diff options
Diffstat (limited to 'tests/unit/db')
| -rw-r--r-- | tests/unit/db/test_audit.py | 3 | ||||
| -rw-r--r-- | tests/unit/db/test_correlation.py | 100 | ||||
| -rw-r--r-- | tests/unit/db/test_datasets.py | 35 | ||||
| -rw-r--r-- | tests/unit/db/test_db.py | 8 | ||||
| -rw-r--r-- | tests/unit/db/test_genotypes.py | 6 | ||||
| -rw-r--r-- | tests/unit/db/test_genotypes2.py | 13 | ||||
| -rw-r--r-- | tests/unit/db/test_sample_data.py | 188 | ||||
| -rw-r--r-- | tests/unit/db/test_species.py | 5 | ||||
| -rw-r--r-- | tests/unit/db/test_traits.py | 60 |
9 files changed, 362 insertions, 56 deletions
diff --git a/tests/unit/db/test_audit.py b/tests/unit/db/test_audit.py index 7480169..884afc6 100644 --- a/tests/unit/db/test_audit.py +++ b/tests/unit/db/test_audit.py @@ -3,6 +3,8 @@ import json from unittest import TestCase from unittest import mock +import pytest + from gn3.db import insert from gn3.db.metadata_audit import MetadataAudit @@ -10,6 +12,7 @@ from gn3.db.metadata_audit import MetadataAudit class TestMetadatAudit(TestCase): """Test cases for fetching chromosomes""" + @pytest.mark.unit_test def test_insert_into_metadata_audit(self): """Test that data is inserted correctly in the audit table diff --git a/tests/unit/db/test_correlation.py b/tests/unit/db/test_correlation.py new file mode 100644 index 0000000..5afe55f --- /dev/null +++ b/tests/unit/db/test_correlation.py @@ -0,0 +1,100 @@ +""" +Tests for the gn3.db.correlations module +""" + +from unittest import TestCase + +import pytest + +from gn3.db.correlations import ( + build_query_sgo_lit_corr, + build_query_tissue_corr) + +class TestCorrelation(TestCase): + """Test cases for correlation data fetching functions""" + maxDiff = None + + @pytest.mark.unit_test + def test_build_query_sgo_lit_corr(self): + """ + Test that the literature correlation query is built correctly. + """ + self.assertEqual( + build_query_sgo_lit_corr( + "Probeset", + "temp_table_xy45i7wd", + "T1.value, T2.value, T3.value", + (("LEFT JOIN ProbesetData AS T1 " + "ON T1.Id = ProbesetXRef.DataId " + "AND T1.StrainId=%(T1_sample_id)s"), + ( + "LEFT JOIN ProbesetData AS T2 " + "ON T2.Id = ProbesetXRef.DataId " + "AND T2.StrainId=%(T2_sample_id)s"), + ( + "LEFT JOIN ProbesetData AS T3 " + "ON T3.Id = ProbesetXRef.DataId " + "AND T3.StrainId=%(T3_sample_id)s"))), + (("SELECT Probeset.Name, temp_table_xy45i7wd.value, " + "T1.value, T2.value, T3.value " + "FROM (Probeset, ProbesetXRef, ProbesetFreeze) " + "LEFT JOIN temp_table_xy45i7wd ON temp_table_xy45i7wd.GeneId2=ProbeSet.GeneId " + "LEFT JOIN ProbesetData AS T1 " + "ON T1.Id = ProbesetXRef.DataId " + "AND T1.StrainId=%(T1_sample_id)s " + "LEFT JOIN ProbesetData AS T2 " + "ON T2.Id = ProbesetXRef.DataId " + "AND T2.StrainId=%(T2_sample_id)s " + "LEFT JOIN ProbesetData AS T3 " + "ON T3.Id = ProbesetXRef.DataId " + "AND T3.StrainId=%(T3_sample_id)s " + "WHERE ProbeSet.GeneId IS NOT NULL " + "AND temp_table_xy45i7wd.value IS NOT NULL " + "AND ProbesetXRef.ProbesetFreezeId = ProbesetFreeze.Id " + "AND ProbesetFreeze.Name = %(db_name)s " + "AND Probeset.Id = ProbesetXRef.ProbesetId " + "ORDER BY Probeset.Id"), + 2)) + + @pytest.mark.unit_test + def test_build_query_tissue_corr(self): + """ + Test that the tissue correlation query is built correctly. + """ + self.assertEqual( + build_query_tissue_corr( + "Probeset", + "temp_table_xy45i7wd", + "T1.value, T2.value, T3.value", + (("LEFT JOIN