Fix uploading Zarr within a BIDS dataset; typing-check guided fix for handling requests exception#1331
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yarikoptic merged 3 commits intomasterfrom Sep 29, 2023
Merged
Fix uploading Zarr within a BIDS dataset; typing-check guided fix for handling requests exception#1331yarikoptic merged 3 commits intomasterfrom
yarikoptic merged 3 commits intomasterfrom
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Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## master #1331 +/- ##
==========================================
+ Coverage 88.81% 88.85% +0.03%
==========================================
Files 76 76
Lines 10200 10216 +16
==========================================
+ Hits 9059 9077 +18
+ Misses 1141 1139 -2
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…n BIDS
could not run tests locally unfortunately - likely due to my custom
configuration of networking for podman (?) or was it also done for docker? TODO to figure it out
ulling django ... done
Creating network "dandiarchive-docker_default" with the default driver
ERROR: Failed to Setup IP tables: Unable to enable SKIP DNAT rule: (iptables failed: iptables --wait -t nat -I DOCKER -i br-c26ebcecb035 -j RETURN: iptables: No chain/target/match by that name.
(exit status 1))
Removing network dandiarchive-docker_default
WARNING: Network dandiarchive-docker_default not found.
ERROR
============================================================ ERRORS =============================================================
____________________________________________ ERROR at setup of test_upload_bids_zarr ____________________________________________
dandi/tests/fixtures.py:403: in docker_compose_setup
run(
/usr/lib/python3.11/subprocess.py:571: in run
raise CalledProcessError(retcode, process.args,
E subprocess.CalledProcessError: Command '['docker-compose', 'run', '--rm', 'django', './manage.py', 'migrate']' returned non-zero exit status 1.
===================================================== slowest 10 durations ======================================================
119.18s setup dandi/tests/test_upload.py::test_upload_bids_zarr
(1 durations < 0.005s hidden. Use -vv to show these durations.)
==================================================== short test summary info ====================================================
ERROR dandi/tests/test_upload.py::test_upload_bids_zarr - subprocess.CalledProcessError: Command '['docker-compose', 'run', '--rm', 'django', './manage.py', 'migrate']' returned non-...
================================================= 1 error in 119.31s (0:01:59) ==================================================
python -m pytest -s -v dandi/tests/test_upload.py::test_upload_bids_zarr 3.87s user 3.43s system 6% cpu 2:01.11 total
Also flake8 was not happy either
flake8...................................................................Failed
- hook id: flake8
- exit code: 1
dandi/tests/test_upload.py:297:5: F821 undefined name 'new_dandiset'
dandi/tests/test_upload.py:298:16: F821 undefined name 'new_dandiset'
dandi/tests/test_upload.py:303:5: F821 undefined name 'new_dandiset'
so it seems it does not know how to deal with those pytest fixtures but odd
that just now and just for that one
Member
Author
issue reproduced!____________________________ test_upload_bids_zarr _____________________________
dandi/tests/test_upload.py:297: in test_upload_bids_zarr
bids_zarr_dandiset.upload()
dandi/tests/fixtures.py:516: in upload
upload(
dandi/upload.py:339: in upload
for v in process_path(dfile):
dandi/upload.py:264: in process_path
for r in dfile.iter_upload(
dandi/files/bases.py:339: in iter_upload
etagger = get_dandietag(self.filepath)
/opt/hostedtoolcache/Python/3.11.5/x64/lib/python3.11/site-packages/fscacher/cache.py:165: in fingerprinter
ret = fingerprinted(*args, **kwargs_)
/opt/hostedtoolcache/Python/3.11.5/x64/lib/python3.11/site-packages/joblib/memory.py:655: in __call__
return self._cached_call(args, kwargs)[0]
/opt/hostedtoolcache/Python/3.11.5/x64/lib/python3.11/site-packages/joblib/memory.py:598: in _cached_call
out, metadata = self.call(*args, **kwargs)
/opt/hostedtoolcache/Python/3.11.5/x64/lib/python3.11/site-packages/joblib/memory.py:856: in call
output = self.func(*args, **kwargs)
/opt/hostedtoolcache/Python/3.11.5/x64/lib/python3.11/site-packages/fscacher/cache.py:101: in fingerprinted
return f(path, *args, **kwargs)
dandi/support/digests.py:100: in get_dandietag
return DandiETag.from_file(filepath)
/opt/hostedtoolcache/Python/3.11.5/x64/lib/python3.11/site-packages/dandischema/digests/dandietag.py:147: in from_file
with open(path, "rb") as f:
E IsADirectoryError: [Errno 21] Is a directory: '/tmp/pytest-of-runner/pytest-0/dandiset236/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr' |
…Zarr is used not of a file Also fixed up test
yarikoptic
changed the title
yarikoptic
changed the title
|
🚀 PR was released in |
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could not run tests locally unfortunately . See first commit for more details
Closes #1307
TODOs: