# pylint: disable-all
import collections
from flask import g
from dataclasses import dataclass

class TheSpecies:
    def __init__(self, dataset=None, species_name=None):
        if species_name is not None:
            self.name = species_name

            self.chromosomes = Chromosomes(species=self.name)

        else:
            self.dataset = dataset
            self.chromosomes = Chromosomes(dataset=self.dataset)


class Chromosomes:
    def __init__(self, dataset=None, species=None):
        self.chromosomes = collections.OrderedDict()

        if species is not None:
            query = """
                Select
                        Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, Species
                where
                        Chr_Length.SpeciesId = Species.SpeciesId AND
                        Species.Name = '%s'
                Order by OrderId
                """ % species.capitalize()

        else:
            self.dataset = dataset

            query = """
                Select
                        Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet
                where
                        Chr_Length.SpeciesId = InbredSet.SpeciesId AND
                        InbredSet.Name = '%s'
                Order by OrderId
                """ % self.dataset.group.name

            # logger.sql(query)

            results = g.db.execute(query).fetchall()

            for item in results:
                self.chromosomes[item.OrderId] = IndChromosome(
                    item.Name, item.Length)


# @dataclass
class IndChromosome:
    def __init__(self,name,length):
        self.name= name
        self.length = length

    @property
    def mb_length(self):
        """Chromosome length in megabases"""
        return self.length/ 1000000