Test the creation of the_species, indchromosomes and chromosome objs

* wqflask/tests/unit/base/test_species.py (TestTheSpecies): Delete.
(TestIndChromosome): Move to pytest and parametrize.
(TestChromosomes): Ditto.
(test_species): Ditto.
(test_create_ind_chromosome): Ditto.
(test_create_chromosomes): Ditto.

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)