Adding line numbers to workflow definitions (broadinstitute#4938)

Add line numbers to workflow definitions (broadinstitute#4938)

core/src/test/scala/cromwell/util/WomMocks.scala

@@ -19,28 +19,28 @@ object WomMocks {
   def mockTaskCall(identifier: WomIdentifier, definition: CommandTaskDefinition = EmptyTaskDefinition) = {
     CommandCallNode(identifier, definition, Set.empty, List.empty, Set.empty, (_, localName) => WomIdentifier(localName = localName))
   }
-  
+
   def mockWorkflowCall(identifier: WomIdentifier, definition: WorkflowDefinition = EmptyWorkflowDefinition) = {
     WorkflowCallNode(identifier, definition, Set.empty, List.empty, Set.empty, (_, localName) => identifier.combine(localName))
   }
 
   def mockWorkflowDefinition(name: String) = {
-    WorkflowDefinition(name, Graph(Set.empty), Map.empty, Map.empty)
+    WorkflowDefinition(name, Graph(Set.empty), Map.empty, Map.empty, None)
   }
 
   def mockTaskDefinition(name: String) = {
     CallableTaskDefinition(name, Function.const(List.empty.validNel), RuntimeAttributes(Map.empty),
       Map.empty, Map.empty, List.empty, List.empty, Set.empty, Map.empty)
   }
-  
+
   def mockOutputPort(name: String, womType: WomType = WomStringType): OutputPort = {
     GraphNodeOutputPort(WomIdentifier(name, name), womType, null)
   }
 
   def mockOutputPort(outputDefinition: OutputDefinition): OutputPort = {
     GraphNodeOutputPort(WomIdentifier(outputDefinition.name, outputDefinition.name), outputDefinition.womType, null)
   }
-  
+
   def mockOutputExpectations(outputs: Map[String, WomValue]): CallOutputs = {
     CallOutputs(outputs.map {
       case (key, value) => WomMocks.mockOutputPort(key, value.womType) -> value

cwl/src/main/scala/cwl/Workflow.scala

@@ -15,6 +15,7 @@ import cwl.Workflow.{WorkflowInputParameter, WorkflowOutputParameter}
 import cwl.command.ParentName
 import shapeless._
 import shapeless.syntax.singleton._
+import wom.SourceFileLocation
 import wom.callable.WorkflowDefinition
 import wom.executable.Executable
 import wom.expression.{IoFunctionSet, ValueAsAnExpression}
@@ -189,13 +190,15 @@ case class Workflow private(
     val name: String = Paths.get(id).getFileName.toString
     val meta: Map[String, String] = Map.empty
     val paramMeta: Map[String, String] = Map.empty
+    val lexInfo : Option[SourceFileLocation] = None
 
     womGraph(name, validator, expressionLib).map(graph =>
       WorkflowDefinition(
         name,
         graph,
         meta,
-        paramMeta
+        paramMeta,
+        lexInfo
       )
     )
   }

wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/LanguageElement.scala

@@ -1,3 +1,6 @@
 package wdl.model.draft3.elements
+import wom.SourceFileLocation
 
-trait LanguageElement
+trait LanguageElement {
+    val srcLoc : Option[SourceFileLocation] = None
+}

wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/WorkflowDefinitionElement.scala

@@ -1,8 +1,10 @@
 package wdl.model.draft3.elements
+import wom.SourceFileLocation
 
 final case class WorkflowDefinitionElement(name: String,
                                            inputsSection: Option[InputsSectionElement],
                                            graphElements: Set[WorkflowGraphElement],
                                            outputsSection: Option[OutputsSectionElement],
                                            metaSection: Option[MetaSectionElement],
-                                           parameterMetaSection: Option[ParameterMetaSectionElement]) extends FileBodyElement
+                                           parameterMetaSection: Option[ParameterMetaSectionElement],
+                                           override val srcLoc : Option[SourceFileLocation]) extends FileBodyElement

wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/ast2wdlom/WdlFileToWdlomSpec.scala

