I have a java code which has R programming steps in it which is running perfectly fine. But the same R programming steps are extracted into a R file (MyScript.r) and I tried to call this file from my java code. When I run my java code nothing seems to be happening. I may look dumb with what I'm trying to achieve, may be it's true as I don't have knowledge on R. So required your help on this.
My Java code with R programming steps inside it.
package com.rtest;
import java.io.IOException;
import org.rosuda.JRI.Rengine;
public class RWithJavaTest {
public static void main(String a[]) {
// Create an R vector in the form of a string.
String javaVector = "c(1,2,3,4,5)";
// System.out.println("System.getProperty(\"java.library.path\")>>"+System.getProperty("java.library.path")); //Prints path in env var
// Start Rengine.
Rengine engine = new Rengine(new String[] { "--no-save" }, false, null);
// The vector that was created in JAVA context is stored in 'rVector'
// which is a variable in R context.
engine.eval("rVector=" + javaVector);
// Calculate MEAN of vector using R syntax.
engine.eval("meanVal=mean(rVector)");
// Retrieve MEAN value
double mean = engine.eval("meanVal").asDouble();
// Print output values
System.out.println("Mean of given vector is=" + mean);
}
}
The above program when run, successfully giving me the output: 3.0
Java code with R programming steps included in R file and calling the R file from the java code.
package com.rtest;
import java.io.IOException;
public class RWithJavaTest {
public static void main(String a[]) {
try {
System.out.println("before..");
Runtime.getRuntime().exec("Rscript D:\\MyScript.R");
System.out.println("after..");
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}
R script:
// Create an R vector in the form of a string.
String javaVector = "c(1,2,3,4,5)";
// System.out.println("System.getProperty(\"java.library.path\")>>"+System.getProperty("java.library.path")); //Prints path in env var
// Start Rengine.
Rengine engine = new Rengine(new String[] { "--no-save" }, false, null);
// The vector that was created in JAVA context is stored in 'rVector'
// which is a variable in R context.
engine.eval("rVector=" + javaVector);
// Calculate MEAN of vector using R syntax.
engine.eval("meanVal=mean(rVector)");
// Retrieve MEAN value
double mean = engine.eval("meanVal").asDouble();
// Print output values
System.out.println("Mean of given vector is=" + mean);
I know what I did here is something completely wrong but seeking help on 2 things here.
1) How to correct my R Script so that it runs with out any issues
2) Java code to call the R Script, so I can see the output 3.0 once I run the code.
Below lines of code obviously worked for me and it calls the R file successfully.
ProcessBuilder pb = new ProcessBuilder("C:/Program Files/R/R-3.4.3/bin/Rscript.exe" ,"D:/RTest/MyScript.R");
pb.start();
Related
I have a problem that I was going to work on arrays in WebAssembly and I wanted to use Java and C ++, and trying to do this, I ran into the following problems and I would like to ask for help:
Java: I'm using JWebAssembly
And we have a class that works on tables
import de.inetsoftware.jwebassembly.api.annotation.Export;
public class Add {
#Export
public static int[] add( int a[], int b ) {
for(int i = 0;i<b-1;i++){
a[i] += b ;
}
return a;
}
}
we convert it to wasm
import de.inetsoftware.jwebassembly.JWebAssembly;
import java.io.File;
import java.net.URL;
public class Wasm {
public static void main(String[] args) {
File wasmFile = new File("testTable.wasm");
JWebAssembly wasm = new JWebAssembly();
Class clazz = Add.class;
URL url = clazz.getResource(
'/' +
clazz.getName().replace('.', '/') +
".class");
wasm.addFile(url);
String txt = wasm.compileToText();
System.out.println(txt);
wasm.compileToBinary(wasmFile);
}
}
and such an error comes out
Exception in thread "main" de.inetsoftware.jwebassembly.WasmException: Unimplemented Java byte code operation: 42 at Add.java:11
