__init__.py

"""Define the top-level command line interface for sourmash

This module handles user input when sourmash is invoked from the command line.
A top-level parser is defined for the `sourmash` command, and subparsers are
defined for each subcommand. Some sourmash operations are grouped together
using the `sourmash <subcmd> <subsubcmd>` pattern, and these are organized in
their own CLI submodules, each with a dedicated directory.
"""

from argparse import ArgumentParser, RawDescriptionHelpFormatter, SUPPRESS
import os
import sys

import sourmash

from . import utils

# Commands
from . import categorize
from . import compare
from . import compute
from . import gather
from . import import_csv
from . import info
from . import index
from . import migrate
from . import multigather
from . import plot
from . import prefetch
from . import sbt_combine
from . import search
from . import watch

# Subcommand groups
from . import lca
from . import sig
from . import sig as signature
from . import sketch
from . import storage
from . import tax


class SourmashParser(ArgumentParser):
    _citation_printed = False

    def __init__(self, citation=True, **kwargs):
        super(SourmashParser, self).__init__(**kwargs)
        self.citation = citation

    @classmethod
    def print_citation(cls):
        if cls._citation_printed:
            return
        from sourmash.logging import notify
        notify(f"\n== This is sourmash version {sourmash.VERSION}. ==")
        notify("== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==\n")
        cls._citation_printed = True

    def _subparser_from_name(self, name):
        """Given a name, get the subparser instance registered with this parser."""
        container = self._actions
        if name is None:
            return None
        for action in container:
            if action.choices is None:
                continue
            elif name in action.choices:
                return action.choices[name]

    def print_help(self):
        self.print_citation()
        super(SourmashParser, self).print_help()


    def parse_args(self, args=None, namespace=None):
        if (args is None and len(sys.argv) == 1) or (args is not None and len(args) == 0):
            self.print_help()
            raise SystemExit(1)
        args = super(SourmashParser, self).parse_args(args=args, namespace=namespace)
        if ('quiet' not in args or not args.quiet) and self.citation:
            self.print_citation()

        if 'subcmd' in args and args.subcmd is None:
            self._subparser_from_name(args.cmd).print_help()
            raise SystemExit(1)

        # BEGIN: dirty hacks to simultaneously support new and previous interface
        if hasattr(args, 'subcmd') and args.subcmd == 'import':
            args.subcmd = 'ingest'
        # END: dirty hacks to simultaneously support new and previous interface
        return args


def get_parser():
    module_descs = {
        'tax': 'Integrate taxonomy information based on "gather" results',
        'lca': 'Taxonomic operations',
        'sketch': 'Create signatures',
        'sig': 'Manipulate signature files',
        'storage': 'Operations on storage',
    }
    alias = {
        "sig": "signature"
    }
    expert = set(['categorize', 'import_csv', 'migrate', 'multigather', 'sbt_combine', 'watch'])

    clidir = os.path.dirname(__file__)
    basic_ops = utils.command_list(clidir)
    user_ops = [op for op in basic_ops if op not in expert]
    usage = '    Basic operations\n'
    for op in user_ops:
        docstring = getattr(sys.modules[__name__], op).__doc__
        helpstring = 'sourmash {op:s} --help'.format(op=op)
        usage += '        {hs:25s} {ds:s}\n'.format(hs=helpstring, ds=docstring)
    cmd_group_dirs = next(os.walk(clidir))[1]
    cmd_group_dirs = filter(utils.opfilter, cmd_group_dirs)
    cmd_group_dirs = sorted(cmd_group_dirs)

    cmd_group_usage = [cmd for cmd in cmd_group_dirs if cmd not in alias.values()]
    for dirpath in cmd_group_usage:
        usage += '\n    ' + module_descs[dirpath] + '\n'
        usage += '        sourmash {gd:s} --help\n'.format(gd=dirpath)
        if dirpath in alias:
            usage += '        sourmash {gd:s} --help\n'.format(gd=alias[dirpath])

    desc = 'Create, compare, and manipulate k-mer sketches of biological sequences.\n\nUsage instructions:\n' + usage
    parser = SourmashParser(prog='sourmash', description=desc, formatter_class=RawDescriptionHelpFormatter, usage=SUPPRESS)
    parser._optionals.title = 'Options'
    parser.add_argument('-v', '--version', action='version', version='sourmash '+ sourmash.VERSION)
    parser.add_argument('-q', '--quiet', action='store_true', help='don\'t print citation information')
    sub = parser.add_subparsers(
        title='Instructions', dest='cmd', metavar='cmd', help=SUPPRESS,
    )
    for op in basic_ops + cmd_group_dirs:
        getattr(sys.modules[__name__], op).subparser(sub)
    parser._action_groups.reverse()
    return parser