CODEWITHSUNDEEP
javarcommand-lineio
CodeMed
CodeMed

Reputation: 9205

Calling R script from Java

I would like to call an R script from Java. I have done google searches on the topic, but almost all of the results I have seen would require me to add a dependency to some third party library. How can I accomplish the same thing without adding any dependencies to my code?

I am using a Windows machine, so perhaps I might use the command line to start R (if it is not already open) and to run a specific R script. But I have never written command line code (or called it from Java) so I would need code examples.

I am including working sample code that I wrote for one possible approach below, using my command line idea. In my in-line-comments below, it can be seen that Step Three in AssembleDataFile.java is intentionally left blank by me. How can I make the command line idea work at this point?

I would be open to another approach that does not involve adding any more dependencies to my code.

Here is what I have so far:

AssembleDataFile.java

import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintWriter;

public class AssembleDataFile {
static String delimiter;
static String localPath = "C:\\test\\cr\\";
static String[][] myDataArray;

public static void main(String[] args) {
    String inputPath = localPath+"pd\\";
    String fileName = "MSData.txt";
    delimiter = "\\t";

    // Step One: Import data in two parts
    try {
        // 1A: get length of data file
        BufferedReader br1 = new BufferedReader(new FileReader(inputPath+fileName));
        int numRows = 0;
        int numCols = 0;
        String currentRow;
        while ((currentRow = br1.readLine()) != null) {
            numRows += 1;
            numCols = currentRow.split(delimiter).length;}
        br1.close();
        //1B: populate data into array
        myDataArray = new String[numRows][numCols+1];
        BufferedReader br2 = new BufferedReader(new FileReader(inputPath+fileName));
        String eachRow;
        int rowIdx = 0;
        while ((eachRow = br2.readLine()) != null) {
            String[] splitRow = eachRow.split(delimiter);
            for(int z = 0;z < splitRow.length;z++){myDataArray[rowIdx][z] = splitRow[z];}
            rowIdx += 1;}
        br2.close();
        
        // Step Two: Write data to csv
        String rPath = localPath+"r\\";
        String sFileName = rPath+"2colData.csv";
        PrintWriter outputWriter = new PrintWriter(sFileName);
        for(int q = 0;q < myDataArray.length; q++){
            outputWriter.println(myDataArray[q][8]+", "+myDataArray[q][9]);
        }
        outputWriter.close();
        
        //Step Three: Call R script named My_R_Script.R that uses 2ColData.csv as input
        // not sure how to write this code.  How can I write this part?
        // For what it is worth, one of the R scripts that I intend to call is included below
        //
        //added the following lines here, per Vincent's suggestion:
            String rScriptFileName = rPath+"My_R_Script.R";
        Runtime.getRuntime().exec("mypathto\\R\\bin\\Rscript "+rScriptFileName);
        //
        //
        
        //Step Four: Import data from R and put it into myDataArray's empty last column
        try {Thread.sleep(30000);}//make this thread sleep for 30 seconds while R creates the needed file
        catch (InterruptedException e) {e.printStackTrace();}
        String matchFileName = rPath+"Matches.csv";
        BufferedReader br3 = new BufferedReader(new FileReader(matchFileName));
        String thisRow;
        int rowIndex = 0;
        while ((thisRow = br3.readLine()) != null) {
            String[] splitRow = thisRow.split(delimiter);
            myDataArray[rowIndex][numCols] = splitRow[0];
            rowIndex += 1;}
        br3.close();
        
        //Step Five: Check work by printing out one row from myDataArray
        //Note that the printout has one more column than the input file had.
        for(int u = 0;u<=numCols;u++){System.out.println(String.valueOf(myDataArray[1][u]));}
    }
    catch (FileNotFoundException e) {e.printStackTrace();}
    catch (IOException ie){ie.printStackTrace();}
}
}

My_R_Script.R

myCSV <- read.csv(file="2colData.csv",head=TRUE,sep=",")  
pts = SpatialPoints(myCSV)
Codes = readShapeSpatial("mypath/myshapefile.shp")  
write.csv(ZipCodes$F[overlay(pts,Codes)], "Matches.csv", quote=FALSE, row.names=FALSE)

Edit

Here is the error message that is being thrown when I add Runtime.getRuntime().exec("Rscript "+rScriptFileName); to the code above:

java.io.IOException: Cannot run program "Rscript": CreateProcess error=2, The system cannot find the file specified
at java.lang.ProcessBuilder.start(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at AssembleDataFile.main(AssembleDataFile.java:52)
Caused by: java.io.IOException: CreateProcess error=2, The system cannot find the file specified
at java.lang.ProcessImpl.create(Native Method)
at java.lang.ProcessImpl.<init>(Unknown Source)
at java.lang.ProcessImpl.start(Unknown Source)
... 5 more

Second Edit

The code above now works because I followed Vincent's suggestions. However, I had to put in a sleep command in order to give the R script enough time to run. Without the sleep command, the Java code above throws an error saying that the Matches.csv file does not exist. I am concerned that a 30 second sleep period is too rough of an instrument. How can I get the Java program to wait until the R program has a chance to create Matches.csv? I hesitate to use thread tools because I have read that poorly designed threads can cause bugs that are nearly impossible to localize and fix.

Upvotes: 19

Views: 46447

Answers (5)

Vasily
Vasily

Reputation: 116

Do not wait for the process to finish with Thread.sleep()...

Use the waitFor() method instead.

Process child = Runtime.getRuntime().exec(command, environments, dataDir);

int code = child.waitFor();

switch (code) {
    case 0:
        //normal termination, everything is fine
        break;
    case 1:
        //Read the error stream then
        String message = IOUtils.toString(child.getErrorStream());
        throw new RExecutionException(message);
}

Upvotes: 6

SUBIN K SOMAN
SUBIN K SOMAN

Reputation: 406

BufferedReader reader = null;
        Process shell = null;
        try {
            shell = Runtime.getRuntime().exec(new String[] { "/usr/bin/Rscript", "/media/subin/works/subzworks/RLanguage/config/predict.R" });

            reader = new BufferedReader(new InputStreamReader(shell.getInputStream()));
            String line;
            while ((line = reader.readLine()) != null) {
                System.out.println(line);

            }

        } catch (IOException e) {
            e.printStackTrace();
        }

Upvotes: 3

Simon Urbanek
Simon Urbanek

Reputation: 13932

You can easily adapt this code: http://svn.rforge.net/org/trunk/rosuda/REngine/Rserve/test/StartRserve.java

Among other things it finds R and runs a fixed script in R - you can replace that script with with your script and ignore the last two methods.

Upvotes: 6

Vincent Zoonekynd
Vincent Zoonekynd

Reputation: 32401

You just want to call an external application: wouldn't the following work?

Runtime.getRuntime().exec("Rscript myScript.R");

Upvotes: 20

duffymo
duffymo

Reputation: 309008

...would require me to add a dependency to some third party library...

Why is that so bad? You make it sound like "...would require me to assault a honeybadger with a baseball bat..." I don't see the harm, especially if it works.

Maybe RCaller can help you. No JNI required.

Upvotes: 2

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