Node Rest API written with Koa that executes R scripts

DEPRECATED: This project is no longer under maintenance. It still exist for the purpose of documentation on how to setup an own API for RScripts in child process using Docker, zeit.co/now, Jest, Travis, codeclimate, Koa, nodemon, husky, ts-node and Typescript for development. We still suggest using projects like opencpu instead of running your own system for a purpose like this.

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Written with Koa (lightweight Express.js alternative. suitable for small APIs) in Typescript.

• Node Rest API written with Koa that executes R scripts
  • Prerequisites
  • Setup
    • Setup Node.js
    • Setup R
  • Development
    • In Node.js
    • In R
    • Running Tests
    • With Docker
  • Deployment

Prerequisites

• docker (version 18.09.1)
• Node.js (version 10.5.0)
• R (version 3.5.2)

Setup

Currently the Docker container is a based in rocker/r-ver with R version 3.5.2 which is based on debian:stretch

Setup Node.js

git clone git@github.com:technologiestiftung/rrest.git
npm install

Setup R

R needs the packrat installed to make a snapshot of all needed libraries. Please open an issue if there is the need to install additional global packages and tools. Run R

cd r-scripts
R

Then in R run:

install.packages("packrat")
packrat::restore("path/to/r-scripts")
q()

Development

In Node.js

# runs nodemon with ts-node
npm run dev

In R

Run R

cd r-scripts
R

If you need to install libraries in R - run:

install.packages('jsonlite')
# packrat should have auto snapshot enabled
# if the package doesn't show up in
# r-scripts/packrat/packrat.lock
# run
packrat::snapshot()
# all local dependencies will be saved into
# the packrat folder and can be restored

Some conventions need to be taken in account.

1. In the docker container the R script gets executed by a subprocess called from the node-app/dist/index.js to make the whole setup work together the R script needs to set its working directory to ./r-scripts when executed from the container by running as first statement setwd("./r-scripts")
2. To make packrat work it also needs to source the provided .Rprofile after that source(".Rprofile")
3. After that libraries can be included library("jsonlite"). Remember to install them in an environment that has packrat available.
4. The should accept input in stdin and have one main function that returns the result. The results will be passed to stdout and the Node server catches it.

Running Tests

This is currently Node.js only.

npm test

With Docker

From the root of the repository run (omit the --build if you did not change source files)

docker-compose up --build

This starts the container. It accepts POST requests with JSON payload on PORT 3000 on the endpoint http://localhost:8080/submit

Example curl POST

curl -X "POST" "http://localhost:8080/submit" \
     -H 'Content-Type: application/json; charset=utf-8' \
     -d $'{
  "foo": "bahh"
}'

To stop the running containers

docker-compose down

Deployment

Could be deployed to a AWS EB Docker setup