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# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from __future__ import annotations
import json
import os
import tempfile
import unittest
import warnings
from unittest.case import skipIf, skipUnless
from unittest.mock import patch
import numpy as np
import torch
from parameterized import parameterized
import monai.networks.nets as nets
from monai.apps import check_hash
from monai.bundle import ConfigParser, create_workflow, load, run
from monai.bundle.scripts import _examine_monai_version, _list_latest_versions, download, download_large_files
from monai.utils import optional_import
from tests.test_utils import (
assert_allclose,
command_line_tests,
skip_if_downloading_fails,
skip_if_no_cuda,
skip_if_quick,
skip_if_windows,
)
_, has_huggingface_hub = optional_import("huggingface_hub")
TEST_CASE_1 = ["test_bundle", None]
TEST_CASE_2 = ["test_bundle", "0.1.1"]
TEST_CASE_3 = [
["model.pt", "model.ts", "network.json", "test_output.pt", "test_input.pt"],
"test_bundle",
"https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/test_bundle.zip",
"a131d39a0af717af32d19e565b434928",
]
TEST_CASE_4 = [
["model.pt", "model.ts", "network.json", "test_output.pt", "test_input.pt"],
"test_bundle",
"monai-test/test_bundle",
]
TEST_CASE_5 = [
["models/model.pt", "models/model.ts", "configs/train.json"],
"brats_mri_segmentation",
"https://api.ngc.nvidia.com/v2/models/nvidia/monaihosting/brats_mri_segmentation/versions/0.4.0/files/brats_mri_segmentation_v0.4.0.zip",
]
TEST_CASE_6 = [["models/model.pt", "configs/train.json"], "renalStructures_CECT_segmentation", "0.1.0"]
TEST_CASE_6_HF = [["models/model.pt", "configs/train.yaml"], "mednist_ddpm", "1.0.1"]
TEST_CASE_7 = [
["model.pt", "model.ts", "network.json", "test_output.pt", "test_input.pt"],
"test_bundle",
"Project-MONAI/MONAI-extra-test-data/0.8.1",
"cuda" if torch.cuda.is_available() else "cpu",
"model.pt",
]
TEST_CASE_8 = [
"spleen_ct_segmentation",
"cuda" if torch.cuda.is_available() else "cpu",
{"spatial_dims": 3, "out_channels": 5},
]
TEST_CASE_9 = [
["test_output.pt", "test_input.pt"],
"test_bundle",
"0.1.1",
"Project-MONAI/MONAI-extra-test-data/0.8.1",
"cuda" if torch.cuda.is_available() else "cpu",
"model.ts",
]
TEST_CASE_10 = [
["network.json", "test_output.pt", "test_input.pt", "large_files.yaml"],
"test_bundle",
"https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/test_bundle_v0.1.3.zip",
{"model.pt": "27952767e2e154e3b0ee65defc5aed38", "model.ts": "97746870fe591f69ac09827175b00675"},
]
