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

21 files changed, 560 insertions, 339 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(
diff --git a/wqflask/tests/unit/utility/test_authentication_tools.py b/wqflask/tests/unit/utility/test_authentication_tools.py
index fff5fd8f..024ab43f 100644
--- a/wqflask/tests/unit/utility/test_authentication_tools.py
+++ b/wqflask/tests/unit/utility/test_authentication_tools.py
@@ -5,6 +5,7 @@ from unittest import mock
 from utility.authentication_tools import check_resource_availability
 from utility.authentication_tools import add_new_resource
 
+
 class TestResponse:
     """Mock Test Response after a request"""
     @property
@@ -18,7 +19,7 @@ class TestUser:
     @property
     def user_id(self):
         """Mockes user id. Used in Flask.g.user_session.user_id"""
-        return "Jane"
+        return b"Jane"
 
 
 class TestUserSession:
diff --git a/wqflask/tests/unit/utility/test_chunks.py b/wqflask/tests/unit/utility/test_chunks.py
index 8d90a1ec..1d349193 100644
--- a/wqflask/tests/unit/utility/test_chunks.py
+++ b/wqflask/tests/unit/utility/test_chunks.py
@@ -7,6 +7,7 @@ from utility.chunks import divide_into_chunks
 
 class TestChunks(unittest.TestCase):
     "Test Utility method for chunking"
+
     def test_divide_into_chunks(self):
         "Check that a list is chunked correctly"
         self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3),
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index d0264b87..1089a36f 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -105,10 +105,10 @@ class TestCorrelations(unittest.TestCase):
         target_dataset = AttributeSetter({"group": group})
 
         target_vals = [3.4, 6.2, 4.1, 3.4, 1.2, 5.6]
-        trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}), 
-        "S3": AttributeSetter(
-            {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}), 
-        "S6": AttributeSetter({"value": 5.0})}
+        trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}),
+                      "S3": AttributeSetter(
+            {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}),
+            "S6": AttributeSetter({"value": 5.0})}
         this_trait = AttributeSetter({"data": trait_data})
         mock_normalize.return_value = ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
                                        [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6)
@@ -127,9 +127,9 @@ class TestCorrelations(unittest.TestCase):
         expected_pearsonr = [-0.21618688834430866, 0.680771605997119, 6]
         expected_spearmanr = [-0.11595420713048969, 0.826848213385815, 6]
         for i, val in enumerate(expected_pearsonr):
-            self.assertAlmostEqual(val, results_pearsonr[i],4)
+            self.assertAlmostEqual(val, results_pearsonr[i], 4)
         for i, val in enumerate(expected_spearmanr):
-            self.assertAlmostEqual(val, results_spearmanr[i],4)
+            self.assertAlmostEqual(val, results_spearmanr[i], 4)
         self.assertEqual(results_num_overlap, None)
 
     @mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits")
diff --git a/wqflask/tests/unit/wqflask/api/test_gen_menu.py b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
index 57eb1650..7e477da2 100644
--- a/wqflask/tests/unit/wqflask/api/test_gen_menu.py
+++ b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
@@ -2,9 +2,7 @@
 import unittest
 from unittest import mock
 
-from wqflask import app
 from wqflask.api.gen_menu import gen_dropdown_json
-from wqflask.api.gen_menu import get_species
 from wqflask.api.gen_menu import get_groups
 from wqflask.api.gen_menu import get_types
 from wqflask.api.gen_menu import get_datasets
@@ -18,8 +16,6 @@ class TestGenMenu(unittest.TestCase):
     """Tests for the gen_menu module"""
 
     def setUp(self):
-        self.app_context = app.app_context()
-        self.app_context.push()
         self.test_group = {
             'mouse': [
                 ['H_T1',
@@ -70,212 +66,225 @@ class TestGenMenu(unittest.TestCase):
             }
         }
 
-    def tearDown(self):
-        self.app_context.pop()
-
-    @mock.patch('wqflask.api.gen_menu.g')
-    def test_get_species(self, db_mock):
-        """Test that assertion is raised when dataset and dataset_name
-        are defined"""
-        db_mock.db.execute.return_value.fetchall.return_value = (
-            ('human', 'Human'),
-            ('mouse', 'Mouse'))
-        self.assertEqual(get_species(),
-                         [['human', 'Human'], ['mouse', 'Mouse']])
-        db_mock.db.execute.assert_called_once_with(
-            "SELECT Name, MenuName FROM Species ORDER BY OrderId"
-        )
-
-    @mock.patch('wqflask.api.gen_menu.g')
-    def test_get_groups(self, db_mock):
+    def test_get_groups(self):
         """Test that species groups are grouped correctly"""
-        db_mock.db.execute.return_value.fetchall.side_effect = [
-            # Mouse
-            (('BXD', 'BXD', None),
-             ('HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)',
-              'Test')),
-            # Human
-            (('H_T1', "H_T", "DescriptionA"),
-             ('H_T2', "H_T'", None))
-        ]
-
-        self.assertEqual(get_groups([["human", "Human"], ["mouse", "Mouse"]]),
-                         self.test_group)
-
-        for name in ["mouse", "human"]:
-            db_mock.db.execute.assert_any_call(
-                ("SELECT InbredSet.Name, InbredSet.FullName, " +
-                 "IFNULL(InbredSet.Family, 'None') " +
-                 "FROM InbredSet, Species WHERE Species.Name " +
-                 "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by " +
-                 "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, " +
-                 "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, " +
-                 "InbredSet.FullName) ASC, InbredSet.FullName ASC, " +
-                 "InbredSet.MenuOrderId ASC").format(name)
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchall.side_effect = [
+                # Mouse
+                (('BXD', 'BXD', None),
+                 ('HLC', ('Liver: Normal Gene Expression '
+                          'with Genotypes (Merck)'),
+                  'Test')),
+                # Human
+                (('H_T1', "H_T", "DescriptionA"),
+                 ('H_T2', "H_T'", None))
+            ]
+            self.assertEqual(get_groups([["human", "Human"],
+                                         ["mouse", "Mouse"]],
+                                        db_mock),
+                             self.test_group)
+
+            for name in ["mouse", "human"]:
+                cursor.execute.assert_any_call(
+                    ("SELECT InbredSet.Name, InbredSet.FullName, "
+                     "IFNULL(InbredSet.Family, 'None') "
+                     "FROM InbredSet, Species WHERE Species.Name "
+                     "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by "
+                     "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, "
+                     "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, "
+                     "InbredSet.FullName) ASC, InbredSet.FullName ASC, "
+                     "InbredSet.MenuOrderId ASC").format(name)
+                )
+
+    def test_phenotypes_exist_called_with_correct_query(self):
+        """Test that phenotypes_exist is called with the correct query"""
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchone.return_value = None
+            phenotypes_exist("test", db_mock)
+            cursor.execute.assert_called_with(
+                "SELECT Name FROM PublishFreeze "
+                "WHERE PublishFreeze.Name = 'testPublish'"
             )
 
