[Core] enh: add method data to output format

openmole/build.sbt

@@ -441,7 +441,7 @@ lazy val onvariableGrouping = OsgiProject(pluginDir, "org.openmole.plugin.groupi
 
 /* Hook */
 
-def allHook = Seq(displayHook, fileHook, modifierHook, jsonHook)
+def allHook = Seq(displayHook, fileHook, modifierHook, jsonHook, omrHook)
 
 lazy val displayHook = OsgiProject(pluginDir, "org.openmole.plugin.hook.display", imports = Seq("*")) dependsOn (openmoleDSL) settings (pluginSettings: _*)
 
@@ -454,6 +454,9 @@ lazy val modifierHook = OsgiProject(pluginDir, "org.openmole.plugin.hook.modifie
 lazy val jsonHook = OsgiProject(pluginDir, "org.openmole.plugin.hook.json", imports = Seq("*")) dependsOn(openmoleDSL,json, replication % "test") settings (
   libraryDependencies += Libraries.scalatest) settings (pluginSettings: _*)
 
+lazy val omrHook = OsgiProject(pluginDir, "org.openmole.plugin.hook.omr", imports = Seq("*")) dependsOn(openmoleDSL,json, replication % "test") settings (
+  libraryDependencies += Libraries.scalatest) settings (pluginSettings: _*)
+
 
 /* Method */
 

openmole/core/org.openmole.core.workflow/src/main/scala/org/openmole/core/workflow/composition/package.scala

@@ -141,7 +141,7 @@ package composition {
     def hook[F](
       output: WritableOutput,
       values: Seq[Val[_]]    = Vector.empty,
-      format: F              = CSVOutputFormat(append = true))(implicit definitionScope: DefinitionScope, fileFormat: OutputFormat[F]): TaskNode = hook(FormattedFileHook(output = output, values = values, format = format))
+      format: F              = CSVOutputFormat(append = true))(implicit definitionScope: DefinitionScope, fileFormat: OutputFormat[F, Any]): TaskNode = hook(FormattedFileHook(output = output, values = values, format = format))
     def source(sources: Source*) = copy(sources = this.sources ++ sources)
   }
 

openmole/core/org.openmole.core.workflow/src/main/scala/org/openmole/core/workflow/mole/CSVHook.scala

@@ -30,8 +30,8 @@ object CSVHook {
 
   object CSVOutputFormat {
 
-    implicit def format: OutputFormat[CSVOutputFormat] = new OutputFormat[CSVOutputFormat] {
-      override def write(format: CSVOutputFormat, output: WritableOutput, variables: Seq[Variable[_]]): FromContext[Unit] = FromContext { p ⇒
+    implicit def format: OutputFormat[CSVOutputFormat, Any] = new OutputFormat[CSVOutputFormat, Any] {
+      override def write(format: CSVOutputFormat, output: WritableOutput, variables: Seq[Variable[_]], method: Any): FromContext[Unit] = FromContext { p ⇒
         import p._
 
         def headerLine = format.header.map(_.from(context)) getOrElse csv.header(variables.map(_.prototype), variables.map(_.value), arrayOnRow = format.arrayOnRow)

openmole/core/org.openmole.core.workflow/src/main/scala/org/openmole/core/workflow/mole/FormattedFileHook.scala

@@ -8,20 +8,21 @@ import org.openmole.core.exception.UserBadDataError
 import org.openmole.core.expansion.FromContext
 import org.openmole.core.workflow.builder._
 
