[英]not able to execute R script from java program?
I have a Rscript in a String variable and I want to execute it from Java program and pass some variable to it. 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。 If I execute that R script standalone, it works fine. 如果我独立执行该R脚本,它可以正常工作。 I have converted that R script to one line by escaping it everything by using Python program as shown below: 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
I use the printed string out and store it in String variable and then I am executing with below code and it doesn't work at all. 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。 I am passing path
and client_users
variable to above R script. 我将path
和client_users
变量传递给上面的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);
}
Above code works fine with bash shell script. 上面的代码适用于bash shell脚本。 Is there anything I need to do special for R script? 我需要为R脚本做些什么特别的事吗? I will be using same code for bash script and R scripts as well. 我将对bash脚本和R脚本使用相同的代码。
And this is the error I am getting: 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')'
And if I remove commandList.add("/bin/bash");
如果我删除commandList.add("/bin/bash");
and add commandList.add("/bin/Rscript");
并添加commandList.add("/bin/Rscript");
then I see below error: 然后我看到下面的错误:
Cannot run program "/bin/Rscript": error=2, No such file or directory
Update:- 更新: -
Instead of using my above script, I decided to use simple print hell script in r to see whether I can execute it through Java or not. 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";
When I execute this script with commandList.add("/bin/bash");
当我用commandList.add("/bin/bash");
执行此脚本时commandList.add("/bin/bash");
, I get this error: ,我收到此错误:
/bin/bash: line 2: syntax error near unexpected token `('
/bin/bash: line 2: `sayHello <- function(){'
But if I execute with this commandList.add("/bin/sh");
但是如果我用这个commandList.add("/bin/sh");
, I get this error: ,我收到此错误:
/bin/sh: 2: Syntax error: "(" unexpected
You will have to run /usr/bin/Rscript
directly. 您必须直接运行/usr/bin/Rscript
。 Also, this program doesn't read scripts from the standard input (you have to specify the path to the script as an argument for Rscript
), so you will have to: 此外,此程序不读取标准输入中的脚本(您必须指定脚本的路径作为Rscript
的参数),因此您必须:
As an example, this is a POC: 例如,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);
}
As an alternative, and if your script has a "shebang" as the first line , you could do these changes: 作为替代方案, 如果您的脚本有第一行“shebang” ,您可以执行以下更改:
commandList.add("/usr/bin/Rscript");
) 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");
) the part of the code to be modified would be: 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);
...
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