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Editing: premium-orphaned-post-query.php

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<?php
/**
 * WPSEO Premium plugin file.
 *
 * @package WPSEO\Premium\Classes
 */

use Yoast\WP\SEO\Repositories\Indexable_Repository;

/**
 * Represents the orphaned post query methods.
 */
class WPSEO_Premium_Orphaned_Post_Query {

/**
	 * Returns the total number of orphaned items for the given post types.
	 *
	 * @param array $post_types The post types to get the counts for.
	 *
	 * @return int[] The counts for all post types.
	 */
	public static function get_counts( array $post_types ) {
		global $wpdb;

$post_type_counts = array_fill_keys( $post_types, 0 );
		$subquery         = self::get_orphaned_content_query();

$results = $wpdb->get_results(
			$wpdb->prepare(
				"SELECT COUNT( ID ) as total_orphaned, post_type
					FROM {$wpdb->posts}
					WHERE
						ID IN ( " . $subquery . " )
						AND post_status = 'publish'
						AND post_type IN ( " . implode( ',', array_fill( 0, count( $post_types ), '%s' ) ) . ' )
					GROUP BY post_type',
				$post_types
			)
		);

foreach ( $results as $result ) {
			$post_type_counts[ $result->post_type ] = (int) $result->total_orphaned;
		}

return $post_type_counts;
	}

/**
	 * Returns a query to retrieve the object ids from the records with an incoming link count of 0.
	 *
	 * @return string Query for get all objects with an incoming link count of 0 from the DB.
	 */
	public static function get_orphaned_content_query() {
		static $query;

if ( $query === null ) {
			$repository = YoastSEO()->classes->get( Indexable_Repository::class );
			$query      = $repository->query()
				->select( 'object_id' )
				->where( 'object_type', 'post' )
				->where_any_is(
					[
						[ 'incoming_link_count' => 0 ],
						[ 'incoming_link_count' => null ],
					]
				);

$frontpage_id = self::get_frontpage_id();
			if ( $frontpage_id ) {
				$query = $query->where_not_equal( 'object_id', $frontpage_id );
			}

$query = sprintf( $query->get_sql(), '\'post\'', 0, $frontpage_id );
		}

return $query;
	}

/**
	 * Returns all the object ids from the records with an incoming link count of 0.
	 *
	 * @return array Array with the object ids.
	 */
	public static function get_orphaned_object_ids() {
		$repository = YoastSEO()->classes->get( Indexable_Repository::class );
		$results    = $repository->query()
			->select( 'object_id' )
			->where( 'object_type', 'post' )
			->where( 'incoming_link_count', 0 )
			->find_array();

$object_ids = wp_list_pluck( $results, 'object_id' );
		$object_ids = self::remove_frontpage_id( $object_ids );

return $object_ids;
	}

/**
	 * Removes the frontpage id from orphaned id's when the frontpage is a static page.
	 *
	 * @param array $object_ids The orphaned object ids.
	 *
	 * @return array The orphaned object ids, without frontpage id.
	 */
	protected static function remove_frontpage_id( $object_ids ) {
		// When the frontpage is a static page, remove it from the object ids.
		if ( get_option( 'show_on_front' ) !== 'page' ) {
			return $object_ids;
		}

$frontpage_id = get_option( 'page_on_front' );

// If the frontpage ID exists in the list, remove it.
		$object_id_key = array_search( $frontpage_id, $object_ids, true );
		if ( $object_id_key !== false ) {
			unset( $object_ids[ $object_id_key ] );
		}

return $object_ids;
	}

/**
	 * Retrieves the frontpage id when set, otherwise null.
	 *
	 * @return int|null The frontpage id when set.
	 */
	protected static function get_frontpage_id() {
		if ( get_option( 'show_on_front' ) !== 'page' ) {
			return null;
		}

$page_on_front = get_option( 'page_on_front', null );
		if ( empty( $page_on_front ) ) {
			return null;
		}

return (int) $page_on_front;
	}
}

Editing: premium-orphaned-post-query.php

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