diff options
Diffstat (limited to 'gn2/tests/unit/base')
| -rw-r--r-- | gn2/tests/unit/base/__init__.py | 0 | ||||
| -rw-r--r-- | gn2/tests/unit/base/test_data_set.py | 238 | ||||
| -rw-r--r-- | gn2/tests/unit/base/test_general_object.py | 40 | ||||
| -rw-r--r-- | gn2/tests/unit/base/test_mrna_assay_tissue_data.py | 81 | ||||
| -rw-r--r-- | gn2/tests/unit/base/test_species.py | 80 | ||||
| -rw-r--r-- | gn2/tests/unit/base/test_trait.py | 262 | ||||
| -rw-r--r-- | gn2/tests/unit/base/test_webqtl_case_data.py | 40 |
7 files changed, 741 insertions, 0 deletions
diff --git a/gn2/tests/unit/base/__init__.py b/gn2/tests/unit/base/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/gn2/tests/unit/base/__init__.py diff --git a/gn2/tests/unit/base/test_data_set.py b/gn2/tests/unit/base/test_data_set.py new file mode 100644 index 00000000..7341314c --- /dev/null +++ b/gn2/tests/unit/base/test_data_set.py @@ -0,0 +1,238 @@ +"""Tests for wqflask/base/data_set.py""" + +import unittest +from unittest import mock +from dataclasses import dataclass +from gn3.monads import MonadicDict + +from gn2.wqflask import app +from gn2.base.data_set import DatasetType +from gn2.base.data_set.dataset import DataSet + +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 MockPhenotypeDataset(DataSet): + def setup(self): + self.type = "Publish" + self.query_for_group = "" + self.group = "" + + + def check_confidentiality(self): + pass + + def retrieve_other_names(self): + pass + +@dataclass +class MockGroup: + name = "Group" + +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() + cursor_mock = mock.Mock() + redis_mock.get.return_value = self.test_dataset + self.assertEqual(DatasetType(redis_mock) + ("All Phenotypes", redis_mock, cursor_mock), "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() + cursor_mock = mock.Mock() + redis_mock.get.return_value = None + data_set = DatasetType(redis_mock) + self.assertEqual(data_set("BXDGeno", redis_mock, cursor_mock), + "Geno") + self.assertEqual(data_set("BXDPublish", redis_mock, cursor_mock), + "Publish") + self.assertEqual(data_set("HLC_0311", redis_mock, cursor_mock), + "ProbeSet") + + redis_mock.set.assert_called_once_with( + "dataset_structure", + ('{"HLC_0311": "ProbeSet", ' + '"HLCPublish": "Publish", ' + '"BXDGeno": "Geno", ' + '"HC_M2_0606_P": "ProbeSet", ' + '"BXDPublish": "Publish"}')) + + +class TestDatasetAccessionId(unittest.TestCase): + """Tests for the DataSetType class""" + + @mock.patch("base.data_set.dataset.query_sql") + @mock.patch("base.data_set.dataset.DatasetGroup") + def test_get_accession_id(self, mock_dataset_group, mock_query_sql): + def mock_fn(): + yield MonadicDict({"accession_id": 7}) + mock_dataset_group.return_value = MockGroup() + mock_query_sql.return_value = mock_fn() + sample_dataset = MockPhenotypeDataset( + name="BXD-LongevityPublish", + get_samplelist=False, + group_name="BXD", + redis_conn=mock.Mock() + ) + sample_dataset\ + .accession_id\ + .bind(lambda x: self.assertEqual(7, x)) + + @mock.patch("base.data_set.dataset.query_sql") + @mock.patch("base.data_set.dataset.DatasetGroup") + def test_get_accession_id_empty_return(self, mock_dataset_group, + mock_query_sql): + mock_dataset_group.return_value = MockGroup() + mock_query_sql.return_value = None + sample_dataset = MockPhenotypeDataset( + name="BXD-LongevityPublish", + get_samplelist=False, + group_name="BXD", + redis_conn=mock.Mock() + ) + sample_dataset\ + .accession_id\ + .bind(lambda x: self.assertNone(x)) diff --git a/gn2/tests/unit/base/test_general_object.py b/gn2/tests/unit/base/test_general_object.py new file mode 100644 index 00000000..1301f18b --- /dev/null +++ b/gn2/tests/unit/base/test_general_object.py @@ -0,0 +1,40 @@ +import unittest + +from gn2.