import os
from busco.BuscoLogger import BuscoLogger
from busco.busco_tools.Toolset import Tool
from shutil import which
from abc import ABCMeta, abstractmethod
from busco.BuscoConfig import BuscoConfigAuto
from busco.Exceptions import BuscoError
import time
import gzip

logger = BuscoLogger.get_logger(__name__)


class ToolException(Exception):
    """
    Module-specific exception
    """

    def __init__(self, value=""):
        self.value = value

    def __str__(self):
        return self.value


class BaseRunner(Tool, metaclass=ABCMeta):

    config = None
    tool_versions = {}

    def __init__(self):
        super().__init__()
        self.run_number = 0
        self.input_file = self.config.get("busco_run", "in")
        # type(self).summary["versions"]["busco"] = busco.__version__
        self.main_out = self.config.get("busco_run", "main_out")
        self.working_dir = (
            os.path.join(self.main_out, "auto_lineage")
            if isinstance(self.config, BuscoConfigAuto)
            else self.main_out
        )
        self.lineage_results_dir = self.config.get("busco_run", "lineage_results_dir")
        self.run_folder = os.path.join(self.working_dir, self.lineage_results_dir)
        self.log_folder = os.path.join(self.main_out, "logs")
        self.cpus = self.config.getint("busco_run", "cpu")
        self.lineage_dataset = self.config.get("busco_run", "lineage_dataset")
        self.domain = self.config.get("busco_run", "domain")

        try:
            self.check_tool_available()
        except ToolException:
            raise ToolException(
                "{} tool cannot be found. Please check the 'path' and 'command' parameters "
                "provided in the config file or make sure the tool is available in your working environment.".format(
                    self.name
                )
            )
        self.version = self.get_version()
        type(self).tool_versions[self.name] = self.version
        self.check_tool_dependencies()

        self.checkpoint_file = None

        self.logfile_path_out = os.path.join(
            self.config.get("busco_run", "main_out"),
            "logs",
            "{}_out.log".format(self.name),
        )
        self.logfile_path_err = (
            self.logfile_path_out.rpartition("_out.log")[0] + "_err.log"
        )
        self.add_args = {}

    def init_checkpoint_file(self):
        self.checkpoint_file = os.path.join(self.output_folder, ".checkpoint")

    def write_checkpoint_file(self, additional_args=[]):
        with open(self.checkpoint_file, "a") as cpt_file:
            cpt_file.write("Tool: {}\n".format(self.name))
            cpt_file.write("Version: {}\n".format(self.version))
            cpt_file.write("Run: {}\n".format(self.run_number))
            for args in additional_args:
                cpt_file.write("{}: {}\n".format(args[0], args[1]))
            cpt_file.write("Time: {}\n".format(time.strftime("%d/%m/%Y %H:%M:%S")))
            cpt_file.write("Completed {} jobs\n\n".format(self.total))

    def check_previous_completed_run(self, additional_args=[]):
        if not os.path.exists(self.checkpoint_file):
            return False
        else:
            with open(self.checkpoint_file, "r") as cpt_file:
                block_size = 6 + len(additional_args)
                lines = cpt_file.readlines()
                tool_names = [s.strip().split(": ")[1] for s in lines[0::block_size]]
                tool_versions = [s.strip().split(": ")[1] for s in lines[1::block_size]]
                tool_run_numbers = [
                    s.strip().split(": ")[1] for s in lines[2::block_size]
                ]
                self.add_args = {}
                for a, arg in enumerate(additional_args):
                    self.add_args[arg] = [
                        s.strip().split(": ")[1]
                        for s in lines[a + 3 :: block_size]
                        if s.strip().split(": ")[0] == arg
                    ]
                try:
                    start_search = 0
                    while True:
                        tool_ind = tool_names.index(self.name, start_search)
                        if int(tool_run_numbers[tool_ind]) == int(self.run_number):
                            if str(self.version) != str(tool_versions[tool_ind]):
                                logger.warning(
                                    "A previous run used {} version {}. "
                                    "The restarted run is using {} version "
                                    "{}".format(
                                        self.name,
                                        tool_versions[tool_ind],
                                        self.name,
                                        self.version,
                                    )
                                )
                            return True
                        elif int(tool_run_numbers[tool_ind]) < int(self.run_number):
                            start_search = tool_ind + 1
                        else:
                            raise BuscoError(
                                "Something went wrong. Information for {} run {} missing but "
                                "information for run {} found.".format(
                                    self.name,
                                    self.run_number,
                                    tool_run_numbers[tool_ind],
                                )
                            )

                except ValueError:
                    return False

                except TypeError:
                    logger.warning(
                        "Unable to parse {} file. Restart mode not available.".format(
                            self.checkpoint_file
                        )
                    )

