case class WdlWorkflow(unqualifiedName: String, workflowOutputWildcards: Seq[WorkflowOutputWildcard], wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter, meta: Map[String, String], parameterMeta: Map[String, String], ast: Ast) extends WdlCallable with Product with Serializable

Linear Supertypes
Serializable, Serializable, Product, Equals, WdlCallable, Scope, AnyRef, Any
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Inherited
  1. WdlWorkflow
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. WdlCallable
  7. Scope
  8. AnyRef
  9. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new WdlWorkflow(unqualifiedName: String, workflowOutputWildcards: Seq[WorkflowOutputWildcard], wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter, meta: Map[String, String], parameterMeta: Map[String, String], ast: Ast)

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. lazy val ancestry: Seq[Scope]

    Seq(parent, grandparent, great grandparent, ..., WdlNamespace)

    Seq(parent, grandparent, great grandparent, ..., WdlNamespace)

    Definition Classes
    Scope
  5. def appearsInFqn: Boolean
    Definition Classes
    Scope
  6. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  7. val ast: Ast
    Definition Classes
    WdlWorkflow → Scope
  8. lazy val calls: Set[WdlCall]

    Descendants that are Calls

    Descendants that are Calls

    Definition Classes
    Scope
  9. def children: Seq[Scope]

    Child scopes, in the order that they appear in the source code

    Child scopes, in the order that they appear in the source code

    Definition Classes
    Scope
  10. def children_=[Child <: Scope](children: Seq[Child]): Unit
    Definition Classes
    Scope
  11. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  12. def closestCommonAncestor(other: Scope): Option[Scope]

    Given another scope, returns the closest common ancestor between the two scopes, if one exists at all

    Given another scope, returns the closest common ancestor between the two scopes, if one exists at all

    returns

    closest common ancestor

    Definition Classes
    Scope
  13. def closestCommonScatter(other: Scope): Option[Scatter]
    Definition Classes
    Scope
  14. lazy val declarations: Seq[Declaration]

    Declarations within this Scope, in the order that they appear in source code

    Declarations within this Scope, in the order that they appear in source code

    Definition Classes
    Scope
  15. lazy val descendants: Set[Scope]

    All children ++ children's children ++ etc

    All children ++ children's children ++ etc

    Definition Classes
    Scope
  16. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  17. def evaluateOutputs(knownInputs: WorkflowCoercedInputs, wdlFunctions: WdlFunctions[WdlValue], outputResolver: OutputResolver = NoOutputResolver, shards: Map[Scatter, Int] = Map.empty[Scatter, Int]): Try[Map[WorkflowOutput, WdlValue]]
  18. lazy val expandedWildcardOutputs: Seq[WorkflowOutput]

    All outputs for this workflow and their associated types

    All outputs for this workflow and their associated types

    returns

    a Map[FullyQualifiedName, WdlType] representing the union of all outputs from all calls within this workflow

  19. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  20. def findCallByName(name: String): Option[WdlCall]

    Find a Call object by name.

    Find a Call object by name. For example,

    workflow w {
  call foobar
}

    calling findCallByName("foobar") will return a Some(call). All other values would return a None

    name

    name of call to return

    returns

    Some(Call) if one with that name was found otherwise None

  21. def findDeclarationByName(name: String): Option[Declaration]
  22. def findWorkflowOutputByName(name: String, relativeTo: Scope): Option[WorkflowOutput]
  23. lazy val fullyQualifiedName: String

    String identifier for this scope.

    String identifier for this scope. this.namespace.resolve(this.fullyQualifiedName) == this

    Definition Classes
    Scope
  24. def fullyQualifiedNameWithIndexScopes: String

    String identifier for this scope, with hidden scope information.

    String identifier for this scope, with hidden scope information.

    this.namespace.resolve(this.fullyQualifiedNameWithIndexScopes) == this

    Definition Classes
    Scope
  25. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  26. lazy val hasEmptyOutputSection: Boolean
  27. def inputs: Map[FullyQualifiedName, WorkflowInput]

    FQNs for all inputs to this workflow and their associated types and possible postfix quantifiers.

