/*
 * Copyright (c) 2012, The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
 * restriction, including without limitation the rights to use,
 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 * OTHER DEALINGS IN THE SOFTWARE.
 */

package org.broadinstitute.sting.queue.function.scattergather

import org.broadinstitute.sting.queue.function.InProcessFunction
import org.broadinstitute.sting.queue.QException
import org.broadinstitute.sting.commandline.Input
import org.apache.commons.io.FileUtils
import java.io.File
import collection.JavaConversions._

/**
 * Concatenate log files to the jobOutputFile.
 */
class ConcatenateLogsFunction extends InProcessFunction {
  analysisName = "Concat"

  @Input(doc="Parts to gather back into the original output")
  var logs: Seq[File] = Nil

  override def description = "%s: %s > %s".format(analysisName, logs, jobOutputFile)
  override def shortDescription = analysisName + ": " + jobOutputFile.getName

  def run() {
    val missing = org.broadinstitute.sting.utils.io.IOUtils.waitFor(logs, 120)
    if (!missing.isEmpty)
      throw new QException("Unable to find log: " + missing.mkString(", "))
    logs.foreach(log => {
      FileUtils.copyFile(log, this.jobOutputStream)
      this.jobOutputStream.println()
    })
  }
}
