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"""Tests wqflask/base/species.py"""
import pytest
from gn2.base.species import TheSpecies
from gn2.base.species import IndChromosome
from gn2.base.species import Chromosomes
from collections import OrderedDict
from dataclasses import dataclass
@dataclass
class MockChromosome:
OrderId: int
Name: str
Length: int
@dataclass
class MockGroup:
name: str
@dataclass
class MockDataset:
group: MockGroup
@pytest.mark.parametrize(
("species_name", "dataset", "expected_name", "chromosome_param"),
(("BXD", None, "BXD", 1),
(None, "Random Dataset", None, 1)))
def test_species(mocker, species_name, dataset,
expected_name, chromosome_param):
_c = mocker.patch("gn2.base.species.Chromosomes",
return_value=chromosome_param)
test_species = TheSpecies(dataset=dataset,
species_name=species_name)
_c.assert_called_with(species=species_name,
dataset=dataset)
assert test_species.name == expected_name
assert test_species.chromosomes == chromosome_param
@pytest.mark.parametrize(
("name", "length", "mb_length"),
(("Test A", 10000000, 10),
("Test B", 100, 0.0001)))
def test_create_ind_chromosome(name, length, mb_length):
_ind = IndChromosome(name=name, length=length)
assert _ind.name == name
assert _ind.length == length
assert _ind.mb_length == mb_length
@pytest.mark.parametrize(
("species", "dataset", "expected_call"),
(("bxd", MockDataset(MockGroup("Random")),
("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", ("Bxd",))),
(None, MockDataset(MockGroup("Random")),
("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", ("Random",)))))
def test_create_chromosomes(mocker, species, dataset, expected_call):
mock_conn = mocker.MagicMock()
with mock_conn.cursor() as cursor:
cursor.fetchall.return_value = (("1", 2, 10,),
("2", 3, 11,),
("4", 5, 15,),)
_c = Chromosomes(dataset=dataset, species=species)
assert _c.chromosomes(cursor) == OrderedDict([
("1", IndChromosome("1", 10)),
("2", IndChromosome("2", 11)),
("4", IndChromosome("4", 15)),
])
cursor.execute.assert_called_with(*expected_call)
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