# (source, repo) pairs covering every `source` accepted by `load()`/`download()`. `repo` only
# matters for sources that read it ("github", "huggingface_hub", "ngc_private"); it's unused
# otherwise but keeps the call shape realistic for each source.
TEST_CASE_SOURCE_GITHUB = ["github", "attacker/repo"]
TEST_CASE_SOURCE_MONAIHOSTING = ["monaihosting", None]
TEST_CASE_SOURCE_NGC = ["ngc", None]
TEST_CASE_SOURCE_HUGGINGFACE_HUB = ["huggingface_hub", "attacker/repo"]
TEST_CASE_NGC_1 = [
"spleen_ct_segmentation",
"0.3.7",
None,
"monai_spleen_ct_segmentation",
"models/model.pt",
"b418a2dc8672ce2fd98dc255036e7a3d",
]
TEST_CASE_NGC_2 = [
"monai_spleen_ct_segmentation",
"0.3.7",
"monai_",
"spleen_ct_segmentation",
"models/model.pt",
"b418a2dc8672ce2fd98dc255036e7a3d",
]
TESTCASE_NGC_WEIGHTS = {
"key": "model.0.conv.unit0.adn.N.bias",
"value": torch.tensor(
[
-0.0705,
-0.0937,
-0.0422,
-0.2068,
0.1023,
-0.2007,
-0.0883,
0.0018,
-0.1719,
0.0116,
0.0285,
-0.0044,
0.1223,
-0.1287,
-0.1858,
0.0460,
]
),
}
class TestDownload(unittest.TestCase):
@parameterized.expand([TEST_CASE_1, TEST_CASE_2])
@skip_if_quick
def test_github_download_bundle(self, bundle_name, version):
bundle_files = ["model.pt", "model.ts", "network.json", "test_output.pt", "test_input.pt"]
repo = "Project-MONAI/MONAI-extra-test-data/0.8.1"
hash_val = "a131d39a0af717af32d19e565b434928"
with skip_if_downloading_fails():
# download a whole bundle from github releases
with tempfile.TemporaryDirectory() as tempdir:
cmd = ["coverage", "run", "-m", "monai.bundle", "download", "--name", bundle_name, "--source", "github"]
cmd += ["--bundle_dir", tempdir, "--repo", repo]
if version is not None:
cmd += ["--version", version]
command_line_tests(cmd)
for file in bundle_files:
file_path = os.path.join(tempdir, "test_bundle", file)
self.assertTrue(os.path.exists(file_path))
if file == "network.json":
self.assertTrue(check_hash(filepath=file_path, val=hash_val, hash_type="md5"))
@parameterized.expand([TEST_CASE_3])
@skip_if_quick
def test_url_download_bundle(self, bundle_files, bundle_name, url, hash_val):
with skip_if_downloading_fails():
# download a single file from url, also use `args_file`
with tempfile.TemporaryDirectory() as tempdir:
def_args = {"name": bundle_name, "bundle_dir": tempdir, "url": ""}
def_args_file = os.path.join(tempdir, "def_args.json")
parser = ConfigParser()
parser.export_config_file(config=def_args, filepath=def_args_file)
cmd = ["coverage", "run", "-m", "monai.bundle", "download", "--args_file", def_args_file]
cmd += ["--url", url, "--source", "github"]
command_line_tests(cmd)
for file in bundle_files:
file_path = os.path.join(tempdir, bundle_name, file)
self.assertTrue(os.path.exists(file_path))
if file == "network.json":
self.assertTrue(check_hash(filepath=file_path, val=hash_val, hash_type="md5"))
@parameterized.expand([TEST_CASE_4])
@skip_if_quick
@skipUnless(has_huggingface_hub, "Requires `huggingface_hub`.")
def test_hf_hub_download_bundle(self, bundle_files, bundle_name, repo):
with skip_if_downloading_fails():
with tempfile.TemporaryDirectory() as tempdir:
cmd = [
"coverage",
"run",
"-m",
"monai.bundle",
"download",
"--name",
bundle_name,
"--source",
"huggingface_hub",
]
cmd += ["--bundle_dir", tempdir, "--repo", repo, "--progress", "False"]
command_line_tests(cmd)
for file in bundle_files:
file_path = os.path.join(tempdir, bundle_name, file)
self.assertTrue(os.path.exists(file_path))
@parameterized.expand([TEST_CASE_5])
@skip_if_quick
def test_monaihosting_url_download_bundle(self, bundle_files, bundle_name, url):
with skip_if_downloading_fails():
# download a single file from url, also use `args_file`
with tempfile.TemporaryDirectory() as tempdir:
