Bookmark.php

<?php
namespace App\Model\Entity;

use Cake\ORM\Entity;

/**
 * Bookmark Entity.
 */
class Bookmark extends Entity
{

    /**
     * Fields that can be mass assigned using newEntity() or patchEntity().
     *
     * @var array
     */
    protected $_accessible = [
        'user_id' => true,
        'title' => true,
        'description' => true,
        'url' => true,
        'user' => true,
        'tags' => true,
        'starred_tags' => true,
        'secondary_tags' => true,
    ];
}

BookmarksTable.php

<?php
namespace App\Model\Table;

use Cake\ORM\Query;
use Cake\ORM\Table;
use Cake\ORM\RulesChecker;
use Cake\Validation\Validator;

/**
 * Bookmarks Model
 */
class BookmarksTable extends Table
{

    /**
     * Initialize method
     *
     * @param array $config The configuration for the Table.
     * @return void
     */
    public function initialize(array $config)
    {
        $this->table('bookmarks');
        $this->displayField('title');
        $this->primaryKey('id');
        $this->addBehavior('Timestamp');

        $this->belongsTo('Users', [
            'foreignKey' => 'user_id',
        ]);
        $this->belongsToMany('Tags', [
            'through' => 'BookmarksTags',
        ]);
        $this->belongsToMany('StarredTags', [
            'className' => 'Tags',
            'targetForeignKey' => 'tag_id',
            'through' => 'BookmarksTags',
            'conditions' => ['BookmarksTags.starred']
        ]);
        $this->belongsToMany('SecondaryTags', [
            'className' => 'Tags',
            'targetForeignKey' => 'tag_id',
            'through' => 'BookmarksTags',
            'conditions' => ['BookmarksTags.starred' => false]
        ]);
    }
}

BugShell.php

<?php
namespace App\Shell;

use Cake\Console\Shell;
use Cake\ORM\TableRegistry;

class BugShell extends Shell
{
    public function main()
    {
        $id = 50;
        $bookmarks = TableRegistry::get('Bookmarks');

        $bookmark = $bookmarks->get($id);
        $data = [
            'starred_tags' => [
                ['id' => 1, '_joinData' => ['starred' => 1]],
                ['id' => 2, '_joinData' => ['starred' => 1]],
                ['id' => 3, '_joinData' => ['starred' => 1]],
            ]
        ];
        $bookmarks->patchEntity($bookmark, $data);
        $bookmarks->save($bookmark);

        $bookmark = $bookmarks->get($id);
        $data = [
            'starred_tags' => [
                ['id' => 1, '_joinData' => ['starred' => 1]]
            ]
        ];
        $bookmarks->patchEntity($bookmark, $data);
        $bookmarks->save($bookmark);
    }
}

