First implementation of JobRunInfo

-- onExecutionDone(Map(QFunction, JobRunInfo)) is the new signature, so that you can walk over your jobs and inspect their success/failure and runtime characteristics

public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala

@@ -114,7 +114,7 @@ class QCommandLine extends CommandLineProgram with Logging {
 
     // walk over each script, calling onExecutionDone
     for (script <- allQScripts) {
-      script.onExecutionDone(script.functions, qGraph.success)
+      script.onExecutionDone(qGraph.getFunctionsAndStatus(script.functions), qGraph.success)
     }
 
     if (!qGraph.success) {

public/scala/src/org/broadinstitute/sting/queue/QScript.scala

@@ -24,6 +24,7 @@
 
 package org.broadinstitute.sting.queue
 
+import engine.JobRunInfo
 import org.broadinstitute.sting.queue.function.QFunction
 import annotation.target.field
 import io.Source
@@ -61,8 +62,9 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon
    * A default handler for the onExecutionDone() function.  By default this doesn't do anything
    * except print out a fine status message.
    */
-  def onExecutionDone(jobs: List[QFunction], success: Boolean) {
+  def onExecutionDone(jobs: Map[QFunction, JobRunInfo], success: Boolean) {
     logger.info("Script %s with %d total jobs".format(if (success) "completed successfully" else "failed", jobs.size))
+    for ( (f, info) <- jobs ) logger.info("  %s %s".format(f.jobName, info))
   }
 
   /**

public/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala

@@ -23,6 +23,8 @@ class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNod
    */
   var depth = -1
 
+  var runInfo: JobRunInfo = JobRunInfo.default // todo: replace after testing with _
+
   /**
    * Initializes with the current status of the function.
    */
@@ -88,6 +90,7 @@ class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNod
             tailError()
           } else if (currentStatus == RunnerStatus.DONE) {
             try {
+              runInfo = runner.getRunInfo
               runner.cleanup()
               function.doneOutputs.foreach(_.createNewFile())
             } catch {

public/scala/src/org/broadinstitute/sting/queue/engine/JobRunInfo.scala

@@ -0,0 +1,75 @@
+/*
+ * Copyright (c) 2011, 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.engine
+
+import java.util.Date
+
+/*
+ * Copyright (c) 2011, 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.
+ */
+
+/**
+ * Base class containing all of the information about a job run.
+ */
+class JobRunInfo(startTime: Date, doneTime: Date, memUsedInGb: Int, hostName: String, status: RunnerStatus.Value) {
+  def getStatus = status
+  def getStartTime = startTime
+  def getDoneTime = doneTime
+  def getMemoryUsedInGb = memUsedInGb
+  def getHostname = hostName
+
+  def getRuntimeInMs: Long = {
+    getDoneTime.getTime - getStartTime.getTime
+  }
+
+  override def toString: String =
+    "started %s ended %s runtime %s on host %s using %d Gb memory".format(getStartTime, getDoneTime, getRuntimeInMs, getHostname, getMemoryUsedInGb)
+}
+
+object JobRunInfo {
+  def default = new JobRunInfo(new Date(), new Date(), 1, "localhost", RunnerStatus.DONE)
+  def detailed(startTime: Date, doneTime: Date, memUsedInGb: Int, hostName: String) =
+    new JobRunInfo(startTime, doneTime, memUsedInGb, hostName, RunnerStatus.DONE)
+}

public/scala/src/org/broadinstitute/sting/queue/engine/JobRunner.scala

@@ -69,6 +69,11 @@ trait JobRunner[TFunction <: QFunction] {
   def cleanup() {
   }
 
+  /**
+   * Must be overloaded
+   */
+  def getRunInfo: JobRunInfo = JobRunInfo.default
+
   /**
    * Calls back to a hook that an expert user can setup to modify a job.
    * @param value Value to modify.

public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala

@@ -38,6 +38,7 @@ import org.apache.commons.lang.StringUtils
 import org.broadinstitute.sting.queue.util._
 import collection.immutable.{TreeSet, TreeMap}
 import org.broadinstitute.sting.queue.function.scattergather.{ScatterFunction, CloneFunction, GatherFunction, ScatterGatherableFunction}
+import java.util.Date
 
 /**
  * The internal dependency tracker between sets of function input and output files.
@@ -939,6 +940,14 @@ class QGraph extends Logging {
     edges.sorted(functionOrdering).foreach(edge => if (running) f(edge))
   }
 
+  /**
+   * Utility function for running a method over all function edges.
+   * @param edgeFunction Function to run for each FunctionEdge.
+   */
+  private def getFunctionEdges: List[FunctionEdge] = {
+    jobGraph.edgeSet.toList.filter(_.isInstanceOf[FunctionEdge]).asInstanceOf[List[FunctionEdge]]
+  }
+
   /**
    * Utility function for running a method over all functions, but traversing the nodes in order of dependency.
    * @param edgeFunction Function to run for each FunctionEdge.
@@ -1028,6 +1037,10 @@ class QGraph extends Logging {
    */
   def isShutdown = !running
 
+  def getFunctionsAndStatus(functions: List[QFunction]): Map[QFunction, JobRunInfo] = {
+    getFunctionEdges.map(edge => (edge.function, edge.runInfo)).toMap
+  }
+
   /**
    * Kills any forked jobs still running.
    */