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Tools API

A FastAPI app providing the tools backend microservice for Ensembl 2020 client.

Endpoints

  • /api/tools/blast/config
  • /api/tools/blast/job
  • /api/tools/blast/jobs/:api_path (e.g. jobs/status/:id, see API docs for details)

Setup

With docker-compose:

docker-compose up

Directly:

pip3 install --no-cache-dir -r requirements.txt
uvicorn app.main:app --proxy-headers --host 0.0.0.0 --port 80

Usage

See the documentation for usage: http://localhost/docs

Deployment

The service/ingress templates in k8s directory root are stored in ensembl-k8s-manifests repo and used for integration to Ensembl 2020 review apps CI/CD pipeline in ensembl-client repo. Rest of the configuration files (in base and overlays subdirs) are used to deploy updates in Tools API (see .gitlab-ci.yml; ingress applied manually).

Testing

  1. pip3 install pytest
  2. pytest (run in the repo root directory)