cli.py 文件源码

def ner(**kwargs):
    kwargs["no_standardize"] = not kwargs["no_standardize"]
    kwargs["no_convert_ions"] = not kwargs["no_convert_ions"]
    kwargs["no_header"] = not kwargs["no_header"]
    kwargs["no_normalize_text"] = not kwargs["no_normalize_text"]
    kwargs["no_annotation"] = not kwargs["no_annotation"]

    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 perform NER: stdin is empty and input file is not provided.")

    kwargs["opsin_types"] = get_opsin_types(kwargs["opsin_types"])

    init_kwargs = get_kwargs(kwargs, KWARGS_CHS_INIT)
    process_kwargs = get_kwargs(kwargs, KWARGS_CHS_PROCESS)

    chemspot = ChemSpot(**init_kwargs)
    result = chemspot.process(input_text=input_text, **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"]))