Legumeinfo Microservices

This repository contains microservices developed and maintained by the Legume Information System to support the Legumeinfo website as well as the various apps developed and maintained by the group. Each subdirectory contains a different microservice, with the exception of the proto/ directory, which contains Protocol Buffers that define common data types used by one or more of the microservices. See the proto/ directory for more information about using these Protocol Buffers.

Usage

Each microservice is distributed as a Docker image via the GitHub container registry. Unless you are a developer, we recommend using these prebuilt images rather trying to compile and run microservices yourself. Additionally, if you are using microservices that depend on other microservices, we especially recommend using a tool for deploying multi-container applications, such as Docker Compose or Kubernetes.

Some containers support gRPC. If you wish to communicate with these containers from a Web client using gRPC Web, then you must use a proxy that supports gRPC Web request, such as Envoy Proxy.

See the Genome Context Viewer Docker Compose repository for an example of deploying Legumeinfo microservices using Docker Compose, Envoy Proxy, and Traefik. The example configures microservices to communicate and supports gRPC Web requests.

Development

Please so our contribution guidelines before contributing to this repository.

See the directories of microservices you wish to compile manually for instructions on doing so. Generally, we recommend still using a solution like Docker Compose to orchestrate container building and cross-talk, even during development.

Pre-Commit Hooks

This project uses pre-commit to manage pre-commit hooks, such as code formatting. These hooks are also applied to all PRs on GitHub. To run the hooks locally before opening a PR (which we recommend), first install pre-commit:

$ pip install pre-commit
$ pre-commit install

The hooks will then be applied every time you make a commit.

If you want to run the hooks manually (i.e. without having to commit), use the following command:

$ pre-commit run --all-files

See the pre-commit documentation for more details and use cases.

Managing Dependencies

Generally, we use the pip-compile command from the pip-tools package to manage microservice dependencies. See the Managing Microservice Dependencies page in this repo's Wiki for details.