"""Tests for wqflask/base/data_set.py""" import unittest from unittest import mock from wqflask import app from base.data_set import DatasetType 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" ] ] } } } """ 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() def test_data_set_type(self): """Test that DatasetType returns correctly if the Redis Instance is not empty and the name variable exists in the dictionary """ with app.app_context(): 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.datasettype.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"}')) @unittest.skip("Too complicated") @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_once_with( ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze " + "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(): 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") ) @unittest.skip("Too complicated") @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") ) @unittest.skip("Too complicated") @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\" "))