def_args = {"name": bundle_name, "bundle_dir": tempdir, "url": ""}
def_args_file = os.path.join(tempdir, "def_args.json")
parser = ConfigParser()
parser.export_config_file(config=def_args, filepath=def_args_file)
cmd = ["coverage", "run", "-m", "monai.bundle", "download", "--args_file", def_args_file]
cmd += ["--url", url, "--progress", "False"]
command_line_tests(cmd)
for file in bundle_files:
file_path = os.path.join(tempdir, bundle_name, file)
self.assertTrue(os.path.exists(file_path))
@parameterized.expand([TEST_CASE_5])
@skip_if_quick
@skipIf(os.getenv("NGC_API_KEY", None) is None, "NGC API key required for this test")
def test_ngc_private_source_download_bundle(self, bundle_files, bundle_name, _url):
with skip_if_downloading_fails():
# download a single file from url, also use `args_file`
with tempfile.TemporaryDirectory() as tempdir:
def_args = {"name": bundle_name, "bundle_dir": tempdir}
def_args_file = os.path.join(tempdir, "def_args.json")
parser = ConfigParser()
parser.export_config_file(config=def_args, filepath=def_args_file)
cmd = ["coverage", "run", "-m", "monai.bundle", "download", "--args_file", def_args_file]
cmd += ["--progress", "False", "--source", "ngc_private"]
command_line_tests(cmd)
for file in bundle_files:
file_path = os.path.join(tempdir, bundle_name, file)
self.assertTrue(os.path.exists(file_path))
@parameterized.expand([TEST_CASE_6])
@skip_if_quick
@skipUnless(has_huggingface_hub, "Requires `huggingface_hub`.")
def test_monaihosting_source_download_bundle(self, bundle_files, bundle_name, version):
with skip_if_downloading_fails():
# download a single file from url, also use `args_file`
with tempfile.TemporaryDirectory() as tempdir:
def_args = {"name": bundle_name, "bundle_dir": tempdir, "version": version}
def_args_file = os.path.join(tempdir, "def_args.json")
parser = ConfigParser()
parser.export_config_file(config=def_args, filepath=def_args_file)
cmd = ["coverage", "run", "-m", "monai.bundle", "download", "--args_file", def_args_file]
cmd += ["--progress", "False", "--source", "monaihosting"]
command_line_tests(cmd)
for file in bundle_files:
file_path = os.path.join(tempdir, bundle_name, file)
self.assertTrue(os.path.exists(file_path))
@patch("monai.bundle.scripts.get_versions", return_value={"version": "1.2"})
def test_examine_monai_version(self, mock_get_versions):
self.assertTrue(_examine_monai_version("1.1")[0]) # Should return True, compatible
self.assertTrue(_examine_monai_version("1.2rc1")[0]) # Should return True, compatible
self.assertFalse(_examine_monai_version("1.3")[0]) # Should return False, not compatible
@patch("monai.bundle.scripts.get_versions", return_value={"version": "1.2rc1"})
def test_examine_monai_version_rc(self, mock_get_versions):
self.assertTrue(_examine_monai_version("1.2")[0]) # Should return True, compatible
self.assertFalse(_examine_monai_version("1.3")[0]) # Should return False, not compatible
def test_list_latest_versions(self):
"""Test listing of the latest versions."""
data = {
"modelVersions": [
{"createdDate": "2021-01-01", "versionId": "1.0"},
{"createdDate": "2021-01-02", "versionId": "1.1"},
{"createdDate": "2021-01-03", "versionId": "1.2"},
]
}
self.assertEqual(_list_latest_versions(data), ["1.2", "1.1", "1.0"])
self.assertEqual(_list_latest_versions(data, max_versions=2), ["1.2", "1.1"])
data = {
"modelVersions": [
{"createdDate": "2021-01-01", "versionId": "1.0"},
{"createdDate": "2021-01-02", "versionId": "1.1"},
]
}
self.assertEqual(_list_latest_versions(data), ["1.1", "1.0"])
@skip_if_quick
@skipUnless(has_huggingface_hub, "Requires `huggingface_hub`.")
