org.biojava.utils
Class ExecRunner

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

public class ExecRunner
extends java.lang.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: ExecRunner.java,v 1.5 2006/12/11 19:00:49 holland Exp $
Author:
Scott McCrory., Francois Pepin, Andreas Dräger

Constructor Summary
ExecRunner()
          Basic ExecRunner constructor.
ExecRunner(java.lang.String command)
          ExecRunner constructor which also conveniently runs exec(String).
ExecRunner(java.lang.String command, java.lang.String[] arguments)
          ExecRunner constructor which also conveniently runs exec(String).
 
Method Summary
 java.lang.Object clone()
          We override the clone method here to prevent cloning of our class.
 int exec(java.lang.String command)
          The exec(String) method runs a process inside of a watched thread.
 int exec(java.lang.String command, java.io.OutputStream stdoutStream, java.io.OutputStream stderrStream)
          Convenience method for calling exec with OutputStreams.
 int exec(java.lang.String command, java.io.PrintWriter stdoutWriter, java.io.PrintWriter stderrWriter)
          The exec(String, PrintWriter, PrintWriter) method runs a process inside of a watched thread.
 int exec(java.lang.String command, java.lang.String[] arguments)
          Sometimes special cases may occur that the arguments of an external program are Strings containing white spaces.
 int exec(java.lang.String command, java.lang.String[] arguments, java.io.OutputStream stdoutStream, java.io.OutputStream stderrStream)
          Convenience method for calling exec with OutputStreams.
 int exec(java.lang.String command, java.lang.String[] arguments, java.io.PrintWriter stdoutWriter, java.io.PrintWriter stderrWriter)
          The exec(String, PrintWriter, PrintWriter) method runs a process inside of a watched thread.
 java.lang.String getErrString()
          Returns the error string if exec(String) was invoked.
 boolean getMaxRunTimeExceeded()
          Returns whether the maximum runtime was exceeded or not.
 int getMaxRunTimeSecs()
          Returns the maximum run time in seconds for this object.
 java.lang.String getOutString()
          Returns the output string if exec(String) was invoked.
static void main(java.lang.String[] args)
          This is for unit testing of the class.
 void setMaxRunTimeSecs(int max)
          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 Detail

ExecRunner

public ExecRunner()
Basic ExecRunner constructor.


ExecRunner

public ExecRunner(java.lang.String command)
           throws java.lang.ExceptionInInitializerError
ExecRunner constructor which also conveniently runs exec(String).

Parameters:
command - The program or command to run
Throws:
java.lang.ExceptionInInitializerError - thrown if a problem occurs

ExecRunner

public ExecRunner(java.lang.String command,
                  java.lang.String[] arguments)
           throws java.lang.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:
java.lang.ExceptionInInitializerError - thrown if a problem occurs
Since:
1.5
Method Detail

clone

public final java.lang.Object clone()
                             throws java.lang.CloneNotSupportedException
We override the clone method here to prevent cloning of our class.

Overrides:
clone in class java.lang.Object
Returns:
Nothing ever really returned since we throw a CloneNotSupportedException
Throws:
java.lang.CloneNotSupportedException - To indicate cloning is not allowed

exec

public int exec(java.lang.String command)
         throws java.io.IOException,
                java.lang.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:
java.io.IOException - thrown if a problem occurs
java.lang.InterruptedException - thrown if a problem occurs

exec

public int exec(java.lang.String command,
                java.lang.String[] arguments)
         throws java.io.IOException,
                java.lang.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:
java.io.IOException - thrown if a problem occurs
java.lang.InterruptedException - thrown if a problem occurs
Since:
1.5

exec

public int exec(java.lang.String command,
                java.io.OutputStream stdoutStream,
                java.io.OutputStream stderrStream)
         throws java.io.IOException,
                java.lang.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:
java.io.IOException - thrown if a problem occurs
java.lang.InterruptedException - thrown if a problem occurs

exec

public int exec(java.lang.String command,
                java.lang.String[] arguments,
                java.io.OutputStream stdoutStream,
                java.io.OutputStream stderrStream)
         throws java.io.IOException,
                java.lang.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:
java.io.IOException - thrown if a problem occurs
java.lang.InterruptedException - thrown if a problem occurs
Since:
1.5

exec

public int exec(java.lang.String command,
                java.io.PrintWriter stdoutWriter,
                java.io.PrintWriter stderrWriter)
         throws java.io.IOException,
                java.lang.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:
java.io.IOException - thrown if a problem occurs
java.lang.InterruptedException - thrown if a problem occurs

exec

public int exec(java.lang.String command,
                java.lang.String[] arguments,
                java.io.PrintWriter stdoutWriter,
                java.io.PrintWriter stderrWriter)
         throws java.io.IOException,
                java.lang.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:
java.io.IOException - thrown if a problem occurs
java.lang.InterruptedException - thrown if a problem occurs
Since:
1.5

getErrString

public java.lang.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 java.lang.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(java.lang.String[] args)
                 throws java.io.IOException
This is for unit testing of the class.

Parameters:
args - an array of command-line arguments
Throws:
java.io.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