76 lines
2.2 KiB
Scala
Executable File
76 lines
2.2 KiB
Scala
Executable File
package org.broadinstitute.sting.queue.engine
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import org.broadinstitute.sting.queue.function.CommandLineFunction
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import org.broadinstitute.sting.queue.util.{JobExitException, Logging, ShellJob}
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/**
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* Runs jobs one at a time locally
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*/
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class ShellJobRunner(val function: CommandLineFunction) extends CommandLineJobRunner with Logging {
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private var runStatus: RunnerStatus.Value = _
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/**
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* Runs the function on the local shell.
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* @param function Command to run.
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*/
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def start() = {
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try {
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val job = new ShellJob
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job.workingDir = function.commandDirectory
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job.outputFile = function.jobOutputFile
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job.errorFile = function.jobErrorFile
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writeExec()
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job.shellScript = exec
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// Allow advanced users to update the job.
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updateJobRun(job)
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if (logger.isDebugEnabled) {
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logger.debug("Starting: " + function.commandDirectory + " > " + function.commandLine)
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} else {
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logger.info("Starting: " + function.commandLine)
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}
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logger.info("Output written to " + function.jobOutputFile)
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if (function.jobErrorFile != null)
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logger.info("Errors written to " + function.jobErrorFile)
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function.deleteLogs()
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function.deleteOutputs()
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function.mkOutputDirectories()
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runStatus = RunnerStatus.RUNNING
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job.run()
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removeTemporaryFiles()
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function.doneOutputs.foreach(_.createNewFile())
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runStatus = RunnerStatus.DONE
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logger.info("Done: " + function.commandLine)
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} catch {
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case jee: JobExitException =>
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runStatus = RunnerStatus.FAILED
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try {
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removeTemporaryFiles()
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function.failOutputs.foreach(_.createNewFile())
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writeError(jee.getMessage)
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} catch {
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case _ => /* ignore errors in the exception handler */
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}
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logger.error("Error: " + function.commandLine)
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logger.error(jee.stdErr)
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case e =>
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runStatus = RunnerStatus.FAILED
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try {
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removeTemporaryFiles()
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function.failOutputs.foreach(_.createNewFile())
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writeStackTrace(e)
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} catch {
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case _ => /* ignore errors in the exception handler */
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}
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logger.error("Error: " + function.commandLine, e)
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}
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}
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def status = runStatus
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}
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