#!/opt/anaconda1anaconda2anaconda3/bin/python
# -*- coding: utf-8

import sys
import argparse

import anvio
import anvio.utils as utils
import anvio.dbops as dbops
import anvio.terminal as terminal
import anvio.constants as constants
import anvio.clustering as clustering

from anvio.errors import ConfigError, FilesNPathsError
from anvio.clusteringconfuguration import ClusteringConfiguration


__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"


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

def experimental_organization(args):
    split_names = []

    if not args.skip_store_in_db and not args.profile_db:
        raise ConfigError("OK. When you don't use the --skip-store-in-db flag, you need to define a\
                            profile database to be explicit about where to store the resulting tree.")

    if args.profile_db:
        utils.is_profile_db(args.profile_db)
    utils.is_contigs_db(args.contigs_db)

    if not args.skip_store_in_db and not args.name:
        raise ConfigError("Since you have not used the --skip-store-in-db flag, this program will attempt\
                            store resulting clustering into the profile database, and it needs a name for\
                            this tree. Please use the --name flag to provide one.")

    if args.name:
        utils.is_this_name_OK_for_database('--name parameter', args.name)

    if args.profile_db:
        profile_db = dbops.ProfileDatabase(args.profile_db)
        if int(profile_db.meta['merged']):
            split_names = profile_db.db.get_single_column_from_table('mean_coverage_splits', 'contig')
        else:
            split_names = profile_db.db.get_single_column_from_table('atomic_data_splits', 'contig')
        profile_db.disconnect()

    db_paths = {'CONTIGS.db': args.contigs_db}
    config = ClusteringConfiguration(args.config_file, args.input_directory, db_paths = db_paths, row_ids_of_interest = split_names)

    config.print_summary(run)

    if args.dry_run:
        sys.exit()

    clustering_id, newick = clustering.order_contigs_simple(config, distance=args.distance, linkage=args.linkage, progress=terminal.Progress(), debug=True)

    _, distance, linkage = clustering_id.split(':')

    run.info('Distance metric used', distance, mc='green')
    run.info('Linkage method used', linkage, mc='green')

    if args.output_file:
        open(args.output_file, 'w').write(newick + '\n')
        run.info('Output', args.output_file, mc='green')

    if args.profile_db and not args.skip_store_in_db:
        dbops.add_items_order_to_db(anvio_db_path=args.profile_db,
                                    order_name=args.name,
                                    order_data=newick,
                                    distance=distance,
                                    linkage=linkage,
                                    make_default=False,
                                    run=run)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='why yes we do stuff here.')
    parser.add_argument('config_file', metavar = 'PATH', default = None, type=str,
                        help = 'Config file for clustering of contigs. See documentation for help.')

    parser.add_argument(*anvio.A('profile-db'), **anvio.K('profile-db', {'required': False}))
    parser.add_argument(*anvio.A('contigs-db'), **anvio.K('contigs-db'))
    parser.add_argument(*anvio.A('experimental-org-input-dir'), **anvio.K('experimental-org-input-dir'))
    parser.add_argument(*anvio.A('clustering-name'), **anvio.K('clustering-name'))
    parser.add_argument(*anvio.A('distance'), **anvio.K('distance', {'default': None, 'help':
                      'The distance metric for the hierarchical clustering. If you do not use this flag,\
                       the distance metric you defined in your clustering config file will be used. If you\
                       have not defined one in your config file, then the system default will be used,\
                       which is "%s".' % constants.distance_metric_default}))
    parser.add_argument(*anvio.A('linkage'), **anvio.K('linkage', {'default': None, 'help':
                      'Same story with the `--distance`, except, the system default for this one\
                       is %s.' % constants.linkage_method_default}))
    parser.add_argument(*anvio.A('skip-store-in-db'), **anvio.K('skip-store-in-db'))
    parser.add_argument(*anvio.A('output-file'), **anvio.K('output-file'))
    parser.add_argument(*anvio.A('dry-run'), **anvio.K('dry-run'))

    args = anvio.get_args(parser)

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