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

26 files changed, 1999 insertions, 0 deletions

diff --git a/wqflask/tests/unit/__init__.py b/wqflask/tests/unit/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/__init__.py
diff --git a/wqflask/tests/unit/base/__init__.py b/wqflask/tests/unit/base/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/base/__init__.py
diff --git a/wqflask/tests/unit/base/data.py b/wqflask/tests/unit/base/data.py
new file mode 100644
index 00000000..06a5a989
--- /dev/null
+++ b/wqflask/tests/unit/base/data.py
@@ -0,0 +1,110 @@
+gen_menu_json = """
+{
+  "datasets": {
+    "human": {
+      "HLC": {
+        "Liver mRNA": [
+          [
+            "320",
+            "HLC_0311",
+            "GSE9588 Human Liver Normal (Mar11) Both Sexes"
+          ]
+        ],
+        "Phenotypes": [
+          [
+            "635",
+            "HLCPublish",
+            "HLC Published Phenotypes"
+          ]
+        ]
+      }
+    },
+    "mouse": {
+      "BXD": {
+        "Genotypes": [
+          [
+            "600",
+            "BXDGeno",
+            "BXD Genotypes"
+          ]
+        ],
+        "Hippocampus mRNA": [
+          [
+            "112",
+            "HC_M2_0606_P",
+            "Hippocampus Consortium M430v2 (Jun06) PDNN"
+          ]
+        ],
+        "Phenotypes": [
+          [
+            "602",
+            "BXDPublish",
+            "BXD Published Phenotypes"
+          ]
+        ]
+      }
+    }
+  },
+  "groups": {
+    "human": [
+      [
+        "HLC",
+        "Liver: Normal Gene Expression with Genotypes (Merck)",
+        "Family:None"
+      ]
+    ],
+    "mouse": [
+      [
+        "BXD",
+        "BXD",
+        "Family:None"
+      ]
+    ]
+  },
+  "species": [
+    [
+      "human",
+      "Human"
+    ],
+    [
+      "mouse",
+      "Mouse"
+    ]
+  ],
+  "types": {
+    "human": {
+      "HLC": [
+        [
+          "Phenotypes",
+          "Traits and Cofactors",
+          "Phenotypes"
+        ],
+        [
+          "Liver mRNA",
+          "Liver mRNA",
+          "Molecular Trait Datasets"
+        ]
+      ]
+    },
+    "mouse": {
+      "BXD": [
+        [
+          "Phenotypes",
+          "Traits and Cofactors",
+          "Phenotypes"
+        ],
+        [
+          "Genotypes",
+          "DNA Markers and SNPs",
+          "Genotypes"
+        ],
+        [
+          "Hippocampus mRNA",
+          "Hippocampus mRNA",
+          "Molecular Trait Datasets"
+        ]
+      ]
+    }
+  }
+}
+"""
diff --git a/wqflask/tests/unit/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py
new file mode 100644
index 00000000..96563a16
--- /dev/null
+++ b/wqflask/tests/unit/base/test_data_set.py
@@ -0,0 +1,181 @@
+"""Tests for wqflask/base/data_set.py"""
+
+import unittest
+from unittest import mock
+
+from wqflask import app
+from .data import gen_menu_json
+from base.data_set import DatasetType
+
+
+class TestDataSetTypes(unittest.TestCase):
+    """Tests for the DataSetType class"""
+
+    def setUp(self):
+        self.test_dataset = """
+            {
+                "AD-cases-controls-MyersGeno": "Geno",
+                "AD-cases-controls-MyersPublish": "Publish",
+                "AKXDGeno": "Geno",
+                "AXBXAGeno": "Geno",
+                "AXBXAPublish": "Publish",
+                "Aging-Brain-UCIPublish": "Publish",
+                "All Phenotypes": "Publish",
+                "B139_K_1206_M": "ProbeSet",
+                "B139_K_1206_R": "ProbeSet"
+            }
+            """
+        self.app_context = app.app_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
+    @mock.patch('base.data_set.g')
+    def test_data_set_type(self, db_mock):
+        """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)
+                             ("All Phenotypes"), "Publish")
+            redis_mock.get.assert_called_once_with("dataset_structure")
+
+    @mock.patch('base.data_set.requests.get')
+    def test_data_set_type_with_empty_redis(self, request_mock):
+        """Test that DatasetType returns correctly if the Redis Instance is empty and
+        the name variable exists in the dictionary
+
+        """
+        with app.app_context():
+            request_mock.return_value.content = gen_menu_json
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = None
+            data_set = DatasetType(redis_mock)
+            self.assertEqual(data_set("BXDGeno"), "Geno")
+            self.assertEqual(data_set("BXDPublish"), "Publish")
+            self.assertEqual(data_set("HLC_0311"), "ProbeSet")
+
+            redis_mock.set.assert_called_once_with(
+                "dataset_structure",
+                ('{"HLC_0311": "ProbeSet", '
+                 '"HLCPublish": "Publish", '
+                 '"BXDGeno": "Geno", '
+                 '"HC_M2_0606_P": "ProbeSet", '
+                 '"BXDPublish": "Publish"}'))
+
+    @mock.patch('base.data_set.g')
+    def test_set_dataset_key_mrna(self, db_mock):
+        with app.app_context():
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            data_set = DatasetType(redis_mock)
+            data_set.set_dataset_key("mrna_expr", "Test")
+            self.assertEqual(data_set("Test"), "ProbeSet")
+            redis_mock.set.assert_called_once_with(
+                "dataset_structure",
+                ('{"AD-cases-controls-MyersGeno": "Geno", '
+                 '"AD-cases-controls-MyersPublish": "Publish", '
+                 '"AKXDGeno": "Geno", '
+                 '"AXBXAGeno": "Geno", '
+                 '"AXBXAPublish": "Publish", '
+                 '"Aging-Brain-UCIPublish": "Publish", '
+                 '"All Phenotypes": "Publish", '
+                 '"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\" ")
+            )
+
+    @mock.patch('base.data_set.g')
+    def test_set_dataset_key_pheno(self, db_mock):
+        with app.app_context():
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            data_set = DatasetType(redis_mock)
+            data_set.set_dataset_key("pheno", "Test")
+            self.assertEqual(data_set("Test"), "Publish")
+            redis_mock.set.assert_called_once_with(
+                "dataset_structure",
+                ('{"AD-cases-controls-MyersGeno": "Geno", '
+                 '"AD-cases-controls-MyersPublish": "Publish", '
+                 '"AKXDGeno": "Geno", '
+                 '"AXBXAGeno": "Geno", '
+                 '"AXBXAPublish": "Publish", '
+                 '"Aging-Brain-UCIPublish": "Publish", '
+                 '"All Phenotypes": "Publish", '
+                 '"B139_K_1206_M": "ProbeSet", '
+                 '"B139_K_1206_R": "ProbeSet", '
+                 '"Test": "Publish"}'))
+            db_mock.db.execute.assert_called_with(
+                ("SELECT InfoFiles.GN_AccesionId "
+                 "FROM InfoFiles, PublishFreeze, InbredSet "
+                 "WHERE InbredSet.Name = 'Test' AND "
+                 "PublishFreeze.InbredSetId = InbredSet.Id AND "
+                 "InfoFiles.InfoPageName = PublishFreeze.Name")
+            )
+
+    @mock.patch('base.data_set.g')
+    def test_set_dataset_other_pheno(self, db_mock):
+        with app.app_context():
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            data_set = DatasetType(redis_mock)
+            data_set.set_dataset_key("other_pheno", "Test")
+            self.assertEqual(data_set("Test"), "Publish")
+
+            redis_mock.set.assert_called_once_with(
+                "dataset_structure",
+                ('{"AD-cases-controls-MyersGeno": "Geno", '
+                 '"AD-cases-controls-MyersPublish": "Publish", '
+                 '"AKXDGeno": "Geno", '
+                 '"AXBXAGeno": "Geno", '
+                 '"AXBXAPublish": "Publish", '
+                 '"Aging-Brain-UCIPublish": "Publish", '
+                 '"All Phenotypes": "Publish", '
+                 '"B139_K_1206_M": "ProbeSet", '
+                 '"B139_K_1206_R": "ProbeSet", '
+                 '"Test": "Publish"}'))
+
+            db_mock.db.execute.assert_called_with(
+                ("SELECT PublishFreeze.Name " +
+                 "FROM PublishFreeze, InbredSet " +
+                 "WHERE InbredSet.Name = 'Test' AND "
+                 "PublishFreeze.InbredSetId = InbredSet.Id")
+            )
+
+    @mock.patch('base.data_set.g')
+    def test_set_dataset_geno(self, db_mock):
+        with app.app_context():
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            data_set = DatasetType(redis_mock)
+            data_set.set_dataset_key("geno", "Test")
+            self.assertEqual(data_set("Test"), "Geno")
+            redis_mock.set.assert_called_once_with(
+                "dataset_structure",
+                ('{"AD-cases-controls-MyersGeno": "Geno", '
+                 '"AD-cases-controls-MyersPublish": "Publish", '
+                 '"AKXDGeno": "Geno", '
