"""Test cases for procedures defined in file_utils.py""" import os import shutil import unittest from dataclasses import dataclass from typing import Callable from unittest import mock from gn3.file_utils import extract_uploaded_file from gn3.file_utils import get_dir_hash from gn3.file_utils import jsonfile_to_dict from gn3.file_utils import lookup_file @dataclass class MockFile: """Mock File object returned by request.files""" filename: str save: Callable class TestFileUtils(unittest.TestCase): """Test cases for procedures defined in file_utils.py""" def test_get_dir_hash(self): """Test that a directory is hashed correctly""" test_dir = os.path.join(os.path.dirname(__file__), "test_data") self.assertEqual("fd9d74a9554b7f13bfeffbdda8e61486", get_dir_hash(test_dir)) def test_get_dir_hash_non_existent_dir(self): """Test thata an error is raised when the dir does not exist""" self.assertRaises(FileNotFoundError, get_dir_hash, "/non-existent-file") @mock.patch("os.path.isfile") @mock.patch.dict(os.environ, {"GENENETWORK_FILES": "/tmp/"}) def test_lookup_genotype_file_exists(self, mock_isfile): """Test whether genotype file exists if file is present""" mock_isfile.return_value = True self.assertEqual(lookup_file("GENENETWORK_FILES", "genotype_files", "genotype.txt"), "/tmp/genotype_files/genotype.txt") @mock.patch("os.path.isfile") @mock.patch.dict(os.environ, {"GENENETWORK_FILES": "/tmp"}) def test_lookup_genotype_file_does_not_exist(self, mock_isfile): """Test whether genotype file exists if file is absent""" mock_isfile.return_value = False self.assertRaises(FileNotFoundError, lookup_file, "GENENETWORK_FILES", "genotype_files", "genotype.txt") def test_lookup_genotype_file_env_does_not_exist(self): """Test whether genotype file exists if GENENETWORK_FILES is absent""" self.assertRaises(FileNotFoundError, lookup_file, "GENENETWORK_FILES", "genotype_files", "genotype.txt") def test_jsonfile_to_dict(self): """Test that a json file is parsed correctly""""" json_file = os.path.join(os.path.dirname(__file__), "test_data", "metadata.json") self.assertEqual("Longer description", jsonfile_to_dict(json_file).get("description")) def test_jsonfile_to_dict_nonexistent_file(self): """Test that a ValueError is raised when the json file is non-existent""" self.assertRaises(FileNotFoundError, jsonfile_to_dict, "/non-existent-dir") @mock.patch("gn3.file_utils.secure_filename") def test_extract_uploaded_file(self, mock_file): """Test that the gzip file is extracted to the right location""" file_loc = os.path.join( os.path.dirname(__file__), "upload-data.tar.gz") mock_file.return_value = file_loc mock_fileobj = MockFile(save=mock.MagicMock(), filename="upload-data.tar.gz") result = extract_uploaded_file(mock_fileobj, "/tmp") mock_fileobj.save.assert_called_once_with(file_loc) mock_file.assert_called_once_with("upload-data.tar.gz") # Clean up! shutil.rmtree(os.path.join("/tmp", "d41d8cd98f00b204e9800998ecf8427e")) self.assertEqual(result, {"status": 0, "token": "d41d8cd98f00b204e9800998ecf8427e"}) @mock.patch("gn3.file_utils.secure_filename") def test_extract_uploaded_file_non_existent_gzip(self, mock_file): """Test that the right error message is returned when there is a problem extracting the file""" file_loc = os.path.join( os.path.dirname(__file__), "CTtyodSTh5") # Does not exist! mock_file.return_value = file_loc mock_fileobj = MockFile(save=mock.MagicMock(), filename="") result = extract_uploaded_file(mock_fileobj, "/tmp") self.assertEqual(result, {"status": 128, "error": "gzip failed to unpack file"})