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proTES

Synopsis

proTES is a robust and scalable Global Alliance for Genomics and Health (GA4GH) Task Execution Service (TES) API gateway that may play a pivotal role in augmenting the capabilities of your GA4GH Cloud ecosystem by offering flexible middleware injection for effectively federating atomic, containerized workloads across on premise, hybrid and multi-cloud environments composed of GA4GH TES nodes.

Description

proTES 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 TES 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 TES requests are received, proTES applies configured middleware before forwarding the requests to appropriate TES 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.

Built-in middleware plugins

Currently, there are two plugins shipped with proTES that each serve as proof-of-concept examples for different task distribution scenarios:

  • Load balancing: The pro_tes.middleware.task_distribution.random plugin evenly (actually: randomly!) distributes workloads across a network of TES endpoints
  • Bringing compute to the data: The pro_tes.middleware.task_distribution.distance plugin selects TES endpoints to relay incoming requests to in such a way that the distance the (input) data of a task has to travel across the network of TES endpoints is minimized.

Implementation notes

proTES is a [Flask][res-flask] microservice that supports [OAuth2][res-oauth2]-based authorization out of the box (bearer authentication) and stores information about incoming and outgoing tasks in a NoSQL database ([MongoDB][res-mongodb]). Based on our [FOCA][res-foca] microservice archetype, it is highly configurable in a declarative (YAML-based!) manner. Forwarded tasks are tracked asynchronously via a [RabbitMQ][res-rabbitmq] broker and [Celery][res-celery] workers that can be easily scaled up. Both a Helm[res-helm] chart and a [Docker Compose][res-docker-compose] configuration are provided for easy deployment in native cloud-based production and development environments, respectively.

Installation

You can find a Helm chart in the GitHub repository of proTES

Follow these instructions

  • Install Helm

  • Clone the proTES repository

    git clone https://github.com/elixir-cloud-aai/proTES.git

  • Browse to deployment to find the Chart.yaml and the values.yaml files

Usage

First you must create a namespace in Kubernetes in which to deploy proTES. The commands below assume that everything is created in the context of this namespace. How the namespace is created depends on the cluster, so we won't document it here.

You need to edit the values.yaml file to specify your applicationDomain and the clusterType

After this you can deploy proTES using helm:

helm install protes . -f values.yaml

Updates

If you want to edit any of the Deployments, you can update them with helm and the values.yaml file. Once edited, you can run this command:

helm upgrade protes . -f values.yaml

Technical details

MongoDB

The MongoDB database is deployed using:

  • templates/mongodb/mongodb-deployment.yaml

RabbitMQ

The message broker RabbitMQ that allows the app to communicate with the worker is deployed using:

  • templates/rabbitmq/rabbitmq-deployment.yaml

proTES

proTES consists of five deployments: a Flask server and a Celery worker. These are deployed using:

  • templates/protes/protes-deployment.yaml
  • templates/protes/celery-deployment.yaml

You can use ReadWriteOnce if you don't have StorageClass that supports RWX. In that case, a podAffinity will be set to have the proTES pods running on the same node.

Destroy

Simply run:

helm uninstall protes