"""Test cases for procedures defined in fs_helpers.py""" import os import unittest from dataclasses import dataclass from typing import Callable from unittest import mock import pytest from gn3.fs_helpers import extract_uploaded_file from gn3.fs_helpers import get_dir_hash from gn3.fs_helpers import jsonfile_to_dict from gn3.fs_helpers import cache_ipfs_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 fs_helpers.py""" @pytest.mark.unit_test 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("3aeafab7d53b4f76d223366ae7ee9738", get_dir_hash(test_dir)) @pytest.mark.unit_test 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") @pytest.mark.unit_test 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")) @pytest.mark.unit_test 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") @pytest.mark.unit_test @mock.patch("gn3.fs_helpers.tarfile") @mock.patch("gn3.fs_helpers.secure_filename") def test_extract_uploaded_file(self, mock_file, mock_tarfile): """Test that the gzip file is extracted to the right location""" mock_file.return_value = "upload-data.tar.gz" mock_fileobj = MockFile(save=mock.MagicMock(), filename="upload-data.tar.gz") mock_tarfile.return_value = mock.Mock() result = extract_uploaded_file(mock_fileobj, "/tmp", token="abcdef-abcdef") mock_fileobj.save.assert_called_once_with("/tmp/abcdef-abcdef/" "upload-data.tar.gz") mock_tarfile.open.assert_called_once_with("/tmp/abcdef-abcdef/" "upload-data.tar.gz") mock_tarfile.open.return_value.__enter__.return_value.extractall.assert_called_once_with( path='/tmp/abcdef-abcdef') mock_file.assert_called_once_with("upload-data.tar.gz") self.assertEqual(result, {"status": 0, "token": "abcdef-abcdef"}) @pytest.mark.unit_test @mock.patch("gn3.fs_helpers.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""" mock_file.return_value = os.path.join(os.path.dirname(__file__), "CTtyodSTh5") # Does not exist! 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" }) @pytest.mark.skip(reason="ipfs http client breaks in Python > 38") @pytest.mark.unit_test def test_cache_ipfs_file_cache_hit(self): """Test that the correct file location is returned if there's a cache hit""" # Create empty file test_dir = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test" if not os.path.exists(test_dir): os.mkdir(test_dir) with open(f"{test_dir}/genotype.txt", "a", encoding="utf8"): pass file_loc = cache_ipfs_file( ipfs_file=("/ipfs/" "QmQPeNsJPyVWPFDVHb" "77w8G42Fvo15z4bG2X8D2GhfbSXc-test/" "genotype.txt"), cache_dir="/tmp") # Clean up os.remove(f"{test_dir}/genotype.txt") os.rmdir(test_dir) self.assertEqual(file_loc, f"{test_dir}/genotype.txt") @pytest.mark.skip(reason="ipfs http client breaks in Python > 38") @pytest.mark.unit_test @mock.patch("gn3.fs_helpers.ipfshttpclient") def test_cache_ipfs_file_cache_miss(self, mock_ipfs): """Test that a file is cached if there's a cache miss""" mock_ipfs_client = mock.MagicMock() mock_ipfs.connect.return_value = mock_ipfs_client test_dir = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test" self.assertEqual(cache_ipfs_file( ipfs_file=("/ipfs/" "QmQPeNsJPyVWPFDVHb" "77w8G42Fvo15z4bG2X8D2GhfbSXc-test/" "genotype.txt"), cache_dir="/tmp" ), f"{test_dir}/genotype.txt") mock_ipfs_client.get.assert_called_once_with( ("/ipfs/" "QmQPeNsJPyVWPFDVHb" "77w8G42Fvo15z4bG2X8D2GhfbSXc-test/" "genotype.txt"), target=f"{test_dir}" )