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

6 files changed, 611 insertions, 0 deletions

diff --git a/wqflask/tests/unit/base/__init__.py b/wqflask/tests/unit/base/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/base/__init__.py
diff --git a/wqflask/tests/unit/base/data.py b/wqflask/tests/unit/base/data.py
new file mode 100644
index 00000000..06a5a989
--- /dev/null
+++ b/wqflask/tests/unit/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/unit/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py
new file mode 100644
index 00000000..96563a16
--- /dev/null
+++ b/wqflask/tests/unit/base/test_data_set.py
@@ -0,0 +1,181 @@
+"""Tests for wqflask/base/data_set.py"""
+
+import unittest
+from unittest import mock
+
+from wqflask import app
+from .data import gen_menu_json
+from base.data_set import DatasetType
+
+
+class TestDataSetTypes(unittest.TestCase):
+    """Tests for the DataSetType class"""
+
+    def setUp(self):
+        self.test_dataset = """
+            {
+                "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"
+            }
+            """
+        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",
+                ('{"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):
+        with app.app_context():
+            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)
+            data_set.set_dataset_key("mrna_expr", "Test")
+            self.assertEqual(data_set("Test"), "ProbeSet")
+            redis_mock.set.assert_called_once_with(
+                "dataset_structure",
+                ('{"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\" ")
+            )
+
+    @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.fetchone.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",
+                ('{"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 "
+                 "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.fetchone.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",
+                ('{"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 " +
+                 "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.fetchone.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",
+                ('{"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\" "))
diff --git a/wqflask/tests/unit/base/test_general_object.py b/wqflask/tests/unit/base/test_general_object.py
new file mode 100644
index 00000000..00fd3c72
--- /dev/null
+++ b/wqflask/tests/unit/base/test_general_object.py
@@ -0,0 +1,40 @@
+import unittest
+
+from base.GeneralObject import GeneralObject
+
+
+class TestGeneralObjectTests(unittest.TestCase):
+    """
+    Test the GeneralObject base class
+    """
+
+    def test_object_contents(self):
+        """Test whether base contents are stored properly"""
+        test_obj = GeneralObject("a", "b", "c")
+        self.assertEqual("abc", ''.join(test_obj.contents))
+        self.assertEqual(len(test_obj), 0)
+
+    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), "name = test\nvalue = 1\n")
+        self.assertEqual(
+            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
+        self.assertEqual(test_obj["test"], 1)
+
+    def test_get_attribute(self):
+        "Test that getattr works"
+        test_obj = GeneralObject("a", name="test", value=1)
+        self.assertEqual(getattr(test_obj, "value", None), 1)
+        self.assertEqual(getattr(test_obj, "non-existent", None), None)
+
+    def test_object_comparisons(self):
+        "Test that 2 objects of the same length are equal"
+        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)
diff --git a/wqflask/tests/unit/base/test_trait.py b/wqflask/tests/unit/base/test_trait.py
new file mode 100644
index 00000000..826ccefd
--- /dev/null
+++ b/wqflask/tests/unit/base/test_trait.py
@@ -0,0 +1,241 @@
+# -*- coding: utf-8 -*-
+"""Tests wqflask/base/trait.py"""
+import unittest
+from unittest import mock
+
+from wqflask import app
+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 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):
+            retrieve_trait_info(trait=mock.MagicMock(),
+                                dataset={})
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g', mock.Mock())
+    def test_retrieve_trait_info_with_empty_trait_info(self,
+                                                       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', mock.Mock())
+    def test_retrieve_trait_info_with_non_empty_trait_info(self,
+                                                           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', mock.Mock())
+    def test_retrieve_trait_info_utf8_parsing(self,
+                                              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。")
+        self.assertEqual(test_trait.authors,
+                         "Jane Doe かいと")
+
+    @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 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")
+
+    @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")
diff --git a/wqflask/tests/unit/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py
new file mode 100644
index 00000000..8e8ba482
--- /dev/null
+++ b/wqflask/tests/unit/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")