-trait OutputFormat[T] {
-  def write(format: T, output: WritableOutput, variables: Seq[Variable[_]]): FromContext[Unit]
+trait OutputFormat[T, -M] {
+  def write(format: T, output: WritableOutput, variables: Seq[Variable[_]], method: M): FromContext[Unit]
   def validate(format: T): FromContextHook.ValidateParameters ⇒ Seq[Throwable]
   def extension: String
 }
 
 object FormattedFileHook {
 
-  def apply[T: OutputFormat](
+  def apply[T, M](
     format:  T,
     output:  WritableOutput,
     values:  Seq[Val[_]]    = Vector.empty,
     exclude: Seq[Val[_]]    = Vector.empty,
-    name:    Option[String] = None)(implicit valName: sourcecode.Name, definitionScope: DefinitionScope, fileFormat: OutputFormat[T]): mole.FromContextHook =
+    method:  M              = None,
+    name:    Option[String] = None)(implicit valName: sourcecode.Name, definitionScope: DefinitionScope, fileFormat: OutputFormat[T, M]): mole.FromContextHook =
 
     Hook(name getOrElse "FileFormatHook") { parameters ⇒
       import parameters._
@@ -30,7 +31,7 @@ object FormattedFileHook {
       val ps = { if (values.isEmpty) context.values.map { _.prototype }.toVector else values }.filter { v ⇒ !excludeSet.contains(v.name) }
       val variables = ps.map(p ⇒ context.variable(p).getOrElse(throw new UserBadDataError(s"Variable $p not found in hook $this")))
 
-      fileFormat.write(format, output, variables).from(context)
+      fileFormat.write(format, output, variables, method).from(context)
 
       context
     } validate { p ⇒

openmole/core/org.openmole.core.workflow/src/main/scala/org/openmole/core/workflow/mole/package.scala

@@ -24,7 +24,7 @@ package mole {
     def CSVHook = mole.CSVHook
     def CSVOutputFormat = mole.CSVHook.CSVOutputFormat
 
-    type OutputFormat[T] = mole.OutputFormat[T]
+    type OutputFormat[T, D] = mole.OutputFormat[T, D]
     type FromContextHook = mole.FromContextHook
     type FromContextSource = mole.FromContextSource
   }

openmole/core/org.openmole.core.workflow/src/test/scala/org/openmole/core/workflow/mole/HookSpec.scala

@@ -37,8 +37,7 @@ class HookSpec extends FlatSpec with Matchers {
 
   "A hook" should "intercept the execution of a task" in {
     val executed = new AtomicInteger(0)
-
-    val p = Val[String]("p")
+    val p = Val[String]
 
     val t1 =
       TestTask { _ + (p → "test") } set (
@@ -66,7 +65,6 @@ class HookSpec extends FlatSpec with Matchers {
 
     val t1 =
       TestTask { _ + (p → "test") } set (
-        name := "Test",
         outputs += p
       )
 
@@ -83,4 +81,10 @@ class HookSpec extends FlatSpec with Matchers {
     executed should equal(true)
   }
 
+  "Display hook" should "be accepted" in {
+    val t1 = EmptyTask()
+    val ex = t1 hook display
+    ex.run
+  }
+
 }

openmole/plugins/org.openmole.plugin.hook.json/src/main/scala/org/openmole/plugin/hook/json/JSONOutputFormat.scala

@@ -7,8 +7,8 @@ import org.openmole.plugin.tool.json._
 
 object JSONOutputFormat {
 
-  implicit def outputFormat = new OutputFormat[JSONOutputFormat] {
-    override def write(format: JSONOutputFormat, output: WritableOutput, variables: Seq[Variable[_]]): FromContext[Unit] = FromContext { p ⇒
+  implicit def outputFormat = new OutputFormat[JSONOutputFormat, Any] {
+    override def write(format: JSONOutputFormat, output: WritableOutput, variables: Seq[Variable[_]], method: Any): FromContext[Unit] = FromContext { p ⇒
       import p._
       import org.json4s._
       import org.json4s.jackson.JsonMethods._

openmole/plugins/org.openmole.plugin.hook.omr/src/main/scala/org/openmole/plugin/hook/omr/Activator.scala

