diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/db/test_traits.py | 195 |
1 files changed, 0 insertions, 195 deletions
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py index a1c1136..434f758 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -5,9 +5,7 @@ from gn3.db.traits import ( build_trait_name, export_trait_data, export_informative, - get_trait_csv_sample_data, set_haveinfo_field, - update_sample_data, retrieve_trait_info, set_confidential_field, set_homologene_id_field, @@ -203,56 +201,6 @@ class TestTraitsDBFunctions(TestCase): expected) @pytest.mark.unit_test - def test_update_sample_data(self): - """Test that the SQL queries when calling update_sample_data are called with - the right calls. - - """ - # pylint: disable=C0103 - db_mock = mock.MagicMock() - PUBLISH_DATA_SQL: str = ( - "UPDATE PublishData SET value = %s " - "WHERE StrainId = %s AND Id = %s") - PUBLISH_SE_SQL: str = ( - "UPDATE PublishSE SET error = %s " - "WHERE StrainId = %s AND DataId = %s") - N_STRAIN_SQL: str = ( - "UPDATE NStrain SET count = %s " - "WHERE StrainId = %s AND DataId = %s") - - with db_mock.cursor() as cursor: - type(cursor).rowcount = 1 - mock_fetchone = mock.MagicMock() - mock_fetchone.return_value = (1, 1) - type(cursor).fetchone = mock_fetchone - self.assertEqual(update_sample_data( - conn=db_mock, strain_name="BXD11", - trait_name="1", - phenotype_id=10, value=18.7, - error=2.3, count=2), - (1, 1, 1)) - cursor.execute.assert_has_calls( - [mock.call(('SELECT Strain.Id, PublishData.Id FROM' - ' (PublishData, Strain, PublishXRef, ' - 'PublishFreeze) LEFT JOIN PublishSE ON ' - '(PublishSE.DataId = PublishData.Id ' - 'AND PublishSE.StrainId = ' - 'PublishData.StrainId) LEFT JOIN NStrain ON ' - '(NStrain.DataId = PublishData.Id AND ' - 'NStrain.StrainId = PublishData.StrainId) WHERE ' - 'PublishXRef.InbredSetId = ' - 'PublishFreeze.InbredSetId AND PublishData.Id = ' - 'PublishXRef.DataId AND PublishXRef.Id = %s AND ' - 'PublishXRef.PhenotypeId = %s AND ' - 'PublishData.StrainId = Strain.Id AND ' - 'Strain.Name = %s'), - ("1", 10, "BXD11")), - mock.call(PUBLISH_DATA_SQL, (18.7, 1, 1)), - mock.call(PUBLISH_SE_SQL, (2.3, 1, 1)), - mock.call(N_STRAIN_SQL, (2, 1, 1))] - ) - - @pytest.mark.unit_test def test_set_haveinfo_field(self): """Test that the `haveinfo` field is set up correctly""" for trait_info, expected in [ @@ -432,146 +380,3 @@ class TestTraitsDBFunctions(TestCase): with self.subTest(trait_data=trait_data): self.assertEqual( export_informative(trait_data, inc_var), expected) - - -class TestRetrieveCsvData(TestCase): - "Test cases for retrieving csv data" - def test_get_trait_csv_sample_data_with_case_attributes(self): - """Test that correct csv is returned when all samples have case attribute -values""" - mock_conn = mock.MagicMock() - with mock_conn.cursor() as cursor: - cursor.fetchall.return_value = [ - ['H1044,25.900000,x,1', 'Strain', 'BXD29'], - ['H1044,25.900000,x,1', 'Condition', 'CD'], - ['H1044,25.900000,x,1', 'EarTag', 1044], - ['H1044,25.900000,x,1', 'Age', 724], - ['H1096,23.700001,x,1', 'EarTag', 1096], - ['H1096,23.700001,x,1', 'Age', 732], - ['H1096,23.700001,x,1', 'Strain', 'BXD90'], - ['H1096,23.700001,x,1', 'Condition', 'CD'], - ['H1163,95.000000,x,1', 'Strain', 'D2B6F1'], - ['H1163,95.000000,x,1', 'Condition', 'HF'], - ['H1163,95.000000,x,1', 'EarTag', 1163], - ['H1163,95.000000,x,1', 'Age', 1114], - ['H1230,88.099998,x,1', 'EarTag', 1230], - ['H1230,88.099998,x,1', 'Age', 726], - ['H1230,88.099998,x,1', 'Strain', 'B6D2F1'], - ['H1230,88.099998,x,1', 'Condition', 'HF'], - ['H1251,24.100000,x,1', 'EarTag', 1251], - ['H1251,24.100000,x,1', 'Age', 711], - ['H1251,24.100000,x,1', 'Strain', 'C57BL/6J'], - ['H1251,24.100000,x,1', 'Condition', 'CD'], - ['H1292,24.900000,x,1', 'Strain', 'C57BL/6J'], - ['H1292,24.900000,x,1', 'Condition', 'CD'], - ['H1292,24.900000,x,1', 'EarTag', 1292], - ['H1292,24.900000,x,1', 'Age', 705], - ] - csv = get_trait_csv_sample_data(conn=mock_conn, - trait_name=10006, - phenotype_id=28409) - self.assertEqual(csv, """Strain