README.md
# 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](https://www.opencpu.org) instead of running your own system for a purpose like this.
---
[](https://travis-ci.org/technologiestiftung/rrest) [](https://github.com/technologiestiftung/rrest/issues?utf8=%E2%9C%93&q=) [](https://codeclimate.com/github/technologiestiftung/rrest/maintainability) [](https://codeclimate.com/github/technologiestiftung/rrest/test_coverage) [](https://greenkeeper.io/)
Written with [Koa](https://www.npmjs.com/package/koa) (lightweight Express.js alternative. suitable for small APIs) in Typescript.
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- [Node Rest API written with Koa that executes R scripts](#node-rest-api-written-with-koa-that-executes-r-scripts)
- [Prerequisites](#prerequisites)
- [Setup](#setup)
- [Setup Node.js](#setup-nodejs)
- [Setup R](#setup-r)
- [Development](#development)
- [In Node.js](#in-nodejs)
- [In R](#in-r)
- [Running Tests](#running-tests)
- [With Docker](#with-docker)
- [Deployment](#deployment)
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## 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](https://hub.docker.com/r/rocker/r-ver) with R version 3.5.2 which is based on [debian:stretch](https://hub.docker.com/_/debian)
### Setup Node.js
```bash
git clone git@github.com:technologiestiftung/rrest.git
npm install
```
### Setup R
R needs the [packrat](https://rstudio.github.io/packrat/) installed to make a snapshot of all needed libraries. Please open [an issue](https://github.com/technologiestiftung/rrest/issues) if there is the need to install additional global packages and tools. Run R
```bash
cd r-scripts
R
```
Then in R run:
```R
install.packages("packrat")
packrat::restore("path/to/r-scripts")
q()
```
## Development
### In Node.js
```bash
# runs nodemon with ts-node
npm run dev
```
### In R
Run R
```bash
cd r-scripts
R
```
If you need to install libraries in R - run:
```R
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.
```bash
npm test
```
### With Docker
From the root of the repository run (omit the `--build` if you did not change source files)
```bash
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`
```bash
curl -X "POST" "http://localhost:8080/submit" \
-H 'Content-Type: application/json; charset=utf-8' \
-d $'{
"foo": "bahh"
}'
```
To stop the running containers
```bash
docker-compose down
```
## Deployment
Could be deployed to a AWS EB Docker setup