+                 '"AXBXAGeno": "Geno", '
+                 '"AXBXAPublish": "Publish", '
+                 '"Aging-Brain-UCIPublish": "Publish", '
+                 '"All Phenotypes": "Publish", '
+                 '"B139_K_1206_M": "ProbeSet", '
+                 '"B139_K_1206_R": "ProbeSet", '
+                 '"Test": "Geno"}'))
+
+            db_mock.db.execute.assert_called_with(
+                ("SELECT GenoFreeze.Id FROM "
+                 "GenoFreeze WHERE GenoFreeze.Name = \"Test\" "))
diff --git a/wqflask/tests/unit/base/test_general_object.py b/wqflask/tests/unit/base/test_general_object.py
new file mode 100644
index 00000000..00fd3c72
--- /dev/null
+++ b/wqflask/tests/unit/base/test_general_object.py
@@ -0,0 +1,40 @@
+import unittest
+
+from base.GeneralObject import GeneralObject
+
+
+class TestGeneralObjectTests(unittest.TestCase):
+    """
+    Test the GeneralObject base class
+    """
+
+    def test_object_contents(self):
+        """Test whether base contents are stored properly"""
+        test_obj = GeneralObject("a", "b", "c")
+        self.assertEqual("abc", ''.join(test_obj.contents))
+        self.assertEqual(len(test_obj), 0)
+
+    def test_object_dict(self):
+        """Test whether the base class is printed properly"""
+        test_obj = GeneralObject("a", name="test", value=1)
+        self.assertEqual(str(test_obj), "name = test\nvalue = 1\n")
+        self.assertEqual(
+            repr(test_obj), "contents = ['a']\nname = test\nvalue = 1\n")
+        self.assertEqual(len(test_obj), 2)
+        self.assertEqual(test_obj["value"], 1)
+        test_obj["test"] = 1
+        self.assertEqual(test_obj["test"], 1)
+
+    def test_get_attribute(self):
+        "Test that getattr works"
+        test_obj = GeneralObject("a", name="test", value=1)
+        self.assertEqual(getattr(test_obj, "value", None), 1)
+        self.assertEqual(getattr(test_obj, "non-existent", None), None)
+
+    def test_object_comparisons(self):
+        "Test that 2 objects of the same length are equal"
+        test_obj1 = GeneralObject("a", name="test", value=1)
+        test_obj2 = GeneralObject("b", name="test2", value=2)
+        test_obj3 = GeneralObject("a", name="test", x=1, y=2)
+        self.assertTrue(test_obj1 == test_obj2)
+        self.assertFalse(test_obj1 == test_obj3)
diff --git a/wqflask/tests/unit/base/test_trait.py b/wqflask/tests/unit/base/test_trait.py
new file mode 100644
index 00000000..826ccefd
--- /dev/null
+++ b/wqflask/tests/unit/base/test_trait.py
@@ -0,0 +1,241 @@
+# -*- coding: utf-8 -*-
+"""Tests wqflask/base/trait.py"""
+import unittest
+from unittest import mock
+
+from wqflask import app
+from base.trait import GeneralTrait
+from base.trait import retrieve_trait_info
+
+
+class TestResponse:
+    """Mock Test Response after a request"""
+    @property
+    def content(self):
+        """Mock the content from Requests.get(params).content"""
+        return "[1, 2, 3, 4]"
+
+
+class TestNilResponse:
+    """Mock Test Response after a request"""
+    @property
+    def content(self):
+        """Mock the content from Requests.get(params).content"""
+        return "{}"
+
+
+class MockTrait(GeneralTrait):
+    @property
+    def wikidata_alias_fmt(self):
+        return "Mock alias"
+
+
+class TestRetrieveTraitInfo(unittest.TestCase):
+    """Tests for 'retrieve_trait_info'"""
+
+    def setUp(self):
+        self.app_context = app.app_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
+    def test_retrieve_trait_info_with_empty_dataset(self):
+        """Test that an exception is raised when dataset is empty"""
+        with self.assertRaises(AssertionError):
+            retrieve_trait_info(trait=mock.MagicMock(),
+                                dataset={})
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g', mock.Mock())
+    def test_retrieve_trait_info_with_empty_trait_info(self,
+                                                       requests_mock):
+        """Empty trait info"""
+        requests_mock.return_value = TestNilResponse()
+        with self.assertRaises(KeyError):
+            retrieve_trait_info(trait=mock.MagicMock(),
+                                dataset=mock.MagicMock())
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g', mock.Mock())
+    def test_retrieve_trait_info_with_non_empty_trait_info(self,
+                                                           requests_mock):
+        """Test that attributes are set"""
+        mock_dataset = mock.MagicMock()
+        requests_mock.return_value = TestResponse()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        test_trait = retrieve_trait_info(trait=MockTrait(dataset=mock_dataset),
+                                         dataset=mock_dataset)
+        self.assertEqual(test_trait.a, 1)
+        self.assertEqual(test_trait.b, 2)
+        self.assertEqual(test_trait.c, 3)
+        self.assertEqual(test_trait.d, 4)
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g', mock.Mock())
+    def test_retrieve_trait_info_utf8_parsing(self,
+                                              requests_mock):
+        """Test that utf-8 strings are parsed correctly"""
+        utf_8_string = "test_string"
+        mock_dataset = mock.MagicMock()
+        requests_mock.return_value = TestResponse()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = 'Publish'
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description=utf_8_string
+        )
+        trait_attrs = {
+            "group_code": "test_code",
+            "pre_publication_description": "test_pre_pub",
+            "pre_publication_abbreviation": "ファイルを画面毎に見て行くには、次のコマンドを使います。",
+            "post_publication_description": None,
+            "pubmed_id": None,
+            'year': "2020",
+            "authors": "Jane Doe かいと",
+        }
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset)
+        self.assertEqual(test_trait.abbreviation,
+                         "ファイルを画面毎に見て行くには、次のコマンドを使います。")
+        self.assertEqual(test_trait.authors,
+                         "Jane Doe かいと")
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_non_empty_lrs(self,
+                                                    resource_id_mock,
+                                                    g_mock,
+                                                    requests_mock):
+        """Test retrieve trait info when lrs has a value"""
+        resource_id_mock.return_value = 1
+        g_mock.db.execute.return_value.fetchone = mock.Mock()
+        g_mock.db.execute.return_value.fetchone.side_effect = [
+            [1, 2, 3, 4],  # trait_info = g.db.execute(query).fetchone()
+            [1, 2.37, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [2.7333, 2.1204]  # trait_info = g.db.execute(query).fetchone()
+        ]
+        requests_mock.return_value = None
+
+        mock_dataset = mock.MagicMock()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = "ProbeSet"
+        type(mock_dataset).name = "RandomName"
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description="test_string"
+        )
+        trait_attrs = {
+            "description": "some description",
+            "probe_target_description": "some description",
+            "cellid": False,
+            "chr": 2.733,
+            "mb": 2.1204
+        }
+
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset,
+                                         get_qtl_info=True)
+        self.assertEqual(test_trait.LRS_score_repr,
+                         "2.4")
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_empty_lrs_field(self,
+                                                      resource_id_mock,
+                                                      g_mock,
+                                                      requests_mock):
+        """Test retrieve trait info with empty lrs field"""
+        resource_id_mock.return_value = 1
+        g_mock.db.execute.return_value.fetchone = mock.Mock()
+        g_mock.db.execute.return_value.fetchone.side_effect = [
+            [1, 2, 3, 4],  # trait_info = g.db.execute(query).fetchone()
+            [1, None, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [2, 3]  # trait_info = g.db.execute(query).fetchone()
+        ]
+        requests_mock.return_value = None
+
+        mock_dataset = mock.MagicMock()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = "ProbeSet"
+        type(mock_dataset).name = "RandomName"
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description="test_string"
+        )
+        trait_attrs = {
+            "description": "some description",
+            "probe_target_description": "some description",
+            "cellid": False,
+            "chr": 2.733,
+            "mb": 2.1204
+        }
+
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset,
+                                         get_qtl_info=True)
