Clarify how to handle a nested array with inputBinding for all levels

[tom-tan]

Related: common-workflow-language/common-workflow-language#783

The spec of CommandLineBinding says:

array: If itemSeparator is specified, add prefix and the join the array into a single string with itemSeparator separating the items. Otherwise first add prefix, then recursively process individual elements.

However, it does not mention how to behave in the case of the combination of itemSeparator and prefix in the different levels.

Current behavior:

• tests/nested-array-inputBinding.cwl

  cwlVersion: v1.2
  class: CommandLineTool
  
  hints:
      - class: DockerRequirement
        dockerPull: docker.io/python:3-slim
  
  baseCommand: python
  inputs:
      script:
          type: File
          default:
              class: File
              location: args.py # use args.py in the conformance tests
          inputBinding:
              position: -1
      inp1:
          type:
              type: array
              items:
                  type: array
                  items: string
                  inputBinding:
                      prefix: "-p"
          inputBinding:
              itemSeparator: ","
  outputs:
      args: string[]

• tests/nested-array-inputBinding-job.yml

  inp1: [["foo", "bar", "buzz"], ["hoge", "fuga"]]

• Result

  $ cwl-runner --quiet tests/nested-array-inputBinding.cwl tests/nested-array-inputBinding-job.yml
  INFO /home/vscode/.local/bin/cwl-runner 3.1.20220502060230
  ...
  {
      "args": [
          "['foo', 'bar', 'buzz'],['hoge', 'fuga']",
          "-p",
          "foo",
          "-p",
          "hoge",
          "-p",
          "bar",
          "-p",
          "fuga",
          "-p",
          "buzz"
      ]
  }

Note: I guess few users write such CWL document but platform developers have to care such cases. I hope we can define this corner case not to make difficult to implement platforms.

[tom-tan]

• Expected types and its resulted types

  • prefix

    • expected: string or string[]
      • e.g., "str", ["elem1", "elem2", "elem3"]
    • result: string[]
      • e.g., ["-pre", "str"], ["-pre", "elem1", "elem2", "elem3"]

  • itemSeparator

    • expected: string[]
      • e.g., ["elem1", "elem2", "elem3"]
    • result: string
      • e.g., "elem1,elem2,elem3"

  • separate: true

    • expected: string
      • e.g., "str"
    • result: string[]
      • e.g., ["-pre", "str"]

  • separate: false

    • expected: string
      • e.g., "str"
    • result: string
      • e.g., "-prestr"

Points to be clarified

1. (not limited to nested arrays) How to behave prefix and separate: false for array?

For example: ["elem1", "elem2", "elem3"]

Possible behavior

• prefix is added only to the first element: "-preelem1 elem2 elem3"
  • It causes another problem: how to interpret string[] as string?
• Same as itemSeparator: "": "-preelem1elem2elem3"
• Reject when prefix and separate: false are specified at the same time

2. How to behave itemSeparator and prefix for nested array?

For example: [["elem1", "elem2", "elem3"], ["elem"]] with the following declaration:

inp1:
  type:
    type: array
    items:
      type: array
      items: string
      inputBinding:
        prefix: -pre
  inputBinding:
    itemSeparator: ","

By processing inputBinding in the leaf level in the above example, we obtain [["-pre", "elem1", "elem2", "elem3"], ["-pre", "elem"]].

Possible behavior

• itemSeparator is applied for all the elements. that is: "-pre,elem1,elem2,elem3,-pre,elem"
• itemSeparator is applied for the first element? "-pre elem1 elem2 elem3,-pre elem"?
  • It causes another problem: how to interpret string[] as string?
• Reject when inputBinding has itemSeparator and any leaves (including their sub-leaves) specify the case of:
  • separate: true if prefix is specified, and
  • itemSeparator is not specified for arrays

---

I prefer the last choice for both cases, that is, rejecting such corner cases.
It makes easier to implement platforms and also enables to delay the decision until we know the real use cases for them.