cli.py 文件源码

def convert(**kwargs):
    kwargs["no_header"] = not kwargs["no_header"]
    kwargs["no_normalize_plurals"] = not kwargs["no_normalize_plurals"]
    kwargs["no_standardize"] = not kwargs["no_standardize"]
    kwargs["opsin_no_allow_acids_without_acid"] = not kwargs["opsin_no_allow_acids_without_acid"]
    kwargs["opsin_no_detailed_failure_analysis"] = not kwargs["opsin_no_detailed_failure_analysis"]
    kwargs["opsin_no_allow_radicals"] = not kwargs["opsin_no_allow_radicals"]
    kwargs["opsin_no_allow_uninterpretable_stereo"] = not kwargs["opsin_no_allow_uninterpretable_stereo"]

    is_output_file = bool(kwargs["output"])

    stdin = click.get_text_stream("stdin")
    input_text = ""
    if not stdin.isatty():
        kwargs["input_file"] = ""
        input_text = click.get_text_stream("stdin").read().strip()
    if not input_text and not kwargs["input_file"]:
        raise click.UsageError("Cannot do conversion: stdin is empty and input file is not provided.")

    init_kwargs = get_kwargs(kwargs, KWARGS_OPSIN_INIT)
    process_kwargs = get_kwargs(kwargs, KWARGS_OPSIN_PROCESS)

    opsin = OPSIN(**init_kwargs)
    result = opsin.process(input=input_text, output_formats=["smiles", "inchi", "inchikey"], **process_kwargs)

    if kwargs["dry_run"]:
        print(result)
        exit(0)

    if kwargs["raw_output"]:
        print(result["stdout"])
        eprint(result["stderr"])
        exit(0)

    if not is_output_file:
        print(dict_to_csv(result["content"], csv_delimiter=kwargs["delimiter"], write_header=kwargs["no_header"]))