Demonstrate the usage of the $import directive in the user guide ?

[Eric Boix]

This is issue was moved to the the cwltool repository where is belongs...

Section 2.4 (Document preprocessing) (of the Common Workflow Language Command Line Tool Description v1.1) mentions the possible usage of the $import directive. One can find some rare examples of usage of this $import directive that don't seem that straightforward to transpose (at least for me and when using cwl-runner version 1.0.20190831161204).

For example suppose we realized the following break down of the first example of the user guide as the following two workflows
to-be-imported.cwl

inputs:
  message:
    type: string
    inputBinding:
      position: 1
outputs: []

and
main.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.1
class: CommandLineTool
baseCommand: echo
$import: to-be-imported.cwl

while keeping the echo-job.yml argument file provided in the user guide. And further assume that you try to run this broken down first example with the following bash commands

virtualenv -p python3 venv
source venv/bin/activate
pip install cwlref-runner
cwl-runner main.cwl echo-job.yml

then you might probably get the following error message

ERROR Tool definition failed initialization:
main.cwl:6:1: '$import' must be the only field in ordereddict([('cwlVersion', 'v1.1'), ('class', 'CommandLineTool'), ('baseCommand', 'echo'), ('$import', 'to-be-imported.cwl'), ('id', 'file:///Users/eboix/SAVED/Divers/Ruses/CWL_examples/main.cwl')])

Wouldn't it be worth documenting the usage of the $import directive in the user guide ?

Notes:

• trying to use the line

  {$import: to-be-imported.cwl}
  

  in place of the line

  $import: to-be-imported.cwl
  

  as suggested by the "Workflow steps and wiring" section of this issue doesn't seem to help.
• trying the following syntax

  "@import": to-be-imported.cwl
  

  as suggested by this issue also fails but with the following different error message

  main.cwl:3:1: "outputs" section is not valid.
  

[Deleted user]

From my reading of https://www.commonwl.org/v1.1/SchemaSalad.html#Import
I see that

cwlVersion: v1.1
class: CommandLineTool
baseCommand: echo
$import: to-be-imported.cwl

is not valid.

From my reading it should be expressed as

cwlVersion: v1.1
class: CommandLineTool
baseCommand: echo
inputs: 
  $import: inputs.cwl
outputs: []

where inputs.cwl is

  message:
    type: string
    inputBinding:
      position: 1

[Deleted user]

Ok, I can't get that to work with cwltool --validate so my understanding is incomplete.

I tried with your trick of @include and get

main.cwl:4:11:   checking object `main.cwl#@include`
main.cwl:4:11:     Field `type` references unknown identifier `inputs.cwl`, tried file:///Users/kghose/Downloads/main.cwl#inputs.cwl

[Eric Boix]

Thanks @kaushik-work . Indeed the version that you propose, that is

cwlVersion: v1.1
class: CommandLineTool
baseCommand: echo
inputs: 
  $import: inputs.cwl
outputs: []

also fails to validate for me (thanks for letting me know about that --validate options) with the message mapping values are not allowed here.
I also tried (I'm pretty despaired on this matter :-) to add a first inputs: line to inputs.cwl (and also fooled around with various indentation levels) but without success...

[Eric Boix]

This is issue was moved to the the cwltool repository where is belongs...