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## org.biojava.utils.process
Class ExternalProcess

    java.lang.Object
      org.biojava.utils.process.ExternalProcess

    public final class ExternalProcess

extends Object

Utility class to execute an external process and to handle the `STDOUT`, `STDERR` and `STDIN` streams in multiple threads managed by a thread pool.

This class is intended for applications that call an external program many times, e.g. in a loop, and that need high performance throughput, i.e. the program's input and output should not be written to disk. The Java `Runtime.exec(java.lang.String)` methods requires the application to read/write the external program's input and output streams in multiple threads. Otherwise the calling application may block. However, instantiating multiple threads for each call is extensive. On Linux systems there is also the problem that each Java thread is represented by a single process and the number of processes is limited on Linux. Because the Java garbage collector does not free the `Thread` objects properly, an application might run out of threads (indicated by a `OutOfMemoryError` exception) after multiple iterations. Therefore, the `ExternalProcess` class uses a thread pool.

The simplest way to use this class is by calling the static methods `execute(String)` and `execute(String, String, StringWriter, StringWriter)`. However, these methods are not thread safe and no configuration is possible. In the former case the program's input, output and error output is redirected to `STDIN`, `STDOUT` and `STDERR` of the calling program. In the latter case input is provided as string and output and error output is written to `StringWriter` objects. The environment, i.e. the current working directory and the environment variables, are inherited from the calling process. In both cases, a static thread pool of size `THREAD_POOL_SIZE` is used. The command that should be executed is provided as a string argument.

In scenarios where the environment has to be changed, the program input is generated just in time, or the program's output is parsed just in time, the use of an explicit instance of the `ExternalProcess` class is recommended. This instance could be initialized with a custom thread pool. Otherwise a `SimpleThreadPool` of size 3 is used. The input and output is managed by multithreaded input handler and output handler objects. There are four predefined handlers that read the program's input from a `Reader` object or a `InputStream` object and write the program's output to a `Writer` object or a `OutputStream` object. These classes are called: `ReaderInputHandler`, `SimpleInputHandler`, `WriterOutputHandler` and `SimpleOutputHandler`. If no handlers are specified the input and output is redirected to the standards streams of the calling process.

Before one of the methods `execute()` or `execute(Properties)` is called, the commands property should be set. One may include placeholders of the form `%PARAM%` within the commands. If a `Properties` object is passed to the `execute(Properties)` method, the placeholders are replaced by the particular property value. Therefore, the `Properties` object must contain a key named `PARAM` (case doesn't matter). The environment for calling the external program can be configured using the properties workingDirectory and environmentProperties.

Finally, the sleepTime property can be increased, in case the output handlers are not able to catch the whole program's output within the given time. The default value is `SLEEP_TIME` [in milliseconds].

Version:
  $Revision: 4023 $
Author:
  Martin Szugat
See Also:
  `Process`

Field Summary
`static int` | `SLEEP_TIME` Number of milliseconds the execute method should pauses after the external process has finished the execution.
`static int` | `THREAD_POOL_SIZE` Size of the thread pool for the static execute methods.

Constructor Summary
`ExternalProcess()` Initializes the external process.
`ExternalProcess(ThreadPool threadPool)` Initializes the external process.

Method Summary
`int` | `execute()` Executes the external process and waits for its termination.
`int` | `execute(Properties variables)` Executes the external process and waits for its termination.
`static int` | `execute(String commands)` Executes an external program.
`static int` | `execute(String commands, String inputString, StringWriter outputString, StringWriter errorString)` Executes an external program.
`protected void` | `finalize()`
`String` | `getCommands()` Gets the command line including the path or name of the external program and its command line arguments.
`String[]` | `getEnvironmentProperties()` Gets environment variables for the external process.
`OutputHandler` | `getErrorHandler()` Gets the output error handler which is responsible for the standard error output of the external process.
`InputHandler` | `getInputHandler()` Gets the input handler which is responsible for the standard input of the external process.
`OutputHandler` | `getOutputHandler()` Gets the output handler which is responsible for the standard output of the external process.
`int` | `getSleepTime()` Gets the number of milliseconds the execute(Properties) method should pauses after the external process is terminated.
`File` | `getWorkingDirectory()` Gets the working directory for the external process.
`static String` | `joinCommands(Object[] commandList)` Joins a command list to a single command string.
`static void` | `main(String[] args)` Runs an external program from the command line.
`static String` | `resolveCommands(String commands, Properties variables)` Resolves the given command line by replacing all placeholder of the format `%NAME%` with the values from the given properties for the corresponding keys of the format `NAME`.
`void` | `setCommands(String commands)` Sets the command line including the path or name of the external program and its command line arguments.
`void` | `setEnvironmentProperties(String[] environmentProperties)` Sets environment variables for the external process.
`void` | `setErrorHandler(OutputHandler errorHandler)` Sets the output error handler which is responsible for the standard error output of the external process.
`void` | `setInputHandler(InputHandler inputHandler)` Sets the input handler which is responsible for the standard input of the external process.
`void` | `setOutputHandler(OutputHandler outputHandler)` Sets the output handler which is responsible for the standard output of the external process.
`void` | `setSleepTime(int sleepTime)` Sets the number of milliseconds the execute(Properties) method should pauses after the external process is terminated.
`void` | `setWorkingDirectory(File workingDirectory)` Sets the working directory for the external process.
`ThreadPool` | `threadPool()` Gets the thread pool which is used for the input and output handlers.

