Parser does not support cwltool extensions

[stxue1]

Given the workflow below:

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
$namespaces:
  cwltool: "http://commonwl.org/cwltool#"

doc: |
  Trivial MPI test that prints the process IDs of each of the parallel
  processes. Requires Python (but you have cwltool running, right?)
  and an MPI implementation.

baseCommand: python
requirements:
  cwltool:MPIRequirement:
    processes: 2
arguments: [-c, 'import os; print(os.getpid())']
inputs: []
outputs:
  pids:
    type: stdout

MPIRequirement is part of the cwltool extensions. This workflow also works with both cwltool and toil-cwl-runner given the right flags, ex:

$ export PATH=$PATH:/home/heaucques/Documents/toil/src/toil/test/cwl/mock_mpi/ # where fake_mpi_run.py exists
$ cwltool --enable-dev --enable-ext --mpi-config-file /home/heaucques/Documents/toil/src/toil/test/cwl/mock_mpi/fake_mpi.yml file:///home/heaucques/Documents/toil/src/toil/test/cwl/mpi_simple.cwl
INFO /home/heaucques/Documents/toil/venv3.12/bin/cwltool 3.1.20240508115724
INFO [job mpi_simple.cwl] /tmp/1ez0it5c$ fake_mpi_run.py \
    --num \
    2 \
    --no-fail \
    python \
    -c \
    'import os; print(os.getpid())' > /tmp/1ez0it5c/c83195d490fa84f03f0cb9b142c6f385d736bd94
INFO [job mpi_simple.cwl] completed success
{
    "pids": {
        "location": "file:///home/heaucques/Documents/toil/c83195d490fa84f03f0cb9b142c6f385d736bd94",
        "basename": "c83195d490fa84f03f0cb9b142c6f385d736bd94",
        "class": "File",
        "checksum": "sha1$010210c4a6298629ae0653165e70c393bc831cad",
        "size": 12,
        "path": "/home/heaucques/Documents/toil/c83195d490fa84f03f0cb9b142c6f385d736bd94"
    }
}INFO Final process status is success

And the toil equivalent

However, running cwl-docker-extract mpi_simple.cwl crashes at parsing as by default, these extensions are disabled.

$ cwl-docker-extract file:///home/heaucques/Documents/toil/src/toil/test/cwl/mpi_simple.cwl
Traceback (most recent call last):
  File "/home/heaucques/Documents/toil/venv3.12/bin/cwl-docker-extract", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/heaucques/Documents/toil/venv3.12/lib/python3.12/site-packages/cwl_utils/docker_extract.py", line 139, in main
    run(arg_parser().parse_args(sys.argv[1:]))
  File "/home/heaucques/Documents/toil/venv3.12/lib/python3.12/site-packages/cwl_utils/docker_extract.py", line 55, in run
    top = cwl.load_document_by_uri(args.input)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/heaucques/Documents/toil/venv3.12/lib/python3.12/site-packages/cwl_utils/parser/__init__.py", line 183, in load_document_by_uri
    return load_document_by_string(doc, real_uri, loadingOptions, id_, load_all)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/heaucques/Documents/toil/venv3.12/lib/python3.12/site-packages/cwl_utils/parser/__init__.py", line 211, in load_document_by_string
    return load_document_by_yaml(result, uri, loadingOptions, id_, load_all)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/heaucques/Documents/toil/venv3.12/lib/python3.12/site-packages/cwl_utils/parser/__init__.py", line 227, in load_document_by_yaml
    result = cwl_v1_0.load_document_by_yaml(
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/heaucques/Documents/toil/venv3.12/lib/python3.12/site-packages/cwl_utils/parser/cwl_v1_0.py", line 21054, in load_document_by_yaml
    result, metadata = _document_load(
                       ^^^^^^^^^^^^^^^
  File "/home/heaucques/Documents/toil/venv3.12/lib/python3.12/site-packages/cwl_utils/parser/cwl_v1_0.py", line 1038, in _document_load
    loader.load(doc, baseuri, loadingOptions, docRoot=baseuri),
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/heaucques/Documents/toil/venv3.12/lib/python3.12/site-packages/cwl_utils/parser/cwl_v1_0.py", line 806, in load
    raise ValidationException("", None, errors, "*")
schema_salad.exceptions.ValidationException: src/toil/test/cwl/mpi_simple.cwl:3:1:   Object `mpi_simple.cwl` is not valid because:
src/toil/test/cwl/mpi_simple.cwl:14:1:   the `requirements` field is not valid because:
                                           Expected a <class 'NoneType'> but got list

cwl-docker-extract does not appear to support extensions:

$ cwl-docker-extract --help
usage: cwl-docker-extract [-h] [--dir DIR] [-s] [--container-engine CONTAINER_ENGINE] [--force-download] input

Save container images specified in a CWL document (Workflow or CommandLineTool). For CWL Workflows, all steps will also be searched (recursively).

positional arguments:
  input                 Input CWL document (CWL Workflow or CWL CommandLineTool)

options:
  -h, --help            show this help message and exit
  --dir DIR             Directory in which to save images
  -s, --singularity     Use singularity to pull the image
  --container-engine CONTAINER_ENGINE
                        Specify which command to use to run OCI containers. Defaults to 'docker' (or 'singularity' if --singularity/-s is passed).
  --force-download      Force pulling a newer container.

Is there a way to enable support for these extensions to allow the parser to pass for these cases?