Merge pull request #422 from BonfaceKilz/build/python3-migration

Build/python3 migration

10 files changed, 237 insertions, 84 deletions

diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py
index dd7f5051..96563a16 100644
--- a/wqflask/tests/base/test_data_set.py
+++ b/wqflask/tests/base/test_data_set.py
@@ -1,10 +1,10 @@
 """Tests for wqflask/base/data_set.py"""
 
 import unittest
-import mock
+from unittest import mock
 
 from wqflask import app
-from data import gen_menu_json
+from .data import gen_menu_json
 from base.data_set import DatasetType
 
 
@@ -59,9 +59,14 @@ class TestDataSetTypes(unittest.TestCase):
             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",
-                '{"BXDGeno": "Geno", "BXDPublish": "Publish", "HLCPublish": "Publish", "HLC_0311": "ProbeSet", "HC_M2_0606_P": "ProbeSet"}')
+                ('{"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):
@@ -74,8 +79,17 @@ class TestDataSetTypes(unittest.TestCase):
             self.assertEqual(data_set("Test"), "ProbeSet")
             redis_mock.set.assert_called_once_with(
                 "dataset_structure",
-                '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "ProbeSet", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
-            expected_db_call = """"""
+                ('{"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\" ")
@@ -92,12 +106,21 @@ class TestDataSetTypes(unittest.TestCase):
             self.assertEqual(data_set("Test"), "Publish")
             redis_mock.set.assert_called_once_with(
                 "dataset_structure",
-                '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
+                ('{"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 " +
+                ("SELECT InfoFiles.GN_AccesionId "
+                 "FROM InfoFiles, PublishFreeze, InbredSet "
                  "WHERE InbredSet.Name = 'Test' AND "
-                 "PublishFreeze.InbredSetId = InbredSet.Id AND " +
+                 "PublishFreeze.InbredSetId = InbredSet.Id AND "
                  "InfoFiles.InfoPageName = PublishFreeze.Name")
             )
 
@@ -110,9 +133,20 @@ class TestDataSetTypes(unittest.TestCase):
             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",
-                '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
+                ('{"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 " +
@@ -131,8 +165,17 @@ class TestDataSetTypes(unittest.TestCase):
             self.assertEqual(data_set("Test"), "Geno")
             redis_mock.set.assert_called_once_with(
                 "dataset_structure",
-                '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Geno", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
-            expected_db_call = """"""
+                ('{"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\" ")
-            )
+                ("SELECT GenoFreeze.Id FROM "
+                 "GenoFreeze WHERE GenoFreeze.Name = \"Test\" "))
diff --git a/wqflask/tests/base/test_general_object.py b/wqflask/tests/base/test_general_object.py
index c7701021..00fd3c72 100644
--- a/wqflask/tests/base/test_general_object.py
+++ b/wqflask/tests/base/test_general_object.py
@@ -17,9 +17,9 @@ class TestGeneralObjectTests(unittest.TestCase):
     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), "value = 1\nname = test\n")
+        self.assertEqual(str(test_obj), "name = test\nvalue = 1\n")
         self.assertEqual(
-            repr(test_obj), "value = 1\nname = test\ncontents = ['a']\n")
+            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
@@ -36,6 +36,5 @@ class TestGeneralObjectTests(unittest.TestCase):
         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 )
-
+        self.assertTrue(test_obj1 == test_obj2)
+        self.assertFalse(test_obj1 == test_obj3)
diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py
index 1a3820f2..826ccefd 100644
--- a/wqflask/tests/base/test_trait.py
+++ b/wqflask/tests/base/test_trait.py
@@ -1,8 +1,9 @@
 # -*- coding: utf-8 -*-
 """Tests wqflask/base/trait.py"""
 import unittest
-import mock
+from unittest import mock
 
+from wqflask import app
 from base.trait import GeneralTrait
 from base.trait import retrieve_trait_info
 
@@ -31,6 +32,14 @@ class MockTrait(GeneralTrait):
 
 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):
@@ -38,9 +47,8 @@ class TestRetrieveTraitInfo(unittest.TestCase):
                                 dataset={})
 
     @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.g', mock.Mock())
     def test_retrieve_trait_info_with_empty_trait_info(self,
-                                                       g_mock,
                                                        requests_mock):
         """Empty trait info"""
         requests_mock.return_value = TestNilResponse()
@@ -49,9 +57,8 @@ class TestRetrieveTraitInfo(unittest.TestCase):
                                 dataset=mock.MagicMock())
 
     @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.g', mock.Mock())
     def test_retrieve_trait_info_with_non_empty_trait_info(self,
-                                                           g_mock,
                                                            requests_mock):
         """Test that attributes are set"""
         mock_dataset = mock.MagicMock()
@@ -66,9 +73,8 @@ class TestRetrieveTraitInfo(unittest.TestCase):
         self.assertEqual(test_trait.d, 4)
 
