Emergency fix for Ryan:

- Catching errors when LSF fails and retrying.
- When LSF retries fail, catching the error, marking the job as failed, and no longer bkilling everything by exiting Queue.
- Caching function fields by class instead of each instance of a function saving a list of its fields.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4490 348d0f76-0448-11de-a6fe-93d51630548a

scala/src/org/broadinstitute/sting/queue/QScriptManager.scala

@@ -10,6 +10,7 @@ import java.lang.String
 import org.apache.log4j.Level
 import scala.tools.nsc.util.{FakePos, NoPosition, Position}
 import org.broadinstitute.sting.utils.classloader.{PackageUtils, PluginManager}
+import org.broadinstitute.sting.queue.util.TextFormatUtils._
 
 /**
  * Plugin manager for QScripts which loads QScripts into the current class loader.
@@ -81,13 +82,6 @@ object QScriptManager extends Logging {
     }
   }
 
-  /**
-   * Returns the string "s" if x is greater than 1.
-   * @param x Value to test.
-   * @return "s" if x is greater than one else "".
-   */
-  private def plural(x: Int) = if (x > 1) "s" else ""
-
   /**
    * NSC (New Scala Compiler) reporter which logs to Log4J.
    * Heavily based on scala/src/compiler/scala/tools/nsc/reporters/ConsoleReporter.scala

scala/src/org/broadinstitute/sting/queue/engine/LsfJobRunner.scala

@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.queue.engine
 
 import java.io.File
-import org.broadinstitute.sting.queue.util.{IOUtils, LsfJob, Logging}
 import org.broadinstitute.sting.queue.function.CommandLineFunction
+import org.broadinstitute.sting.queue.util._
 
 /**
  * Runs jobs on an LSF compute cluster.
@@ -45,6 +45,8 @@ class LsfJobRunner(function: CommandLineFunction) extends DispatchJobRunner with
     if (!IOUtils.CURRENT_DIR.getCanonicalFile.equals(function.commandDirectory))
       job.workingDir = function.commandDirectory
 
+    job.extraBsubArgs ++= function.extraArgs
+
     if (function.jobRestartable)
       job.extraBsubArgs :+= "-r"
 
@@ -74,9 +76,19 @@ class LsfJobRunner(function: CommandLineFunction) extends DispatchJobRunner with
       function.jobErrorFile.delete()
 
     runStatus = RunnerStatus.RUNNING
-    job.run()
-    jobStatusPath = IOUtils.absolute(new File(function.commandDirectory, "." + job.bsubJobId)).toString
-    logger.info("Submitted LSF job id: " + job.bsubJobId)
+    try {
+      Retry.attempt(() => job.run(), 1, 5, 10)
+      jobStatusPath = IOUtils.absolute(new File(function.commandDirectory, "." + job.bsubJobId)).toString
+      logger.info("Submitted LSF job id: " + job.bsubJobId)
+    } catch {
+      case re: RetryException =>
+        removeTemporaryFiles()
+        runStatus = RunnerStatus.FAILED
+      case e =>
+        logger.error("Error trying to start job.", e)
+        removeTemporaryFiles()
+        runStatus = RunnerStatus.FAILED
+    }
   }
 
   /**

scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala

@@ -33,6 +33,9 @@ trait CommandLineFunction extends QFunction with Logging {
   /** Job queue to run the command */
   var jobQueue: String = _
 
+  /** Extra arguments to specify on the command line */
+  var extraArgs: List[String] = Nil
+
   /** Temporary directory to write any files */
   var jobTempDir: File = IOUtils.javaTempDir
 

scala/src/org/broadinstitute/sting/queue/function/QFunction.scala

@@ -85,14 +85,14 @@ trait QFunction {
   def failOutputs = statusPaths.map(path => new File(path + ".fail"))
 
