implement first ui binding: manipulating using a slider

Dockerfile

@@ -1,13 +1,34 @@
-FROM node:8-alpine
+FROM rocker/geospatial:latest
+
+SHELL ["/bin/bash", "-c"]
+
+RUN R -e 'install.packages(c("diveMove", "trip", "adehabitatLT", "plm", "cshapes", "plumber"))'
+# based on https://gist.github.com/remarkablemark/aacf14c29b3f01d6900d13137b21db3a
+RUN apt-get update \
+    && apt-get install -y curl \
+    && apt-get -y autoclean
+
+ENV NVM_DIR /usr/local/nvm
+ENV NODE_VERSION 8.10.0
+RUN curl --silent -o- https://raw.githubusercontent.com/creationix/nvm/v0.33.8/install.sh | bash
+RUN source $NVM_DIR/nvm.sh \
+    && nvm install $NODE_VERSION \
+    && nvm alias default $NODE_VERSION \
+    && nvm use default
+
+# add node and npm to path so the commands are available
+ENV NODE_PATH $NVM_DIR/v$NODE_VERSION/lib/node_modules
+ENV PATH $NVM_DIR/versions/node/v$NODE_VERSION/bin:$PATH
+
+#WORKDIR /bindings
 
 COPY package.json package.json
 
-RUN apk add --no-cache
 RUN npm install --production
 
 COPY config config
+COPY index.js index.js
 COPY controllers controllers
 COPY controllers/bindings.js controllers/bindings.js 
-COPY index.js index.js
-
-CMD ["node", "index.js"]
+
+CMD ["node", "index.js"]

controllers/bindings.js

@@ -20,8 +20,13 @@
 const express = require('express');
 const bodyParser = require('body-parser');
 const debug = require('debug')('bindings');
+const rscript = require('r-script');
+const path = require('path');
+const fs = require('fs')
+
 const fn = require('./generalFunctions');
 
+
 let bindings = {};
 
 bindings.start = (conf) => {
@@ -30,22 +35,43 @@ bindings.start = (conf) => {
         app.use(bodyParser.json());
         app.use(bodyParser.urlencoded({extended: true}));
         debug('Receiving data to create bindings');
-        app.post('/api/v1/bindings', function(req, res) {
-            debug('Received the following data: %s', req.body.id);
-            switch (req.body.purpose) {
-                case 'showFigureCode':
-                    bindings.showCode(req.body);
-                    break;
-                case 'showResultCode':
-                    bindings.showCode(req.body);
-                    break;
-                default:
-                    break;
-            }
+        app.post('/api/v1/bindings/discover/discoverNumber', function(req, res) {
+            res.send({
+                callback: 'ok',
+                data: req.body});
+        });
+        app.post('/api/v1/bindings/discover/discoverFigure', function(req, res) {
+            res.send({
+                callback: 'ok',
+                data: req.body});
+        });
+        app.post('/api/v1/bindings/inspect/inspectPaperDataCode', function(req, res) {
             res.send({
                 callback: 'ok',
-                temp: 'bla',
-                data: req.body.id});
+                data: req.body});
+        });
+        app.post('/api/v1/bindings/inspect/inspectNumberDataCode', function(req, res) {
+            res.send({
+                callback: 'ok',
+                data: req.body});
+        });
+        app.post('/api/v1/bindings/inspect/inspectFigureDataCode', function(req, res) {
+            res.send({
+                callback: 'ok',
+                data: req.body});
+        });
+        app.post('/api/v1/bindings/manipulate/manipulateFigure', function(req, res) {
+            bindings.manipulateFigure(req.body);
+            res.send({
+                callback: 'ok',
+                data: req.body});
+        });
+        app.post('/api/v1/bindings/manipulate/run', function(req, res) {
+            debug('Start running plumber service for %s', req.body.id);
+            bindings.runR(req.body);
+            res.send({
+                callback: 'ok',
+                data: req.body});
         });
         let bindingsListen = app.listen(conf.port, () => {
             debug('Bindings server listening on port %s', conf.port);
@@ -54,6 +80,17 @@ bindings.start = (conf) => {
     });
 };
 
