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"""Test cases for procedures defined in file_utils.py"""
import os
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.tarfile")
@mock.patch("gn3.file_utils.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_file.assert_called_once_with("upload-data.tar.gz")
self.assertEqual(result,
{"status": 0,
"token": "abcdef-abcdef"})
@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"""
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"})
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