+        self.assertEqual(test_trait.LRS_score_repr,
+                         "N/A")
+        self.assertEqual(test_trait.LRS_location_repr,
+                         "Chr2: 3.000000")
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_empty_chr_field(self,
+                                                      resource_id_mock,
+                                                      g_mock,
+                                                      requests_mock):
+        """Test retrieve trait info with empty chr field"""
+        resource_id_mock.return_value = 1
+        g_mock.db.execute.return_value.fetchone = mock.Mock()
+        g_mock.db.execute.return_value.fetchone.side_effect = [
+            [1, 2, 3, 4],  # trait_info = g.db.execute(query).fetchone()
+            [1, 2, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [None, 3]  # trait_info = g.db.execute(query).fetchone()
+        ]
+
+        requests_mock.return_value = None
+
+        mock_dataset = mock.MagicMock()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = "ProbeSet"
+        type(mock_dataset).name = "RandomName"
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description="test_string"
+        )
+        trait_attrs = {
+            "description": "some description",
+            "probe_target_description": "some description",
+            "cellid": False,
+            "chr": 2.733,
+            "mb": 2.1204
+        }
+
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset,
+                                         get_qtl_info=True)
+        self.assertEqual(test_trait.LRS_score_repr,
+                         "N/A")
+        self.assertEqual(test_trait.LRS_location_repr,
+                         "N/A")
diff --git a/wqflask/tests/unit/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py
new file mode 100644
index 00000000..8e8ba482
--- /dev/null
+++ b/wqflask/tests/unit/base/test_webqtl_case_data.py
@@ -0,0 +1,39 @@
+"""Tests for wqflask/base/webqtlCaseData.py"""
+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")
+
+    def test_webqtl_case_data_repr(self):
+        self.assertEqual(
+            repr(self.w),
+            "<webqtlCaseData> value=0.000 variance=0.000 ndata=10 name=Test name2=Test2"
+        )
+
+    def test_class_outlier(self):
+        self.assertEqual(self.w.class_outlier, "")
+
+    def test_display_value(self):
+        self.assertEqual(self.w.display_value, "0.000")
+        self.w.value = None
+        self.assertEqual(self.w.display_value, "x")
+
+    def test_display_variance(self):
+        self.assertEqual(self.w.display_variance, "0.000")
+        self.w.variance = None
+        self.assertEqual(self.w.display_variance, "x")
+
+    def test_display_num_cases(self):
+        self.assertEqual(self.w.display_num_cases, "10")
+        self.w.num_cases = None
+        self.assertEqual(self.w.display_num_cases, "x")
diff --git a/wqflask/tests/unit/utility/__init__.py b/wqflask/tests/unit/utility/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/utility/__init__.py
diff --git a/wqflask/tests/unit/utility/test_authentication_tools.py b/wqflask/tests/unit/utility/test_authentication_tools.py
new file mode 100644
index 00000000..5c391be5
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_authentication_tools.py
@@ -0,0 +1,189 @@
+"""Tests for authentication tools"""
+import unittest
+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
+    def content(self):
+        """Mock the content from Requests.get(params).content"""
+        return '["foo"]'
+
+
+class TestUser:
+    """Mock user"""
+    @property
+    def user_id(self):
+        """Mockes user id. Used in Flask.g.user_session.user_id"""
+        return "Jane"
+
+
+class TestUserSession:
+    """Mock user session"""
+    @property
+    def user_session(self):
+        """Mock user session. Mocks Flask.g.user_session object"""
+        return TestUser()
+
+
+def mock_add_resource(resource_ob, update=False):
+    return resource_ob
+
+
+class TestCheckResourceAvailability(unittest.TestCase):
+    """Test methods related to checking the resource availability"""
+    @mock.patch('utility.authentication_tools.add_new_resource')
+    @mock.patch('utility.authentication_tools.Redis')
+    @mock.patch('utility.authentication_tools.g', mock.Mock())
+    @mock.patch('utility.authentication_tools.get_resource_id')
+    def test_check_resource_availability_default_mask(
+            self,
+            resource_id_mock,
+            redis_mock,
+            add_new_resource_mock):
+        """Test the resource availability with default mask"""
+        resource_id_mock.return_value = 1
+        redis_mock.smembers.return_value = []
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Test")
+        add_new_resource_mock.return_value = {"default_mask": 2}
+        self.assertEqual(check_resource_availability(test_dataset), 2)
+
+    @mock.patch('utility.authentication_tools.requests.get')
+    @mock.patch('utility.authentication_tools.add_new_resource')
+    @mock.patch('utility.authentication_tools.Redis')
+    @mock.patch('utility.authentication_tools.g', TestUserSession())
+    @mock.patch('utility.authentication_tools.get_resource_id')
+    def test_check_resource_availability_non_default_mask(
+            self,
+            resource_id_mock,
+            redis_mock,
+            add_new_resource_mock,
+            requests_mock):
+        """Test the resource availability with default mask"""
+        resource_id_mock.return_value = 1
+        redis_mock.smembers.return_value = []
+        add_new_resource_mock.return_value = {"default_mask": 2}
+        requests_mock.return_value = TestResponse()
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Test")
+        self.assertEqual(check_resource_availability(test_dataset),
+                         ['foo'])
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.SUPER_PRIVILEGES',
+                "SUPERUSER")
+    @mock.patch('utility.authentication_tools.requests.get')
+    @mock.patch('utility.authentication_tools.add_new_resource')
+    @mock.patch('utility.authentication_tools.Redis')
+    @mock.patch('utility.authentication_tools.g', TestUserSession())
+    @mock.patch('utility.authentication_tools.get_resource_id')
+    def test_check_resource_availability_of_super_user(
+            self,
+            resource_id_mock,
+            redis_mock,
+            add_new_resource_mock,
+            requests_mock):
+        """Test the resource availability if the user is the super user"""
+        resource_id_mock.return_value = 1
+        redis_mock.smembers.return_value = ["Jane"]
+        add_new_resource_mock.return_value = {"default_mask": 2}
+        requests_mock.return_value = TestResponse()
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Test")
+        self.assertEqual(check_resource_availability(test_dataset),
+                         "SUPERUSER")
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    def test_check_resource_availability_string_dataset(self):
+        """Test the resource availability if the dataset is a string"""
+        self.assertEqual(check_resource_availability("Test"),
+                         "John Doe")
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    def test_check_resource_availability_temp(self):
+        """Test the resource availability if the dataset is a string"""
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Temp")
+        self.assertEqual(check_resource_availability(test_dataset),
+                         "John Doe")
+
+
+class TestAddNewResource(unittest.TestCase):
+    """Test cases for add_new_resource method"""
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('utility.authentication_tools.get_group_code')
+    def test_add_new_resource_if_publish_datatype(self, group_code_mock):
+        """Test add_new_resource if dataset type is 'publish'"""
+        group_code_mock.return_value = "Test"
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Publish")
+        type(test_dataset).id = mock.PropertyMock(return_value=10)
+        expected_value = {
+            "owner_id": "none",
+            "default_mask": "John Doe",
+            "group_masks": {},
+            "name": "Test_None",
+            "data": {
+                "dataset": 10,
+                "trait": None
+            },
+            "type": "dataset-publish"
+        }
+        self.assertEqual(add_new_resource(test_dataset),
+                         expected_value)
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('utility.authentication_tools.get_group_code')
+    def test_add_new_resource_if_geno_datatype(self, group_code_mock):
+        """Test add_new_resource if dataset type is 'geno'"""
+        group_code_mock.return_value = "Test"
+        test_dataset = mock.MagicMock()
+        type(test_dataset).name = mock.PropertyMock(return_value="Geno")
+        type(test_dataset).type = mock.PropertyMock(return_value="Geno")
