CLI

Researcher CLI

Attributes

cli module-attribute 

cli = ResearcherCLI()

Classes

ResearcherCLI 

ResearcherCLI()

Bases: CommonCLI

Researcher CLI

Source code in fedbiomed/researcher/cli.py 
def __init__(self):
    super().__init__()
    self.description = f"{__intro__}\nA CLI app for fedbiomed researchers."
    self.initialize()

Attributes

description instance-attribute 
description = f'{__intro__}
A CLI app for fedbiomed researchers.'

Functions

initialize 
initialize()

Initializes Researcher CLI

Source code in fedbiomed/researcher/cli.py 
def initialize(self):
    """Initializes Researcher CLI"""


    class ConfigNameActionResearcher(ConfigNameAction):
        _this = self
        _component = ComponentType.RESEARCHER

        def import_environ(self) -> 'fedbiomed.researcher.environ.Environ':
            """Import environ"""
            return importlib.import_module("fedbiomed.researcher.environ").environ


    # Config parameter is not necessary. Python client (user in jupyter notebook)
    # will always use default config file which is `researcher_config`
    # However, this argument will play important role once researcher back-end (orhestrator)
    # and researcher is seperated
    self._parser.add_argument(
        "--config",
        "-cf",
        nargs="?",
        action=ConfigNameActionResearcher,
        default="config_researcher.ini",
        help="Name of the config file that the CLI will be activated for. Default is 'config_researcher.ini'.")

    super().initialize()

ResearcherControl 

ResearcherControl(subparser)

Bases: CLIArgumentParser

Source code in fedbiomed/common/cli.py 
def __init__(self, subparser: argparse.ArgumentParser):

    self._subparser = subparser
    # Parser that is going to be add using subparser
    self._parser = None

Functions

initialize 
initialize()
Source code in fedbiomed/researcher/cli.py 
def initialize(self):

    start = self._subparser.add_parser(
        "start", help="Starts Jupyter (server) Notebook for researcher API. The default"
                      "directory will be  notebook directory.")

    start.add_argument(
        "--directory",
        "-dir",
        type=str,
        nargs="?",
        required=False,
        help="The directory where jupyter notebook will be started.")
    start.set_defaults(func=self.start)
start 
start(args)

Starts jupyter notebook

Source code in fedbiomed/researcher/cli.py 
def start(self, args):
    """Starts jupyter notebook"""


    options = ['--NotebookApp.use_redirect_file=false']

    if args.directory:
        options.append(f"--notebook-dir={args.directory}")

    command = ["jupyter", "notebook"]
    command = [*command, *options]
    process = subprocess.Popen(command)

    try:
        process.wait()
    except KeyboardInterrupt:
        try:
            process.terminate()
        except Exception:
            pass
        process.wait()