id = false ) {

		$post_args = array(	'post_type'         => 'lesson',
							'posts_per_page'    => -1,
//							'orderby'           => 'menu_order date',

54% of this comment could be valid code. Did you maybe forget this after debugging?

//							'order'             => 'ASC',
							'post_status'       => $post_status,
							'suppress_filters'  => 0,
							'fields'            => 'ids',
							);
		if( $course_id ) {
			$post_args['meta_query'][] = array(
				'key' => '_lesson_course',
				'value' => $course_id,
			);
		}
		else {
			// Simple check for connection to a Course
			$post_args['meta_query'][] = array(
				'key' => '_lesson_course',
				'value' => 0,
				'compare' => '>=',
			);
		}

		// Allow WP to generate the complex final query, just shortcut to only do an overall count
//		add_filter( 'posts_clauses', array( 'WooThemes_Sensei_Utils', 'get_posts_count_only_filter' ) );
		$lessons_query = new WP_Query( apply_filters( 'sensei_lesson_count', $post_args ) );
//		remove_filter( 'posts_clauses', array( 'WooThemes_Sensei_Utils', 'get_posts_count_only_filter' ) );

58% of this comment could be valid code. Did you maybe forget this after debugging?

		return count( $lessons_query->posts );
	} // End lesson_count()


	/**
	 * lesson_quizzes function.
	 *
	 * @access public
	 * @param int $lesson_id (default: 0)
	 * @param string $post_status (default: 'publish')
	 * @param string $fields (default: 'ids')
	 * @return int $quiz_id
	 */
	public function lesson_quizzes( $lesson_id = 0, $post_status = 'any', $fields = 'ids' ) {

This method seems to be duplicated in your project.

		$posts_array = array();

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

		$post_args = array(	'post_type' 		=> 'quiz',
							'posts_per_page' 		=> 1,
							'orderby'         	=> 'title',
    						'order'           	=> 'DESC',
    						'post_parent'      	=> $lesson_id,
    						'post_status'		=> $post_status,
							'suppress_filters' 	=> 0,
							'fields'            => $fields
							);
		$posts_array = get_posts( $post_args );
        $quiz_id = array_shift($posts_array);

		return $quiz_id;
	} // End lesson_quizzes()


	/**
	 * Fetches all the questions for a quiz depending on certain conditions.
     *
     * Determine which questions should be shown depending on:
     * - admin/teacher selected questions to be shown
     * - questions shown to a user previously (saved as asked questions)
     * - limit number of questions lesson setting
	 *
     * @since 1.0
	 * @param int $quiz_id (default: 0)
	 * @param string $post_status (default: 'publish')
	 * @param string $orderby (default: 'meta_value_num title')
	 * @param string $order (default: 'ASC')
     *
	 * @return array $questions { $question type WP_Post }
	 */
	public function lesson_quiz_questions( $quiz_id = 0, $post_status = 'any', $orderby = 'meta_value_num title', $order = 'ASC' ) {

		$quiz_id = (string) $quiz_id;
        $quiz_lesson_id = Sensei()->quiz->get_lesson_id( $quiz_id );

        // setup the user id
        if( is_admin() ) {
            $user_id = isset( $_GET['user'] ) ? $_GET['user'] : '' ;
        } else {
            $user_id = get_current_user_id();
        }

        // get the users current status on the lesson
        $user_lesson_status = Sensei_Utils::user_lesson_status( $quiz_lesson_id, $user_id );

		// Set the default question order if it has not already been set for this quiz
		$this->set_default_question_order( $quiz_id );

		// If viewing quiz on the frontend then show questions in random order if set
		if ( ! is_admin() ) {
			$random_order = get_post_meta( $quiz_id, '_random_question_order', true );
			if( $random_order && $random_order == 'yes' ) {
				$orderby = 'rand';
			}
		}

		// Get all questions and multiple questions
		$question_query_args = array(
			'post_type' 		=> array( 'question', 'multiple_question' ),
			'posts_per_page' 	=> -1,
			'meta_key'        	=> '_quiz_question_order' . $quiz_id,
			'orderby'         	=> $orderby,
			'order'           	=> $order,
			'meta_query'		=> array(
				array(
					'key'       => '_quiz_id',
					'value'     => $quiz_id,
				)
			),
			'post_status'		=> $post_status,
			'suppress_filters' 	=> 0
		);

        //query the questions
		$questions_query = new WP_Query( $question_query_args );

        // Set return array to initially include all items
        $questions = $questions_query->posts;

        // set the questions array that will be manipulated within this function
        $questions_array = $questions_query->posts;

		// If viewing quiz on frontend or in grading then only single questions must be shown
		$selected_questions = false;
		if( ! is_admin() || ( is_admin() && isset( $_GET['page'] ) && 'sensei_grading' == $_GET['page'] && isset( $_GET['user'] ) && isset( $_GET['quiz_id'] ) ) ) {

			// Fetch the questions that the user was asked in their quiz if they have already completed it
			$questions_asked_string = !empty( $user_lesson_status->comment_ID) ? get_comment_meta( $user_lesson_status->comment_ID, 'questions_asked', true ) : false;
			if( !empty($questions_asked_string) ) {

				$selected_questions = explode( ',', $questions_asked_string );

				// Fetch each question in the order in which they were asked
				$questions = array();
				foreach( $selected_questions as $question_id ) {
					if( ! $question_id ) continue;
					$question = get_post( $question_id );
					if( ! isset( $question ) || ! isset( $question->ID ) ) continue;
					$questions[] = $question;
				}

			} else {

				// Otherwise, make sure that we convert all multiple questions into single questions

