[Bug]: Cannot Detect Files in Nested Symlinked Folders

[garrettmflynn]

What happened?

The following code is a demo that shows NWB files in nested symlinked folders are not found by the NWB Inspector—though these same files are found when inspect_all is run directly on the base folder as well as a direct symlink to that folder.

from datetime import datetime
from shutil import rmtree
from pathlib import Path

from nwbinspector import inspect_all
from nwbinspector.nwbinspector import InspectorOutputJSONEncoder

paths = [
   # Path(s) to directories containing NWB files
]

tmp_base_folder_path =  Path(__file__).parent / ".temp"
def get_temp_folder_path():
    return tmp_base_folder_path / f"temp_{datetime.now().strftime('%Y%m%d-%H%M%S')}"

tmp_folder_path = get_temp_folder_path()
tmp_folder_path.mkdir(parents=True)

for path in paths:
    path = Path(path)
    (tmp_folder_path / path.name).symlink_to(path, path.is_dir())

messages = inspect_all(path=tmp_folder_path)

print('Messages (nested symlink)', len(list(messages)))

direct_path = Path(paths[0])
print('Messages (direct)', len(list(inspect_all(path=direct_path))))

direct_symlink_path = tmp_base_folder_path / direct_path.name
direct_symlink_path.symlink_to(direct_path, direct_path.is_dir())
print('Messages (symlink)', len(list(inspect_all(path=direct_symlink_path))))
rmtree(tmp_base_folder_path)

Operating System

macOS

Python Version

3.10

Were you streaming with ROS3?

No

Package Versions

Package Version

---

altgraph 0.17.3
aniso8601 9.0.1
annotated-types 0.5.0
appdirs 1.4.4
arrow 1.2.3
asciitree 0.3.3
attrs 23.1.0
bidsschematools 0.7.1
blessed 1.20.0
blinker 1.6.2
boto3 1.28.23
botocore 1.31.23
certifi 2023.7.22
chardet 5.1.0
charset-normalizer 3.2.0
ci-info 0.3.0
click 8.1.6
click-didyoumean 0.3.0
configparser 6.0.0
contourpy 1.1.0
cycler 0.11.0
dandi 0.55.1
dandischema 0.8.4
dnspython 2.4.2
elephant 0.13.0
email-validator 2.0.0.post2
entrypoints 0.4
etelemetry 0.3.0
exceptiongroup 1.1.2
fasteners 0.18
Flask 2.3.2
Flask-Cors 4.0.0
flask-restx 1.1.0
fonttools 4.42.0
fparse 1.20.1
fqdn 1.5.1
fscacher 0.3.0
h5py 3.9.0
hdf5storage 0.1.19
hdmf 3.8.1
humanize 4.7.0
idna 3.4
importlib-metadata 6.8.0
importlib-resources 6.0.1
iniconfig 2.0.0
interleave 0.2.1
isodate 0.6.1
isoduration 20.11.0
itsdangerous 2.1.2
jaraco.classes 3.3.0
Jinja2 3.1.2
jmespath 1.0.1
joblib 1.3.2
jsonpointer 2.4
jsonschema 4.18.0
jsonschema-specifications 2023.7.1
keyring 24.2.0
keyrings.alt 5.0.0
kiwisolver 1.4.4
lazy-ops 0.2.0
lxml 4.9.3
macholib 1.16.2
MarkupSafe 2.1.3
matplotlib 3.7.2
MEArec 1.9.0
MEAutility 1.5.1
more-itertools 10.1.0
msgpack 1.0.5
natsort 8.4.0
neo 0.12.0
neuroconv 0.4.2
numcodecs 0.11.0
numpy 1.25.2
nwbinspector 0.4.29
packaging 21.3
pandas 2.0.3
Pillow 10.0.0
pip 23.2.1
pkgutil_resolve_name 1.3.10
pluggy 1.2.0
probeinterface 0.2.17
psutil 5.9.5
pycryptodomex 3.18.0
pydantic 1.10.12
pydantic_core 2.1.2
pyEDFlib 0.1.32
pyinstaller 5.13.0
pyinstaller-hooks-contrib 2023.6
pyintan 0.3.0
pymatreader 0.0.32
pynwb 2.4.0
pyopenephys 1.1.6
pyout 0.7.3
pyparsing 3.0.9
pytest 7.4.0
python-dateutil 2.8.2
pytz 2023.3
PyYAML 6.0.1
quantities 0.14.1
referencing 0.30.2
requests 2.31.0
rfc3339-validator 0.1.4
rfc3987 1.3.8
rpds-py 0.9.2
ruamel.yaml 0.17.32
ruamel.yaml.clib 0.2.7
s3transfer 0.6.1
scipy 1.11.2
semantic-version 2.10.0
setuptools 68.0.0
six 1.16.0
spikeextractors 0.9.11
spikeinterface 0.98.2
tenacity 8.2.2
threadpoolctl 3.2.0
tomli 2.0.1
tqdm 4.66.0
typing_extensions 4.7.1
tzdata 2023.3
uri-template 1.3.0
urllib3 1.26.16
wcwidth 0.2.6
webcolors 1.13
Werkzeug 2.3.6
wheel 0.41.1
xmltodict 0.13.0
zarr 2.16.0
zarr-checksum 0.2.9
zipp 3.16.2

Code of Conduct

• I agree to follow this project's Code of Conduct
• Have you ensured this bug was not already reported?
• To the best of your ability, have you ensured this is a bug within the code that checks the NWBFile, rather than a bug in the NWBFile reader (e.g., PyNWB or MatNWB)?