Project Structure

Core Repos

• https://github.com/renalreg/ukrdc-fastapi

  • API interface to data

  • Python, FastAPI, Pydantic

• https://github.com/renalreg/ukrdc-nuxt-3

  • Frontend client app

  • Nuxt 3 (Vue.js), Typescript, NuxtUI, Tailwind

• https://github.com/renalreg/ukrdc-compose

  • Reference Docker Compose for deployment

Auxiliary repos

• https://github.com/renalreg/python-mirth-client

  • Async client for Mirth API

• https://github.com/renalreg/ukrdc-sqla

  • Minimal SQLAlchemy models for the UKRDC

Auth management

• https://

  renalregistry-admin

  sso.

  okta

  ukkidney.

  com

  org/admin/dashboard

  • Non-admins can manage accounts at https://

    renalregistry

    sso.

    okta

    ukkidney.

    com

    org

Issue trackers

• https://jira.ukrdc.org/projects/UI/summary

  • Project-wide issue trackers

Sentry

• https://sentry.io/organizations/uk-renal-registry/projects/

  • Request access

UKRDC-FastAPI

...

Pydantic and Type Hints

• Familiar with MyPy and Python type-hints?

• Our data goes through 2 “conversions”:

  • SQLAlchemy ORM turns database rows into Python objects

  • Pydantic (via FastAPI response_model) turns Python objects into JSON

UKRDC-Nuxt

• See ARCHITECTURE.md

TypeScript

...

• Initially it often just looks like a source of frustration, but it does a tonne of good for catching errors early on

• Interfaces are roughly equivalent to Pydantic models. They give the expected fields and types for objects (JS dictionaries)

Tailwind

• One of the most divisive web dev libraries I’ve ever come across

• I’ve found it excellent for rapidly developing new components

• We abstract a lot of styling away at the component level

  • E.g. we have a “TextH1” component which acts a lot like html “h1” but with extra styling

  • This means we can easily bulk-change styles across the whole application without a web of CSS files

Docker-Compose

• We use Docker images to deploy the applications

  • I’m assuming everyone is familiar with Docker but if not let me know and I’ll run through why we use it

• Docker images can have tags, so we use these to separate environments (dev, staging, production etc)

• Our Docker-Compose file pulls and configures all images required to run the whole stack

• Runtime configuration is handled by .env files or environment variables

Devops Flow

Branches

• Main

  main

  • Current "snapshot" branch

  • Code here should be as stable as possible

  • Code should not be committed directly

  • Base for feature/fix branches

• Feature branches

  • When working on a specific feature/fix, create a new branch for that work item 

  • Either submit a PR when ready, or create a draft PR whenever

  • PRs should pass all tests and code-quality checks before merging

  • PRs should be reviewed by someone else on the project before merging

GitHub Actions

• All testing and build automation is handled by GitHub Actions

• If you’ve used Bamboo it’s the same thing but with a sensible configuration system

• Example config file:

  • https://github.com/renalreg/ukrdc-fastapi/blob/main/.github/workflows/main.yml

How to deploy a new release

Build and publish Docker images

This guide is broadly applicable to both "ukrdc-fastapi" and "ukrdc-nuxt"

• Create a new GitHub Release, or push a tag

• The tag and release should be named as the approximate release datetime, in the format YYYY-MM-DD-HHMME.g. 2021-11-22-1410 for a release made on November 22nd 2021 at 14:10

  See https://github.com/renalreg/ukrdc-nuxt#github-release-versions and https://github.com/renalreg/ukrdc-fastapi#github-release-versions

• A docker image will be published with 2 tags, the version number, and 'latest'

Update containers on the app server

• Once the image has been published, connect to the app server via SSH
• Run:

• cd /srv/ukrdc-compose

• docker-compose pull 

• docker-compose down

• docker-compose up -d

• Ideally also run

• docker system prune

• You can view real-time logs from the entire stack with:

• docker-compose log -f

• See /wiki/spaces/SI/pages/2249424968

Reverting/redeploying an old version

• Modify your docker-compose file, and instead of pointing to the image tag 'latest', point to a specific version tag.

Active Instances

...

/wiki/spaces/SI/pages/2441183233

ukrdc-app-staging_7 - Systems Infrastructure - Confluence (atlassian.net)