无法从java程序执行R脚本？

Question

我在String变量中有一个Rscript,我想从Java程序执行它并将一些变量传递给它.如果我独立执行该R脚本,它可以正常工作.我通过使用Python程序将所有R脚本转换为一行,如下所示:

import json

jsonstr = json.dumps({"script": """\
#!/usr/bin/Rscript

# read the data file
library('jsonlite')
library('rpart')

args <- as.list(Sys.getenv(c(
                        "path",
                        "client_users")))

if (args[["path"]]==""){
    args[["path"]] <- "."
}

# other stuff here
# other stuff here

"""})

print jsonstr

我使用打印出来的字符串并将其存储在String变量中,然后我执行下面的代码,它根本不起作用.我传递path和client_users变量到上面的R脚本.

public static void main(String[] args) throws IOException, InterruptedException {

    // this is your script in a string
    // String script = "#!/bin/bash\n\necho \"Hello World\"\n\n readonly PARAM1=$param1\n echo $PARAM1\n\nreadonly PARAM2=$param2\n echo $PARAM2\n\n";
    String script = "above R Script here";

    List<String> commandList = new ArrayList<>();
    commandList.add("/bin/bash");

    ProcessBuilder builder = new ProcessBuilder(commandList);
    builder.environment().put("path", "/home/david");
    builder.environment().put("client_users", "1000");
    builder.redirectErrorStream(true);
    Process shell = builder.start();

    // Send your script to the input of the shell, something
    // like doing cat script.sh | bash in the terminal
    try(OutputStream commands = shell.getOutputStream()) {
        commands.write(script.getBytes());
    }

    // read the outcome
    try(BufferedReader reader = new BufferedReader(new InputStreamReader(shell.getInputStream()))) {
        String line;
        while((line = reader.readLine()) != null) {
            System.out.println(line);
        }
    }

    // check the exit code
    int exitCode = shell.waitFor();
    System.out.println("EXIT CODE: " + exitCode);
}

上面的代码适用于bash shell脚本.我需要为R脚本做些什么特别的事吗？我将对bash脚本和R脚本使用相同的代码.

这是我得到的错误:

/bin/bash: line 7: -: No such file or directory /bin/bash: line 10: syntax error near unexpected token `'jsonlite'' /bin/bash: line 10: `library('jsonlite')' 

如果我删除commandList.add("/bin/bash");并添加,commandList.add("/bin/Rscript");那么我看到下面的错误:

Cannot run program "/bin/Rscript": error=2, No such file or directory

更新: -

我没有使用上面的脚本,而是决定在r中使用简单的打印地狱脚本来查看是否可以通过Java执行它.

// this will print hello
String script = "#!/usr/bin/env Rscript\nsayHello <- function(){\n   print('hello')\n}\n\nsayHello()\n";

当我执行此脚本时commandList.add("/bin/bash");,我收到此错误:

/bin/bash: line 2: syntax error near unexpected token `('
/bin/bash: line 2: `sayHello <- function(){'

但是,如果我执行此操作commandList.add("/bin/sh");,我会收到此错误:

/bin/sh: 2: Syntax error: "(" unexpected

Answer 1

您必须/usr/bin/Rscript直接运行。此外，该程序不会从标准输入读取脚本（您必须指定脚本的路径作为 的参数Rscript），因此您必须：

• 创建临时文件
• 写你的脚本
• 使用 Rscript 执行脚本
• 删除临时文件（作为良好的编程实践）

举个例子，这是一个 POC：

public static void main(String[] args) throws IOException, InterruptedException {

    // Your script
    String script = "#!/usr/bin/env Rscript\n" +
            "\n" +
            "sayHello <- function() {\n" +
            "    print('hello')\n" +
            "}\n" +
            "\n" +
            "sayHello()\n";

    // create a temp file and write your script to it
    File tempScript = File.createTempFile("test_r_scripts_", "");
    try(OutputStream output = new FileOutputStream(tempScript)) {
        output.write(script.getBytes());
    }

    // build the process object and start it
    List<String> commandList = new ArrayList<>();
    commandList.add("/usr/bin/Rscript");
    commandList.add(tempScript.getAbsolutePath());
    ProcessBuilder builder = new ProcessBuilder(commandList);
    builder.redirectErrorStream(true);
    Process shell = builder.start();

    // read the output and show it
    try(BufferedReader reader = new BufferedReader(
            new InputStreamReader(shell.getInputStream()))) {
        String line;
        while((line = reader.readLine()) != null) {
            System.out.println(line);
        }
    }

    // wait for the process to finish
    int exitCode = shell.waitFor();

    // delete your temp file
    tempScript.delete();

    // check the exit code (exit code = 0 usually means "executed ok")
    System.out.println("EXIT CODE: " + exitCode);
}

作为替代方案，如果您的脚本第一行有“shebang”，您可以进行以下更改：

• 将其可执行属性设置为“true”
• 使用临时文件的路径作为 commandList 中的第一个元素（即删除commandList.add("/usr/bin/Rscript");）

要修改的代码部分是：

...

// create a temp file and write your script to it
File tempScript = File.createTempFile("test_r_scripts_", "");
tempScript.setExecutable(true);
try(OutputStream output = new FileOutputStream(tempScript)) {
    output.write(script.getBytes());
}

// build the process object and start it
List<String> commandList = new ArrayList<>();
commandList.add(tempScript.getAbsolutePath());
ProcessBuilder builder = new ProcessBuilder(commandList);

...