Open
Description
What would you like to see added to HDMF-ZARR?
See #238 and NeurodataWithoutBorders/nwb_benchmarks#77
Error:
For parameters: 's3://dandiarchive/zarr/18e75d22-f527-4051-a4c8-c7e0f1e7dad1/'
. Using tshark at: /Applications/Wireshark.app/Contents/MacOS/tshark
Traceback (most recent call last):
File "/Users/rly/miniconda3/envs/nwb_benchmarks/lib/python3.11/site-packages/asv/benchmark.py", line 68, in <module>
main()
File "/Users/rly/miniconda3/envs/nwb_benchmarks/lib/python3.11/site-packages/asv/benchmark.py", line 60, in main
commands[mode](args)
File "/Users/rly/miniconda3/envs/nwb_benchmarks/lib/python3.11/site-packages/asv_runner/run.py", line 72, in _run
result = benchmark.do_run()
^^^^^^^^^^^^^^^^^^
File "/Users/rly/miniconda3/envs/nwb_benchmarks/lib/python3.11/site-packages/asv_runner/benchmarks/_base.py", line 661, in do_run
return self.run(*self._current_params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/miniconda3/envs/nwb_benchmarks/lib/python3.11/site-packages/asv_runner/benchmarks/track.py", line 64, in run
return self.func(*param)
^^^^^^^^^^^^^^^^^
File "/Users/rly/miniconda3/envs/nwb_benchmarks/lib/python3.11/site-packages/asv_runner/benchmarks/mark.py", line 105, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/miniconda3/envs/nwb_benchmarks/lib/python3.11/site-packages/asv_runner/benchmarks/mark.py", line 164, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/Documents/NWB/nwb_benchmarks/src/nwb_benchmarks/benchmarks/network_tracking_remote_file_reading.py", line 327, in track_network_activity_during_read
self.nwbfile, self.io = read_zarr_nwbfile(s3_url=s3_url, mode="r")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/Documents/NWB/nwb_benchmarks/src/nwb_benchmarks/core/_streaming.py", line 264, in read_zarr_nwbfile
nwbfile = io.read()
^^^^^^^^^
File "/Users/rly/miniconda3/envs/nwb_benchmarks/lib/python3.11/site-packages/hdmf/utils.py", line 668, in func_call
return func(args[0], **pargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/miniconda3/envs/nwb_benchmarks/lib/python3.11/site-packages/hdmf/backends/io.py", line 56, in read
f_builder = self.read_builder()
^^^^^^^^^^^^^^^^^^^
File "/Users/rly/miniconda3/envs/nwb_benchmarks/lib/python3.11/site-packages/hdmf/utils.py", line 668, in func_call
return func(args[0], **pargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/Documents/NWB/hdmf-zarr/src/hdmf_zarr/backend.py", line 1467, in read_builder
f_builder = self.__read_group(self.__file, ROOT_NAME)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/Documents/NWB/hdmf-zarr/src/hdmf_zarr/backend.py", line 1545, in __read_group
sub_builder = self.__read_group(sub_group, sub_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/Documents/NWB/hdmf-zarr/src/hdmf_zarr/backend.py", line 1545, in __read_group
sub_builder = self.__read_group(sub_group, sub_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/Documents/NWB/hdmf-zarr/src/hdmf_zarr/backend.py", line 1554, in __read_group
self.__read_links(zarr_obj=zarr_obj, parent=ret)
File "/Users/rly/Documents/NWB/hdmf-zarr/src/hdmf_zarr/backend.py", line 1573, in __read_links
target_name, target_zarr_obj = self.resolve_ref(link)
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/Documents/NWB/hdmf-zarr/src/hdmf_zarr/backend.py", line 819, in resolve_ref
target_zarr_obj = self.__open_file_consolidated(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/Documents/NWB/hdmf-zarr/src/hdmf_zarr/backend.py", line 566, in __open_file_consolidated
return zarr.open_consolidated(
^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/miniconda3/envs/nwb_benchmarks/lib/python3.11/site-packages/zarr/convenience.py", line 1345, in open_consolidated
store = normalize_store_arg(
^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/miniconda3/envs/nwb_benchmarks/lib/python3.11/site-packages/zarr/storage.py", line 201, in normalize_store_arg
return normalize_store(store, storage_options, mode)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/rly/miniconda3/envs/nwb_benchmarks/lib/python3.11/site-packages/zarr/storage.py", line 173, in _normalize_store_arg_v2
raise ValueError("storage_options passed with non-fsspec path")
ValueError: storage_options passed with non-fsspec path
Is your feature request related to a problem?
No response
What solution would you like?
Add tests for this
Do you have any interest in helping implement the feature?
Yes.