From 77d026e042a3eac9e3de4177ee374a37f2e24127 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 15 Sep 2020 20:53:11 +0300 Subject: Fix failing tests * wqflask/tests/base/test_data_set.py: Update failing tests introduced by the change in 301bdd2f4. --- wqflask/tests/base/test_data_set.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) (limited to 'wqflask/tests') 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) -- cgit v1.2.3 From 6e776e94bdc2cea9923d70ff836ce1c02a1e1af9 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 15 Sep 2020 23:19:30 +0300 Subject: Add tests for authentication tools Catches bugs in: - https://github.com/genenetwork/genenetwork2/pull/422/commits/70dbeeb5832711ed5271434e482c18bc7ea095b8 * wqflask/tests/utility/test_authentication_tools.py: New file. Add tests for "check_resource_availability". --- wqflask/tests/utility/test_authentication_tools.py | 113 +++++++++++++++++++++ 1 file changed, 113 insertions(+) create mode 100644 wqflask/tests/utility/test_authentication_tools.py (limited to 'wqflask/tests') diff --git a/wqflask/tests/utility/test_authentication_tools.py b/wqflask/tests/utility/test_authentication_tools.py new file mode 100644 index 00000000..59c53879 --- /dev/null +++ b/wqflask/tests/utility/test_authentication_tools.py @@ -0,0 +1,113 @@ +"""Tests for authentication tools""" +import unittest +import mock + +from utility.authentication_tools import check_resource_availability + + +class TestResponse: + """Mock Test Response after a request""" + @property + def content(self): + """Mock the content from Requests.get(params).content""" + return '["foo"]' + + +class TestUser: + """Mock user""" + @property + def user_id(self): + """Mockes user id. Used in Flask.g.user_session.user_id""" + return "Jane" + + +class TestUserSession: + """Mock user session""" + @property + def user_session(self): + """Mock user session. Mocks Flask.g.user_session object""" + return TestUser() + + +class TestCheckResourceAvailability(unittest.TestCase): + """Test methods related to checking the resource availability""" + @mock.patch('utility.authentication_tools.add_new_resource') + @mock.patch('utility.authentication_tools.Redis') + @mock.patch('utility.authentication_tools.g') + @mock.patch('utility.authentication_tools.get_resource_id') + def test_check_resource_availability_default_mask( + self, + resource_id_mock, + g_mock, + redis_mock, + add_new_resource_mock): + """Test the resource availability with default mask""" + resource_id_mock.return_value = 1 + g_mock.return_value = mock.Mock() + redis_mock.smembers.return_value = [] + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Test") + add_new_resource_mock.return_value = {"default_mask": 2} + self.assertEqual(check_resource_availability(test_dataset), 2) + + @mock.patch('utility.authentication_tools.requests.get') + @mock.patch('utility.authentication_tools.add_new_resource') + @mock.patch('utility.authentication_tools.Redis') + @mock.patch('utility.authentication_tools.g') + @mock.patch('utility.authentication_tools.get_resource_id') + def test_check_resource_availability_non_default_mask( + self, + resource_id_mock, + g_mock, + redis_mock, + add_new_resource_mock, + requests_mock): + """Test the resource availability with default mask""" + resource_id_mock.return_value = 1 + g_mock.return_value = mock.Mock() + redis_mock.smembers.return_value = [] + add_new_resource_mock.return_value = {"default_mask": 2} + requests_mock.return_value = TestResponse() + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Test") + self.assertEqual(check_resource_availability(test_dataset), + ['foo']) + + @mock.patch('utility.authentication_tools.webqtlConfig.SUPER_PRIVILEGES', + "SUPERUSER") + @mock.patch('utility.authentication_tools.requests.get') + @mock.patch('utility.authentication_tools.add_new_resource') + @mock.patch('utility.authentication_tools.Redis') + @mock.patch('utility.authentication_tools.g', TestUserSession()) + @mock.patch('utility.authentication_tools.get_resource_id') + def test_check_resource_availability_of_super_user( + self, + resource_id_mock, + redis_mock, + add_new_resource_mock, + requests_mock): + """Test the resource availability if the user is the super user""" + resource_id_mock.return_value = 1 + redis_mock.smembers.return_value = ["Jane"] + add_new_resource_mock.return_value = {"default_mask": 2} + requests_mock.return_value = TestResponse() + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Test") + self.assertEqual(check_resource_availability(test_dataset), + "SUPERUSER") + + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + def test_check_resource_availability_string_dataset(self): + """Test the resource availability if the dataset is a string""" + self.assertEqual(check_resource_availability("Test"), + "John Doe") + + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + def test_check_resource_availability_temp(self): + """Test the resource availability if the dataset is a string""" + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Temp") + self.assertEqual(check_resource_availability(test_dataset), + "John Doe") -- cgit v1.2.3 From cad9d0e4c913eba5ae3c74912b59051885833f90 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 16 Sep 2020 00:03:28 +0300 Subject: Add tests for "add_new_resource" method * wqflask/tests/utility/test_authentication_tools.py: Add them. --- wqflask/tests/utility/test_authentication_tools.py | 80 ++++++++++++++++++++++ 1 file changed, 80 insertions(+) (limited to 'wqflask/tests') diff --git a/wqflask/tests/utility/test_authentication_tools.py b/wqflask/tests/utility/test_authentication_tools.py index 59c53879..99c74245 100644 --- a/wqflask/tests/utility/test_authentication_tools.py +++ b/wqflask/tests/utility/test_authentication_tools.py @@ -3,6 +3,7 @@ import unittest import mock from utility.authentication_tools import check_resource_availability +from utility.authentication_tools import add_new_resource class TestResponse: @@ -29,6 +30,10 @@ class TestUserSession: return TestUser() +def mock_add_resource(resource_ob, update=False): + return resource_ob + + class TestCheckResourceAvailability(unittest.TestCase): """Test methods related to checking the resource availability""" @mock.patch('utility.authentication_tools.add_new_resource') @@ -111,3 +116,78 @@ class TestCheckResourceAvailability(unittest.TestCase): type(test_dataset).type = mock.PropertyMock(return_value="Temp") self.assertEqual(check_resource_availability(test_dataset), "John Doe") + + +class TestAddNewResource(unittest.TestCase): + """Test cases for add_new_resource method""" + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + @mock.patch('utility.authentication_tools.add_resource', mock_add_resource) + @mock.patch('utility.authentication_tools.get_group_code') + def test_add_new_resource_if_publish_datatype(self, group_code_mock): + """Test add_new_resource if dataset type is 'publish'""" + group_code_mock.return_value = "Test" + test_dataset = mock.MagicMock() + type(test_dataset).type = mock.PropertyMock(return_value="Publish") + type(test_dataset).id = mock.PropertyMock(return_value=10) + expected_value = { + "owner_id": "none", + "default_mask": "John Doe", + "group_masks": {}, + "name": "Test_None", + "data": { + "dataset": 10, + "trait": None + }, + "type": "dataset-publish" + } + self.assertEqual(add_new_resource(test_dataset), + expected_value) + + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + @mock.patch('utility.authentication_tools.add_resource', mock_add_resource) + @mock.patch('utility.authentication_tools.get_group_code') + def test_add_new_resource_if_geno_datatype(self, group_code_mock): + """Test add_new_resource if dataset type is 'geno'""" + group_code_mock.return_value = "Test" + test_dataset = mock.MagicMock() + type(test_dataset).name = mock.PropertyMock(return_value="Geno") + type(test_dataset).type = mock.PropertyMock(return_value="Geno") + type(test_dataset).id = mock.PropertyMock(return_value=20) + expected_value = { + "owner_id": "none", + "default_mask": "John Doe", + "group_masks": {}, + "name": "Geno", + "data": { + "dataset": 20, + }, + "type": "dataset-geno" + } + self.assertEqual(add_new_resource(test_dataset), + expected_value) + + @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES', + "John Doe") + @mock.patch('utility.authentication_tools.add_resource', mock_add_resource) + @mock.patch('utility.authentication_tools.get_group_code') + def test_add_new_resource_if_other_datatype(self, group_code_mock): + """Test add_new_resource if dataset type is not 'geno' or 'publish'""" + group_code_mock.return_value = "Test" + test_dataset = mock.MagicMock() + type(test_dataset).name = mock.PropertyMock(return_value="Geno") + type(test_dataset).type = mock.PropertyMock(return_value="other") + type(test_dataset).id = mock.PropertyMock(return_value=20) + expected_value = { + "owner_id": "none", + "default_mask": "John Doe", + "group_masks": {}, + "name": "Geno", + "data": { + "dataset": 20, + }, + "type": "dataset-probeset" + } + self.assertEqual(add_new_resource(test_dataset), + expected_value) -- cgit v1.2.3 From 32f434e9f49583b731f1393328a3ff645c2f9af7 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 16 Sep 2020 03:11:01 +0300 Subject: Add new tests for "base/trait.py" * wqflask/tests/base/test_trait.py: New tests. --- wqflask/tests/base/test_trait.py | 101 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 101 insertions(+) create mode 100644 wqflask/tests/base/test_trait.py (limited to 'wqflask/tests') diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py new file mode 100644 index 00000000..53b0d440 --- /dev/null +++ b/wqflask/tests/base/test_trait.py @@ -0,0 +1,101 @@ +# -*- 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。") + self.assertEqual(test_trait.authors, + "Jane Doe かいと") -- cgit v1.2.3 From b13ca26da67855f9d32f3209176af052ed46617f Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 17 Sep 2020 15:55:05 +0300 Subject: Add tests for hmac utility * wqflask/tests/utility/test_hmac.py: New tests. --- wqflask/tests/utility/test_hmac.py | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 wqflask/tests/utility/test_hmac.py (limited to 'wqflask/tests') diff --git a/wqflask/tests/utility/test_hmac.py b/wqflask/tests/utility/test_hmac.py new file mode 100644 index 00000000..c7927685 --- /dev/null +++ b/wqflask/tests/utility/test_hmac.py @@ -0,0 +1,35 @@ +# -*- coding: utf-8 -*- +"""Test hmac utility functions""" + +import unittest +import mock + +from utility.hmac import data_hmac +from utility.hmac import url_for_hmac +from utility.hmac import hmac_creation + + +class TestHmacUtil(unittest.TestCase): + """Test Utility method for hmac creation""" + + def test_hmac_creation(self): + """Test hmac creation with a utf-8 string""" + self.assertEqual(hmac_creation("ファイ"), "21fa1d935bbbb07a7875") + + def test_data_hmac(self): + """Test data_hmac fn with a utf-8 string""" + self.assertEqual(data_hmac("ファイ"), "ファイ:21fa1d935bbbb07a7875") + + @mock.patch("utility.hmac.url_for") + def test_url_for_hmac_with_plain_url(self, mock_url): + """Test url_for_hmac without params""" + mock_url.return_value = "https://mock_url.com/ファイ/" + self.assertEqual(url_for_hmac("ファイ"), + "https://mock_url.com/ファイ/?hm=a62896a50d9ffcff7deb") + + @mock.patch("utility.hmac.url_for") + def test_url_for_hmac_with_param_in_url(self, mock_url): + """Test url_for_hmac with params""" + mock_url.return_value = "https://mock_url.com/?ファイ=1" + self.assertEqual(url_for_hmac("ファイ"), + "https://mock_url.com/?ファイ=1&hm=b2128fb28bc32da3b5b7") -- cgit v1.2.3 From 0fd23995fa21c32c2a6005b2fd70b0bd99d13214 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 17 Sep 2020 18:05:54 +0300 Subject: Mock "SECRET_HMAC_CODE" * wqflask/tests/utility/test_hmac.py: Mock app.config's "SECRET_HMAC_CODE" value. --- wqflask/tests/utility/test_hmac.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) (limited to 'wqflask/tests') diff --git a/wqflask/tests/utility/test_hmac.py b/wqflask/tests/utility/test_hmac.py index c7927685..16b50771 100644 --- a/wqflask/tests/utility/test_hmac.py +++ b/wqflask/tests/utility/test_hmac.py @@ -12,24 +12,28 @@ from utility.hmac import hmac_creation class TestHmacUtil(unittest.TestCase): """Test Utility method for hmac creation""" + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) def test_hmac_creation(self): """Test hmac creation with a utf-8 string""" - self.assertEqual(hmac_creation("ファイ"), "21fa1d935bbbb07a7875") + self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946") + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) def test_data_hmac(self): """Test data_hmac fn with a utf-8 string""" - self.assertEqual(data_hmac("ファイ"), "ファイ:21fa1d935bbbb07a7875") + self.assertEqual(data_hmac("ファイ"), "ファイ:7410466338cfe109e946") + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) @mock.patch("utility.hmac.url_for") def test_url_for_hmac_with_plain_url(self, mock_url): """Test url_for_hmac without params""" mock_url.return_value = "https://mock_url.com/ファイ/" self.assertEqual(url_for_hmac("ファイ"), - "https://mock_url.com/ファイ/?hm=a62896a50d9ffcff7deb") + "https://mock_url.com/ファイ/?hm=05bc39e659b1948f41e7") + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) @mock.patch("utility.hmac.url_for") def test_url_for_hmac_with_param_in_url(self, mock_url): """Test url_for_hmac with params""" mock_url.return_value = "https://mock_url.com/?