diff options
Diffstat (limited to 'wqflask/tests')
| -rw-r--r-- | wqflask/tests/__init__.py | 0 | ||||
| -rw-r--r-- | wqflask/tests/base/__init__.py | 0 | ||||
| -rw-r--r-- | wqflask/tests/base/data.py | 110 | ||||
| -rw-r--r-- | wqflask/tests/base/test_data_set.py | 140 | ||||
| -rw-r--r-- | wqflask/tests/base/test_general_object.py | 41 | ||||
| -rw-r--r-- | wqflask/tests/base/test_webqtl_case_data.py | 39 | ||||
| -rw-r--r-- | wqflask/tests/utility/__init__.py | 0 | ||||
| -rw-r--r-- | wqflask/tests/utility/test_chunks.py | 19 | ||||
| -rw-r--r-- | wqflask/tests/utility/test_corestats.py | 55 | ||||
| -rw-r--r-- | wqflask/tests/utility/test_corr_result_helpers.py | 32 | ||||
| -rw-r--r-- | wqflask/tests/utility/test_formatting.py | 33 | ||||
| -rw-r--r-- | wqflask/tests/wqflask/__init__.py | 0 | ||||
| -rw-r--r-- | wqflask/tests/wqflask/api/__init__.py | 0 | ||||
| -rw-r--r-- | wqflask/tests/wqflask/api/test_gen_menu.py | 407 | ||||
| -rw-r--r-- | wqflask/tests/wqflask/marker_regression/__init__.py | 0 | ||||
| -rw-r--r-- | wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py | 151 |
16 files changed, 1027 insertions, 0 deletions
diff --git a/wqflask/tests/__init__.py b/wqflask/tests/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/tests/__init__.py diff --git a/wqflask/tests/base/__init__.py b/wqflask/tests/base/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/tests/base/__init__.py 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 new file mode 100644 index 00000000..94780a5d --- /dev/null +++ b/wqflask/tests/base/test_data_set.py @@ -0,0 +1,140 @@ +"""Tests for wqflask/base/data_set.py""" + +import 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", + '{"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\" ") + ) diff --git a/wqflask/tests/base/test_general_object.py b/wqflask/tests/base/test_general_object.py new file mode 100644 index 00000000..c7701021 --- /dev/null +++ b/wqflask/tests/base/test_general_object.py @@ -0,0 +1,41 @@ +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), "value = 1\nname = test\n") + self.assertEqual( + repr(test_obj), "value = 1\nname = test\ncontents = ['a']\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/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), + "<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") diff --git a/wqflask/tests/utility/__init__.py b/wqflask/tests/utility/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/tests/utility/__init__.py diff --git a/wqflask/tests/utility/test_chunks.py b/wqflask/tests/utility/test_chunks.py new file mode 100644 index 00000000..8d90a1ec --- /dev/null +++ b/wqflask/tests/utility/test_chunks.py @@ -0,0 +1,19 @@ +"""Test chunking""" + +import unittest + +from utility.chunks import divide_into_chunks + + +class TestChunks(unittest.TestCase): + "Test Utility method for chunking" + def test_divide_into_chunks(self): + "Check that a list is chunked correctly" + self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3), + [[1, 2, 7], [3, 22, 8], [5, 22, 333]]) + self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4), + [[1, 2, 7], [3, 22, 8], [5, 22, 333]]) + self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5), + [[1, 2], [7, 3], [22, 8], [5, 22], [333]]) + self.assertEqual(divide_into_chunks([], 5), + [[]]) diff --git a/wqflask/tests/utility/test_corestats.py b/wqflask/tests/utility/test_corestats.py new file mode 100644 index 00000000..cf91a248 --- /dev/null +++ b/wqflask/tests/utility/test_corestats.py @@ -0,0 +1,55 @@ +"""Test Core Stats""" + +import unittest + +from utility.corestats import Stats + + +class TestChunks(unittest.TestCase): + "Test Utility method for chunking" + + def setUp(self): + self.stat_test = Stats((x for x in range(1, 11))) + + def test_stats_sum(self): + """ Test sequence sum """ + self.assertEqual(self.stat_test.sum(), 55) + self.stat_test = Stats([]) + self.assertEqual(self.stat_test.sum(), None) + + def test_stats_count(self): + """ Test sequence count """ + self.assertEqual(self.stat_test.count(), 10) + self.stat_test = Stats([]) + self.assertEqual(self.stat_test.count(), 0) + + def test_stats_min(self): + """ Test min value in sequence""" + self.assertEqual(self.stat_test.min(), 1) + self.stat_test = Stats([]) + self.assertEqual(self.stat_test.min(), None) + + def test_stats_max(self): + """ Test max value in sequence """ + self.assertEqual(self.stat_test.max(), 10) + self.stat_test = Stats([]) + self.assertEqual(self.stat_test.max(), None) + + def test_stats_avg(self): + """ Test avg of sequence """ + self.assertEqual(self.stat_test.avg(), 5.5) + self.stat_test = Stats([]) + self.assertEqual(self.stat_test.avg(), None) + + def test_stats_stdev(self): + """ Test standard deviation of sequence """ + self.assertEqual(self.stat_test.stdev(), 3.0276503540974917) + self.stat_test = Stats([]) + self.assertEqual(self.stat_test.stdev(), None) + + def test_stats_percentile(self): + """ Test percentile of sequence """ + self.assertEqual(self.stat_test.percentile(20), 3.0) + self.assertEqual(self.stat_test.percentile(101), None) + self.stat_test = Stats([]) + self.assertEqual(self.stat_test.percentile(20), None) diff --git a/wqflask/tests/utility/test_corr_result_helpers.py b/wqflask/tests/utility/test_corr_result_helpers.py new file mode 100644 index 00000000..e196fbdf --- /dev/null +++ b/wqflask/tests/utility/test_corr_result_helpers.py @@ -0,0 +1,32 @@ +""" Test correlation helper methods """ + +import unittest +from utility.corr_result_helpers import normalize_values, common_keys, normalize_values_with_samples + + +class TestCorrelationHelpers(unittest.TestCase): + """Test methods for normalising lists""" + + def test_normalize_values(self): + """Test that a list is normalised correctly""" + self.assertEqual( + normalize_values([2.3, None, None, 3.2, 4.1, 5], [ + 3.4, 7.2, 1.3, None, 6.2, 4.1]), + ([2.3, 4.1, 5], [3.4, 6.2, 4.1], 3) + ) + + def test_common_keys(self): + """Test that common keys are returned as a list""" + a = dict(BXD1=9.113, BXD2=9.825, BXD14=8.985, BXD15=9.300) + b = dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300) + self.assertEqual(sorted(common_keys(a, b)), ['BXD1', 'BXD14']) + + def test_normalize_values_with_samples(self): + """Test that a sample(dict) is normalised correctly""" + self.assertEqual( + normalize_values_with_samples( + dict(BXD1=9.113, BXD2=9.825, BXD14=8.985, + BXD15=9.300, BXD20=9.300), + dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300)), + (({'BXD1': 9.113, 'BXD14': 8.985}, {'BXD1': 9.723, 'BXD14': 9.124}, 2)) + ) diff --git a/wqflask/tests/utility/test_formatting.py b/wqflask/tests/utility/test_formatting.py new file mode 100644 index 00000000..9d3033d1 --- /dev/null +++ b/wqflask/tests/utility/test_formatting.py @@ -0,0 +1,33 @@ +import unittest +from utility.formatting import numify, commify + + +class TestFormatting(unittest.TestCase): + """Test formatting numbers by numifying or commifying""" + + def test_numify(self): + "Test that a number