import collections from dataclasses import dataclass from typing import Optional, Dict from flask import g from utility.logger import getLogger logger = getLogger(__name__) @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) 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 class Chromosomes: def __init__(self, dataset=None, species=None): self.chromosomes = collections.OrderedDict() if species != 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)