#!/opt/anaconda1anaconda2anaconda3/bin/python
# -*- coding: utf-8
"""Entry point to the interactive interface.

The massage of the data is being taken care of in the interactive module,
and this file implements the bottle callbacks."""

import sys
import argparse

import anvio
import anvio.utils as utils
import anvio.terminal as terminal
import anvio.interactive as interactive
from anvio.bottleroutes import BottleApplication

from anvio.errors import ConfigError, FilesNPathsError, GenesDBError 

__author__ = "Developers of anvi'o (see AUTHORS.txt)"
__copyright__ = "Copyleft 2015-2018, the Meren Lab (http://merenlab.org/)"
__credits__ = ["Doğan Can Kilment", "Gökmen Göksel", "Gökmen Görgen"]
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "A. Murat Eren"
__email__ = "a.murat.eren@gmail.com"
__requires__ = ['profile-db', 'single-profile-db', 'contigs-db', 'genes-db', 'bin', 'view-data', 'dendrogram', 'phylogeny']
__provides__ = ['collection', 'bin', 'interactive', 'svg']


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

if __name__ == '__main__':
    # setup the command line user interface
    parser = argparse.ArgumentParser(description="Start an anvi'o server for the interactive interface")

    groupA = parser.add_argument_group('DEFAULT INPUTS', "The interavtive interface can be started with and without\
                                                          anvi'o databases. The default use assumes you have your\
                                                          profile and contigs database, however, it is also possible\
                                                          to start the interface using ad hoc input files. See 'MANUAL\
                                                          INPUT' section for required parameters.")
    groupB = parser.add_argument_group('MANUAL INPUTS', "Mandatory input parameters to start the interactive interface\
                                                         without anvi'o databases.")
    groupC = parser.add_argument_group('ADDITIONAL STUFF', "Parameters to provide additional layers, views, or layer data.")
    groupD = parser.add_argument_group('GENE MODE', "Gene mode related parameters.")
    groupE = parser.add_argument_group('VISUALS RELATED', "Parameters that give access to various adjustements regarding\
                                                           the interface.")
    groupF = parser.add_argument_group('SWEET PARAMS OF CONVENIENCE', "Parameters and flags that are not quite essential (but\
                                                                       nice to have).")
    groupG = parser.add_argument_group('SERVER CONFIGURATION', "For power users.")

    groupA.add_argument(*anvio.A('profile-db'), **anvio.K('profile-db', {'required': False}))
    groupA.add_argument(*anvio.A('contigs-db'), **anvio.K('contigs-db', {'required': False}))
    groupA.add_argument(*anvio.A('collection-name'), **anvio.K('collection-name', {'help':
                                    "If you have a collection in your profile database, you can use this flag to start the\
                                    interactive interface with a tree showing your bins in your collection, instead of each\
                                    split. This is very useful when you have imported your external binning results into\
                                    anvi'o, and want to see the distribution of your bins across samples. In these cases\
                                    anvi'o will cluster your bins and based on multiple metrics. Because this particular\
                                    clustering will be done on the fly within anvi'o interactive class, you get to define\
                                    a disntance metric and a linkage method using --linkage and --distance parameters if\
                                    you want!"}))
    groupB.add_argument(*anvio.A('manual-mode'), **anvio.K('manual-mode'))
    groupB.add_argument(*anvio.A('fasta-file'), **anvio.K('fasta-file'))
    groupB.add_argument(*anvio.A('view-data'), **anvio.K('view-data'))
    groupB.add_argument(*anvio.A('tree'), **anvio.K('tree'))
    groupB.add_argument(*anvio.A('items-order'), **anvio.K('items-order'))
    groupC.add_argument(*anvio.A('additional-view'), **anvio.K('additional-view'))
    groupC.add_argument(*anvio.A('additional-layers'), **anvio.K('additional-layers'))
    groupE.add_argument(*anvio.A('view'), **anvio.K('view'))
    groupE.add_argument(*anvio.A('title'), **anvio.K('title'))
    groupE.add_argument(*anvio.A('taxonomic-level'), **anvio.K('taxonomic-level'))
    groupE.add_argument(*anvio.A('split-hmm-layers'), **anvio.K('split-hmm-layers'))
    groupE.add_argument(*anvio.A('hide-outlier-SNVs'), **anvio.K('hide-outlier-SNVs'))
    groupE.add_argument(*anvio.A('state-autoload'), **anvio.K('state-autoload'))
    groupE.add_argument(*anvio.A('collection-autoload'), **anvio.K('collection-autoload'))
    groupE.add_argument(*anvio.A('export-svg'), **anvio.K('export-svg'))
    groupD.add_argument(*anvio.A('gene-mode'), **anvio.K('gene-mode'))
    groupD.add_argument(*anvio.A('bin-id'), **anvio.K('bin-id'))
    groupF.add_argument(*anvio.A('show-views'), **anvio.K('show-views'))
    groupF.add_argument(*anvio.A('skip-check-names'), **anvio.K('skip-check-names'))
    groupF.add_argument(*anvio.A('output-dir'), **anvio.K('output-dir'))
    groupF.add_argument(*anvio.A('dry-run'), **anvio.K('dry-run'))
    groupF.add_argument(*anvio.A('show-states'), **anvio.K('show-states'))
    groupF.add_argument(*anvio.A('list-collections'), **anvio.K('list-collections'))
    groupF.add_argument(*anvio.A('skip-init-functions'), **anvio.K('skip-init-functions'))
    groupF.add_argument(*anvio.A('skip-auto-ordering'), **anvio.K('skip-auto-ordering'))
    groupF.add_argument(*anvio.A('distance'), **anvio.K('distance', {'help':
                                    'The distance metric for the hierarchical clustering. Only relevant if you are running\
                                     the interactive interface in "collection" mode. The default is "%(default)s".'}))
    groupF.add_argument(*anvio.A('linkage'), **anvio.K('linkage', {'help':
                                    'The linkage method for the hierarchical clustering. Only relevant if you are running\
                                     the interactive interface in "collection" mode. The default is "%(default)s".'}))
    groupG.add_argument(*anvio.A('ip-address'), **anvio.K('ip-address'))
    groupG.add_argument(*anvio.A('port-number'), **anvio.K('port-number'))
    groupG.add_argument(*anvio.A('browser-path'), **anvio.K('browser-path'))
    groupG.add_argument(*anvio.A('read-only'), **anvio.K('read-only'))
    groupG.add_argument(*anvio.A('server-only'), **anvio.K('server-only'))
    groupG.add_argument(*anvio.A('password-protected'), **anvio.K('password-protected'))
    groupG.add_argument(*anvio.A('user-server-shutdown'), **anvio.K('user-server-shutdown'))

    args = anvio.get_args(parser)

    try:
        d = interactive.Interactive(args)
        args.port_number = utils.get_port_num(args.port_number, args.ip_address, run=run)
    except ConfigError as e:
        print(e)
        sys.exit(-1)
    except FilesNPathsError as e:
        print(e)
        sys.exit(-2)
    except GenesDBError as e:
        print(e)
        sys.exit(-3)

    if args.dry_run:
        run.info_single('Dry run, eh? Fine. Bai!', nl_after=1)
        sys.exit()

    app = BottleApplication(d)
    app.run_application(args.ip_address, args.port_number)