is correctly converted to a English readable string" + self.assertEqual(numify(1, 'item', 'items'), + 'one item') + self.assertEqual(numify(2, 'book'), 'two') + self.assertEqual(numify(2, 'book', 'books'), 'two books') + self.assertEqual(numify(0, 'book', 'books'), 'zero books') + self.assertEqual(numify(0), 'zero') + self.assertEqual(numify(5), 'five') + self.assertEqual(numify(14, 'book', 'books'), '14 books') + self.assertEqual(numify(999, 'book', 'books'), '999 books') + self.assertEqual(numify(1000000, 'book', 'books'), '1,000,000 books') + self.assertEqual(numify(1956), '1956') + + def test_commify(self): + "Test that commas are added correctly" + self.assertEqual(commify(1), '1') + self.assertEqual(commify(123), '123') + self.assertEqual(commify(1234), '1234') + self.assertEqual(commify(12345), '12,345') + self.assertEqual(commify(1234567890), '1,234,567,890') + self.assertEqual(commify(123.0), '123.0') + self.assertEqual(commify(1234.5), '1234.5') + self.assertEqual(commify(1234.56789), '1234.56789') + self.assertEqual(commify(123456.789), '123,456.789') + self.assertEqual(commify(None), None) diff --git a/wqflask/tests/wqflask/__init__.py b/wqflask/tests/wqflask/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/tests/wqflask/__init__.py diff --git a/wqflask/tests/wqflask/api/__init__.py b/wqflask/tests/wqflask/api/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/tests/wqflask/api/__init__.py diff --git a/wqflask/tests/wqflask/api/test_gen_menu.py b/wqflask/tests/wqflask/api/test_gen_menu.py new file mode 100644 index 00000000..239484aa --- /dev/null +++ b/wqflask/tests/wqflask/api/test_gen_menu.py @@ -0,0 +1,407 @@ +"""Test cases for wqflask.api.gen_menu""" +import unittest +import mock + +from wqflask.api.gen_menu import gen_dropdown_json +from wqflask.api.gen_menu import get_species +from wqflask.api.gen_menu import get_groups +from wqflask.api.gen_menu import get_types +from wqflask.api.gen_menu import get_datasets +from wqflask.api.gen_menu import phenotypes_exist +from wqflask.api.gen_menu import genotypes_exist +from wqflask.api.gen_menu import build_datasets +from wqflask.api.gen_menu import build_types + + +class TestGenMenu(unittest.TestCase): + """Tests for the gen_menu module""" + + def setUp(self): + self.test_group = { + 'mouse': [ + ['H_T1', + 'H_T', + 'Family:DescriptionA' + ], + ['H_T2', "H_T'", 'Family:None'] + ], + 'human': [ + ['BXD', 'BXD', 'Family:None'], + ['HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)', + 'Family:Test'] + ] + } + + self.test_type = { + 'mouse': { + 'H_T2': [('Phenotypes', + 'Traits and Cofactors', + 'Phenotypes'), + ('Genotypes', + 'DNA Markers and SNPs', + 'Genotypes'), + ['M', 'M', 'Molecular Trait Datasets']], + 'H_T1': [('Phenotypes', + 'Traits and Cofactors', + 'Phenotypes'), + ('Genotypes', + 'DNA Markers and SNPs', + 'Genotypes'), + ['M', 'M', 'Molecular Trait Datasets']] + }, + 'human': { + 'HLC': [('Phenotypes', + 'Traits and Cofactors', + 'Phenotypes'), + ('Genotypes', + 'DNA Markers and SNPs', + 'Genotypes'), + ['M', 'M', 'Molecular Trait Datasets']], + 'BXD': [('Phenotypes', + 'Traits and Cofactors', + 'Phenotypes'), + ('Genotypes', + 'DNA Markers and SNPs', + 'Genotypes'), + ['M', 'M', 'Molecular Trait Datasets']] + } + } + + @mock.patch('wqflask.api.gen_menu.g') + def test_get_species(self, db_mock): + """Test that assertion is raised when dataset and dataset_name + are defined""" + db_mock.db.execute.return_value.fetchall.return_value = ( + ('human', 