init

Author: fridgerator

.gitignore

@@ -0,0 +1,106 @@
+
+# Created by https://www.gitignore.io/api/node,visualstudiocode
+# Edit at https://www.gitignore.io/?templates=node,visualstudiocode
+
+### Node ###
+# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+lerna-debug.log*
+
+# Diagnostic reports (https://nodejs.org/api/report.html)
+report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+*.lcov
+
+# nyc test coverage
+.nyc_output
+
+# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# Bower dependency directory (https://bower.io/)
+bower_components
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (https://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directories
+node_modules/
+jspm_packages/
+
+# TypeScript v1 declaration files
+typings/
+
+# TypeScript cache
+*.tsbuildinfo
+
+# Optional npm cache directory
+.npm
+
+# Optional eslint cache
+.eslintcache
+
+# Optional REPL history
+.node_repl_history
+
+# Output of 'npm pack'
+*.tgz
+
+# Yarn Integrity file
+.yarn-integrity
+
+# dotenv environment variables file
+.env
+.env.test
+
+# parcel-bundler cache (https://parceljs.org/)
+.cache
+
+# next.js build output
+.next
+
+# nuxt.js build output
+.nuxt
+
+# vuepress build output
+.vuepress/dist
+
+# Serverless directories
+.serverless/
+
+# FuseBox cache
+.fusebox/
+
+# DynamoDB Local files
+.dynamodb/
+
+### VisualStudioCode ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+
+# End of https://www.gitignore.io/api/node,visualstudiocode

R/launch.R

@@ -0,0 +1,38 @@
+# based on https://github.com/joshkatz/r-script/blob/master/R/launch.R
+suppressMessages(library(jsonlite))
+
+run <- function(dataIn) {
+
+  # set up environment
+  input <- unname(dataIn[[1]])
+  .e <- as.environment(list(
+    path = dataIn[[2]],
+    out = modifyList(list(x = NULL, auto_unbox = T),
+      dataIn[[3]], keep.null = T)
+  ))
+  lockBinding(".e", environment())
+
+  # run source, capture output
+  captured <- tryCatch(capture.output({
+    temp <- source(.e$path, local = T)$value
+  }), error = function(err) err)
+  unlockBinding(".e", environment())
+
+  # process and return
+  if (inherits(captured, "error")) {
+    msg <- conditionMessage(captured)
+    cat("Error in R script", .e$path, "\n", sQuote(msg), file = stderr())
+    return(invisible(F))
+  }
+  .e$out$x <- if (is.null(temp)) {
+     ""
+  } else {
+    temp
+  }
+  do.call(toJSON, .e$out)
+
+}
+
+suppressWarnings(
+  run(fromJSON(Sys.getenv("input")))
+)

README.md

@@ -0,0 +1,39 @@
+# r-script
+
+### In development, still a WIP
+
+Module for running R scripts from node
+
+Based on [r-script](https://github.com/joshkatz/r-script) by [joshkatz](https://github.com/joshkatz).  Decided to re-write this project because I need similar functionality and that project seems unmaintained.
+
+## Installation
+
+R needs to already be installed, and [jsonlite](https://cran.r-project.org/web/packages/jsonlite/index.html) R library needs to be installed.
+
+`yarn add @fridgerator/r-script` or `npm install @fridgerator/r-script`
+
+## Usage
+
+In an R file: 
+
+```R
+input[[1]] + input[[2]]
+```
+
+In node:
+
+```javascript
+const { R } = require('@fridgerator/r-script')
+
+// optionally pass an environment object if Rscript is not in your system PATH
+// `process.env` will be used as default
+let r = new R('./add.R', {PATH: '/bin:/location/to/R/bin'})
+
+// data is converted to a list variable `input` in the R script
+r.data(2, 3)
+
+// call the script async
+r.call()
+  .then(response => response === 5) // true
+  .catch(e => console.log('error : ', e))
+```

dist/R/launch.R

@@ -0,0 +1,38 @@
+# based on https://github.com/joshkatz/r-script/blob/master/R/launch.R
+suppressMessages(library(jsonlite))
+
+run <- function(dataIn) {
+
+  # set up environment
+  input <- unname(dataIn[[1]])
+  .e <- as.environment(list(
+    path = dataIn[[2]],
+    out = modifyList(list(x = NULL, auto_unbox = T),
+      dataIn[[3]], keep.null = T)
+  ))
+  lockBinding(".e", environment())
+
+  # run source, capture output
+  captured <- tryCatch(capture.output({
+    temp <- source(.e$path, local = T)$value
+  }), error = function(err) err)
+  unlockBinding(".e", environment())
+
+  # process and return
+  if (inherits(captured, "error")) {
+    msg <- conditionMessage(captured)
+    cat("Error in R script", .e$path, "\n", sQuote(msg), file = stderr())
+    return(invisible(F))
+  }
+  .e$out$x <- if (is.null(temp)) {
+     ""
+  } else {
+    temp
+  }
+  do.call(toJSON, .e$out)
+
+}
+
+suppressWarnings(
+  run(fromJSON(Sys.getenv("input")))
+)