ProbesetData AS T1 " + "ON T1.Id = ProbesetXRef.DataId " + "AND T1.StrainId=%(T1_sample_id)s"), + ( + "LEFT JOIN ProbesetData AS T2 " + "ON T2.Id = ProbesetXRef.DataId " + "AND T2.StrainId=%(T2_sample_id)s"), + ( + "LEFT JOIN ProbesetData AS T3 " + "ON T3.Id = ProbesetXRef.DataId " + "AND T3.StrainId=%(T3_sample_id)s"))), + (("SELECT Probeset.Name, temp_table_xy45i7wd.Correlation, " + "temp_table_xy45i7wd.PValue, " + "T1.value, T2.value, T3.value " + "FROM (Probeset, ProbesetXRef, ProbesetFreeze) " + "LEFT JOIN temp_table_xy45i7wd ON temp_table_xy45i7wd.Symbol=ProbeSet.Symbol " + "LEFT JOIN ProbesetData AS T1 " + "ON T1.Id = ProbesetXRef.DataId " + "AND T1.StrainId=%(T1_sample_id)s " + "LEFT JOIN ProbesetData AS T2 " + "ON T2.Id = ProbesetXRef.DataId " + "AND T2.StrainId=%(T2_sample_id)s " + "LEFT JOIN ProbesetData AS T3 " + "ON T3.Id = ProbesetXRef.DataId " + "AND T3.StrainId=%(T3_sample_id)s " + "WHERE ProbeSet.Symbol IS NOT NULL " + "AND temp_table_xy45i7wd.Correlation IS NOT NULL " + "AND ProbesetXRef.ProbesetFreezeId = ProbesetFreeze.Id " + "AND ProbesetFreeze.Name = %(db_name)s " + "AND Probeset.Id = ProbesetXRef.ProbesetId " + "ORDER BY Probeset.Id"), + 3)) diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py index 39f4af9..e4abd2f 100644 --- a/tests/unit/db/test_datasets.py +++ b/tests/unit/db/test_datasets.py @@ -1,6 +1,7 @@ """Tests for gn3/db/datasets.py""" from unittest import mock, TestCase +import pytest from gn3.db.datasets import ( retrieve_dataset_name, retrieve_group_fields, @@ -11,35 +12,36 @@ from gn3.db.datasets import ( class TestDatasetsDBFunctions(TestCase): """Test cases for datasets functions.""" + @pytest.mark.unit_test def test_retrieve_dataset_name(self): """Test that the function is called correctly.""" - for trait_type, thresh, trait_name, dataset_name, columns, table in [ - ["ProbeSet", 9, "probesetTraitName", "probesetDatasetName", - "Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze"], - ["Geno", 3, "genoTraitName", "genoDatasetName", - "Id, Name, FullName, ShortName", "GenoFreeze"], - ["Publish", 6, "publishTraitName", "publishDatasetName", - "Id, Name, FullName, ShortName", "PublishFreeze"], - ["Temp", 4, "tempTraitName", "tempTraitName", - "Id, Name, FullName, ShortName", "TempFreeze"]]: + for trait_type, thresh, dataset_name, columns, table, expected in [ + ["ProbeSet", 9, "probesetDatasetName", + "Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze", + {"dataset_id": None, "dataset_name": "probesetDatasetName", + "dataset_fullname": "probesetDatasetName"}], + ["Geno", 3, "genoDatasetName", + "Id, Name, FullName, ShortName", "GenoFreeze", {}], + ["Publish", 6, "publishDatasetName", + "Id, Name, FullName, ShortName", "PublishFreeze", {}]]: db_mock = mock.MagicMock() with self.subTest(trait_type=trait_type): with db_mock.cursor() as cursor: cursor.fetchone.return_value = {} self.assertEqual( retrieve_dataset_name( - trait_type, thresh, trait_name, dataset_name, db_mock), - {}) + trait_type, thresh, dataset_name, db_mock), + expected) cursor.execute.assert_called_once_with( - "SELECT {cols} " - "FROM {table} " + f"SELECT {columns} " + f"FROM {table} " "WHERE public > %(threshold)s AND " "(Name = %(name)s " "OR FullName = %(name)s " - "OR ShortName = %(name)s)".format( - table=table, cols=columns), + "OR ShortName = %(name)s)", {"threshold": thresh, "name": dataset_name}) + @pytest.mark.unit_test def test_retrieve_probeset_group_fields(self): """ Test that the `group` and `group_id` fields are retrieved appropriately @@ -63,6 +65,7 @@ class TestDatasetsDBFunctions(TestCase): " AND ProbeSetFreeze.Name = %(name)s"), {"name": trait_name}) + @pytest.mark.unit_test def test_retrieve_group_fields(self): """ Test that the group fields are set up correctly for the different trait @@ -88,6 +91,7 @@ class TestDatasetsDBFunctions(TestCase): trait_type, trait_name, dataset_info, db_mock), expected) + @pytest.mark.unit_test def test_retrieve_publish_group_fields(self): """ Test that the `group` and `group_id` fields are retrieved appropriately @@ -110,6 +114,7 @@ class TestDatasetsDBFunctions(TestCase): " AND PublishFreeze.Name = %(name)s"), {"name": trait_name}) + @pytest.mark.unit_test def test_retrieve_geno_group_fields(self): """ Test that the `group` and `group_id` fields are retrieved appropriately diff --git a/tests/unit/db/test_db.py b/tests/unit/db/test_db.py index e47c9fd..8ac468c 100644 --- a/tests/unit/db/test_db.py +++ b/tests/unit/db/test_db.py @@ -2,6 +2,8 @@ from unittest import TestCase from unittest import mock +import pytest + from gn3.db import fetchall from gn3.db import fetchone from gn3.db import update @@ -14,6 +16,7 @@ from gn3.db.metadata_audit import MetadataAudit class TestCrudMethods(TestCase): """Test cases for CRUD methods""" + @pytest.mark.unit_test def test_update_phenotype_with_no_data(self): """Test that a phenotype is updated correctly if an empty Phenotype dataclass is provided @@ -24,6 +27,7 @@ class TestCrudMethods(TestCase): conn=db_mock, table="Phenotype", data=Phenotype(), where=Phenotype()), None) + @pytest.mark.unit_test def test_update_phenotype_with_data(self): """ Test that a phenotype is updated correctly if some @@ -46,6 +50,7 @@ class TestCrudMethods(TestCase): "Submitter = %s WHERE id = %s AND Owner = %s", ('Test Pre Pub', 'Test Post Pub', 'Rob', 1, 'Rob')) + @pytest.mark.unit_test def test_fetch_phenotype(self): """Test that a single phenotype is fetched properly @@ -68,6 +73,7 @@ class TestCrudMethods(TestCase): "SELECT * FROM Phenotype WHERE id = %s AND Owner = %s", (35, 'Rob')) + @pytest.mark.unit_test def test_fetchall_metadataaudit(self): """Test that multiple metadata_audit entries are fetched properly @@ -96,6 +102,7 @@ class TestCrudMethods(TestCase): "dataset_id = %s AND editor = %s"), (35, 'Rob')) + @pytest.mark.unit_test # pylint: disable=R0201 def test_probeset_called_with_right_columns(self): """Given a columns argument, test that the correct sql query is @@ -112,6 +119,7 @@ class TestCrudMethods(TestCase): "Name = %s", ("1446112_at",)) + @pytest.mark.unit_test def test_diff_from_dict(self): """Test that a correct diff is generated""" self.assertEqual(diff_from_dict({"id": 1, "data": "a"}, diff --git a/tests/unit/db/test_genotypes.py b/tests/unit/db/test_genotypes.py index c125224..28728bf 100644 --- a/tests/unit/db/test_genotypes.py +++ b/tests/unit/db/test_genotypes.py @@ -1,5 +1,6 @@ """Tests gn3.db.genotypes""" from unittest import TestCase +import pytest from gn3.db.genotypes import ( parse_genotype_file, parse_genotype_labels, @@ -10,6 +11,7 @@ from gn3.db.genotypes import ( class TestGenotypes(TestCase): """Tests for functions in `gn3.db.genotypes`.""" + @pytest.mark.unit_test def test_parse_genotype_labels(self): """Test that the genotype labels are parsed correctly.""" self.assertEqual( @@ -22,6 +24,7 @@ class