case class WdlNamespaceWithWorkflow(importedAs: Option[String], workflow: WdlWorkflow, imports: Seq[Import], namespaces: Seq[WdlNamespace], tasks: Seq[WdlTask], terminalMap: Map[Terminal, WorkflowSource], wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter, ast: Ast) extends WdlNamespace with Product with Serializable

A WdlNamespace which has exactly one workflow defined.

Linear Supertypes
Serializable, Serializable, Product, Equals, WdlNamespace, Scope, WdlValue, AnyRef, Any
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Inherited
  1. WdlNamespaceWithWorkflow
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. WdlNamespace
  7. Scope
  8. WdlValue
  9. AnyRef
  10. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new WdlNamespaceWithWorkflow(importedAs: Option[String], workflow: WdlWorkflow, imports: Seq[Import], namespaces: Seq[WdlNamespace], tasks: Seq[WdlTask], terminalMap: Map[Terminal, WorkflowSource], wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter, 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. def add(rhs: WdlValue): Try[WdlValue]
    Definition Classes
    WdlValue
  5. lazy val ancestry: Seq[Scope]

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

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

    Definition Classes
    Scope
  6. def and(rhs: WdlValue): Try[WdlBoolean]
    Definition Classes
    WdlValue
  7. def appearsInFqn: Boolean
    Definition Classes
    WdlNamespace → Scope
  8. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  9. val ast: Ast
    Definition Classes
    WdlNamespaceWithWorkflow → WdlNamespace → Scope
  10. lazy val calls: Set[WdlCall]

    Descendants that are Calls

    Descendants that are Calls

    Definition Classes
    Scope
  11. 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
  12. def children_=[Child <: Scope](children: Seq[Child]): Unit
    Definition Classes
    Scope
  13. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  14. 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
  15. def closestCommonScatter(other: Scope): Option[Scatter]
    Definition Classes
    Scope
  16. def coerceRawInputs(rawInputs: WorkflowRawInputs): Try[WorkflowCoercedInputs]

    Confirm all required inputs are present and attempt to coerce raw inputs to WdlValues.

    Confirm all required inputs are present and attempt to coerce raw inputs to WdlValues. This can fail if required raw inputs are missing or if the values for a specified raw input cannot be coerced to the target type of the input as specified in the namespace.

  17. def collectAsSeq[T <: WdlValue](filterFn: PartialFunction[WdlValue, T]): Seq[T]
    Definition Classes
    WdlValue
  18. def computeHash(implicit hasher: FileHasher): SymbolHash
    Definition Classes
    WdlValue
  19. 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
  20. lazy val descendants: Set[Scope]

    All children ++ children's children ++ etc

    All children ++ children's children ++ etc

    Definition Classes
    Scope
  21. def divide(rhs: WdlValue): Try[WdlValue]
    Definition Classes
    WdlValue
  22. def emptyValueFailure(operationName: String): Failure[Nothing]
    Definition Classes
    WdlValue
  23. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  24. def equals(rhs: WdlValue): Try[WdlBoolean]
    Definition Classes
    WdlValue
  25. def evaluateIfDefined[A <: WdlValue](operationName: String, optionalValue: WdlOptionalValue, operation: (WdlValue) ⇒ Try[A]): Try[A]
    Definition Classes
    WdlValue
  26. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  27. def findTask(name: String): Option[WdlTask]
    Definition Classes
    WdlNamespace
  28. lazy val fullyQualifiedName: String

    String identifier for this scope.

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

    Definition Classes
    Scope
  29. 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
  30. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  31. def greaterThan(rhs: WdlValue): Try[WdlBoolean]
    Definition Classes
    WdlValue
  32. def greaterThanOrEqual(rhs: WdlValue): Try[WdlBoolean]
    Definition Classes
    WdlValue
  33. val importedAs: Option[String]
    Definition Classes
    WdlNamespaceWithWorkflow → WdlNamespace
  34. val imports: Seq[Import]
    Definition Classes
    WdlNamespaceWithWorkflow → WdlNamespace
  35. def invalid(operation: String): Failure[Nothing]
    Definition Classes
    WdlValue
  36. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  37. def lessThan(rhs: WdlValue): Try[WdlBoolean]
    Definition Classes
    WdlValue
  38. def lessThanOrEqual(rhs: WdlValue): Try[WdlBoolean]
    Definition Classes
    WdlValue
  39. 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
  40. 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