Name,Value,SE,Count,Age,Condition,EarTag,Strain -H1044,25.900000,x,1,724,CD,1044,BXD29 -H1096,23.700001,x,1,732,CD,1096,BXD90 -H1163,95.000000,x,1,1114,HF,1163,D2B6F1 -H1230,88.099998,x,1,726,HF,1230,B6D2F1 -H1251,24.100000,x,1,711,CD,1251,C57BL/6J -H1292,24.900000,x,1,705,CD,1292,C57BL/6J -""") - - def test_get_trait_csv_sample_data_with_missing_case_attributes(self): - """Test that the correct csv is returned when some case attributes are not -present from some samples""" - mock_conn = mock.MagicMock() - with mock_conn.cursor() as cursor: - cursor.fetchall.return_value = [ - ['H1044,25.900000,x,1', 'Strain', 'BXD29'], - ['H1044,25.900000,x,1', 'Condition', 'CD'], - ['H1044,25.900000,x,1', 'Age', 724], - ['H1096,23.700001,x,1', 'Age', 732], - ['H1096,23.700001,x,1', 'Strain', 'BXD90'], - ['H1096,23.700001,x,1', 'Condition', 'CD'], - ['H1163,95.000000,x,1', 'Condition', 'HF'], - ['H1163,95.000000,x,1', 'EarTag', 1163], - ['H1163,95.000000,x,1', 'Age', 1114], - ['H1230,88.099998,x,1', 'EarTag', 1230], - ['H1230,88.099998,x,1', 'Age', 726], - ['H1230,88.099998,x,1', 'Strain', 'B6D2F1'], - ['H1230,88.099998,x,1', 'Condition', 'HF'], - ['H1251,24.100000,x,1', 'EarTag', 1251], - ['H1251,24.100000,x,1', 'Age', 711], - ['H1251,24.100000,x,1', 'Strain', 'C57BL/6J'], - ['H1251,24.100000,x,1', 'Condition', 'CD'], - ['H1292,24.900000,x,1', 'Strain', 'C57BL/6J'], - ['H1292,24.900000,x,1', 'Condition', 'CD'], - ['H1292,24.900000,x,1', 'EarTag', 1292], - ] - csv = get_trait_csv_sample_data(conn=mock_conn, - trait_name=10006, - phenotype_id=28409) - self.assertEqual(csv, """Strain Name,Value,SE,Count,Age,Condition,EarTag,Strain -H1044,25.900000,x,1,724,CD,x,BXD29 -H1096,23.700001,x,1,732,CD,x,BXD90 -H1163,95.000000,x,1,1114,HF,1163,x -H1230,88.099998,x,1,726,HF,1230,B6D2F1 -H1251,24.100000,x,1,711,CD,1251,C57BL/6J -H1292,24.900000,x,1,x,CD,1292,C57BL/6J -""") - - def test_get_trait_csv_sample_data_with_varying_case_attributes(self): - """Test that the correct csv is returned when case attributes are entirely -missing from same samples, and only one sample has a case attribute that is -not present in all other samples""" - mock_conn = mock.MagicMock() - with mock_conn.cursor() as cursor: - cursor.fetchall.return_value = [ - ['H1044,25.900000,x,1', 'x', 'x'], - ['H1096,23.700001,x,1', 'x', 'x'], - ['H1163,95.000000,x,1', 'x', 'x'], - ['H1230,88.099998,x,1', 'x', 'x'], - ['H1251,24.100000,x,1', 'x', 'x'], - ['H1292,24.900000,x,1', 'x', 'x'], - ] - csv = get_trait_csv_sample_data(conn=mock_conn, - trait_name=10006, - phenotype_id=28409) - self.assertEqual(csv, """Strain Name,Value,SE,Count -H1044,25.900000,x,1 -H1096,23.700001,x,1 -H1163,95.000000,x,1 -H1230,88.099998,x,1 -H1251,24.100000,x,1 -H1292,24.900000,x,1""") - - def test_get_trait_csv_sample_data_with_empty_case_attributes(self): - mock_conn = mock.MagicMock() - with mock_conn.cursor() as cursor: - cursor.fetchall.return_value = [ - ['H1044,25.900000,x,1', 'x', 'x'], - ['H1096,23.700001,x,1', 'Age', 732], - ['H1096,23.700001,x,1', 'Sex', "M"], - ['H1096,23.700001,x,1', 'Strain', 'BXD90'], - ['H1096,23.700001,x,1', 'Condition', 'CD'], - ['H1163,95.000000,x,1', 'Condition', 'HF'], - ['H1163,95.000000,x,1', 'EarTag', 1163], - ['H1163,95.000000,x,1', 'Age', 1114], - ['H1230,88.099998,x,1', 'EarTag', 1230], - ['H1230,88.099998,x,1', 'Age', 726], - ['H1230,88.099998,x,1', 'Strain', 'B6D2F1'], - ['H1230,88.099998,x,1', 'Condition', 'HF'], - ['H1251,24.100000,x,1', 'x', 'x'], - ['H1292,24.900000,x,1', 'Strain', 'C57BL/6J'], - ['H1292,24.900000,x,1', 'Condition', 'CD'], - ['H1292,24.900000,x,1', 'EarTag', 1292], - ] - csv = get_trait_csv_sample_data(conn=mock_conn, - trait_name=10006, - phenotype_id=28409) - self.assertEqual(csv, """Strain Name,Value,SE,Count,Age,Condition,EarTag,Sex,Strain -H1044,25.900000,x,1,x,x,x,x,x -H1096,23.700001,x,1,732,CD,x,M,BXD90 -H1163,95.000000,x,1,1114,HF,1163,x,x -H1230,88.099998,x,1,726,HF,1230,x,B6D2F1 -H1251,24.100000,x,1,x,x,x,x,x -H1292,24.900000,x,1,x,CD,1292,x,C57BL/6J -""") |