Hypsipyle is a GraphQL API developed to provide variant visualisations on Ensembl beta website which utilises VCF files produced by Ensembl Variant Effect Predictor (VEP) and enables querying and faster access of data
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 ./graphql_service/resolver.
More details about the schema are available here: https://github.com/Ensembl/ensembl-vdm-docs
The API resolvers use VEP annotated VCF data to provide visualisations
The API can be queried against a single endpoint specifying the payload to be returned
The deployment assumes that we have a directory mounted with the convention <data_root>/<genome_uuid>/variation.vcf.gz. This VEP annotated VCF file generated using a Nextflow VEP pipeline.
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.
A template file ./example_connections.conf is available. Copy this file and rename to ./connections.conf and add path to the datafile.
The file follows the following template:
data_root = /app/data
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.
Once the container starts running, the GraphQL server will be running at the endpoint 0.0.0.0:8000 A simple query would look like:
query variant_example {
variant(
by_id: {genome_id: "a7335667-93e7-11ec-a39d-005056b38ce3", variant_id: "1:10153:rs1639547929"}
) {
name
primary_source {
description
url
}
}
}
More example queries can be found in examples/