@@ -7,6 +7,7 @@ import wom.types._
 import wdl.model.draft3.elements.CommandPartElement.{PlaceholderCommandPartElement, StringCommandPartElement}
 import wdl.model.draft3.elements._
 import wdl.model.draft3.elements.ExpressionElement._
+import wom.SourceFileLocation
 import wom.values.WomInteger
 
 class WdlFileToWdlomSpec extends FlatSpec with Matchers {
@@ -65,7 +66,9 @@ object WdlFileToWdlomSpec {
           ),
           outputsSection = None,
           metaSection = None,
-          parameterMetaSection = None)),
+          parameterMetaSection = None,
+          srcLoc = Some(SourceFileLocation(3)))
+        ),
         tasks = Vector(
           TaskDefinitionElement(
             name = "no_inputs",
@@ -92,7 +95,9 @@ object WdlFileToWdlomSpec {
           outputsSection = Some(OutputsSectionElement(Vector(
             OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "out", IdentifierMemberAccess("in_n_out", "out", List.empty))))),
           metaSection = None,
-          parameterMetaSection = None)),
+          parameterMetaSection = None,
+          srcLoc = Some(SourceFileLocation(14)))
+        ),
         tasks = Vector(TaskDefinitionElement(
           name = "in_n_out",
           inputsSection = Some(InputsSectionElement(Vector(
@@ -124,7 +129,9 @@ object WdlFileToWdlomSpec {
           ),
           outputsSection = None,
           metaSection = None,
-          parameterMetaSection = None)),
+          parameterMetaSection = None,
+          srcLoc = Some(SourceFileLocation(3)))
+        ),
         tasks = Vector(TaskDefinitionElement(
           name = "foo",
           inputsSection = Some(InputsSectionElement(Vector(
@@ -188,7 +195,8 @@ object WdlFileToWdlomSpec {
           ),
           outputsSection = None,
           metaSection = None,
-          parameterMetaSection = None
+          parameterMetaSection = None,
+          srcLoc = Some(SourceFileLocation(3))
         )),
         tasks = Vector.empty)
   )

wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomWorkflowDefinitionMaker.scala

@@ -1,22 +1,27 @@
 package wdl.transforms.draft2.wdlom2wom
 
 import common.validation.ErrorOr.ErrorOr
-import wdl.draft2.model.WdlWorkflow
-import wdl.draft2.model.{Scope, WdlWorkflow}
+import wdl.draft2.model.{AstTools, Scope, WdlWorkflow}
+import wdl.draft2.parser.WdlParser.Terminal
 import wom.callable.WorkflowDefinition
 import wom.transforms.WomWorkflowDefinitionMaker
 import wom.transforms.WomGraphMaker.ops._
+import wom.SourceFileLocation
 
 object WdlDraft2WomWorkflowDefinitionMaker extends WomWorkflowDefinitionMaker[WdlWorkflow] {
   override def toWomWorkflowDefinition(wdlWorkflow: WdlWorkflow, isASubworkflow: Boolean): ErrorOr[WorkflowDefinition] = {
     // NB: We don't allow "OuterGraphInputNode"s when building this (the Map is empty), so preserveScatterForExternalLookups isn't ever actually used.
 
+    // Figure out the start line of the workflow in the source file
+    val t: Terminal = AstTools.findTerminals(wdlWorkflow.ast).head
+
     (wdlWorkflow: Scope).toWomGraph(Set.empty, Map.empty, preserveIndexForOuterLookups = true, isASubworkflow: Boolean) map { wg =>
       WorkflowDefinition(
         wdlWorkflow.fullyQualifiedName,
         wg,
         wdlWorkflow.meta,
-        wdlWorkflow.parameterMeta)
+        wdlWorkflow.parameterMeta,
+        Some(SourceFileLocation(t.getLine)))
     }
   }
 }

wdl/transforms/draft3/src/test/cases/cmd_whitespace_spaces.wdl

@@ -1,5 +1,10 @@
 version 1.0
 
+
+
+
+
+
 workflow Test {
 
   call Echo as echo

wdl/transforms/draft3/src/test/cases/simple_conditional.wdl

@@ -1,5 +1,7 @@
 version 1.0
 
+
+
 workflow simple_conditional {
   Boolean bool = true