				$multiple_array = array();

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

				$existing_questions = array();

				// Set array of questions that already exist so we can prevent duplicates from appearing
				foreach( $questions_array as $question ) {
					if( 'question' != $question->post_type ) continue;
					$existing_questions[] = $question->ID;
				}

				// Include only single questions in the return array
				$questions_loop = $questions_array;
				$questions_array = array();
				foreach( $questions_loop as $k => $question ) {

					// If this is a single question then include it
					if( 'question' == $question->post_type ) {
						$questions_array[] = $question;
					} else {

						// If this is a multiple question then get the specified amount of questions from the specified category
						$question_cat = intval( get_post_meta( $question->ID, 'category', true ) );
						$question_number = intval( get_post_meta( $question->ID, 'number', true ) );

						$qargs = array(
							'post_type' 		=> 'question',
							'posts_per_page' 		=> $question_number,
							'orderby'         	=> $orderby,
							'tax_query'			=> array(
								array(
									'taxonomy'  => 'question-category',
									'field'     => 'term_id',
									'terms'		=> $question_cat
								)
							),
							'post_status'		=> $post_status,
							'suppress_filters' 	=> 0,
							'post__not_in'		=> $existing_questions,
						);
						$cat_questions = get_posts( $qargs );

						// Merge results into return array
						$questions_array = array_merge( $questions_array, $cat_questions );

						// Add selected questions to existing questions array to prevent duplicates from being added
						foreach( $questions_array as $cat_question ) {
							if( in_array( $cat_question->ID, $existing_questions ) ) continue;
							$existing_questions[] = $cat_question->ID;
						}
					}
				}

				// Set return data
				$questions = $questions_array;
			}
		}

		// If user has not already taken the quiz and a limited number of questions are to be shown, then show a random selection of the specified amount of questions
		if( ! $selected_questions ) {

			// Only limit questions like this on the frontend
			if( ! is_admin() ) {

				// Get number of questions to show
				$show_questions = intval( get_post_meta( $quiz_id, '_show_questions', true ) );
				if( $show_questions ) {

					// Get random set of array keys from selected questions array
					$selected_questions = array_rand( $questions_array, $show_questions );

					// Loop through all questions and pick the the ones to be shown based on the random key selection
					$questions = array();
					foreach( $questions_array as $k => $question ) {

						// Random keys will always be an array, unless only one question is to be shown
						if( is_array( $selected_questions ) ) {
							if( in_array( $k, $selected_questions ) ) {
								$questions[] = $question;
							}
						} elseif( 1 == $show_questions ) {
							if ( $selected_questions == $k ) {
								$questions[] = $question;
							}
						}
					}
				}
			}
		}

        // Save the questions that will be asked for the current user
        // this happens only once per user/quiz, unless the user resets the quiz
        if( ! is_admin() ){

            if( $user_lesson_status ) {

                $questions_asked = get_comment_meta($user_lesson_status->comment_ID, 'questions_asked', true);
                if ( empty($questions_asked) && $user_lesson_status) {

                    $questions_asked = array();
                    foreach ($questions as $question) {

                        $questions_asked[] = $question->ID;

                    }

                    // save the questions asked id
                    $questions_asked_csv = implode(',', $questions_asked);
                    update_comment_meta($user_lesson_status->comment_ID, 'questions_asked', $questions_asked_csv);

                }
            }
        }

        /**
         * Filter the questions returned by Sensei_Lesson::lessons_quiz_questions
         *
         * @hooked Sensei_Teacher::allow_teacher_access_to_questions
         * @since 1.8.0
         */
		return apply_filters( 'sensei_lesson_quiz_questions', $questions,  $quiz_id  );

	} // End lesson_quiz_questions()

	/**
	 * Set the default quiz order
	 * @param integer $quiz_id ID of quiz
	 */
	public function set_default_question_order( $quiz_id = 0 ) {

		if( $quiz_id ) {

			$question_order = get_post_meta( $quiz_id, '_question_order', true );

			if( ! $question_order ) {

				$args = array(
					'post_type' 		=> 'question',
					'posts_per_page' 		=> -1,
					'orderby'         	=> 'ID',
					'order'           	=> 'ASC',
					'meta_query'		=> array(
						array(
							'key'       => '_quiz_id',
							'value'     => $quiz_id
						)
					),
					'post_status'		=> 'any',
					'suppress_filters' 	=> 0
				);
				$questions = get_posts( $args );

				$o = 1;
				foreach( $questions as $question ) {
					add_post_meta( $question->ID, '_quiz_question_order' . $quiz_id, $quiz_id . '000' . $o, true );
					$o++;
				}
			}
		}

	}

	/**
	 * lesson_image function.
	 *
	 * Handles output of the lesson image
	 *
	 * @access public
	 * @param int $lesson_id (default: 0)
	 * @param string $width (default: '100')
	 * @param string $height (default: '100')
	 * @return string
	 */
	public function lesson_image( $lesson_id = 0, $width = '100', $height = '100', $widget = false ) {

		$html = '';

		// Get Width and Height settings
		if ( ( $width == '100' ) && ( $height == '100' ) ) {

			if ( is_singular( 'lesson' ) ) {

				if ( ! $widget && ! Sensei()->settings->settings[ 'lesson_single_image_enable' ] ) {

					return '';

				} // End If Statement

				$image_thumb_size = 'lesson_single_image';
				$dimensions = Sensei()->get_image_size( $image_thumb_size );
				$width = $dimensions['width'];
				$height = $dimensions['height'];
				$crop = $dimensions['crop'];

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

			} else {

				if ( ! $widget && ! Sensei()->settings->settings[ 'course_lesson_image_enable' ] ) {

					return '';
				} // End If Statement

				$image_thumb_size = 'lesson_archive_image';
				$dimensions = Sensei()->get_image_size( $image_thumb_size );
				$width = $dimensions['width'];
				$height = $dimensions['height'];
				$crop = $dimensions['crop'];

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

			} // End If Statement

		} // End If Statement

		$img_url = '';

		if ( has_post_thumbnail( $lesson_id ) ) {

   			// Get Featured Image
   			$img_url = get_the_post_thumbnail( $lesson_id, array( $width, $height ), array( 'class' => 'woo-image thumbnail alignleft') );

 		} else {

This code seems to be duplicated across your project.

