Dev4.1 new chain

.gitignore

@@ -20,3 +20,6 @@ project/plugins/project/
 .classpath
 .project
 /bin/
+
+#IntelliJ
+.idea/

Figaro/.gitignore

@@ -1 +1,4 @@
 /bin/
+/.cache-main
+/.cache-tests
+/build.properties

Figaro/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Figaro
 Bundle-SymbolicName: com.cra.figaro
-Bundle-Version: 3.2.0
+Bundle-Version: 4.1.0
 Export-Package: com.cra.figaro.algorithm,
  com.cra.figaro.algorithm.decision,
  com.cra.figaro.algorithm.decision.index,
@@ -13,16 +13,16 @@ Export-Package: com.cra.figaro.algorithm,
  com.cra.figaro.language,
  com.cra.figaro.library.atomic.continuous,
  com.cra.figaro.library.atomic.discrete,
+ com.cra.figaro.library.collection,
  com.cra.figaro.library.compound,
  com.cra.figaro.library.decision,
  com.cra.figaro.util
 Bundle-Vendor: Charles River Analytics
 Bundle-RequiredExecutionEnvironment: JavaSE-1.6
 Require-Bundle: org.scala-lang.scala-library,
  org.scala-lang.scala-reflect,
- com.typesafe.akka.actor;bundle-version="2.3.3",
- com.typesafe.config;bundle-version="1.2.1",
- org.scalatest;bundle-version="2.1.6"
+ com.typesafe.config,
+ com.typesafe.akka.actor
 Import-Package: org.apache.commons.math3.distribution;version="3.3.0"
 
 

Figaro/figaro_build.properties

@@ -1 +1 @@
-version=3.2.0.0
+version=4.1.0.0

Figaro/src/main/scala/com/cra/figaro/algorithm/Algorithm.scala

@@ -26,7 +26,6 @@ class UnsupportedAlgorithmException(element: Element[_]) extends RuntimeExceptio
 class AlgorithmException extends RuntimeException
 class AlgorithmInactiveException extends AlgorithmException
 class AlgorithmActiveException extends AlgorithmException
-class NotATargetException[T](target: Element[T]) extends AlgorithmException
 
 /**
  * The general class of Figaro algorithms. The Algorithm class is defined to generalize both
@@ -47,22 +46,22 @@ trait Algorithm {
   /*
    * Start the algorithm. After it returns, the algorithm must be ready to provide answers.
    */
-  protected def doStart(): Unit
+  protected[algorithm] def doStart(): Unit
 
   /*
    * Stop the algorithm from computing. The algorithm is still ready to provide answers after it returns.
    */
-  protected def doStop(): Unit
+  protected[algorithm] def doStop(): Unit
 
   /*
    * Resume the computation of the algorithm, if it has been stopped.
    */
-  protected def doResume(): Unit
+  protected[algorithm] def doResume(): Unit
 
   /*
    * Kill the algorithm so that it is inactive. It will no longer be able to provide answers.
    */
-  protected def doKill(): Unit
+  protected[algorithm] def doKill(): Unit
 
   protected var active = false
 

Figaro/src/main/scala/com/cra/figaro/algorithm/Anytime.scala

@@ -16,6 +16,13 @@ package com.cra.figaro.algorithm
 import com.cra.figaro.language._
 import akka.actor._
 import com.typesafe.config.ConfigFactory
+import akka.util.Timeout
+import java.util.concurrent.TimeUnit
+import akka.pattern.{ ask }
+import scala.concurrent.Await
+import scala.concurrent.Future
+import java.util.concurrent.TimeoutException
+import scala.concurrent.duration.Duration
 
 /**
  * Class of services implemented by the anytime algorithm.
@@ -26,8 +33,14 @@ abstract class Service
  * Class of responses to services.
  */
 abstract class Response
+
+/**
+ * Ack Response (String)
+ */
+case object AckResponse extends Response
+
 /**
- * General Response (String)
+ * Exception Response (String)
  */
 case class ExceptionResponse(msg: String) extends Response
 
@@ -40,6 +53,9 @@ sealed abstract class Message
  */
 case class Handle(service: Service) extends Message
 
+
+class AnytimeAlgorithmException(s: String) extends RuntimeException(s)
+
 /**
  * An anytime algorithm is able to improve its estimated answers over time. Anytime algorithms run in their
  * own thread using an actor.
@@ -50,15 +66,6 @@ case class Handle(service: Service) extends Message
  */
 
 trait Anytime extends Algorithm {
-  /**
-   * Run a single step of the algorithm. The algorithm must be able to provide answers after each step.
-   */
-  def runStep(): Unit
-
-  /**
-   * Optional function to run when the algorithm is stopped (not killed). Used in samplers to update lazy values.
-   */
-  def stopUpdate(): Unit = {  }
 
