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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.

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NDMS-1460

Background

Logical model

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

API structure

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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.

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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",

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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)

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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.

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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.

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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)

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Patient Status: Key Actions

Deactivating a patient

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

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

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Patient

Request

POST /sample-message/patient

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