How to use ProcessBuilder when using redirection in Linux

Question

I want to run this command using ProcessBuilder:

sort -m -u -T /dir -o output <(zcat big-zipped-file1.gz | sort -u) <(zcat big-zipped-file2.gz | sort -u) <(zcat big-zipped-file3.gz | sort -u)

I have tried the following:

// This doesn't recognise the redirection.
String[] args = new String[] {"sort", "-m", "-u", "-T", "/dir", "-o", "output", "<(zcat big-zipped-file1.gz | sort -u)", "<(zcat big-zipped-file2.gz | sort -u)", "<(zcat big-zipped-file3.gz | sort -u)"};

// This gives:
// /bin/sh: -c: line 0: syntax error near unexpected token `('
String[] args = new String[] {"/bin/sh", "-c", "\"sort -m -u -T /dir -o output <(zcat big-zipped-file1.gz | sort -u) <(zcat big-zipped-file2.gz | sort -u) <(zcat big-zipped-file3.gz | sort -u)\""};

I am using args like this: processBuilder.command(args);

Updated my question. I want to redirect the output from several zcat commands to the sort. — tourniquet_grab
– tourniquet_grab, Commented Jun 12, 2016 at 3:28
ProcessBuilder is not a shell. either invoke the shell explicitly or do the redirection yourself. — jtahlborn
– jtahlborn, Commented Jun 12, 2016 at 3:59
This is not a duplicate. The problem here is different. I did invoke the shell explicitly in my second attempt. — tourniquet_grab
– tourniquet_grab, Commented Jun 12, 2016 at 6:35
First, remove internal quotes around sort .... Second, I don't think sh understands <(...) syntax - it's more of a bash thing. — Roman
– Roman, Commented Jun 12, 2016 at 12:05
You are correct! I figured this out a few hours after I posted the question but could not add an answer since this question was marked duplicate. — tourniquet_grab
– tourniquet_grab, Commented Jun 12, 2016 at 22:00

tourniquet_grab · Accepted Answer · 2016-06-13 20:37:08Z

0

I finally figured it out. As Roman has mentioned in his comment, sh does not understand redirection so I had to use bash. I also had to consume both the input stream and the error stream.

String[] args = new String[] {"/bin/bash", "-c", "sort -m -u -T /dir -o output <(zcat big-zipped-file1.gz | sort -u) <(zcat big-zipped-file2.gz | sort -u) <(zcat big-zipped-file3.gz | sort -u)"};

ProcessBuilder builder = new ProcessBuilder();
builder.command(args);
Process process = builder.start();
BufferedReader input = new BufferedReader(new InputStreamReader(process.getInputStream()));
BufferedReader error = new BufferedReader(new InputStreamReader(process.getErrorStream()));
while((line = input.readLine()) != null);
while((line = error.readLine()) != null);

process.waitFor();

edited Jun 13, 2016 at 20:37

answered Jun 12, 2016 at 21:55

tourniquet_grab

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1 Comment

Roman Over a year ago

You used process.getInputStream() twice. Second one should be error stream.

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