From d63e7554d6dfce4e80c2570667a0fa371235beb7 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 27 Jul 2020 14:31:31 +0300 Subject: Apply py-lint * wqflask/tests/base/test_data_set.py: Apply pylint --- wqflask/tests/base/test_data_set.py | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) (limited to 'wqflask/tests/base') diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py index 44a54c7e..74799e49 100644 --- a/wqflask/tests/base/test_data_set.py +++ b/wqflask/tests/base/test_data_set.py @@ -1,3 +1,5 @@ +"""Tests for wqflask/base/data_set.py""" + import unittest import mock @@ -5,8 +7,10 @@ from wqflask import app from base.data_set import DatasetType - + class TestDataSetTypes(unittest.TestCase): + """Tests for the DataSetType class""" + def setUp(self): self.app_context = app.app_context() self.app_context.push() @@ -16,10 +20,14 @@ class TestDataSetTypes(unittest.TestCase): @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() - r = mock.Mock() - r.get.return_value = """ + redis_mock = mock.Mock() + redis_mock.get.return_value = """ { "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", @@ -32,4 +40,6 @@ class TestDataSetTypes(unittest.TestCase): "B139_K_1206_R": "ProbeSet" } """ - self.assertEqual(DatasetType(r)("All Phenotypes"), "Publish") + self.assertEqual(DatasetType(redis_mock) + ("All Phenotypes"), "Publish") + -- cgit v1.2.3 From 5cad720187b3c53b6d64c64d45be4bc020eed52d Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 27 Jul 2020 14:32:26 +0300 Subject: Add test case for empty redis instance for DatasetType * wqflask/tests/base/test_data_set.py(tests): Check correct results are returned when Redis is empty * wqflask/tests/base/data.py(tests): New file. Adds json test data. --- wqflask/tests/base/data.py | 110 ++++++++++++++++++++++++++++++++++++ wqflask/tests/base/test_data_set.py | 16 +++++- 2 files changed, 125 insertions(+), 1 deletion(-) create mode 100644 wqflask/tests/base/data.py (limited to 'wqflask/tests/base') 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 74799e49..835d786a 100644 --- a/wqflask/tests/base/test_data_set.py +++ b/wqflask/tests/base/test_data_set.py @@ -4,7 +4,7 @@ import unittest import mock from wqflask import app - +from data import gen_menu_json from base.data_set import DatasetType @@ -43,3 +43,17 @@ class TestDataSetTypes(unittest.TestCase): self.assertEqual(DatasetType(redis_mock) ("All Phenotypes"), "Publish") + @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") -- cgit v1.2.3 From 957e05d33eb423df99181a99e7c25891810a21f7 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 27 Jul 2020 15:06:02 +0300 Subject: Check that Redis is called correctly * wqflask/tests/base/test_data_set.py: assert that `set` and `get` are called correctly --- wqflask/tests/base/test_data_set.py | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'wqflask/tests/base') diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py index 835d786a..3ac1b6d6 100644 --- a/wqflask/tests/base/test_data_set.py +++ b/wqflask/tests/base/test_data_set.py @@ -42,6 +42,7 @@ class TestDataSetTypes(unittest.TestCase): """ 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): @@ -57,3 +58,6 @@ class TestDataSetTypes(unittest.TestCase): 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"}') -- cgit v1.2.3 From 79b8cf45c1c40b9c20278762b6e8f587a2820b43 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 27 Jul 2020 19:10:36 +0300 Subject: Test that non-existent keys in Dataset are set correctly * wqflask/tests/base/test_data_set.py: Add more tests. --- wqflask/tests/base/test_data_set.py | 103 +++++++++++++++++++++++++++++++----- 1 file changed, 90 insertions(+), 13 deletions(-) (limited to 'wqflask/tests/base') diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py index 3ac1b6d6..94780a5d 100644 --- a/wqflask/tests/base/test_data_set.py +++ b/wqflask/tests/base/test_data_set.py @@ -12,6 +12,19 @@ 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() @@ -27,19 +40,7 @@ class TestDataSetTypes(unittest.TestCase): with app.app_context(): db_mock.get = mock.Mock() redis_mock = mock.Mock() - redis_mock.get.return_value = """ - { - "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" - } - """ + 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") @@ -61,3 +62,79 @@ class TestDataSetTypes(unittest.TestCase): 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\" ") + ) -- cgit v1.2.3 From 7732204662bf395eb8ed55b6d26fd208998c1067 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 27 Jul 2020 19:48:16 +0300 Subject: Add unittests for WebqtlCaseData * wqflask/tests/base/test_webqtl_case_data.py: Add it --- wqflask/tests/base/test_webqtl_case_data.py | 39 +++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 wqflask/tests/base/test_webqtl_case_data.py (limited to 'wqflask/tests/base') 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), + " 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") -- cgit v1.2.3