Is awk a good tool for data extraction along with java?

Question

I am using awk for data extraction on .csv file and am trying to display the extracted data using java. The bash script (awk) is running perfect individually but when run with java, the program crashes for data greater than 3000 values (in csv).Is there a problem with my awk expression or awk is not a good combination with java?

Bash script:

#!/bin/bash
echo "hello"
echo "gracias"
awk -F "\"*,\"*" '{print $1,$2}' data3.csv

Java Code:

import java.io.*;
public class Test {

    public static void main(String[] args) throws Exception {

        int count = 0;
            try {
                    String target = new String("/home/arohan/ab/assignment/test.sh");

                    Runtime rt = Runtime.getRuntime();
                    Process proc = rt.exec(target);
                    proc.waitFor();
                    StringBuffer output = new StringBuffer();
                    BufferedReader reader = new BufferedReader(new InputStreamReader(proc.getInputStream()));
                    String line = "";                       
                    while ((line = reader.readLine())!= null) {
                            output.append(line + "\n");
            count++;
                    }
                    System.out.println("### " + output);
        System.out.println(count);
            } catch (Throwable t) {
                    t.printStackTrace();
            }
    }

}

csv file:

38.55042047 39.55042047
39.55042047 40.55042047
40.55042047 41.55042047
41.55042047 42.55042047
42.55042047 43.55042047
43.55042047 44.55042047
44.55042047 45.55042047
45.55042047 46.55042047
46.55042047 47.55042047
47.55042047 48.55042047
48.55042047 49.55042047
49.55042047 50.55042047
50.55042047 51.55042047
51.55042047 52.55042047
52.55042047 53.55042047
53.55042047 54.55042047
54.55042047 55.55042047
55.55042047 56.55042047
56.55042047 57.55042047
57.55042047 58.55042047
58.55042047 59.55042047
59.55042047 60.55042047
60.55042047 61.55042047
61.55042047 62.55042047
62.55042047 63.55042047
63.55042047 64.55042047
64.55042047 65.55042047
65.55042047 66.55042047
66.55042047 67.55042047
67.55042047 68.55042047
68.55042047 69.55042047
69.55042047 70.55042047
70.55042047 71.55042047
71.55042047 72.55042047
72.55042047 73.55042047
73.55042047 74.55042047
74.55042047 75.55042047
75.55042047 76.55042047
76.55042047 77.55042047
77.55042047 78.55042047
78.55042047 79.55042047
79.55042047 80.55042047
80.55042047 81.55042047
81.55042047 82.55042047
82.55042047 83.55042047
83.55042047 84.55042047
84.55042047 85.55042047
85.55042047 86.55042047
86.55042047 87.55042047
87.55042047 88.55042047
88.55042047 89.55042047
89.55042047 90.55042047
90.55042047 91.55042047
91.55042047 92.55042047
92.55042047 93.55042047
93.55042047 94.55042047
94.55042047 95.55042047
95.55042047 96.55042047
96.55042047 97.55042047
97.55042047 98.55042047
98.55042047 99.55042047
99.55042047 100.55042047
100.55042047    101.55042047
101.55042047    102.55042047
102.55042047    103.55042047
103.55042047    104.55042047
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106.55042047    107.55042047
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111.55042047    112.55042047
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131.55042047    132.55042047
132.55042047    133.55042047
133.55042047    134.55042047
134.55042047    135.55042047
135.55042047    136.55042047
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560.55042047    561.55042047
561.55042047    562.55042047
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980.55042047    981.55042047
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998.55042047    999.55042047
999.55042047    1000.55042047
1000.55042047   1001.55042047
1001.55042047   1002.55042047
1002.55042047   1003.55042047

Ps: I am attaching a sample of the csv file.

Expected Output: Display the values extracted from the csv file. (which gets displayed for values upto 2000).

Answer 1

The quick solution

Move your proc.waitFor(); after the read loop.

Explanation: you haven't specified which error you are getting, but when you call waitFor right after you open the process, it means that the process has limited space for its output before it floods the buffer (see the answer by Bibz). Once that buffer is full, you get deadlocked.

So it will work for small data, but not for large. What you should do is let the process run and keep reading its output. Since you don't have to provide it with input at the same time, this is relatively easy - you just read until you get null. The null indicates that awk closed its output, as it finished working and terminated.

At that point, you waitFor() the process (this should return immediately, unless your script somehow does additional operations after output has been closed). This allows you to process any size of data from your subprocess.

The correct solution

As the many comments tell you, you shouldn't really be using awk or a subprocess here.

• Awk is not designed to process standard CSV files, which may have escaped quotes and commas in them. You need a CSV parser for this.
• Simple text processing can be done by any language. The use for awk is for times when you don't actually want to write a program in a general-purpose language at all. If you are going to write a program in any language - Java, Python, PHP, C++ - then you should be using that same language for your text processing as well.
• Subprocesses require extra work. What if there is an error in the process? The file is not found or doesn't have permissions? In that case, the subprocess will issue an error, but you have no error checking in your code, and it's going to become very complicated once you put in the appropriate error checks and set up a thread to read the standard error as well as the standard output.

So the correct solution would be to use a CSV Parser. For example, there's Apache Commons CSV.

Where you would use something like:

 Path path = Paths.get("/path/to/data3.csv");
 try (CSVParser parser = CSVFormat.DEFAULT.parse(Files.newBufferedReader(path));) {
     for (CSVRecord csvRecord : parser) {
         System.output.println( "### " + csvRecord.get(0) + " " + csvRecord.get(1) + "\n";
     }
 }

Answer 2

Your script's output might be too large for the buffer, from the Process API reference (emphasis mine):

By default, the created subprocess does not have its own terminal or console. All its standard I/O (i.e. stdin, stdout, stderr) operations will be redirected to the parent process, where they can be accessed via the streams obtained using the methods getOutputStream(), getInputStream(), and getErrorStream(). The parent process uses these streams to feed input to and get output from the subprocess. Because some native platforms only provide limited buffer size for standard input and output streams, failure to promptly write the input stream or read the output stream of the subprocess may cause the subprocess to block, or even deadlock.

You could try to start reading your script's output before it completes, but it would not be a robust way of doing it; since both are in parallel, the script could still run all the way and overflow the buffer.

As stated in your question's comment, you should do your sting extraction directly in Java, not in an external script (read the file line by line, do extract, save output, repeat)