@patch("monai.bundle.scripts.get_versions", return_value={"version": "1.2"})
def test_download_monaihosting(self, mock_get_versions):
"""Test checking MONAI version from a metadata file."""
with patch("monai.bundle.scripts.logger") as mock_logger:
with tempfile.TemporaryDirectory() as tempdir:
with skip_if_downloading_fails():
download(name="spleen_ct_segmentation", bundle_dir=tempdir, source="monaihosting")
# Should have a warning message because the latest version is using monai > 1.2
mock_logger.warning.assert_called_once()
@skip_if_quick
@patch("monai.bundle.scripts.get_versions", return_value={"version": "1.3"})
def test_download_ngc(self, mock_get_versions):
"""Test checking MONAI version from a metadata file."""
with skip_if_downloading_fails():
with patch("monai.bundle.scripts.logger") as mock_logger:
with tempfile.TemporaryDirectory() as tempdir:
download(name="spleen_ct_segmentation", bundle_dir=tempdir, source="ngc")
mock_logger.warning.assert_not_called()
@skip_if_no_cuda
class TestLoad(unittest.TestCase):
@parameterized.expand([TEST_CASE_7])
@skip_if_quick
def test_load_weights(self, bundle_files, bundle_name, repo, device, model_file):
with skip_if_downloading_fails():
with tempfile.TemporaryDirectory() as tempdir:
bundle_root = os.path.join(tempdir, bundle_name)
# load weights
model_1 = load(
name=bundle_name,
model_file=model_file,
bundle_dir=tempdir,
repo=repo,
source="github",
progress=False,
device=device,
)
# prepare network
with open(os.path.join(bundle_root, bundle_files[2])) as f:
net_args = json.load(f)["network_def"]
model_name = net_args["_target_"]
del net_args["_target_"]
model = getattr(nets, model_name)(**net_args)
model.to(device)
model.load_state_dict(model_1)
model.eval()
# prepare data and test
input_tensor = torch.load(
os.path.join(bundle_root, bundle_files[4]), map_location=device, weights_only=True
)
output = model.forward(input_tensor)
expected_output = torch.load(
os.path.join(bundle_root, bundle_files[3]), map_location=device, weights_only=True
)
assert_allclose(output, expected_output, atol=1e-3, rtol=1e-3, type_test=False)
# load instantiated model directly and test, since the bundle has been downloaded,
# there is no need to input `repo`
_model_2 = getattr(nets, model_name)(**net_args)
model_2 = load(
name=bundle_name,
model=_model_2,
model_file=model_file,
bundle_dir=tempdir,
progress=False,
device=device,
source="github",
)
model_2.eval()
output_2 = model_2.forward(input_tensor)
assert_allclose(output_2, expected_output, atol=1e-3, rtol=1e-3, type_test=False)
@parameterized.expand([TEST_CASE_8])
@skip_if_quick
@skipUnless(has_huggingface_hub, "Requires `huggingface_hub`.")
def test_load_weights_with_net_override(self, bundle_name, device, net_override):
with skip_if_downloading_fails():
# download bundle, and load weights from the downloaded path
with tempfile.TemporaryDirectory() as tempdir:
# load weights
model = load(name=bundle_name, bundle_dir=tempdir, source="monaihosting", progress=False, device=device)
# prepare data and test
input_tensor = torch.rand(1, 1, 96, 96, 96).to(device)
output = model(input_tensor)
model_path = f"{tempdir}/spleen_ct_segmentation/models/model.pt"
workflow = create_workflow(
config_file=f"{tempdir}/spleen_ct_segmentation/configs/train.json", workflow_type="train"
)
expected_model = workflow.network_def.to(device)
expected_model.load_state_dict(torch.load(model_path, weights_only=True))
expected_output = expected_model(input_tensor)
assert_allclose(output, expected_output, atol=1e-4, rtol=1e-4, type_test=False)
# using net_override to override kwargs in network directly
model_2 = load(
name=bundle_name,
bundle_dir=tempdir,
source="monaihosting",
progress=False,
device=device,
net_override=net_override,
)
# prepare data and test
input_tensor = torch.rand(1, 1, 96, 96, 96).to(device)
output = model_2(input_tensor)
