From 204a308be0f741726b9a620d88fbc22b22124c81 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 29 Dec 2023 18:55:37 +0000 Subject: Namespace all modules under gn2. We move all modules under a gn2 directory. This is important for "correct" packaging and deployment as a Guix service. --- wqflask/tests/unit/base/__init__.py | 0 wqflask/tests/unit/base/test_data_set.py | 238 ------------------- wqflask/tests/unit/base/test_general_object.py | 40 ---- .../tests/unit/base/test_mrna_assay_tissue_data.py | 81 ------- wqflask/tests/unit/base/test_species.py | 80 ------- wqflask/tests/unit/base/test_trait.py | 262 --------------------- wqflask/tests/unit/base/test_webqtl_case_data.py | 40 ---- 7 files changed, 741 deletions(-) delete mode 100644 wqflask/tests/unit/base/__init__.py delete mode 100644 wqflask/tests/unit/base/test_data_set.py delete mode 100644 wqflask/tests/unit/base/test_general_object.py delete mode 100644 wqflask/tests/unit/base/test_mrna_assay_tissue_data.py delete mode 100644 wqflask/tests/unit/base/test_species.py delete mode 100644 wqflask/tests/unit/base/test_trait.py delete mode 100644 wqflask/tests/unit/base/test_webqtl_case_data.py (limited to 'wqflask/tests/unit/base') diff --git a/wqflask/tests/unit/base/__init__.py b/wqflask/tests/unit/base/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/wqflask/tests/unit/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py deleted file mode 100644 index 744c8a94..00000000 --- a/wqflask/tests/unit/base/test_data_set.py +++ /dev/null @@ -1,238 +0,0 @@ -"""Tests for wqflask/base/data_set.py""" - -import unittest -from unittest import mock -from dataclasses import dataclass -from gn3.monads import MonadicDict - -from wqflask import app -from base.data_set import DatasetType -from 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/wqflask/tests/unit/base/test_general_object.py b/wqflask/tests/unit/base/test_general_object.py deleted file mode 100644 index 00fd3c72..00000000 --- a/wqflask/tests/unit/base/test_general_object.py +++ /dev/null @@ -1,40 +0,0 @@ -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), "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/wqflask/tests/unit/base/test_mrna_assay_tissue_data.py b/wqflask/tests/unit/base/test_mrna_assay_tissue_data.py deleted file mode 100644 index c43fb4b6..00000000 --- a/wqflask/tests/unit/base/test_mrna_assay_tissue_data.py +++ /dev/null @@ -1,81 +0,0 @@ -import pytest -from 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/wqflask/tests/unit/base/test_species.py b/wqflask/tests/unit/base/test_species.py deleted file mode 100644 index f12bde6d..00000000 --- a/wqflask/tests/unit/base/test_species.py +++ /dev/null @@ -1,80 +0,0 @@ -"""Tests wqflask/base/species.py""" -import pytest -from base.species import TheSpecies -from base.species import IndChromosome -from 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/wqflask/tests/unit/base/test_trait.py b/wqflask/tests/unit/base/test_trait.py deleted file mode 100644 index 5a27e243..00000000 --- a/wqflask/tests/unit/base/test_trait.py +++ /dev/null @@ -1,262 +0,0 @@ -# -*- coding: utf-8 -*- -"""Tests wqflask/base/trait.py""" -import unittest -from 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'""" - @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/wqflask/tests/unit/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py deleted file mode 100644 index e1555cb4..00000000 --- a/wqflask/tests/unit/base/test_webqtl_case_data.py +++ /dev/null @@ -1,40 +0,0 @@ -"""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), - " 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") -- cgit v1.2.3