#!/opt/anaconda1anaconda2anaconda3/bin/python
# -*- coding: utf-8
"""A program to import an items order into an anvi'o database"""

import sys

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

from anvio.errors import ConfigError, FilesNPathsError


__author__ = "Developers of anvi'o (see AUTHORS.txt)"
__copyright__ = "Copyleft 2015-2019, the Meren Lab (http://merenlab.org/)"
__credits__ = []
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "A. Murat Eren"
__email__ = "a.murat.eren@gmail.com"
__requires__ = ['genes-db', 'pan-db', 'profile-db', 'misc-data-item-orders-txt', 'dendrogram', 'phylogeny',]
__provides__ = ['misc-data-item-orders',]

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


def main(args):
    A = lambda x: args.__dict__[x] if x in args.__dict__ else None
    input_file_path = A('input_order')
    db_path = A('db_path')
    order_name = A('name') or 'LAZY_USERS_UNKNOWN_ITEMS_ORDER'
    make_default = A('make_default')

    if not input_file_path or not db_path:
        raise ConfigError("Probably it will come as a surprise, but you *must* provide a file path for the\
                           input order and the target database :/")

    filesnpaths.is_file_plain_text(input_file_path)
    utils.is_pan_or_profile_db(db_path, genes_db_is_also_accepted=True)

    order_data = [l.strip() for l in open(input_file_path).readlines() if len(l.strip())]

    # Determine the nature of the incoming order data:
    if len(order_data) == 1:
        try:
            filesnpaths.is_proper_newick(order_data[0])
        except Exception as e:
            raise ConfigError("Your input file contained a single line and anvi'o thought that it shold be a \
                               newick tree, but then ETE complained about it, so we are all upset here: '%s'\
                               :(" % (e))

        order_data = order_data[0]
        order_data_type_newick = True
    else:
        order_data_type_newick = False
        order_data = ','.join(order_data)

    run.info("Target database", db_path)
    run.info("Database type", utils.get_db_type(db_path), nl_after=1)
    run.info("Order file path", input_file_path)
    run.info("Order data type", 'newick' if order_data_type_newick else 'basic')
    run.info("Order name", order_name, mc='red', nl_after=1)

    if order_data_type_newick:
        dbops.add_items_order_to_db(db_path, order_name, order_data, order_data_type_newick=order_data_type_newick,
                                    distance='NA', linkage='NA', dont_overwrite=True, make_default=make_default,
                                    check_names_consistency=True)
    else:
        dbops.add_items_order_to_db(db_path, order_name, order_data, order_data_type_newick=order_data_type_newick,
                                    dont_overwrite=True, make_default=make_default, check_names_consistency=True)


if __name__ == '__main__':
    import argparse

    parser = argparse.ArgumentParser(description="Import a new items order into an anvi'o database")

    groupI = parser.add_argument_group('CRITICAL INPUT', 'Basically the input file and the target database')
    groupI.add_argument('-i', '--input-order', metavar = 'FILE', help = "One of the two important things you must provide: the file\
                                that contains the items order. The format of this file is important. It can either contain a\
                                proper newick tree in it, or a complete list of 'items' in the target database where every line\
                                of the file is simply an item name. If you are providing a newick tree, the entire file should\
                                be a single line. I know it sounds hard, but you seriously can do this.")
    groupI.add_argument('-p', '--db-path', metavar = 'DB PATH', help = "An appropriate anvi'o database to import the items order. Currently\
                                it can be a profile, pan, or genes database. But you should try your chances with other kinds of\
                                databases for fun and games. Basically, if the database contains an items order table, then things\
                                will work. Otherwise, you will probably get angry errors back in the worst case scenario.")

    groupZ = parser.add_argument_group('NOT SO CRITICAL INPUT', 'Because not all parameters are created equal')
    groupZ.add_argument('--name', metavar='ORDER NAME', help="What should we call this order? Give it a concise, single-word name.")
    groupZ.add_argument('--make-default', default=False, action="store_true", help="You have the option to make this order the \
                                default order in the database. Which means, anvi'o will use this one when someone runs the\
                                program anvi-interactive and presses draw. Big responsibility. But if you have a 'default' state,\
                                it will not work because the default items order in the state file overwrites the one that comes\
                                from the database. So not that big of a responsibility.")

    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)