   /**
    * A class representing the actor running the algorithm.
@@ -71,7 +78,8 @@ trait Anytime extends Algorithm {
         sender ! handle(service)
       case "stop" =>
         stopUpdate()
-        become (inactive)
+        sender ! AckResponse
+        become(inactive)
       case "next" =>
         runStep()
         self ! "next"
@@ -89,9 +97,11 @@ trait Anytime extends Algorithm {
       case "resume" =>
         resume()
         become(active)
-      	self ! "next"
+        self ! "next"
       case "kill" =>
-         become(shuttingDown)
+        cleanUp()
+        sender ! AckResponse
+        become(shuttingDown)
       case _ =>
         sender ! ExceptionResponse("Algorithm is stopped")
     }
@@ -102,8 +112,6 @@ trait Anytime extends Algorithm {
     }
 
     def receive = inactive
-
-
   }
 
   /**
@@ -121,41 +129,80 @@ trait Anytime extends Algorithm {
   var runner: ActorRef = null
   var running = false;
 
+  /**
+   * default message timeout. Increase if queries to the algorithm fail due to timeout
+   */
+  implicit var messageTimeout = Timeout(5000, TimeUnit.MILLISECONDS)
+
+  /**
+   * Run a single step of the algorithm. The algorithm must be able to provide answers after each step.
+   */
+  def runStep(): Unit
+
+  /**
+   * Optional function to run when the algorithm is stopped (not killed). Used in samplers to update lazy values.
+   */
+  def stopUpdate(): Unit = {}
+
   /**
    * A handler of services provided by the algorithm.
    */
   def handle(service: Service): Response
 
 
-  protected def doStart() = {
+  protected[algorithm] def doStart() = {
     if (!running) {
-    	system = ActorSystem("Anytime", ConfigFactory.load(customConf))
-    	runner = system.actorOf(Props(new Runner))
-    	initialize()
-    	running = true
+      system = ActorSystem("Anytime", ConfigFactory.load(customConf))
+      runner = system.actorOf(Props(new Runner))
+      initialize()
+      running = true
     }
 
     runner ! "start"
   }
 
-  protected def doStop() = runner ! "stop"
+  protected[algorithm] def doStop() = runner ! "stop"
 
-  protected def doResume() = runner ! "resume"
+  protected[algorithm] def doResume() = runner ! "resume"
 
-  protected def doKill() = {
+  protected[algorithm] def doKill() = {
     shutdown
   }
 
   /**
    * Release all resources from this anytime algorithm.
    */
   def shutdown {
-    cleanUp()
-    if (running)
-    {
-    	runner ! "kill"
-    	system.stop(runner)
-    	system.shutdown
+    if (running) {      
+      awaitResponse(runner ? "kill", messageTimeout.duration)      
+      system.stop(runner)
+      system.shutdown
     }
   }
+
+  /*
+   * A helper function to query the running thread and await a response.
+   * In the case that it times out, it will print a message that it timed out and return an exception response.
+   * Note, on a time, it does NOT throw an exception.
+   */
+  protected def awaitResponse(response: Future[Any], duration: Duration): Response = {
+    try {
+      val result = Await.result(response, duration) 
+      result match {
+        case e: ExceptionResponse => {
+          println(e.msg)
+          e
+        }
+        case r: Response => r
+        case _ => throw new AnytimeAlgorithmException("Unknown Response")
+      }
+    } catch {
+      case to: TimeoutException => {
+        println("Error! Did not receive a response from algorithm thread - it may be hanging or taking an exceptionally long time to respond. Try increasing messageTimeout.")
+        ExceptionResponse("Timeout")
+      }
+      case e: Exception => throw e
+    } 
+  }
+
 }

Figaro/src/main/scala/com/cra/figaro/algorithm/AnytimeMPE.scala

@@ -14,6 +14,7 @@
 package com.cra.figaro.algorithm
 
 import com.cra.figaro.language._
+import akka.pattern.{ask}
 
 /**
  * Anytime algorithms that compute most likely values of elements.
@@ -25,7 +26,7 @@ trait AnytimeMPE extends MPEAlgorithm with Anytime {
    * A message instructing the handler to compute the most likely value of the target element.
    */
   case class ComputeMostLikelyValue[T](target: Element[T]) extends Service
-  
+
   /**
    * A message from the handler containing the most likely value of the previously requested element.
    */
@@ -36,4 +37,14 @@ trait AnytimeMPE extends MPEAlgorithm with Anytime {
       case ComputeMostLikelyValue(target) =>
         MostLikelyValue(mostLikelyValue(target))
     }
+
+  protected def doMostLikelyValue[T](target: Element[T]): T = {
+    awaitResponse(runner ? Handle(ComputeMostLikelyValue(target)), messageTimeout.duration) match {
+      case MostLikelyValue(result) => result.asInstanceOf[T]
+      case _ => {
+        println("Error: Response not recognized from algorithm")
+        target.value 
+      }
+    }
+  }
 }