     @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.g', mock.Mock())
     def test_retrieve_trait_info_utf8_parsing(self,
-                                              g_mock,
                                               requests_mock):
         """Test that utf-8 strings are parsed correctly"""
         utf_8_string = "test_string"
@@ -96,9 +102,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
         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。".decode('utf-8'))
+                         "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".decode('utf-8'))
+                         "Jane Doe かいと")
 
     @mock.patch('base.trait.requests.get')
     @mock.patch('base.trait.g')
@@ -107,7 +113,7 @@ class TestRetrieveTraitInfo(unittest.TestCase):
                                                     resource_id_mock,
                                                     g_mock,
                                                     requests_mock):
-        """Test """
+        """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 = [
diff --git a/wqflask/tests/utility/test_authentication_tools.py b/wqflask/tests/utility/test_authentication_tools.py
index 99c74245..5c391be5 100644
--- a/wqflask/tests/utility/test_authentication_tools.py
+++ b/wqflask/tests/utility/test_authentication_tools.py
@@ -1,6 +1,6 @@
 """Tests for authentication tools"""
 import unittest
-import mock
+from unittest import mock
 
 from utility.authentication_tools import check_resource_availability
 from utility.authentication_tools import add_new_resource
@@ -38,17 +38,15 @@ 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.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,
-            g_mock,
             redis_mock,
             add_new_resource_mock):
         """Test the resource availability with default mask"""
         resource_id_mock.return_value = 1
-        g_mock.return_value = mock.Mock()
         redis_mock.smembers.return_value = []
         test_dataset = mock.MagicMock()
         type(test_dataset).type = mock.PropertyMock(return_value="Test")
@@ -58,18 +56,16 @@ class TestCheckResourceAvailability(unittest.TestCase):
     @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')
+    @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,
-            g_mock,
             redis_mock,
             add_new_resource_mock,
             requests_mock):
         """Test the resource availability with default mask"""
         resource_id_mock.return_value = 1
-        g_mock.return_value = mock.Mock()
         redis_mock.smembers.return_value = []
         add_new_resource_mock.return_value = {"default_mask": 2}
         requests_mock.return_value = TestResponse()
diff --git a/wqflask/tests/utility/test_hmac.py b/wqflask/tests/utility/test_hmac.py
index 16b50771..7c61c0a6 100644
--- a/wqflask/tests/utility/test_hmac.py
+++ b/wqflask/tests/utility/test_hmac.py
@@ -2,7 +2,7 @@
 """Test hmac utility functions"""
 
 import unittest
-import mock
+from unittest import mock
 
 from utility.hmac import data_hmac
 from utility.hmac import url_for_hmac
diff --git a/wqflask/tests/wqflask/api/test_gen_menu.py b/wqflask/tests/wqflask/api/test_gen_menu.py
index 239484aa..84898bd1 100644
--- a/wqflask/tests/wqflask/api/test_gen_menu.py
+++ b/wqflask/tests/wqflask/api/test_gen_menu.py
@@ -1,7 +1,8 @@
 """Test cases for wqflask.api.gen_menu"""
 import unittest
-import mock
+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
@@ -17,6 +18,8 @@ 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',
@@ -67,6 +70,9 @@ 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
diff --git a/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py
index 6f791df1..8ae0f09f 100644
--- a/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py
+++ b/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py
@@ -1,6 +1,6 @@
 import unittest
 
-from htmlgen import HTMLgen2 as HT
+import htmlgen as HT
 from wqflask.marker_regression.display_mapping_results import (
     DisplayMappingResults,
     HtmlGenWrapper
@@ -26,9 +26,9 @@ class TestHtmlGenWrapper(unittest.TestCase):
                                                 width="10",
                                                 height="13",
                                                 usemap="#webqtlmap")),
-            ("""<IMG src="test.png" height="13" width="10" """
-             """alt="random" border="0" """
-             """usemap="#webqtlmap">""")
+            ("""<img alt="random" border="0" height="13" """
+             """src="test.png" usemap="#webqtlmap" """
+             """width="10"/>""")
         )
 
