cli.py

#!/usr/bin/env python

# hifis-surveyval
# Framework to help developing analysis scripts for the HIFIS Software survey.
#
# SPDX-FileCopyrightText: 2021 HIFIS Software <support@hifis.net>
#
# SPDX-License-Identifier: GPL-3.0-or-later
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.

# -*- coding: utf-8 -*-

"""
This is the entry point for the command-line interface (CLI) application.

It can be used as a handy facility for running the task from a command line.

.. note::

    To learn more about Click visit the
    `project website <http://click.pocoo.org/7/>`_.
    There is also a very helpful `tutorial video
    <https://www.youtube.com/watch?v=kNke39OZ2k0>`_.

    To learn more about running Luigi, visit the Luigi project's
    `Read-The-Docs <http://luigi.readthedocs.io/en/stable/>`_ page.

.. currentmodule:: hifis_surveyval.cli
.. moduleauthor:: HIFIS Software <software@hifis.net>
"""
import logging
import pathlib
from csv import reader

import click
import pkg_resources
import yaml

from hifis_surveyval.core import util
from hifis_surveyval.core.dispatch import Dispatcher
from hifis_surveyval.core.preprocess import Preprocessor
from hifis_surveyval.core.settings import Settings
from hifis_surveyval.data_container import DataContainer
from hifis_surveyval.hifis_surveyval import HIFISSurveyval

settings: Settings = Settings()


@click.group()
@click.option(
    "--verbose",
    "-v",
    count=True,
    default=0,
    show_default=True,
    help="Enable verbose output. "
    "Increase verbosity by setting this option up to 3 times.",
)
def cli(verbose: int) -> None:
    """
    Analyze a given CSV file with a set of independent python scripts.

    Args:
        verbose (int): Indicates the verbosity level on the CLI.
    """
    # NOTE that click takes above documentation for generating help text
    # Thus the documentation refers to the application per se and not the
    # function (as it should)

    settings.set_verbosity(verbose)
    if not settings.VERBOSITY == logging.ERROR:
        click.echo(
            click.style(
                f"Verbose logging is enabled. "
                f"(LEVEL={logging.getLogger().getEffectiveLevel()})",
                fg="yellow",
            )
        )


@cli.command()
def version() -> None:
    """Get the library version."""
    version_string: str = pkg_resources.require("hifis_surveyval")[0].version
    click.echo(click.style(f"{version_string}", bold=True))


@cli.command()
@click.option(
    "--config",
    "-c",
    is_flag=True,
    show_default=True,
    help="Create a default config as file. "
    "Overwrites any existing configuration file.",
)
@click.option(
    "--script",
    "-s",
    is_flag=True,
    show_default=True,
    help="Create an example script in the given script folder. "
    "Overwrites any existing example script file.",
)
@click.option(
    "--preprocess",
    "-p",
    is_flag=True,
    show_default=True,
    help="Create an empty preprocessing script in the given location. "
    "Overwrites any existing preprocessing script.",
)
def init(config: bool, script: bool, preprocess: bool) -> None:
    """
    Create a configuration file and an example script in the default locations.

    It will overwrite any existing configuration and example file.

    Args:
        config (bool): Indicates whether to create a configuration file.
        script (bool): Indicates whether to create an example analysis
                       script.
    """
    if not config and not script and not preprocess:
        config = True
        script = True
        preprocess = True

    if config:
        settings.create_default_config_file()
    if script:
        util.create_example_script(settings)
    if preprocess:
        util.create_preprocessing_script(settings)


@click.argument(
    "survey_data",
    type=click.Path(exists=True, dir_okay=False, path_type=pathlib.Path),
)
@cli.command()
def analyze(survey_data: click.Path) -> None:
    """
    Read the survey data and run all defined analysis scripts.

    The metadata are read from a file specified in the settings.

    Args:
        survey_data (click.File): File that contains all data for the analysis.
    """
    settings.load_config_file()

    surveyval: HIFISSurveyval = HIFISSurveyval(settings=settings)
    raw_data: DataContainer = DataContainer()
    logging.info(f"Analyzing file {survey_data.name}")

    # Load the metadata
    logging.info(f"Attempt to load metadata from {settings.METADATA}")

    with settings.METADATA.open(mode="r") as metadata_io_stream:
        metadata_yaml = yaml.safe_load(metadata_io_stream)
        raw_data.load_metadata(metadata_yaml)

    #  Load the actual survey data
    with survey_data.open(mode="r") as data_io_stream:
        csv_reader = reader(data_io_stream)
        raw_data.load_survey_data(csv_data=list(csv_reader))

    # preproces the data
    preprocessed_data: DataContainer = Preprocessor.preprocess(
        settings=settings, data=raw_data
    )

    # run analysis scripts
    dispatcher: Dispatcher = Dispatcher(
        surveyval=surveyval, data=preprocessed_data
    )
    dispatcher.discover()
    dispatcher.load_all_modules()