Figaro/src/main/scala/com/cra/figaro/algorithm/AnytimeProbEvidence.scala

@@ -37,18 +37,12 @@ trait AnytimeProbEvidence extends ProbEvidenceAlgorithm with Anytime {
   /**
    * Returns the probability of evidence of the universe on which the algorithm operates.
    * Throws AlgorithmInactiveException if the algorithm is not active.
-   */
-  implicit val timeout = Timeout(5000, TimeUnit.MILLISECONDS)
+   */  
   def probabilityOfEvidence(): Double = {
-    if (!active) throw new AlgorithmInactiveException
-    val response = runner ? Handle(ComputeProbEvidence)
-    Await.result(response, timeout.duration ).asInstanceOf[Response] match {
+    awaitResponse(runner ? Handle(ComputeProbEvidence), messageTimeout.duration) match {
       case ProbEvidence(result) => result
-      case ExceptionResponse(msg) =>
-        println(msg)
-        0.0
       case _ => 0.0
-    }
+    }    
   }
 
 }

Figaro/src/main/scala/com/cra/figaro/algorithm/AnytimeProbQuery.scala

@@ -50,6 +50,14 @@ trait AnytimeProbQuery extends ProbQueryAlgorithm with Anytime {
    * A message from the handler containing the probability of the previously requested predicate and element.
    */
   case class Probability(probability: Double) extends Response
+ /**
+   * A message instructing the handler to compute the projection of the target element.
+   */
+  case class ComputeProjection[T](target: Element[T]) extends Service
+ /**
+   * A message from the handler containing the projection of the previously requested element.
+   */
+  case class Projection[T](projection: List[(T, Double)]) extends Response
 
   def handle(service: Service): Response =
     service match {
@@ -60,38 +68,33 @@ trait AnytimeProbQuery extends ProbQueryAlgorithm with Anytime {
       case ComputeProbability(target, predicate) =>
         Probability(computeProbability(target, predicate))
     }
-
-  implicit val timeout = Timeout(5000, TimeUnit.MILLISECONDS)
+
   protected def doDistribution[T](target: Element[T]): Stream[(Double, T)] = {
-    val response = runner ? Handle(ComputeDistribution(target))
-    Await.result(response, timeout.duration ).asInstanceOf[Response] match {
+    awaitResponse(runner ? Handle(ComputeDistribution(target)), messageTimeout.duration) match {
       case Distribution(result) => result.asInstanceOf[Stream[(Double, T)]]
-      case ExceptionResponse(msg) =>
-        println(msg)
-        Stream()
       case _ => Stream()
-    }
+    } 
   }
 
   protected def doExpectation[T](target: Element[T], function: T => Double): Double = {
-    val response = runner ? Handle(ComputeExpectation(target, function))
-    Await.result(response, timeout.duration ).asInstanceOf[Response] match {
+    awaitResponse(runner ? Handle(ComputeExpectation(target, function)), messageTimeout.duration) match {
       case Expectation(result) => result
-      case ExceptionResponse(msg) =>
-        println(msg)
-        0.0
       case _ => 0.0
-    }
+    }     
   }
 
   protected override def doProbability[T](target: Element[T], predicate: T => Boolean): Double = {
-    val response = runner ? Handle(ComputeProbability(target, predicate))
-    Await.result(response, timeout.duration ).asInstanceOf[Response] match {
+    awaitResponse(runner ? Handle(ComputeProbability(target, predicate)), messageTimeout.duration) match {
       case Probability(result) => result
-      case ExceptionResponse(msg) =>
-        println(msg)
-        0.0
       case _ => 0.0
-    }
+    }     
   }
+
+  protected override def doProjection[T](target: Element[T]): List[(T, Double)] = {
+    awaitResponse(runner ? Handle(ComputeProjection(target)), messageTimeout.duration) match {
+      case Projection(result) => result.asInstanceOf[List[(T, Double)]]
+      case _ => List()
+    }     
+  }
+
 }

Figaro/src/main/scala/com/cra/figaro/algorithm/MPEAlgorithm.scala

@@ -28,4 +28,7 @@ trait MPEAlgorithm extends Algorithm {
    * Returns the most likely value for the target element.
    */
   def mostLikelyValue[T](target: Element[T]): T
+
+  // Defined in one time or anytime versions
+  protected def doMostLikelyValue[T](target: Element[T]): T
 }