diff options
| -rw-r--r-- | wqflask/tests/unit/base/test_species.py | 151 |
1 files changed, 59 insertions, 92 deletions
diff --git a/wqflask/tests/unit/base/test_species.py b/wqflask/tests/unit/base/test_species.py index 87f89607..d7ba30a3 100644 --- a/wqflask/tests/unit/base/test_species.py +++ b/wqflask/tests/unit/base/test_species.py @@ -1,12 +1,9 @@ """Tests wqflask/base/species.py""" - -import unittest -from unittest import mock +import pytest 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 @@ -27,91 +24,61 @@ 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) - - -@unittest.skip("Too complicated") -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) - self.assertEqual( - list(test_chromosomes.chromosomes.keys()), - [1, 2, 3] - ) - self.assertEqual(test_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" - ) - - @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") - self.assertEqual( - list(test_chromosomes.chromosomes.keys()), - [1, 2, 3] - ) - 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" - ) +@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): + mock_conn = mocker.patch("base.species.database_connection") + mock_conn.return_value.__enter__.return_value = mocker.MagicMock() + _c = mocker.patch("base.species.Chromosomes", + return_value=chromosome_param) + with mock_conn() as conn: + test_species = TheSpecies(dataset=dataset, + species_name=species_name) + _c.assert_called_with(conn=conn, 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(conn=mock_conn, + dataset=dataset, species=species) + assert _c.chromosomes == OrderedDict([ + ("1", IndChromosome("1", 10)), + ("2", IndChromosome("2", 11)), + ("4", IndChromosome("4", 15)), + ]) + cursor.execute.assert_called_with(*expected_call) |