Controller.php

<?php
class FooController {
    public function __construct(FooService $foo) {
        $this->foo = $foo;
    }
    
    public function indexAction() {
        return new ViewModel([
            'data' => $foo->listStuff();
        ]);
    }
}

FooService.php

<?php
class FooService {
    __construct(ObjectRepository $er) {
        $this->er = $er;
    }

    public function listStuff() {
        return $this->er->findAll();
    }
}

FooServiceFactory.php

class FooServiceFactory {
    public function createService($sl) {
        return new FooService(
            $sl->get('Doctrine\ORM\EntityManager')->getRepository('My\Entity\Foo')
        );
    }
}