diff options
Diffstat (limited to 'wqflask/tests/base')
| -rw-r--r-- | wqflask/tests/base/test_data_set.py | 10 | ||||
| -rw-r--r-- | wqflask/tests/base/test_trait.py | 235 |
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") |