    FQNs for all inputs to this workflow and their associated types and possible postfix quantifiers.

    returns

    a Map[FullyQualifiedName, WorkflowInput] representing the inputs that the user needs to provide to this workflow

  28. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  29. def locallyQualifiedName(relativeTo: Scope): String

    Similar to fullyQualifiedName but relatively to an ancestry scope.

    Similar to fullyQualifiedName but relatively to an ancestry scope. e.g. Workflow w Call a Output o

    o.locallyQualified(a) = "a.o" o.locallyQualified(w) = o.fullyQualifiedName = "w.a.o"

    Definition Classes
    Scope
  30. def lookupFunction(knownInputs: WorkflowCoercedInputs, wdlFunctions: WdlFunctions[WdlValue], outputResolver: OutputResolver = NoOutputResolver, shards: Map[Scatter, Int] = Map.empty[Scatter, Int], relativeTo: Scope = this): (String) ⇒ WdlValue

    This will return a lookup function for evaluating expressions which will traverse up the scope hierarchy to find a value for name.

    This will return a lookup function for evaluating expressions which will traverse up the scope hierarchy to find a value for name. An exception will be thrown if a value cannot be found for name

    knownInputs

    All known values of FQNs

    wdlFunctions

    Implementation of WDL functions for expression evaluation

    shards

    For resolving specific shards of scatter blocks

    returns

    String => WdlValue lookup function rooted at scope

    Definition Classes
    Scope
    Exceptions thrown

    VariableLookupException if anything else goes wrong in looking up a value for name

    VariableNotFoundException If no errors occurred, but also name didn't resolve to any value

  31. val meta: Map[String, String]
  32. def namespace: WdlNamespace

    Containing namespace

    Containing namespace

    Definition Classes
    Scope
  33. def namespace_=[Child <: WdlNamespace](ns: WdlNamespace): Unit
    Definition Classes
    Scope
  34. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  35. final def notify(): Unit
    Definition Classes
    AnyRef
  36. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  37. lazy val outputs: Seq[WorkflowOutput]
    Definition Classes
    WdlWorkflow → WdlCallable
  38. val parameterMeta: Map[String, String]
  39. def parent: Option[Scope]

    Parent scope

    Parent scope

    Definition Classes
    Scope
  40. def parent_=[Child <: Scope](scope: Scope): Unit
    Definition Classes
    Scope
  41. def resolveVariable(name: String, relativeTo: Scope = this): Option[WdlGraphNode]

    First tries to find any Call with name name.

    First tries to find any Call with name name. If not found, Fallback to looking at immediate children or delegating to parent node

    Definition Classes
    WdlWorkflow → Scope
  42. lazy val scatters: Set[Scatter]

    Descendants that are Scatters

    Descendants that are Scatters

    Definition Classes
    Scope
  43. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  44. lazy val taskCalls: Set[WdlTaskCall]
    Definition Classes
    Scope
  45. def toString(): String
    Definition Classes
    WdlWorkflow → AnyRef → Any
  46. lazy val transitiveDeclarations: Set[Declaration]

    Declarations within the workflow scope (including inside scatters and ifs)

  47. val unqualifiedName: String
    Definition Classes
    WdlWorkflow → Scope
  48. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  49. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  50. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  51. val wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter
  52. lazy val womDefinition: WorkflowDefinition

    Convert this WdlWorkflow into a wom.components.Workflow

    Convert this WdlWorkflow into a wom.components.Workflow

    Definition Classes
    WdlWorkflow → WdlCallable
  53. lazy val workflowCalls: Set[WdlWorkflowCall]
    Definition Classes
    Scope
  54. val workflowOutputWildcards: Seq[WorkflowOutputWildcard]

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from WdlCallable

Inherited from Scope

Inherited from AnyRef

Inherited from Any

Ungrouped