+/*
+ * Copyright (C) 2015 Romain Reuillon
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.openmole.plugin.hook.omr
+
+import org.openmole.core.pluginmanager._
+import org.openmole.core.preference.ConfigurationInfo
+import org.osgi.framework.BundleContext
+
+class Activator extends PluginInfoActivator {
+  override def keyWordTraits = List()
+
+  override def stop(context: BundleContext): Unit = {
+    PluginInfo.unregister(this)
+    ConfigurationInfo.unregister(this)
+  }
+
+  override def start(context: BundleContext): Unit = {
+    import org.openmole.core.pluginmanager.KeyWord._
+
+    val keyWords: Vector[KeyWord] =
+      Vector( //        TaskKeyWord(objectName(JSONHook)),
+      //        OtherKeyWord(objectName(JSONOutputFormat))
+      )
+
+    PluginInfo.register(this, Vector(this.getClass.getPackage), keyWords = keyWords)
+    ConfigurationInfo.register(
+      this,
+      ConfigurationInfo.list()
+    )
+  }
+}
\ No newline at end of file

openmole/plugins/org.openmole.plugin.hook.omr/src/main/scala/org/openmole/plugin/hook/omr/OMROutputFormat.scala

+//package org.openmole.plugin.hook.omr
+//
+//import org.openmole.core.dsl._
+//import org.openmole.core.dsl.extension._
+//import org.openmole.core.workflow.mole.FromContextHook
+//import org.openmole.plugin.tool.json._
+//
+//object OMROutputFormat {
+//
+//  implicit def outputFormat = new OutputFormat[OMROutputFormat, Any] {
+//    override def write(format: OMROutputFormat, output: WritableOutput, variables: Seq[Variable[_]]): FromContext[Unit] = FromContext { p ⇒
+//      import p._
+//      import org.json4s._
+//      import org.json4s.jackson.JsonMethods._
+//
+//      implicit val formats = DefaultFormats
+//
+//      output match {
+//        case WritableOutput.FileValue(file) ⇒
+//          file.from(context).withPrintStream(append = false, create = true) { ps ⇒
+//            ps.print(compact(render(variablesToJValue(variables))))
+//          }
+//        case WritableOutput.StreamValue(ps, prelude) ⇒
+//          prelude.foreach(ps.print)
+//          ps.println(pretty(render(variablesToJValue(variables))))
+//      }
+//    }
+//
+//    override def validate(format: OMROutputFormat): FromContextHook.ValidateParameters ⇒ Seq[Throwable] = { p ⇒ Seq() }
+//    override def extension = ".omr"
+//  }
+//
+//}
+//
+//case class OMROutputFormat()

openmole/plugins/org.openmole.plugin.method.directsampling/src/main/scala/org/openmole/plugin/method/directsampling/package.scala

@@ -35,24 +35,24 @@ package object directsampling {
   type Aggregation = AggregateTask.AggregateVal[_, _]
 
   implicit class DirectSamplingDSL(dsl: DSLContainer[DirectSampling]) extends DSLContainerHook(dsl) {
-    def hook[T: OutputFormat](
+    def hook[T](
       output: WritableOutput,
       values: Seq[Val[_]]    = Vector.empty,
-      format: T              = CSVOutputFormat(append = true)): DSLContainer[DirectSampling] = {
+      format: T              = CSVOutputFormat(append = true))(implicit outputFormat: OutputFormat[T, DirectSampling]): DSLContainer[DirectSampling] = {
       implicit val defScope = dsl.scope
-      dsl hook FormattedFileHook(output = output, values = values, format = format)
+      dsl hook FormattedFileHook(output = output, values = values, format = format, method = dsl.data)
     }
   }
 