TestGenotypes(TestCase): ("type", "test_type"), ("mat", "test_mat"), ("pat", "test_pat"), ("het", "test_het"), ("unk", "test_unk"))) + @pytest.mark.unit_test def test_parse_genotype_header(self): """Test that the genotype header is parsed correctly.""" for header, expected in [ @@ -43,6 +46,7 @@ class TestGenotypes(TestCase): with self.subTest(header=header): self.assertEqual(parse_genotype_header(header), expected) + @pytest.mark.unit_test def test_parse_genotype_data_line(self): """Test parsing of data lines.""" for line, geno_obj, parlist, expected in [ @@ -76,6 +80,7 @@ class TestGenotypes(TestCase): parse_genotype_marker(line, geno_obj, parlist), expected) + @pytest.mark.unit_test def test_build_genotype_chromosomes(self): """ Given `markers` and `geno_obj`, test that `build_genotype_chromosomes` @@ -115,6 +120,7 @@ class TestGenotypes(TestCase): build_genotype_chromosomes(geno_obj, markers), expected) + @pytest.mark.unit_test def test_parse_genotype_file(self): """Test the parsing of genotype files. """ self.assertEqual( diff --git a/tests/unit/db/test_genotypes2.py b/tests/unit/db/test_genotypes2.py new file mode 100644 index 0000000..453120b --- /dev/null +++ b/tests/unit/db/test_genotypes2.py @@ -0,0 +1,13 @@ +"""Module to test functions in gn3.db.genotypes""" + +import pytest + +from gn3.db.genotypes import load_genotype_samples + +@pytest.mark.unit_test +@pytest.mark.parametrize( + "genotype_filename,file_type,expected", ( + ("tests/unit/test_data/genotype.txt", "geno", ("BXD1","BXD2")),)) +def test_load_genotype_samples(genotype_filename, file_type, expected): + """Test that the genotype samples are loaded correctly""" + assert load_genotype_samples(genotype_filename, file_type) == expected diff --git a/tests/unit/db/test_sample_data.py b/tests/unit/db/test_sample_data.py new file mode 100644 index 0000000..2524e07 --- /dev/null +++ b/tests/unit/db/test_sample_data.py @@ -0,0 +1,188 @@ +"""Tests for gn3.db.sample_data""" +import pytest +import gn3 + +from gn3.db.sample_data import __extract_actions +from gn3.db.sample_data import delete_sample_data +from gn3.db.sample_data import insert_sample_data +from gn3.db.sample_data import update_sample_data + + +@pytest.mark.unit_test +def test_insert_sample_data(mocker): + """Test that inserts work properly""" + mock_conn = mocker.MagicMock() + strain_id, data_id, inbredset_id = 1, 17373, 20 + with mock_conn.cursor() as cursor: + cursor.fetchone.side_effect = ( + 0, + [ + 19, + ], + 0, + ) + mocker.patch( + "gn3.db.sample_data.get_sample_data_ids", + return_value=(strain_id, data_id, inbredset_id), + ) + insert_sample_data( + conn=mock_conn, + trait_name=35, + data="BXD1,18,3,0,M", + csv_header="Strain Name,Value,SE,Count,Sex", + phenotype_id=10007, + ) + calls = [ + mocker.call( + "SELECT Id FROM PublishData where Id = %s " "AND StrainId = %s", + (data_id, strain_id), + ), + mocker.call( + "INSERT INTO PublishData " "(StrainId, Id, value) VALUES (%s, %s, %s)", + (strain_id, data_id, "18"), + ), + mocker.call( + "INSERT INTO PublishSE " + "(StrainId, DataId, error) VALUES (%s, %s, %s)", + (strain_id, data_id, "3"), + ), + mocker.call( + "INSERT INTO NStrain " "(StrainId, DataId, count) VALUES (%s, %s, %s)", + (strain_id, data_id, "0"), + ), + mocker.call("SELECT Id FROM CaseAttribute WHERE Name = %s", ("Sex",)), + mocker.call( + "SELECT StrainId FROM CaseAttributeXRefNew " + "WHERE StrainId = %s AND " + "CaseAttributeId = %s AND