dist/bundle.js

@@ -0,0 +1,11 @@
+interface R {
+  data(...args: any[]): R;
+  call(_opts?: R.Options): Promise<object>;
+  callSync(_opts?: R.Options): object;
+}
+declare namespace R {
+  interface Options {
+    [key: string]: any;
+  }
+}
+export = R;

index.d.ts

@@ -0,0 +1,29 @@
+{
+  "name": "@fridgerator/r-script",
+  "version": "0.1.0",
+  "description": "Module for running R scripts from node",
+  "main": "./dist/bundle.js",
+  "repository": "https://github.com/fridgerator/r-script",
+  "author": "Nick Franken <[email protected]>",
+  "license": "MIT",
+  "scripts": {
+    "build": "webpack --config webpack.config.js",
+    "test": "mocha"
+  },
+  "files": [
+    "dist",
+    "src",
+    "index.d.ts"
+  ],
+  "devDependencies": {
+    "@types/node": "^12.6.6",
+    "chai": "^4.2.0",
+    "copy-webpack-plugin": "^5.0.3",
+    "mocha": "^6.1.4",
+    "ts-loader": "^6.0.4",
+    "typescript": "^3.5.3",
+    "webpack": "^4.36.1",
+    "webpack-cli": "^3.3.6"
+  },
+  "types": "index.d.ts"
+}

package.json

@@ -0,0 +1,67 @@
+import { spawn, spawnSync } from 'child_process'
+
+interface Options {
+  [key: string]: any
+}
+
+export class R {
+  rData: Options
+  path: string
+  options: Options
+  idCounter: number
+  args: string[]
+
+  constructor(path: string, env?: Options) {
+    let _env = env || process.env
+    this.rData = {}
+    this.path = path
+    this.options = {
+      env: Object.assign({}, {DIRNAME: __dirname}, _env),
+      encoding: 'utf8'
+    }
+    this.idCounter = 0
+    this.args = ['--vanilla', __dirname + '/R/launch.R']
+  }
+
+  private setInputEnv (opts: Options): void {
+    this.options.env.input = JSON.stringify([this.rData, this.path, opts])
+  }
+
+  data (...args: any[]): R {
+    for (let i = 0; i < args.length; i++)
+      this.rData[++this.idCounter] = args[i]
+    
+    return this
+  }
+
+  call (_opts?: Options): Promise<object> {
+    return new Promise((resolve: any, reject: any) => {
+      let opts = _opts || {}
+      this.setInputEnv(opts)
+      let child = spawn('Rscript', this.args, this.options)
+      let body = ""
+      child.stderr.on('data', d => {
+        let msg = d.toString()
+        if (msg.includes('Warning message')) return
+        reject(msg)
+      })
+      child.stdout.on('data', d => body += d)
+      child.on('close', () => resolve(JSON.parse(body)))
+    })
+  }
+
+  callSync (_opts?: Options): object | undefined {
+    let opts = _opts || {}
+    this.setInputEnv(opts)
+    let child = spawnSync('Rscript', this.args, this.options)
+    if (child.stderr) {
+      let msg = child.stderr.toString()
+      if (!msg.includes('Warning message'))
+        throw msg
+    }
+    if (child.stdout) {
+      return JSON.parse(child.stdout.toString())
+    }
+    return undefined
+  }
+}

src/index.ts

@@ -0,0 +1,44 @@
+const { expect } = require('chai')
+const { R } = require('./dist/bundle')
+
+describe('R', () => {
+  describe('#call', () => {
+    it('should add two numbers', done => {
+      let r = new R('./test_files/add.R')
+      r.data(2, 3)
+      r.call()
+        .then(result => {
+          expect(result).to.equal(5)
+          done()
+        })
+        .catch(e => console.log('err : ', e))
+    })
+
+    it('should return what was passed', done => {
+      let r = new R('./test_files/return_immediate.R')
+      r.data({stuff: [1, 2, 9999999]}, 'hello', 99.9)
+      r.call()
+        .then(result => {
+          expect(result).to.deep.equal([{stuff: [1, 2, 9999999]}, 'hello', 99.9])
+          done()
+        })
+        .catch(e => console.log('err : ', e))
+    })
+  })
+
+  describe('#callSync', () => {
+    it('should add two numbers', () => {
+      let r = new R('./test_files/add.R')
+      r.data(2, 3)
+      let result = r.callSync()
+      expect(result).to.equal(5)
+    })
+
+    it('should return what was passed', () => {
+      let r = new R('./test_files/return_immediate.R')
+      r.data({stuff: [1, 2, 9999999]}, 'hello', 99.9)
+      let result = r.callSync()
+      expect(result).to.deep.equal([{stuff: [1, 2, 9999999]}, 'hello', 99.9])
+    })
+  })
+})

test.js

@@ -0,0 +1 @@
+input[[1]] + input[[2]]