-    @mock.patch('wqflask.api.gen_menu.g')
-    def test_phenotypes_exist_called_with_correct_query(self, db_mock):
-        """Test that phenotypes_exist is called with the correct query"""
-        db_mock.db.execute.return_value.fetchone.return_value = None
-        phenotypes_exist("test")
-        db_mock.db.execute.assert_called_with(
-            "SELECT Name FROM PublishFreeze "
-            "WHERE PublishFreeze.Name = 'testPublish'"
-        )
-
-    @mock.patch('wqflask.api.gen_menu.g')
-    def test_phenotypes_exist_with_falsy_values(self, db_mock):
+    def test_phenotypes_exist_with_falsy_values(self):
         """Test that phenotype check returns correctly when given
         a None value"""
-        for x in [None, False, (), [], ""]:
-            db_mock.db.execute.return_value.fetchone.return_value = x
-            self.assertFalse(phenotypes_exist("test"))
-
-    @mock.patch('wqflask.api.gen_menu.g')
-    def test_phenotypes_exist_with_truthy_value(self, db_mock):
-        """Test that phenotype check returns correctly when given Truthy """
-        for x in ["x", ("result"), ["result"], [1]]:
-            db_mock.db.execute.return_value.fetchone.return_value = (x)
-            self.assertTrue(phenotypes_exist("test"))
-
-    @mock.patch('wqflask.api.gen_menu.g')
-    def test_genotypes_exist_called_with_correct_query(self, db_mock):
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            for x in [None, False, (), [], ""]:
+                cursor.fetchone.return_value = x
+            self.assertFalse(phenotypes_exist("test", db_mock))
+
+    def test_phenotypes_exist_with_truthy_value(self):
+        """Test that phenotype check returns correctly when given Truthy"""
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as conn:
+            with conn.cursor() as cursor:
+                for x in ["x", ("result"), ["result"], [1]]:
+                    cursor.fetchone.return_value = (x)
+                self.assertTrue(phenotypes_exist("test", db_mock))
+
+    def test_genotypes_exist_called_with_correct_query(self):
         """Test that genotypes_exist is called with the correct query"""
-        db_mock.db.execute.return_value.fetchone.return_value = None
-        genotypes_exist("test")
-        db_mock.db.execute.assert_called_with(
-            "SELECT Name FROM GenoFreeze WHERE GenoFreeze.Name = 'testGeno'"
-        )
-
-    @mock.patch('wqflask.api.gen_menu.g')
-    def test_genotypes_exist_with_falsy_values(self, db_mock):
-        """Test that genotype check returns correctly when given
-        a None value"""
-        for x in [None, False, (), [], ""]:
-            db_mock.db.execute.return_value.fetchone.return_value = x
-            self.assertFalse(genotypes_exist("test"))
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchone.return_value = None
+            genotypes_exist("test", db_mock)
+            cursor.execute.assert_called_with(
+                "SELECT Name FROM GenoFreeze WHERE "
+                "GenoFreeze.Name = 'testGeno'"
+            )
+
+    def test_genotypes_exist_with_falsy_values(self):
+        """Test that genotype check returns correctly when given a None value
 
-    @mock.patch('wqflask.api.gen_menu.g')
-    def test_genotypes_exist_with_truthy_value(self, db_mock):
+        """
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            for x in [None, False, (), [], ""]:
+                cursor.fetchone.return_value = x
+                self.assertFalse(genotypes_exist("test", db_mock))
+
+    def test_genotypes_exist_with_truthy_value(self):
         """Test that genotype check returns correctly when given Truthy """
-        for x in ["x", ("result"), ["result"], [1]]:
-            db_mock.db.execute.return_value.fetchone.return_value = (x)
-            self.assertTrue(phenotypes_exist("test"))
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            for x in ["x", ("result"), ["result"], [1]]:
+                cursor.fetchone.return_value = (x)
+                self.assertTrue(phenotypes_exist("test", db_mock))
 
