diff options
Diffstat (limited to 'tests/unit/db')
| -rw-r--r-- | tests/unit/db/test_traits.py | 126 |
1 files changed, 117 insertions, 9 deletions
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py index 0e69bbe..c8f28b5 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -1,12 +1,120 @@ -"""Tests for db/traits.py""" -from unittest import TestCase -from unittest import mock +"""Tests for gn3/db/traits.py""" +from unittest import mock, TestCase +from gn3.db.traits import ( + GENO_TRAIT_INFO_QUERY, + TEMP_TRAIT_INFO_QUERY, + PUBLISH_TRAIT_INFO_QUERY, + PROBESET_TRAIT_INFO_QUERY) +from gn3.db.traits import ( + retrieve_trait_info, + retrieve_geno_trait_info, + retrieve_temp_trait_info, + retrieve_trait_dataset_name, + retrieve_publish_trait_info, + retrieve_probeset_trait_info, + update_sample_data) -from gn3.db.traits import update_sample_data +class TestTraitsDBFunctions(TestCase): + "Test cases for traits functions" + + def test_retrieve_trait_dataset_name(self): + """Test that the function is called correctly.""" + for trait_type, thresh, trait_dataset_name, columns in [ + ["ProbeSet", 9, "testName", + "Id, Name, FullName, ShortName, DataScale"], + ["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName"], + ["Publish", 6, "publishTraitName", + "Id, Name, FullName, ShortName"], + ["Temp", 4, "tempTraitName", "Id, Name, FullName, ShortName"]]: + db_mock = mock.MagicMock() + with self.subTest(trait_type=trait_type): + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = ( + "testName", "testNameFull", "testNameShort", + "dataScale") + self.assertEqual( + retrieve_trait_dataset_name( + trait_type, thresh, trait_dataset_name, db_mock), + ("testName", "testNameFull", "testNameShort", + "dataScale")) + cursor.execute.assert_called_once_with( + "SELECT {cols} " + "FROM {ttype}Freeze " + "WHERE public > %(threshold)s AND " + "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)".format( + cols=columns, ttype=trait_type), + {"threshold": thresh, "name": trait_dataset_name}) + + def test_retrieve_publish_trait_info(self): + """Test retrieval of type `Publish` traits.""" + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = tuple() + trait_source = { + "trait_name": "PublishTraitName", "trait_dataset_id": 1} + self.assertEqual( + retrieve_publish_trait_info( + trait_source, + db_mock), + tuple()) + cursor.execute.assert_called_once_with( + PUBLISH_TRAIT_INFO_QUERY, trait_source) + + def test_retrieve_probeset_trait_info(self): + """Test retrieval of type `Probeset` traits.""" + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = tuple() + trait_source = { + "trait_name": "ProbeSetTraitName", + "trait_dataset_name": "ProbeSetDatasetTraitName"} + self.assertEqual( + retrieve_probeset_trait_info(trait_source, db_mock), tuple()) + cursor.execute.assert_called_once_with( + PROBESET_TRAIT_INFO_QUERY, trait_source) + + def test_retrieve_geno_trait_info(self): + """Test retrieval of type `Geno` traits.""" + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = tuple() + trait_source = { + "trait_name": "GenoTraitName", + "trait_dataset_name": "GenoDatasetTraitName"} + self.assertEqual( + retrieve_geno_trait_info(trait_source, db_mock), tuple()) + cursor.execute.assert_called_once_with( + GENO_TRAIT_INFO_QUERY, trait_source) + + def test_retrieve_temp_trait_info(self): + """Test retrieval of type `Temp` traits.""" + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = tuple() + trait_source = {"trait_name": "TempTraitName"} + self.assertEqual( + retrieve_temp_trait_info(trait_source, db_mock), tuple()) + cursor.execute.assert_called_once_with( + TEMP_TRAIT_INFO_QUERY, trait_source) + + def test_retrieve_trait_info(self): + """Test that information on traits is retrieved as appropriate.""" + for trait_type, trait_name, trait_dataset_id, trait_dataset_name, in [ + ["Publish", "PublishTraitName", 1, "PublishDatasetTraitName"], + ["ProbeSet", "ProbeSetTraitName", 2, "ProbeSetDatasetTraitName"], + ["Geno", "GenoTraitName", 3, "GenoDatasetTraitName"], + ["Temp", "TempTraitName", 4, "TempDatasetTraitName"]]: + db_mock = mock.MagicMock() + with self.subTest(trait_type=trait_type): + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = tuple() + self.assertEqual( + retrieve_trait_info( + trait_type, trait_name, trait_dataset_id, + trait_dataset_name, db_mock), + tuple()) -class TestTraitsSqlMethods(TestCase): - """Test cases for sql operations that affect traits""" def test_update_sample_data(self): """Test that the SQL queries when calling update_sample_data are called with the right calls. @@ -14,12 +122,12 @@ class TestTraitsSqlMethods(TestCase): """ db_mock = mock.MagicMock() - STRAIN_ID_SQL: str = "UPDATE Strain SET Name = '%s' WHERE Id = %s" + 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 DataId = %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' " + N_STRAIN_SQL: str = ("UPDATE NStrain SET count = %s " "WHERE StrainId = %s AND DataId = %s") with db_mock.cursor() as cursor: |