Saving data from form with multiple objects

okay. So the problem is the following:

Patient is an independent entity, which is good. It has two associations, one with each PatientSample and PatientOrder. PatientSample and PatientOrder also have an association

Your form creates a new PatientOrder, that is automatically associated with the Patient, since PatientOrder is the owning side of that association, and also automatically persisted, due to the cascade="PERSIST" in the mapping.

PatientOrder also is automatically associated with the PatientSample, which you probably marked as cascade persisted as well. However, the patient property/association of the PatientSample is not automatically set, as far as I can see. That is at least a problem, if not the problem. - This luckily is a small problem, since it only creates a triangle in your dependency graph, however - since Patient is independent, it doesn't create a cycle (that would be a big problem). However, your form isn't easily capable of setting those kinds of dependencies, especially since they're not obvious. Technically, the sample could belong to another patient... (see validation comment at the end of answer)

the easy solution: set it explicitly

There are probably several solutions, the easiest, but not the best:

    if($form->isSubmitted() && $form->isValid()){

        $patientOrder = $form->getData();
        // NEW! However, I don't know if this violates the Law of Demeter:
        $patientOrder->getSample()->setPatient($patientOrder->getPatient());

        $entityManager = $this->getDoctrine()->getManager();
        $entityManager->persist($patientOrder);
        $entityManager->flush();

        return $this->redirectToRoute('patient_order_index');
    }

the cleaner way would be to do this somewhere in a form event though...

adding a form event handler (instead)

you should adapt the PatientOrderType code to something like this:

// be aware you need to set the following use clauses:
// use Symfony\Component\Form\FormEvent;
// use Symfony\Component\Form\FormEvents;

$builder
   // ...
   ->addEventListener(FormEvents::POST_SUBMIT, function(FormEvent $event) {
         $patientOrder = $event->getData(); // view data, i.e. your objects
         $patientSample = $patientOrder->getPatientSample();
         if(!$patientSample->getPatient()) { 
             $patientSample->setPatient($patientOrder->getPatient());
         }
   })
;

This approach is somewhat tame. You could potentially also throw an exception if $patientSample already has a different Patient assigned (a form can be pre-filled/pre-set with entities). However, this approach will set a missing patient, which avoids the form leaving a PatientSample without a Patient.

why do this in a form event instead of directly setting it in the controller? because this way the form type is reusable without remembering "oh, i have to explicitly set the person on the PersonSample with this form type".

bonus: adding validation

for validating that a patient sample belongs to a patient order for the same patient, you could add the following Expression constraint on the PatientOrder (the entity, not the form type):

use Symfony\Component\Validator\Constraints as Assert;

/**
 * @ORM\Entity(...)
 * @Assert\Expression("this.getPatientSample().getPatient() == this.getPatient()",
      message="PatientOrder's patient must be PatientSample's patient")
 */
class PatientOrder {...}

or a callback constraint and essentially do the same ... actually it feels weird to write code in an annotation (IDEs on average won't be of much help)

update: mixed up patient order and patient sample in validation part