APPS-1149 optional elements in structs

[YuxinShi0423]

This PR is to fix the evaluation of structs as input parameters of workflow/scatter:

• hash inputs should be coerced from object to struct

• their optional elements should be assigned to Null if not specified in job inputs.

• add tests

  • task struct input
  • workflow struct input
  • workflow struct input to scatter input

[YuxinShi0423]

All test WDL files I added can be compiled and executed successfully. Also all WDL integration tests with this version of wdlTools are passed. (CWL is not affected so I did not run the tests.)

[commandlinegirl]

LGTM, thank you for working on that!

[commandlinegirl]

LGTM, thank you for adding a release note!

[commandlinegirl]

@YuxinShi0423 Are you planning to release a snapshot for wdlTools once this this merged and create a PR in dxCompiler to run integration tests on this?

[YuxinShi0423]

@commandlinegirl I have run the integration test with this snapshot. Shall I release a new version of wdlTools? Or is there a way to build a snapshot (but not release it) which dxCompiler can use?

[commandlinegirl]

@commandlinegirl I have run the integration test with this snapshot. Shall I release a new version of wdlTools? Or is there a way to build a snapshot (but not release it) which dxCompiler can use?

You don't have to create a new full wdlTools release. You can run the "Publish snapshot" workflow from the Actions tab in the wdlTools repo:

And then use the released version (it will be 0.17.9-SNAPSHOT) in dxCompiler (it's already set to 0.17.9 as shown here).

[commandlinegirl]

@YuxinShi0423 Oh, re my previous comment - I can see you already ran it!:) So now you'd just need to create PR in dxCompiler to run integration tests.