Merge branch 'testing' of github.com:genenetwork/genenetwork2 into acenteno

3 files changed, 128 insertions, 14 deletions

diff --git a/wqflask/tests/unit/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py
index 96563a16..66ad361d 100644
--- a/wqflask/tests/unit/base/test_data_set.py
+++ b/wqflask/tests/unit/base/test_data_set.py
@@ -31,14 +31,12 @@ class TestDataSetTypes(unittest.TestCase):
     def tearDown(self):
         self.app_context.pop()
 
-    @mock.patch('base.data_set.g')
-    def test_data_set_type(self, db_mock):
+    def test_data_set_type(self):
         """Test that DatasetType returns correctly if the Redis Instance is not empty
         and the name variable exists in the dictionary
 
         """
         with app.app_context():
-            db_mock.get = mock.Mock()
             redis_mock = mock.Mock()
             redis_mock.get.return_value = self.test_dataset
             self.assertEqual(DatasetType(redis_mock)
@@ -89,10 +87,9 @@ class TestDataSetTypes(unittest.TestCase):
                  '"B139_K_1206_M": "ProbeSet", '
                  '"B139_K_1206_R": "ProbeSet", '
                  '"Test": "ProbeSet"}'))
-
-            db_mock.db.execute.assert_called_with(
-                ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze " +
-                 "WHERE ProbeSetFreeze.Name = \"Test\" ")
+            db_mock.db.execute.assert_called_once_with(
+                ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze "
+                 + "WHERE ProbeSetFreeze.Name = \"Test\" ")
             )
 
     @mock.patch('base.data_set.g')
@@ -148,9 +145,9 @@ class TestDataSetTypes(unittest.TestCase):
                  '"Test": "Publish"}'))
 
             db_mock.db.execute.assert_called_with(
-                ("SELECT PublishFreeze.Name " +
-                 "FROM PublishFreeze, InbredSet " +
-                 "WHERE InbredSet.Name = 'Test' AND "
+                ("SELECT PublishFreeze.Name "
+                 + "FROM PublishFreeze, InbredSet "
+                 + "WHERE InbredSet.Name = 'Test' AND "
                  "PublishFreeze.InbredSetId = InbredSet.Id")
             )
 
diff --git a/wqflask/tests/unit/base/test_species.py b/wqflask/tests/unit/base/test_species.py
new file mode 100644
index 00000000..9b5c023c
--- /dev/null
+++ b/wqflask/tests/unit/base/test_species.py
@@ -0,0 +1,116 @@
+"""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)
+        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"
+        )
diff --git a/wqflask/tests/unit/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py
index 8e8ba482..e1555cb4 100644
--- a/wqflask/tests/unit/base/test_webqtl_case_data.py
+++ b/wqflask/tests/unit/base/test_webqtl_case_data.py
@@ -4,15 +4,16 @@ import unittest
 from wqflask import app  # Required because of utility.tools in webqtlCaseData.py
 from base.webqtlCaseData import webqtlCaseData
 
+
 class TestWebqtlCaseData(unittest.TestCase):
     """Tests for WebqtlCaseData class"""
 
     def setUp(self):
         self.w = webqtlCaseData(name="Test",
-                           value=0,
-                           variance=0.0,
-                           num_cases=10,
-                           name2="Test2")
+                                value=0,
+                                variance=0.0,
+                                num_cases=10,
+                                name2="Test2")
 
     def test_webqtl_case_data_repr(self):
         self.assertEqual(