'Human'), + ('mouse', 'Mouse')) + self.assertEqual(get_species(), + [['human', 'Human'], ['mouse', 'Mouse']]) + db_mock.db.execute.assert_called_once_with( + "SELECT Name, MenuName FROM Species ORDER BY OrderId" + ) + + @mock.patch('wqflask.api.gen_menu.g') + def test_get_groups(self, db_mock): + """Test that species groups are grouped correctly""" + db_mock.db.execute.return_value.fetchall.side_effect = [ + # Mouse + (('BXD', 'BXD', None), + ('HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)', + 'Test')), + # Human + (('H_T1', "H_T", "DescriptionA"), + ('H_T2', "H_T'", None)) + ] + + self.assertEqual(get_groups([["human", "Human"], ["mouse", "Mouse"]]), + self.test_group) + + for name in ["mouse", "human"]: + db_mock.db.execute.assert_any_call( + ("SELECT InbredSet.Name, InbredSet.FullName, " + + "IFNULL(InbredSet.Family, 'None') " + + "FROM InbredSet, Species WHERE Species.Name " + + "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by " + + "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, " + + "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, " + + "InbredSet.FullName) ASC, InbredSet.FullName ASC, " + + "InbredSet.MenuOrderId ASC").format(name) + ) + + @mock.patch('wqflask.api.gen_menu.g') + def test_phenotypes_exist_called_with_correct_query(self, db_mock): + """Test that phenotypes_exist is called with the correct query""" + db_mock.db.execute.return_value.fetchone.return_value = None + phenotypes_exist("test") + db_mock.db.execute.assert_called_with( + "SELECT Name FROM PublishFreeze " + "WHERE PublishFreeze.Name = 'testPublish'" + ) + + @mock.patch('wqflask.api.gen_menu.g') + def test_phenotypes_exist_with_falsy_values(self, db_mock): + """Test that phenotype check returns correctly when given + a None value""" + for x in [None, False, (), [], ""]: + db_mock.db.execute.return_value.fetchone.return_value = x + self.assertFalse(phenotypes_exist("test")) + + @mock.patch('wqflask.api.gen_menu.g') + def test_phenotypes_exist_with_truthy_value(self, db_mock): + """Test that phenotype check returns correctly when given Truthy """ + for x in ["x", ("result"), ["result"], [1]]: + db_mock.db.execute.return_value.fetchone.return_value = (x) + self.assertTrue(phenotypes_exist("test")) + + @mock.patch('wqflask.api.gen_menu.g') + def test_genotypes_exist_called_with_correct_query(self, db_mock): + """Test that genotypes_exist is called with the correct query""" + db_mock.db.execute.return_value.fetchone.return_value = None + genotypes_exist("test") + db_mock.db.execute.assert_called_with( + "SELECT Name FROM GenoFreeze WHERE GenoFreeze.Name = 'testGeno'" + ) + + @mock.patch('wqflask.api.gen_menu.g') + def test_genotypes_exist_with_falsy_values(self, db_mock): + """Test that genotype check returns correctly when given + a None value""" + for x in [None, False, (), [], ""]: + db_mock.db.execute.return_value.fetchone.return_value = x + self.assertFalse(genotypes_exist("test")) + + @mock.patch('wqflask.api.gen_menu.g') + def test_genotypes_exist_with_truthy_value(self, db_mock): + """Test that genotype check returns correctly when given Truthy """ + for x in ["x", ("result"), ["result"], [1]]: + db_mock.db.execute.return_value.fetchone.return_value = (x) + self.assertTrue(phenotypes_exist("test")) + + @mock.patch('wqflask.api.gen_menu.g') + def test_build_datasets_with_type_phenotypes(self, db_mock): + """Test that correct dataset is returned for a phenotype type""" + db_mock.db.execute.return_value.fetchall.return_value = ( + (602, "BXDPublish", "BXD Published Phenotypes"), + ) + self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"), + [['602', "BXDPublish", "BXD Published Phenotypes"]]) + db_mock.db.execute.assert_called_with( + "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, " + + "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, " + + "InbredSet WHERE InbredSet.Name = 'BXD' AND " + + "PublishFreeze.InbredSetId = InbredSet.Id AND " + + "InfoFiles.InfoPageName = PublishFreeze.Name " + + "ORDER BY PublishFreeze.CreateTime ASC" + ) + self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"), + [['602', "BXDPublish", "Mouse Phenome Database"]]) + + db_mock.db.execute.return_value.fetchall.return_value = () + db_mock.db.execute.return_value.fetchone.return_value = ( + "BXDPublish", "Mouse Phenome Database" + ) + self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"), + [["None", "BXDPublish", "Mouse Phenome Database"]]) + + @mock.patch('wqflask.api.gen_menu.g') + def test_build_datasets_with_type_phenotypes_and_no_results(self, db_mock): + """Test that correct dataset is returned for a phenotype type with no + results + + """ + db_mock.db.execute.return_value.fetchall.return_value = None + db_mock.db.execute.return_value.fetchone.return_value = (121, + "text value") + self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"), + [["None", "121", "text value"]]) + db_mock.db.execute.assert_called_with( + "SELECT PublishFreeze.Name, PublishFreeze.FullName " + "FROM PublishFreeze, InbredSet " + "WHERE InbredSet.Name = 'BXD' AND " + "PublishFreeze.InbredSetId = InbredSet.Id " + "ORDER BY PublishFreeze.CreateTime ASC" + ) + + @mock.patch('wqflask.api.gen_menu.g') + def test_build_datasets_with_type_genotypes(self, db_mock): + """Test that correct dataset is returned for a phenotype type""" + db_mock.db.execute.return_value.fetchone.return_value = ( + 635, "HLCPublish", "HLC Published Genotypes" + ) + + self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"), + [["635", "HLCGeno", "HLC Genotypes"]]) + db_mock.db.execute.assert_called_with( + "SELECT InfoFiles.GN_AccesionId FROM InfoFiles, " + "GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND " + "GenoFreeze.InbredSetId = InbredSet.Id AND " + "InfoFiles.InfoPageName = GenoFreeze.ShortName " + + "ORDER BY GenoFreeze.CreateTime DESC" + ) + db_mock.db.execute.return_value.fetchone.return_value = () + self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"), + [["None", "HLCGeno", "HLC Genotypes"]]) + + @mock.patch('wqflask.api.gen_menu.g') + def test_build_datasets_with_type_mrna(self, db_mock): + """Test that correct dataset is returned for a mRNA + expression/ Probeset""" + db_mock.db.execute.return_value.fetchall.return_value = ( + (112, "HC_M2_0606_P", + "Hippocampus Consortium M430v2 (Jun06) PDNN"), ) + self.assertEqual(build_datasets("Mouse", "HLC", "mRNA"), [[ + "112", 'HC_M2_0606_P', "Hippocampus Consortium M430v2 (Jun06) PDNN" + ]]) + db_mock.db.execute.assert_called_once_with( + "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, " + + "ProbeSetFreeze.FullName FROM ProbeSetFreeze, " + + "ProbeFreeze, InbredSet, Tissue, Species WHERE " + + "Species.Name = 'Mouse' AND Species.Id = " + + "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND " + + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and " + + "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = " + + "Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id " + + "ORDER BY ProbeSetFreeze.CreateTime