     def test_create_form(self):
@@ -37,7 +37,7 @@ class TestHtmlGenWrapper(unittest.TestCase):
             cgi="/testing/",
             enctype='multipart/form-data',
             name="formName",
-            submit=HT.Input(type='hidden')
+            submit=HtmlGenWrapper.create_input_tag(type_='hidden', name='Default_Name')
         )
         test_image = HtmlGenWrapper.create_image_tag(
             src="test.png",
@@ -49,10 +49,10 @@ class TestHtmlGenWrapper(unittest.TestCase):
         )
         self.assertEqual(
             str(test_form).replace("\n", ""),
-            ("""<FORM METHOD="POST" ACTION="/testing/" """
-             """ENCTYPE="multipart/form-data" """
-             """NAME="formName"><INPUT TYPE="hidden" """
-             """NAME="Default_Name"></FORM>"""))
+            ("""<form action="/testing/" enctype="multipart/form-data" """
+             """method="POST" """
+             """name="formName"><input name="Default_Name" """
+             """type="hidden"/></form>"""))
         hddn = {
             'FormID': 'showDatabase',
             'ProbeSetID': '_',
@@ -62,21 +62,26 @@ class TestHtmlGenWrapper(unittest.TestCase):
             'incparentsf1': 'ON'
         }
         for key in hddn.keys():
-            test_form.append(HT.Input(name=key, value=hddn[key],
-                                      type='hidden'))
+            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 METHOD="POST" ACTION="/testing/" """
-            """ENCTYPE="multipart/form-data" NAME="formName">"""
-            """<INPUT TYPE="hidden" NAME="database" VALUE="TestGeno">"""
-            """<INPUT TYPE="hidden" NAME="incparentsf1" VALUE="ON">"""
-            """<INPUT TYPE="hidden" NAME="FormID" VALUE="showDatabase">"""
-            """<INPUT TYPE="hidden" NAME="ProbeSetID" VALUE="_">"""
-            """<INPUT TYPE="hidden" NAME="RISet" VALUE="Test">"""
-            """<INPUT TYPE="hidden" NAME="CellID" VALUE="_">"""
-            """<IMG src="test.png" height="13" width="10" alt="random" """
-            """border="0" usemap="#webqtlmap">"""
-            """<INPUT TYPE="hidden" NAME="Default_Name"></FORM>"""))
+            """<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"""
@@ -89,48 +94,48 @@ class TestHtmlGenWrapper(unittest.TestCase):
         )
         self.assertEqual(
             str(test_p_element),
-            """<P id="smallSize"></P>"""
+            """<p id="smallSize"></p>"""
         )
-        test_p_element.append(HT.BR())
+        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)
+            """<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>")
+                         "<br/>")
 
     def test_create_input_tag(self):
         """Test HT.Input method"""
         self.assertEqual(
             str(HtmlGenWrapper.create_input_tag(
-                type="hidden",
+                type_="hidden",
                 name="name",
                 value="key",
                 Class="trait trait_")).replace("\n", ""),
-            ("""<INPUT TYPE="hidden" NAME="name" """
-             """class="trait trait_" VALUE="key">"""))
+            ("""<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(areas=[])
-        gifmap.areas.append(HT.Area(shape="rect",
-                                    coords='1 2 3', href='#area1'))
-        gifmap.areas.append(HT.Area(shape="rect",
-                                    coords='1 2 3', href='#area2'))
+            """<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="">"""
-             """<AREA coords="1 2 3" """
-             """href="#area1" shape="rect">"""
-             """<AREA coords="1 2 3" href="#area2" shape="rect">"""
-             """</MAP>"""))
+            ("""<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"""
@@ -140,12 +145,12 @@ class TestHtmlGenWrapper(unittest.TestCase):
                 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">"""))
+            ("""<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>""")
+            """<a href="www.test.com" target="_blank">test</a>""")
diff --git a/wqflask/tests/wqflask/test_collect.py b/wqflask/tests/wqflask/test_collect.py
index 6b8d7931..9a36132d 100644
--- a/wqflask/tests/wqflask/test_collect.py
+++ b/wqflask/tests/wqflask/test_collect.py
@@ -1,7 +1,7 @@
 """Test cases for some methods in collect.py"""
 
 import unittest
-import mock
+from unittest import mock
 
 from flask import Flask
 from wqflask.collect import process_traits
@@ -41,10 +41,10 @@ class TestCollect(unittest.TestCase):
         self.app_context.pop()
 
     @mock.patch("wqflask.collect.g", MockFlaskG())
-    def test_process_traits_when_user_is_logged_out(self):
+    def test_process_traits_with_bytestring(self):
         """
         Test that the correct traits are returned when the user is logged
-        out
+        out and bytes are used.
         """
         self.assertEqual(process_traits(
             b'1452452_at:HC_M2_0606_P:163d04f7db7c9e110de6,'
@@ -55,3 +55,19 @@ class TestCollect(unittest.TestCase):
                  '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/wqflask/test_pbkdf2.py b/wqflask/tests/wqflask/test_pbkdf2.py
new file mode 100644
index 00000000..a33fbd4f
--- /dev/null
+++ b/wqflask/tests/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/wqflask/test_user_login.py b/wqflask/tests/wqflask/test_user_login.py
new file mode 100644
index 00000000..61cd9ab9
--- /dev/null
+++ b/wqflask/tests/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')