#(c) 2013-2014 by Authors
#This file is a part of Ragout program.
#Released under the BSD license (see LICENSE file)

"""
The main Ragout module. It defines top-level logic of the program
"""

import os
import sys
import shutil
import logging
import argparse
from collections import namedtuple
from copy import deepcopy

import ragout.assembly_graph.assembly_refine as asref
import ragout.scaffolder.scaffolder as scfldr
import ragout.scaffolder.merge_iters as merge
import ragout.scaffolder.output_generator as out_gen
import ragout.maf2synteny.maf2synteny as m2s
import ragout.overlap.overlap as overlap
import ragout.shared.config as config
from ragout.overlap.overlap import OverlapException
from ragout.phylogeny.phylogeny import Phylogeny, PhyloException
from ragout.breakpoint_graph.permutation import (PermutationContainer,
                                                 PermException)
from ragout.synteny_backend.synteny_backend import (SyntenyBackend,
                                                    BackendException)
from ragout.parsers.recipe_parser import parse_ragout_recipe, RecipeException
from ragout.parsers.fasta_parser import read_fasta_dict, FastaError
from ragout.shared.debug import DebugConfig
from ragout.breakpoint_graph.breakpoint_graph import BreakpointGraph
from ragout.breakpoint_graph.inferer import AdjacencyInferer
from ragout.breakpoint_graph.chimera_detector import ChimeraDetector
from ragout.__version__ import __version__

#register backends
import synteny_backend.sibelia
import synteny_backend.cactus
import synteny_backend.maf
import synteny_backend.hal

logger = logging.getLogger()
debugger = DebugConfig.get_instance()


RunStage = namedtuple("RunStage", ["name", "block_size", "ref_indels",
                                   "repeats", "rearrange"])


def enable_logging(log_file, debug):
    """
    Turns on logging, sets debug levels and assigns a log file
    """
    log_formatter = logging.Formatter("[%(asctime)s] %(name)s: %(levelname)s: "
                                      "%(message)s", "%H:%M:%S")
    console_formatter = logging.Formatter("[%(asctime)s] %(levelname)s: "
                                          "%(message)s", "%H:%M:%S")
    console_log = logging.StreamHandler()
    console_log.setFormatter(console_formatter)
    if not debug:
        console_log.setLevel(logging.INFO)

    file_handler = logging.FileHandler(log_file, mode="w")
    file_handler.setFormatter(log_formatter)

    logger.setLevel(logging.DEBUG)
    logger.addHandler(console_log)
    logger.addHandler(file_handler)


def check_extern_modules(backend):
    """
    Checks if all necessary native modules are available
    """
    backends = SyntenyBackend.get_available_backends()
    if backend not in backends:
        raise BackendException("\"{0}\" is not installed.".format(backend))

    if not m2s.check_binary():
        raise BackendException("maf2synteny binary is missing, "
                               "did you run 'make'?")

    if not overlap.check_binary():
        raise BackendException("overlap binary is missing, "
                               "did you run 'make'?")


def run_ragout(args):
    """
    A wrapper to catch possible exceptions
    """
    try:
        run_unsafe(args)
    except (RecipeException, PhyloException, PermException,
            BackendException, OverlapException, FastaError) as e:
        logger.error("An error occured while running Ragout:")
        logger.error(e)
        return 1

    return 0


def make_run_stages(block_sizes, resolve_repeats):
    """
    Setting parameters of run stages
    """
    stages = []
    for block in block_sizes:
        stages.append(RunStage(name=str(block), block_size=block,
                               ref_indels=False, repeats=False,
                               rearrange=True))
    stages.append(RunStage(name="refine", block_size=block_sizes[-1],
                           ref_indels=True, repeats=resolve_repeats,
                           rearrange=False))
    return stages


def get_phylogeny_and_name_ref(recipe, permutation_file):
    """
    Retrieves phylogeny (infers if necessary) as well as
    naming reference genome
    """
    if "tree" in recipe:
        logger.info("Phylogeny is taken from the recipe")
        phylogeny = Phylogeny.from_newick(recipe["tree"])
    else:
        logger.info("Inferring phylogeny from synteny blocks data")
        perm_cont = PermutationContainer(permutation_file,
                                           recipe, False, True, None)
        phylogeny = Phylogeny.from_permutations(perm_cont)
        logger.info(phylogeny.tree_string)

    leaves_sorted = phylogeny.leaves_by_distance(recipe["target"])
    if "naming_ref" in recipe:
        naming_ref = recipe["naming_ref"]
    else:
        naming_ref = leaves_sorted[0]
        logger.info("'{0}' is chosen as a naming reference".format(naming_ref))

    return phylogeny, naming_ref


def run_unsafe(args):
    """
    Top-level logic of the program
    """
    if not os.path.isdir(args.out_dir):
        os.mkdir(args.out_dir)

    debug_root = os.path.join(args.out_dir, "debug")
    debugger.set_debugging(args.debug)
    debugger.set_debug_dir(debug_root)
    debugger.clear_debug_dir()

    out_log = os.path.join(args.out_dir, "ragout.log")
    enable_logging(out_log, args.debug)
    logger.info("Cooking Ragout...")