https://en.wikipedia.org/wiki/List_of_Java_bytecode_instructions
And I don't understand why because in this guy's presentation https://www.youtube.com/watch?v=93z9SaLQVVw (40 min+) you can see that it works and compiles
Now C++
I use emscripten, I wanted to do a bubble sort but for the sake of simplicity an example showing the problem
#include <emscripten.h>
using namespace std;
EMSCRIPTEN_KEEPALIVE
int* mainFunction(int table[], int length)
{
int* outTable = new int[length];
for(int i = 0;i<length; i++){
outTable[i] = table[i];
}
return table;
}
By running it with this command test.cpp -s WASM=1 -o test.html
after compiling it, files appear to me from which I extract the appropriate data and in javascript I set and import everything
let wasmExports = null;
let asmLibraryArg = {
abort: () => {},
emscripten_resize_heap: () => {},
};
let info = {
env: asmLibraryArg,
wasi_snapshot_preview1: asmLibraryArg,
};
async function loadWasm() {
let response = await fetch("test.wasm");
let bytes = await response.arrayBuffer();
let wasmObj = await WebAssembly.instantiate(bytes, info);
wasmExports = wasmObj.instance.exports;
}
loadWasm();
and later in the code I use
console.log(wasmExports);
console.log(wasmExports._Z12mainFunctionPii(table, table.length));
results
and when I throw in some array of integers it only throws me the number 0 and I have no idea how to get out of it. Or maybe someone knows another language in which it is possible to compile for wasm and then run it on the website?
Hello working on a small program that just needs to run a python script I have. This python script will play a given .wav file, and draw a shape on the turtle screen. As such, I'm not looking for an output to be returned to java. Here is my java code:
public class Driver {
public static void main(String[] args){
try {
Process p = Runtime.getRuntime().exec("python " +
" D:/Coding Files/Python/MusicColors.py" +" teenagers.wav");
}
catch (Exception e){
System.out.println(e);
}
}
}
The exception I get is:
java.io.IOException: Cannot run program "python":
CreateProcess error=2, The system cannot find the file specified
I probably am making a very stupid mistake as I have limited knowledge in the subject of processes and such. I added python to my system path, so whenever I put "python" into command line, it returns with
Python 3.5.2 (v3.5.2:4def2a2901a5, Jun 25 2016, 22:01:18) [MSC v.1900 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
And makes it the python shell.
Here is the exact line I added to my environment path:
C:\Users\Joe\AppData\Local\Programs\Python\Python35-32
If anyone can figure out where I went wrong I'd really appreciate it!
The $PATH variable you've set is not inherited in Java's execution context. Try passing the Python's bin path to exec()'s execution environment.
To do this, the code below first retrieve all the environment variables and create an array of ENV_KEY=ENV_VALUE pairs.
Then, the path to your Python's bin is appended to the PATH value.
Finally, we pass the array of all environment variables to exec() (via the second parameter).
import java.util.HashMap;
import java.util.Map;
public class Driver {
public static void main(String[] args){
try {
String[] commands = {"python D:/Coding Files/Python/MusicColors.py teenagers.wav"};
// Get a list of all environment variables
final Map<String, String> envMap = new HashMap<String, String>(System.getenv());
// Append Python bin path to Path
envMap.put("Path", envMap.get("Path") + ";C:/Users/Joe/AppData/Local/Programs/Python/Python35-32");
// Convert to an array of ENV_KEY=ENV_VALUE format strings
final String[] envs = new String[envMap.size()];
int i = 0;
for (Map.Entry<String, String> e : envMap.entrySet()) {
envs[i] = e.getKey() + '=' + e.getValue();
i++;
}
// Exec with the environment variables
Process p = Runtime.getRuntime().exec(commands, envs);
}
catch (Exception e){
System.out.println(e);
}
}
}
I have build an application connecting R and java using the Rserve package.
