struct with optional fields

[adthrasher]

I have run into a potential issue when using a struct that contains optional fields.

For example, consider this WDL document.

version 1.1

struct ReadGroup {
    String ID
    String? BC
    String? CN
    String? DS
    String? DT
    String? FO
    String? KS
    String? LB
    String? PG
    Int? PI
    String? PL
    String? PM
    String? PU
    String? SM
}

task test_task {
    input {
        ReadGroup read_group 
    }

    command <<<
        if [ -z "~{read_group.KS}" ]
        then
            echo "KS is empty"
        fi  
    >>>
}

I have a struct that represents a SAM read group. When I run miniwdl check, there are no issues reported. However, if I then run miniwdl, with the following input json:

{
    "read_group": {
        "ID": "test"
    }
}

I get an error (Token('CNAME', 'KS')) at ~{read_group.KS}. I have tried alternative methods such as ~{if defined(read_group.KS) then read_group.KS else ""} and ~{select_first([read_group.KS, ""])} which both have the same issue.

Based on the error and the fact that it only occurs at runtime, is it possible that the KS field is not being created on the internal data structure so miniwdl doesn't recognize that token? I would expect that it would exist and simply be undefined similar to other optional variables, but that doesn't seem to be the case.

[mlin]

Thanks @adthrasher, your diagnosis was correct in the case where the struct is initialized from the runner input JSON file. I've checked in a fix.

[adthrasher]

Excellent! As always, thanks for the rapid response and fix!