DESC") + + @mock.patch('wqflask.api.gen_menu.build_datasets') + @mock.patch('wqflask.api.gen_menu.g') + def test_build_types(self, db_mock, datasets_mock): + """Test that correct tissue metadata is returned""" + datasets_mock.return_value = [ + ["112", 'HC_M2_0606_P', + "Hippocampus Consortium M430v2 (Jun06) PDNN"] + ] + db_mock.db.execute.return_value.fetchall.return_value = ( + ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue') + ) + self.assertEqual(build_types('mouse', 'random group'), + [['M', 'M', 'Molecular Traits'], + ['H', 'H', 'Molecular Traits'], + ['R', 'R', 'Molecular Traits']]) + db_mock.db.execute.assert_called_once_with( + "SELECT DISTINCT Tissue.Name " + + "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, " + + "Tissue, Species WHERE Species.Name = 'mouse' " + + "AND Species.Id = InbredSet.SpeciesId AND " + + "InbredSet.Name = 'random group' AND " + + "ProbeFreeze.TissueId = Tissue.Id AND " + + "ProbeFreeze.InbredSetId = InbredSet.Id AND " + + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " + + "ORDER BY Tissue.Name" + ) + + @mock.patch('wqflask.api.gen_menu.build_types') + @mock.patch('wqflask.api.gen_menu.genotypes_exist') + @mock.patch('wqflask.api.gen_menu.phenotypes_exist') + def test_get_types_with_existing_genotype_and_phenotypes( + self, + phenotypes_exist_mock, + genotypes_exist_mock, + build_types_mock): + """Test that build types are constructed correctly if phenotypes and genotypes + exist + + """ + phenotypes_exist_mock.return_value = True + genotypes_exist_mock.return_value = True + + expected_result = self.test_type + + build_types_mock.return_value = [ + ['M', 'M', 'Molecular Trait Datasets'] + ] + self.assertEqual(get_types(self.test_group), expected_result) + + @mock.patch('wqflask.api.gen_menu.build_types') + @mock.patch('wqflask.api.gen_menu.genotypes_exist') + @mock.patch('wqflask.api.gen_menu.phenotypes_exist') + def test_get_types_with_buildtype_and_non_existent_genotype_and_phenotypes( + self, + phenotypes_exist_mock, + genotypes_exist_mock, + build_types_mock): + """Test that build types are constructed correctly if phenotypes_exist and + genotypes_exist are false but build_type is falsy + + """ + phenotypes_exist_mock.return_value = False + genotypes_exist_mock.return_value = False + + build_types_mock.return_value = [] + self.assertEqual(get_types(self.test_group), { + 'mouse': {}, + 'human': {} + }) + + @mock.patch('wqflask.api.gen_menu.build_types') + @mock.patch('wqflask.api.gen_menu.genotypes_exist') + @mock.patch('wqflask.api.gen_menu.phenotypes_exist') + def test_get_types_with_non_existent_genotype_phenotypes_and_buildtype( + self, + phenotypes_exist_mock, + genotypes_exist_mock, + build_types_mock): + """Test that build types are constructed correctly if phenotypes_exist, + genotypes_exist and build_types are truthy + + """ + phenotypes_exist_mock.return_value = False + genotypes_exist_mock.return_value = False + + build_types_mock.return_value = [ + ['M', 'M', 'Molecular Trait Datasets'] + ] + expected_result = { + 'mouse': { + 'H_T2': [['M', 'M', 'Molecular Trait Datasets']], + 'H_T1': [['M', 'M', 'Molecular Trait Datasets']]}, + 'human': { + 'HLC': [['M', 'M', 'Molecular Trait Datasets']], + 'BXD': [['M', 'M', 'Molecular Trait Datasets']]}} + self.assertEqual(get_types(self.test_group), + expected_result) + + @mock.patch('wqflask.api.gen_menu.build_datasets') + def test_get_datasets_with_existent_datasets(self, + build_datasets_mock): + """Test correct dataset is