Jack Smith jacksmith15

Django Update Summary

PR-343 Migrates a large part of the Genomic Record codebase to use [Django] and [Django REST Framework]. Both of these frameworks are well-documented, and it is recommended that developers take some time to familiarise themselves.

This migration also changes the directory structure of the project, and it is recommended that developers take a fresh git clone the respository.

The project continues to use the SQLAlchemy ORM, and so a few helpers have been implemented to simplify the integration between [Django Rest Framework] and SQLAlchemy ORM.

`app.base.views.BaseAlchemyViewSet`

BaseAlchemyViewSet is a subclass of rest_framework.viewsets.ViewSet, designed to provide sensible default behaviour for SQLAlchemy models as resources.

NDMS-1460

Background

Logical model

Each referral may have one responsible_clinician
Each referral may have many additional_clinicians

API structure

Questions

What to do if a JWT is not supplied:

Kong currently enforces JWTs in higher environments
In lower environments we rely on the ability to send requests without JWTs for integration testing.
- This applies to latest and release2.
- It would be a non-trivial amount of work to overhaul this system (but not out of the question).
In all environments we rely on the ability to send requests between services without JWTS.
- Currently this only includes GET requests (i.e. not editing a referral).

In future it may be required that LIMS systems will send requests to edit a referral via this method, but not for beta.

Referral Status API

Handle status transition logic as state in GET

GET /referral/{id}/status

{
    "data": {
        "id": "2b074729-376b-4dfa-963c-39ddbc6a2a2c",
        "code": "draft",
        "display": "Draft",

Clinician change summary

Summary of changes to DDF payload triggered by data model change

Before

Clinicians are found as an array of referral_clinicians, under an attribute with the same name.
Each referral_clinician contains:
- a clinician (see below)
- an organisation_uid reference
- a referral_clinician_role_uid reference (always null)
a referral_uid reference (always the same as the outer referral)

Unique NHS Number

How to enforce at the data model layer whilst being compatible with cohorts?
1. Currently sits in generic identifier table - this is hard to constrain at the model layer.
2. Could be an attribute on the table - easier to constrain but NHS-specific. Would need to split NHS specific fields using inheritance.
How to enforce at the API layer?
- If (1) above then would need to do an explicit lookup in the serializer to check uniqueness.
- If (2) above then can use standard handling.
How to communicate correct error to UI?
- This should be a 400 - will need an extra message or code to distinguish.

Overview

This document provides some JSON examples to aid with re-integration of consumers to breaking API changes for patient records brought about by NDMS-1984.

Included are happy path before/after examples for common cases:

With and without NHS Number
Read and write payloads
With and without explicit reason for missing NHS Number

as well as some canonical invalid payloads.

Patient Status: Key Actions

Deactivating a patient

Display the available reason concepts for the user to select GET /codes-search/patient_deactivation_reason

{
  "total": 2,
  "limit": 10,
  "offset": 0,

Patient

Request

POST /sample-message/patient

{
  "query": {
    "human_readable_id": [
      "p10001400859"

	from collections import namedtuple

	class ImmutableNamespaceMeta(type):
	def __new__(cls, name, bases, dct):
	x = super().__new__(cls, name, bases, dct)
	public = {key: value for key, value in dct.items() if not key.startswith("_")}
	typ_ = namedtuple(name + "Type", public.keys())
	return typ_(**public)