"""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) 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())