+bindings.manipulateFigure = function(binding) {
+    debug('Start creating the binding %s for the result %s for the compendium %s', binding.purpose, binding.figure, binding.id);
+    let fileContent = fn.readRmarkdown(binding.id, binding.mainfile);
+        fileContent = fn.replaceVariable(fileContent, binding.variable);
+    let codeLines = fn.handleCodeLines(binding.codeLines);
+    let code = fn.extractCode(fileContent, codeLines);
+    let wrappedCode = fn.wrapCode(code, binding.id, binding.figure);
+    fn.saveResult(wrappedCode, binding.id, binding.figure.replace(/\s/g, '').toLowerCase());
+    fn.createRunFile(binding.id, binding.figure.replace(/\s/g, '').toLowerCase());
+};
+
 bindings.showCode = function(binding) {
     debug('Start creating the binding %s for the result %s', binding.purpose, binding.result);
     let fileContent = fn.readRmarkdown(binding.id, binding.mainfile);
@@ -63,4 +100,19 @@ bindings.showCode = function(binding) {
     fn.modifyMainfile(binding, fileContent);
 };
 
+bindings.createInteractiveFigure = function(binding) {
+    debug('Start creating manipulation binding for %s for figure %s', binding.id, binding.figure);
+};
+
+bindings.runR = function(binding) {
+    debug('Start running R script %s', binding.id);
+    // debug('File exists? %s', fs.existsSync(path.join('tmp', 'o2r', 'compendium', binding.id, 'figure4.R')));
+    // debug('File exists? %s', fs.existsSync(path.join('tmp', 'o2r', 'compendium', binding.id, 'main.Rmd')));
+    // debug('File exists? %s', fs.existsSync(path.join('tmp', 'o2r', 'compendium', binding.id, 'figure4run.R')));
+    let run = rscript(path.join(path.join('tmp', 'o2r', 'compendium', binding.id, binding.figure.replace(/\s/g, '').toLowerCase() + 'run.R')))
+        .data(binding.id)
+        .callSync();
+    //console.log(run);
+};
+
 module.exports = bindings;

controllers/generalFunctions.js

@@ -40,28 +40,45 @@ fn.modifyMainfile = function(binding, fileContent) {
 };
 
 fn.extractCode = function(fileContent, codeLines) {
-    let newContent = '---' + fileContent.split('---')[1] + '---\n' + '```{r}';
+    let newContent = '';
     let splitFileContent = fileContent.split('\n');
     codeLines.forEach(function(elem) {
-        newContent = newContent + '\n' + splitFileContent[elem] + '\n';
+        newContent += splitFileContent[elem] + '\n';
     });
-    newContent += '```';
+    return newContent;
+};
+
+fn.wrapCode = function(sourcecode, compendiumId, result) {
+    let get = "#' @get /" + result.replace(/\s/g, '').toLowerCase() + '\n' +
+                "#' @png \n" +
+                'function(newValue){ \n' +
+                'newValue = as.numeric(newValue) \n';
+                //'newValue = as.numeric(newValue) \n' + 'library("xts") \n library("RColorBrewer") \n library("foreign") \n library("plm") \n library("sp") \n library("spacetime") \n library("gstat") \n library("mapdata") \n library("rgdal") \n library("maps") \n library("maptools") \n';
+    let code = sourcecode.split('\n');
+        code[code.length-2] = 'print(' + code[code.length-2] + ')';
+    let newCode = '';
+        code.forEach(function(elem) {
+            newCode += elem + '\n';
+        });
+    let newContent = get + newCode + '}';
+    return newContent;
+};
+
+fn.replaceVariable = function(code, variable) {
+    let newContent = code.replace(variable.text, variable.varName + ' = newValue');
     return newContent;
 };
 
 fn.handleCodeLines = function(lines) {
     let codeLines = [];
     lines.forEach(function(elem) {
-        if (elem.toString().indexOf(/-/i) > -1) {
-            let range = elem.split('-');
-            for (let i = range[0]; i <= range[1]; i++) {
-                codeLines.push(Number(i)-1); // -1 is required as the code lines from the front end start counting at 1.
-            };
-        } else {
-            codeLines.push(Number(elem)-1);
-        }
+        for (let i = elem.start; i <= elem.end; i++) {
+            codeLines.push(Number(i)-1); // -1 is required as the code lines from the front end start counting at 1.
+        };
+    });
+    return codeLines.sort(function(a, b) {
+        return a-b;
     });
-    return codeLines.sort();
 };
 