 			// Display Image Placeholder if none
			if ( Sensei()->settings->settings[ 'placeholder_images_enable' ] ) {

                $img_url = apply_filters( 'sensei_lesson_placeholder_image_url', '<img src="http://placehold.it/' . $width . 'x' . $height . '" class="woo-image thumbnail alignleft" />' );

			} // End If Statement

		} // End If Statement

		$html .= '<a href="' . get_permalink( $lesson_id ) . '" title="' . esc_attr( get_post_field( 'post_title', $lesson_id ) ) . '">' . $img_url . '</a>';

		return $html;

	} // End lesson_image()

	/**
	 * Returns the the lesson excerpt.
	 *
	 * @param WP_Post $lesson
     * @param bool $add_p_tags should the excerpt be wrapped by calling wpautop()
	 * @return string
	 */
	public static function lesson_excerpt( $lesson = null, $add_p_tags = true ) {
		$html = '';
		if ( is_a( $lesson, 'WP_Post' ) && 'lesson' == $lesson->post_type ) {

            $excerpt =  $lesson->post_excerpt;

            // if $add_p_tags true wrap with <p> else return the excerpt as is
            $html =  $add_p_tags ? wpautop( $excerpt ) : $excerpt;

		}
		return apply_filters( 'sensei_lesson_excerpt', $html );

	} // End lesson_excerpt()

    /**
     * Returns the course for a given lesson
     *
     * @since 1.7.4
     * @access public
     *
     * @param int $lesson_id
     * @return int|bool $course_id or bool when nothing is found.
     */
     public function get_course_id( $lesson_id ){

         if( ! isset( $lesson_id ) || empty( $lesson_id )
         ||  'lesson' != get_post_type( $lesson_id ) ){
             return false;
         }

         $lesson_course_id = get_post_meta( $lesson_id, '_lesson_course', true);

         // make sure the course id is valid
         if( empty( $lesson_course_id )
             || is_array( $lesson_course_id )
             || intval( $lesson_course_id ) < 1
             || 'course' != get_post_type( $lesson_course_id ) ){

             return false;

         }

         return $lesson_course_id;

     }// en get_course_id

    /**
     * Add the admin all lessons screen edit options.
     *
     * The fields in this function work for both quick and bulk edit. The ID attributes is used
     * by bulk edit javascript in the front end to retrieve the new values set byt the user. Then
     * name attribute is will be used by the quick edit and submitted via standard POST. This
     * will use this classes save_post_meta function to save the new field data.
     *
     * @hooked quick_edit_custom_box
     * @hooked bulk_edit_custom_box
     *
     * @since 1.8.0
     *
     * @param string $column_name
     * @param string $post_type
     * @return void
     */
    public function all_lessons_edit_fields( $column_name, $post_type ) {

        // only show these options ont he lesson post type edit screen
        if( 'lesson' != $post_type || 'lesson-course' != $column_name ){
            return;
        }

        ?>
        <fieldset class="sensei-edit-field-set inline-edit-lesson">
            <div class="sensei-inline-edit-col column-<?php echo $column_name ?>">
                    <?php
                    echo '<h4>' . __('Lesson Information', 'woothemes-sensei') . '</h4>';
                    // create a nonce field to be  used as a security measure when saving the data
                    wp_nonce_field( 'bulk-edit-lessons', '_edit_lessons_nonce' );
                    wp_nonce_field( 'sensei-save-post-meta','woo_' . $this->token . '_nonce'  );

                    // unchanged option - we need this in because
                    // the default option in bulk edit should not be empty. If it is
                    // the user will erase data they didn't want to touch.
                    $no_change_text = '-- ' . __('No Change', 'woothemes-sensei') . ' --';

                    //
                    //course selection
                    //
                    $courses =  WooThemes_Sensei_Course::get_all_courses();
                    $course_options = array();
                    if ( count( $courses ) > 0 ) {
                        foreach ($courses as $course ){
                            $course_options[ $course->ID ] = get_the_title( $course->ID );
                        }
                    }
                    //pre-append the no change option
                    $course_options['-1']=  $no_change_text;
                    $course_attributes = array( 'name'=> 'lesson_course', 'id'=>'sensei-edit-lesson-course' , 'class'=>' ' );
                    $course_field =  Sensei_Utils::generate_drop_down( '-1', $course_options, $course_attributes );
                    echo $this->generate_all_lessons_edit_field( __('Lesson Course', 'woothemes-sensei'),   $course_field  );

                    //
                    // lesson complexity selection
                    //
                    $lesson_complexities =  $this->lesson_complexities();
                    //pre-append the no change option
                    $lesson_complexities['-1']=  $no_change_text;
                    $complexity_dropdown_attributes = array( 'name'=> 'lesson_complexity', 'id'=>'sensei-edit-lesson-complexity' , 'class'=>' ');
                    $complexity_filed =  Sensei_Utils::generate_drop_down( '-1', $lesson_complexities, $complexity_dropdown_attributes );
                    echo $this->generate_all_lessons_edit_field( __('Lesson Complexity', 'woothemes-sensei'),   $complexity_filed  );

