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

3 files changed, 269 insertions, 15 deletions

diff --git a/wqflask/tests/base/data.py b/wqflask/tests/base/data.py
new file mode 100644
index 00000000..06a5a989
--- /dev/null
+++ b/wqflask/tests/base/data.py
@@ -0,0 +1,110 @@
+gen_menu_json = """
+{
+  "datasets": {
+    "human": {
+      "HLC": {
+        "Liver mRNA": [
+          [
+            "320",
+            "HLC_0311",
+            "GSE9588 Human Liver Normal (Mar11) Both Sexes"
+          ]
+        ],
+        "Phenotypes": [
+          [
+            "635",
+            "HLCPublish",
+            "HLC Published Phenotypes"
+          ]
+        ]
+      }
+    },
+    "mouse": {
+      "BXD": {
+        "Genotypes": [
+          [
+            "600",
+            "BXDGeno",
+            "BXD Genotypes"
+          ]
+        ],
+        "Hippocampus mRNA": [
+          [
+            "112",
+            "HC_M2_0606_P",
+            "Hippocampus Consortium M430v2 (Jun06) PDNN"
+          ]
+        ],
+        "Phenotypes": [
+          [
+            "602",
+            "BXDPublish",
+            "BXD Published Phenotypes"
+          ]
+        ]
+      }
+    }
+  },
+  "groups": {
+    "human": [
+      [
+        "HLC",
+        "Liver: Normal Gene Expression with Genotypes (Merck)",
+        "Family:None"
+      ]
+    ],
+    "mouse": [
+      [
+        "BXD",
+        "BXD",
+        "Family:None"
+      ]
+    ]
+  },
+  "species": [
+    [
+      "human",
+      "Human"
+    ],
+    [
+      "mouse",
+      "Mouse"
+    ]
+  ],
+  "types": {
+    "human": {
+      "HLC": [
+        [
+          "Phenotypes",
+          "Traits and Cofactors",
+          "Phenotypes"
+        ],
+        [
+          "Liver mRNA",
+          "Liver mRNA",
+          "Molecular Trait Datasets"
+        ]
+      ]
+    },
+    "mouse": {
+      "BXD": [
+        [
+          "Phenotypes",
+          "Traits and Cofactors",
+          "Phenotypes"
+        ],
+        [
+          "Genotypes",
+          "DNA Markers and SNPs",
+          "Genotypes"
+        ],
+        [
+          "Hippocampus mRNA",
+          "Hippocampus mRNA",
+          "Molecular Trait Datasets"
+        ]
+      ]
+    }
+  }
+}
+"""
diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py
index 44a54c7e..94780a5d 100644
--- a/wqflask/tests/base/test_data_set.py
+++ b/wqflask/tests/base/test_data_set.py
@@ -1,25 +1,18 @@
+"""Tests for wqflask/base/data_set.py"""
+
 import unittest
 import mock
 
 from wqflask import app
-
+from data import gen_menu_json
 from base.data_set import DatasetType
 
-    
-class TestDataSetTypes(unittest.TestCase):
-    def setUp(self):
-        self.app_context = app.app_context()
-        self.app_context.push()
 
-    def tearDown(self):
-        self.app_context.pop()
+class TestDataSetTypes(unittest.TestCase):
+    """Tests for the DataSetType class"""
 
