--codegen python: have normal __init__ , add method for parsing from a doc

[mr-c]

using @classmethod

example generated code:

class Workflow(Process):
  def __init__(self, id, inputs, outputs, requirements, hints, label, doc, steps): 
     # or use attrs, or use 3.7's dataclasses
    pass # init code here

  @staticmethod
  def from_doc(cls, doc, baseurl, loadingOptions, docRoot=None):
    pass # regular loading code here

• Generate the __init__ as part of codegen? Or go Python3.7+ only by using @dataclass/PEP-0557?

[illusional]

I believe this is implemented right as it's in the parser in common-workflow-language/cwl-utils#5? Secondary to this @tetron / @mr-c, it would be great if optional values (like label in this example had a default =None on the __init__. Then we've covered just about all the bases from common-workflow-lab/python-cwlgen#27).

eg:

class Workflow(Process):
  def __init__(self, id, inputs, outputs, steps, requirements=None, hints=None, label=None, doc=None): 
    pass # init code here

Some things I could forsee being an issue are ordering of optional and non-optional params. And when I was doing the automatic parsing, I needed to make sure that these param names match up properly.

def get_required_input_params_for_cls(cls, valuesdict):
    try:
        argspec = inspect.getfullargspec(cls.__init__)
    except:
        # we're in Python 2
        argspec = inspect.getargspec(cls.__init__)

    args, defaults = argspec.args, argspec.defaults
    required_param_keys = set(args[1:-len(defaults)]) if defaults is not None and len(defaults) > 0 else args[1:]

    inspect_ignore_keys = {"self", "args", "kwargs"}

    required_init_kwargs = {k: valuesdict[k] for k in required_param_keys if (k not in inspect_ignore_keys)}

    return required_init_kwargs

And then splat (**kwarg) the result: T(**get_required_input_params_for_cls(T, _doc)).

[illusional]

Bump on this to deprecate the cwlgen project.

[mr-c]

@tetron How hard do you think it would be to add the =None to the optional items?

[tetron]

I haven't been keeping up, is the question about how hard it is for codegen to make some Python parameters optional? It should be very easy.

[illusional]

@tetron, exactly that. If the parameter is optional, it should have a default of None. Better mirrors the CWLGen project, which can then be deprecated as doesn't really support v1.1 nor will it support v1.2 without a bit of work.

[multimeric]

At least in the short term, here's my hack to work around this issue:

import inspect

def with_default_none(func, *args, **kwargs):
    """
    Calls a function, and inserts None for all arguments you didn't provide
    """
    spec = inspect.getfullargspec(func)
    defaults = {arg: None for arg in spec.args}
    defaults.pop('self', None)
    return func(*args, **{**defaults, **kwargs})

This then lets you:

tool = with_default_none(
    CommandLineTool,
    id=cmd.as_filename + ".cwl",
    baseCommand=list(cmd.command),
    cwlVersion="v1.1",
    inputs=[],
    outputs=[]
)

tool.inputs.append(
    with_default_none(
        CommandInputParameter,
        id=self.choose_variable_name(pos),
        type=self.to_cwl_type(pos.get_type()),
        inputBinding=with_default_none(
            CommandLineBinding,
            position=pos.position
        ),
        doc=pos.description,
    )
)

[mr-c]

@TMiguelT Nice hack! We could apply this as a decorator to the generated code. PRs very welcome!