InbredSetId = %s", + (strain_id, 19, inbredset_id), + ), + mocker.call( + "INSERT INTO CaseAttributeXRefNew " + "(StrainId, CaseAttributeId, Value, " + "InbredSetId) VALUES (%s, %s, %s, %s)", + (strain_id, 19, "M", inbredset_id), + ), + ] + cursor.execute.assert_has_calls(calls, any_order=False) + + +@pytest.mark.unit_test +def test_delete_sample_data(mocker): + """Test that deletes work properly""" + mock_conn = mocker.MagicMock() + strain_id, data_id, inbredset_id = 1, 17373, 20 + with mock_conn.cursor() as cursor: + cursor.fetchone.side_effect = ( + 0, + [ + 19, + ], + 0, + ) + mocker.patch( + "gn3.db.sample_data.get_sample_data_ids", + return_value=(strain_id, data_id, inbredset_id), + ) + delete_sample_data( + conn=mock_conn, + trait_name=35, + data="BXD1,18,3,0,M", + csv_header="Strain Name,Value,SE,Count,Sex", + phenotype_id=10007, + ) + calls = [ + mocker.call( + "DELETE FROM PublishData WHERE " "StrainId = %s AND Id = %s", + (strain_id, data_id), + ), + mocker.call( + "DELETE FROM PublishSE WHERE " "StrainId = %s AND DataId = %s", + (strain_id, data_id), + ), + mocker.call( + "DELETE FROM NStrain WHERE " "StrainId = %s AND DataId = %s", + (strain_id, data_id), + ), + mocker.call( + "DELETE FROM CaseAttributeXRefNew WHERE " + "StrainId = %s AND CaseAttributeId = " + "(SELECT CaseAttributeId FROM " + "CaseAttribute WHERE Name = %s) " + "AND InbredSetId = %s", + (strain_id, "Sex", inbredset_id), + ), + ] + cursor.execute.assert_has_calls(calls, any_order=False) + + +@pytest.mark.unit_test +def test_extract_actions(): + """Test that extracting the correct dict of 'actions' work properly""" + assert __extract_actions( + original_data="BXD1,18,x,0,x", + updated_data="BXD1,x,2,1,F", + csv_header="Strain Name,Value,SE,Count,Sex", + ) == { + "delete": {"data": "BXD1,18", "csv_header": "Strain Name,Value"}, + "insert": {"data": "BXD1,2,F", "csv_header": "Strain Name,SE,Sex"}, + "update": {"data": "BXD1,1", "csv_header": "Strain Name,Count"}, + } + assert __extract_actions( + original_data="BXD1,18,x,0,x", + updated_data="BXD1,19,2,1,F", + csv_header="Strain Name,Value,SE,Count,Sex", + ) == { + "delete": None, + "insert": {"data": "BXD1,2,F", "csv_header": "Strain Name,SE,Sex"}, + "update": {"data": "BXD1,19,1", "csv_header": "Strain Name,Value,Count"}, + } + + +@pytest.mark.unit_test +def test_update_sample_data(mocker): + """Test that updates work properly""" + mock_conn = mocker.MagicMock() + strain_id, data_id, inbredset_id = 1, 17373, 20 + with mock_conn.cursor() as cursor: + # cursor.fetchone.side_effect = (0, [19, ], 0) + mocker.patch( + "gn3.db.sample_data.get_sample_data_ids", + return_value=(strain_id, data_id, inbredset_id), + ) + mocker.patch("gn3.db.sample_data.insert_sample_data", return_value=1) + mocker.patch("gn3.db.sample_data.delete_sample_data", return_value=1) + update_sample_data( + conn=mock_conn, + trait_name=35, + original_data="BXD1,18,x,0,x", + updated_data="BXD1,x,2,1,F", + csv_header="Strain Name,Value,SE,Count,Sex", + phenotype_id=10007, + ) + # pylint: disable=[E1101] + gn3.db.sample_data.insert_sample_data.assert_called_once_with( + conn=mock_conn, + trait_name=35, + data="BXD1,2,F", + csv_header="Strain Name,SE,Sex", + phenotype_id=10007, + ) + # pylint: disable=[E1101] + gn3.db.sample_data.delete_sample_data.assert_called_once_with( + conn=mock_conn, + trait_name=35, + data="BXD1,18", + csv_header="Strain