-    @mock.patch('wqflask.api.gen_menu.g')
-    def test_build_datasets_with_type_phenotypes(self, db_mock):
+    def test_build_datasets_with_type_phenotypes(self):
         """Test that correct dataset is returned for a phenotype type"""
-        db_mock.db.execute.return_value.fetchall.return_value = (
-            (602, "BXDPublish", "BXD Published Phenotypes"),
-        )
-        self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"),
-                         [['602', "BXDPublish", "BXD Published Phenotypes"]])
-        db_mock.db.execute.assert_called_with(
-            "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, " +
-            "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, " +
-            "InbredSet WHERE InbredSet.Name = 'BXD' AND " +
-            "PublishFreeze.InbredSetId = InbredSet.Id AND " +
-            "InfoFiles.InfoPageName = PublishFreeze.Name " +
-            "ORDER BY PublishFreeze.CreateTime ASC"
-        )
-        self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"),
-                         [['602', "BXDPublish", "Mouse Phenome Database"]])
-
-        db_mock.db.execute.return_value.fetchall.return_value = ()
-        db_mock.db.execute.return_value.fetchone.return_value = (
-            "BXDPublish", "Mouse Phenome Database"
-        )
-        self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"),
-                         [["None", "BXDPublish", "Mouse Phenome Database"]])
-
-    @mock.patch('wqflask.api.gen_menu.g')
-    def test_build_datasets_with_type_phenotypes_and_no_results(self, db_mock):
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchall.return_value = (
+                (602, "BXDPublish", "BXD Published Phenotypes"),
+            )
+            self.assertEqual(build_datasets("Mouse", "BXD",
+                                            "Phenotypes", db_mock),
+                             [['602', "BXDPublish",
+                               "BXD Published Phenotypes"]])
+            cursor.execute.assert_called_with(
+                "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, "
+                + "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, "
+                + "InbredSet WHERE InbredSet.Name = 'BXD' AND "
+                + "PublishFreeze.InbredSetId = InbredSet.Id AND "
+                + "InfoFiles.InfoPageName = PublishFreeze.Name "
+                + "ORDER BY PublishFreeze.CreateTime ASC"
+            )
+            self.assertEqual(build_datasets("Mouse", "MDP",
+                                            "Phenotypes", db_mock),
+                             [['602', "BXDPublish",
+                               "Mouse Phenome Database"]])
+
+            cursor.fetchall.return_value = ()
+            cursor.fetchone.return_value = (
+                "BXDPublish", "Mouse Phenome Database"
+            )
+            self.assertEqual(build_datasets("Mouse", "MDP",
+                                            "Phenotypes", db_mock),
+                             [["None", "BXDPublish",
+                               "Mouse Phenome Database"]])
+
+    def test_build_datasets_with_type_phenotypes_and_no_results(self):
         """Test that correct dataset is returned for a phenotype type with no
         results
 
         """
-        db_mock.db.execute.return_value.fetchall.return_value = None
-        db_mock.db.execute.return_value.fetchone.return_value = (121,
-                                                                 "text value")
-        self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"),
-                         [["None", "121", "text value"]])
-        db_mock.db.execute.assert_called_with(
-            "SELECT PublishFreeze.Name, PublishFreeze.FullName "
-            "FROM PublishFreeze, InbredSet "
-            "WHERE InbredSet.Name = 'BXD' AND "
-            "PublishFreeze.InbredSetId = InbredSet.Id "
-            "ORDER BY PublishFreeze.CreateTime ASC"
-        )
-
-    @mock.patch('wqflask.api.gen_menu.g')
-    def test_build_datasets_with_type_genotypes(self, db_mock):
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchall.return_value = None
+            cursor.fetchone.return_value = (121,
+                                            "text value")
+            self.assertEqual(build_datasets("Mouse", "BXD",
+                                            "Phenotypes", db_mock),
+                             [["None", "121",
+                               "text value"]])
+            cursor.execute.assert_called_with(
+                "SELECT PublishFreeze.Name, PublishFreeze.FullName "
+                "FROM PublishFreeze, InbredSet "
+                "WHERE InbredSet.Name = 'BXD' AND "
+                "PublishFreeze.InbredSetId = InbredSet.Id "
+                "ORDER BY PublishFreeze.CreateTime ASC"
+            )
+
+    def test_build_datasets_with_type_genotypes(self):
         """Test that correct dataset is returned for a phenotype type"""
-        db_mock.db.execute.return_value.fetchone.return_value = (
-            635, "HLCPublish", "HLC Published Genotypes"
-        )
-
-        self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"),
-                         [["635", "HLCGeno", "HLC Genotypes"]])
-        db_mock.db.execute.assert_called_with(
-            "SELECT InfoFiles.GN_AccesionId FROM InfoFiles, "
-            "GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND "
-            "GenoFreeze.InbredSetId = InbredSet.Id AND "
-            "InfoFiles.InfoPageName = GenoFreeze.ShortName " +
-            "ORDER BY GenoFreeze.CreateTime DESC"
-        )
-        db_mock.db.execute.return_value.fetchone.return_value = ()
-        self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"),
-                         [["None", "HLCGeno", "HLC Genotypes"]])
-
-    @mock.patch('wqflask.api.gen_menu.g')
-    def test_build_datasets_with_type_mrna(self, db_mock):
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchone.return_value = (
+                635, "HLCPublish", "HLC Published Genotypes"
+            )
+            self.assertEqual(build_datasets("Mouse", "HLC",
+                                            "Genotypes", db_mock),
+                             [["635", "HLCGeno", "HLC Genotypes"]])
+            cursor.execute.assert_called_with(
+                "SELECT InfoFiles.GN_AccesionId FROM InfoFiles, "
+                "GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND "
+                "GenoFreeze.InbredSetId = InbredSet.Id AND "
+                "InfoFiles.InfoPageName = GenoFreeze.ShortName "
+                "ORDER BY GenoFreeze.CreateTime DESC"
+            )
+            cursor.fetchone.return_value = ()
+            self.assertEqual(build_datasets("Mouse", "HLC",
+                                            "Genotypes", db_mock),
+                             [["None", "HLCGeno", "HLC Genotypes"]])
+
+    def test_build_datasets_with_type_mrna(self):
         """Test that correct dataset is returned for a mRNA
         expression/ Probeset"""
-        db_mock.db.execute.return_value.fetchall.return_value = (
-            (112, "HC_M2_0606_P",
-             "Hippocampus Consortium M430v2 (Jun06) PDNN"), )
-        self.assertEqual(build_datasets("Mouse", "HLC", "mRNA"), [[
-            "112", 'HC_M2_0606_P', "Hippocampus Consortium M430v2 (Jun06) PDNN"
-        ]])
-        db_mock.db.execute.assert_called_once_with(
-            "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, " +
-            "ProbeSetFreeze.FullName FROM ProbeSetFreeze, " +
-            "ProbeFreeze, InbredSet, Tissue, Species WHERE " +
-            "Species.Name = 'Mouse' AND Species.Id = " +
-            "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND " +
-            "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND " +
-            "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = " +
-            "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND " +
-            "ProbeSetFreeze.public > 0 " +
-            "ORDER BY -ProbeSetFreeze.OrderList DESC, ProbeSetFreeze.CreateTime DESC")
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchall.return_value = (
+                (112, "HC_M2_0606_P",
+                 "Hippocampus Consortium M430v2 (Jun06) PDNN"), )
+            self.assertEqual(build_datasets("Mouse",
+                                            "HLC", "mRNA", db_mock),
+                             [["112", 'HC_M2_0606_P',
+                               "Hippocampus Consortium M430v2 (Jun06) PDNN"
+                               ]])
+            cursor.execute.assert_called_once_with(
+                "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, "
+                "ProbeSetFreeze.FullName FROM ProbeSetFreeze, "
+                "ProbeFreeze, InbredSet, Tissue, Species WHERE "
+                "Species.Name = 'Mouse' AND Species.Id = "
+                "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND "
+                "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND "
+                "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = "
+                "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND "
+                "ProbeSetFreeze.public > 0 "
+                "ORDER BY -ProbeSetFreeze.OrderList DESC, "
+                "ProbeSetFreeze.CreateTime DESC")
 