In that, i am getting the error as "evaluation successful but object is too big to transport". i have tried increasing the send buffer size value in Rconnection class also. but that doesn't seem to work.
The object size which is being transported is 4 MB
here is the code from the R connection file
public void setSendBufferSize(long sbs) throws RserveException {
if (!connected || rt == null) {
throw new RserveException(this, "Not connected");
}
try {
RPacket rp = rt.request(RTalk.CMD_setBufferSize, (int) sbs);
System.out.println("rp is send buffer "+rp);
if (rp != null && rp.isOk()) {
System.out.println("in if " + rp);
return;
}
} catch (Exception e) {
e.printStackTrace();
LogOut.log.error("Exception caught" + e);
}
//throw new RserveException(this,"setSendBufferSize failed",rp);
}
The full java class is available here :Rconnection.java
Instead of RServe, you can use JRI, that is shipped with rJava package.
In my opinion JRI is better than RServe, because instead of creating a separate process it uses native calls to integrate Java and R.
With JRI you don't have to worry about ports, connections, watchdogs, etc... The calls to R are done using an operating system library (libjri).
The methods are pretty similar to RServe, and you can still use REXP objects.
Here is an example:
public void testMeanFunction() {
// just making sure we have the right version of everything
if (!Rengine.versionCheck()) {
System.err.println("** Version mismatch - Java files don't match library version.");
fail(String.format("Invalid versions. Rengine must have the same version of native library. Rengine version: %d. RNI library version: %d", Rengine.getVersion(), Rengine.rniGetVersion()));
}
// Enables debug traces
Rengine.DEBUG = 1;
System.out.println("Creating Rengine (with arguments)");
// 1) we pass the arguments from the command line
// 2) we won't use the main loop at first, we'll start it later
// (that's the "false" as second argument)
// 3) no callback class will be used
engine = REngine.engineForClass("org.rosuda.REngine.JRI.JRIEngine", new String[] { "--no-save" }, null, false);
System.out.println("Rengine created...");
engine.parseAndEval("rVector=c(1,2,3,4,5)");
REXP result = engine.parseAndEval("meanVal=mean(rVector)");
// generic vectors are RVector to accomodate names
assertThat(result.asDouble()).isEqualTo(3.0);
}
I have a demo project that exposes a REST API and calls R functions using this package.
Take a look at: https://github.com/jfcorugedo/RJavaServer
I am using Rserve to access an R script through my Java project. The java code asks for a user input to enter the file location and stores in a String variable. This variable is then passes through to the R function which should read the file location perform some processes and then create a new folder and write the processed data in individual files and then print out on the console that all the files have been generated. I initially checked the R connection with a smaller version of the program and it worked. But, when I include the steps to write data to files, it shows the following error:
Enter the file path:
/home/workspace/TestR/test_file
Exception in thread "main" org.rosuda.REngine.Rserve.RserveException: eval failed, request status: error code: 127
at org.rosuda.REngine.Rserve.RConnection.eval(RConnection.java:234)
at testMain.main(testMain.java:23)
Moreover, the code also does not print any statements on the console which have to be printed via R from the Rscript. Here is the Java code:
import java.util.Scanner;
import org.rosuda.REngine.REXP;
import org.rosuda.REngine.REXPMismatchException;
import org.rosuda.REngine.REngineException;
import org.rosuda.REngine.Rserve.RConnection;
import org.rosuda.REngine.Rserve.RserveException;
public class testMain {
static String dirPath;
public static void main(String[] args) throws REXPMismatchException, REngineException {
// For user input
Scanner scanner = new Scanner(System.in );
System.out.println("Enter the file path: ");
dirPath = scanner.nextLine();
RConnection c = new RConnection();
// source the Palindrome function