-    @mock.patch('base.data_set.g')
-    def test_data_set_type(self, db_mock):
-        with app.app_context():
-            db_mock.get = mock.Mock()
-            r = mock.Mock()
-            r.get.return_value = """
+    def setUp(self):
+        self.test_dataset = """
             {
                 "AD-cases-controls-MyersGeno": "Geno",
                 "AD-cases-controls-MyersPublish": "Publish",
@@ -32,4 +25,116 @@ class TestDataSetTypes(unittest.TestCase):
                 "B139_K_1206_R": "ProbeSet"
             }
             """
-            self.assertEqual(DatasetType(r)("All Phenotypes"), "Publish")
+        self.app_context = app.app_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
+    @mock.patch('base.data_set.g')
+    def test_data_set_type(self, db_mock):
+        """Test that DatasetType returns correctly if the Redis Instance is not empty
+        and the name variable exists in the dictionary
+
+        """
+        with app.app_context():
+            db_mock.get = mock.Mock()
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            self.assertEqual(DatasetType(redis_mock)
+                             ("All Phenotypes"), "Publish")
+            redis_mock.get.assert_called_once_with("dataset_structure")
+
+    @mock.patch('base.data_set.requests.get')
+    def test_data_set_type_with_empty_redis(self, request_mock):
+        """Test that DatasetType returns correctly if the Redis Instance is empty and
+        the name variable exists in the dictionary
+
+        """
+        with app.app_context():
+            request_mock.return_value.content = gen_menu_json
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = None
+            data_set = DatasetType(redis_mock)
+            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"}')
+
+    @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]
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            data_set = DatasetType(redis_mock)
+            data_set.set_dataset_key("mrna_expr", "Test")
+            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 = """"""
+            db_mock.db.execute.assert_called_with(
+                ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze " +
+                 "WHERE ProbeSetFreeze.Name = \"Test\" ")
+            )
+
+    @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]
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            data_set = DatasetType(redis_mock)
+            data_set.set_dataset_key("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 = """"""
+            db_mock.db.execute.assert_called_with(
+                ("SELECT InfoFiles.GN_AccesionId " +
+                 "FROM InfoFiles, PublishFreeze, InbredSet " +
+                 "WHERE InbredSet.Name = 'Test' AND "
+                 "PublishFreeze.InbredSetId = InbredSet.Id AND " +
+                 "InfoFiles.InfoPageName = PublishFreeze.Name")
+            )
+
+    @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]
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            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 = """"""
+            db_mock.db.execute.assert_called_with(
+                ("SELECT PublishFreeze.Name " +
+                 "FROM PublishFreeze, InbredSet " +
+                 "WHERE InbredSet.Name = 'Test' AND "
+                 "PublishFreeze.InbredSetId = InbredSet.Id")
+            )
+
+    @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]
+            redis_mock = mock.Mock()
+            redis_mock.get.return_value = self.test_dataset
+            data_set = DatasetType(redis_mock)
+            data_set.set_dataset_key("geno", "Test")
+            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 = """"""
+            db_mock.db.execute.assert_called_with(
+                ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE GenoFreeze.Name = \"Test\" ")
+            )
diff --git a/wqflask/tests/base/test_webqtl_case_data.py b/wqflask/tests/base/test_webqtl_case_data.py
new file mode 100644
index 00000000..8e8ba482
--- /dev/null
+++ b/wqflask/tests/base/test_webqtl_case_data.py
@@ -0,0 +1,39 @@
+"""Tests for wqflask/base/webqtlCaseData.py"""
+import unittest
+
+from wqflask import app  # Required because of utility.tools in webqtlCaseData.py
+from base.webqtlCaseData import webqtlCaseData
+
+class TestWebqtlCaseData(unittest.TestCase):
+    """Tests for WebqtlCaseData class"""
+
+    def setUp(self):
+        self.w = webqtlCaseData(name="Test",
+                           value=0,
+                           variance=0.0,
+                           num_cases=10,
+                           name2="Test2")
+
+    def test_webqtl_case_data_repr(self):
+        self.assertEqual(
+            repr(self.w),
+            "<webqtlCaseData> value=0.000 variance=0.000 ndata=10 name=Test name2=Test2"
+        )
+
+    def test_class_outlier(self):
+        self.assertEqual(self.w.class_outlier, "")
+
+    def test_display_value(self):
+        self.assertEqual(self.w.display_value, "0.000")
+        self.w.value = None
+        self.assertEqual(self.w.display_value, "x")
+
+    def test_display_variance(self):
+        self.assertEqual(self.w.display_variance, "0.000")
+        self.w.variance = None
+        self.assertEqual(self.w.display_variance, "x")
+
+    def test_display_num_cases(self):
+        self.assertEqual(self.w.display_num_cases, "10")
+        self.w.num_cases = None
+        self.assertEqual(self.w.display_num_cases, "x")