     @mock.patch('wqflask.api.gen_menu.build_datasets')
-    @mock.patch('wqflask.api.gen_menu.g')
-    def test_build_types(self, db_mock, datasets_mock):
+    def test_build_types(self, datasets_mock):
         """Test that correct tissue metadata is returned"""
+        db_mock = mock.MagicMock()
         datasets_mock.return_value = [
             ["112", 'HC_M2_0606_P',
                 "Hippocampus Consortium M430v2 (Jun06) PDNN"]
         ]
-        db_mock.db.execute.return_value.fetchall.return_value = (
-            ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue')
-        )
-        self.assertEqual(build_types('mouse', 'random group'),
-                         [['M', 'M', 'Molecular Traits'],
-                          ['H', 'H', 'Molecular Traits'],
-                          ['R', 'R', 'Molecular Traits']])
-        db_mock.db.execute.assert_called_once_with(
-            "SELECT DISTINCT Tissue.Name " +
-            "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, " +
-            "Tissue, Species WHERE Species.Name = 'mouse' " +
-            "AND Species.Id = InbredSet.SpeciesId AND " +
-            "InbredSet.Name = 'random group' AND " +
-            "ProbeFreeze.TissueId = Tissue.Id AND " +
-            "ProbeFreeze.InbredSetId = InbredSet.Id AND " +
-            "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " +
-            "ORDER BY Tissue.Name"
-        )
+        with db_mock.cursor() as cursor:
+            cursor.fetchall.return_value = (
+                ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue')
+            )
+            self.assertEqual(build_types('mouse', 'random group', db_mock),
+                             [['M', 'M', 'Molecular Traits'],
+                              ['H', 'H', 'Molecular Traits'],
+                              ['R', 'R', 'Molecular Traits']])
+            cursor.execute.assert_called_once_with(
+                "SELECT DISTINCT Tissue.Name "
+                "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, "
+                "Tissue, Species WHERE Species.Name = 'mouse' "
+                "AND Species.Id = InbredSet.SpeciesId AND "
+                "InbredSet.Name = 'random group' AND "
+                "ProbeFreeze.TissueId = Tissue.Id AND "
+                "ProbeFreeze.InbredSetId = InbredSet.Id AND "
+                "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+                "ORDER BY Tissue.Name"
+            )
 
     @mock.patch('wqflask.api.gen_menu.build_types')
     @mock.patch('wqflask.api.gen_menu.genotypes_exist')
@@ -297,7 +306,9 @@ class TestGenMenu(unittest.TestCase):
         build_types_mock.return_value = [
             ['M', 'M', 'Molecular Trait Datasets']
         ]
-        self.assertEqual(get_types(self.test_group), expected_result)
+        self.assertEqual(get_types(self.test_group,
+                                   mock.MagicMock()),
+                         expected_result)
 
     @mock.patch('wqflask.api.gen_menu.build_types')
     @mock.patch('wqflask.api.gen_menu.genotypes_exist')
@@ -315,10 +326,8 @@ class TestGenMenu(unittest.TestCase):
         genotypes_exist_mock.return_value = False
 
         build_types_mock.return_value = []
-        self.assertEqual(get_types(self.test_group), {
-            'mouse': {},
-            'human': {}
-        })
+        self.assertEqual(get_types(self.test_group, mock.MagicMock()),
+                         {'mouse': {}, 'human': {}})
 
     @mock.patch('wqflask.api.gen_menu.build_types')
     @mock.patch('wqflask.api.gen_menu.genotypes_exist')
@@ -345,7 +354,7 @@ class TestGenMenu(unittest.TestCase):
             'human': {
                 'HLC': [['M', 'M', 'Molecular Trait Datasets']],
                 'BXD': [['M', 'M', 'Molecular Trait Datasets']]}}
-        self.assertEqual(get_types(self.test_group),
+        self.assertEqual(get_types(self.test_group, mock.MagicMock()),
                          expected_result)
 
     @mock.patch('wqflask.api.gen_menu.build_datasets')
@@ -367,7 +376,7 @@ class TestGenMenu(unittest.TestCase):
                       'BXD': {'Genotypes': 'Test',
                               'M': 'Test',
                               'Phenotypes': 'Test'}}}
-        self.assertEqual(get_datasets(self.test_type),
+        self.assertEqual(get_datasets(self.test_type, mock.MagicMock()),
                          expected_result)
 
     @mock.patch('wqflask.api.gen_menu.build_datasets')
@@ -381,13 +390,13 @@ class TestGenMenu(unittest.TestCase):
                 'H_T1': {}},
             'human': {'HLC': {},
                       'BXD': {}}}
-        self.assertEqual(get_datasets(self.test_type),
+        self.assertEqual(get_datasets(self.test_type, mock.MagicMock()),
                          expected_result)
 
     @mock.patch('wqflask.api.gen_menu.get_datasets')
     @mock.patch('wqflask.api.gen_menu.get_types')
     @mock.patch('wqflask.api.gen_menu.get_groups')
-    @mock.patch('wqflask.api.gen_menu.get_species')
+    @mock.patch('wqflask.api.gen_menu.get_all_species')
     def test_gen_dropdown_json(self,
                                species_mock,
                                groups_mock,
@@ -411,4 +420,4 @@ class TestGenMenu(unittest.TestCase):
             'groups': ['groupA', 'groupB', 'groupC', 'groupD'],
             'species': ['speciesA', 'speciesB', 'speciesC', 'speciesD']}
 
