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 | 4 | ||||
| -rw-r--r-- | tests/unit/db/test_datasets.py | 6 | ||||
| -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_species.py | 5 | ||||
| -rw-r--r-- | tests/unit/db/test_traits.py | 15 |
7 files changed, 47 insertions, 0 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 index 3f940b2..5afe55f 100644 --- a/tests/unit/db/test_correlation.py +++ b/tests/unit/db/test_correlation.py @@ -4,6 +4,8 @@ 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) @@ -12,6 +14,7 @@ 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. @@ -53,6 +56,7 @@ class TestCorrelation(TestCase): "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. diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py index 0b8c2fe..5b86db9 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, @@ -11,6 +12,7 @@ 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, expected in [ @@ -42,6 +44,7 @@ class TestDatasetsDBFunctions(TestCase): table=table, cols=columns), {"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 @@ -65,6 +68,7 @@ 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 @@ -90,6 +94,7 @@ 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 @@ -112,6 +117,7 @@ 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_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 f3e0bab..d7c0b27 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -1,5 +1,6 @@ """Tests for gn3/db/traits.py""" from unittest import mock, TestCase +import pytest from gn3.db.traits import ( build_trait_name, export_trait_data, @@ -49,6 +50,7 @@ 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() @@ -83,6 +85,7 @@ class TestTraitsDBFunctions(TestCase): " 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() @@ -118,6 +121,7 @@ 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() @@ -141,6 +145,7 @@ class TestTraitsDBFunctions(TestCase): "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() @@ -153,6 +158,7 @@ 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. @@ -169,6 +175,7 @@ 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. @@ -178,6 +185,7 @@ 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 [ @@ -194,6 +202,7 @@ class TestTraitsDBFunctions(TestCase): threshold, trait_fullname, db_mock), 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. @@ -242,6 +251,7 @@ class TestTraitsDBFunctions(TestCase): 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 [ @@ -250,6 +260,7 @@ 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 [ @@ -264,6 +275,7 @@ 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 [ @@ -275,6 +287,7 @@ 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 @@ -290,6 +303,7 @@ 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 @@ -331,6 +345,7 @@ 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 |