Merge branch 'testing' into scroller_testing

2 files changed, 239 insertions, 6 deletions

diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py
index 94780a5d..dd7f5051 100644
--- a/wqflask/tests/base/test_data_set.py
+++ b/wqflask/tests/base/test_data_set.py
@@ -66,7 +66,7 @@ class TestDataSetTypes(unittest.TestCase):
     @mock.patch('base.data_set.g')
     def test_set_dataset_key_mrna(self, db_mock):
         with app.app_context():
-            db_mock.db.execute.return_value = [1, 2, 3]
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
             redis_mock = mock.Mock()
             redis_mock.get.return_value = self.test_dataset
             data_set = DatasetType(redis_mock)
@@ -84,7 +84,7 @@ class TestDataSetTypes(unittest.TestCase):
     @mock.patch('base.data_set.g')
     def test_set_dataset_key_pheno(self, db_mock):
         with app.app_context():
-            db_mock.db.execute.return_value = [1, 2, 3]
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
             redis_mock = mock.Mock()
             redis_mock.get.return_value = self.test_dataset
             data_set = DatasetType(redis_mock)
@@ -93,7 +93,6 @@ class TestDataSetTypes(unittest.TestCase):
             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 = """"""
             db_mock.db.execute.assert_called_with(
                 ("SELECT InfoFiles.GN_AccesionId " +
                  "FROM InfoFiles, PublishFreeze, InbredSet " +
@@ -105,7 +104,7 @@ class TestDataSetTypes(unittest.TestCase):
     @mock.patch('base.data_set.g')
     def test_set_dataset_other_pheno(self, db_mock):
         with app.app_context():
-            db_mock.db.execute.return_value = [1, 2, 3]
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
             redis_mock = mock.Mock()
             redis_mock.get.return_value = self.test_dataset
             data_set = DatasetType(redis_mock)
@@ -114,7 +113,6 @@ class TestDataSetTypes(unittest.TestCase):
             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 = """"""
             db_mock.db.execute.assert_called_with(
                 ("SELECT PublishFreeze.Name " +
                  "FROM PublishFreeze, InbredSet " +
@@ -125,7 +123,7 @@ class TestDataSetTypes(unittest.TestCase):
     @mock.patch('base.data_set.g')
     def test_set_dataset_geno(self, db_mock):
         with app.app_context():
-            db_mock.db.execute.return_value = [1, 2, 3]
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
             redis_mock = mock.Mock()
             redis_mock.get.return_value = self.test_dataset
             data_set = DatasetType(redis_mock)
diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py
new file mode 100644
index 00000000..1a3820f2
--- /dev/null
+++ b/wqflask/tests/base/test_trait.py
@@ -0,0 +1,235 @@
+# -*- coding: utf-8 -*-
+"""Tests wqflask/base/trait.py"""
+import unittest
+import mock
+
+from base.trait import GeneralTrait
+from base.trait import retrieve_trait_info
+
+
+class TestResponse:
+    """Mock Test Response after a request"""
+    @property
+    def content(self):
+        """Mock the content from Requests.get(params).content"""
+        return "[1, 2, 3, 4]"
+
+
+class TestNilResponse:
+    """Mock Test Response after a request"""
+    @property
+    def content(self):
+        """Mock the content from Requests.get(params).content"""
+        return "{}"
+
+
+class MockTrait(GeneralTrait):
+    @property
+    def wikidata_alias_fmt(self):
+        return "Mock alias"
+
+
+class TestRetrieveTraitInfo(unittest.TestCase):
+    """Tests for 'retrieve_trait_info'"""
+    def test_retrieve_trait_info_with_empty_dataset(self):
+        """Test that an exception is raised when dataset is empty"""
+        with self.assertRaises(AssertionError):
+            retrieve_trait_info(trait=mock.MagicMock(),
+                                dataset={})
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    def test_retrieve_trait_info_with_empty_trait_info(self,
+                                                       g_mock,
+                                                       requests_mock):
+        """Empty trait info"""
+        requests_mock.return_value = TestNilResponse()
+        with self.assertRaises(KeyError):
+            retrieve_trait_info(trait=mock.MagicMock(),
+                                dataset=mock.MagicMock())
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    def test_retrieve_trait_info_with_non_empty_trait_info(self,
+                                                           g_mock,
+                                                           requests_mock):
+        """Test that attributes are set"""
+        mock_dataset = mock.MagicMock()
+        requests_mock.return_value = TestResponse()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        test_trait = retrieve_trait_info(trait=MockTrait(dataset=mock_dataset),
+                                         dataset=mock_dataset)
+        self.assertEqual(test_trait.a, 1)
+        self.assertEqual(test_trait.b, 2)
+        self.assertEqual(test_trait.c, 3)
+        self.assertEqual(test_trait.d, 4)
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    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"
+        mock_dataset = mock.MagicMock()
+        requests_mock.return_value = TestResponse()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = 'Publish'
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description=utf_8_string
+        )
+        trait_attrs = {
+            "group_code": "test_code",
+            "pre_publication_description": "test_pre_pub",
+            "pre_publication_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。",
+            "post_publication_description": None,
+            "pubmed_id": None,
+            'year': "2020",
+            "authors": "Jane Doe かいと",
+        }
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        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'))
+        self.assertEqual(test_trait.authors,
+                         "Jane Doe かいと".decode('utf-8'))
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_non_empty_lrs(self,
+                                                    resource_id_mock,
+                                                    g_mock,
+                                                    requests_mock):
+        """Test """
+        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")
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_empty_lrs_field(self,
+                                                      resource_id_mock,
+                                                      g_mock,
+                                                      requests_mock):
+        """Test retrieve trait info with empty lrs field"""
+        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, None, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [2, 3]  # 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,
+                         "N/A")
+        self.assertEqual(test_trait.LRS_location_repr,
+                         "Chr2: 3.000000")
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_empty_chr_field(self,
+                                                      resource_id_mock,
+                                                      g_mock,
+                                                      requests_mock):
+        """Test retrieve trait info with empty chr field"""
+        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, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [None, 3]  # 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,
+                         "N/A")
+        self.assertEqual(test_trait.LRS_location_repr,
+                         "N/A")