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

   WdlTask → 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.  val commandTemplate: Seq[CommandPart]
15.  def commandTemplateString: String
16.  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

17.  lazy val descendants: Set[Scope]

    All children ++ children's children ++ etc

    All children ++ children's children ++ etc

    Definition Classes

    Scope

18.  final def eq(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

19.  def evaluateFilesFromCommand(inputs: WorkflowCoercedInputs, functions: WdlFunctions[WdlValue]): Map[WdlExpression, WdlFile]

    Finds all write_* expressions in the command line, evaluates them, and return the corresponding created file for them.

20.  def evaluateOutputs(inputs: EvaluatedTaskInputs, wdlFunctions: WdlStandardLibraryFunctions, postMapper: (WdlValue) ⇒ Try[WdlValue] = v => Success(v)): Try[Map[TaskOutput, WdlValue]]
21.  def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

22.  def findOutputFiles(inputs: WorkflowCoercedInputs, functions: WdlFunctions[WdlValue], silenceEvaluationErrors: Boolean = true): Seq[WdlFile]

    Tries to determine files that will be created by the outputs of this task.

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.  def inputsFromMap(inputs: Map[FullyQualifiedName, WdlValue]): EvaluatedTaskInputs

    Assign declaration values from the given input map.

    Assign declaration values from the given input map. Fqn must be task declaration fqns e.g.: task t { String s } inputMap = Map("t.s" -> WdlString("hello"))

27.  def inputsLookupFunction(inputs: WorkflowCoercedInputs, wdlFunctions: WdlFunctions[WdlValue], shards: Map[Scatter, Int] = Map.empty[Scatter, Int]): (String) ⇒ WdlValue

    A lookup function that restricts known task values to input declarations

28.  def instantiateCommand(taskInputs: EvaluatedTaskInputs, functions: WdlFunctions[WdlValue], valueMapper: (WdlValue) ⇒ WdlValue = (v) => v): Try[String]

    Given a map of task-local parameter names and WdlValues, create a command String.

    Given a map of task-local parameter names and WdlValues, create a command String.

    Instantiating a command line is the process of taking a command in this form:

    sh script.sh $${var1} -o $${var2}

    This command is stored as a Seq[CommandPart] in the Command class (e.g. [sh script.sh, $${var1}, -o, $${var2}]). Then, given a map of variable -> value:

    {
      "var1": "foo",
      "var2": "bar"
    }

    It calls instantiate() on each part, and passes this map. The ParameterCommandPart are the $${var1} and $${var2} pieces and they lookup var1 and var2 in that map.

    The command that's returned from Command.instantiate() is:

    sh script.sh foo -o bar

    taskInputs

    Map[String, WdlValue] of inputs to this call, keys should be declarations

    functions

    Implementation of the WDL standard library functions to evaluate functions in expressions

    valueMapper

    Optional WdlValue => WdlValue function that is called on the result of each expression evaluation (i.e. evaluation of $${...} blocks).

    returns

    String instantiation of the command

29.  final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

30.  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

31.  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

32.  val meta: Map[String, String]
33.  val name: String
34.  def namespace: WdlNamespace

    Containing namespace

    Containing namespace

    Definition Classes

    Scope

35.  def namespace_=[Child <: WdlNamespace](ns: WdlNamespace): Unit

    Definition Classes

    Scope

36.  final def ne(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

37.  final def notify(): Unit

    Definition Classes

    AnyRef

38.  final def notifyAll(): Unit

    Definition Classes

    AnyRef

39.  lazy val outputs: Seq[TaskOutput]

    Definition Classes

    WdlTask → WdlCallable

40.  val parameterMeta: Map[String, String]
41.  def parent: Option[Scope]

    Parent scope

    Parent scope

    Definition Classes

    Scope

42.  def parent_=[Child <: Scope](scope: Scope): Unit

    Definition Classes

    Scope

43.  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

44.  val runtimeAttributes: RuntimeAttributes
45.  lazy val scatters: Set[Scatter]

    Descendants that are Scatters

    Descendants that are Scatters

    Definition Classes

    Scope

46.  final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes

    AnyRef

47.  lazy val taskCalls: Set[WdlTaskCall]

    Definition Classes

    Scope

48.  def toString(): String

    Definition Classes

    WdlTask → AnyRef → Any

49.  val unqualifiedName: LocallyQualifiedName

    Definition Classes

    WdlTask → Scope

50.  final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

51.  final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

52.  final def wait(arg0: Long): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

53.  lazy val womDefinition: TaskDefinition

    Definition Classes

    WdlTask → WdlCallable

54.  lazy val workflowCalls: Set[WdlWorkflowCall]

    Definition Classes

    Scope