diff options
Diffstat (limited to 'tests/unit/db/test_traits.py')
| -rw-r--r-- | tests/unit/db/test_traits.py | 60 |
1 files changed, 19 insertions, 41 deletions
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 |