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), "name = test\nvalue = 1\n") + self.assertEqual( + repr(test_obj), "contents = ['a']\nname = test\nvalue = 1\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/gn2/tests/unit/base/test_mrna_assay_tissue_data.py b/gn2/tests/unit/base/test_mrna_assay_tissue_data.py new file mode 100644 index 00000000..5bc28ffa --- /dev/null +++ b/gn2/tests/unit/base/test_mrna_assay_tissue_data.py @@ -0,0 +1,81 @@ +import pytest +from gn2.base.mrna_assay_tissue_data import MrnaAssayTissueData + + +@pytest.mark.parametrize( + ('gene_symbols', 'expected_query', 'sql_fetch_all_results'), + ( + (None, + (("SELECT t.Symbol, t.GeneId, t.DataId, " + "t.Chr, t.Mb, t.description, " + "t.Probe_Target_Description " + "FROM (SELECT Symbol, " + "max(Mean) AS maxmean " + "FROM TissueProbeSetXRef WHERE " + "TissueProbeSetFreezeId=1 AND " + "Symbol != '' AND Symbol IS NOT " + "Null GROUP BY Symbol) " + "AS x INNER JOIN TissueProbeSetXRef " + "AS t ON t.Symbol = x.Symbol " + "AND t.Mean = x.maxmean"),), + (("symbol", "gene_id", + "data_id", "chr", "mb", + "description", + "probe_target_description"),)), + (["k1", "k2", "k3"], + ("SELECT t.Symbol, t.GeneId, t.DataId, " + "t.Chr, t.Mb, t.description, " + "t.Probe_Target_Description FROM (SELECT Symbol, " + "max(Mean) AS maxmean " + "FROM TissueProbeSetXRef WHERE " + "TissueProbeSetFreezeId=1 AND " + "Symbol IN (%s, %s, %s) " + "GROUP BY Symbol) AS x INNER JOIN " + "TissueProbeSetXRef AS " + "t ON t.Symbol = x.Symbol " + "AND t.Mean = x.maxmean", + ("k1", "k2", "k3")), + (("k1", "203", + "112", "xy", "20.11", + "Sample Description", + "Sample Probe Target Description"),)), + ), +) +def test_mrna_assay_tissue_data_initialisation(mocker, gene_symbols, + expected_query, + sql_fetch_all_results): + mock_conn = mocker.MagicMock() + with mock_conn.cursor() as cursor: + cursor.fetchall.return_value = sql_fetch_all_results + MrnaAssayTissueData(conn=mock_conn, gene_symbols=gene_symbols) + cursor.execute.assert_called_with(*expected_query) + + +def test_get_trait_symbol_and_tissue_values(mocker): + """Test for getting trait symbol and tissue_values""" + mock_conn = mocker.MagicMock() + with mock_conn.cursor() as cursor: + cursor.fetchall.side_effect = [ + (("k1", "203", + "112", "xy", "20.11", + "Sample Description", + "Sample Probe Target Description"),), + (("k1", "v1"), + ("k2", "v2"), + ("k3", "v3")), + ] + _m = MrnaAssayTissueData(conn=mock_conn, + gene_symbols=["k1", "k2", "k3"]) + assert _m.get_symbol_values_pairs() == { + "k1": ["v1"], + "k2": ["v2"], + "k3": ["v3"], + } + cursor.execute.assert_called_with( + "SELECT TissueProbeSetXRef.Symbol, " + "TissueProbeSetData.value FROM " + "TissueProbeSetXRef, TissueProbeSetData " + "WHERE TissueProbeSetData.Id IN (%s) " + "AND TissueProbeSetXRef.DataId = " + "TissueProbeSetData.Id", + ('112',)) diff --git a/gn2/tests/unit/base/test_species.py b/gn2/tests/unit/base/test_species.py new file mode 100644 index 00000000..239e8b3f --- /dev/null +++ b/gn2/tests/unit/base/test_species.py @@ -0,0 +1,80 @@ +"""Tests wqflask/base/species.py""" +import pytest +from gn2.base.species import TheSpecies +from gn2.base.species import IndChromosome +from gn2.base.species import Chromosomes +from collections import OrderedDict +from dataclasses import dataclass + + +@dataclass +class MockChromosome: + OrderId: int + Name: str + Length: int + + +@dataclass +class MockGroup: + name: str + + +@dataclass +class MockDataset: + group: MockGroup + + +@pytest.mark.parametrize( + ("species_name", "dataset", "expected_name", "chromosome_param"), + (("BXD", None, "BXD", 1), + (None, "Random Dataset", None, 1))) +def test_species(mocker, species_name, dataset, + expected_name, chromosome_param): + _c = mocker.patch("base.species.Chromosomes", + return_value=chromosome_param) + test_species = TheSpecies(dataset=dataset, + species_name=species_name) + _c.assert_called_with(species=species_name, + dataset=dataset) + assert test_species.name == expected_name + assert test_species.chromosomes == chromosome_param + + +@pytest.mark.parametrize( + ("name", "length", "mb_length"), + (("Test A", 10000000, 10), + ("Test B", 100, 0.0001))) +def test_create_ind_chromosome(name, length, mb_length): + _ind = IndChromosome(name=name, length=length) + assert _ind.name == name + assert _ind.length == length + assert _ind.mb_length == mb_length + + +@pytest.mark.parametrize( + ("species", "dataset", "expected_call"), + (("bxd", MockDataset(MockGroup("Random")), + ("SELECT Chr_Length.Name, Chr_Length.OrderId, Length " + "FROM Chr_Length, Species WHERE " + "Chr_Length.SpeciesId = Species.SpeciesId AND " + "Species.Name = %s " + "ORDER BY