-        self.assertEqual(gen_dropdown_json(), expected_result)
+        self.assertEqual(gen_dropdown_json(mock.MagicMock()), expected_result)
diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py
index b094294a..159c982b 100644
--- a/wqflask/tests/unit/wqflask/api/test_mapping.py
+++ b/wqflask/tests/unit/wqflask/api/test_mapping.py
@@ -58,7 +58,7 @@ class TestMapping(unittest.TestCase):
 
         self.assertEqual(results_2, expected_results)
 
-    @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl_geno")
+    @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl")
     @mock.patch("wqflask.api.mapping.gemma_mapping.run_gemma")
     @mock.patch("wqflask.api.mapping.initialize_parameters")
     @mock.patch("wqflask.api.mapping.retrieve_sample_data")
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
index 44d2e0fc..a8cf6006 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -1,11 +1,31 @@
+"""module contains tests for correlation functions"""
+
 import unittest
 from unittest import mock
+
 from wqflask.correlation.correlation_functions import get_trait_symbol_and_tissue_values
 from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_tiss
 
 
 class TestCorrelationFunctions(unittest.TestCase):
-    
+    """test for correlation helper functions"""
+
+    @mock.patch("wqflask.correlation.correlation_functions.compute_corr_coeff_p_value")
+    def test_tissue_corr_computation(self, mock_tiss_corr_computation):
+        """test for cal_zero_order_corr_for_tiss"""
+
+        primary_values = [9.288, 9.313, 8.988, 9.660, 8.21]
+        target_values = [9.586, 8.498, 9.362, 8.820, 8.786]
+
+        mock_tiss_corr_computation.return_value = (0.51, 0.7)
+
+        results = cal_zero_order_corr_for_tiss(primary_values, target_values)
+        mock_tiss_corr_computation.assert_called_once_with(
+            primary_values=primary_values, target_values=target_values,
+            corr_method="pearson")
+
+        self.assertEqual(len(results), 3)
+
     @mock.patch("wqflask.correlation.correlation_functions.MrnaAssayTissueData")
     def test_get_trait_symbol_and_tissue_values(self, mock_class):
         """test for getting trait symbol and tissue_values"""
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py
new file mode 100644
index 00000000..e1bd6d86
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py
@@ -0,0 +1,14 @@
+"""this module contains tests for code used in integrating to gn3 api"""
+from unittest import TestCase
+from base.data_set import create_dataset
+
+class TestCorrelation(TestCase):
+
+    def test_create_dataset(self):
+        """test for creating datasets"""
+
+        pass
+    def test_fetch_dataset_info(self):
+        """test for fetching dataset info data"""
+
+        pass
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
index 8ae0f09f..f4869c45 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
@@ -9,6 +9,7 @@ from wqflask.marker_regression.display_mapping_results import (
 
 class TestDisplayMappingResults(unittest.TestCase):
     """Basic Methods to test Mapping Results"""
+
     def test_pil_colors(self):
         """Test that colors use PILLOW color format"""
         self.assertEqual(DisplayMappingResults.CLICKABLE_WEBQTL_REGION_COLOR,
@@ -17,6 +18,7 @@ class TestDisplayMappingResults(unittest.TestCase):
 
 class TestHtmlGenWrapper(unittest.TestCase):
     """Test Wrapper around HTMLGen"""
+
     def test_create_image(self):
         """Test HT.Image method"""
         self.assertEqual(
@@ -37,7 +39,8 @@ class TestHtmlGenWrapper(unittest.TestCase):
             cgi="/testing/",
             enctype='multipart/form-data',
             name="formName",
-            submit=HtmlGenWrapper.create_input_tag(type_='hidden', name='Default_Name')
+            submit=HtmlGenWrapper.create_input_tag(
+                type_='hidden', name='Default_Name')
         )
         test_image = HtmlGenWrapper.create_image_tag(
             src="test.png",
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index fe2569b8..58a44b2a 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -47,11 +47,11 @@ class TestGemmaMapping(unittest.TestCase):
     @mock.patch("wqflask.marker_regression.run_mapping.random.choice")
     @mock.patch("wqflask.marker_regression.gemma_mapping.os")
     @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file")
-    def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files,mock_parse_loco):
+    def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_parse_loco):
         """add tests for run_gemma where first run is set to true"""
-        this_chromosomes={}
+        this_chromosomes = {}
         for i in range(1, 5):
-            this_chromosomes[f'CH{i}']=(AttributeSetter({"name": f"CH{i}"}))
+            this_chromosomes[f'CH{i}'] = (AttributeSetter({"name": f"CH{i}"}))
         chromosomes = AttributeSetter({"chromosomes": this_chromosomes})
 
         dataset_group = MockGroup(
@@ -68,9 +68,10 @@ class TestGemmaMapping(unittest.TestCase):
         mock_parse_loco.return_value = []
         results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[
         ], vals=[], covariates="", use_loco=True)
-        self.assertEqual(mock_os.system.call_count,2)
+        self.assertEqual(mock_os.system.call_count, 2)
         mock_gen_pheno_txt.assert_called_once()
-        mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR",True)
+        mock_parse_loco.assert_called_once_with(
+            dataset, "GP1_GWA_RRRRRR", True)
         mock_os.path.isfile.assert_called_once_with(
             ('/home/user/imgfile_output.assoc.txt'))
         self.assertEqual(mock_flat_files.call_count, 4)
@@ -80,10 +81,12 @@ class TestGemmaMapping(unittest.TestCase):
     def test_gen_pheno_txt_file(self):
         """add tests for generating pheno txt file"""
         with mock.patch("builtins.open", mock.mock_open())as mock_open:
-            gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[
-                               "x", "w", "q", "we", "R"], trait_filename="fitr.re")
+            gen_pheno_txt_file(
+                this_dataset=AttributeSetter({"name": "A"}),
+                genofile_name="", vals=[
+                    "x", "w", "q", "we", "R"])
             mock_open.assert_called_once_with(
-                '/home/user/data/gn2/fitr.re.txt', 'w')
+                '/home/user/data/gn2/PHENO_KiAEKlCvM6iGTM9Kh_TAlQ.txt', 'w')
             filehandler = mock_open()
             values = ["x", "w", "q", "we", "R"]
             write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call(
@@ -102,7 +105,8 @@ class TestGemmaMapping(unittest.TestCase):
         create_trait_side_effect = []
 
         for i in range(4):
-            create_dataset_side_effect.append(AttributeSetter({"name": f'name_{i}'}))
+            create_dataset_side_effect.append(
+                AttributeSetter({"name": f'name_{i}'}))
             create_trait_side_effect.append(
                 AttributeSetter({"data": [f'data_{i}']}))
 