                    ?>

                    <h4><?php _e('Quiz Settings', 'woothemes-sensei'); ?> </h4>

                    <?php

                    //
                    // Lesson require pass to complete
                    //
                    $pass_required_options = array(
                        '-1' => $no_change_text,
                         '0' => __('No','woothemes'),
                         '1' => __('Yes','woothemes'),
                    );

                    $pass_required_select_attributes = array( 'name'=> 'pass_required',
                                                                'id'=> 'sensei-edit-lesson-pass-required',
                                                                'class'=>' '   );
                    $require_pass_field =  Sensei_Utils::generate_drop_down( '-1', $pass_required_options, $pass_required_select_attributes, false );
                    echo $this->generate_all_lessons_edit_field( __('Pass required', 'woothemes-sensei'),   $require_pass_field  );

                    //
                    // Quiz pass percentage
                    //
                    $quiz_pass_percentage_field = '<input name="quiz_passmark" id="sensei-edit-quiz-pass-percentage" type="number" />';
                    echo $this->generate_all_lessons_edit_field( __('Pass Percentage', 'woothemes-sensei'), $quiz_pass_percentage_field  );

                    //
                    // Enable quiz reset button
                    //
                    $quiz_reset_select__options = array(
                        '-1' => $no_change_text,
                        '0' => __('No','woothemes'),
                        '1' => __('Yes','woothemes'),
                    );
                    $quiz_reset_name_id = 'sensei-edit-enable-quiz-reset';
                    $quiz_reset_select_attributes = array( 'name'=> 'enable_quiz_reset', 'id'=>$quiz_reset_name_id, 'class'=>' ' );
                    $quiz_reset_field =  Sensei_Utils::generate_drop_down( '-1', $quiz_reset_select__options, $quiz_reset_select_attributes, false );
                    echo $this->generate_all_lessons_edit_field( __('Enable quiz reset button', 'woothemes-sensei'), $quiz_reset_field  );

                    ?>
            </div>
        </fieldset>
    <?php
    }// all_lessons_edit_fields

    /**
     * Create the html for the edit field
     *
     * Wraps the passed in field and title combination with the correct html.
     *
     * @since 1.8.0
     *
     * @param string $title that will stand to the left of the field.
     * @param string $field type markup for the field that must be wrapped.
     * @return string $field_html
     */
    public function generate_all_lessons_edit_field( $title  ,$field ){

        $html = '';

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

        $html = '<div class="inline-edit-group" >';
        $html .=  '<span class="title">'. $title .'</span> ';
        $html .= '<span class="input-text-wrap">';
        $html .= $field;
        $html .= '</span>';
        $html .= '</label></div>';

        return $html ;

    }//end generate_all_lessons_edit_field

    /**
     * Respond to the ajax call from the bulk edit save function. This comes
     * from the admin all lesson screen.
     *
     * @since 1.8.0
     * @return void
     */
    function save_all_lessons_edit_fields() {

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

        // verify all the data before attempting to save
        if( ! isset( $_POST['security'] ) || ! check_ajax_referer( 'bulk-edit-lessons', 'security' )
            ||  empty( $_POST[ 'post_ids' ] )  || ! is_array( $_POST[ 'post_ids' ] ) ) {
            die();
        }

        // get our variables
        $new_course = sanitize_text_field(  $_POST['sensei_edit_lesson_course'] );
        $new_complexity = sanitize_text_field(  $_POST['sensei_edit_complexity'] );
        $new_pass_required = sanitize_text_field(  $_POST['sensei_edit_pass_required'] );
        $new_pass_percentage = sanitize_text_field(  $_POST['sensei_edit_pass_percentage'] );
        $new_enable_quiz_reset = sanitize_text_field(  $_POST['sensei_edit_enable_quiz_reset'] );
        // store the values for all selected posts
        foreach( $_POST[ 'post_ids' ] as $lesson_id ) {

            // get the quiz id needed for the quiz meta
            $quiz_id = Sensei()->lesson->lesson_quizzes( $lesson_id );

            // do not save the items if the value is -1 as this
            // means it was not changed

            // update lesson course
            if( -1 != $new_course ){
                update_post_meta( $lesson_id, '_lesson_course', $new_course );
            }
            // update lesson complexity
            if( -1 != $new_complexity ){
                update_post_meta( $lesson_id, '_lesson_complexity', $new_complexity );
            }

            // Quiz Related settings
            if( isset( $quiz_id) && 0 < intval( $quiz_id ) ) {

                // update pass required
                if (-1 != $new_pass_required) {

                    $checked = $new_pass_required  ? 'on' : '';
                    update_post_meta($quiz_id, '_pass_required', $checked);
                    unset( $checked );
                }

                // update pass percentage
                if( !empty( $new_pass_percentage) && is_numeric( $new_pass_percentage ) ){

                        update_post_meta($quiz_id, '_quiz_passmark', $new_pass_percentage);

                }

                //
                // update enable quiz reset
                //
                if (-1 != $new_enable_quiz_reset ) {

                    $checked = $new_enable_quiz_reset ? 'on' : ''  ;
                    update_post_meta($quiz_id, '_enable_quiz_reset', $checked);
                    unset( $checked );

                }


            } // end if quiz

        }// end for each

        die();

