#!/opt/anaconda1anaconda2anaconda3/bin/python
# -*- coding: utf-8
"""Adds a DEAFULT collection with EVERYTHING in it into a pan or profile database."""

import sys
import argparse

import anvio
import anvio.utils as utils
import anvio.dbops as dbops
import anvio.terminal as terminal

from anvio.tables import splits_info_table_name
from anvio.errors import ConfigError, FilesNPathsError
from anvio.tables.collections import TablesForCollections


__author__ = "Developers of anvi'o (see AUTHORS.txt)"
__copyright__ = "Copyleft 2015-2018, the Meren Lab (http://merenlab.org/)"
__credits__ = []
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "A. Murat Eren"
__email__ = "a.murat.eren@gmail.com"


pp = terminal.pretty_print
run = terminal.Run()
progress = terminal.Progress()


def main(args):
    utils.is_pan_or_profile_db(args.pan_or_profile_db)

    if utils.get_db_type(args.pan_or_profile_db) == 'profile' and utils.is_blank_profile(args.pan_or_profile_db):
        if not args.contigs_db:
            raise ConfigError("Yes but anvi'o can't add a 'default' collection into a blank profile database (yes, yours is a\
                               blank profile database). The reason to that is because blank profile databases do not know about\
                               the items names they pretend to know. Why? Well, it is a long story, BUT FORTUNATELY, you can\
                               recover from this by providing the contigs database your blank profile is associated with, and\
                               things would likely work.")
        else:
            utils.is_profile_db_and_contigs_db_compatible(args.pan_or_profile_db, args.contigs_db)
            all_items = dbops.ContigsDatabase(args.contigs_db).db.get_single_column_from_table(splits_info_table_name, 'split')
    else:
        if args.contigs_db:
            run.warning("You should provide a contigs database to this script only if you are working with an anvi'o blank\
                         profile database, which doesn't seem to be the case here. Anvi'o did think about raising an error\
                         and killing your awesome analysis on its track in the name of being explicit, but then it decided\
                         to ignore it for this once. Basically, the contigs database you provided will not be utilized for\
                         anything.")

        all_items = utils.get_all_item_names_from_the_database(args.pan_or_profile_db)

    collections_table = TablesForCollections(args.pan_or_profile_db)
    collections_table.append('DEFAULT', {'EVERYTHING': all_items})

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description="A script to add a 'DEFAULT' collection in an anvi'o pan or profile database with a bin\
                                                  named 'EVERYTHING' that describes all items available in the profile databse.")

    parser.add_argument(*anvio.A('pan-or-profile-db'), **anvio.K('pan-or-profile-db'))
    parser.add_argument(*anvio.A('contigs-db'), **anvio.K('contigs-db', {'required': False}))

    args = anvio.get_args(parser)

    try:
        main(args)
    except ConfigError as e:
        print(e)
        sys.exit(-1)
    except FilesNPathsError as e:
        print(e)
        sys.exit(-2)