@@ -110,7 +114,7 @@ class TestGemmaMapping(unittest.TestCase):
         create_trait.side_effect = create_trait_side_effect
 
         group = MockGroup({"name": "group_X", "samplelist": samplelist})
-        this_dataset = AttributeSetter({"group": group})
+        this_dataset = AttributeSetter({"group": group, "name": "A"})
         flat_files.return_value = "Home/Genenetwork"
 
         with mock.patch("builtins.open", mock.mock_open())as mock_open:
@@ -130,7 +134,7 @@ class TestGemmaMapping(unittest.TestCase):
 
             flat_files.assert_called_once_with('mapping')
             mock_open.assert_called_once_with(
-                'Home/Genenetwork/group_X_covariates.txt', 'w')
+                'Home/Genenetwork/COVAR_anFZ_LfZYV0Ulywo+7tRCw.txt', 'w')
             filehandler = mock_open()
             filehandler.write.assert_has_calls([mock.call(
                 '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')])
@@ -144,7 +148,7 @@ class TestGemmaMapping(unittest.TestCase):
             "files": [["file_name", "user", "~/file1"],
                       ["file_name", "user", "~/file2"]]
         }
-        return_file="""X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t
+        return_file = """X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t
 chr4\tM2\t12\tQ\tE\tMMB\tR\t24\tW\t0.87\t0.5
 Y\tM4\t12\tQ\tE\tMMB\tR\t11.6\tW\t0.21\t0.7
 X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
@@ -159,11 +163,14 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
             mock_open.side_effect = handles
             results = parse_loco_output(
                 this_dataset={}, gwa_output_filename=".xw/")
-            expected_results= [
-            {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, 'additive': 23.3, 'lod_score': 0.07058107428570727},
-            {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, 'additive': 24.0, 'lod_score': 0.3010299956639812},
-            {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, 'additive': 11.6, 'lod_score': 0.1549019599857432},
-            {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}]
+            expected_results = [
+                {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85,
+                 'additive': 23.3, 'lod_score': 0.07058107428570727},
+                {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5,
+                 'additive': 24.0, 'lod_score': 0.3010299956639812},
+                {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7,
+                 'additive': 11.6, 'lod_score': 0.1549019599857432},
+                {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}]
 
             self.assertEqual(expected_results, results)
 
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
index 5eec93f1..fd21a825 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
@@ -12,9 +12,10 @@ class AttributeSetter:
     def __init__(self, obj):
         for key, val in obj.items():
             setattr(self, key, val)
-class TestPlinkMapping(unittest.TestCase):
 
 
+class TestPlinkMapping(unittest.TestCase):
+
     def test_build_line_list(self):
         """test for building line list"""
         line_1 = "this is line one test"
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index b47f877a..8b4337ec 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -1,21 +1,24 @@
 import unittest
-from unittest import  mock
-from wqflask.marker_regression.qtlreaper_mapping import  gen_pheno_txt_file
+from unittest import mock
+from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
+
+# issues some methods in genofile object are not defined
+# modify samples should equal to vals
 
-#issues some methods in genofile object are not defined
-#modify samples should equal to vals
-class TestQtlReaperMapping(unittest.TestCase):
-	@mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
-	def  test_gen_pheno_txt_file(self):                   
-		vals=["V1","x","V4","V3","x"]
-		samples=["S1","S2","S3","S4","S5"]
-		trait_filename="trait_file"
-		with mock.patch("builtins.open", mock.mock_open())as mock_open:
-			gen_pheno_txt_file(samples=samples,vals=vals,trait_filename=trait_filename)
-			mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt","w")
-			filehandler=mock_open()
-			write_calls= [mock.call('Trait\t'),mock.call('S1\tS3\tS4\n'),mock.call('T1\t'),mock.call('V1\tV4\tV3')]
 
-			filehandler.write.assert_has_calls(write_calls)
+class TestQtlReaperMapping(unittest.TestCase):
+    @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
+    def test_gen_pheno_txt_file(self):
+        vals = ["V1", "x", "V4", "V3", "x"]
+        samples = ["S1", "S2", "S3", "S4", "S5"]
+        trait_filename = "trait_file"
+        with mock.patch("builtins.open", mock.mock_open())as mock_open:
+            gen_pheno_txt_file(samples=samples, vals=vals,
+                               trait_filename=trait_filename)
+            mock_open.assert_called_once_with(
+                "/home/user/data/gn2/trait_file.txt", "w")
+            filehandler = mock_open()
+            write_calls = [mock.call('Trait\t'), mock.call(
+                'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
 
-	                                                                                                                    
+            filehandler.write.assert_has_calls(write_calls)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index c585f1df..9d13e943 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -1,48 +1,43 @@
 import unittest
 from unittest import mock
-from wqflask import app
-from wqflask.marker_regression.rqtl_mapping import get_trait_data_type
-from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_phenotype
-from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names
+from dataclasses import dataclass
 
-class TestRqtlMapping(unittest.TestCase):
-
-	def setUp(self):
-		self.app_context=app.app_context()
-		self.app_context.push()
-
-	def tearDown(self):
-		self.app_context.pop()
-
-
-	@mock.patch("wqflask.marker_regression.rqtl_mapping.g")
-	@mock.patch("wqflask.marker_regression.rqtl_mapping.logger")
-	def test_get_trait_data(self,mock_logger,mock_db):
-		"""test for getting trait data_type return True"""
-		query_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'"""
-		mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""]
-		results=get_trait_data_type("traid_id")
-		mock_db.db.execute.assert_called_with(query_value)
-		self.assertEqual(results,"fer434f")
-
-	def test_sanitize_rqtl_phenotype(self):
-		"""test for sanitizing rqtl phenotype"""
-		vals=['f',"x","r","x","x"]
-		results=sanitize_rqtl_phenotype(vals)
-		expected_phenotype_string='c(f,NA,r,NA,NA)'
-
-		self.assertEqual(results,expected_phenotype_string)
-
-	def test_sanitize_rqtl_names(self):
-		"""test for sanitzing rqtl names"""
-		vals=['f',"x","r","x","x"]
-		expected_sanitized_name="c('f',NA,'r',NA,NA)"
-		results=sanitize_rqtl_names(vals)
-		self.assertEqual(expected_sanitized_name,results)
-
-
-		
-		
+from wqflask.marker_regression.rqtl_mapping import run_rqtl
 
