Replace "g.db" mocks with "database_connection" mocks

* wqflask/tests/unit/base/test_trait.py: Delete "wqflask.app" import.
(TestRetrieveTraitInfo.setUp): Delete it.
(TestRetrieveTraitInfo.tearDown): Ditto.
(TestRetrieveTraitInfo.test_retrieve_trait_info_with_empty_dataset):
Replace "g" mock with "database_connection" mock.
(test_retrieve_trait_info_with_empty_trait_info): Ditto.
(test_retrieve_trait_info_with_non_empty_trait_info): Ditto.
(test_retrieve_trait_info_utf8_parsing): Ditto.
* wqflask/tests/wqflask/show_trait/test_show_trait.py (TestTraits):
(test_get_nearest_marker): Ditto.
(test_get_nearest_marker_empty_db): Ditto.

2 files changed, 56 insertions, 40 deletions

diff --git a/wqflask/tests/unit/base/test_trait.py b/wqflask/tests/unit/base/test_trait.py
index 71fe0a44..e8c01ca9 100644
--- a/wqflask/tests/unit/base/test_trait.py
+++ b/wqflask/tests/unit/base/test_trait.py
@@ -3,7 +3,6 @@
 import unittest
 from unittest import mock
 
-from wqflask import app
 from base.trait import GeneralTrait
 from base.trait import retrieve_trait_info
 
@@ -32,25 +31,24 @@ 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):
+    @mock.patch('base.trait.database_connection')
+    def test_retrieve_trait_info_with_empty_dataset(self, mock_db):
         """Test that an exception is raised when dataset is empty"""
-        with self.assertRaises(AssertionError):
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
+        with self.assertRaises(ValueError):
             retrieve_trait_info(trait=mock.MagicMock(),
                                 dataset={})
 
     @mock.patch('base.trait.requests.get')
     @mock.patch('base.trait.g', mock.Mock())
+    @mock.patch('base.trait.database_connection')
     def test_retrieve_trait_info_with_empty_trait_info(self,
+                                                       mock_db,
                                                        requests_mock):
         """Empty trait info"""
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
         requests_mock.return_value = TestNilResponse()
         with self.assertRaises(KeyError):
             retrieve_trait_info(trait=mock.MagicMock(),
@@ -58,10 +56,14 @@ class TestRetrieveTraitInfo(unittest.TestCase):
 
     @mock.patch('base.trait.requests.get')
     @mock.patch('base.trait.g', mock.Mock())
+    @mock.patch('base.trait.database_connection')
     def test_retrieve_trait_info_with_non_empty_trait_info(self,
+                                                           mock_db,
                                                            requests_mock):
         """Test that attributes are set"""
         mock_dataset = mock.MagicMock()
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
         requests_mock.return_value = TestResponse()
         type(mock_dataset).display_fields = mock.PropertyMock(
             return_value=["a", "b", "c", "d"])
@@ -74,10 +76,14 @@ class TestRetrieveTraitInfo(unittest.TestCase):
 
     @mock.patch('base.trait.requests.get')
     @mock.patch('base.trait.g', mock.Mock())
+    @mock.patch('base.trait.database_connection')
     def test_retrieve_trait_info_utf8_parsing(self,
+                                              mock_db,
                                               requests_mock):
         """Test that utf-8 strings are parsed correctly"""
         utf_8_string = "test_string"
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
         mock_dataset = mock.MagicMock()
         requests_mock.return_value = TestResponse()
         type(mock_dataset).display_fields = mock.PropertyMock(
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index 5f4598f5..6a6b1587 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -143,39 +143,49 @@ class TestTraits(unittest.TestCase):
         self.assertEqual(results, "this is a descriptionN/A")
         self.assertEqual(results_no_unit, "Value")
 
-    @mock.patch("wqflask.show_trait.show_trait.g")
+    @mock.patch("wqflask.show_trait.show_trait.database_connection")
     def test_get_nearest_marker(self, mock_db):
         """test for getting nearest marker with non-empty db"""
-
-        mock_db.db.execute.return_value.fetchall.return_value = [
-            ["Geno1", "Geno2"], ["Geno3"]]
-
-        trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"})
-        group_name = TraitObject({"name": "group_name"})
-        this_db = TraitObject({"group": group_name})
-        results_with_item_db = get_nearest_marker(trait, this_db)
-        called_with_value = """SELECT Geno.Name
-               FROM Geno, GenoXRef, GenoFreeze
-               WHERE Geno.Chr = 'test_chr' AND
-                     GenoXRef.GenoId = Geno.Id AND
-                     GenoFreeze.Id = GenoXRef.GenoFreezeId AND
-                     GenoFreeze.Name = 'group_nameGeno'
-               ORDER BY ABS( Geno.Mb - test_mb) LIMIT 1"""
-
-        mock_db.db.execute.assert_called_with(called_with_value)
-
-        self.assertEqual(results_with_item_db, "Geno1")
-
-    @mock.patch("wqflask.show_trait.show_trait.g")
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
+        with conn.cursor() as cursor:
+            cursor.fetchall.return_value = [
+                ["Geno1", "Geno2"], ["Geno3"]]
+
+            trait = TraitObject({
+                "locus_chr": "test_chr",
+                "locus_mb": "test_mb"
+            })
+            group_name = TraitObject({"name": "group_name"})
+            this_db = TraitObject({"group": group_name})
+            results_with_item_db = get_nearest_marker(trait, this_db)
+            cursor.execute.assert_called_with(
+                "SELECT Geno.Name FROM Geno, GenoXRef, "
+                "GenoFreeze WHERE Geno.Chr = %s "
+                "AND GenoXRef.GenoId = Geno.Id AND "
+                "GenoFreeze.Id = GenoXRef.GenoFreezeId "
+                "AND GenoFreeze.Name = %s "
+                "ORDER BY ABS( Geno.Mb - %s) LIMIT 1",
+                ('test_chr', 'group_nameGeno', 'test_mb'))
+
+            self.assertEqual(results_with_item_db, "Geno1")
+
+    @mock.patch("wqflask.show_trait.show_trait.database_connection")
     def test_get_nearest_marker_empty_db(self, mock_db):
         """test for getting nearest marker with empty db"""
-        mock_db.db.execute.return_value.fetchall.return_value = []
-        trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"})
-        group_name = TraitObject({"name": "group_name"})
-        this_db = TraitObject({"group": group_name})
-        results_empty_db = get_nearest_marker(trait, this_db)
-        mock_db.db.execute.assert_called_once()
-        self.assertEqual(results_empty_db, "")
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
+        with conn.cursor() as cursor:
+            cursor.fetchall.return_value = []
+            trait = TraitObject({
+                "locus_chr": "test_chr",
+                "locus_mb": "test_mb"
+            })
+            group_name = TraitObject({"name": "group_name"})
+            this_db = TraitObject({"group": group_name})
+            results_empty_db = get_nearest_marker(trait, this_db)
+            cursor.execute.assert_called_once()
+            self.assertEqual(results_empty_db, "")
 
     @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
     def test_get_genotype_scales_with_genofile_is_list(self, mock_get_scales):