Package fr.ens.biologie.genomique.eoulsan.util

Class ProcessUtils

java.lang.Object
fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
public final class ProcessUtils extends Object
Utility class for launching external process.
Since:
1.0
Author:
Laurent Jourdren

  • Method Details

    • system

      public static int system(String cmd) throws IOException
      Execute a command.
      Parameters:
      cmd - command to execute
      Returns:
      the exit error of the program
      Throws:
      IOException - if an error occurs while executing the command

    • sh

      public static int sh(List<String> cmd) throws IOException
      Execute a command.
      Parameters:
      cmd - command to execute
      Returns:
      the exit error of the program
      Throws:
      IOException - if an error occurs while executing the command

    • sh

      public static int sh(List<String> cmd, File temporaryDirectory) throws IOException
      Execute a command.
      Parameters:
      cmd - command to execute
      temporaryDirectory - temporary where create the temporary shell file
      Returns:
      the exit error of the program
      Throws:
      IOException - if an error occurs while executing the command

    • exec

      public static void exec(String cmd, boolean stdOutput) throws IOException
      Execute a command with the OS.
      Parameters:
      cmd - Command to execute
      stdOutput - don't show the result of the command on the standard output
      Throws:
      IOException - if an error occurs while running the process

    • execWriteOutput

      public static void execWriteOutput(String cmd, File outputFile) throws IOException
      Execute a command with the OS and save the output in file.
      Parameters:
      cmd - Command to execute
      outputFile - The output file
      Throws:
      IOException - if an error occurs while running the process

    • execToString

      public static String execToString(String cmd) throws IOException
      Execute a command with the OS and return the output in a string.
      Parameters:
      cmd - Command to execute
      Returns:
      a string with the output the command
      Throws:
      IOException - if an error occurs while running the process

    • execToString

      public static String execToString(String cmd, boolean addStdErr, boolean checkExitCode) throws IOException
      Execute a command with the OS and return the output in a string.
      Parameters:
      cmd - Command to execute
      addStdErr - add the output of stderr in the result
      checkExitCode - if true exit code will be checked
      Returns:
      a string with the output the command
      Throws:
      IOException - if an error occurs while running the process

    • logEndTime

      public static void logEndTime(Process p, String cmd, long startTime) throws IOException
      Log the time of execution of a process.
      Parameters:
      p - Process to log
      cmd - Command of the process
      startTime - Start time in ms
      Throws:
      IOException - if an error occurs at the end of the process

    • throwExitCodeException

      public static void throwExitCodeException(int exitCode, String command) throws IOException
      Throw an IOException if the exit code of a process is not equals to 0.
      Parameters:
      exitCode - the exit code
      command - the executed command
      Throws:
      IOException - if the exit code if not 0

    • getExecutablePids

      public static Set<Integer> getExecutablePids(String executableName)
      Return a set withs pid of existing executable.
      Parameters:
      executableName - executable name
      Returns:
      a set of integers with pid of existing executable

    • waitUntilExecutableRunning

      public static void waitUntilExecutableRunning(String executableName)
      Wait the end of the execution of all the instance of an executable.
      Parameters:
      executableName - name of the executable

    • waitRandom

      public static void waitRandom(int maxMilliseconds)
      Wait a random number of milliseconds.
      Parameters:
      maxMilliseconds - the maximum number of milliseconds to wait

    • execThreadOutput

      public static void execThreadOutput(String cmd) throws IOException
      Execute a command and write the content of the standard output and error to System.out and System.err.
      Parameters:
      cmd - Command to execute
      Throws:
      IOException - if an error occurs while executing the command

    • execThreadOutput

      public static void execThreadOutput(String[] cmd) throws IOException
      Execute a command and write the content of the standard output and error to System.out and System.err.
      Parameters:
      cmd - array with the command to execute
      Throws:
      IOException - if an error occurs while executing the command