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"""Tests wqflask/base/species.py"""
import unittest
from unittest import mock
from base.species import TheSpecies
from base.species import IndChromosome
from base.species import Chromosomes
from collections import OrderedDict
from wqflask import app
from dataclasses import dataclass
@dataclass
class MockChromosome:
OrderId: int
Name: str
Length: int
@dataclass
class MockGroup:
name: str
@dataclass
class MockDataset:
group: MockGroup
class TestTheSpecies(unittest.TestCase):
"""Tests for TheSpecies class"""
@mock.patch('base.species.Chromosomes')
def test_create_species_with_null_species_name(self, mock_chromosome):
"""Test that TheSpecies is instantiated correctly when the
species_name is provided."""
mock_chromosome.return_value = 1
test_species = TheSpecies(dataset="random_dataset", species_name="a")
self.assertEqual(test_species.name, "a")
self.assertEqual(test_species.chromosomes, 1)
@mock.patch('base.species.Chromosomes')
def test_create_species_with_species_name(self, mock_chromosome):
"""Test that TheSpecies is instantiated correctly when the
species_name is not provided."""
mock_chromosome.return_value = 1
test_species = TheSpecies(dataset="random_dataset")
self.assertEqual(test_species.dataset, "random_dataset")
self.assertEqual(test_species.chromosomes, 1)
mock_chromosome.assert_called_once_with(dataset="random_dataset")
class TestIndChromosome(unittest.TestCase):
"""Tests for IndChromosome class"""
def test_create_ind_chromosome(self):
"""Test that IndChromosome is instantiated correctly"""
test_ind_chromosome = IndChromosome(name="Test", length=10000000)
self.assertEqual(test_ind_chromosome.name, "Test")
self.assertEqual(test_ind_chromosome.length, 10000000)
self.assertEqual(test_ind_chromosome.mb_length, 10)
class TestChromosomes(unittest.TestCase):
"""Tests for Chromosomes class"""
maxDiff = None
def setUp(self):
self.app_context = app.app_context()
self.app_context.push()
def tearDown(self):
self.app_context.pop()
@mock.patch("base.species.g")
def test_create_chromosomes_with_no_species(self, mock_db):
"""Test instantiating a chromosome without a species"""
mock_db.db.execute.return_value.fetchall.return_value = [
MockChromosome(1, "X", 100),
MockChromosome(2, "Y", 1000),
MockChromosome(3, "Z", 10000),
]
mock_dataset = MockDataset(MockGroup("Random"))
test_chromosomes = Chromosomes(dataset=mock_dataset)
mock_db.db.execute.assert_called_with(
"SELECT Chr_Length.Name, Chr_Length.OrderId, Length "
"FROM Chr_Length, InbredSet WHERE "
"Chr_Length.SpeciesId = InbredSet.SpeciesId AND "
"InbredSet.Name = 'Random' ORDER BY OrderId"
)
self.assertEqual(
list(test_chromosomes.chromosomes.keys()),
[1, 2, 3]
)
self.assertEqual(test_chromosomes.dataset, mock_dataset)
@mock.patch("base.species.g")
def test_create_chromosomes_with_species(self, mock_db):
"""Test instantiating a chromosome with a species"""
mock_db.db.execute.return_value.fetchall.return_value = [
MockChromosome(1, "X", 100),
MockChromosome(2, "Y", 1000),
MockChromosome(3, "Z", 10000),
]
mock_dataset = MockDataset(MockGroup("Random"))
test_chromosomes = Chromosomes(dataset=mock_dataset,
species="testSpecies")
mock_db.db.execute.assert_called_with(
"SELECT Chr_Length.Name, Chr_Length.OrderId, Length "
"FROM Chr_Length, Species WHERE "
"Chr_Length.SpeciesId = Species.SpeciesId AND "
"Species.Name = 'Testspecies' ORDER BY OrderId"
)
self.assertEqual(
list(test_chromosomes.chromosomes.keys()),
[1, 2, 3]
)
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