+@dataclass
+class MockGroup:
+    name: str
+    genofile: str
 
+@dataclass
+class MockDataset:
+    group: MockGroup
 
+class TestRqtlMapping(unittest.TestCase):
+    """Tests for functions in rqtl_mapping.py"""
+    @mock.patch("wqflask.marker_regression.rqtl_mapping.requests.post")
+    @mock.patch("wqflask.marker_regression.rqtl_mapping.locate")
+    @mock.patch("wqflask.marker_regression.rqtl_mapping.write_phenotype_file")
+    def test_run_rqtl_with_perm(self, mock_write_pheno_file, mock_locate, mock_post):
+        """Test for run_rqtl with permutations > 0"""
+        dataset_group = MockGroup("GP1", "file_geno")
+        dataset = MockDataset(dataset_group)
+
+        mock_write_pheno_file.return_value = "pheno_filename"
+        mock_locate.return_value = "geno_filename"
+        mock_post.return_value = mock.Mock(ok=True)
+        mock_post.return_value.json.return_value = {"perm_results": [],
+                                                    "suggestive": 3,
+                                                    "significant": 4,
+                                                    "results" : []}
+
+        results = run_rqtl(trait_name="the_trait", vals=[], samples=[],
+        dataset=dataset, mapping_scale="cM", model="normal", method="hk",
+        num_perm=5, perm_strata_list=[], do_control="false", control_marker="",
+        manhattan_plot=True, cofactors="")
+
+        mock_write_pheno_file.assert_called_once()
+        mock_locate.assert_called_once()
+        mock_post.assert_called_once()
+
+        self.assertEqual(results, ([], 3, 4, []))
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
index a29d8cfb..868b0b0b 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -43,11 +43,11 @@ class TestRunMapping(unittest.TestCase):
             })
         }
         self.dataset = AttributeSetter(
-            {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"})
+            {"fullname": "dataset_1", "group": self.group, "type": "ProbeSet"})
 
         self.chromosomes = AttributeSetter({"chromosomes": chromosomes})
         self.trait = AttributeSetter(
-            {"symbol": "IGFI", "chr": "X1", "mb": 123313})
+            {"symbol": "IGFI", "chr": "X1", "mb": 123313, "display_name": "Test Name"})
 
     def tearDown(self):
         self.dataset = AttributeSetter(
@@ -180,33 +180,36 @@ class TestRunMapping(unittest.TestCase):
 
             with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
                 export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers,
-                                       results_path="~/results", mapping_scale="physic", score_type="-log(p)",
-                                       transform="qnorm", covariates="Dataset1:Trait1,Dataset2:Trait2", n_samples="100")
+                                       results_path="~/results", mapping_method="gemma", mapping_scale="physic",
+                                       score_type="-logP", transform="qnorm",
+                                       covariates="Dataset1:Trait1,Dataset2:Trait2",
+                                       n_samples="100", vals_hash="")
 
                 write_calls = [
                     mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
                     mock.call('Population: Human GP1_\n'), mock.call(
-                        'Data Set: dataser_1\n'),
-                    mock.call('N Samples: 100\n'), mock.call('Transform - Quantile Normalized\n'),
+                        'Data Set: dataset_1\n'),
+                    mock.call('Trait: Test Name\n'),
+                    mock.call('Trait Hash: \n'),
+                    mock.call('N Samples: 100\n'),
+                    mock.call('Mapping Tool: gemma\n'),
+                    mock.call('Transform - Quantile Normalized\n'),
                     mock.call('Gene Symbol: IGFI\n'), mock.call(
                         'Location: X1 @ 123313 Mb\n'),
                     mock.call('Cofactors (dataset - trait):\n'),
                     mock.call('Trait1 - Dataset1\n'),
                     mock.call('Trait2 - Dataset2\n'),
                     mock.call('\n'), mock.call('Name,Chr,'),
-                    mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'),
+                    mock.call('Mb,-logP'),
                     mock.call(',Additive'), mock.call(',Dominance'),
                     mock.call('\n'), mock.call('MK1,C1,'),
-                    mock.call('12000,'), mock.call('1,'),
-                    mock.call('3'), mock.call(',VA'),
-                    mock.call(',TT'), mock.call('\n'),
-                    mock.call('MK2,C2,'), mock.call('10000,'),
-                    mock.call('15,'), mock.call('7'),
+                    mock.call('12000,'), mock.call('3'),
+                    mock.call(',VA'), mock.call(',TT'),
+                    mock.call('\n'), mock.call('MK2,C2,'),
+                    mock.call('10000,'), mock.call('7'),
                     mock.call('\n'), mock.call('MK1,C3,'),
-                    mock.call('1,'), mock.call('45,'),
-                    mock.call('7'), mock.call(',VE'),
-                    mock.call(',Tt')
-
+                    mock.call('1,'), mock.call('7'),
+                    mock.call(',VE'), mock.call(',Tt')
                 ]
                 mock_open.assert_called_once_with("~/results", "w+")
                 filehandler = mock_open()
@@ -228,28 +231,23 @@ class TestRunMapping(unittest.TestCase):
         used_samples = ["S1", "S2"]
         sample_list = AttributeSetter({"sample_attribute_values": {
             "S1": {
-                "C1": "c1_value",
-                "C2": "c2_value",
-                "W1": "w1_value"
-
+                "c1": "c1_value",
+                "c2": "c2_value",
+                "w1": "w1_value"
             },
             "S2": {
-                "W1": "w2_value",
-                "W2": "w2_value"
-
+                "w1": "w2_value",
+                "w2": "w2_value"
             },
             "S3": {
 