   implicit class ReplicationDSL(dsl: DSLContainer[Replication]) extends DSLContainerHook(dsl) {
-    def hook[T: OutputFormat](
+    def hook[T](
       output:      WritableOutput,
       values:      Seq[Val[_]]    = Vector.empty,
       includeSeed: Boolean        = false,
-      format:      T              = CSVOutputFormat(append = true)): DSLContainer[Replication] = {
+      format:      T              = CSVOutputFormat(append = true))(implicit outputFormat: OutputFormat[T, Replication]): DSLContainer[Replication] = {
       implicit val defScope = dsl.scope
       val exclude = if (!includeSeed) Seq(dsl.data.seed) else Seq()
-      dsl hook FormattedFileHook(output = output, values = values, exclude = exclude, format = format)
+      dsl hook FormattedFileHook(output = output, values = values, exclude = exclude, format = format, method = dsl.data)
     }
   }
 

openmole/plugins/org.openmole.plugin.method.directsampling/src/test/scala/org/openmole/plugin/method/directsampling/PatternCompositionSpec.scala → openmole/plugins/org.openmole.plugin.method.directsampling/src/test/scala/org/openmole/plugin/method/directsampling/DirectSamplingSpec.scala

@@ -11,7 +11,7 @@ import org.openmole.plugin.tool.pattern._
 import org.scalatest._
 import org.openmole.core.workflow.test._
 
-class PatternCompositionSpec extends FlatSpec with Matchers {
+class DirectSamplingSpec extends FlatSpec with Matchers {
   import org.openmole.core.workflow.test.Stubs._
 
   "Direct sampling" should "transmit explored inputs" in {
@@ -193,4 +193,15 @@ class PatternCompositionSpec extends FlatSpec with Matchers {
     mole.run
   }
 
+  "Direct samplings" should "accept display hook" in {
+    val l = Val[Double]
+
+    val model = EmptyTask() set (inputs += l)
+
+    DirectSampling(
+      model,
+      ExplicitSampling(l, Seq(1.0, 2.0))
+    ) hook display
+  }
+
 }
\ No newline at end of file

openmole/plugins/org.openmole.plugin.method.evolution/src/main/scala/org/openmole/plugin/method/evolution/SavePopulationHook.scala

@@ -22,13 +22,17 @@ import org.openmole.core.dsl.extension._
 
 object SavePopulationHook {
 
+  case class EvolutionData()
+
+  def evolutionData(t: EvolutionWorkflow) = EvolutionData()
+
   def resultVariables(t: EvolutionWorkflow) = FromContext { p ⇒
     import p._
     context.variable(t.generationPrototype).toSeq ++
       t.operations.result(context(t.populationPrototype).toVector, context(t.statePrototype)).from(context)
   }
 
-  def hook[F](t: EvolutionWorkflow, output: WritableOutput, frequency: Option[Long], last: Boolean, format: F)(implicit name: sourcecode.Name, definitionScope: DefinitionScope, outputFormat: OutputFormat[F]) = {
+  def hook[F](t: EvolutionWorkflow, output: WritableOutput, frequency: Option[Long], last: Boolean, format: F)(implicit name: sourcecode.Name, definitionScope: DefinitionScope, outputFormat: OutputFormat[F, EvolutionData]) = {
     Hook("SavePopulationHook") { p ⇒
       import p._
 
@@ -44,7 +48,7 @@ object SavePopulationHook {
       output match {
         case WritableOutput.FileValue(dir) ⇒
           saveFile(dir) match {
-            case Some(outputFile) ⇒ outputFormat.write(format, outputFile.from(context), resultVariables(t).from(context)).from(context)
+            case Some(outputFile) ⇒ outputFormat.write(format, outputFile.from(context), resultVariables(t).from(context), evolutionData(t)).from(context)
             case None             ⇒
           }
         case o ⇒
@@ -55,7 +59,7 @@ object SavePopulationHook {
               case _            ⇒ false
             }
 
