Replay

core/src/main/scala/dagr/core/cmdline/DagrCoreMain.scala

@@ -28,7 +28,7 @@ import java.net.InetAddress
 import java.nio.file.{Files, Path}
 import java.text.DecimalFormat
 
-import com.fulcrumgenomics.commons.CommonsDef.unreachable
+import com.fulcrumgenomics.commons.CommonsDef.{FilePath, unreachable}
 import com.fulcrumgenomics.commons.io.{Io, PathUtil}
 import com.fulcrumgenomics.commons.util.{LazyLogging, LogLevel, Logger}
 import com.fulcrumgenomics.sopt.cmdline.{CommandLineProgramParserStrings, ValidationException}
@@ -41,7 +41,8 @@ import dagr.core.execsystem._
 import dagr.core.execsystem2.GraphExecutor
 import dagr.core.execsystem2.{TopLikeStatusReporter => TopLikeStatusReporter2}
 import dagr.core.execsystem2.local.LocalTaskExecutor
-import dagr.core.reporting.{FinalStatusReporter, PeriodicRefreshingReporter, Terminal}
+import dagr.core.execsystem2.replay.TaskCache
+import dagr.core.reporting.{ExecutionLogger, FinalStatusReporter, PeriodicRefreshingReporter, Terminal}
 import dagr.core.tasksystem.Pipeline
 
 import scala.collection.mutable.ListBuffer
@@ -112,7 +113,9 @@ class DagrCoreArgs(
   @arg(doc = "Provide an top-like interface for tasks with the give delay in seconds. This suppress info logging.")
   var interactive: Boolean = false,
   @arg(doc = "Use the experimental execution system.")
-  val experimentalExecution: Boolean = false
+  val experimentalExecution: Boolean = false,
+  @arg(doc = "Attempt to replay using the provided replay log")
+  val replayLog: Option[FilePath] = None
 ) extends LazyLogging {
 
   // These are not optional, but are only populated during configure()
@@ -184,7 +187,12 @@ class DagrCoreArgs(
     * an execution report.
     */
   protected[cmdline] def execute(pipeline : Pipeline)(implicit ex: ExecutionContext): Int = {
-    val report  = this.reportPath.getOrElse(throw new IllegalStateException("execute() called before configure()"))
+    val report = this.reportPath.getOrElse(throw new IllegalStateException("execute() called before configure()"))
+    // FIXME: should this path be exposed on the command line?
+    val executionLog = {
+      if (report == Io.StdOut.toAbsolutePath) None // FIXME
+      else Some(report.getParent.resolve("execution_log.txt"))
+    }
 
     if (interactive && !Terminal.supportsAnsi) {
       logger.warning("ANSI codes are not supported in your terminal.  Interactive mode will not be used.")
@@ -210,6 +218,15 @@ class DagrCoreArgs(
         )
         graphExecutor.withLogger(reporter)
       }
+      executionLog.foreach { log =>
+        val executionLogger = new ExecutionLogger(log)
+        graphExecutor.withLogger(executionLogger)
+        graphExecutor.withTaskRegister(executionLogger)
+      }
+      this.replayLog.foreach { log =>
+        val taskCache = TaskCache(log)
+        graphExecutor.withTaskCache(taskCache)
+      }
       (graphExecutor, graphExecutor execute pipeline)
     }
     else {

core/src/main/scala/dagr/core/execsystem/TaskStatus.scala

@@ -29,7 +29,7 @@ sealed trait TaskStatus extends RootTaskStatus {
   override def toString: String = description
 }
 
-object TaskStatus extends {
+object TaskStatus {
   /** Checks if a task with a given status is done.
     *
     * @param taskStatus the status of the task

core/src/main/scala/dagr/core/execsystem2/GraphExecutor.scala

@@ -26,15 +26,17 @@
 package dagr.core.execsystem2
 
 import com.fulcrumgenomics.commons.util.LazyLogging
+import dagr.core.execsystem2.replay.TaskCache
 import dagr.core.reporting.FinalStatusReporter
-import dagr.core.tasksystem.{Retry, Task}
+import dagr.core.reporting.ReportingDef.{TaskLogger, TaskRegister}
 import dagr.core.tasksystem.Task.{TaskInfo => RootTaskInfo}
+import dagr.core.tasksystem.{Retry, Task}
 
 import scala.collection.mutable
 import scala.collection.mutable.ListBuffer
 import scala.concurrent.duration.Duration
 import scala.concurrent.{Await, ExecutionContext, Future, blocking}
-import scala.util.{Failure, Success, Try}
+import scala.util.{Failure, Success}
 
 /** Coordinates between the dependency graph ([[DependencyGraph]]) and task executor ([[TaskExecutor]]) given a (root)
   * task to execute.
@@ -51,6 +53,14 @@ trait GraphExecutor[T<:Task] extends FinalStatusReporter {
   /** Adds the [[TaskLogger]] to the list of loggers to be notified when a task's status is updated. */
   def withLogger(logger: TaskLogger): this.type
 
+  /** Adds the [[TaskRegister]] to the list of registers to be notified when a list of tasks is returned by [[Task.getTasks]] */
+  def withTaskRegister(register: TaskRegister): this.type
+
+  /** Adds the [[TaskCache]] to the list of registers to be notified when a list of tasks is returned by [[Task.getTasks]] */
+  def withTaskCache(taskCache: TaskCache): this.type = {
+    withTaskRegister(taskCache)
+  }
+
   /** Returns the executor that execute tasks. */
   protected def taskExecutor: TaskExecutor[T]
 
