从Java调用R脚本

Question

我想从Java调用R脚本。我已经对该主题进行了google搜索，但是我看到的几乎所有结果都需要我向某些第三方库添加依赖项。任何人都可以向我展示一种在不添加任何依赖项的情况下完成同一件事的好方法吗？

我正在使用Windows计算机，因此也许我可以使用命令行来启动R（如果尚未打开）并运行特定的R脚本。但是我从未写过命令行代码（或从Java调用过），因此我需要代码示例。

我将使用命令行思路包含为以下一种可能的方法编写的工作示例代码。在下面的在线注释中，您可以看到AssembleDataFile.java中的
第三步
被我故意留为空白。如果您认为可以使命令行提示生效，那么请告诉我在第三步中编写什么代码。

另外，请随意提出另一种方法，希望该方法不涉及在我的代码中添加任何其他依赖项。

而且，一如既往，我非常感谢您可能发布到与此问题相关的文章/教程/等的任何链接。

这是我到目前为止的内容：

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.  Can anyone help me 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)

编辑：
这是当我添加Runtime.getRuntime（）。exec（“ Rscript” + rScriptFileName）;时抛出的错误消息；上面的代码：

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

第二编辑：
上面的代码现在可用，因为我遵循了Vincent的建议。但是，我必须输入sleep命令才能给R脚本足够的运行时间。如果没有sleep命令，则上面的Java代码将引发错误，指出Matches.csv文件不存在。我担心30秒的睡眠时间太长了。
谁能给我展示让Java程序等待R程序有机会创建Matches.csv的代码吗？
我很犹豫使用线程工具，因为我读到设计不良的线程可能会导致几乎无法本地化和修复的错误。

Answer 1

您只想调用一个外部应用程序：以下工作行不通？

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