-          if (save) outputFormat.write(format, o, resultVariables(t).from(context)).from(context)
+          if (save) outputFormat.write(format, o, resultVariables(t).from(context), evolutionData(t)).from(context)
       }
 
       context
@@ -63,7 +67,7 @@ object SavePopulationHook {
 
   }
 
-  def apply[T, F: OutputFormat](algorithm: T, output: WritableOutput, frequency: OptionalArgument[Long] = None, last: Boolean = false, format: F = CSVOutputFormat(unrollArray = true))(implicit wfi: WorkflowIntegration[T], name: sourcecode.Name, definitionScope: DefinitionScope) = {
+  def apply[T, F](algorithm: T, output: WritableOutput, frequency: OptionalArgument[Long] = None, last: Boolean = false, format: F = CSVOutputFormat(unrollArray = true))(implicit wfi: WorkflowIntegration[T], name: sourcecode.Name, definitionScope: DefinitionScope, outputFormat: OutputFormat[F, EvolutionData]) = {
     val t = wfi(algorithm)
     hook(t, output, frequency.option, last = last, format = format)
   }
@@ -72,14 +76,14 @@ object SavePopulationHook {
 
 object SaveLastPopulationHook {
 
-  def apply[T, F](algorithm: T, output: WritableOutput, format: F = CSVOutputFormat(unrollArray = true))(implicit wfi: WorkflowIntegration[T], name: sourcecode.Name, definitionScope: DefinitionScope, outputFormat: OutputFormat[F]) = {
+  def apply[T, F](algorithm: T, output: WritableOutput, format: F = CSVOutputFormat(unrollArray = true))(implicit wfi: WorkflowIntegration[T], name: sourcecode.Name, definitionScope: DefinitionScope, outputFormat: OutputFormat[F, SavePopulationHook.EvolutionData]) = {
     val t = wfi(algorithm)
 
     Hook("SaveLastPopulationHook") { p ⇒
       import p._
       import org.openmole.core.csv
 
-      outputFormat.write(format, output, SavePopulationHook.resultVariables(t).from(context)).from(context)
+      outputFormat.write(format, output, SavePopulationHook.resultVariables(t).from(context), SavePopulationHook.evolutionData(t)).from(context)
       context
     } set (inputs += (t.populationPrototype, t.statePrototype))
 

openmole/plugins/org.openmole.plugin.method.evolution/src/main/scala/org/openmole/plugin/method/evolution/package.scala

@@ -99,7 +99,7 @@ package object evolution {
   implicit def workflowIntegration = WorkflowIntegration[DSLContainer[EvolutionWorkflow]](_.data)
 
   implicit class EvolutionMethodContainer(dsl: DSLContainer[EvolutionWorkflow]) extends DSLContainerHook(dsl) {
-    def hook[F: OutputFormat](output: WritableOutput, frequency: OptionalArgument[Long] = None, last: Boolean = false, format: F = CSVOutputFormat()): DSLContainer[EvolutionWorkflow] = {
+    def hook[F](output: WritableOutput, frequency: OptionalArgument[Long] = None, last: Boolean = false, format: F = CSVOutputFormat())(implicit outputFormat: OutputFormat[F, SavePopulationHook.EvolutionData]): DSLContainer[EvolutionWorkflow] = {
       implicit val defScope = dsl.scope
       dsl.hook(SavePopulationHook(dsl, output, frequency = frequency, last = last, format = format))
     }

openmole/plugins/org.openmole.plugin.method.sensitivity/src/main/scala/org/openmole/plugin/method/sensitivity/MorrisHook.scala

@@ -5,7 +5,7 @@ import org.openmole.core.dsl.extension._
 
 object MorrisHook {
 
-  def apply[F](dsl: DSLContainer[Sensitivity.MorrisParams], output: WritableOutput, format: F = CSVOutputFormat())(implicit name: sourcecode.Name, definitionScope: DefinitionScope, outputFormat: OutputFormat[F]) =
+  def apply[F](dsl: DSLContainer[Sensitivity.MorrisParams], output: WritableOutput, format: F = CSVOutputFormat())(implicit name: sourcecode.Name, definitionScope: DefinitionScope, outputFormat: OutputFormat[F, Sensitivity.MorrisParams]) =
     Hook("MorrisHook") { p ⇒
       import p._
       import WritableOutput._
@@ -14,13 +14,13 @@ object MorrisHook {
 