+        type(test_dataset).id = mock.PropertyMock(return_value=20)
+        expected_value = {
+            "owner_id": "none",
+            "default_mask": "John Doe",
+            "group_masks": {},
+            "name": "Geno",
+            "data": {
+                "dataset": 20,
+            },
+            "type": "dataset-geno"
+        }
+        self.assertEqual(add_new_resource(test_dataset),
+                         expected_value)
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('utility.authentication_tools.get_group_code')
+    def test_add_new_resource_if_other_datatype(self, group_code_mock):
+        """Test add_new_resource if dataset type is not 'geno' or 'publish'"""
+        group_code_mock.return_value = "Test"
+        test_dataset = mock.MagicMock()
+        type(test_dataset).name = mock.PropertyMock(return_value="Geno")
+        type(test_dataset).type = mock.PropertyMock(return_value="other")
+        type(test_dataset).id = mock.PropertyMock(return_value=20)
+        expected_value = {
+            "owner_id": "none",
+            "default_mask": "John Doe",
+            "group_masks": {},
+            "name": "Geno",
+            "data": {
+                "dataset": 20,
+            },
+            "type": "dataset-probeset"
+        }
+        self.assertEqual(add_new_resource(test_dataset),
+                         expected_value)
diff --git a/wqflask/tests/unit/utility/test_chunks.py b/wqflask/tests/unit/utility/test_chunks.py
new file mode 100644
index 00000000..8d90a1ec
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_chunks.py
@@ -0,0 +1,19 @@
+"""Test chunking"""
+
+import unittest
+
+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),
+                         [[1, 2, 7], [3, 22, 8], [5, 22, 333]])
+        self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4),
+                         [[1, 2, 7], [3, 22, 8], [5, 22, 333]])
+        self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5),
+                         [[1, 2], [7, 3], [22, 8], [5, 22], [333]])
+        self.assertEqual(divide_into_chunks([], 5),
+                         [[]])
diff --git a/wqflask/tests/unit/utility/test_corestats.py b/wqflask/tests/unit/utility/test_corestats.py
new file mode 100644
index 00000000..cf91a248
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_corestats.py
@@ -0,0 +1,55 @@
+"""Test Core Stats"""
+
+import unittest
+
+from utility.corestats import Stats
+
+
+class TestChunks(unittest.TestCase):
+    "Test Utility method for chunking"
+
+    def setUp(self):
+        self.stat_test = Stats((x for x in range(1, 11)))
+
+    def test_stats_sum(self):
+        """ Test sequence sum """
+        self.assertEqual(self.stat_test.sum(), 55)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.sum(), None)
+
+    def test_stats_count(self):
+        """ Test sequence count """
+        self.assertEqual(self.stat_test.count(), 10)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.count(), 0)
+
+    def test_stats_min(self):
+        """ Test min value in sequence"""
+        self.assertEqual(self.stat_test.min(), 1)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.min(), None)
+
+    def test_stats_max(self):
+        """ Test max value in sequence """
+        self.assertEqual(self.stat_test.max(), 10)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.max(), None)
+
+    def test_stats_avg(self):
+        """ Test avg of sequence """
+        self.assertEqual(self.stat_test.avg(), 5.5)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.avg(), None)
+
+    def test_stats_stdev(self):
+        """ Test standard deviation of sequence """
+        self.assertEqual(self.stat_test.stdev(), 3.0276503540974917)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.stdev(), None)
+
+    def test_stats_percentile(self):
+        """ Test percentile of sequence """
+        self.assertEqual(self.stat_test.percentile(20), 3.0)
+        self.assertEqual(self.stat_test.percentile(101), None)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.percentile(20), None)
diff --git a/wqflask/tests/unit/utility/test_corr_result_helpers.py b/wqflask/tests/unit/utility/test_corr_result_helpers.py
new file mode 100644
index 00000000..e196fbdf
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_corr_result_helpers.py
@@ -0,0 +1,32 @@
+""" Test correlation helper methods """
+
+import unittest
+from utility.corr_result_helpers import normalize_values, common_keys, normalize_values_with_samples
+
+
+class TestCorrelationHelpers(unittest.TestCase):
+    """Test methods for normalising lists"""
+
+    def test_normalize_values(self):
+        """Test that a list is normalised correctly"""
+        self.assertEqual(
+            normalize_values([2.3, None, None, 3.2, 4.1, 5], [
+                             3.4, 7.2, 1.3, None, 6.2, 4.1]),
+            ([2.3, 4.1, 5], [3.4, 6.2, 4.1], 3)
+        )
+
+    def test_common_keys(self):
+        """Test that common keys are returned as a list"""
+        a = dict(BXD1=9.113, BXD2=9.825, BXD14=8.985, BXD15=9.300)
+        b = dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300)
+        self.assertEqual(sorted(common_keys(a, b)), ['BXD1', 'BXD14'])
+
+    def test_normalize_values_with_samples(self):
+        """Test that a sample(dict) is normalised correctly"""
+        self.assertEqual(
+            normalize_values_with_samples(
+                dict(BXD1=9.113, BXD2=9.825, BXD14=8.985,
+                     BXD15=9.300, BXD20=9.300),
+                dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300)),
+            (({'BXD1': 9.113, 'BXD14': 8.985}, {'BXD1': 9.723, 'BXD14': 9.124}, 2))
+        )
diff --git a/wqflask/tests/unit/utility/test_formatting.py b/wqflask/tests/unit/utility/test_formatting.py
new file mode 100644
index 00000000..9d3033d1
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_formatting.py
@@ -0,0 +1,33 @@
+import unittest
+from utility.formatting import numify, commify
+
+
+class TestFormatting(unittest.TestCase):
+    """Test formatting numbers by numifying or commifying"""
+
+    def test_numify(self):
+        "Test that a number is correctly converted to a English readable string"
+        self.assertEqual(numify(1, 'item', 'items'),
+                         'one item')
+        self.assertEqual(numify(2, 'book'), 'two')
+        self.assertEqual(numify(2, 'book', 'books'), 'two books')
+        self.assertEqual(numify(0, 'book', 'books'), 'zero books')
+        self.assertEqual(numify(0), 'zero')
+        self.assertEqual(numify(5), 'five')
+        self.assertEqual(numify(14, 'book', 'books'), '14 books')
+        self.assertEqual(numify(999, 'book', 'books'), '999 books')
+        self.assertEqual(numify(1000000, 'book', 'books'), '1,000,000 books')
+        self.assertEqual(numify(1956), '1956')
+
+    def test_commify(self):
+        "Test that commas are added correctly"
+        self.assertEqual(commify(1), '1')
+        self.assertEqual(commify(123), '123')
+        self.assertEqual(commify(1234), '1234')
+        self.assertEqual(commify(12345), '12,345')
+        self.assertEqual(commify(1234567890), '1,234,567,890')
+        self.assertEqual(commify(123.0), '123.0')
+        self.assertEqual(commify(1234.5), '1234.5')
+        self.assertEqual(commify(1234.56789), '1234.56789')
+        self.assertEqual(commify(123456.789), '123,456.789')
+        self.assertEqual(commify(None), None)
diff --git a/wqflask/tests/unit/utility/test_hmac.py b/wqflask/tests/unit/utility/test_hmac.py
new file mode 100644
index 00000000..13d6261d
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_hmac.py
@@ -0,0 +1,51 @@
+"""Test hmac utility functions"""
+
+import unittest
+from unittest import mock
+
+from utility.hmac import data_hmac
+from utility.hmac import url_for_hmac
+from utility.hmac import hmac_creation
+
+
+class TestHmacUtil(unittest.TestCase):
+    """Test Utility method for hmac creation"""
+
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    def test_hmac_creation(self):
+        """Test hmac creation with a utf-8 string"""
+        self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946")
+
+    @mock.patch("utility.hmac.app.config",
+                {'SECRET_HMAC_CODE': ('\x08\xdf\xfa\x93N\x80'
+                                      '\xd9\\H@\\\x9f`\x98d^'
+                                      '\xb4a;\xc6OM\x946a\xbc'
+                                      '\xfc\x80:*\xebc')})
+    def test_hmac_creation_with_cookie(self):
+        """Test hmac creation with a cookie"""
+        cookie = "3f4c1dbf-5b56-4260-87d6-f35445bda37e:af4fcf5eace9e7c864ce"
+        uuid_, _, signature = cookie.partition(":")
+        self.assertEqual(
+            hmac_creation(uuid_),
+            "af4fcf5eace9e7c864ce")
+
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    def test_data_hmac(self):
