Process.execute() throws exception when trying to run command on shell using java

Question

I have written this code which should execute a command on shell to search pattern ">" in a text file , when I try same command on shell it works fine but when I try execute same command using java , it doesn't work for me as buffered reader returns null.Can somebody tell that what I have done wrong in this.

Code:

            String filename="/home/abhijeet/sample.txt";

            Process contigcount_p;

            String command_to_count="grep  \">\" "+filename+" | wc -l";

            System.out.println("command for counting contigs "+command_to_count); 

            contigcount_p=Runtime.getRuntime().exec(command_to_count);


             contigcount_p.wait();


            BufferedReader reader = 
                        new BufferedReader(new InputStreamReader(contigcount_p.getInputStream()));    

            System.out.println("chkk buffer"+reader.readLine());

Those are two commands, connected by a pipe. You probably need to wrap this in a shell. — Thilo
– Thilo, Commented Jun 20, 2014 at 9:12
@Thilo I tried which solution was described in comments.It worked as i tested it with redirecting its output to a file in command.Command sends output to file but buffered reader still returns null value. — Abhijeet Panwar
– Abhijeet Panwar, Commented Jun 20, 2014 at 9:27

Community · Accepted Answer · 2017-05-23 12:05:43Z

1

According to comments i have resolved thsi issue by wrapping commands in a shell by using

Runtime.getRuntime().exec(new String[]{"sh", "-c", "grep  \">\" "+filename+" | wc -l"});

By this command was executing successfully but i was still not able to get its output by bufferedreader , as still output value was NULL, so what i have done is that i in first command i have redicted it's output to a temporary file

 Runtime.getRuntime().exec(new String[]{"sh", "-c", "grep  \">\" "+filename+" | wc -l > temp"});

and I have created one more process to execute a read on this command and then to remove that temporary file.

Please refer to :- shell Command execution Failing when executed from Java

Note: I know that this is not a perfect solution for this as output should be directly available by bufferedreader, but could'd find any solution yet, Any answer is still welcom, for temporary purpose i have used this answer will remove and accept answer if someone gives a solution for this.

edited May 23, 2017 at 12:05

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answered Jun 26, 2014 at 11:15

Abhijeet Panwar

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1 Comment

dethorpe Over a year ago

not sure, but should contigcount_p.wait(); be contigcount_p.waitFor(); to ensure the execed shell command as completed before continuing.

dethorpe · Accepted Answer · 2014-06-26 13:26:40Z

0

Think you have to read inputStream in loop before waiting and use waitFor() rather than wait() to wait for the process to finish if needed, although thats not necassary in this case it will have finished when the reading loop completes.

e.g:

.... 

contigcount_p=Runtime.getRuntime().exec(command_to_count);

BufferedReader reader = new BufferedReader(new InputStreamReader(contigcount_p.getInputStream()));  

String line;
while ((line = reader.readLine()) != null) { 
    System.out.println("chkk buffer"+line);
}

reader.close()

contigcount_p.waitFor();

answered Jun 26, 2014 at 13:26

dethorpe

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2 Comments

dethorpe Over a year ago

Are there any errors? Is the command pipeline itself failing for some reason so no stdout generated, try reading and printing stderr as well to see if anything is there.

Abhijeet Panwar Over a year ago

In java it shows illegal state exceptions. I have posted a new question regarding this :stackoverflow.com/questions/24445942/…

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