"""Tests for db/phenotypes.py""" from unittest import TestCase from unittest import mock from gn3.db import fetchall from gn3.db import fetchone from gn3.db import update from gn3.db import diff_from_dict from gn3.db.phenotypes import Phenotype from gn3.db.metadata_audit import MetadataAudit class TestCrudMethods(TestCase): """Test cases for CRUD methods""" def test_update_phenotype_with_no_data(self): """Test that a phenotype is updated correctly if an empty Phenotype dataclass is provided """ db_mock = mock.MagicMock() self.assertEqual(update( conn=db_mock, table="Phenotype", data=Phenotype(), where=Phenotype()), None) def test_update_phenotype_with_data(self): """ Test that a phenotype is updated correctly if some data is provided """ db_mock = mock.MagicMock() with db_mock.cursor() as cursor: type(cursor).rowcount = 1 self.assertEqual(update( conn=db_mock, table="Phenotype", data=Phenotype( pre_pub_description="Test Pre Pub", submitter="Rob", post_pub_description="Test Post Pub"), where=Phenotype(id_=1, owner="Rob")), 1) cursor.execute.assert_called_once_with( "UPDATE Phenotype SET " "Pre_publication_description = %s, " "Post_publication_description = %s, " "Submitter = %s WHERE id = %s AND Owner = %s", ('Test Pre Pub', 'Test Post Pub', 'Rob', 1, 'Rob')) def test_fetch_phenotype(self): """Test that a single phenotype is fetched properly """ db_mock = mock.MagicMock() with db_mock.cursor() as cursor: test_data = ( 35, "Test pre-publication", "Test post-publication", "Original description A", "cm^2", "pre-abbrev", "post-abbrev", "LAB001", "R. W.", "R. W.", "R. W." ) cursor.fetchone.return_value = test_data phenotype = fetchone(db_mock, "Phenotype", where=Phenotype(id_=35, owner="Rob")) self.assertEqual(phenotype.id_, 35) self.assertEqual(phenotype.pre_pub_description, "Test pre-publication") cursor.execute.assert_called_once_with( "SELECT * FROM Phenotype WHERE id = %s AND Owner = %s", (35, 'Rob')) def test_fetchall_metadataaudit(self): """Test that multiple metadata_audit entries are fetched properly """ db_mock = mock.MagicMock() with db_mock.cursor() as cursor: test_data = ( 1, 35, "Rob", ('{"pages": ' '{"old": "5099-5109", ' '"new": "5099-5110"}, ' '"month": {"old": "July", ' '"new": "June"}, ' '"year": {"old": "2001", ' '"new": "2002"}}'), "2021-06-04 09:01:05") cursor.fetchall.return_value = (test_data,) metadata = list(fetchall(db_mock, "metadata_audit", where=MetadataAudit(dataset_id=35, editor="Rob")))[0] self.assertEqual(metadata.dataset_id, 35) self.assertEqual(metadata.time_stamp, "2021-06-04 09:01:05") cursor.execute.assert_called_once_with( ("SELECT * FROM metadata_audit WHERE " "dataset_id = %s AND editor = %s"), (35, 'Rob')) def test_diff_from_dict(self): """Test that a correct diff is generated""" self.assertEqual(diff_from_dict({"id": 1, "data": "a"}, {"id": 2, "data": "b"}), {"id": {"old": 1, "new": 2}, "data": {"old": "a", "new": "b"}})