+        """Test data_hmac fn with a utf-8 string"""
+        self.assertEqual(data_hmac("ファイ"), "ファイ:7410466338cfe109e946")
+
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("utility.hmac.url_for")
+    def test_url_for_hmac_with_plain_url(self, mock_url):
+        """Test url_for_hmac without params"""
+        mock_url.return_value = "https://mock_url.com/ファイ/"
+        self.assertEqual(url_for_hmac("ファイ"),
+                         "https://mock_url.com/ファイ/?hm=05bc39e659b1948f41e7")
+
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("utility.hmac.url_for")
+    def test_url_for_hmac_with_param_in_url(self, mock_url):
+        """Test url_for_hmac with params"""
+        mock_url.return_value = "https://mock_url.com/?ファイ=1"
+        self.assertEqual(url_for_hmac("ファイ"),
+                         "https://mock_url.com/?ファイ=1&hm=4709c1708270644aed79")
diff --git a/wqflask/tests/unit/wqflask/__init__.py b/wqflask/tests/unit/wqflask/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/__init__.py
diff --git a/wqflask/tests/unit/wqflask/api/__init__.py b/wqflask/tests/unit/wqflask/api/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/api/__init__.py
diff --git a/wqflask/tests/unit/wqflask/api/test_gen_menu.py b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
new file mode 100644
index 00000000..84898bd1
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
@@ -0,0 +1,413 @@
+"""Test cases for wqflask.api.gen_menu"""
+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
+from wqflask.api.gen_menu import phenotypes_exist
+from wqflask.api.gen_menu import genotypes_exist
+from wqflask.api.gen_menu import build_datasets
+from wqflask.api.gen_menu import build_types
+
+
+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',
+                 'H_T',
+                 'Family:DescriptionA'
+                 ],
+                ['H_T2', "H_T'", 'Family:None']
+            ],
+            'human': [
+                ['BXD', 'BXD', 'Family:None'],
+                ['HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)',
+                 'Family:Test']
+            ]
+        }
+
+        self.test_type = {
+            'mouse': {
+                'H_T2': [('Phenotypes',
+                          'Traits and Cofactors',
+                          'Phenotypes'),
+                         ('Genotypes',
+                          'DNA Markers and SNPs',
+                          'Genotypes'),
+                         ['M', 'M', 'Molecular Trait Datasets']],
+                'H_T1': [('Phenotypes',
+                          'Traits and Cofactors',
+                          'Phenotypes'),
+                         ('Genotypes',
+                          'DNA Markers and SNPs',
+                          'Genotypes'),
+                         ['M', 'M', 'Molecular Trait Datasets']]
+            },
+            'human': {
+                'HLC': [('Phenotypes',
+                         'Traits and Cofactors',
+                         'Phenotypes'),
+                        ('Genotypes',
+                         'DNA Markers and SNPs',
+                         'Genotypes'),
+                        ['M', 'M', 'Molecular Trait Datasets']],
+                'BXD': [('Phenotypes',
+                         'Traits and Cofactors',
+                         'Phenotypes'),
+                        ('Genotypes',
+                         'DNA Markers and SNPs',
+                         'Genotypes'),
+                        ['M', 'M', 'Molecular Trait Datasets']]
+            }
+        }
+
+    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):
+        """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)
+            )
+
+    @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):
+        """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):
+        """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"))
+
+    @mock.patch('wqflask.api.gen_menu.g')
+    def test_genotypes_exist_with_truthy_value(self, db_mock):
+        """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"))
+
+    @mock.patch('wqflask.api.gen_menu.g')
+    def test_build_datasets_with_type_phenotypes(self, db_mock):
+        """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):
+        """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):
+        """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):
+        """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 " +
+            "ORDER BY 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):
+        """Test that correct tissue metadata is returned"""
+        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"
+        )
+
+    @mock.patch('wqflask.api.gen_menu.build_types')
+    @mock.patch('wqflask.api.gen_menu.genotypes_exist')
+    @mock.patch('wqflask.api.gen_menu.phenotypes_exist')
+    def test_get_types_with_existing_genotype_and_phenotypes(
+            self,
+            phenotypes_exist_mock,
+            genotypes_exist_mock,
+            build_types_mock):
+        """Test that build types are constructed correctly if phenotypes and genotypes
+        exist
+
+        """
+        phenotypes_exist_mock.return_value = True
+        genotypes_exist_mock.return_value = True
+
+        expected_result = self.test_type
+
+        build_types_mock.return_value = [
+            ['M', 'M', 'Molecular Trait Datasets']
+        ]
+        self.assertEqual(get_types(self.test_group), expected_result)
+
+    @mock.patch('wqflask.api.gen_menu.build_types')
+    @mock.patch('wqflask.api.gen_menu.genotypes_exist')
+    @mock.patch('wqflask.api.gen_menu.phenotypes_exist')
+    def test_get_types_with_buildtype_and_non_existent_genotype_and_phenotypes(
+            self,
+            phenotypes_exist_mock,
+            genotypes_exist_mock,
+            build_types_mock):
+        """Test that build types are constructed correctly if phenotypes_exist and
+        genotypes_exist are false but build_type is falsy
+
+        """
+        phenotypes_exist_mock.return_value = False
+        genotypes_exist_mock.return_value = False
+
+        build_types_mock.return_value = []
+        self.assertEqual(get_types(self.test_group), {
+            'mouse': {},
+            'human': {}
+        })
+
+    @mock.patch('wqflask.api.gen_menu.build_types')
+    @mock.patch('wqflask.api.gen_menu.genotypes_exist')
+    @mock.patch('wqflask.api.gen_menu.phenotypes_exist')
+    def test_get_types_with_non_existent_genotype_phenotypes_and_buildtype(
+            self,
+            phenotypes_exist_mock,
+            genotypes_exist_mock,
+            build_types_mock):
+        """Test that build types are constructed correctly if phenotypes_exist,
+        genotypes_exist and build_types are truthy
+
+        """
+        phenotypes_exist_mock.return_value = False
+        genotypes_exist_mock.return_value = False
+
+        build_types_mock.return_value = [
+            ['M', 'M', 'Molecular Trait Datasets']
+        ]
+        expected_result = {
+            'mouse': {
+                'H_T2': [['M', 'M', 'Molecular Trait Datasets']],
+                'H_T1': [['M', 'M', 'Molecular Trait Datasets']]},
+            'human': {
+                'HLC': [['M', 'M', 'Molecular Trait Datasets']],
+                'BXD': [['M', 'M', 'Molecular Trait Datasets']]}}
+        self.assertEqual(get_types(self.test_group),
+                         expected_result)
+
+    @mock.patch('wqflask.api.gen_menu.build_datasets')
+    def test_get_datasets_with_existent_datasets(self,
+                                                 build_datasets_mock):
+        """Test correct dataset is returned with existent build_datasets"""
+        build_datasets_mock.return_value = "Test"
+        expected_result = {
+            'mouse': {
+                'H_T2': {'Genotypes': 'Test',
+                         'M': 'Test',
+                         'Phenotypes': 'Test'},
+                'H_T1': {'Genotypes': 'Test',
+                         'M': 'Test',
+                         'Phenotypes': 'Test'}},
+            'human': {'HLC': {'Genotypes': 'Test',
+                              'M': 'Test',
+                              'Phenotypes': 'Test'},
+                      'BXD': {'Genotypes': 'Test',
+                              'M': 'Test',
+                              'Phenotypes': 'Test'}}}
+        self.assertEqual(get_datasets(self.test_type),
+                         expected_result)
+
+    @mock.patch('wqflask.api.gen_menu.build_datasets')
+    def test_get_datasets_with_non_existent_datasets(self,
+                                                     build_datasets_mock):
+        """Test correct dataset is returned with non-existent build_datasets"""
+        build_datasets_mock.return_value = None
+        expected_result = {
+            'mouse': {
+                'H_T2': {},
+                'H_T1': {}},
+            'human': {'HLC': {},
