APPS-1149 optional elements in structs

dnanexus / wdlTools

WDL tools for parsing, type-checking, and more

Apache License 2.0

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APPS-1149 optional elements in structs #218

Closed YuxinShi0423 closed 2 years ago

YuxinShi0423 commented 2 years ago

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

[x] hash inputs should be coerced from object to struct
[x] their optional elements should be assigned to Null if not specified in job inputs.
[x] add tests
- [x] task struct input
- [x] workflow struct input
- [x] workflow struct input to scatter input

YuxinShi0423 commented 2 years ago

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 commented 2 years ago

@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 commented 2 years ago

@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 commented 2 years ago

@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 commented 2 years ago

@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.