    check_extern_modules(args.synteny_backend)
    all_backends = SyntenyBackend.get_available_backends()
    backend = all_backends[args.synteny_backend]
    recipe = parse_ragout_recipe(args.recipe)

    #Setting synteny block sizes
    if "blocks" in recipe:
        scale = recipe["blocks"]
    else:
        scale = backend.infer_block_scale(recipe)
        logger.info("Synteny block scale set to '{0}'".format(scale))
    synteny_blocks = config.vals["blocks"][scale]

    #Running backend to get synteny blocks
    perm_files = backend.make_permutations(recipe, synteny_blocks, args.out_dir,
                                           args.overwrite, args.threads)
    run_stages = make_run_stages(synteny_blocks, args.resolve_repeats)
    phylo_perm_file = perm_files[synteny_blocks[-1]]
    phylogeny, naming_ref = get_phylogeny_and_name_ref(recipe, phylo_perm_file)

    logger.info("Processing permutation files")
    raw_bp_graphs = {}
    stage_perms = {}
    for stage in run_stages:
        debugger.set_debug_dir(os.path.join(debug_root, stage.name))
        stage_perms[stage] = PermutationContainer(perm_files[stage.block_size],
                                                  recipe, stage.repeats,
                                                  stage.ref_indels, phylogeny)
        raw_bp_graphs[stage] = BreakpointGraph(stage_perms[stage])
    chim_detect = ChimeraDetector(raw_bp_graphs, run_stages)

    #####
    scaffolds = None
    prev_stages = []
    last_stage = run_stages[-1]
    for stage in run_stages:
        logger.info("Stage \"{0}\"".format(stage.name))
        debugger.set_debug_dir(os.path.join(debug_root, stage.name))
        prev_stages.append(stage)

        fixed_container = chim_detect.break_contigs(stage_perms[stage], [stage])
        breakpoint_graph = BreakpointGraph(fixed_container)

        adj_inferer = AdjacencyInferer(breakpoint_graph, phylogeny)
        adjacencies = adj_inferer.infer_adjacencies()
        cur_scaffolds = scfldr.build_scaffolds(adjacencies, fixed_container)

        if scaffolds is not None:
            all_breaks = chim_detect.break_contigs(stage_perms[stage],
                                                   prev_stages)
            scaffolds = merge.merge_scaffolds(scaffolds, cur_scaffolds,
                                              all_breaks, stage.rearrange)
        else:
            scaffolds = cur_scaffolds
    debugger.set_debug_dir(debug_root)
    ####

    scfldr.assign_scaffold_names(scaffolds, stage_perms[last_stage], naming_ref)
    target_sequences = read_fasta_dict(backend.get_target_fasta())

    if not args.no_refine:
        out_overlap = os.path.join(args.out_dir, "contigs_overlap.dot")
        overlap.make_overlap_graph(backend.get_target_fasta(), out_overlap)
        scaffolds = asref.refine_scaffolds(out_overlap, scaffolds,
                                           target_sequences)
        if args.debug:
            shutil.copy(out_overlap, debugger.debug_dir)
        os.remove(out_overlap)

    out_gen.make_output(target_sequences, scaffolds,
                        args.out_dir, recipe["target"])
    logger.info("Done!")


def main():
    parser = argparse.ArgumentParser(description="A tool for reference-assisted"
                                                 " assembly", formatter_class= \
                                        argparse.ArgumentDefaultsHelpFormatter)

    parser.add_argument("recipe", metavar="recipe_file",
                        help="path to recipe file")
    parser.add_argument("-o", "--outdir", dest="out_dir",
                        metavar="output_dir",
                        help="output directory",
                        default="ragout-out")
    parser.add_argument("-s", "--synteny", dest="synteny_backend",
                        default="sibelia",
                        choices=["sibelia", "cactus", "maf", "hal"],
                        help="backend for synteny block decomposition")
    parser.add_argument("--no-refine", action="store_true",
                        dest="no_refine", default=False,
                        help="disable refinement with assembly graph")
    parser.add_argument("--overwrite", action="store_true", default=False,
                        dest="overwrite",
                        help="overwrite results from the previous run")
    parser.add_argument("--repeats", action="store_true", default=False,
                        dest="resolve_repeats",
                        help="resolve repetitive input sequences")
    parser.add_argument("--debug", action="store_true",
                        dest="debug", default=False,
                        help="enable debug output")
    parser.add_argument("-t", "--threads", dest="threads", type=int,
                        default=1, help="number of threads for synteny backend")
    parser.add_argument("--version", action="version", version=__version__)
    args = parser.parse_args()

    return run_ragout(args)