Merge remote-tracking branch 'origin/testing' into feature/add_rqtl_pairscan

3 files changed, 51 insertions, 37 deletions

diff --git a/wqflask/tests/unit/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py
index 66ad361d..505449a5 100644
--- a/wqflask/tests/unit/base/test_data_set.py
+++ b/wqflask/tests/unit/base/test_data_set.py
@@ -66,6 +66,7 @@ class TestDataSetTypes(unittest.TestCase):
                  '"HC_M2_0606_P": "ProbeSet", '
                  '"BXDPublish": "Publish"}'))
 
+    @unittest.skip("Too complicated")
     @mock.patch('base.data_set.g')
     def test_set_dataset_key_mrna(self, db_mock):
         with app.app_context():
@@ -92,6 +93,7 @@ class TestDataSetTypes(unittest.TestCase):
                  + "WHERE ProbeSetFreeze.Name = \"Test\" ")
             )
 
+    @unittest.skip("Too complicated")
     @mock.patch('base.data_set.g')
     def test_set_dataset_key_pheno(self, db_mock):
         with app.app_context():
@@ -121,6 +123,7 @@ class TestDataSetTypes(unittest.TestCase):
                  "InfoFiles.InfoPageName = PublishFreeze.Name")
             )
 
+    @unittest.skip("Too complicated")
     @mock.patch('base.data_set.g')
     def test_set_dataset_other_pheno(self, db_mock):
         with app.app_context():
@@ -151,6 +154,7 @@ class TestDataSetTypes(unittest.TestCase):
                  "PublishFreeze.InbredSetId = InbredSet.Id")
             )
 
+    @unittest.skip("Too complicated")
     @mock.patch('base.data_set.g')
     def test_set_dataset_geno(self, db_mock):
         with app.app_context():
diff --git a/wqflask/tests/unit/base/test_species.py b/wqflask/tests/unit/base/test_species.py
index 9b5c023c..87f89607 100644
--- a/wqflask/tests/unit/base/test_species.py
+++ b/wqflask/tests/unit/base/test_species.py
@@ -60,6 +60,7 @@ class TestIndChromosome(unittest.TestCase):
         self.assertEqual(test_ind_chromosome.mb_length, 10)
 
 
+@unittest.skip("Too complicated")
 class TestChromosomes(unittest.TestCase):
     """Tests for Chromosomes class"""
     maxDiff = None
diff --git a/wqflask/tests/unit/base/test_trait.py b/wqflask/tests/unit/base/test_trait.py
index 826ccefd..71fe0a44 100644
--- a/wqflask/tests/unit/base/test_trait.py
+++ b/wqflask/tests/unit/base/test_trait.py
@@ -106,49 +106,57 @@ class TestRetrieveTraitInfo(unittest.TestCase):
         self.assertEqual(test_trait.authors,
                          "Jane Doe かいと")
 
+
+    @unittest.skip("Too complicated")
     @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.database_connection')
     @mock.patch('base.trait.get_resource_id')
     def test_retrieve_trait_info_with_non_empty_lrs(self,
                                                     resource_id_mock,
-                                                    g_mock,
+                                                    mock_db,
                                                     requests_mock):
         """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 = [
-            [1, 2, 3, 4],  # trait_info = g.db.execute(query).fetchone()
-            [1, 2.37, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
-            [2.7333, 2.1204]  # trait_info = g.db.execute(query).fetchone()
-        ]
-        requests_mock.return_value = None
-
-        mock_dataset = mock.MagicMock()
-        type(mock_dataset).display_fields = mock.PropertyMock(
-            return_value=["a", "b", "c", "d"])
-        type(mock_dataset).type = "ProbeSet"
-        type(mock_dataset).name = "RandomName"
-
-        mock_trait = MockTrait(
-            dataset=mock_dataset,
-            pre_publication_description="test_string"
-        )
-        trait_attrs = {
-            "description": "some description",
-            "probe_target_description": "some description",
-            "cellid": False,
-            "chr": 2.733,
-            "mb": 2.1204
-        }
-
-        for key, val in list(trait_attrs.items()):
-            setattr(mock_trait, key, val)
-        test_trait = retrieve_trait_info(trait=mock_trait,
-                                         dataset=mock_dataset,
-                                         get_qtl_info=True)
-        self.assertEqual(test_trait.LRS_score_repr,
-                         "2.4")
-
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
+        with conn.cursor() as cursor:
+            cursor.fetchone.side_effect = [
+                # trait_info = g.db.execute(query).fetchone()
+                [1, 2, 3, 4],
+                # trait_qtl = g.db.execute(query).fetchone()
+                [1, 2.37, 3, 4, 5],
+                # trait_info = g.db.execute(query).fetchone()
+                [2.7333, 2.1204]
+            ]
+            requests_mock.return_value = None
+
+            mock_dataset = mock.MagicMock()
+            type(mock_dataset).display_fields = mock.PropertyMock(
+                return_value=["a", "b", "c", "d"])
+            type(mock_dataset).type = "ProbeSet"
+            type(mock_dataset).name = "RandomName"
+
+            mock_trait = MockTrait(
+                dataset=mock_dataset,
+                pre_publication_description="test_string"
+            )
+            trait_attrs = {
+                "description": "some description",
+                "probe_target_description": "some description",
+                "cellid": False,
+                "chr": 2.733,
+                "mb": 2.1204
+            }
+
+            for key, val in list(trait_attrs.items()):
+                setattr(mock_trait, key, val)
+            test_trait = retrieve_trait_info(trait=mock_trait,
+                                             dataset=mock_dataset,
+                                             get_qtl_info=True)
+            self.assertEqual(test_trait.LRS_score_repr,
+                             "2.4")
+
+    @unittest.skip("Too complicated")
     @mock.patch('base.trait.requests.get')
     @mock.patch('base.trait.g')
     @mock.patch('base.trait.get_resource_id')
@@ -193,7 +201,8 @@ class TestRetrieveTraitInfo(unittest.TestCase):
                          "N/A")
         self.assertEqual(test_trait.LRS_location_repr,
                          "Chr2: 3.000000")
-
+        
+    @unittest.skip("Too complicated")
     @mock.patch('base.trait.requests.get')
     @mock.patch('base.trait.g')
     @mock.patch('base.trait.get_resource_id')