Methods inherited from class java.lang.Object
`clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Field Detail

### THREAD_POOL_SIZE

    public static final int THREAD_POOL_SIZE

  Size of the thread pool for the static execute methods.

  See Also:
    Constant Field Values

### SLEEP_TIME

    public static final int SLEEP_TIME

  Number of milliseconds the execute method should pauses after the external process has finished the execution.

  See Also:
    Constant Field Values

Constructor Detail

### ExternalProcess

    public ExternalProcess()

  Initializes the external process.

### ExternalProcess

    public ExternalProcess(ThreadPool threadPool)

  Initializes the external process.

  Parameters:
    `threadPool` - a thread pool with at least three threads or `null` if the default thread pool should be used

Method Detail

### main

    public static void main(String[] args)

  Runs an external program from the command line. The external process inherits the environment variables and the current working directory from the parent process.

  Parameters:
    `args` - the path or the name of the external program and its command line arguments

### resolveCommands

    public static String resolveCommands(String commands,
                                         Properties variables)
                                  throws NullPointerException

  Resolves the given command line by replacing all placeholder of the format `%NAME%` with the values from the given properties for the corresponding keys of the format `NAME`.

  Parameters:
    `commands` - the given command line
    `variables` - the placeholders or `null` if no resolvement should be performed
  Returns:
    the new command line
  Throws:
    `NullPointerException` - if `commands` is `null`.

### execute

    public static int execute(String commands)
                       throws IOException,
                              InterruptedException,
                              NullPointerException,
                              SecurityException,
                              IllegalArgumentException

  Executes an external program. The working directory and the environment variables are inherited from the parent process. The program input is read from `STDIN`, the program output is written to `STDOUT` and the program error output is written to `STDERR`.

  Note: This method is not thread-safe.

  Parameters:
    `commands` - the command line including the path or the name of the external program and its command line arguments
  Returns:
    the exit code from the external program
  Throws:
    `SecurityException` - if a security manager exists and its `checkExec` method doesn't allow creation of a subprocess.
    `IOException` - if an I/O error occurs.
    `NullPointerException` - if `commands` is `null`.
    `IllegalArgumentException` - if `commandList` is empty.
    `InterruptedException` - if the current thread is `interrupted` by another thread while it is waiting, then the wait is ended and an `InterruptedException` is thrown.

### execute

    public static int execute(String commands,
                              String inputString,
                              StringWriter outputString,
                              StringWriter errorString)
                       throws IOException,
                              InterruptedException,
                              NullPointerException,
                              SecurityException,
                              IllegalArgumentException

  Executes an external program. The working directory and the environment variables are inherited from the parent process.

  Note: This method is not thread-safe.

  Parameters:
    `commands` - the command line including the path or the name of the external program and its command line arguments
    `inputString` - the input for the external programm or `null` if the input should be read from `STDIN`
    `outputString` - the output of the external programm or `null` if the output should be written to `STDOUT`
    `errorString` - the error output of the external program or `null` if the error output should be written to `STDERR`
  Returns:
    the exit code from the external program
  Throws:
    `SecurityException` - if a security manager exists and its `checkExec` method doesn't allow creation of a subprocess.
    `IOException` - if an I/O error occurs.
    `NullPointerException` - if `commandList` is `null`.
    `IllegalArgumentException` - if `commandList` is empty.
    `InterruptedException` - if the current thread is `interrupted` by another thread while it is waiting, then the wait is ended and an `InterruptedException` is thrown.

### joinCommands

    public static String joinCommands(Object[] commandList)
                               throws NullPointerException

  Joins a command list to a single command string.

  Parameters:
    `commandList` - the list of the command and its arguments
  Returns:
    the joined command line
  Throws:
    `NullPointerException` - if `commandList` is `null`.

