gatk-3.8/scala/src/org/broadinstitute/sting/queue/engine/InProcessRunner.scala

package org.broadinstitute.sting.queue.engine

import org.broadinstitute.sting.queue.function.InProcessFunction
import org.broadinstitute.sting.queue.util.Logging

/**
 * Runs a function that executes in process and does not fork out an external process.
 */
class InProcessRunner(val function: InProcessFunction) extends JobRunner[InProcessFunction] with Logging {
  private var runStatus: RunnerStatus.Value = _

  def start() = {
    try {
      if (logger.isDebugEnabled) {
        logger.debug("Starting: " + function.commandDirectory + " > " + function.description)
      } else {
        logger.info("Starting: " + function.description)
      }

      function.deleteLogs()
      function.deleteOutputs()
      function.mkOutputDirectories()
      runStatus = RunnerStatus.RUNNING
      function.run()
      function.doneOutputs.foreach(_.createNewFile())
      writeDone()
      runStatus = RunnerStatus.DONE
      logger.info("Done: " + function.description)
    } catch {
      case e => {
        runStatus = RunnerStatus.FAILED
        try {
          function.failOutputs.foreach(_.createNewFile())
          writeStackTrace(e)
        } catch {
          case _ => /* ignore errors in the exception handler */
        }
        logger.error("Error: " + function.description, e)
      }
    }
  }

  def status = runStatus
}