OrderId", ("Bxd",))), + (None, MockDataset(MockGroup("Random")), + ("SELECT Chr_Length.Name, Chr_Length.OrderId, " + "Length FROM Chr_Length, InbredSet WHERE " + "Chr_Length.SpeciesId = InbredSet.SpeciesId AND " + "InbredSet.Name = " + "%s ORDER BY OrderId", ("Random",))))) +def test_create_chromosomes(mocker, species, dataset, expected_call): + mock_conn = mocker.MagicMock() + with mock_conn.cursor() as cursor: + cursor.fetchall.return_value = (("1", 2, 10,), + ("2", 3, 11,), + ("4", 5, 15,),) + _c = Chromosomes(dataset=dataset, species=species) + assert _c.chromosomes(cursor) == OrderedDict([ + ("1", IndChromosome("1", 10)), + ("2", IndChromosome("2", 11)), + ("4", IndChromosome("4", 15)), + ]) + cursor.execute.assert_called_with(*expected_call) diff --git a/gn2/tests/unit/base/test_trait.py b/gn2/tests/unit/base/test_trait.py new file mode 100644 index 00000000..417956ae --- /dev/null +++ b/gn2/tests/unit/base/test_trait.py @@ -0,0 +1,262 @@ +# -*- coding: utf-8 -*- +"""Tests wqflask/base/trait.py""" +import unittest +from unittest import mock + +from gn2.base.trait import GeneralTrait +from gn2.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'""" + @mock.patch('base.trait.database_connection') + def test_retrieve_trait_info_with_empty_dataset(self, mock_db): + """Test that an exception is raised when dataset is empty""" + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn + with self.assertRaises(ValueError): + retrieve_trait_info(trait=mock.MagicMock(), + dataset={}) + + @mock.patch('base.trait.requests.get') + @mock.patch('base.trait.g', mock.Mock()) + @mock.patch('base.trait.database_connection') + def test_retrieve_trait_info_with_empty_trait_info(self, + mock_db, + requests_mock): + """Empty trait info""" + conn = mock.MagicMock() + cursor = mock.MagicMock() + cursor.fetchone.return_value = {} + conn.cursor.return_value.__enter__.return_value = cursor + mock_db.return_value.__enter__.return_value = conn + 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', mock.Mock()) + @mock.patch('base.trait.database_connection') + def test_retrieve_trait_info_with_non_empty_trait_info(self, + mock_db, + requests_mock): + """Test that attributes are set""" + mock_dataset = mock.MagicMock() + conn = mock.MagicMock() + cursor = mock.MagicMock() + cursor.fetchone.return_value = [1, 2, 3, 4] + conn.cursor.return_value.__enter__.return_value = cursor + mock_db.return_value.__enter__.return_value = conn + 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', mock.Mock()) + @mock.patch('base.trait.database_connection') + def test_retrieve_trait_info_utf8_parsing(self, + mock_db, + requests_mock): + """Test that utf-8 strings are parsed correctly""" + utf_8_string = "test_string" + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn + 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") + + + @unittest.skip("Too complicated") + @mock.patch('base.trait.requests.get') + @mock.patch('base.trait.database_connection') + @mock.patch('base.trait.get_resource_id') + def test_retrieve_trait_info_with_non_empty_lrs(self, + resource_id_mock, + mock_db, + requests_mock): + """Test retrieve trait info when lrs has a value""" + resource_id_mock.return_value = 1 + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn + with conn.cursor() as cursor: + cursor.fetchone.side_effect = [ + # trait_info = g.db.execute(query).fetchone() + [1, 2, 3, 4], + # trait_qtl = g.db.execute(query).fetchone() + [1, 2.37, 3, 4, 5], + # trait_info = g.db.execute(query).fetchone() + [2.7333, 2.1204] + ] + 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") + + @unittest.skip("Too complicated") + @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") + + @unittest.skip("Too complicated") + @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") diff --git a/gn2/tests/unit/base/test_webqtl_case_data.py b/gn2/tests/unit/base/test_webqtl_case_data.py new file mode 100644 index 00000000..250b8358 --- /dev/null +++ b/gn2/tests/unit/base/test_webqtl_case_data.py @@ -0,0 +1,40 @@ +"""Tests for wqflask/base/webqtlCaseData.py""" +import unittest + +from gn2.wqflask import app # Required because of utility.tools in webqtlCaseData.py +from gn2.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") |