Flask microservice implementing the Global Alliance for Genomics and Health (GA4GH) Task Execution Service (TES) API specification for injecting middleware (such as task distribution logic) into TES requests.
proTES is a proxy-like implementation of the [GA4GH TES OpenAPI specification] based on Flask and Connexion built for distributing TES tasks over different TES service instances and injecting other middleware into TES requests.
proTES 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.
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:
- Docker (18.06.1-ce, build e68fc7a)
- docker-compose (1.22.0, build f46880fe)
- Git (1.8.3.1)
Note: These indicated versions are those that were used for developing/testing. Other versions may or may not work.
Create data directory and required subdiretories
export PROTES_DATA_DIR=/path/to/data/directory
mkdir -p $PROTES_DATA_DIR/{db,specs}Note: If the
PROTES_DATA_DIRenvironment variable is not set, proTES will require the following default directories to be available:
../data/pro_tes/db../data/pro_tes/specs
Clone repository
git clone https://github.com/elixir-europe/proTES.gitTraverse to app directory
cd proTESThe following user-configurable files are available:
Build/pull and run services
docker-compose up -d --buildVisit Swagger UI
firefox http://localhost:8080/ga4gh/tes/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, or fixes and 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.
Development of the app is currently still in alpha stage, and current "versions" are for internal use only. We are aiming to have a fully spec-compliant ("feature complete") version of the app available by the end of 2018. The plan is to then adopt a semantic versioning scheme in which we would shadow TES spec versioning for major and minor versions, and release patched versions intermittently.
This project is covered by the Apache License 2.0 also shipped with this repository.
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.
