proWES is a robust and scalable Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API gateway that may play a pivotal role in augmenting the capabilities of your GA4GH Cloud ecosystem by offering flexible middleware injection for effective workflow deployment across a range of federated workflow management system deployments.
proWES gateway may serve as a crucial component in federated compute networks based on the GA4GH Cloud ecosystem. Its primary purpose is to provide centralized features to a federated network of independently operated GA4GH WES instances. As such, it can serve, for example, as a compatibility layer, a load balancer workload distribution layer, a public entry point to an enclave of independent compute nodes, or a means of collecting telemetry.
When WES requests are received, proWES applies one or more configurable middlewares before forwarding the requests to appropriate WES instances in the network. A plugin system makes it easy to write and inject middlewares tailored to specific requirements, such as for access control, request/response processing or validation, or the selection of suitable endpoints considering data use restrictions and client preferences.
TBA
proWES is a Flask microservice that supports OAuth2-based authorization out of the box (bearer authentication) and stores information about incoming and outgoing tasks in a NoSQL database (MongoDB). Based on our FOCA microservice archetype, it is highly configurable in a declarative (YAML-based!) manner. Forwarded tasks are tracked asynchronously via a RabbitMQ broker and Celery workers that can be easily scaled up. Both a Helm chart and a Docker Compose configuration are provided for easy deployment in native cloud-based production and development environments, respectively.
For production-grade Kubernetes-based deployment, see separate instructions. For testing/development purposes, you can use the instructions described below.
Ensure you have the following software installed:
Create data directory and required subdirectories
export PROWES_DATA_DIR=/path/to/data/directory
mkdir -p $PROWES_DATA_DIR/{db,specs}Note: If the
PROWES_DATA_DIRenvironment variable is not set, proWES will require the following default directories to be available:
../data/pro_wes/db../data/pro_wes/specs
Clone repository
git clone https://github.com/elixir-europe/proWES.gitTraverse to app directory
cd proWESThe following user-configurable files are available:
Build/pull and run services
docker-compose up -d --buildVisit Swagger UI
firefox http://localhost:8090/ga4gh/wes/v1/uiNote: Host and port may differ if you have changed the configuration or use an HTTP server to reroute calls to a different host.
This project is a community effort and lives off your contributions, be it in the form of bug reports, feature requests, discussions, ideas, fixes, or other code changes. Please read these guidelines if you want to contribute. And please mind the code of conduct for all interactions with the community.
The project adopts the semantic versioning scheme for versioning. Currently the service is in beta stage, so the API may change and even break without further notice. However, once we deem the service stable and "feature complete", the major, minor and patch version will shadow the supported WES version, with the build version representing proWES-internal updates.
This project is covered by the Apache License 2.0 also shipped with this repository.
proWES is part of ELIXIR Cloud & AAI, a multinational effort at establishing and implementing FAIR data sharing and promoting reproducible data analyses and responsible data handling in the life sciences.
If you have suggestions for or find issue with this app, please use the issue tracker. If you would like to reach out to us for anything else, you can join our Slack board, start a thread in our Q&A forum, or send us an email.