### execute

    public int execute()
                throws IOException,
                       InterruptedException,
                       SecurityException,
                       IllegalArgumentException

  Executes the external process and waits for its termination.

  Returns:
    the exit code from the external process
  Throws:
    `IllegalArgumentException` - if the command is empty
    `SecurityException` - if a security manager exists and its `checkExec` method doesn't allow creation of a subprocess.
    `IOException` - if an I/O error occurs.
    `InterruptedException` - if the current thread is `interrupted` by another thread while it is waiting, then the wait is ended and an `InterruptedException` is thrown.

### execute

    public int execute(Properties variables)
                throws IOException,
                       InterruptedException,
                       SecurityException,
                       IllegalArgumentException

  Executes the external process and waits for its termination.

  Parameters:
    `variables` - a list of key-value-pairs that should be used to replace placeholders in the command line. May be `null`.
  Returns:
    the exit code from the external process
  Throws:
    `SecurityException` - if a security manager exists and its `checkExec` method doesn't allow creation of a subprocess.
    `IllegalArgumentException` - if the command is empty
    `IOException` - if an I/O error occurs.
    `InterruptedException` - if the current thread is `interrupted` by another thread while it is waiting, then the wait is ended and an `InterruptedException` is thrown.

### getCommands

    public String getCommands()

  Gets the command line including the path or name of the external program and its command line arguments.

  Returns:
    the command line

### setCommands

    public void setCommands(String commands)
                     throws NullPointerException

  Sets the command line including the path or name of the external program and its command line arguments.

  Parameters:
    `commands` - the command line
  Throws:
    `NullPointerException` - if `commands` is `null`.

### getEnvironmentProperties

    public String[] getEnvironmentProperties()

  Gets environment variables for the external process.

  Returns:
    a list of strings in the format `name=value` or `null` if the environment variables should be inherited from the parent process

### setEnvironmentProperties

    public void setEnvironmentProperties(String[] environmentProperties)

  Sets environment variables for the external process.

  Parameters:
    `environmentProperties` - a list of strings in the format `name=value` or `null` if the environment variables should be inherited from the parent process

### getErrorHandler

    public OutputHandler getErrorHandler()

  Gets the output error handler which is responsible for the standard error output of the external process.

  Returns:
    the error output handler

### setErrorHandler

    public void setErrorHandler(OutputHandler errorHandler)

  Sets the output error handler which is responsible for the standard error output of the external process.

  Parameters:
    `errorHandler` - the error output handler or `null` if the error output should be redirected to `STDERR`

### getInputHandler

    public InputHandler getInputHandler()

  Gets the input handler which is responsible for the standard input of the external process.

  Returns:
    the input handler

### setInputHandler

    public void setInputHandler(InputHandler inputHandler)

  Sets the input handler which is responsible for the standard input of the external process.

  Parameters:
    `inputHandler` - the input handler or `null` if the input should be read from `STDIN`

### getOutputHandler

    public OutputHandler getOutputHandler()

  Gets the output handler which is responsible for the standard output of the external process.

  Returns:
    the output handler

### setOutputHandler

    public void setOutputHandler(OutputHandler outputHandler)

  Sets the output handler which is responsible for the standard output of the external process.

  Parameters:
    `outputHandler` - the output handler or `null` if the output should be redirected to `STDOUT`

### threadPool

    public ThreadPool threadPool()

  Gets the thread pool which is used for the input and output handlers.

  Returns:
    a thread pool with at least three threads

### getWorkingDirectory

    public File getWorkingDirectory()

  Gets the working directory for the external process.

  Returns:
    the working directory or `null` if it should be inherited from the parent process

### setWorkingDirectory

    public void setWorkingDirectory(File workingDirectory)

  Sets the working directory for the external process.

  Parameters:
    `workingDirectory` - the working directory or `null` if it should be inherited from the parent process

### getSleepTime

    public int getSleepTime()

  Gets the number of milliseconds the execute(Properties) method should pauses after the external process is terminated. This gives the stream handlers the time to complete their work.

  Returns:
    time in milliseconds

### setSleepTime

    public void setSleepTime(int sleepTime)
                      throws IllegalArgumentException

  Sets the number of milliseconds the execute(Properties) method should pauses after the external process is terminated. Increase this value if the output handlers didn't catch the whole program output.

  Parameters:
    `sleepTime` - time in milliseconds
  Throws:
    `IllegalArgumentException` - if `sleepTime` is negative.

### finalize

    protected void finalize()

  Overrides:
    `finalize` in class `Object`

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