from __future__ import print_function, division, absolute_import

import json

import logging

import os

import sys

from os.path import join

import astropy

import dask.dataframe as dd

import pandas as pd

"""Top-level package for openomics."""

__author__ = """Nhat (Jonny) Tran"""

__email__ = 'nhat.tran@mavs.uta.edu'

__version__ = '0.8.9'

# Initialize configurations

this = sys.modules[__name__]

this.config = {}

# Set pandas backend

this.config["backend"] = pd

# Set cache download directory

this.config["cache_dir"] = astropy.config.get_cache_dir(this.__name__)

logging.info("Cache directory is", this.config["cache_dir"])

home_dir = os.path.expanduser('~')

user_conf_path = join(home_dir, ".openomics/conf.json")

# Initialize user configuration file at ~/.openomics/conf.json

if not os.path.exists(user_conf_path):

    if not os.path.exists(join(home_dir, ".openomics")):

        os.makedirs(join(home_dir, ".openomics"))

    if not os.path.isfile(user_conf_path):

        base_conf = {}

        base_conf['cache_dir'] = astropy.config.get_cache_dir(this.__name__)

        with open(user_conf_path, 'w', encoding='utf-8') as file:

            json.dump(base_conf, fp=file, indent=4)

# Read configuration from ~/.openomics/conf.json

if os.path.isfile(user_conf_path):

    try:

        with open(user_conf_path, 'r', encoding='utf-8') as file:

            user_conf = json.load(fp=file)

        if user_conf:

            for p in user_conf.get('database', []):

                this.config.update(p)

    except Exception as e:

        logging.info("Could not import configurations from", user_conf_path)

# Import submodules

from .transcriptomics import *

from .genomics import *

from .proteomics import *

from .clinical import *

from .multiomics import *

def set_backend(new: str = "pandas"):

    """Set the dataframe processing backend to either Pandas or Dask.

    Args:

        new (str): Either "dask" or "pandas". Default "pandas.

    """

    assert new in ["dask", "pandas", "modin"]

    if new == "dask":

        this.config["backend"] = dd

    else:

        this.config["backend"] = pd

def set_cache_dir(path: str, delete_temp: bool = False):

    """Set the path where external databases downloaded from URL are saved.

    Args:

        path (str):

        delete_temp (bool):

    """

    if not os.path.exists(path):

        raise NotADirectoryError(path)

    this.config["cache_dir"] = path

    astropy.config.set_temp_cache(path=path, delete=delete_temp)

    logging.info("Cache directory is", this.config["cache_dir"])