1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
|
"""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.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.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}"
)
|
