annotations

Annotations service backend

Docker

The project provides two images (a fpm and a cli one) that run as the www-data user. They work in concert with others to allow to run the service locally, or to run tasks such as tests.

Build images with:

docker-compose build

Run a shell as www-data inside a new cli container:

docker-compose run cli /bin/bash

Run composer:

docker-compose run composer composer install

Run a PHP interpreter:

docker-compose run cli /usr/bin/env php ...

Run PHPUnit:

docker-compose run cli vendor/bin/phpunit

Run all project tests:

docker-compose -f docker-compose.yml -f docker-compose.ci.yml build
docker-compose -f docker-compose.yml -f docker-compose.ci.yml run ci

Journey of a request to the annotations api

1. Query received via the annotations api.
2. Retrieve annotation listing from hypothes.is/api based on query parameters.
3. Denormalize the annotations into an object model.
4. Normalize the annotations to prepare the response which conforms to the eLife json schema. We rely on CommonMark to step through the Markdown content and prepare the structure that we need, sanitizing each HTML value as it is rendered with HTMLPurifier.
5. Return the response to the client.