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Automated CWL and Galaxy XML generation for Python tools that use argparse and click

License: Apache License 2.0

Python 100.00%

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anton-khodak

gxargparse's Issues

unnecessary InlineJavascriptRequirement

Seems to be added to all files, regardless of being needed

requirements:
  - class: InlineJavascriptRequirement

Flag to override outputs with provided output section

Remove `posititon` field for optional arguments

common-workflow-library/legacy#93

Open PR to add cnvkit wrappers to https://github.com/common-workflow-language/workflows

It can be a "standing" or "[WIP]" (work in progress) pull request.

use optional arguments shortcut

type: ["null", str] -> type: str?

Switch from jinja2 templates to yaml writer

use array shortcuts

If an array of a single type then type: string[] is simpler

Error when trying to convert click command to cwl

I'd like to convert click commands to cwl command line tools. After installing gxargparse I get an error if I run the command with or without --generate_cwl_tool:

> python -m nlppln.replace_ner --generate_cwl_tool
Traceback (most recent call last):
  File "/usr/lib/python3.5/runpy.py", line 184, in _run_module_as_main
    "__main__", mod_spec)
  File "/usr/lib/python3.5/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/jvdzwaan/code/nlppln/nlppln/replace_ner.py", line 2, in <module>
    import click
  File "/home/jvdzwaan/code/gxargparse/click/__init__.py", line 20, in <module>
    setattr(__selfmodule__, x, getattr(click, x))
AttributeError: module 'random_name_1' has no attribute 'cwlt'

> python -m nlppln.replace_ner
Traceback (most recent call last):
  File "/usr/lib/python3.5/runpy.py", line 184, in _run_module_as_main
    "__main__", mod_spec)
  File "/usr/lib/python3.5/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/jvdzwaan/code/nlppln/nlppln/replace_ner.py", line 2, in <module>
    import click
  File "/home/jvdzwaan/code/gxargparse/click/__init__.py", line 20, in <module>
    setattr(__selfmodule__, x, getattr(click, x))
AttributeError: module 'random_name_1' has no attribute 'cwlt'
(cwl3) jvdzwaan@ESLT0062:~/code/gxargparse$

The error also occurs in Python 2.7:

> python -m nlppln.replace_ner --generate_cwl_tool
Traceback (most recent call last):
  File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/jvdzwaan/code/nlppln/nlppln/replace_ner.py", line 2, in <module>
    import click
  File "click/__init__.py", line 20, in <module>
    setattr(__selfmodule__, x, getattr(click, x))
AttributeError: 'module' object has no attribute 'cwlt'

> python -m nlppln.replace_ner
Traceback (most recent call last):
  File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/jvdzwaan/code/nlppln/nlppln/replace_ner.py", line 2, in <module>
    import click
  File "click/__init__.py", line 20, in <module>
    setattr(__selfmodule__, x, getattr(click, x))
AttributeError: 'module' object has no attribute 'cwlt'

In both instances gxargparse_check_path gives Ready to go!

Running example.py creates file named `example.cwl` unexpectedly

Took me a few minutes to understand why my changes weren't sticking as I had created an example.cwl for testing.

When example.py is run, it outputs the CWL tool to both stdout + example.cwl (one also has an extra newline). This seems like odd behaviour to me (a linux admin). If it outputs to stdout, I don't expect it to also be writing to a file.

$ strace -e open python example.py --generate_cwl_tool 2>&1 | grep example.cwl
open("example.cwl", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3

Additionally one of them has an extra newline at the end (stdout vs updated file).

no empty defaults

Needs merging into erasche/gxargparse

cwlVersion can be simplified

cwlVersion: v1.0

CWL booleans are default false, saying so is redundant

Repository name

As @mr-c mentioned in a private conversation, Galaxy will be gaining CWL support, and the development of the original gxargparse basically stopped, so Galaxy specific parts can be ripped off. I need them now as a sample, but as soon as CWL tool wrapper will be finished, I'll remove them as much as the docs. Should the repository bear the old name along with that?

/cc @brainstorm

parse_known_args() cwl generation?

Hi,

I looked through the issues before posting, apologies if this has been asked or explained elsewhere or I missed it...

I noticed that if my argparse objects call parse_known_args instead of parse_args, the --generate_cwl_tool doesn't fire. Is that by design? I can see the logic if so, just wondering.

optional CWL tool output definitions in external file

Hey @anton-khodak, this is looking great!

In the resulting CWL tool definition I see that the output sections are all blank.

One way to fix that is to accept a file with the definitions written by hand.

Missing future and jinja2 from requirements.txt and install_requires in setup.py

From hexylena#31 (comment)

Error when running --generate_cwl_tool on example.py

I get an error when I run python example.py --generate_cwl_tool:

Traceback (most recent call last):
  File "example.py", line 29, in <module>
    args = parser.parse_args()
  File "/home/jvdzwaan/code/gxargparse/argparse/__init__.py", line 78, in parse_args
    self.parse_args_cwl(*args, **kwargs)
  File "/home/jvdzwaan/code/gxargparse/argparse/__init__.py", line 115, in parse_args_cwl
    cwlt_parameter = methodToCall(result)
  File "/home/jvdzwaan/code/gxargparse/argparse/argparse_cwl_translation.py", line 85, in _StoreAction
    cwlparam = self.__cwl_param_from_type(param)
  File "/home/jvdzwaan/code/gxargparse/argparse/argparse_cwl_translation.py", line 58, in __cwl_param_from_type
    'type': self.get_cwl_type(param.type) or 'str'}
  File "/home/jvdzwaan/code/gxargparse/argparse/argparse_cwl_translation.py", line 131, in get_cwl_type
    return PY_TO_CWL_TYPES[py_type]
KeyError: <class 'io.IOBase'>