Merge branch 'develop' into WX-1506

centaur/src/main/resources/standardTestCases/failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.inputs

@@ -0,0 +1,4 @@
+{
+    "MinimalStructExample.test": "Hello World",
+    "MinimalStructExample.integer": 2
+}

centaur/src/main/resources/standardTestCases/failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.wdl

@@ -0,0 +1,27 @@
+version 1.0
+
+
+struct firstLayer {
+    String first
+    Int number
+}
+
+struct secondLayer {
+    String second
+    firstLayer lowerLayer
+}
+
+
+workflow MinimalStructExample {
+    input {
+        String test
+        Int integer
+    }
+
+    firstLayer example1 = {"first": test, "number": integer}
+    secondLayer example2 = {"second": test, "lowerLayer": example1}
+
+    output {
+        String example3 = example2.second
+    }
+}

centaur/src/main/resources/standardTestCases/nested_struct_bad_instantiation.test

@@ -0,0 +1,14 @@
+name: nested_struct_bad_instantiation
+testFormat: workflowfailure
+
+files {
+  workflow: failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.wdl
+  inputs: failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.inputs
+}
+
+metadata {
+  workflowName: MinimalStructExample
+  status: Failed
+  "failures.0.message": "Workflow failed"
+  "failures.0.causedBy.0.message": "Failed to evaluate 'example2' (reason 1 of 1): Evaluating { \"second\": test, \"lowerLayer\": example1 } failed: Cannot construct WomMapType(WomStringType,WomAnyType) with mixed types in map values: [WomString(Hello World), WomObject(Map(first -> WomString(Hello World), number -> WomInteger(2)),WomCompositeType(Map(first -> WomStringType, number -> WomIntegerType),Some(firstLayer)))]"
+}

engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ExpressionKey.scala

@@ -6,7 +6,7 @@ import common.validation.ErrorOr._
 import common.validation.Validation._
 import cromwell.core.ExecutionIndex._
 import cromwell.core.{ExecutionStatus, JobKey}
-import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionDiff
+import cromwell.engine.workflow.lifecycle.execution.{WdlRuntimeException, WorkflowExecutionDiff}
 import cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.{
   ExpressionEvaluationFailedResponse,
   ExpressionEvaluationSucceededResponse
@@ -32,7 +32,7 @@ final case class ExpressionKey(node: ExpressionNodeLike, index: ExecutionIndex)
       .contextualizeErrors(s"evaluate '${node.fullyQualifiedName}'") match {
       case Right(result) => workflowExecutionActor ! ExpressionEvaluationSucceededResponse(this, result)
       case Left(f) =>
-        workflowExecutionActor ! ExpressionEvaluationFailedResponse(this, new RuntimeException(f.toList.mkString(", ")))
+        workflowExecutionActor ! ExpressionEvaluationFailedResponse(this, WdlRuntimeException(f.toList.mkString(", ")))
     }
 
     WorkflowExecutionDiff(Map(this -> ExecutionStatus.Running)).validNel

engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/package.scala

@@ -5,6 +5,16 @@ package execution {
   import cromwell.core.CallKey
   import wom.values.WomEvaluatedCallInputs
 
+  import scala.util.control.NoStackTrace
+
   final case class JobRunning(key: CallKey, inputs: WomEvaluatedCallInputs)
   final case class JobStarting(callKey: CallKey)
+
+  /**
+    * An exception specific to conditions inside the executing WDL, as opposed to one that is "Cromwell's fault"
+    * @param message Description suitable for user display
+    */
+  final case class WdlRuntimeException(message: String) extends RuntimeException with NoStackTrace {
+    override def getMessage: String = message
+  }
 }

server/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala

@@ -192,7 +192,7 @@ class SimpleWorkflowActorSpec extends CromwellTestKitWordSpec with BeforeAndAfte
         workflowActor ! StartWorkflowCommand
       }
       Await.result(promise.future, TestExecutionTimeout)
-      probe.expectTerminated(workflowActor, 2.seconds)
+      probe.expectTerminated(workflowActor, 15.seconds)
       supervisor.expectMsgPF(AwaitAlmostNothing, "parent should get a failed response") {
         case x: WorkflowFailedResponse =>
           x.workflowId should be(workflowId)

wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LiteralEvaluators.scala

@@ -4,7 +4,9 @@ import cats.syntax.apply._
 import cats.syntax.traverse._
 import cats.syntax.validated._
 import cats.instances.list._
+import common.validation.ErrorOr
 import common.validation.ErrorOr.ErrorOr
+import common.validation.ErrorOr.NestedErrorOr
 import wdl.model.draft3.elements.ExpressionElement
 import wdl.model.draft3.elements.ExpressionElement._
 import wdl.model.draft3.graph.expression.{EvaluatedValue, ForCommandInstantiationOptions, ValueEvaluator}
@@ -84,11 +86,11 @@ object LiteralEvaluators {
           ) mapN { (key, value) => key -> value }
       }
 
-      evaluated map { kvps =>
+      (evaluated map { kvps =>
         val value = kvps.map(entry => entry._1.value -> entry._2.value).toMap
         val sideEffectFiles = kvps.flatMap(entry => entry._1.sideEffectFiles ++ entry._2.sideEffectFiles)
-        EvaluatedValue(WomMap(value.toMap), sideEffectFiles)
-      }
+        ErrorOr(EvaluatedValue(WomMap.apply(value.toMap), sideEffectFiles))
+      }).flatten
     }
   }
 
@@ -103,11 +105,11 @@ object LiteralEvaluators {
         entry.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
       }
 
-      evaluated map { evaluateds =>
+      (evaluated map { evaluateds =>
         val value = evaluateds.map(_.value)
         val sideEffectFiles = evaluateds.flatMap(_.sideEffectFiles)
-        EvaluatedValue(WomArray(value), sideEffectFiles)
-      }
+        ErrorOr(EvaluatedValue(WomArray.apply(value), sideEffectFiles))
+      }).flatten
     }
   }