expected_shape = (1, 5, 96, 96, 96)
np.testing.assert_equal(output.shape, expected_shape)
@parameterized.expand([TEST_CASE_9])
@skip_if_quick
def test_load_ts_module(self, bundle_files, bundle_name, version, repo, device, model_file):
with skip_if_downloading_fails():
# load ts module
with tempfile.TemporaryDirectory() as tempdir:
bundle_root = os.path.join(tempdir, bundle_name)
# load ts module
model_ts, metadata, extra_file_dict = load(
name=bundle_name,
version=version,
model_file=model_file,
load_ts_module=True,
bundle_dir=tempdir,
repo=repo,
progress=False,
device=device,
source="github",
config_files=("network.json",),
)
# prepare and test ts
input_tensor = torch.load(
os.path.join(bundle_root, bundle_files[1]), map_location=device, weights_only=True
)
output = model_ts.forward(input_tensor)
expected_output = torch.load(
os.path.join(bundle_root, bundle_files[0]), map_location=device, weights_only=True
)
assert_allclose(output, expected_output, atol=1e-3, rtol=1e-3, type_test=False)
# test metadata
self.assertTrue(metadata["pytorch_version"] == "1.7.1")
# test extra_file_dict
self.assertTrue("network.json" in extra_file_dict.keys())
class TestDownloadLargefiles(unittest.TestCase):
def test_large_files_rejects_path_traversal(self):
with tempfile.TemporaryDirectory() as tempdir:
large_files_path = os.path.join(tempdir, "large_files.yaml")
with open(large_files_path, "w") as f:
f.write("large_files:\n" " - path: ../evil.pt\n" " url: https://example.com/evil.pt\n")
with self.assertRaises(ValueError):
download_large_files(bundle_path=tempdir)
@parameterized.expand([TEST_CASE_10])
@skip_if_quick
def test_url_download_large_files(self, bundle_files, bundle_name, url, hash_val):
with skip_if_downloading_fails():
# download a single file from url, also use `args_file`
with tempfile.TemporaryDirectory() as tempdir:
def_args = {"name": bundle_name, "bundle_dir": tempdir, "url": ""}
def_args_file = os.path.join(tempdir, "def_args.json")
parser = ConfigParser()
parser.export_config_file(config=def_args, filepath=def_args_file)
cmd = ["coverage", "run", "-m", "monai.bundle", "download", "--args_file", def_args_file]
cmd += ["--url", url, "--source", "github"]
command_line_tests(cmd)
for file in bundle_files:
file_path = os.path.join(tempdir, bundle_name, file)
print(file_path)
self.assertTrue(os.path.exists(file_path))
# download large files
bundle_path = os.path.join(tempdir, bundle_name)
cmd = ["coverage", "run", "-m", "monai.bundle", "download_large_files", "--bundle_path", bundle_path]
command_line_tests(cmd)
for file in ["model.pt", "model.ts"]:
file_path = os.path.join(tempdir, bundle_name, f"models/{file}")
self.assertTrue(check_hash(filepath=file_path, val=hash_val[file], hash_type="md5"))
@skip_if_windows
class TestNgcBundleDownload(unittest.TestCase):
@parameterized.expand([TEST_CASE_NGC_1, TEST_CASE_NGC_2])
@skip_if_quick
def test_ngc_download_bundle(self, bundle_name, version, remove_prefix, download_name, file_path, hash_val):
with skip_if_downloading_fails():
with tempfile.TemporaryDirectory() as tempdir:
download(
name=bundle_name, source="ngc", version=version, bundle_dir=tempdir, remove_prefix=remove_prefix
)
full_file_path = os.path.join(tempdir, download_name, file_path)
self.assertTrue(os.path.exists(full_file_path))
self.assertTrue(check_hash(filepath=full_file_path, val=hash_val, hash_type="md5"))
model = load(
name=bundle_name, source="ngc", version=version, bundle_dir=tempdir, remove_prefix=remove_prefix
)
assert_allclose(
model.state_dict()[TESTCASE_NGC_WEIGHTS["key"]],
TESTCASE_NGC_WEIGHTS["value"],
atol=1e-4,
rtol=1e-4,
type_test=False,
)
class TestLoadWarnsOnConfigExecution(unittest.TestCase):
"""Regression tests for GHSA-873f-pvrv-4x83: `load()`/`create_workflow()` parse and execute a
bundle's own config (arbitrary `_target_`/`$`-expression content) whenever `model` is `None`.
