Unable to use the $import directive

[EricBoix]

Expected Behavior

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

The expected behavior is thus that the import directive does indeed import the designated piece of workflow.

Actual Behavior

Instead, when running the above mentioned command 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')])

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.
  

Workflow Code

The following import_problem.zip zip file provides all the code: start with the extracted Readme.md and refer to the above description.

Full Traceback

INFO /private/tmp/import_problem/venv/bin/cwl-runner 1.0.20190915164430
INFO Resolved 'main.cwl' to 'file:///private/tmp/import_problem/main.cwl'
ERROR I'm sorry, I couldn't load this CWL file.
The error was: 
Traceback (most recent call last):
  File "/private/tmp/import_problem/venv/lib/python3.7/site-packages/cwltool/main.py", line 661, in main
    uri, loadingContext)
  File "/private/tmp/import_problem/venv/lib/python3.7/site-packages/cwltool/load_tool.py", line 113, in fetch_document
    workflowobj = loadingContext.loader.fetch(fileuri)
  File "/private/tmp/import_problem/venv/lib/python3.7/site-packages/schema_salad/ref_resolver.py", line 1192, in fetch
    result = next(attachments)
  File "/private/tmp/import_problem/venv/lib/python3.7/site-packages/ruamel/yaml/main.py", line 959, in load_all
    while loader._constructor.check_data():
  File "/private/tmp/import_problem/venv/lib/python3.7/site-packages/ruamel/yaml/constructor.py", line 98, in check_data
    return self.composer.check_node()
  File "/private/tmp/import_problem/venv/lib/python3.7/site-packages/ruamel/yaml/composer.py", line 58, in check_node
    if self.parser.check_event(StreamStartEvent):
  File "/private/tmp/import_problem/venv/lib/python3.7/site-packages/ruamel/yaml/parser.py", line 141, in check_event
    self.current_event = self.state()
  File "/private/tmp/import_problem/venv/lib/python3.7/site-packages/ruamel/yaml/parser.py", line 177, in parse_stream_start
    token.move_comment(self.scanner.peek_token())
  File "/private/tmp/import_problem/venv/lib/python3.7/site-packages/ruamel/yaml/scanner.py", line 1775, in peek_token
    self._gather_comments()
  File "/private/tmp/import_problem/venv/lib/python3.7/site-packages/ruamel/yaml/scanner.py", line 1803, in _gather_comments
    self.fetch_more_tokens()
  File "/private/tmp/import_problem/venv/lib/python3.7/site-packages/ruamel/yaml/scanner.py", line 282, in fetch_more_tokens
    return self.fetch_value()
  File "/private/tmp/import_problem/venv/lib/python3.7/site-packages/ruamel/yaml/scanner.py", line 655, in fetch_value
    self.reader.get_mark(),
ruamel.yaml.scanner.ScannerError: mapping values are not allowed here
  in "file:///private/tmp/import_problem/main.cwl", line 4, column 11

Your Environment

(venv): cwltool --version
/private/tmp/import_problem/venv/bin/cwltool 1.0.20190915164430
(venv) : python --version
Python 3.7.4