-                "C1": "c1_value",
-                "C2": "c2_value"
-
+                "c1": "c1_value",
+                "c2": "c2_value"
             },
-
         }})
-
         results = get_perm_strata(this_trait={}, sample_list=sample_list,
                                   categorical_vars=categorical_vars, used_samples=used_samples)
-        self.assertEqual(results, [2, 1])
+        self.assertEqual(results, [1, 1])
 
     def test_get_chr_length(self):
         """test for getting chromosome length"""
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
index ce3e7b83..89442c47 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -21,11 +21,11 @@ class TestSnpBrowser(unittest.TestCase):
                          "transcript": "false", "exon": "false", "domain_2": "true", "function": "false", "function_details": "true"}
         strains = {"mouse": ["S1", "S2", "S3", "S4", "S5"], "rat": []}
         expected_results = ([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore',
-                              'Domain 1', 'Domain 2', 'Details'], 
-                              ['S1', 'S2', 'S3', 'S4', 'S5']], 5, 
-                              ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 
-                              'conservation_score', 'domain_1', 'domain_2',
-                              'function_details', 'S1', 'S2', 'S3', 'S4', 'S5'])
+                              'Domain 1', 'Domain 2', 'Details'],
+                             ['S1', 'S2', 'S3', 'S4', 'S5']], 5,
+                            ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles',
+                             'conservation_score', 'domain_1', 'domain_2',
+                             'function_details', 'S1', 'S2', 'S3', 'S4', 'S5'])
 
         results_with_snp = get_header_list(
             variant_type="SNP", strains=strains, species="Mouse", empty_columns=empty_columns)
@@ -33,9 +33,9 @@ class TestSnpBrowser(unittest.TestCase):
             variant_type="InDel", strains=strains, species="rat", empty_columns=[])
         expected_results_with_indel = (
             ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start',
-             'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0, 
-             ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s',
-            'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'])
+             'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0,
+            ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s',
+             'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'])
 
         self.assertEqual(expected_results, results_with_snp)
         self.assertEqual(expected_results_with_indel, results_with_indel)
diff --git a/wqflask/tests/unit/wqflask/test_collect.py b/wqflask/tests/unit/wqflask/test_collect.py
index 9a36132d..2a914fb2 100644
--- a/wqflask/tests/unit/wqflask/test_collect.py
+++ b/wqflask/tests/unit/wqflask/test_collect.py
@@ -11,6 +11,7 @@ app = Flask(__name__)
 
 class MockSession:
     """Helper class for mocking wqflask.collect.g.user_session.logged_in"""
+
     def __init__(self, is_logged_in=False):
         self.is_logged_in = is_logged_in
 
@@ -21,6 +22,7 @@ class MockSession:
 
 class MockFlaskG:
     """Helper class for mocking wqflask.collect.g.user_session"""
+
     def __init__(self, is_logged_in=False):
         self.is_logged_in = is_logged_in
 
diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py
index 4f91d8ca..be7ca2df 100644
--- a/wqflask/tests/unit/wqflask/test_server_side.py
+++ b/wqflask/tests/unit/wqflask/test_server_side.py
@@ -17,15 +17,18 @@ class TestServerSideTableTests(unittest.TestCase):
     def test_get_page(self):
         rows_count = 3
         table_rows = [
-            {'first': 'd', 'second': 4, 'third': 'zz'}, 
-            {'first': 'b', 'second': 2, 'third': 'aa'}, 
+            {'first': 'd', 'second': 4, 'third': 'zz'},
+            {'first': 'b', 'second': 2, 'third': 'aa'},
             {'first': 'c', 'second': 1, 'third': 'ss'},
         ]
         headers = ['first', 'second', 'third']
-        request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1', 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'}
+        request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1',
+                        'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'}
 
-        test_page = ServerSideTable(rows_count, table_rows, headers, request_args).get_page()
+        test_page = ServerSideTable(
+            rows_count, table_rows, headers, request_args).get_page()
         self.assertEqual(test_page['sEcho'], '1')
         self.assertEqual(test_page['iTotalRecords'], 'nan')
         self.assertEqual(test_page['iTotalDisplayRecords'], '3')
-        self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, {'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}])
+        self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, {
+                         'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}])
diff --git a/wqflask/tests/unit/wqflask/wgcna/__init__.py b/wqflask/tests/unit/wqflask/wgcna/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/wgcna/__init__.py
diff --git a/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py b/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py
new file mode 100644
index 00000000..8e947e2f
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py
@@ -0,0 +1,50 @@
+
+"""module contains for processing gn3 wgcna data"""
+from unittest import TestCase
+
+from wqflask.wgcna.gn3_wgcna import process_wgcna_data
+
+
+class DataProcessingTests(TestCase):
+    """class contains data processing tests"""
+
+    def test_data_processing(self):
+        """test for parsing data for datatable"""
+        output = {
+            "input": {
+                "sample_names": ["BXD1", "BXD2", "BXD3", "BXD4", "BXD5", "BXD6"],
+
+            },
+            "output": {
+                "ModEigens": {
+                    "MEturquoise": [
+                        0.0646677768085351,
+                        0.137200224277058,
+                        0.63451113720732,
+                        -0.544002665501479,
+                        -0.489487590361863,
+                        0.197111117570427
+                    ],
+                    "MEgrey": [
+                        0.213,
+                        0.214,
+                        0.3141,
+                        -0.545,
+                        -0.423,
+                        0.156,
+                    ]
+                }}}
+
+        row_data = [['BXD1', 0.065, 0.213],
+                    ['BXD2', 0.137, 0.214],
+                    ['BXD3', 0.635, 0.314],
+                    ['BXD4', -0.544, -0.545],
+                    ['BXD5', -0.489, -0.423],
+                    ['BXD6', 0.197, 0.156]]
+
+        expected_results = {
+            "col_names": ["sample_names", "MEturquoise", "MEgrey"],
+            "mod_dataset": row_data
+        }
+
+        self.assertEqual(process_wgcna_data(output), expected_results)