Name,Value", + phenotype_id=10007, + ) + cursor.execute.assert_has_calls( + [ + mocker.call( + "UPDATE NStrain SET count = %s " + "WHERE StrainId = %s AND DataId = %s", + ("1", strain_id, data_id), + ) + ], + any_order=False, + ) diff --git a/tests/unit/db/test_species.py b/tests/unit/db/test_species.py index b2c4844..e883b21 100644 --- a/tests/unit/db/test_species.py +++ b/tests/unit/db/test_species.py @@ -2,6 +2,8 @@ from unittest import TestCase from unittest import mock +import pytest + from gn3.db.species import get_chromosome from gn3.db.species import get_all_species @@ -9,6 +11,7 @@ from gn3.db.species import get_all_species class TestChromosomes(TestCase): """Test cases for fetching chromosomes""" + @pytest.mark.unit_test def test_get_chromosome_using_species_name(self): """Test that the chromosome is fetched using a species name""" db_mock = mock.MagicMock() @@ -24,6 +27,7 @@ class TestChromosomes(TestCase): "Species.Name = 'TestCase' ORDER BY OrderId" ) + @pytest.mark.unit_test def test_get_chromosome_using_group_name(self): """Test that the chromosome is fetched using a group name""" db_mock = mock.MagicMock() @@ -39,6 +43,7 @@ class TestChromosomes(TestCase): "InbredSet.Name = 'TestCase' ORDER BY OrderId" ) + @pytest.mark.unit_test def test_get_all_species(self): """Test that species are fetched correctly""" db_mock = mock.MagicMock() diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py index 4aa9389..434f758 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -1,11 +1,11 @@ """Tests for gn3/db/traits.py""" from unittest import mock, TestCase +import pytest from gn3.db.traits import ( build_trait_name, export_trait_data, export_informative, set_haveinfo_field, - update_sample_data, retrieve_trait_info, set_confidential_field, set_homologene_id_field, @@ -49,6 +49,7 @@ trait_data = { class TestTraitsDBFunctions(TestCase): "Test cases for traits functions" + @pytest.mark.unit_test def test_retrieve_publish_trait_info(self): """Test retrieval of type `Publish` traits.""" db_mock = mock.MagicMock() @@ -75,15 +76,15 @@ class TestTraitsDBFunctions(TestCase): " Publication.Year, PublishXRef.Sequence, Phenotype.Units," " PublishXRef.comments" " FROM" - " PublishXRef, Publication, Phenotype, PublishFreeze" + " PublishXRef, Publication, Phenotype" " WHERE" " PublishXRef.Id = %(trait_name)s" " AND Phenotype.Id = PublishXRef.PhenotypeId" " AND Publication.Id = PublishXRef.PublicationId" - " AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId" - " AND PublishFreeze.Id =%(trait_dataset_id)s"), + " AND PublishXRef.InbredSetId = %(trait_dataset_id)s"), trait_source) + @pytest.mark.unit_test def test_retrieve_probeset_trait_info(self): """Test retrieval of type `Probeset` traits.""" db_mock = mock.MagicMock() @@ -119,6 +120,7 @@ class TestTraitsDBFunctions(TestCase): "AND ProbeSetFreeze.Name = %(trait_dataset_name)s " "AND ProbeSet.Name = %(trait_name)s"), trait_source) + @pytest.mark.unit_test def test_retrieve_geno_trait_info(self): """Test retrieval of type `Geno` traits.""" db_mock = mock.MagicMock() @@ -134,14 +136,14 @@ class TestTraitsDBFunctions(TestCase): "SELECT " "Geno.name, Geno.chr, Geno.mb, Geno.source2, Geno.sequence " "FROM " - "Geno, GenoFreeze, GenoXRef " + "Geno INNER JOIN GenoXRef ON GenoXRef.GenoId = Geno.Id " + "INNER JOIN GenoFreeze ON GenoFreeze.Id = GenoXRef.GenoFreezeId " "WHERE " - "GenoXRef.GenoFreezeId = GenoFreeze.Id " - "AND GenoXRef.GenoId = Geno.Id " - "AND