    } // end save_all_lessons_edit_fields

    /**
     * Loading the quick edit fields defaults.
     *
     * This function will localise the default values along with the script that will
     * add these values to the inputs.
     *
     * NOTE: this function runs for each row in the edit column
     *
     * @since 1.8.0
     * @return void
     */
    public function set_quick_edit_admin_defaults( $column_name, $post_id ){

        if( 'lesson-course' != $column_name ){
            return;
        }
        // load the script
        $suffix = defined( 'SCRIPT_DEBUG') && SCRIPT_DEBUG ? '' : '.min';
        wp_enqueue_script( 'sensei-lesson-quick-edit', Sensei()->plugin_url . 'assets/js/admin/lesson-quick-edit' . $suffix . '.js', array( 'jquery' ), Sensei()->version, true );

        // setup the values for all meta fields
        $data = array();
        foreach( $this->meta_fields as $field ){

            $data[$field] =  get_post_meta( $post_id, '_'.$field, true );

        }
        // add quiz meta fields
        $quiz_id = Sensei()->lesson->lesson_quizzes( $post_id );
        foreach( Sensei()->quiz->meta_fields as $field ){

            $data[$field] =  get_post_meta( $quiz_id, '_'.$field, true );

        }

        wp_localize_script( 'sensei-lesson-quick-edit', 'sensei_quick_edit_'.$post_id, $data );

    }// end quick edit admin defaults

    /**
     * Filter the classes for lessons on the single course page.
     *
     * Adds the nesecary classes depending on the user data
     *
     * @since 1.9.0
     * @param array $classes
     * @return array $classes
     */
    public static function single_course_lessons_classes( $classes ){

        if(  is_singular('course') ){

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

            $lesson_classes = array( 'course', 'post' );
            if ( is_user_logged_in() ) {

                // Check if Lesson is complete
                $single_lesson_complete = Sensei_Utils::user_completed_lesson( get_the_ID(), get_current_user_id() );
                if ( $single_lesson_complete ) {

                    $lesson_classes[] = 'lesson-completed';

                } // End If Statement

            } // End If Statement

            $is_user_taking_course = Sensei_Utils::user_started_course( $course_id, get_current_user_id() );
            if (  Sensei_Utils::is_preview_lesson( get_the_ID() ) && !$is_user_taking_course ) {

The expression $is_user_taking_course of type false|string is loosely compared to false; this is ambiguous if the string can be empty. You might want to explicitly use === false instead.

                $lesson_classes[] = 'lesson-preview';

            }

            $classes = array_merge( $classes, $lesson_classes  );

        }

        return $classes;

    }// end single_course_lessons_classes

    /**
     * Output the lesson meta for the given lesson
     *
     * @since 1.9.0
     * @param $lesson_id
     */
    public static function the_lesson_meta( $lesson_id ){

        global $wp_query;
        $loop_lesson_number = $wp_query->current_post + 1;

        $course_id = Sensei()->lesson->get_course_id( $lesson_id );
        $single_lesson_complete = false;
        $is_user_taking_course = Sensei_Utils::user_started_course( $course_id, get_current_user_id() );

It seems like $course_id defined by Sensei()->lesson->get_course_id($lesson_id) on line 3221 can also be of type boolean; however, Sensei_Utils::user_started_course() does only seem to accept integer, maybe add an additional type check?

        // Get Lesson data
        $complexity_array = Sensei()->lesson->lesson_complexities();

        $lesson_complexity = get_post_meta( $lesson_id, '_lesson_complexity', true );
        if ( '' != $lesson_complexity ) {

            $lesson_complexity = $complexity_array[$lesson_complexity];

        }
        $user_info = get_userdata( absint( get_post()->post_author ) );
        $is_preview = Sensei_Utils::is_preview_lesson( $lesson_id);
        $preview_label = '';
        if ( $is_preview && !$is_user_taking_course ) {

The expression $is_user_taking_course of type false|string is loosely compared to false; this is ambiguous if the string can be empty. You might want to explicitly use === false instead.

            $preview_label = Sensei()->frontend->sensei_lesson_preview_title_text( $lesson_id);
            $preview_label = '<span class="preview-heading">' . $preview_label . '</span>';

        }


        $count_markup= '';
        /**
         * Filter for if you want the $lesson_count to show next to the lesson.
         *
         * @since 1.0
         * @param bool default false.
         */
        if( apply_filters( 'sensei_show_lesson_numbers', false ) ) {

            $count_markup =  '<span class="lesson-number">' . $loop_lesson_number. '</span>';

        }

        $heading_link_title = sprintf( __( 'Start %s', 'woothemes-sensei' ), get_the_title( $lesson_id ) );

        ?>
        <header>
            <h2>
                <a href="<?php echo esc_url_raw( get_permalink( $lesson_id ) ) ?>"
                   title="<?php esc_attr_e( $heading_link_title ) ?>" >
                    <?php echo $count_markup. get_the_title( $lesson_id ) . $preview_label; ?>
                </a>
            </h2>

            <p class="lesson-meta">

                <?php

                $meta_html = '';
                $user_lesson_status = Sensei_Utils::user_lesson_status( get_the_ID(), get_current_user_id() );

                $lesson_length = get_post_meta( $lesson_id, '_lesson_length', true );
                if ( '' != $lesson_length ) {

This code seems to be duplicated across your project.

                    $meta_html .= '<span class="lesson-length">' .  __( 'Length: ', 'woothemes-sensei' ) . $lesson_length . __( ' minutes', 'woothemes-sensei' ) . '</span>';

                }

                if ( Sensei()->settings->get( 'lesson_author' ) ) {

                    $meta_html .= '<span class="lesson-author">' .  __( 'Author: ', 'woothemes-sensei' ) . '<a href="' . get_author_posts_url( absint( get_post()->post_author ) ) . '" title="' . esc_attr( $user_info->display_name ) . '">' . esc_html( $user_info->display_name ) . '</a></span>';

                } // End If Statement
                if ( '' != $lesson_complexity ) {

                    $meta_html .= '<span class="lesson-complexity">' .  __( 'Complexity: ', 'woothemes-sensei' ) . $lesson_complexity .'</span>';

                }

                if ( $single_lesson_complete ) {

This code seems to be duplicated across your project.