    @abstractmethod
    def check_tool_dependencies(self):
        pass

    @abstractmethod
    def configure_job(self, *args):
        pass

    @abstractmethod
    def configure_runner(self, *args):
        self.init_checkpoint_file()

    @abstractmethod
    def generate_job_args(self):
        pass

    @staticmethod
    def decompress_refseq_file(gzip_file):  # todo: probably doesn't belong in this class as it is only applicable to metaeuk and miniprot
        unzipped_filename = gzip_file.split(".gz")[0]
        if not os.path.exists(unzipped_filename):
            with gzip.open(gzip_file, "rb") as compressed_file:
                with open(unzipped_filename, "wb") as decompressed_file:
                    for line in compressed_file:
                        decompressed_file.write(line)
        if os.path.exists(gzip_file):
            try:
                os.remove(gzip_file)
            except OSError:
                logger.warning(
                    "Unable to remove compressed refseq file in dataset download"
                )
                pass
        return unzipped_filename

    @property
    @abstractmethod
    def output_folder(self):
        raise NotImplementedError

    @property
    @abstractmethod
    def name(self):
        raise NotImplementedError

    @abstractmethod
    def run(self):
        if self.version is not None:
            logger.debug("Tool: {}".format(self.name))
            logger.debug("Version: {}".format(self.version))

    @staticmethod
    def create_dirs(dirnames):
        """
        Create all required directories

        :param dirnames: list of paths already constructed
        :return:
        """
        if isinstance(dirnames, str):
            os.makedirs(dirnames, exist_ok=True)
        elif isinstance(dirnames, list):
            for d in dirnames:
                os.makedirs(d, exist_ok=True)
        else:
            raise TypeError("'dirnames' should be either a str or a list")

    def check_tool_available(self):
        """
        Check tool's availability.


        :return: True if the tool can be run, False if it is not the case
        :rtype: bool
        """
        try:
            self.get_tool_from_config()
        except ToolException:
            try:
                self.get_tool_from_environment()
            except ToolException:
                raise

        return which(self.cmd) is not None  # True if tool available

    def get_tool_from_environment(self):
        which_tool = which(self.cmd)
        if not which_tool:
            raise ToolException()

    def get_tool_from_config(self):
        """
        1. The section ['name'] is available in the config
        2. This section contains keys 'path' and 'command'
        3. The string resulted from concatenation of values of these two keys
        represents the full path to the command
        :return:
        """
        if not self.config.has_section(self.name):
            raise ToolException()

        if not self.config.has_option(self.name, "path") or not self.config.get(
            self.name, "path"
        ):
            raise ToolException()

        if self.config.has_option(self.name, "command"):
            executable = self.config.get(self.name, "command")
        else:
            executable = self.name

        self.cmd = os.path.join(self.config.get(self.name, "path"), executable)

        return

    @staticmethod
    def get_matches(results_grouped, seq):
        g1 = results_grouped.get_group(seq)
        g1_sorted = g1.sort_values(
            "Low coord"
        )  # sort to facilitate a single-pass coordinate check
        for idx1, row1 in g1_sorted.iterrows():
            strand = g1_sorted.loc[idx1]["Strand"]
            if strand == "-":
                start_val = high_coord = g1_sorted.loc[idx1]["High coord"]
                stop_val = low_coord = g1_sorted.loc[idx1]["Low coord"]
            else:
                start_val = low_coord = g1_sorted.loc[idx1]["Low coord"]
                stop_val = high_coord = g1_sorted.loc[idx1]["High coord"]
            current_seqid = "{}:{}-{}".format(
                g1_sorted.loc[idx1], start_val, stop_val
            )
            matches = g1_sorted[g1_sorted["Low coord"] >= low_coord].loc[
                g1_sorted["Low coord"] < high_coord
                ]  # find entries with a start coordinate between the current exon start and end
            yield idx1, current_seqid, g1_sorted, matches

    @abstractmethod
    def get_version(self):
        return

    @classmethod
    def reset(cls):
        BaseRunner.config = None
        BaseRunner.tool_versions = {}


class NoGenesError(Exception):
    def __init__(self, gene_predictor):
        self.gene_predictor = gene_predictor


class NoRerunFile(Exception):
    def __init__(self):
        pass