GenoFreeze.Name = %(trait_dataset_name)s " + "GenoFreeze.Name = %(trait_dataset_name)s " "AND Geno.Name = %(trait_name)s"), trait_source) + @pytest.mark.unit_test def test_retrieve_temp_trait_info(self): """Test retrieval of type `Temp` traits.""" db_mock = mock.MagicMock() @@ -154,6 +156,7 @@ class TestTraitsDBFunctions(TestCase): "SELECT name, description FROM Temp WHERE Name = %(trait_name)s", trait_source) + @pytest.mark.unit_test def test_build_trait_name_with_good_fullnames(self): """ Check that the name is built correctly. @@ -170,6 +173,7 @@ class TestTraitsDBFunctions(TestCase): with self.subTest(fullname=fullname): self.assertEqual(build_trait_name(fullname), expected) + @pytest.mark.unit_test def test_build_trait_name_with_bad_fullnames(self): """ Check that an exception is raised if the full name format is wrong. @@ -179,6 +183,7 @@ class TestTraitsDBFunctions(TestCase): with self.assertRaises(AssertionError, msg="Name format error"): build_trait_name(fullname) + @pytest.mark.unit_test def test_retrieve_trait_info(self): """Test that information on traits is retrieved as appropriate.""" for threshold, trait_fullname, expected in [ @@ -195,39 +200,7 @@ class TestTraitsDBFunctions(TestCase): threshold, trait_fullname, db_mock), expected) - 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() - - STRAIN_ID_SQL: str = "UPDATE Strain SET Name = %s WHERE Id = %s" - 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 - self.assertEqual(update_sample_data( - conn=db_mock, strain_name="BXD11", - strain_id=10, publish_data_id=8967049, - value=18.7, error=2.3, count=2), - (1, 1, 1, 1)) - cursor.execute.assert_has_calls( - [mock.call(STRAIN_ID_SQL, ('BXD11', 10)), - mock.call(PUBLISH_DATA_SQL, (18.7, 10, 8967049)), - mock.call(PUBLISH_SE_SQL, (2.3, 10, 8967049)), - mock.call(N_STRAIN_SQL, (2, 10, 8967049))] - ) - + @pytest.mark.unit_test def test_set_haveinfo_field(self): """Test that the `haveinfo` field is set up correctly""" for trait_info, expected in [ @@ -236,6 +209,7 @@ class TestTraitsDBFunctions(TestCase): with self.subTest(trait_info=trait_info, expected=expected): self.assertEqual(set_haveinfo_field(trait_info), expected) + @pytest.mark.unit_test def test_set_homologene_id_field(self): """Test that the `homologene_id` field is set up correctly""" for trait_type, trait_info, expected in [ @@ -250,6 +224,7 @@ class TestTraitsDBFunctions(TestCase): self.assertEqual( set_homologene_id_field(trait_type, trait_info, db_mock), expected) + @pytest.mark.unit_test def test_set_confidential_field(self): """Test that the `confidential` field is set up correctly""" for trait_type, trait_info, expected in [ @@ -261,6 +236,7 @@ class TestTraitsDBFunctions(TestCase): self.assertEqual( set_confidential_field(trait_type, trait_info), expected) + @pytest.mark.unit_test def test_export_trait_data_dtype(self): """ Test `export_trait_data` with different values for the `dtype` keyword @@ -276,6 +252,7 @@ class TestTraitsDBFunctions(TestCase): export_trait_data(trait_data, samplelist, dtype=dtype), expected) + @pytest.mark.unit_test def test_export_trait_data_dtype_all_flags(self): """ Test `export_trait_data` with different values for the `dtype` keyword @@ -317,6 +294,7 @@ class TestTraitsDBFunctions(TestCase): n_exists=nflag), expected) + @pytest.mark.unit_test def test_export_informative(self): """Test that the function exports appropriate data.""" # pylint: disable=W0621 |