                    $meta_html .= '<span class="lesson-status complete">' .__( 'Complete', 'woothemes-sensei' ) .'</span>';

                } elseif ( $user_lesson_status ) {

                    $meta_html .= '<span class="lesson-status in-progress">' . __( 'In Progress', 'woothemes-sensei' ) .'</span>';

                } // End If Statement

                echo $meta_html;

                ?>

            </p> <!-- lesson meta -->

        </header>

    <?php

    } // end the_lesson_meta

    /**
     * Output the lessons thumbnail
     *
     * 1.9.0
     *
     * @param $lesson_id
     */
    public static function the_lesson_thumbnail( $lesson_id ){

        if( empty( $lesson_id ) ){

            $lesson_id = get_the_ID();

        }

        if( 'lesson' != get_post_type( $lesson_id ) ){
            return;
        }

        echo Sensei()->lesson->lesson_image( $lesson_id );
    }


    /**
     * Alter the sensei lesson excerpt.
     *
     * @since 1.9.0
     * @param string $excerpt
     * @return string $excerpt
     */
    public static function alter_the_lesson_excerpt( $excerpt ) {

        if ('lesson' == get_post_type(get_the_ID())){

            // remove this hooks to avoid an infinite loop.
            remove_filter( 'get_the_excerpt', array( 'WooThemes_Sensei_Lesson','alter_the_lesson_excerpt') );

            return WooThemes_Sensei_Lesson::lesson_excerpt( get_post( get_the_ID() ) );
        }

        return $excerpt;

    }// end the_lesson_excerpt

    /**
     * Returns the lesson prerequisite for the given lesson id.
     *
     * @since 1.9.0
     *
     * @param $current_lesson_id
     * @return mixed | bool | int $prerequisite_lesson_id or false
     */
    public static function get_lesson_prerequisite_id( $current_lesson_id  ){

        $prerequisite_lesson_id = get_post_meta( $current_lesson_id , '_lesson_prerequisite', true );

        // set ti to false if not a valid prerequisite lesson id
        if(  empty( $prerequisite_lesson_id )
            || 'lesson' != get_post_type( $prerequisite_lesson_id )
            || $prerequisite_lesson_id == $current_lesson_id  ) {

            $prerequisite_lesson_id = false;

        }

        return apply_filters( 'sensei_lesson_prerequisite', $prerequisite_lesson_id, $current_lesson_id );

    }

    /**
     * This function requires that you pass in the lesson you would like to check for
     * a pre-requisite and not the pre-requisite. It will check if the
     * lesson has a pre-requiste and then check if it is completed.
     *
     * @since 1.9.0
     *
     * @param $lesson_id
     * @param $user_id
     * @return bool
     */
    public  static function is_prerequisite_complete( $lesson_id, $user_id  ){

        if( empty( $lesson_id ) || empty( $user_id )

This code seems to be duplicated across your project.

        || 'lesson' != get_post_type( $lesson_id )
        ||  ! is_a( get_user_by( 'id', $user_id ), 'WP_User' )){

            return false;

        }

        $pre_requisite_id = (string) self::get_lesson_prerequisite_id( $lesson_id );

        // not a valid pre-requisite so pre-requisite is completed
        if( 'lesson' != get_post_type( $pre_requisite_id )
            || ! is_numeric( $pre_requisite_id ) ){

            return true;

        }

        return  Sensei_Utils::user_completed_lesson( $pre_requisite_id, $user_id );

    }// end is_prerequisite_complete

    /**
     * Show the user not taking course message if it is the case
     *
     * @since 1.9.0
     */
    public  static function user_not_taking_course_message(){

        $lesson_id = get_the_ID();

        if( 'lesson' != get_post_type( $lesson_id ) ){
            return;
        }

        $is_preview = Sensei_Utils::is_preview_lesson( $lesson_id );
        $pre_requisite_complete = self::is_prerequisite_complete( $lesson_id , get_current_user_id() );
        $lesson_course_id = get_post_meta( $lesson_id, '_lesson_course', true );
        $user_taking_course = Sensei_Utils::user_started_course( $lesson_course_id, get_current_user_id() );

        if ( $pre_requisite_complete && $is_preview && !$user_taking_course ) {

The expression $user_taking_course of type false|string is loosely compared to false; this is ambiguous if the string can be empty. You might want to explicitly use === false instead.

            ?>

            <div class="sensei-message alert">
                <?php echo Sensei()->permissions_message['message']; ?>
            </div>

            <?php

        }// end if

    } // end user_not_taking_course_message

    /**
     * Outputs the lessons course signup lingk
     *
     * This hook runs inside the single lesson page.
     *
     * @since 1.9.0
     */
    public static function course_signup_link( ){

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

        if ( empty( $course_id ) || 'course' != get_post_type( $course_id ) || sensei_all_access() ) {

            return;

        }
        ?>

        <section class="course-signup lesson-meta">

            <?php
            $wc_post_id = (int) get_post_meta( $course_id, '_course_woocommerce_product', true );

            if ( Sensei_WC::is_woocommerce_active() && ( 0 < $wc_post_id ) ) {

                global $current_user;
                if( is_user_logged_in() ) {
                    wp_get_current_user();

