teodortymon/nbis_bioinformatics_assignment

National Bioinformatic Institute of Sweden assigment: relay server with a cache

Table of Contents

• Relay server
  • Live versions
  • Code structure
  • Endpoints
  • Docker containers
  • Running
  • Testing
• CLI
• Extra tasks & rationales
  • Cache
  • Multi threading
  • Load tests

Quick overview

To spin up the relay server, redis cache and redis insights:

git clone git@github.com:NBISweden/devops-umu-teodortymon.git
cd devops-umu-teodortymon
make run-dev

Then open http://localhost:80/docs to access the api documentation.

Relay server

Relay server is based on FastAPI.

Rationale

• Since operations will be mostly I/O bound, leveraging asyncronity could provide a siginificant speedup compared to a standard WSGI (ex. Flask). (Benchmarks)

• Great documentation that hints at a nice level of conventions and sensible defaults, but also a possibility to dig deeper in the stack by directly calling the underlying Starlette.

• Auto generated interactive api schema documentation can be accessed at thanks to Swagger UI

• Since this assignment is at its' core quite straightforward, I though it would be a great opportunity to try something new and hyped by the Python community.

Live versions

• Server can be accessed at a small GoogleCloudEngine instance at: http://34.67.173.3
• API schema docs at: http://34.67.173.3/docs
• Redis insights at: http://34.67.173.3:8001

Code structure

.
├── Dockerfile              -> Used to create the relay image
├── README.md
├── app
│   ├── __init__.py
│   ├── main.py             -> Server entrypoint code
│   └── models.py           -> Used for validating data and creating API docs
├── cli
│   ├── __init__.py
│   ├── error_msgs.py
│   ├── main.py             -> Typer App with bells & whistles
│   ├── requirements.txt
│   └── simple_lunch.sh     -> Maximizes OS compability without dependencies
├── config.yml              -> Holds URL, PATHs and cache TTL configs
├── docker-compose-dev.yml  -> Live reload with mounted local volume
├── docker-compose.yml      -> Production ready with auto thread scaling
├── makefile                -> Holds useful container management macros
├── requirements.txt
└── tests
    ├── __init__.py
    ├── app
    │   ├── __init__.py
    │   └── test_main.py
    ├── cli
    │   ├── __init__.py
    │   └── test_main.py
    ├── locustfile.py
    └── test_constants.py

Endpoints

There are three endpoints:

1. /relay_anything/{query} which accepts any type of path string and relays the response from the menu.dckube server. It is the simplest implemementation in 10 lines of code and it satisfies the assignment requirements (although for simiplicity I opted for always returning responses in a "text" format)

As a warm up & exercise in using type hints, type validations and Pydantic two other endpoints were implemented. There's a considerate amount of code overhead for such a small project and in a production scenario for a simple relay option 1. would be completely sufficient.

2. /restaurant which lists all the available restaurants
3. /restaurant/{restaurant_id} which lists queried restaurants menu & detailed information

Code is formatted by black & statically type checked by mypy.

Docker containers

Docker compose is used to orchestrate the:

• relay server as relay on :80
• redis cache as redis on :6379
• redis insights as redis-insights on :8001 for easy cache monitoring

Running

There is a makefile that contains commands for interacting with the server.

run-prod: ## Run containers with worker count optimized to available CPUs
	docker compose up

run-dev: ## Run containers in development mode with code reloading and /app volume mounted in local workspace for active development
	docker compose -f docker-compose-dev.yml up

test: ## Run mypy & pytests. Spin up all the containers in dev mode first as integration tests rely on redis cache and local test files
	docker compose exec web pytest
	docker compose exec web mypy */*.py

shell: ## Atttach a bash shell to the relay container
	docker exec -it relay /bin/bash

rebuild: ## Rebuild all containers
	docker compose build --force-rm --no-cache

If you want to modify the relay code, execute make run-dev as it will mount the the current directory in the container allowing you to run new code directly in the container.

Running manually

It is recommended to run docker compose -f docker-compose-dev.yml or make run-dev as that will also spin up the redis cache which the relay relies on but if you'd wish to run just the relay with a single worker and reload on code change:

pip install -r requirements.txt
uvicorn main:app --reload

Testing

Based on FastAPI documentation recommendations and my own past experience I've chosen Pytest for the testing framework. Easiest way to run tests is to:

1. make run-dev to first spin the containers in dev mode as integrations tests rely on redis
2. make test which will execute pytest inside the containers testing the relay, cache & cli. Type checking by Mypy is also a part of the command.

CLI

There are two ways to interact with the API from the shell:

1. By using ./cli/simple_lunch [restaurant_id OR no argument for restaurant listing] which strives to maximize compatibility with any OS by using only curl for API calls and inlined python json.load for formatting.

2. By running a full fledged Typer shell app:

   
   pip3 install cli/requirements.txt
   python3 -m cli.main
   
   

Extra tasks & rationales

Cache

For caching I chose Redis as it's one of the most popular production caching solutions. I could have went with simpler solutions that would have resulted in a slightly easier implementation (like memcached or some in memory solutions).

I used a simple layer on top of aioredis (important for using only async methods and preserving async performance) for FastAPI provided by fastapi-cache that mostly just abstracts an easier to use cache object for FastAPI routes. I made sure to check that package had quite good test coverage, clean code and was actively maintained.

To monitor redis use redis-insight provisioned by one of the docker images. Insights GUI will ask you to provide the cache url. Use make ip to easily see the containers url.

Multi threading

By implementing only async methods and using an ASGI stack (Uvicorn, Starlette and FastAPI), there are no blocking methods and a decent speedup with low developer effort is achieved compared to WSGI stacks (benchmarks). Production image will start the relay with the same amount of workers as available CPU cores. More information in documentation.

Load tests

Load tests are orchestrated by Locust from tests/locustfile.py.

1. Consistently increasing 0->500RPS in ~10RPS intervals.

   The server can fault free handle up to ~600 RPS/instance until it becomes throttled down. My first guess would be that the external API is rate limiting the relay.

   Also it's worth noting that on CKE the less expensive CPU units are only allowed to "burst" (docs) to increase the processing for a short period of time. That could also contribute to throttling especially when compared to the CPU metrics which show ~300% usage spikes followed by rapid drops.

2. Cold boot, empty cache, high load

   Running a concentrated swarm of 1000 users through 20 workers and spinning RPS from 0 to ~500 results in a server worker crash. I guess that the next step would be attaching some log & crash reporting service to the server to get rudimentary observability. It would also be worth the investigating other factors such as the number of open connections, memory and disk I/O and bandwidth of the instance