       output match {
         case FileValue(dirFC) ⇒
-          Sensitivity.writeResults(format, FileValue(dirFC / s"mu${outputFormat.extension}"), inputs, dsl.data.outputs, Morris.mu(_, _)).from(context)
-          Sensitivity.writeResults(format, FileValue(dirFC / s"muStar${outputFormat.extension}"), inputs, dsl.data.outputs, Morris.muStar(_, _)).from(context)
-          Sensitivity.writeResults(format, FileValue(dirFC / s"sigma${outputFormat.extension}"), inputs, dsl.data.outputs, Morris.sigma(_, _)).from(context)
+          Sensitivity.writeResults(format, dsl.data, FileValue(dirFC / s"mu${outputFormat.extension}"), inputs, dsl.data.outputs, Morris.mu(_, _)).from(context)
+          Sensitivity.writeResults(format, dsl.data, FileValue(dirFC / s"muStar${outputFormat.extension}"), inputs, dsl.data.outputs, Morris.muStar(_, _)).from(context)
+          Sensitivity.writeResults(format, dsl.data, FileValue(dirFC / s"sigma${outputFormat.extension}"), inputs, dsl.data.outputs, Morris.sigma(_, _)).from(context)
         case StreamValue(ps, prelude) ⇒
-          Sensitivity.writeResults(format, StreamValue(ps, Some(prelude.getOrElse("") + "mu\n")), inputs, dsl.data.outputs, Morris.mu(_, _)).from(context)
-          Sensitivity.writeResults(format, StreamValue(ps, Some("muStar\n")), inputs, dsl.data.outputs, Morris.muStar(_, _)).from(context)
-          Sensitivity.writeResults(format, StreamValue(ps, Some("sigma\n")), inputs, dsl.data.outputs, Morris.sigma(_, _)).from(context)
+          Sensitivity.writeResults(format, dsl.data, StreamValue(ps, Some(prelude.getOrElse("") + "mu\n")), inputs, dsl.data.outputs, Morris.mu(_, _)).from(context)
+          Sensitivity.writeResults(format, dsl.data, StreamValue(ps, Some("muStar\n")), inputs, dsl.data.outputs, Morris.muStar(_, _)).from(context)
+          Sensitivity.writeResults(format, dsl.data, StreamValue(ps, Some("sigma\n")), inputs, dsl.data.outputs, Morris.sigma(_, _)).from(context)
       }
       context
     }

openmole/plugins/org.openmole.plugin.method.sensitivity/src/main/scala/org/openmole/plugin/method/sensitivity/SaltelliHook.scala

@@ -5,7 +5,7 @@ import org.openmole.core.dsl.extension._
 
 object SaltelliHook {
 
-  def apply[F](dsl: DSLContainer[Sensitivity.SaltelliParams], output: WritableOutput, format: F = CSVOutputFormat())(implicit name: sourcecode.Name, definitionScope: DefinitionScope, outputFormat: OutputFormat[F]) =
+  def apply[F](dsl: DSLContainer[Sensitivity.SaltelliParams], output: WritableOutput, format: F = CSVOutputFormat())(implicit name: sourcecode.Name, definitionScope: DefinitionScope, outputFormat: OutputFormat[F, Sensitivity.SaltelliParams]) =
     Hook("SaltelliHook") { p ⇒
       import p._
       import WritableOutput._
@@ -14,11 +14,11 @@ object SaltelliHook {
 
       output match {
         case FileValue(dirFC) ⇒
-          Sensitivity.writeResults(format, FileValue(dirFC / s"firstOrderIndices${outputFormat.extension}"), inputs, dsl.data.outputs, Saltelli.firstOrder(_, _)).from(context)
+          Sensitivity.writeResults(format, dsl.data, FileValue(dirFC / s"firstOrderIndices${outputFormat.extension}"), inputs, dsl.data.outputs, Saltelli.firstOrder(_, _)).from(context)