Class ExecRunner

java.lang.Object
org.biojava.utils.ExecRunner

public class ExecRunner extends Object

Makes running external executables easier, optionally under a watched thread. In addition, probably the most useful feature of ExecRunner is using it to run a command-line program and obtain its stdout and stderr results in two strings. This is done with exec(String) - see that method for an example. With acknowledgements to Michael C. Daconta, author of "Java Pitfalls, Time Saving Solutions, and Workarounds to Improve Programs." and his article in JavaWorld "When Runtime.exec() Won't".

Version:
CVS $Id$
Author:
Scott McCrory., Francois Pepin, Andreas Dräger
  • Constructor Summary

    Constructors
    Constructor
    Description
    Basic ExecRunner constructor.
    ExecRunner(String command)
    ExecRunner constructor which also conveniently runs exec(String).
    ExecRunner(String command, String[] arguments)
    ExecRunner constructor which also conveniently runs exec(String).
  • Method Summary

    Modifier and Type
    Method
    Description
    final Object
    We override the clone method here to prevent cloning of our class.
    int
    exec(String command)
    The exec(String) method runs a process inside of a watched thread.
    int
    exec(String command, OutputStream stdoutStream, OutputStream stderrStream)
    Convenience method for calling exec with OutputStreams.
    int
    exec(String command, PrintWriter stdoutWriter, PrintWriter stderrWriter)
    The exec(String, PrintWriter, PrintWriter) method runs a process inside of a watched thread.
    int
    exec(String command, String[] arguments)
    Sometimes special cases may occur that the arguments of an external program are Strings containing white spaces.
    int
    exec(String command, String[] arguments, OutputStream stdoutStream, OutputStream stderrStream)
    Convenience method for calling exec with OutputStreams.
    int
    exec(String command, String[] arguments, PrintWriter stdoutWriter, PrintWriter stderrWriter)
    The exec(String, PrintWriter, PrintWriter) method runs a process inside of a watched thread.
    Returns the error string if exec(String) was invoked.
    boolean
    Returns whether the maximum runtime was exceeded or not.
    int
    Returns the maximum run time in seconds for this object.
    Returns the output string if exec(String) was invoked.
    static void
    main(String[] args)
    This is for unit testing of the class.
    void
    Sets the maximum run time in seconds.

    Methods inherited from class java.lang.Object

    equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Constructor Details

    • ExecRunner

      public ExecRunner()
      Basic ExecRunner constructor.
    • ExecRunner

      ExecRunner constructor which also conveniently runs exec(String).
      Parameters:
      command - The program or command to run
      Throws:
      ExceptionInInitializerError - thrown if a problem occurs
    • ExecRunner

      public ExecRunner(String command, String[] arguments) throws ExceptionInInitializerError
      ExecRunner constructor which also conveniently runs exec(String).
      Parameters:
      command - The program or command to run
      arguments - An array of Strings in which every single String is exactly one of the program's arguments. So these arguments are allowed to contain white spaces and are marked as Strings by the system.
      Throws:
      ExceptionInInitializerError - thrown if a problem occurs
      Since:
      1.5
  • Method Details

    • clone

      public final Object clone() throws CloneNotSupportedException
      We override the clone method here to prevent cloning of our class.
      Overrides:
      clone in class Object
      Returns:
      Nothing ever really returned since we throw a CloneNotSupportedException
      Throws:
      CloneNotSupportedException - To indicate cloning is not allowed
    • exec

      public int exec(String command) throws IOException, InterruptedException
      The exec(String) method runs a process inside of a watched thread. It returns the client's exit code and feeds its STDOUT and STDERR to ExecRunner's out and err strings, where you then use getOutString() and getErrString() to obtain these values. If the command String contains arguments which are Strings containing white spaces, the method
      exec(program, arguments)
      should be used instead, where arguments is a String[] array containing the arguments of the program. Example:
       // Execute the program and grab the results
       String out = "";
       String err = "";
       try {
      
           ExecRunner er = new ExecRunner();
           er.setMaxRunTimeSecs(maxRunTime);
           er.exec(program);
           if (!er.getMaxRunTimeExceeded()) {
               out = er.getOutString();
               err = er.getErrString();
           }
           else {
               log.error("Maximum run time exceeded!");
               continue;
           }
      
       }
       catch (Exception e) {
           log.error("Error executing " + program + ": " + e.getMessage());
           continue;
       }
       