queries.log

2015-12-23 03:08:25 Debug: SELECT `Bookmarks`.`id` AS `Bookmarks__id`, `Bookmarks`.`user_id` AS `Bookmarks__user_id`, `Bookmarks`.`title` AS `Bookmarks__title`, `Bookmarks`.`description` AS `Bookmarks__description`, `Bookmarks`.`url` AS `Bookmarks__url`, `Bookmarks`.`created` AS `Bookmarks__created`, `Bookmarks`.`updated` AS `Bookmarks__updated`, `Bookmarks`.`starred` AS `Bookmarks__starred` FROM `bookmarks` `Bookmarks` WHERE `Bookmarks`.`id` = 50 LIMIT 1
2015-12-23 03:08:25 Debug: SELECT `StarredTags`.`id` AS `StarredTags__id`, `StarredTags`.`title` AS `StarredTags__title`, `StarredTags`.`created` AS `StarredTags__created`, `StarredTags`.`updated` AS `StarredTags__updated` FROM `tags` `StarredTags` WHERE (`StarredTags`.`id` = 1 OR `StarredTags`.`id` = 2 OR `StarredTags`.`id` = 3)
2015-12-23 03:08:25 Debug: BEGIN
2015-12-23 03:08:25 Debug: SELECT `BookmarksTags`.`bookmark_id` AS `BookmarksTags__bookmark_id`, `BookmarksTags`.`tag_id` AS `BookmarksTags__tag_id`, `BookmarksTags`.`starred` AS `BookmarksTags__starred`, `StarredTags`.`id` AS `StarredTags__id`, `StarredTags`.`title` AS `StarredTags__title`, `StarredTags`.`created` AS `StarredTags__created`, `StarredTags`.`updated` AS `StarredTags__updated` FROM `bookmarks_tags` `BookmarksTags` LEFT JOIN `tags` `StarredTags` ON `StarredTags`.`id` = (`BookmarksTags`.`tag_id`) WHERE (`bookmark_id` = 50 AND BookmarksTags.starred)
2015-12-23 03:08:25 Debug: DELETE FROM `bookmarks_tags` WHERE (`bookmark_id` = 50 AND `tag_id` = 1)
2015-12-23 03:08:25 Debug: DELETE FROM `bookmarks_tags` WHERE (`bookmark_id` = 50 AND `tag_id` = 2)
2015-12-23 03:08:25 Debug: DELETE FROM `bookmarks_tags` WHERE (`bookmark_id` = 50 AND `tag_id` = 3)
2015-12-23 03:08:25 Debug: SELECT 1 AS `existing` FROM `bookmarks_tags` `BookmarksTags` WHERE (`BookmarksTags`.`bookmark_id` = 50 AND `BookmarksTags`.`tag_id` = 1) LIMIT 1
2015-12-23 03:08:25 Debug: INSERT INTO `bookmarks_tags` (`bookmark_id`, `tag_id`, `starred`) VALUES (50, 1, 1)
2015-12-23 03:08:25 Debug: SELECT 1 AS `existing` FROM `bookmarks_tags` `BookmarksTags` WHERE (`BookmarksTags`.`bookmark_id` = 50 AND `BookmarksTags`.`tag_id` = 2) LIMIT 1
2015-12-23 03:08:25 Debug: INSERT INTO `bookmarks_tags` (`bookmark_id`, `tag_id`, `starred`) VALUES (50, 2, 1)
2015-12-23 03:08:25 Debug: SELECT 1 AS `existing` FROM `bookmarks_tags` `BookmarksTags` WHERE (`BookmarksTags`.`bookmark_id` = 50 AND `BookmarksTags`.`tag_id` = 3) LIMIT 1
2015-12-23 03:08:25 Debug: INSERT INTO `bookmarks_tags` (`bookmark_id`, `tag_id`, `starred`) VALUES (50, 3, 1)
2015-12-23 03:08:25 Debug: COMMIT
2015-12-23 03:08:25 Debug: SELECT `Bookmarks`.`id` AS `Bookmarks__id`, `Bookmarks`.`user_id` AS `Bookmarks__user_id`, `Bookmarks`.`title` AS `Bookmarks__title`, `Bookmarks`.`description` AS `Bookmarks__description`, `Bookmarks`.`url` AS `Bookmarks__url`, `Bookmarks`.`created` AS `Bookmarks__created`, `Bookmarks`.`updated` AS `Bookmarks__updated`, `Bookmarks`.`starred` AS `Bookmarks__starred` FROM `bookmarks` `Bookmarks` WHERE `Bookmarks`.`id` = 50 LIMIT 1
2015-12-23 03:08:25 Debug: SELECT `StarredTags`.`id` AS `StarredTags__id`, `StarredTags`.`title` AS `StarredTags__title`, `StarredTags`.`created` AS `StarredTags__created`, `StarredTags`.`updated` AS `StarredTags__updated` FROM `tags` `StarredTags` WHERE `StarredTags`.`id` = 1
2015-12-23 03:08:25 Debug: BEGIN
2015-12-23 03:08:25 Debug: SELECT `BookmarksTags`.`bookmark_id` AS `BookmarksTags__bookmark_id`, `BookmarksTags`.`tag_id` AS `BookmarksTags__tag_id`, `BookmarksTags`.`starred` AS `BookmarksTags__starred`, `StarredTags`.`id` AS `StarredTags__id`, `StarredTags`.`title` AS `StarredTags__title`, `StarredTags`.`created` AS `StarredTags__created`, `StarredTags`.`updated` AS `StarredTags__updated` FROM `bookmarks_tags` `BookmarksTags` LEFT JOIN `tags` `StarredTags` ON `StarredTags`.`id` = (`BookmarksTags`.`tag_id`) WHERE (`bookmark_id` = 50 AND BookmarksTags.starred)
2015-12-23 03:08:25 Debug: DELETE FROM `bookmarks_tags` WHERE (`bookmark_id` = 50 AND `tag_id` = 1)
2015-12-23 03:08:25 Debug: DELETE FROM `bookmarks_tags` WHERE (`bookmark_id` = 50 AND `tag_id` = 2)
2015-12-23 03:08:25 Debug: DELETE FROM `bookmarks_tags` WHERE (`bookmark_id` = 50 AND `tag_id` = 3)
2015-12-23 03:08:25 Debug: SELECT 1 AS `existing` FROM `bookmarks_tags` `BookmarksTags` WHERE (`BookmarksTags`.`bookmark_id` = 50 AND `BookmarksTags`.`tag_id` = 1) LIMIT 1
2015-12-23 03:08:25 Debug: INSERT INTO `bookmarks_tags` (`bookmark_id`, `tag_id`, `starred`) VALUES (50, 1, 1)
2015-12-23 03:08:25 Debug: COMMIT

schema.sql

CREATE TABLE `bookmarks` (
  `id` int(11) NOT NULL AUTO_INCREMENT,
  `user_id` int(11) NOT NULL,
  `title` varchar(50) DEFAULT NULL,
  `description` text,
  `url` text,
  `created` datetime DEFAULT NULL,
  `updated` datetime DEFAULT NULL,
  PRIMARY KEY (`id`)
);
CREATE TABLE `tags` (
  `id` int(11) NOT NULL AUTO_INCREMENT,
  `title` varchar(255) DEFAULT NULL,
  `created` datetime DEFAULT NULL,
  `updated` datetime DEFAULT NULL,
  PRIMARY KEY (`id`),
  UNIQUE KEY `title` (`title`)
);
CREATE TABLE `bookmarks_tags` (
  `bookmark_id` int(11) NOT NULL,
  `tag_id` int(11) NOT NULL,
  `starred` tinyint(1) DEFAULT '0',
  PRIMARY KEY (`bookmark_id`,`tag_id`),
  KEY `tag_idx` (`tag_id`,`bookmark_id`),
  CONSTRAINT `bookmarks_tags_ibfk_1` FOREIGN KEY (`tag_id`) REFERENCES `tags` (`id`),
  CONSTRAINT `bookmarks_tags_ibfk_2` FOREIGN KEY (`bookmark_id`) REFERENCES `bookmarks` (`id`)
);