Linux Shell command from java [duplicate]

Question

I am trying to run a Linux command from Java. The command runs perfect from command line itself but from Java it does not. The command from command line is

curl -H "Content-Type: text/plain" -d "$(printf '#Genes\nPIK3C2A\nPTEN\nUNC5B')" -X POST --url https://reactome.org/AnalysisService/identifiers/projection/

The command from Java is

 String $notifyMsg="\"$(printf '#Genes\nPIK3C2A\nPTEN\nUNC5B')\"";
 String $reactome = "https://reactome.org/AnalysisService/identifiers/projection/";
 String $notifyTitle= "\"Content-Type: text/plain\"";
 String $command = "curl" + " " + "-H"+ " " +  $notifyTitle + " "+ "-d " + $notifyMsg +" "+ "-X" + " " + "POST" + " " +  " " + "--url" +" " + $reactome;
 System.out.println("Command is: " + $command);

      Process p=Runtime.getRuntime().exec($command);
      p.waitFor();
      System.out.println("Run Result " + p.exitValue() )

I am supprosed to get an output like this

{"summary":{"token":"MjAxODAxMjMxNjQyMDZfNjcy","projection":true,"interactors":false,"type":"OVERREPRESENTATION","sampleName":"Genes","text":true},"expression":{"columnNames":[]},"identifiersNotFound":0,"pathwaysFound":51,"pathways":

But instead i get 0 . Can anyone tell me what could be wrong?

Consider using jsoup or apache http components or any other Java library. You don't need to use curl here. — Elliott Frisch
– Elliott Frisch, Commented Jan 28, 2018 at 18:12
Why would you want to download a file by launching curl when there are a number of native Java libraries to do this? — Joe C
– Joe C, Commented Jan 28, 2018 at 18:12

John Kugelman · Accepted Answer · 2018-01-28 18:06:36Z

2

Quoting and escaping are your enemies. The best thing to do is avoid them entirely. Start the process with a method that lets you pass the individual arguments as separate strings without having to split them apart.

Process p = new ProcessBuilder(
    "curl",
    "-H", "Content-Type: text/plain",
    "-d", "#Genes\nPIK3C2A\nPTEN\nUNC5B",
    "-X", "POST",
    "--url", "https://reactome.org/AnalysisService/identifiers/projection/"
).start();

Your code calls exitValue(), which gives you the exit code of the process. To read its output, read from its input stream.

InputStream s = p.getInputStream();

answered Jan 28, 2018 at 18:06

John Kugelman

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ballmerspeak · Accepted Answer · 2018-01-28 18:08:33Z

1

p.exitValue() will give you the exit code of the process. It returns 0 because the curl succeeded with exit code 0.

I would consider looking into the HttpClient library to perform these natively in Java.

answered Jan 28, 2018 at 18:08

ballmerspeak

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John Kugelman · Accepted Answer · 2018-01-29 00:28:51Z

This is what worked for me:

String notifyMsg = "#Genes\nPIK3C2A\nPTEN\nUNC5B";
String reactome = "https://reactome.org/AnalysisService/identifiers/projection/";
String notifyTitle = "Content-Type: text/plain";

Process p = new ProcessBuilder("curl", "-H", notifyTitle, "-d", notifyMsg, "-X", "POST", "--url", reactome).start();
p.waitFor();
try (Scanner scanner = new Scanner(new InputStreamReader(p.getInputStream()))) {
    while (scanner.hasNextLine()) {
        System.out.println(scanner.nextLine());
    }
}
System.out.println("Run Result " + p.exitValue());

Don't concat the command line manually, use vararg constructor of the ProcessBuilder
There were extra double quotes in your Content-Type instruction and your -d
$(printf is something that shell interprets, but Java doesn't. Just use \n in Java string literals to get new lines.

I've also added some code to read the output.

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