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

3 files changed, 77 insertions, 29 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 = [