                    $course_purchased = Sensei_Utils::sensei_customer_bought_product( $current_user->user_email, $current_user->ID, $wc_post_id );

The method Sensei_Utils::sensei_customer_bought_product() has been deprecated with message: since 1.9.0 use Sensei_WC::has_customer_bought_product($user_id, $product_id)

                    if( $course_purchased ) {

                        $prereq_course_id = get_post_meta( $course_id, '_course_prerequisite',true );
                        $course_link = '<a href="' . esc_url( get_permalink( $prereq_course_id ) ) . '" title="' . esc_attr( get_the_title( $prereq_course_id ) ) . '">' . __( 'the previous course', 'woothemes-sensei' )  . '</a>';
                        ?>
                            <div class="sensei-message info">

                                <?php  echo sprintf( __( 'Please complete %1$s before starting the lesson.', 'woothemes-sensei' ), $course_link ); ?>

                            </div>

                    <?php } else { ?>

This code seems to be duplicated across your project.

                        <div class="sensei-message info">

                            <?php
                            $course_link = '<a href="' . esc_url( get_permalink( $course_id ) )
                                            . '"title="' . __( 'Sign Up', 'woothemes-sensei' )
                                            . '">' . __( 'course', 'woothemes-sensei' )
                                            . '</a>';

                            echo  sprintf( __( 'Please purchase the %1$s before starting the lesson.', 'woothemes-sensei' ), $course_link );

                            ?>

                        </div>
                    <?php } ?>

                <?php } else { ?>

This code seems to be duplicated across your project.

                    <div class="sensei-message info"><?php echo sprintf( __( 'Please purchase the %1$s before starting the lesson.', 'woothemes-sensei' ), '<a href="' . esc_url( get_permalink( $course_id ) ) . '" title="' . __( 'Sign Up', 'woothemes-sensei' )  . '">' . __( 'course', 'woothemes-sensei' ) . '</a>' ); ?></div>

                <?php } ?>

            <?php } else { ?>

            <?php if( ! Sensei_Utils::user_started_course( $course_id, get_current_user_id() ) &&  sensei_is_login_required() )  : ?>

It seems like $course_id defined by Sensei()->lesson->get_course_id(get_the_ID()) on line 3460 can also be of type boolean; however, Sensei_Utils::user_started_course() does only seem to accept integer, maybe add an additional type check?

The expression \Sensei_Utils::user_started_course($course_id, get_current_user_id()) of type false|string is loosely compared to false; this is ambiguous if the string can be empty. You might want to explicitly use === false instead.

                <div class="sensei-message info">
                    <?php
                    $course_link =  '<a href="'
                                        . esc_url( get_permalink( $course_id ) )
                                        . '" title="' . __( 'Sign Up', 'woothemes-sensei' )
                                        . '">' . __( 'course', 'woothemes-sensei' )
                                    . '</a>';

                    echo sprintf( __( 'Please sign up for the %1$s before starting the lesson.', 'woothemes-sensei' ),  $course_link );
                    ?>
                </div>

            <?php endif; ?>

            <?php } // End If Statement ?>

        </section>

        <?php
    }// end course_signup_link

    /**
     * Show a message telling the user to complete the previous message if they haven't done so yet
     *
     * @since 1.9.0
     */
    public  static function prerequisite_complete_message(){

        $lesson_prerequisite =  WooThemes_Sensei_Lesson::get_lesson_prerequisite_id( get_the_ID() );
        $lesson_has_pre_requisite = $lesson_prerequisite > 0;
        if ( ! WooThemes_Sensei_Lesson::is_prerequisite_complete(  get_the_ID(), get_current_user_id() ) && $lesson_has_pre_requisite ) {

            $prerequisite_lesson_link  = '<a href="' . esc_url( get_permalink( $lesson_prerequisite ) ) . '" title="' . esc_attr(  sprintf( __( 'You must first complete: %1$s', 'woothemes-sensei' ), get_the_title( $lesson_prerequisite ) ) ) . '">' . get_the_title( $lesson_prerequisite ). '</a>';
            echo sprintf( __( 'You must first complete %1$s before viewing this Lesson', 'woothemes-sensei' ), $prerequisite_lesson_link );

        }

    }

    /**
     * Deprecate the sensei_lesson_archive_header hook but keep it
     * active for backwards compatibility.
     *
     * @deprecated since 1.9.0
     */
    public static function deprecate_sensei_lesson_archive_header_hook(){

        sensei_do_deprecated_action('sensei_lesson_archive_header', '1.9.0', 'sensei_loop_lesson_inside_before');

    }

    /**
     * Outputs the the lesson archive header.
     *
     * @since  1.9.0
     * @return void
     */
    public function the_archive_header( ) {

        $before_html = '<header class="archive-header"><h1>';
        $after_html = '</h1></header>';
        $html = $before_html .  __( 'Lessons Archive', 'woothemes-sensei' ) . $after_html;

        echo apply_filters( 'sensei_lesson_archive_title', $html );

    } // sensei_course_archive_header()

    /**
     * Output the title for the single lesson page
     *
     * @global $post
     * @since 1.9.0
     */
    public static function the_title(){

        global $post;

        ?>
        <header>

            <h1>

                <?php
                /**
                 * Filter documented in class-sensei-messages.php the_title
                 */
                echo apply_filters( 'sensei_single_title', get_the_title( $post ), $post->post_type );
                ?>

            </h1>

        </header>

        <?php

    }//the_title

    /**
     * Flush the rewrite rules for a lesson post type
     *
     * @since 1.9.0
     *
     * @param $post_id
     */
    public static function flush_rewrite_rules( $post_id ){

