MODELS ---------------------------------------
models/user.php
<?php
class User extends Doctrine_Record {

	public function setTableDefinition() {
		// this contains the table definition
		$this->hasColumn('username', 'string', 255, array('unique' => 'true'));
		$this->hasColumn('password', 'string', 255);
		$this->hasColumn('karma', 'integer', 4);
		$this->hasColumn('ratings', 'array', 1000);
	}

	public function setUp() {
		// this contains additional methods
		$this->setTableName('user');
		/* adds 2 fields to the table and manages them. They are called created_at and updated_at. */
		$this->actAs('Timestampable');
		$this->hasMutator('password', '_encrypt_password');

		// a User has many Resource
		$this->hasMany('Resource', array(
			'local' => 'id',
			'foreign' => 'resource_id'
		));

		// relation a user hasOne Profile User->Profile
		$this->hasOne('Profile', array(
			'local' => 'id',
			'foreign' => 'user_id'
			));
	}

	protected function _encrypt_password($value) {
		$salt = '#*seCrEt!@-*%';
		$this->_set('password', md5($salt . $value));
	}
}

models/resource.php
<?php
class Resource extends Doctrine_Record {

	public function setTableDefinition() {
		$this->hasColumn('resource_id', 'integer',4); // foreign key for user->resource relation
		$this->hasColumn('user_id', 'integer',4);
		$this->hasColumn('name', 'string', 255, array('unique' => 'true'));
		$this->hasColumn('url', 'string', 255);
		$this->hasColumn('description', 'string', 255);
		$this->hasColumn('karma', 'integer', 4);
		$this->hasColumn('ratings','array', 1000);

	}

	public function setUp() {
		// this contains additional methods
		$this->setTableName('resource');
		/* adds 2 fields to the table and manages them. They are called created_at and updated_at. */
		$this->actAs('Timestampable');

		// relation for resources->user
		$this->hasOne('User', array(
			'local' => 'resource_id',
			'foreign' => 'id'
		));

		//relation for resource->comments a resource has many comments
		$this->hasMany('Comment',array(
			'local' => 'id',
			'foreign' => 'comment_id'
		));

		//relation for resource->file
		$this->hasMany('File',array(
			'local' => 'id',
			'foreign' => 'file_id'
		));

	}
}


models/profile.php
<?php
class Profile extends Doctrine_Record {
	public function setTableDefinition() {
		$this->hasColumn('user_id', 'integer',array('unique' => 'true')); // foreign key for user->profile relation
		$this->hasColumn('title', 'string', 50);
		$this->hasColumn('first_name', 'string', 50);
		$this->hasColumn('last_name', 'string', 50);
		$this->hasColumn('town', 'string', 50);
		$this->hasColumn('country', 'string', 50);
		$this->hasColumn('email', 'string', 255, array('unique' => 'true'));
		$this->hasColumn('phone', 'integer', 20);
		$this->hasColumn('office', 'string', 100);
		$this->hasColumn('webpage', 'string', 100);

		$this->hasColumn('fields_of_research', 'string', 30);
		$this->hasColumn('research_summary', 'string',50);
		$this->hasColumn('institution', 'string', 50);
		$this->hasColumn('publications', 'string', 550);

	}

	public function setUp() {
		$this->setTableName('profile');
		$this->actAs('Timestampable');

		// a Profile has one User
		$this->hasOne('User', array(
			'local' => 'user_id',
			'foreign' => 'id'
			));
	}
}
models/file.php
<?php
class File extends Doctrine_Record {

	public function setTableDefinition() {
		$this->hasColumn('name', 'string', 255, array('unique' => 'true'));
		$this->hasColumn('url', 'string', 255);
		$this->hasColumn('type', 'string',255);
	}

	public function setUp() {
		// this contains additional methods
		$this->setTableName('file');
		/* adds 2 fields to the table and manages them. They are called created_at and updated_at. */
		$this->actAs('Timestampable');

		// relations
		$this->hasOne('User', array(
			'local' => 'user_id',
			'foreign' => 'id'
		));

		// relation for file->resources
		$this->hasOne('Resource',array(
			'local' => 'file_id',
			'foreign' => 'id'
		));


		$this->hasMany('Tag', array(
            'local' => 'resource_id',
            'foreign' => 'tag_id',
            'refClass' => 'ResourceTag'
                ));
	}
}
models/comment.php
<?php
class Comment extends Doctrine_Record {

	public function setTableDefinition() {
		$this->hasColumn('comment_id', 'integer',4); // foreign key for resource->comment relation
		$this->hasColumn('text', 'string', 255);
	}

	public function setUp() {
		// this contains additional methods
		$this->setTableName('comment');
		/* adds 2 fields to the table and manages them. They are called created_at and updated_at. */
		$this->actAs('Timestampable');

		// relation for resources->user, a resource has one user
		$this->hasOne('Resource',array(
			'local' => 'comment_id',
			'foreign' => 'id'
			));

			// relation for comment->subcomment
			$this->hasMany('Subcomment',array(
			'local' => 'id',
			'foreign' => 'subcomment_id'
			));
	}
}

models/subcomment.php
<?php
class Subcomment extends Doctrine_Record {

	public function setTableDefinition() {
		$this->hasColumn('subcomment_id', 'integer',4);
		$this->hasColumn('text', 'string', 255);
	}

	public function setUp() {
		// this contains additional methods
		$this->setTableName('subcomment');
		/* adds 2 fields to the table and manages them. They are called created_at and updated_at. */
		$this->actAs('Timestampable');

		// relation for subcomment->comment
		$this->hasOne('Comment', array(
			'local' => 'subcomment_id',
			'foreign' => 'id'
		));
	}
}

and I also have a php5 class in the same directory
models/current_user.php
<?php
class Current_User {
    /** Returns the User object for the logged in user. */
    private static $user;

    private function __construct() {

    }

    /** returns the private $user variable */
    public static function user() {

        if(!isset(self::$user)) {
            // we use the $CI object to load the session library because this is a static class.
            $CI =& get_instance();

            if (!$user_id = $CI->session->userdata('user_id')) {
                return FALSE;
            }

            if (!$u = Doctrine::getTable('User')->find($user_id)) {
                return FALSE;
            }

            self::$user = $u;
        }
        return self::$user;
    }

    /** returns the id of the current logged in user */
    public static function get_user_id() {
        $CI =& get_instance();
        $user_id = $CI->session->userdata('user_id');
        return $user_id;
    }

    public static function get_username() {
        return self::user()->username;
    }

    public static function login($username, $password) {

        // get User object by username
        if ($u = Doctrine::getTable('User')->findOneByUsername($username)) {

            // this mutates (encrypts) the input password
            $u_input = new User();
            $u_input->password = $password;

            // password match (comparing encrypted passwords)
            if ($u->password == $u_input->password) {
                unset($u_input);

                $CI =& get_instance();
                $CI->load->library('session');
                $CI->session->set_userdata('user_id',$u->id);
                self::$user = $u;

                return TRUE;
            }

            unset($u_input);
        }

        // login failed
        return FALSE;

    }

    public function __clone() {
        trigger_error('Clone is not allowed.', E_USER_ERROR);
    }

}