+                      'BXD': {}}}
+        self.assertEqual(get_datasets(self.test_type),
+                         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')
+    def test_gen_dropdown_json(self,
+                               species_mock,
+                               groups_mock,
+                               types_mock,
+                               datasets_mock):
+        "Test that the correct dictionary is constructed properly"
+        species_mock.return_value = ("speciesA speciesB speciesC speciesD"
+                                     .split(" "))
+        datasets_mock.return_value = ("datasetA datasetB datasetC datasetD"
+                                      .split(" "))
+        groups_mock.return_value = ("groupA groupB groupC groupD"
+                                    .split(" "))
+        types_mock.return_value = ("typeA typeB typeC typeD"
+                                   .split(" "))
+        datasets_mock.return_value = ("datasetA datasetB datasetC datasetD"
+                                      .split(" "))
+
+        expected_result = {
+            'datasets': ['datasetA', 'datasetB', 'datasetC', 'datasetD'],
+            'types': ['typeA', 'typeB', 'typeC', 'typeD'],
+            'groups': ['groupA', 'groupB', 'groupC', 'groupD'],
+            'species': ['speciesA', 'speciesB', 'speciesC', 'speciesD']}
+
+        self.assertEqual(gen_dropdown_json(), expected_result)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/__init__.py b/wqflask/tests/unit/wqflask/marker_regression/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/marker_regression/__init__.py
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
new file mode 100644
index 00000000..8ae0f09f
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
@@ -0,0 +1,156 @@
+import unittest
+
+import htmlgen as HT
+from wqflask.marker_regression.display_mapping_results import (
+    DisplayMappingResults,
+    HtmlGenWrapper
+)
+
+
+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,
+                         (245, 211, 211))
+
+
+class TestHtmlGenWrapper(unittest.TestCase):
+    """Test Wrapper around HTMLGen"""
+    def test_create_image(self):
+        """Test HT.Image method"""
+        self.assertEqual(
+            str(HtmlGenWrapper.create_image_tag(src="test.png",
+                                                alt="random",
+                                                border="0",
+                                                width="10",
+                                                height="13",
+                                                usemap="#webqtlmap")),
+            ("""<img alt="random" border="0" height="13" """
+             """src="test.png" usemap="#webqtlmap" """
+             """width="10"/>""")
+        )
+
+    def test_create_form(self):
+        """Test HT.Form method"""
+        test_form = HtmlGenWrapper.create_form_tag(
+            cgi="/testing/",
+            enctype='multipart/form-data',
+            name="formName",
+            submit=HtmlGenWrapper.create_input_tag(type_='hidden', name='Default_Name')
+        )
+        test_image = HtmlGenWrapper.create_image_tag(
+            src="test.png",
+            alt="random",
+            border="0",
+            width="10",
+            height="13",
+            usemap="#webqtlmap"
+        )
+        self.assertEqual(
+            str(test_form).replace("\n", ""),
+            ("""<form action="/testing/" enctype="multipart/form-data" """
+             """method="POST" """
+             """name="formName"><input name="Default_Name" """
+             """type="hidden"/></form>"""))
+        hddn = {
+            'FormID': 'showDatabase',
+            'ProbeSetID': '_',
+            'database': "TestGeno",
+            'CellID': '_',
+            'RISet': "Test",
+            'incparentsf1': 'ON'
+        }
+        for key in hddn.keys():
+            test_form.append(
+                HtmlGenWrapper.create_input_tag(
+                    name=key,
+                    value=hddn[key],
+                    type_='hidden'))
+        test_form.append(test_image)
+
+        self.assertEqual(str(test_form).replace("\n", ""), (
+            """<form action="/testing/" enctype="multipart/form-data" """
+            """method="POST" name="formName">"""
+            """<input name="Default_Name" type="hidden"/>"""
+            """<input name="FormID" type="hidden" value="showDatabase"/>"""
+            """<input name="ProbeSetID" type="hidden" value="_"/>"""
+            """<input name="database" type="hidden" value="TestGeno"/>"""
+            """<input name="CellID" type="hidden" value="_"/>"""
+            """<input name="RISet" type="hidden" value="Test"/>"""
+            """<input name="incparentsf1" type="hidden" value="ON"/>"""
+            """<img alt="random" border="0" height="13" src="test.png" """
+            """usemap="#webqtlmap" width="10"/>"""
+            """</form>"""))
+
+    def test_create_paragraph(self):
+        """Test HT.Paragraph method"""
+        test_p_element = HtmlGenWrapper.create_p_tag(id="smallSize")
+        par_text = (
+            "Mapping using genotype data as "
+            "a trait will result in infinity LRS at one locus. "
+            "In order to display the result properly, all LRSs "
+            "higher than 100 are capped at 100."
+        )
+        self.assertEqual(
+            str(test_p_element),
+            """<p id="smallSize"></p>"""
+        )
+        test_p_element.append(HtmlGenWrapper.create_br_tag())
+        test_p_element.append(par_text)
+        self.assertEqual(
+            str(test_p_element),
+            """<p id="smallSize"><br/>{}</p>""".format(par_text)
+        )
+
+    def test_create_br_tag(self):
+        """Test HT.BR() method"""
+        self.assertEqual(str(HtmlGenWrapper.create_br_tag()),
+                         "<br/>")
+
+    def test_create_input_tag(self):
+        """Test HT.Input method"""
+        self.assertEqual(
+            str(HtmlGenWrapper.create_input_tag(
+                type_="hidden",
+                name="name",
+                value="key",
+                Class="trait trait_")).replace("\n", ""),
+            ("""<input class="trait trait_" name="name" """
+             """type="hidden" value="key"/>"""))
+
+    def test_create_map_tag(self):
+        """Test HT.Map method"""
+        self.assertEqual(str(HtmlGenWrapper.create_map_tag(
+            name="WebqTLImageMap")).replace("\n", ""),
+            """<map name="WebqTLImageMap"></map>""")
+        gifmap = HtmlGenWrapper.create_map_tag(name="test")
+        gifmap.append(HtmlGenWrapper.create_area_tag(shape="rect",
+                                                     coords='1 2 3', href='#area1'))
+        gifmap.append(HtmlGenWrapper.create_area_tag(shape="rect",
+                                                     coords='1 2 3', href='#area2'))
+        self.assertEqual(
+            str(gifmap).replace("\n", ""),
+            ("""<map name="test">"""
+             """<area coords="1 2 3" """
+             """href="#area1" shape="rect"/>"""
+             """<area coords="1 2 3" href="#area2" shape="rect"/>"""
+             """</map>"""))
+
+    def test_create_area_tag(self):
+        """Test HT.Area method"""
+        self.assertEqual(
+            str(HtmlGenWrapper.create_area_tag(
+                shape="rect",
+                coords="1 2",
+                href="http://test.com",
+                title="Some Title")).replace("\n", ""),
+            ("""<area coords="1 2" href="http://test.com" """
+             """shape="rect" title="Some Title"/>"""))
+
+    def test_create_link_tag(self):
+        """Test HT.HREF method"""
+        self.assertEqual(
+            str(HtmlGenWrapper.create_link_tag(
+                "www.test.com", "test", target="_blank")).replace("\n", ""),
+            """<a href="www.test.com" target="_blank">test</a>""")
diff --git a/wqflask/tests/unit/wqflask/show_trait/__init__.py b/wqflask/tests/unit/wqflask/show_trait/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/show_trait/__init__.py
diff --git a/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py b/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py
new file mode 100644
index 00000000..41761944
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py
@@ -0,0 +1,212 @@
+import unittest
+from unittest import mock
+from wqflask.show_trait.export_trait_data import dict_to_sorted_list
+from wqflask.show_trait.export_trait_data import cmp_samples
+from wqflask.show_trait.export_trait_data import export_sample_table
+from wqflask.show_trait.export_trait_data import get_export_metadata
+
+
+class AttributesSetter:
+    def __init__(self, obj):
+        for key, value in obj.items():
+            setattr(self, key, value)
+
+
+class TestExportTraits(unittest.TestCase):