This method seems to be duplicated in your project.

        if (defined('DOING_AUTOSAVE') && DOING_AUTOSAVE){

            return;

        }


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

            Sensei()->initiate_rewrite_rules_flush();

        }

    }

    /**
     * Output the quiz specific buttons and messaging on the single lesson page
     *
     *
     * @since 1.0.0 moved here from frontend class
     *
     * @param int $lesson_id
     * @param int $user_id
     */
    public static function footer_quiz_call_to_action( $lesson_id = 0, $user_id = 0 ) {


        $lesson_id                 =  empty( $lesson_id ) ?  get_the_ID() : $lesson_id;
        $user_id                   = empty( $lesson_id ) ?  get_current_user_id() : $user_id;
        $lesson_prerequisite       = (int) get_post_meta( $lesson_id, '_lesson_prerequisite', true );
        $lesson_course_id          = (int) get_post_meta( $lesson_id, '_lesson_course', true );

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

        $quiz_id                   = Sensei()->lesson->lesson_quizzes( $lesson_id );
        $has_user_completed_lesson = Sensei_Utils::user_completed_lesson( intval( $lesson_id ), $user_id );
        $show_actions              = is_user_logged_in() ? true : false;

        if( intval( $lesson_prerequisite ) > 0 ) {

            // If the user hasn't completed the prereq then hide the current actions
            $show_actions = Sensei_Utils::user_completed_lesson( $lesson_prerequisite, $user_id );

        }
        ?>

        <footer>

            <?php
            if( $show_actions && $quiz_id && Sensei()->access_settings() ) {

                $has_quiz_questions = get_post_meta( $lesson_id, '_quiz_has_questions', true );
                if( $has_quiz_questions ) {
                    ?>

                    <p>

                        <a class="button"
                           href="<?php echo esc_url_raw( get_permalink( $quiz_id ) ); ?>"
                           title="<?php _e( 'View the Lesson Quiz', 'woothemes-sensei'  ); ?>">

                            <?php  _e( 'View the Lesson Quiz', 'woothemes-sensei' ); ?>

                        </a>

                    </p>

                    <?php
                }

            } // End If Statement

            if ( $show_actions && ! $has_user_completed_lesson ) {

                sensei_complete_lesson_button();

            } elseif( $show_actions ) {

                sensei_reset_lesson_button();

            } // End If Statement
            ?>

        </footer>

        <?php
    } // End sensei_lesson_quiz_meta()

    /**
     * Show the lesson comments. This should be used in the loop.
     *
     * @since 1.9.0
     */
    public static function output_comments(){

        if( ! is_user_logged_in() ){
            return;
        }

        $pre_requisite_complete = Sensei()->lesson->is_prerequisite_complete( get_the_ID(), get_current_user_id() );
        $course_id = Sensei()->lesson->get_course_id( get_the_ID() );
        $allow_comments = Sensei()->settings->settings[ 'lesson_comments' ];
        $user_taking_course = Sensei_Utils::user_started_course($course_id );

It seems like $course_id defined by Sensei()->lesson->get_course_id(get_the_ID()) on line 3723 can also be of type boolean; however, Sensei_Utils::user_started_course() does only seem to accept integer, maybe add an additional type check?

        $lesson_allow_comments = $allow_comments && $pre_requisite_complete  && $user_taking_course;

The expression $user_taking_course of type false|string is loosely compared to true; this is ambiguous if the string can be empty. You might want to explicitly use !== false instead.

        if (  $lesson_allow_comments || is_singular( 'sensei_message' ) ) {

            comments_template();

        } // End If Statement

    } //output_comments

    /**
     * Display the leeson quiz status if it should be shown
     *
     * @param int $lesson_id defaults to the global lesson id
     * @param int $user_id defaults to the current user id
     *
     * @since 1.9.0
     */
    public static function user_lesson_quiz_status_message( $lesson_id = 0, $user_id = 0){

        $lesson_id                 =  empty( $lesson_id ) ?  get_the_ID() : $lesson_id;
        $user_id                   = empty( $lesson_id ) ?  get_current_user_id() : $user_id;
        $lesson_course_id          = (int) get_post_meta( $lesson_id, '_lesson_course', true );
        $quiz_id                   = Sensei()->lesson->lesson_quizzes( $lesson_id );
        $has_user_completed_lesson = Sensei_Utils::user_completed_lesson( intval( $lesson_id ), $user_id );


        if ( $quiz_id && is_user_logged_in()
            && Sensei_Utils::user_started_course( $lesson_course_id, $user_id ) ) {

The expression \Sensei_Utils::user_started_course($lesson_course_id, $user_id) of type false|string is loosely compared to true; this is ambiguous if the string can be empty. You might want to explicitly use !== false instead.

            $no_quiz_count = 0;

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

            $has_quiz_questions = get_post_meta( $lesson_id, '_quiz_has_questions', true );

            // Display lesson quiz status message
            if ( $has_user_completed_lesson || $has_quiz_questions ) {
                $status = Sensei_Utils::sensei_user_quiz_status_message( $lesson_id, $user_id, true );
                echo '<div class="sensei-message ' . $status['box_class'] . '">' . $status['message'] . '</div>';
                if( $has_quiz_questions ) {

This if statement is empty and can be removed.

                   // echo $status['extra'];

75% of this comment could be valid code. Did you maybe forget this after debugging?

                } // End If Statement
            } // End If Statement

        }

    }

} // End Class

/**
 * Class WooThemes_Sensei_Lesson
 * for backward compatibility
 * @since 1.9.0
 */
class WooThemes_Sensei_Lesson extends Sensei_Lesson{}