from collections import OrderedDict from dataclasses import dataclass from dataclasses import InitVar from typing import Optional, Dict from flask import g @dataclass class TheSpecies: """Data related to species.""" dataset: Optional[Dict] = None species_name: Optional[str] = None def __post_init__(self): if self.species_name is not None: self.name = self.species_name self.chromosomes = Chromosomes(species=self.name) else: self.dataset = self.dataset self.chromosomes = Chromosomes(dataset=self.dataset) @dataclass class IndChromosome: """Data related to IndChromosome""" name: str length: int @property def mb_length(self): """Chromosome length in mega-bases""" return self.length / 1000000 @dataclass class Chromosomes: """Data related to a chromosome""" dataset: InitVar[Dict] = None species: Optional[str] = None def __post_init__(self, dataset): if self.species is None: self.dataset = dataset @property def chromosomes(self): """Lazily fetch the chromosomes""" chromosomes = OrderedDict() if self.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" % self.species.capitalize()) else: 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) results = g.db.execute(query).fetchall() for item in results: chromosomes[item.OrderId] = IndChromosome( item.Name, item.Length) return chromosomes