+    """Test methods related to converting dict to sortedlist"""
+    @mock.patch("wqflask.show_trait.export_trait_data.create_trait")
+    @mock.patch("wqflask.show_trait.export_trait_data.data_set")
+    def test_get_export_metadata_no_publish(self, mock_dataset, mock_trait):
+        """test for exporting metadata with no publish"""
+        mock_dataset_attributes = AttributesSetter(
+            {"type": "no_publish", "dataset_name": "Temp", "name": "Temp"})
+
+        mock_nested_attributes = AttributesSetter({"name": "name"})
+        mock_dataset_attributes.group = mock_nested_attributes
+        mock_dataset.create_dataset.return_value = mock_dataset_attributes
+        mock_trait.return_value = AttributesSetter({"symbol": "", "description_display": "Description",
+                                                    "title": "research1", "journal": "", "authors": ""})
+
+        results = get_export_metadata("random_id", "Temp")
+        expected = [["Record ID: random_id"],
+                    ["Trait URL: http://genenetwork.org/show_trait?trait_id=random_id&dataset=Temp"],
+                    ["Dataset: Temp"],
+                    ["Group: name"], []]
+
+        mock_dataset.create_dataset.assert_called_with("Temp")
+        mock_trait.assert_called_with(
+            dataset=mock_dataset_attributes, name="random_id", cellid=None, get_qtl_info=False)
+        self.assertEqual(results, expected)
+
+    @mock.patch("wqflask.show_trait.export_trait_data.create_trait")
+    @mock.patch("wqflask.show_trait.export_trait_data.data_set")
+    def test_get_export_metadata_with_publish(self, data_mock, trait_mock):
+        """test for exporting metadata with dataset.type=Publish"""
+        mock_dataset_attributes = AttributesSetter({"type": "Publish", "dataset_name": "Temp",
+                                                    "name": "Temp", "description_display": "Description goes here"})
+
+        mock_nested_attributes = AttributesSetter({"name": "name"})
+        mock_dataset_attributes.group = mock_nested_attributes
+        data_mock.create_dataset.return_value = mock_dataset_attributes
+        trait_instance = AttributesSetter({"symbol": "", "description_display": "Description",
+                                           "title": "research1", "journal": "", "authors": ""})
+        trait_mock.return_value = trait_instance
+
+        results = get_export_metadata(
+            "29ae0615-0d77-4814-97c7-c9e91f6bfd7b", "Temp")
+
+        expected = [['Phenotype ID: 29ae0615-0d77-4814-97c7-c9e91f6bfd7b'],
+                    ['Phenotype URL: http://genenetwork.org/show_trait?trait_id=29ae0615-0d77-4814-97c7-c9e91f6bfd7b&dataset=Temp'], [
+                        'Group: name'], ['Phenotype: Description'],
+                    ['Authors: N/A'], ['Title: research1'],
+                    ['Journal: N/A'], ['Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=Temp'], []]
+
+        self.assertEqual(results, expected)
+
+    @mock.patch("wqflask.show_trait.export_trait_data.dict_to_sorted_list")
+    @mock.patch("wqflask.show_trait.export_trait_data.get_export_metadata")
+    def test_export_sample_table(self, exp_metadata, dict_list):
+        """test for  exporting sample table"""
+        targs_obj = {
+            "export_data": """{
+                "primary_samples": [
+                    {
+                        "other": "germanotta",
+                        "name": "Sauroniops",
+                        "se":{
+                        "name":"S2"
+                        },
+                        "num_cases":{
+                        "k1":"value"
+
+                        }
+                    }
+                ],
+                "other_samples": [
+                    {
+                        "se": 1,
+                        "num_cases": 4,
+                        "value": 6,
+                        "name": 3
+                    }
+                ]
+            }""",
+            "trait_display_name": "Hair_color",
+            "trait_id": "23177fdc-312e-4084-ad0c-f3eae785fff5",
+            "dataset": {
+            }
+        }
+        exp_metadata.return_value = [
+            ["Phenotype ID:0a2be192-57f5-400b-bbbd-0cf50135995f"], ['Group:gp1'],
+            ["Phenotype:p1"], [
+                "Authors:N/A"],
+            ["Title:research1"],
+            ["Journal:N/A"],
+            ["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=name1"], []]
+        expected = ('Hair_color',
+                    [['Phenotype ID:0a2be192-57f5-400b-bbbd-0cf50135995f'],
+                     ['Group:gp1'],
+                     ['Phenotype:p1'],
+                     ['Authors:N/A'],
+                     ['Title:research1'],
+                     ['Journal:N/A'],
+                     ['Dataset Link: '
+                      'http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=name1'],
+                     [],
+                     ['Name', 'Value', 'SE', 'N'],
+                     ['Sauroniops', 'germanotta'],
+                     [3, 6, 1, 4]])
+
+        dict_list.side_effect = [['Sauroniops', 'germanotta'], [3, 6, 1, 4]]
+
+        self.assertEqual(export_sample_table(targs_obj), expected)
+        exp_metadata.assert_called_with(
+            "23177fdc-312e-4084-ad0c-f3eae785fff5", {})
+        self.assertEqual(dict_list.call_count, 2)
+
+    def test_dict_to_sortedlist(self):
+        """test for conversion of dict to sorted list"""
+        sample1 = {
+            "other": "exp1",
+            "name": "exp2"
+        }
+        sample2 = {
+            "se": 1,
+            "num_cases": 4,
+            "value": 6,
+            "name": 3
+
+        }
+        rever = {
+            "name": 3,
+            "value": 6,
+            "num_cases": 4,
+            "se": 1
+        }
+        oneItem = {
+            "item1": "one"
+        }
+
+        self.assertEqual(["exp2", "exp1"], dict_to_sorted_list(sample1))
+        self.assertEqual([3, 6, 1, 4], dict_to_sorted_list(sample2))
+        self.assertEqual([3, 6, 1, 4], dict_to_sorted_list(rever))
+        self.assertEqual(["one"], dict_to_sorted_list(oneItem))
+        """test that the func returns the values not the keys"""
+        self.assertFalse(["other", "name"] == dict_to_sorted_list(sample1))
+
+    def test_cmp_samples(self):
+        """test for comparing samples function"""
+        sampleA = [
+            [
+                ("value", "other"),
+                ("name", "test_name")
+            ]
+        ]
+        sampleB = [
+            [
+                ("value", "other"),
+                ("unknown", "test_name")
+            ]
+        ]
+        sampleC = [
+            [("other", "value"),
+             ("name", "value")
+             ],
+            [
+                ("name", "value"),
+                ("value", "name")
+            ],
+            [
+                ("other", "value"),
+                ("name", "value"
+                 )],
+            [
+                ("name", "name1"),
+                ("se", "valuex")
+            ],
+            [(
+                "value", "name1"),
+                ("se", "valuex")
+             ],
+            [(
+                "other", "name1"),
+                ("se", "valuex"
+                 )
+             ],
+            [(
+                "name", "name_val"),
+                ("num_cases", "num_val")
+             ],
+            [(
+                "other_a", "val_a"),
+                ("other_b", "val"
+                 )
+             ]
+        ]
+        results = [cmp_samples(val[0], val[1]) for val in sampleA]
+        resultB = [cmp_samples(val[0], val[1]) for val in sampleB]
+        resultC = [cmp_samples(val[0], val[1]) for val in sampleC]
+
+        self.assertEqual(1, *results)
+        self.assertEqual(-1, *resultB)
+        self.assertEqual([1, -1, 1, -1, -1, 1, -1, -1], resultC)
diff --git a/wqflask/tests/unit/wqflask/test_collect.py b/wqflask/tests/unit/wqflask/test_collect.py
new file mode 100644
index 00000000..9a36132d
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/test_collect.py
@@ -0,0 +1,73 @@
+"""Test cases for some methods in collect.py"""
+
+import unittest
+from unittest import mock
+
+from flask import Flask
+from wqflask.collect import process_traits
+
+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
+
+    @property
+    def logged_in(self):
+        return self.is_logged_in
+
+
+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
+
+    @property
+    def user_session(self):
+        if self.is_logged_in:
+            return MockSession(is_logged_in=True)
+        return MockSession()
+
+
+class TestCollect(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.collect.g", MockFlaskG())
+    def test_process_traits_with_bytestring(self):
+        """
+        Test that the correct traits are returned when the user is logged
+        out and bytes are used.