returned with existent build_datasets""" + build_datasets_mock.return_value = "Test" + expected_result = { + 'mouse': { + 'H_T2': {'Genotypes': 'Test', + 'M': 'Test', + 'Phenotypes': 'Test'}, + 'H_T1': {'Genotypes': 'Test', + 'M': 'Test', + 'Phenotypes': 'Test'}}, + 'human': {'HLC': {'Genotypes': 'Test', + 'M': 'Test', + 'Phenotypes': 'Test'}, + 'BXD': {'Genotypes': 'Test', + 'M': 'Test', + 'Phenotypes': 'Test'}}} + self.assertEqual(get_datasets(self.test_type), + expected_result) + + @mock.patch('wqflask.api.gen_menu.build_datasets') + def test_get_datasets_with_non_existent_datasets(self, + build_datasets_mock): + """Test correct dataset is returned with non-existent build_datasets""" + build_datasets_mock.return_value = None + expected_result = { + 'mouse': { + 'H_T2': {}, + 'H_T1': {}}, + 'human': {'HLC': {}, + 'BXD': {}}} + self.assertEqual(get_datasets(self.test_type), + expected_result) + + @mock.patch('wqflask.api.gen_menu.get_datasets') + @mock.patch('wqflask.api.gen_menu.get_types') + @mock.patch('wqflask.api.gen_menu.get_groups') + @mock.patch('wqflask.api.gen_menu.get_species') + def test_gen_dropdown_json(self, + species_mock, + groups_mock, + types_mock, + datasets_mock): + "Test that the correct dictionary is constructed properly" + species_mock.return_value = ("speciesA speciesB speciesC speciesD" + .split(" ")) + datasets_mock.return_value = ("datasetA datasetB datasetC datasetD" + .split(" ")) + groups_mock.return_value = ("groupA groupB groupC groupD" + .split(" ")) + types_mock.return_value = ("typeA typeB typeC typeD" + .split(" ")) + datasets_mock.return_value = ("datasetA datasetB datasetC datasetD" + .split(" ")) + + expected_result = { + 'datasets': ['datasetA', 'datasetB', 'datasetC', 'datasetD'], + 'types': ['typeA', 'typeB', 'typeC', 'typeD'], + 'groups': ['groupA', 'groupB', 'groupC', 'groupD'], + 'species': ['speciesA', 'speciesB', 'speciesC', 'speciesD']} + + self.assertEqual(gen_dropdown_json(), expected_result) diff --git a/wqflask/tests/wqflask/marker_regression/__init__.py b/wqflask/tests/wqflask/marker_regression/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/tests/wqflask/marker_regression/__init__.py diff --git a/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py new file mode 100644 index 00000000..6f791df1 --- /dev/null +++ b/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py @@ -0,0 +1,151 @@ +import unittest + +from htmlgen import HTMLgen2 as HT +from wqflask.marker_regression.display_mapping_results import ( + DisplayMappingResults, + HtmlGenWrapper +) + + +class TestDisplayMappingResults(unittest.TestCase): + """Basic Methods to test Mapping Results""" + def test_pil_colors(self): + """Test that colors use PILLOW color format""" + self.assertEqual(DisplayMappingResults.CLICKABLE_WEBQTL_REGION_COLOR, + (245, 211, 211)) + + +class TestHtmlGenWrapper(unittest.TestCase): + """Test Wrapper around HTMLGen""" + def test_create_image(self): + """Test HT.Image method""" + self.assertEqual( + str(HtmlGenWrapper.create_image_tag(src="test.png", + alt="random", + border="0", + width="10", + height="13", + usemap="#webqtlmap")), + ("""<IMG src="test.png" height="13" width="10" """ + """alt="random" border="0" """ + """usemap="#webqtlmap">""") + ) + + def test_create_form(self): + """Test HT.Form method""" + test_form = HtmlGenWrapper.create_form_tag( + cgi="/testing/", + enctype='multipart/form-data', + name="formName", + submit=HT.Input(type='hidden') + ) + test_image = HtmlGenWrapper.create_image_tag( + src="test.png", + alt="random", + border="0", + width="10", + height="13", + usemap="#webqtlmap" + ) + self.assertEqual( + str(test_form).replace("\n", ""), + ("""<FORM METHOD="POST" ACTION="/testing/" """ + """ENCTYPE="multipart/form-data" """ + """NAME="formName"><INPUT TYPE="hidden" """ + """NAME="Default_Name"></FORM>""")) + hddn = { + 'FormID': 'showDatabase', + 'ProbeSetID': '_', + 'database': "TestGeno", + 'CellID': '_', + 'RISet': "Test", + 'incparentsf1': 'ON' + } + for key in hddn.keys(): + test_form.append(HT.Input(name=key, value=hddn[key], + type='hidden')) + test_form.append(test_image) + self.assertEqual(str(test_form).replace("\n", ""), ( + """<FORM METHOD="POST" ACTION="/testing/" """ + """ENCTYPE="multipart/form-data" NAME="formName">""" + """<INPUT TYPE="hidden" NAME="database" VALUE="TestGeno">""" + """<INPUT TYPE="hidden" NAME="incparentsf1" VALUE="ON">""" + """<INPUT TYPE="hidden" NAME="FormID" VALUE="showDatabase">""" + """<INPUT TYPE="hidden" NAME="ProbeSetID" VALUE="_">""" + """<INPUT TYPE="hidden" NAME="RISet" VALUE="Test">""" + """<INPUT TYPE="hidden" NAME="CellID" VALUE="_">""" + """<IMG src="test.png" height="13" width="10" alt="random" """ + """border="0" usemap="#webqtlmap">""" + """<INPUT TYPE="hidden" NAME="Default_Name"></FORM>""")) + + def test_create_paragraph(self): + """Test HT.Paragraph method""" + test_p_element = HtmlGenWrapper.create_p_tag(id="smallSize") + par_text = ( + "Mapping using genotype data as " + "a trait will result in infinity LRS at one locus. " + "In order to display the result properly, all LRSs " + "higher than 100 are capped at 100." + ) + self.assertEqual( + str(test_p_element), + """<P id="smallSize"></P>""" + ) + test_p_element.append(HT.BR()) + test_p_element.append(par_text) + self.assertEqual( + str(test_p_element), + """<P id="smallSize"><BR>{}</P>""".format(par_text) + ) + + def test_create_br_tag(self): + """Test HT.BR() method""" + self.assertEqual(str(HtmlGenWrapper.create_br_tag()), + "<BR>") + + def test_create_input_tag(self): + """Test HT.Input method""" + self.assertEqual( + str(HtmlGenWrapper.create_input_tag( + type="hidden", + name="name", + value="key", + Class="trait trait_")).replace("\n", ""), + ("""<INPUT TYPE="hidden" NAME="name" """ + """class="trait trait_" VALUE="key">""")) + + def test_create_map_tag(self): + """Test HT.Map method""" + self.assertEqual(str(HtmlGenWrapper.create_map_tag( + name="WebqTLImageMap")).replace("\n", ""), + """<MAP NAME="WebqTLImageMap"></MAP>""") + gifmap = HtmlGenWrapper.create_map_tag(areas=[]) + gifmap.areas.append(HT.Area(shape="rect", + coords='1 2 3', href='#area1')) + gifmap.areas.append(HT.Area(shape="rect", + coords='1 2 3', href='#area2')) + self.assertEqual( + str(gifmap).replace("\n", ""), + ("""<MAP NAME="">""" + """<AREA coords="1 2 3" """ + """href="#area1" shape="rect">""" + """<AREA coords="1 2 3" href="#area2" shape="rect">""" + """</MAP>""")) + + def test_create_area_tag(self): + """Test HT.Area method""" + self.assertEqual( + str(HtmlGenWrapper.create_area_tag( + shape="rect", + coords="1 2", + href="http://test.com", + title="Some Title")).replace("\n", ""), + ("""<AREA coords="1 2" href="http://test.com" """ + """shape="rect" title="Some Title">""")) + + def test_create_link_tag(self): + """Test HT.HREF method""" + self.assertEqual( + str(HtmlGenWrapper.create_link_tag( + "www.test.com", "test", target="_blank")).replace("\n", ""), + """<A HREF="www.test.com" TARGET="_blank">test</A>""") |