import sys

from anvio.argparse import ArgumentParser

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, DictIOError

__copyright__ = "Copyleft 2015-2024, The Anvi'o Project (http://anvio.org/)"

__credits__ = []

__license__ = "GPL 3.0"

__version__ = anvio.__version__

__authors__ = ['ivagljiva']

__requires__ = ['contigs-db', "kegg-data", "kegg-functions", "profile-db", "collection", "bin"]

__provides__ = ['interactive']

__description__ = "Start the anvi'o interactive interactive for viewing KEGG metabolism data"

run = terminal.Run()

progress = terminal.Progress()

if __name__ == '__main__':

parser = ArgumentParser(description=__description__)

groupI = parser.add_argument_group('INPUT', "The minimum you must provide this program is a contigs database. In which case "

"anvi'o will attempt to estimate and display metabolism for all contigs in it, assuming that "

"the contigs database represents a single genome. If the contigs database is actually "

"a metagenome, you should use the `--metagenome` flag to explicitly declare that.")

groupI.add_argument(*anvio.A('contigs-db'), **anvio.K('contigs-db', {'required': True}))

groupI.add_argument(*anvio.A('metagenome-mode'), **anvio.K('metagenome-mode'))

groupI.add_argument(*anvio.A('kegg-data-dir'), **anvio.K('kegg-data-dir'))

groupP = parser.add_argument_group('ADDITIONAL INPUT', "If you also provide a profile database AND a collection name, anvi'o will "

"estimate metabolism separately for each bin in your collection. You can also limit "

"those estimates to a specific bin or set of bins in the collection using the parameters "

"`--bin-id` or `--bin-ids-file`, respectively.")

groupP.add_argument(*anvio.A('profile-db'), **anvio.K('profile-db', {'required': False}))

groupP.add_argument(*anvio.A('collection-name'), **anvio.K('collection-name'))

groupP.add_argument(*anvio.A('bin-id'), **anvio.K('bin-id'))

groupP.add_argument(*anvio.A('bin-ids-file'), **anvio.K('bin-ids-file'))

groupC = parser.add_argument_group('OUTPUT', "Parameters for controlling estimation output. The output will be TAB-delimited files which by "

"default are prefixed with 'kegg-metabolism', but you can of course change that name here.")

groupC.add_argument(*anvio.A('module-completion-threshold'), **anvio.K('module-completion-threshold'))

groupB = parser.add_argument_group('SERVER CONFIGURATION', "For power users.")

groupB.add_argument(*anvio.A('ip-address'), **anvio.K('ip-address'))

groupB.add_argument(*anvio.A('port-number'), **anvio.K('port-number'))

groupB.add_argument(*anvio.A('browser-path'), **anvio.K('browser-path'))

groupB.add_argument(*anvio.A('server-only'), **anvio.K('server-only'))

groupB.add_argument(*anvio.A('password-protected'), **anvio.K('password-protected'))

args = parser.get_args(parser)

A = lambda x: args.__dict__[x] if x in args.__dict__ else None

try:

utils.is_all_npm_packages_installed()

args.mode = 'metabolism'

d = interactive.MetabolismInteractive(args)

args.port_number = utils.get_port_num(args.port_number, args.ip_address, run=run)

app = BottleApplication(d)

app.run_application(args.ip_address, args.port_number)

except ConfigError as e:

print(e)

sys.exit(-1)

except FilesNPathsError as e:

print(e)

sys.exit(-2)

except DictIOError as e:

print(e)

sys.exit(-3)