+        """
+        self.assertEqual(process_traits(
+            b'1452452_at:HC_M2_0606_P:163d04f7db7c9e110de6,'
+            b'1452447_at:HC_M2_0606_P:eeece8fceb67072debea,'
+            b'1451401_a_at:HC_M2_0606_P:a043d23b3b3906d8318e,'
+            b'1429252_at:HC_M2_0606_P:6fa378b349bc9180e8f5'),
+            set(['1429252_at:HC_M2_0606_P',
+                 '1451401_a_at:HC_M2_0606_P',
+                 '1452447_at:HC_M2_0606_P',
+                 '1452452_at:HC_M2_0606_P']))
+
+    @mock.patch("wqflask.collect.g", MockFlaskG())
+    def test_process_traits_with_normal_string(self):
+        """
+        Test that the correct traits are returned when the user is logged
+        out and a normal string is used.
+        """
+        self.assertEqual(process_traits(
+            '1452452_at:HC_M2_0606_P:163d04f7db7c9e110de6,'
+            '1452447_at:HC_M2_0606_P:eeece8fceb67072debea,'
+            '1451401_a_at:HC_M2_0606_P:a043d23b3b3906d8318e,'
+            '1429252_at:HC_M2_0606_P:6fa378b349bc9180e8f5'),
+            set(['1429252_at:HC_M2_0606_P',
+                 '1451401_a_at:HC_M2_0606_P',
+                 '1452447_at:HC_M2_0606_P',
+                 '1452452_at:HC_M2_0606_P']))
diff --git a/wqflask/tests/unit/wqflask/test_markdown_routes.py b/wqflask/tests/unit/wqflask/test_markdown_routes.py
new file mode 100644
index 00000000..3adf63e5
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/test_markdown_routes.py
@@ -0,0 +1,58 @@
+"""Test functions in markdown utils"""
+
+import unittest
+from unittest import mock
+
+from wqflask.markdown_routes import render_markdown
+
+
+class MockRequests404:
+    @property
+    def status_code(self):
+        return 404
+
+class MockRequests200:
+    @property
+    def status_code(self):
+        return 200
+
+    @property
+    def content(self):
+        return b"""
+# Glossary
+This is some content
+
+## Sub-heading
+This is another sub-heading
+        """
+
+class TestMarkdownRoutesFunctions(unittest.TestCase):
+    """Test cases for functions in markdown_routes"""
+
+    @mock.patch('wqflask.markdown_routes.requests.get')
+    def test_render_markdown_when_fetching_locally(self, requests_mock):
+        requests_mock.return_value = MockRequests404()
+        markdown_content = render_markdown("glossary.md")
+        requests_mock.assert_called_with(
+            "https://raw.githubusercontent.com"
+            "/genenetwork/genenetwork2/"
+            "wqflask/wqflask/static/"
+            "glossary.md")
+        self.assertRegexpMatches(markdown_content,
+                                 "Glossary of Terms and Features")
+
+    @mock.patch('wqflask.markdown_routes.requests.get')
+    def test_render_markdown_when_fetching_remotely(self, requests_mock):
+        requests_mock.return_value = MockRequests200()
+        markdown_content = render_markdown("glossary.md")
+        requests_mock.assert_called_with(
+            "https://raw.githubusercontent.com"
+            "/genenetwork/genenetwork2/"
+            "wqflask/wqflask/static/"
+            "glossary.md")
+        self.assertEqual("""<h1>Glossary</h1>
+<p>This is some content</p>
+<h2>Sub-heading</h2>
+<p>This is another sub-heading</p>
+""",
+                         markdown_content)
diff --git a/wqflask/tests/unit/wqflask/test_pbkdf2.py b/wqflask/tests/unit/wqflask/test_pbkdf2.py
new file mode 100644
index 00000000..a33fbd4f
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/test_pbkdf2.py
@@ -0,0 +1,61 @@
+"""Test cases pbkdf2"""
+
+import unittest
+from wqflask.pbkdf2 import pbkdf2_hex
+
+
+class TestPbkdf2(unittest.TestCase):
+    def test_pbkdf2_hex(self):
+        """
+        Test pbkdf2_hex function
+        """
+
+        for password, salt, iterations, keylen, expected_value in [
+                ('password', 'salt', 1, 20,
+                 '0c60c80f961f0e71f3a9b524af6012062fe037a6'),
+                ('password', 'salt', 2, 20,
+                 'ea6c014dc72d6f8ccd1ed92ace1d41f0d8de8957'),
+                ('password', 'salt', 4096, 20,
+                 '4b007901b765489abead49d926f721d065a429c1'),
+                ('passwordPASSWORDpassword',
+                 'saltSALTsaltSALTsaltSALTsaltSALTsalt',
+                 4096, 25,
+                 '3d2eec4fe41c849b80c8d83662c0e44a8b291a964cf2f07038'),
+                ('pass\x00word', 'sa\x00lt', 4096, 16,
+                 '56fa6aa75548099dcc37d7f03425e0c3'),
+                ('password', 'ATHENA.MIT.EDUraeburn', 1, 16,
+                 'cdedb5281bb2f801565a1122b2563515'),
+                ('password', 'ATHENA.MIT.EDUraeburn', 1, 32,
+                 ('cdedb5281bb2f80'
+                  '1565a1122b256351'
+                  '50ad1f7a04bb9f3a33'
+                  '3ecc0e2e1f70837')),
+                ('password', 'ATHENA.MIT.EDUraeburn', 2, 16,
+                 '01dbee7f4a9e243e988b62c73cda935d'),
+                ('password', 'ATHENA.MIT.EDUraeburn', 2, 32,
+                 ('01dbee7f4a9e243e9'
+                  '88b62c73cda935da05'
+                  '378b93244ec8f48a99'
+                  'e61ad799d86')),
+                ('password', 'ATHENA.MIT.EDUraeburn', 1200, 32,
+                 ('5c08eb61fdf71e'
+                  '4e4ec3cf6ba1f55'
+                  '12ba7e52ddbc5e51'
+                  '42f708a31e2e62b1e13')),
+                ('X' * 64, 'pass phrase equals block size', 1200, 32,
+                 ('139c30c0966bc32ba'
+                  '55fdbf212530ac9c5'
+                  'ec59f1a452f5cc9ad'
+                  '940fea0598ed1')),
+                ('X' * 65, 'pass phrase exceeds block size', 1200, 32,
+                 ('9ccad6d468770cd'
+                  '51b10e6a68721be6'
+                  '11a8b4d282601db3'
+                  'b36be9246915ec82a'))
+        ]:
+            self.assertEqual(
+                pbkdf2_hex(data=password,
+                           salt=salt,
+                           iterations=iterations,
+                           keylen=keylen),
+                expected_value)
diff --git a/wqflask/tests/unit/wqflask/test_user_login.py b/wqflask/tests/unit/wqflask/test_user_login.py
new file mode 100644
index 00000000..61cd9ab9
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/test_user_login.py
@@ -0,0 +1,21 @@
+"""Test cases for some methods in login.py"""
+
+import unittest
+from wqflask.user_login import encode_password
+
+
+class TestUserLogin(unittest.TestCase):
+    def test_encode_password(self):
+        """
+        Test encode password
+        """
+        pass_gen_fields = {
+            "salt": "salt",
+            "hashfunc": "sha1",
+            "iterations": 4096,
+            "keylength": 20,
+        }
+        self.assertEqual(
+            encode_password(pass_gen_fields,
+                            "password").get("password"),
+            '4b007901b765489abead49d926f721d065a429c1')
diff --git a/wqflask/tests/unit/wqflask/test_user_session.py b/wqflask/tests/unit/wqflask/test_user_session.py
new file mode 100644
index 00000000..ebb0334a
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/test_user_session.py
@@ -0,0 +1,15 @@
+"""Test cases for some methods in user_session.py"""
+
+import unittest
+from wqflask.user_session import verify_cookie
+
+
+class TestUserSession(unittest.TestCase):
+    def test_verify_cookie(self):
+        """
+        Test cookie verification
+        """
+        self.assertEqual(
+            "3f4c1dbf-5b56-4260-87d6-f35445bda37e",
+            verify_cookie(("3f4c1dbf-5b56-4260-87d6-"
+                           "f35445bda37e:af4fcf5eace9e7c864ce")))