Parent Post From Another Post Type And A New URL Structure In WordPress

functions.php

<?php
// Flush rewrite rules after switch theme
function my_rewrite_flush() {
   	flush_rewrite_rules();
}
add_action( 'after_switch_theme', 'my_rewrite_flush' );

// A little help so we can get the stylesheet from parent theme
// Remove line 10-19 if this is not a child theme
function my_enqueue_styles() {
	$parent_style = 'parent-style';

	wp_enqueue_style( $parent_style, get_template_directory_uri() . '/style.css' );
	wp_enqueue_style( 'child-style',
        	get_stylesheet_directory_uri() . '/style.css',
        	array( $parent_style )
	);
}
add_action( 'wp_enqueue_scripts', 'my_enqueue_styles' );

// Register Custom Post Types
function my_register_cpt() {
	$labels = array(
		'name'                  => _x( 'Courses', 'Post Type General Name', '1fix' ),
		'singular_name'         => _x( 'Course', 'Post Type Singular Name', '1fix' ),
		'menu_name'             => __( 'Courses', '1fix' ),
		'name_admin_bar'        => __( 'Courses', '1fix' )
	);
	$args = array(
		'label'                 => __( 'Course', '1fix' ),
		'labels'                => $labels,
		'hierarchical'          => true,
		'public'                => true
	);
	register_post_type( 'course', $args );

	$labels = array(
		'name'                  => _x( 'Lessons', 'Post Type General Name', '1fix' ),
		'singular_name'         => _x( 'Lesson', 'Post Type Singular Name', '1fix' ),
		'menu_name'             => __( 'Lessons', '1fix' ),
		'name_admin_bar'        => __( 'Lessons', '1fix' )
	);
	$args = array(
		'label'                 => __( 'Lesson', '1fix' ),
		'labels'                => $labels,
		'hierarchical'          => false,
		'public'                => true
	);
	register_post_type( 'lesson', $args );

}
add_action( 'init', 'my_register_cpt' );

// Add our Course parent meta box
function my_add_meta_boxes() {
	add_meta_box( 'lesson-parent', 'Course', 'lesson_attributes_meta_box', 'lesson', 'side', 'high' );
}
add_action( 'add_meta_boxes', 'my_add_meta_boxes' );

// Get the Course dropdown
function lesson_attributes_meta_box( $post ) {
	$post_type_object = get_post_type_object( $post->post_type );
	$pages = wp_dropdown_pages( array( 'post_type' => 'course', 'selected' => $post->post_parent, 'name' => 'parent_id', 'show_option_none' => __( '(no parent)' ), 'sort_column'=> 'menu_order, post_title', 'echo' => 0 ) );
	if ( ! empty( $pages ) ) {
		echo $pages;
	}
}

// Add our own URL strucutre and rewrite rules
function my_add_rewrite_rules() {
	add_rewrite_tag('%lesson%', '([^/]+)', 'lesson=');
	add_permastruct('lesson', '/lesson/%course%/%lesson%', false);
	add_rewrite_rule('^lesson/([^/]+)/([^/]+)/?','index.php?lesson=$matches[2]','top');
}
add_action( 'init', 'my_add_rewrite_rules' );

// Set permalink for Lessons
function my_permalinks($permalink, $post, $leavename) {
	$post_id = $post->ID;
	if($post->post_type != 'lesson' || empty($permalink) || in_array($post->post_status, array('draft', 'pending', 'auto-draft')))
	 	return $permalink;

	$parent = $post->post_parent;
	$parent_post = get_post( $parent );

	$permalink = str_replace('%course%', $parent_post->post_name, $permalink);

	return $permalink;
}
add_filter('post_type_link', 'my_permalinks', 10, 3);

parent-meta-box.php

<?php
function my_add_meta_boxes() {
	add_meta_box( 'lesson-parent', 'Course', 'lesson_attributes_meta_box', 'lesson', 'side', 'high' );
}
add_action( 'add_meta_boxes', 'my_add_meta_boxes' );

function lesson_attributes_meta_box( $post ) {
	$post_type_object = get_post_type_object( $post->post_type );
	$pages = wp_dropdown_pages( array( 'post_type' => 'course', 'selected' => $post->post_parent, 'name' => 'parent_id', 'show_option_none' => __( '(no parent)' ), 'sort_column'=> 'menu_order, post_title', 'echo' => 0 ) );
	if ( ! empty( $pages ) ) {
		echo $pages;
	}
}

permalink.php

<?php
function my_permalinks($permalink, $post, $leavename) {
	$post_id = $post->ID;
	if($post->post_type != 'lesson' || empty($permalink) || in_array($post->post_status, array('draft', 'pending', 'auto-draft')))
	 	return $permalink;

	$parent = $post->post_parent;
	$parent_post = get_post( $parent );

	$permalink = str_replace('%course%', $parent_post->post_name, $permalink);

	return $permalink;
}
add_filter('post_type_link', 'my_permalinks', 10, 3);

register-cpt.php

<?php
// Register Custom Post Types
function my_register_cpt() {
	$labels = array(
		'name'                  => _x( 'Courses', 'Post Type General Name', '1fix' ),
		'singular_name'         => _x( 'Course', 'Post Type Singular Name', '1fix' ),
		'menu_name'             => __( 'Courses', '1fix' ),
		'name_admin_bar'        => __( 'Courses', '1fix' )
	);
	$args = array(
		'label'                 => __( 'Course', '1fix' ),
		'labels'                => $labels,
		'hierarchical'          => true,
		'public'                => true
	);
	register_post_type( 'course', $args );
	$labels = array(
		'name'                  => _x( 'Lessons', 'Post Type General Name', '1fix' ),
		'singular_name'         => _x( 'Lesson', 'Post Type Singular Name', '1fix' ),
		'menu_name'             => __( 'Lessons', '1fix' ),
		'name_admin_bar'        => __( 'Lessons', '1fix' )
	);
	$args = array(
		'label'                 => __( 'Lesson', '1fix' ),
		'labels'                => $labels,
		'hierarchical'          => false,
		'public'                => true
	);
	register_post_type( 'lesson', $args );
}
add_action( 'init', 'my_register_cpt' );

url-structure.php

<?php
function my_add_rewrite_rules() {
	add_rewrite_tag('%lesson%', '([^/]+)', 'lesson=');
	add_permastruct('lesson', '/lesson/%course%/%lesson%', false);
	add_rewrite_rule('^lesson/([^/]+)/([^/]+)/?','index.php?lesson=$matches[2]','top');
}
add_action( 'init', 'my_add_rewrite_rules' );