Fix failing tests

3 files changed, 66 insertions, 20 deletions

diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py
index 94780a5d..e6000e56 100644
--- a/wqflask/tests/base/test_data_set.py
+++ b/wqflask/tests/base/test_data_set.py
@@ -4,7 +4,7 @@ import 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\" ")
@@ -92,13 +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"}')
-            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": "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")
             )
 
@@ -111,10 +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"}')
-            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": "Publish"}'))
+
             db_mock.db.execute.assert_called_with(
                 ("SELECT PublishFreeze.Name " +
                  "FROM PublishFreeze, InbredSet " +
@@ -133,8 +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/wqflask/api/test_gen_menu.py b/wqflask/tests/wqflask/api/test_gen_menu.py
index 239484aa..bf41054d 100644
--- a/wqflask/tests/wqflask/api/test_gen_menu.py
+++ b/wqflask/tests/wqflask/api/test_gen_menu.py
@@ -2,6 +2,7 @@
 import 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