   /** The complete list of fields on this CommandLineFunction. */
-  lazy val functionFields: List[ArgumentSource] = initFunctionFields
+  def functionFields = QFunction.classFields(this.getClass).functionFields
   /** The @Input fields on this CommandLineFunction. */
-  lazy val inputFields = functionFields.filter(source => ReflectionUtils.hasAnnotation(source.field, classOf[Input]))
+  def inputFields = QFunction.classFields(this.getClass).inputFields
   /** The @Output fields on this CommandLineFunction. */
-  lazy val outputFields = functionFields.filter(source => ReflectionUtils.hasAnnotation(source.field, classOf[Output]))
+  def outputFields = QFunction.classFields(this.getClass).outputFields
   /** The @Argument fields on this CommandLineFunction. */
-  lazy val argumentFields = functionFields.filter(source => ReflectionUtils.hasAnnotation(source.field, classOf[Argument]))
-
+  def argumentFields = QFunction.classFields(this.getClass).argumentFields
+  
   /**
    * Called at most once, returns the list of fields for this function.
    */
@@ -344,3 +344,40 @@ trait QFunction {
    */
   private def invokeObj(source: ArgumentSource) = source.parentFields.foldLeft[AnyRef](this)(ReflectionUtils.getValue(_, _))
 }
+
+object QFunction {
+  /**
+   * The list of fields defined on a class
+   * @param clazz The class to lookup fields.
+   */
+  private class ClassFields(clazz: Class[_]) {
+    /** The complete list of fields on this CommandLineFunction. */
+    val functionFields: List[ArgumentSource] = ParsingEngine.extractArgumentSources(clazz).toList
+    /** The @Input fields on this CommandLineFunction. */
+    val inputFields = functionFields.filter(source => ReflectionUtils.hasAnnotation(source.field, classOf[Input]))
+    /** The @Output fields on this CommandLineFunction. */
+    val outputFields = functionFields.filter(source => ReflectionUtils.hasAnnotation(source.field, classOf[Output]))
+    /** The @Argument fields on this CommandLineFunction. */
+    val argumentFields = functionFields.filter(source => ReflectionUtils.hasAnnotation(source.field, classOf[Argument]))
+  }
+
+  /**
+   * The mapping from class to fields.
+   */
+  private var classFieldsMap = Map.empty[Class[_], ClassFields]
+
+  /**
+   * Returns the fields for a class.
+   * @param clazz Class to retrieve fields for.
+   * @return the fields for the class.
+   */
+  private def classFields(clazz: Class[_]) = {
+    classFieldsMap.get(clazz) match {
+      case Some(classFields) => classFields
+      case None =>
+        val classFields = new ClassFields(clazz)
+        classFieldsMap += clazz -> classFields
+        classFields
+    }
+  }
+}

scala/src/org/broadinstitute/sting/queue/util/Retry.scala

@@ -0,0 +1,45 @@
+package org.broadinstitute.sting.queue.util
+
+import org.broadinstitute.sting.queue.util.TextFormatUtils._
+
+/**
+ * Utilities for retrying a function and waiting a number of minutes.
+ */
+object Retry extends Logging {
+  /**
+   * Attempt the function and return the value on success.
+   * Each time the function fails the stack trace is logged.
+   * @param f Function to run and return its value.
+   * @param wait The length in minutes to wait before each attempt.
+   * @throws RetryException when all retries are exhausted.
+   * @return The successful result of f.
+   */
+  def attempt[A](f: () => A, wait: Double*): A = {
+    var count = 0
+    var success = false
+    val tries = wait.size + 1
+    var result = null.asInstanceOf[A]
+    while (!success && count < tries) {
+      try {
+        result = f()
+        success = true
+      } catch {
+        case e => {
+          count += 1
+          if (count < tries) {
+            val minutes = wait(count-1)
+            logger.error("Caught error during attempt %s of %s."
+                    .format(count, tries), e)
+            logger.error("Retrying in %.1f minute%s.".format(minutes, plural(minutes)))
+            Thread.sleep((minutes * 1000 * 60).toLong)
+          } else {
+            logger.error("Caught error during attempt %s of %s. Giving up."
+                    .format(count, tries), e)
+            throw new RetryException("Gave up after %s attempts.".format(tries), e)
+          }
+        }
+      }
+    }
+    result
+  }
+}

scala/src/org/broadinstitute/sting/queue/util/RetryException.scala

@@ -0,0 +1,9 @@
+package org.broadinstitute.sting.queue.util
+
+import org.broadinstitute.sting.queue.QException
+
+/**
+ * Thrown after giving up on retrying.
+ */
+class RetryException(private val message: String, private val throwable: Throwable)
+        extends QException(message, throwable) {}

scala/src/org/broadinstitute/sting/queue/util/TextFormatUtils.scala

@@ -0,0 +1,31 @@
+package org.broadinstitute.sting.queue.util
+
+object TextFormatUtils {
+  /**
+   * Returns the string "s" if x is greater than 1.
+   * @param x Value to test.
+   * @return "s" if x is greater than one else "".
+   */
+  def plural(x: Int) = if (x > 1) "s" else ""
+
+  /**
+   * Returns the string "s" if x is greater than 1.
+   * @param x Value to test.
+   * @return "s" if x is greater than one else "".
+   */
+  def plural(x: Long) = if (x > 1) "s" else ""
+
+  /**
+   * Returns the string "s" if x is not equal to 1.
+   * @param x Value to test.
+   * @return "s" if x is greater than one else "".
+   */
+  def plural(x: Float) = if (x != 1) "s" else ""
+
+  /**
+   * Returns the string "s" if x is not equal to 1.
+   * @param x Value to test.
+   * @return "s" if x is greater than one else "".
+   */
+  def plural(x: Double) = if (x != 1) "s" else ""
+}