ファイ=1" self.assertEqual(url_for_hmac("ファイ"), - "https://mock_url.com/?ファイ=1&hm=b2128fb28bc32da3b5b7") + "https://mock_url.com/?ファイ=1&hm=4709c1708270644aed79") -- cgit v1.2.3 From fd151ade1d9f12157bc0ae25570e982122be0c7d Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 23 Sep 2020 02:23:02 +0300 Subject: Fix failing tests * wqflask/tests/base/test_trait.py: In python2 it's necessary to decode the utf-8 string. --- wqflask/tests/base/test_trait.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask/tests') diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py index 53b0d440..960f2c81 100644 --- a/wqflask/tests/base/test_trait.py +++ b/wqflask/tests/base/test_trait.py @@ -96,6 +96,6 @@ class TestRetrieveTraitInfo(unittest.TestCase): 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。") + "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") + "Jane Doe かいと".decode('utf-8')) -- cgit v1.2.3 From e247f43bf9bc31164948760694ff796bb469ae4c Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 28 Sep 2020 02:25:58 +0300 Subject: Update trait tests * wqflask/tests/base/test_trait.py (test_retrieve_trait_info_with_non_empty_lrs): Check trait.LRS_score_repr is set correctly if trait.lrs is None. (test_retrieve_trait_info_with_empty_lrs_field): Check trait.LRS_score_repr and test_trait.LRS_location_repr is set correctly if trait.lrs is None. (test_retrieve_trait_info_with_empty_chr_field): Check test_trait.LRS_score_repr and test_trait.LRS_location_repr is set correctly if trait.locus is None. --- wqflask/tests/base/test_trait.py | 134 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 134 insertions(+) (limited to 'wqflask/tests') diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py index 960f2c81..1a3820f2 100644 --- a/wqflask/tests/base/test_trait.py +++ b/wqflask/tests/base/test_trait.py @@ -99,3 +99,137 @@ class TestRetrieveTraitInfo(unittest.TestCase): "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") -- cgit v1.2.3 From 4d16656304b9702c124721e82ea0dcda3c40ae44 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 29 Sep 2020 15:57:01 +0300 Subject: Add test for process_traits from collections.py * wqflask/tests/wqflask/test_collect.py: Add it. --- wqflask/tests/wqflask/test_collect.py | 57 +++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 wqflask/tests/wqflask/test_collect.py (limited to 'wqflask/tests') diff --git a/wqflask/tests/wqflask/test_collect.py b/wqflask/tests/wqflask/test_collect.py new file mode 100644 index 00000000..6b8d7931 --- /dev/null +++ b/wqflask/tests/wqflask/test_collect.py @@ -0,0 +1,57 @@ +"""Test cases for some methods in collect.py""" + +import unittest +import mock + +from flask import Flask +from wqflask.collect import process_traits + +app = Flask(__name__) + + +class MockSession: + """Helper class for mocking wqflask.collect.g.user_session.logged_in""" + def __init__(self, is_logged_in=False): + self.is_logged_in = is_logged_in + + @property + def logged_in(self): + return self.is_logged_in + + +class MockFlaskG: + """Helper class for mocking wqflask.collect.g.user_session""" + def __init__(self, is_logged_in=False): + self.is_logged_in = is_logged_in + + @property + def user_session(self): + if self.is_logged_in: + return MockSession(is_logged_in=True) + return MockSession() + + +class TestCollect(unittest.TestCase): + + def setUp(self): + self.app_context = app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + @mock.patch("wqflask.collect.g", MockFlaskG()) + def test_process_traits_when_user_is_logged_out(self): + """ + Test that the correct traits are returned when the user is logged + out + """ + self.assertEqual(process_traits( + b'1452452_at:HC_M2_0606_P:163d04f7db7c9e110de6,' + b'1452447_at:HC_M2_0606_P:eeece8fceb67072debea,' + b'1451401_a_at:HC_M2_0606_P:a043d23b3b3906d8318e,' + b'1429252_at:HC_M2_0606_P:6fa378b349bc9180e8f5'), + set(['1429252_at:HC_M2_0606_P', + '1451401_a_at:HC_M2_0606_P', + '1452447_at:HC_M2_0606_P', + '1452452_at:HC_M2_0606_P'])) -- cgit v1.2.3