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.
Requires Python 3.8+.
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.
The deployment assumes that we have a directory mounted with the convention <data_root>/<genome_uuid>/variation.vcf.gz
The code currently fetches a single vcf file within the genome_uuid folder. In the future, we plan to fetch data from multiple VCFs for a single genome_uuid.
Add path to the datafile in ./connections.conf.
The file follows the following template:
data_root = /usr/data/variation_vcfs
The command below will start the server:
uvicorn --workers 1 --host=0.0.0.0 graphql_service.server:APP
Build the image using ./Dockerfile.dev:
docker build -t $NAME:$VERSION -f ./Dockerfile.dev .
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 -v <ensembl-hysipile-dir>:/app $NAME:$VERSION
Build the image using ./Dockerfile.prod:
docker build -t $NAME:$VERSION -f ./Dockerfile.prod .
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.