test_nwb2asset_remote_asset timed out in test (ubuntu-latest, 3.8, dandi-api)
- Dominant language
- Python
- Stars
- 28
- Forks
- 37
- Avg merge
- 1d 17h
- Merged PRs (30d)
- 9
Description
https://github.com/dandi/dandi-cli/actions/runs/9395898413/job/25876096821
```
_________________________ test_nwb2asset_remote_asset __________________________
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/fscacher/cache.py:133: in fingerprinter
path = op.realpath(path_orig)
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/posixpath.py:390: in realpath
filename = os.fspath(filename)
E TypeError: expected str, bytes or os.PathLike object, not RemoteReadableAsset
During handling of the above exception, another exception occurred:
dandi/tests/test_metadata.py:889: in test_nwb2asset_remote_asset
assert nwb2asset(r, digest=digest) == BareAsset.model_construct(
dandi/metadata/nwb.py:149: in nwb2asset
metadata = get_metadata(nwb_path)
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/fscacher/cache.py:138: in fingerprinter
return f(*args, **kwargs)
dandi/metadata/nwb.py:106: in get_metadata
meta.update(_get_pynwb_metadata(r))
dandi/pynwb_utils.py:206: in _get_pynwb_metadata
with open_readable(path) as fp, h5py.File(fp, "r") as h5, NWBHDF5IO(
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/h5py/_hl/files.py:562: in __init__
fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/h5py/_hl/files.py:235: in make_fid
fid = h5f.open(name, flags, fapl=fapl)
h5py/_objects.pyx:54: in h5py._objects.with_phil.wrapper
???
h5py/_objects.pyx:55: in h5py._objects.with_phil.wrapper
???
h5py/h5f.pyx:102: in h5py.h5f.open
???
h5py/h5fd.pyx:163: in h5py.h5fd.H5FD_fileobj_read
???
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/fsspec/spec.py:1915: in readinto
data = self.read(out.nbytes)
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/fsspec/implementations/http.py:598: in read
return super().read(length)
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/fsspec/spec.py:1897: in read
out = self.cache._fetch(self.loc, self.loc + length)
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/fsspec/caching.py:481: in _fetch
self.cache = self.fetcher(start, bend)
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/fsspec/asyn.py:118: in wrapper
return sync(self.loop, func, *args, **kwargs)
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/fsspec/asyn.py:91: in sync
if event.wait(1):
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/threading.py:558: in wait
signaled = self._cond.wait(timeout)
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/threading.py:306: in wait
gotit = waiter.acquire(True, timeout)
E Failed: Timeout >300.0s
------------------------------ Captured log setup ------------------------------
DEBUG dandi:dandiapi.py:197 POST http://localhost:8000/api/dandisets/
DEBUG dandi:dandiapi.py:261 Response: 200
DEBUG dandi:dandiapi.py:197 GET http://localhost:8000/api/info/
DEBUG dandi:dandiapi.py:261 Response: 200
DEBUG dandi:dandiapi.py:493 Using api key from DANDI_API_KEY environment variable
DEBUG dandi:dandiapi.py:197 GET http://localhost:8000/api/auth/token
DEBUG dandi:dandiapi.py:261 Response: 200
DEBUG dandi:dandiset.py:128 Found identifier 000112 in top level 'identifier'
INFO dandi:upload.py:214 Found 2 files to consider
DEBUG dandi:dandiapi.py:197 GET http://localhost:8000/api/dandisets/000112/versions/draft/assets/
DEBUG dandi:dandiapi.py:261 Response: 200
DEBUG dandi:bases.py:342 Calculated dandi-etag of 2dfea6d6ebb6018f3a5c59707bc69ed3-1 for /tmp/pytest-of-runner/pytest-0/dandiset107/sub-mouse001/sub-mouse001.nwb
DEBUG dandi:bases.py:351 sub-mouse001/sub-mouse001.nwb: Beginning upload
DEBUG dandi:dandiapi.py:197 POST http://localhost:8000/api/uploads/initialize/
DEBUG dandi:dandiapi.py:261 Response: 409
DEBUG dandi:dandiapi.py:268 Error 409 while sending POST request to http://localhost:8000/api/uploads/initialize/: "Blob already exists."
DEBUG dandi:bases.py:367 sub-mouse001/sub-mouse001.nwb: Blob already exists on server
DEBUG dandi:bases.py:446 sub-mouse001/sub-mouse001.nwb: Assigning asset blob to dandiset & version
DEBUG dandi:dandiapi.py:197 POST http://localhost:8000/api/dandisets/000112/versions/draft/assets/
DEBUG dandi:dandiapi.py:261 Response: 200
INFO dandi:bases.py:460 sub-mouse001/sub-mouse001.nwb: Asset successfully uploaded
------------------------------ Captured log call -------------------------------
DEBUG dandi:dandiapi.py:197 GET http://localhost:8000/api/dandisets/000112/versions/draft/assets/
DEBUG dandi:dandiapi.py:261 Response: 200
DEBUG dandi:dandiapi.py:197 GET http://localhost:8000/api/dandisets/000112/versions/draft/assets/b770f47f-b67f-4a58-8883-09a2466eb577/
DEBUG dandi:dandiapi.py:261 Response: 200
DEBUG dandi:dandiapi.py:197 GET http://localhost:8000/api/dandisets/000112/versions/draft/assets/b770f47f-b67f-4a58-8883-09a2466eb577/
DEBUG dandi:dandiapi.py:261 Response: 200
DEBUG dandi:dandiapi.py:197 GET http://localhost:8000/api/dandisets/000112/versions/draft/assets/b770f47f-b67f-4a58-8883-09a2466eb577/
DEBUG dandi:dandiapi.py:261 Response: 200
---------- coverage: platform linux, python 3.8.18-final-0 -----------
```
@jwodder please remind what those trailing requests are for -- waiting for validation or smth? I wonder if it is result of some recent change...
Contributor guide
No contributing guide indexed for this repository
Assessment
This issue has not been assessed yet.