      Parameters:
      command - The program or command to run
      Returns:
      The command's return code
      Throws:
      IOException - thrown if a problem occurs
      InterruptedException - thrown if a problem occurs
    • exec

      public int exec(String command, String[] arguments) throws IOException, InterruptedException
      Sometimes special cases may occur that the arguments of an external program are Strings containing white spaces. Another example are external processes needing the String arguments to be characterized in a special way. In this cases it is sensefull to write every single argument in an String array. The system itselfe will mark these arguments as Strings so that these special encoding can be omitted.
      Parameters:
      command - The external program to be executed.
      arguments - An array of Strings. Every entry of this array is an argument of the external program to be executed.
      Returns:
      The command's return code
      Throws:
      IOException - thrown if a problem occurs
      InterruptedException - thrown if a problem occurs
      Since:
      1.5
    • exec

      public int exec(String command, OutputStream stdoutStream, OutputStream stderrStream) throws IOException, InterruptedException
      Convenience method for calling exec with OutputStreams.
      Parameters:
      command - The program or command to run
      stdoutStream - java.io.OutputStream
      stderrStream - java.io.OutputStream
      Returns:
      The command's return code
      Throws:
      IOException - thrown if a problem occurs
      InterruptedException - thrown if a problem occurs
    • exec

      public int exec(String command, String[] arguments, OutputStream stdoutStream, OutputStream stderrStream) throws IOException, InterruptedException
      Convenience method for calling exec with OutputStreams.
      Parameters:
      command - The program or command to run
      arguments - An array of Strings containing the program's arguments.
      stdoutStream - java.io.OutputStream
      stderrStream - java.io.OutputStream
      Returns:
      The command's return code
      Throws:
      IOException - thrown if a problem occurs
      InterruptedException - thrown if a problem occurs
      Since:
      1.5
    • exec

      public int exec(String command, PrintWriter stdoutWriter, PrintWriter stderrWriter) throws IOException, InterruptedException
      The exec(String, PrintWriter, PrintWriter) method runs a process inside of a watched thread. It returns the client's exit code and feeds its STDOUT and STDERR to the passed-in streams.
      Parameters:
      command - The program or command to run
      stdoutWriter - java.io.PrintWriter
      stderrWriter - java.io.PrintWriter
      Returns:
      The command's return code
      Throws:
      IOException - thrown if a problem occurs
      InterruptedException - thrown if a problem occurs
    • exec

      public int exec(String command, String[] arguments, PrintWriter stdoutWriter, PrintWriter stderrWriter) throws IOException, InterruptedException
      The exec(String, PrintWriter, PrintWriter) method runs a process inside of a watched thread. It returns the client's exit code and feeds its STDOUT and STDERR to the passed-in streams. The arguments for the external program or command are passed as an array of Strings. This has the advantage that the arguments are allowed to contain white spaces and are marked to be Strings by the System itselfe, which is sometimes important. Every single argument has to be exactly one dimension of the arguments array.
      Parameters:
      command - The program or command to run
      arguments - An array of Strings containing the program's arguments/options.
      stdoutWriter - java.io.PrintWriter
      stderrWriter - java.io.PrintWriter
      Returns:
      The command's return code
      Throws:
      IOException - thrown if a problem occurs
      InterruptedException - thrown if a problem occurs
      Since:
      1.5
    • getErrString

      public String getErrString()
      Returns the error string if exec(String) was invoked.
      Returns:
      The error string if exec(String) was invoked.
    • getMaxRunTimeExceeded

      public boolean getMaxRunTimeExceeded()
      Returns whether the maximum runtime was exceeded or not.
      Returns:
      boolean indicating whether the maximum runtime was exceeded or not.
    • getMaxRunTimeSecs

      public int getMaxRunTimeSecs()
      Returns the maximum run time in seconds for this object.
      Returns:
      the maximum run time in seconds for this object.
    • getOutString

      public String getOutString()
      Returns the output string if exec(String) was invoked.
      Returns:
      The output string if exec(String) was invoked.
    • main

      public static void main(String[] args) throws IOException
      This is for unit testing of the class.
      Parameters:
      args - an array of command-line arguments
      Throws:
      IOException - thrown if a problem occurs
    • setMaxRunTimeSecs

      public void setMaxRunTimeSecs(int max)
      Sets the maximum run time in seconds. If you do not want to limit the executable's run time, simply pass in a 0 (which is also the default).
      Parameters:
      max - Maximim number of seconds to let program run