  41. def mod(rhs: WdlValue): Try[WdlValue]
    Definition Classes
    WdlValue
  42. def multiply(rhs: WdlValue): Try[WdlValue]
    Definition Classes
    WdlValue
  43. def namespace: WdlNamespace

    Containing namespace

    Containing namespace

    Definition Classes
    WdlNamespace → Scope
  44. def namespace_=[Child <: WdlNamespace](ns: WdlNamespace): Unit
    Definition Classes
    Scope
  45. val namespaces: Seq[WdlNamespace]
    Definition Classes
    WdlNamespaceWithWorkflow → WdlNamespace
  46. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  47. def not: Try[WdlValue]
    Definition Classes
    WdlValue
  48. def notEquals(rhs: WdlValue): Try[WdlBoolean]
    Definition Classes
    WdlValue
  49. final def notify(): Unit
    Definition Classes
    AnyRef
  50. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  51. def or(rhs: WdlValue): Try[WdlBoolean]
    Definition Classes
    WdlValue
  52. def parent: Option[Scope]

    Parent scope

    Parent scope

    Definition Classes
    Scope
  53. def parent_=[Child <: Scope](scope: Scope): Unit
    Definition Classes
    Scope
  54. def resolve(fqn: FullyQualifiedName): Option[Scope]
    Definition Classes
    WdlNamespace
  55. def resolveCallOrOutputOrDeclaration(fqn: FullyQualifiedName): Option[Scope]
    Definition Classes
    WdlNamespace
  56. def resolveVariable(name: String, relativeTo: Scope = this): Option[WdlGraphNode]

    Performs scope resolution starting from this scope and walking up the lexical hierarchy until it finds a GraphNode with the name as its unqualifiedName

    Performs scope resolution starting from this scope and walking up the lexical hierarchy until it finds a GraphNode with the name as its unqualifiedName

    Definition Classes
    Scope
  57. def resource: String
    Definition Classes
    WdlNamespace
  58. lazy val scatters: Set[Scatter]

    Descendants that are Scatters

    Descendants that are Scatters

    Definition Classes
    Scope
  59. def staticDeclarationsRecursive(userInputs: WorkflowCoercedInputs, wdlFunctions: WdlStandardLibraryFunctions): Try[WorkflowCoercedInputs]

    Some declarations need a value from the user and some have an expression attached to them.

    Some declarations need a value from the user and some have an expression attached to them. For the declarations that have an expression attached to it already, evaluate the expression and return the value. Only evaluates workflow level declarations. Other declarations will be evaluated at runtime.

  60. def subtract(rhs: WdlValue): Try[WdlValue]
    Definition Classes
    WdlValue
  61. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  62. lazy val taskCalls: Set[WdlTaskCall]
    Definition Classes
    Scope
  63. val tasks: Seq[WdlTask]
    Definition Classes
    WdlNamespaceWithWorkflow → WdlNamespace
  64. val terminalMap: Map[Terminal, WorkflowSource]
    Definition Classes
    WdlNamespaceWithWorkflow → WdlNamespace
  65. def toString(): String
    Definition Classes
    WdlNamespaceWithWorkflow → AnyRef → Any
  66. def toWdlString: String
    Definition Classes
    WdlValue
  67. def typeName: String
    Definition Classes
    WdlValue
  68. def unaryMinus: Try[WdlValue]
    Definition Classes
    WdlValue
  69. def unaryPlus: Try[WdlValue]
    Definition Classes
    WdlValue
  70. def unqualifiedName: LocallyQualifiedName
    Definition Classes
    WdlNamespace → Scope
  71. def valueString: String
    Definition Classes
    WdlValue
  72. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  73. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  74. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  75. val wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter
  76. final val wdlType: WdlNamespaceType.type
    Definition Classes
    WdlNamespace → WdlValue
  77. lazy val womExecutable: Executable
  78. val workflow: WdlWorkflow
  79. lazy val workflowCalls: Set[WdlWorkflowCall]
    Definition Classes
    Scope
  80. val workflows: Seq[WdlWorkflow]
    Definition Classes
    WdlNamespaceWithWorkflow → WdlNamespace

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from WdlNamespace

Inherited from Scope

Inherited from WdlValue

Inherited from AnyRef

Inherited from Any

Ungrouped