There is no opt-in flag -- MONAI has no way to establish whether a bundle is actually
trustworthy, so a flag would only teach callers to always pass it and ignore the risk. Instead,
a `UserWarning` is raised every time this happens, in both `load()` (via `create_workflow()`)
and `run()` (also via `create_workflow()`)."""
def _stage_malicious_bundle(self, tempdir: str, marker: str) -> str:
name = "evil_bundle"
bundle_root = os.path.join(tempdir, name)
os.makedirs(os.path.join(bundle_root, "configs"))
os.makedirs(os.path.join(bundle_root, "models"))
torch.save({"state_dict": {}}, os.path.join(bundle_root, "models", "model.pt"))
# writes the marker directly via `pathlib` instead of shelling out through `os.system` --
# `!r` yields a Python-source-safe literal (handling spaces and Windows backslashes alike)
# with no shell involved to reintroduce quoting/splitting issues.
payload = f"$__import__('pathlib').Path({marker!r}).write_text('pwned')"
# included under both keys so the payload runs whether the config is consumed via
# `network_def` (the `load()` tests) or via `initialize` (the `run()` test).
malicious_config = {"network_def": payload, "initialize": [payload]}
with open(os.path.join(bundle_root, "configs", "train.json"), "w") as f:
json.dump(malicious_config, f)
return name
@parameterized.expand(
[TEST_CASE_SOURCE_GITHUB, TEST_CASE_SOURCE_MONAIHOSTING, TEST_CASE_SOURCE_NGC, TEST_CASE_SOURCE_HUGGINGFACE_HUB]
)
def test_default_warns_and_executes_config(self, source, repo):
# `source`/`repo` only steer where `download()` would fetch from -- irrelevant here since
# the bundle is already staged on disk, so `load()` never calls `download()`. Parameterized
# anyway to confirm the warning fires the same way regardless of `source`.
with tempfile.TemporaryDirectory() as tempdir:
marker = os.path.join(tempdir, "PWNED")
name = self._stage_malicious_bundle(tempdir, marker)
with self.assertWarnsRegex(UserWarning, r"GHSA-873f-pvrv-4x83"):
with self.assertRaises(AttributeError):
# the malicious config is missing metadata.json and returns a plain `int` for
# `network_def`, so the workflow construction fails after the payload has already
# run -- this mirrors the advisory's own PoC, where the failure happens *after* RCE.
load(name=name, bundle_dir=tempdir, source=source, repo=repo)
self.assertTrue(os.path.exists(marker))
def test_explicit_model_skips_config_parsing(self):
with tempfile.TemporaryDirectory() as tempdir:
marker = os.path.join(tempdir, "PWNED")
name = self._stage_malicious_bundle(tempdir, marker)
model = nets.UNet(spatial_dims=2, in_channels=1, out_channels=1, channels=(4, 8), strides=(2,))
with warnings.catch_warnings():
warnings.simplefilter("error", UserWarning)
load(name=name, model=model, bundle_dir=tempdir, source="github", repo="attacker/repo")
self.assertFalse(os.path.exists(marker))
def test_run_warns_on_config_execution(self):
with tempfile.TemporaryDirectory() as tempdir:
marker = os.path.join(tempdir, "PWNED")
name = self._stage_malicious_bundle(tempdir, marker)
config_file = os.path.join(tempdir, name, "configs", "train.json")
with self.assertWarnsRegex(UserWarning, r"GHSA-873f-pvrv-4x83"):
with self.assertRaises(ValueError):
# no "run" ID is defined, so `workflow.run()` fails after `initialize()` has
# already evaluated the payload above.
run(config_file=config_file)
self.assertTrue(os.path.exists(marker))
if __name__ == "__main__":
unittest.main()