 fn.readRmarkdown = function(compendiumId, mainfile) {
@@ -82,14 +99,22 @@ fn.saveResult = function(data, compendiumId, fileName) {
     fileName = fileName.replace(' ', '');
     fileName = fileName.replace('.', '_');
     fileName = fileName.replace(',', '_');
-    if (!fs.existsSync(path.join('tmp', 'o2r', 'compendium', compendiumId, 'bindings'))) {
-        fs.mkdirSync(path.join('tmp', 'o2r', 'compendium', compendiumId, 'bindings'));
+    if (!fs.existsSync(path.join('tmp', 'o2r', 'compendium', compendiumId))) {
+        fs.mkdirSync(path.join('tmp', 'o2r', 'compendium', compendiumId));
     }
-    fileName = path.join('bindings', fileName + '.Rmd');
-    fn.saveRmarkdown(data, compendiumId, fileName);
+    fileName = path.join(fileName + '.R');
+    fn.saveRFile(data, compendiumId, fileName);
+};
+
+fn.createRunFile = function(compendiumId, result) {
+    let content = 'library("plumber")' + '\n' +
+                    'path = paste("/tmp/o2r/compendium/' + compendiumId + '/' + result + '.R", sep = "")\n' +
+                    'r <- plumb(path)\n' +
+                    'r$run(host = "0.0.0.0", port=8000)';
+    fn.saveRFile(content, compendiumId, result+'run.R');
 };
 
-fn.saveRmarkdown = function(data, compendiumId, fileName) {
+fn.saveRFile = function(data, compendiumId, fileName) {
     let dir = path.join('tmp', 'o2r', 'compendium', compendiumId, fileName);
     fs.writeFile(dir, data, 'utf8', function(err) {
         debug(err);

