GraphQL for Ensembl

A GraphQL trial for Ensembl to reduce the need for RESTful web services.

This application is implemented with Ariadne, a schema-first graphql framework for Python

GraphQL requires a schema (in /common) and implementation of resolver functions that know how to interpret specific parts of a GraphQL query. Resolvers are found in /resolver, and may also make use of "data loaders" to overcome inherent deficiencies in GraphQL implementations.

https://www.ebi.ac.uk/seqdb/confluence/display/EA/Thoas+Docs

Installation

Requires Python 3.10+.

To install dependencies, run:

pip install -r requirements.txt for just the API. Use this when deploying the service.

pip install -r requirements-dev.txt installs everything including dev dependencies like pytest, mypy etc.

Running the API locally

Rename example_connections.conf to connections.conf and update the config values accordingly.

This command will start the server:

uvicorn --workers 1 --host=0.0.0.0 graphql_service.server:APP

To run a Uvicorn server with automatic reload for development purposes, you can use the --reload flag. This flag will make Uvicorn watch your code for changes and automatically restart the server when it detects any changes.

uvicorn --workers 1 --host 0.0.0.0 --reload graphql_service.server:APP

Also, if you're developing in PyCharm, you will probably find it useful to create a run configuration so that you can use the debugger. Create a run configuration that looks like this:

Development

Pre-commit hook (local)

To run Black, Pylint, and Mypy automatically before each commit, create pre-commit hook under .git/hooks/:

cat <<'EOF' > .git/hooks/pre-commit
#!/bin/sh
set -e

black . --check --verbose --diff --color
pylint $(git ls-files '*.py') --fail-under=9.5
mypy graphql_service
EOF
chmod +x .git/hooks/pre-commit

Note:

• .git/hooks is not versioned, so each developer needs to run this once locally.
• You can test it by running .git/hooks/pre-commit
• If any of Black/pylint/mypy fails, the commit will be blocked.

Testing

cd ensembl-thoas
pytest .

Linting

From the root of the repository:

cd ensembl-thoas
pylint $(git ls-files '*.py') --fail-under=9.5

Type checking

cd ensembl-thoas
mypy graphql_service

Formatting

black . --check --diff previews the formatting.

black . applies the formatting in-place.

Containerisation

Build the image using ./Dockerfile:

docker build -t $NAME:$VERSION .

Run a container with the image (--publish below is exposing the container's ports to the host network):

docker container run --publish 0.0.0.0:80:80/tcp --publish 0.0.0.0:8000:8000/tcp -ti $NAME:$VERSION

The connection configuration is assumed to exist in the repo as the file ./connections.conf and gets built into the Docker image. On Kubernetes cluster, these configs are passed through k8s objects called a escrets. If we want to emulate this in Docker then we could look into using Docker bind mounts.