Merge branch 'build/python3-migration' of github.com:BonfaceKilz/genenetwork2 into build/python3-migration

7 files changed, 126 insertions, 80 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..60ebaee0 100644
--- a/wqflask/tests/base/test_trait.py
+++ b/wqflask/tests/base/test_trait.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 """Tests wqflask/base/trait.py"""
 import unittest
-import mock
+from unittest import mock
 
 from base.trait import GeneralTrait
 from base.trait import retrieve_trait_info
@@ -38,9 +38,8 @@ 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 +48,8 @@ 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 +64,8 @@ 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 +93,9 @@ 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')
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>""")