controllers/plumber/.Rhistory

@@ -0,0 +1,134 @@
+file.exists("plumber.R")
+file.exists("plumber.R")
+print(file.exists("plumber.R"))
+library(here)
+print(file.exists(here("plumber.R"))
+print(file.exists(here("plumber.R")))
+print(file.exists(here("plumber.R")))
+print(file.exists(here("plumber/plumber.R")))
+print(file.exists(here("plumber","plumber.R")))
+print(file.exists(here("plumber","plumber.R")))
+print(file.exists(here("plumber/plumber.R")))
+print(file.exists(here("plumber.R")))
+here()
+print(file.exists(here("plumber.R")))
+setwd("~/o2r-platform/bindings/o2r-bindings/controllers/plumber")
+print(file.exists(here("plumber.R")))
+here()
+print(file.exists(here("plumber","plumber.R")))
+print(file.exists(here("controllers", "plumber","plumber.R")))
+needs(magrittr)
+set.seed(512)
+do.call(rep, input) %>%
+strsplit(NULL) %>%
+sapply(sample) %>%
+apply(2, paste, collapse = "")
+install.packages("magrittr")
+needs(magrittr)
+library(magrittr)
+set.seed(512)
+do.call(rep, input) %>%
+strsplit(NULL) %>%
+sapply(sample) %>%
+apply(2, paste, collapse = "")
+do.call(rep) %>%
+strsplit(NULL) %>%
+sapply(sample) %>%
+apply(2, paste, collapse = "")
+do.call(rep) %>%
+print(set.seed(512))
+r <- plumb(here("controllers", "plumber","plumber.R"))  # Where 'myfile.R' is the location of the file shown above
+r$run(port=8000)
+library(plumber)
+library(here)
+here()
+r <- plumb(here("controllers", "plumber","plumber.R"))  # Where 'myfile.R' is the location of the file shown above
+r$run(port=8000)
+install.package("plumber", repos = "http://cran.us.r-project.org")
+install.packages("plumber", repos = "http://cran.us.r-project.org")
+install.packages("plumber", repos = "http://cran.us.r-project.org")
+install.packages("here", repos = "http://cran.us.r-project.org")
+install.packages("here", repos = "http://cran.us.r-project.org")
+install.packages('plumber', repos='http://cran.us.r-project.org')
+2+2
+install.packages('here',dependencies=TRUE, repos='http://cran.rstudio.com/')
+install.packages("here", dependencies = TRUE, repos = "http://cran.rstudio.com/")
+file.exists("plumber.R")
+here()
+#r <- plumb("indings/o2r-bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+r <- plumb("/home/markus/o2r-platform/bindings/o2r-bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+r$run(port=8000)
+install.packages("plumber")
+r$run(port=8000)
+#install.packages('plumber', dependencies=TRUE, repos='http://cran.rstudio.com/')
+library(plumber)
+#r <- plumb("indings/o2r-bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+r <- plumb("/home/markus/o2r-platform/bindings/o2r-bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+r$run(port=8000)
+#r <- plumb(here("bindings", "controllers", "plumber", "plumber.R"))  # Where 'myfile.R' is the location of the file shown above
+#r <- plumb("home", "markus", "o2r-platform", "bindings", "o2r-bindings", "controllers", "plumber", "plumber.R")
+here()
+library(here)
+library(here)
+#r <- plumb(here("bindings", "controllers", "plumber", "plumber.R"))  # Where 'myfile.R' is the location of the file shown above
+#r <- plumb("home", "markus", "o2r-platform", "bindings", "o2r-bindings", "controllers", "plumber", "plumber.R")
+here()
+#r <- plumb(here("bindings", "controllers", "plumber", "plumber.R"))  # Where 'myfile.R' is the location of the file shown above
+r <- plumb("home", "markus", "o2r-platform", "bindings", "o2r-bindings", "controllers", "plumber", "plumber.R")
+#install.packages('plumber', dependencies=TRUE, repos='http://cran.rstudio.com/')
+library(plumber)
+#r <- plumb(here("bindings", "controllers", "plumber", "plumber.R"))  # Where 'myfile.R' is the location of the file shown above
+r <- plumb("home", "markus", "o2r-platform", "bindings", "o2r-bindings", "controllers", "plumber", "plumber.R")
+#r <- plumb(here("bindings", "controllers", "plumber", "plumber.R"))  # Where 'myfile.R' is the location of the file shown above
+r <- plumb(here("home", "markus", "o2r-platform", "bindings", "o2r-bindings", "controllers", "plumber", "plumber.R"))
+#r <- plumb(here("bindings", "controllers", "plumber", "plumber.R"))  # Where 'myfile.R' is the location of the file shown above
+r <- plumb(here("plumber.R"))
+#r <- plumb("/home/markus/o2r-platform/bindings/o2r-bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+r$run(port=8000)
+#r <- plumb(here("bindings", "controllers", "plumber", "plumber.R"))  # Where 'myfile.R' is the location of the file shown above
+here()
+install.packages("magrittr")
+# ex-async.R
+needs(dplyr)
+attach(input[[1]])
+# output of final expression is returned to node
+df %>%
+mutate(group = cut(rating, nGroups, ordered = T)) %>%
+group_by(group) %>%
+summarize_each(funs_(fxn)) %>%
+select(group, rating, advance) %>%
+mutate(group = as.character(group))
+getwd()
+getwd() + "/test"
+getwd()."/test"
+paste(getwd(),"/test")
+paste(getwd(),"/test", sep="")
+file.exists(paste(getwd(),"/plumer.R", sep=""))
+file.exists(paste(getwd(),"/plumber.R", sep=""))
+#install.packages('plumber', dependencies=TRUE, repos='http://cran.rstudio.com/')
+library(plumber)
+r <- plumb("/bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+#install.packages('plumber', dependencies=TRUE, repos='http://cran.rstudio.com/')
+library(plumber)
+r <- plumb("bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+#r <- plumb("/home/markus/o2r-platform/bindings/o2r-bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+r$run(port=8000)
+#r <- plumb("bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+r <- plumb("/home/markus/o2r-platform/bindings/o2r-bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+r$run(port=8000)
+#install.packages('plumber', dependencies=TRUE, repos='http://cran.rstudio.com/')
+library(plumber)
+#r <- plumb("bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+r <- plumb("/home/markus/o2r-platform/bindings/o2r-bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+r$run(port=8000)
+knitr::opts_chunk$set(echo = TRUE)
+plot(pressure)
+plot(pressure*2)
+plot(pressure)
+pressure
+install.packages("rgdal")
+installed.packages(c("dplyr"))
+library("dplyr")
+installed.packages(c("dplyr"))
+installed.packages(c("dplyr"), repos='http://cran.rstudio.com/')
+install.packages(c("dplyr"), repos='http://cran.rstudio.com/')

controllers/plumber/plumber.R

@@ -0,0 +1,20 @@
+#' Plot out data from the iris dataset
+#' @get /plot
+#' @png
+
+function (spec){
+  myData <- iris
+  title <- "All Species"
+
+  # Filter if the species was specified
+  if (!missing(spec)){
+    title <- paste0("Only the '", spec, "' Species")
+    myData <- subset(iris, Species == spec)
+  }
+
+
+  plot(myData$Sepal.Length, myData$Petal.Length,
+       main=title, xlab="Sepal Length", ylab="Petal Length")  
+}
+
+

controllers/plumber/runPlumber.R

@@ -0,0 +1,5 @@
+#install.packages('plumber', repos='http://cran.rstudio.com/')
+library("plumber")
+#r <- plumb("/bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+r <- plumb("/home/markus/o2r-platform/bindings/o2r-bindings/controllers/plumber/plumber.R")  # Where 'myfile.R' is the location of the file shown above
+r$run(host = '0.0.0.0', port=8000)