Converting WDL into WDLOM

To provide a concrete example, we will see how Cromwell parses the following line of WDL into WDLOM:

Int foo = min(100, max(1,2))

How Hermes interprets the WDL

Hermes can be asked to show its parse tree for a valid WDL file by running:

$ hermes analyze grammar.hgr <WDL FILE>

This allows us to see how Hermes interprets our line of WDL:

  type=<string:5:5 type "SW50">,
  name=<string:5:9 identifier "Zl9yb3VuZA==">,
    name=<string:5:19 identifier "bWlu">,
      <string:5:23 integer "MTAw">,
        name=<string:5:28 identifier "bWF4">,
          <string:5:32 integer "MQ==">,
          <string:5:34 integer "Mg==">

In graphical form this is (with string hashes replaced by values, for convenience):

Hermes AST Graph

How WDLOM represents WDL

WDLOM tries to be a programmer-friendlier, WDL version agnostic data model to hold WDL syntax trees.

It would use the following data structure to represent this declaration:

    typeElement = PrimitiveTypeElement(WomIntegerType),
    name = "foo",
    expression = Min(
        arg1 = PrimitiveLiteralExpressionElement(WomInteger(100)),
        arg2 = Max(
            arg1 = PrimitiveLiteralExpressionElement(WomInteger(1)),
            arg2 = PrimitiveLiteralExpressionElement(WomInteger(2))

Again, attempting to show this graphically:


Transliteration functions from Hermes ASTs to WDLOM

The various classes in the wdl.transforms.base.ast2wdlom package implement conversions from various types of AST element into various types of WDLOM.

Let's look at AstToInputDeclarationElement:

  • The conversion from AST to WDLOM relies on two other conversions, astNodeToTypeElement and astNodeToExpressionElement, to validate the attributes on the AST it is given, and construct WDLOM from Hermes ASTs.
  • The resulting function can itself be used as a building block to construct higher-level WDLOM types.

How AST-to-WDLOM building blocks are chained together

To see how these building blocks are pieced together we can look at WDL 1.0's ast2wdlom package object.

Notice how - and where - the astToInputDeclarationElement value is declared:

  • It follows the implicit vals astNodeToTypeElement and astNodeToExpressionElement and so can use those in its processing.
  • It is, as an implicit val, used later on by astNodeToInputsSectionElement, which is then used by astNodeToWorkflowBodyElement and astNodeToTaskSectionElement, and so on.

How different WDL versions convert to WDLOM differently

These package objects ultimately control how different WDL versions are parsed differently. These differences can be seen most easily by comparing package objects for different WDL versions:

diff \
  wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/ast2wdlom/ast2wdlom.scala \

In an extreme case, these could contain fundamentally different conversion logic from AST to WDLOM for different WDL versions. Luckily, between WDL 1.0 and the WDL development version, there are only a few minor changes, amongst which are:

  • Importing a new Hermes parser.
  • Specifying that additional functions are available when constructing the astNodeToExpressionElement conversion.
  • Specifying that a new Directory type is available when constructing the astNodeToTypeElement conversion.