@@ -88,9 +98,25 @@ private class GraphExecutorImpl[T<:Task](protected val taskExecutor: TaskExecuto
   /** A list of [[TaskLogger]]s that will be notified when a task's status is updated. */
   private val loggers: ListBuffer[TaskLogger] = ListBuffer[TaskLogger](new TaskStatusLogger)
 
+  /** A list of [[TaskLogger]]s that will be notified when a task's status is updated. */
+  private val registers: ListBuffer[TaskRegister] = ListBuffer[TaskRegister]()
+
+  /** A list of [[TaskLogger]]s that will be notified when a task's status is updated. */
+  private val taskCaches: ListBuffer[TaskCache] = ListBuffer[TaskCache]()
+
   /** Adds the [[TaskLogger]] to the list of loggers to be notified when a task's status is updated. */
   def withLogger(logger: TaskLogger): this.type = { this.loggers.append(logger); this }
 
+  /** Adds the [[TaskRegister]] to the list of registers to be notified when a list of tasks is returned by [[Task.getTasks]] */
+  def withTaskRegister(register: TaskRegister): this.type = { this.registers.append(register); this }
+
+  /** Adds the [[TaskCache]] to the list of registers to be notified when a list of tasks is returned by [[Task.getTasks]] */
+  override def withTaskCache(taskCache: TaskCache): this.type = {
+    super.withTaskCache(taskCache)
+    this.taskCaches.append(taskCache)
+    this
+  }
+
   /** The tasks currently known by the executor. */
   def tasks: Traversable[Task] = this._tasks
 
@@ -105,6 +131,7 @@ private class GraphExecutorImpl[T<:Task](protected val taskExecutor: TaskExecuto
     val rootFuture: Future[Task] = failFutureWithTaskStatus(rootTask) {
       Future {
         lockIt {
+          this.registers.foreach(_.register(rootTask, rootTask))
           registerTask(rootTask) match {
             case None        => throw new IllegalArgumentException(s"Task '${rootTask.name}' already attempted.")
             case Some(false) => throw new IllegalArgumentException(s"Task '${rootTask.name}' depends on ${rootTask.tasksDependedOn.size} tasks.")
@@ -168,9 +195,17 @@ private class GraphExecutorImpl[T<:Task](protected val taskExecutor: TaskExecuto
     buildTask(parent) flatMap {
       case x :: Nil if x == parent => // one task and it returned itself, so execute it
         requireNoDependencies(parent)
-        executeWithTaskExecutor(parent)
+        registers.foreach(_.register(parent, parent))
+        if (this.taskCaches.isEmpty || this.taskCaches.exists(_.execute(parent))) {
+          executeWithTaskExecutor(parent)
+        }
+        else {
+          updateMetadata(parent, ManuallySucceeded)
+          Future.successful(parent)
+        }
       case childTasks              => // a different task, or more than one task, so build those tasks and execute them
         requireNoDependencies(parent)
+        registers.foreach(_.register(parent, childTasks:_*))
         executeMultiTask(parent, childTasks)
     }
   }

core/src/main/scala/dagr/core/execsystem2/TaskStatusLogger.scala

@@ -0,0 +1,40 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2017 Fulcrum Genomics LLC
+ *
+ * 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 dagr.core.execsystem2
+
+import com.fulcrumgenomics.commons.util.{LazyLogging, Logger}
+import dagr.core.reporting.ReportingDef.TaskLogger
+import dagr.core.tasksystem.Task.{TaskInfo => RootTaskInfo}
+
+/** A simple logger that delegates to [[dagr.core.tasksystem.Task.TaskInfo#logTaskMessage]]. */
+class TaskStatusLogger extends TaskLogger {
+  // NB: rename this class to set the name on the command line
+  private class Dagr extends LazyLogging {
+    override lazy val logger: Logger = new Logger(getClass)
+  }
+  private val logger = new Dagr().logger
+  def record(info: RootTaskInfo): Unit = info.logTaskMessage(this.logger)
+}

core/src/main/scala/dagr/core/execsystem2/TaskLogger.scala → core/src/main/scala/dagr/core/execsystem2/TopLikeStatusReporter.scala

@@ -27,31 +27,15 @@ package dagr.core.execsystem2
 
 import java.io.ByteArrayOutputStream
 
-import com.fulcrumgenomics.commons.util.{LazyLogging, Logger}
 import dagr.core.execsystem.SystemResources
+import dagr.core.execsystem2.ExecDef.concurrentSet
+import dagr.core.reporting.ReportingDef.TaskLogger
 import dagr.core.reporting.{TopLikeStatusReporter => BaseTopLikeStatusReporter}
 import dagr.core.tasksystem.Task
 import dagr.core.tasksystem.Task.{TaskInfo => RootTaskInfo}
-import dagr.core.execsystem2.ExecDef.concurrentSet
 
 import scala.collection.mutable
 
-/** Base trait for all classes interested in when the task status changes for any task. */
-trait TaskLogger {
-  /** The method that will be called with updated task information. */
-  def record(info: RootTaskInfo): Unit
-}
-
-/** A simple logger that delegates to [[dagr.core.tasksystem.Task.TaskInfo#logTaskMessage]]. */
-class TaskStatusLogger extends TaskLogger {
-  // NB: rename this class to set the name on the command line
-  private class Dagr extends LazyLogging {
-    override lazy val logger: Logger = new Logger(getClass)
-  }
-  private val logger = new Dagr().logger
-  def record(info: RootTaskInfo): Unit = info.logTaskMessage(this.logger)
-}
-
 /** A simple top-like status reporter for [[dagr.core.execsystem2.GraphExecutor]].
   * @param systemResources the system resources used while executing
   * @param loggerOut the stream to which log messages are written, or none if no stream is available.