c.eval("source('/home/workspace/TestR/Main.R')");
REXP valueReturned = c.eval("Main(\""+dirPath+"\")");
//c.eval("Main(\""+dirPath+"\")");
System.out.println(valueReturned.length());
}
}
And, here is the R script:
Main <- function(FILE_PATH)
{
## load libraries
library(MALDIquant)
library(MALDIquantForeign)
library(dcemriS4)
require(gridExtra) # also loads grid
library(lattice)
library(fields)
library(matlab)
library(rJava)
#Call the source files of the function which this script will use
source('/home/workspace/TestR/importAnalyzeFormat.R', echo=TRUE)
source('/home/workspace/TestR/exportFile.R', echo=TRUE)
source('/home/workspace/TestR/readRecalibratedSpectra.R', echo=TRUE)
spectralDataObjects <- importAnalyzeFormat(FILE_PATH)
p <- detectPeaks(spectralDataObjects, method="MAD", halfWindowSize=1, SNR=1)
# Assign the p to preprocessedDataObjects
preprocessedDataObjects<-p
dir.create("PreprocessedSpectra", showWarnings = FALSE)
setwd("PreprocessedSpectra")
for(i in 1:length(preprocessedDataObjects))
{
coordinateValue<-metaData(preprocessedDataObjects[[i]])
coordinates<-coordinateValue$imaging$pos
mzValues<-mass(preprocessedDataObjects[[i]])
intensityValues<-intensity(preprocessedDataObjects[[i]])
exportFile(coordinates,mzValues,intensityValues)
}
print("Files exported. Program will now terminate")
print("############################################################")
return(preprocessedDataObjects)
}
Can someone please help me?
You have an error in your script, a 127 means that there is a parse exception.
If you use something like this it will print out the error in the script.
c is the rserve connection in this case.
c.assign(".tmp.", myCode);
REXP r = c.parseAndEval("try(eval(parse(text=.tmp.)),silent=TRUE)");
if (r.inherits("try-error")) System.err.println("Error: "+r.toString())
else { // success .. }
Error code 127 means parsing exception.
Change your line:
c.eval("source('/home/workspace/TestR/Main.R')");
to
c.eval("source(\"/home/workspace/TestR/Main.R\")");
Now it is suppose to work.
I m passing multiple tab delim files into R via Java.The R programm merges those tab delim files as single file and sends back to java and it is captured in the variable "name".Now I want to rename and save that file stored in "name" as tab delim using save dialog box in windows.Any help highly appreciated.Here is the java code:
import org.rosuda.REngine.*;
public class rjava {
// Before this run Rserve() command in R
public String ana(String filenames)
{
String name = "";
try{
System.out.println("INFO: Trying to connect to R ");
RConnection c = new RConnection();
System.out.println("INFO: Connected to R");
System.out.println("INFO: The Server version is "+ c.getServerVersion());
// c.voidEval("source('D:/combine/combining_files.r')");
c.voidEval("source('D:/combine/merge.r')");
c.assign("file",filenames);
// name = (c.eval("fn(file)").asString());
name = (c.eval("combine (file)").asString());
c.close();
}
catch(Exception e)
{
System.out.println("ERROR: In Connection to R");
System.out.println("The Exception is "+ e.getMessage());
e.printStackTrace();
}
return name;
}
}
I find passing complex objects between R and Java to be a pain the ass. I would not pass the full data, but rather would pass only file names as a string. Either have Java tell R to write out the new file (my pref) or have Java read in the file and then write out with a new name.
Can you modify the R program, so that it outputs files in the same path with a given file name, such as [path]/filename.out?
Otherwise, you can modify the execte string so that the R program outputs in a given location.
See http://cran.r-project.org/doc/manuals/R-intro.html#Invoking-R-from-the-command-line
When working at a command line on UNIX or Windows, the command ‘R’ can be used both for starting the main R program in the form R [options] [<infile] [>outfile]
-- EDIT
I just saw that you are using an RConnection. According to the R docs, you can define where to pipe stdout
The function sink, sink("record.lis") will divert all subsequent output from the console to an external file, record.lis.