fsspec / fsspec/kerchunk

JSON not properly decoded by backends

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Description

Kerchunk doesn't properly decode the JSON for zarr array-level attributes, instead leaving dictionaries as long strings. For example:

# create example netCDF4 file
xr.tutorial.open_dataset('air_temperature').to_netcdf('air.nc')

kerchunk.backends.SingleHdf5ToZarr('air.nc', inline_threshold=300).translate()
{'version': 1,
 'refs': {'.zgroup': '{"zarr_format":2}',
  '.zattrs': '{"Conventions":"COARDS","description":"Data is from NMC initialized reanalysis\\n(4x\\/day).  These are the 0.9950 sigma level values.","platform":"Model","references":"http:\\/\\/[www.esrl.noaa.gov\\/psd\\/data\\/gridded\\/data.ncep.reanalysis.html](https://www.esrl.noaa.gov///psd///data///gridded///data.ncep.reanalysis.html)","title":"4x daily NMC reanalysis (1948)"}',
  'air/.zarray': '{"chunks":[2920,25,53],"compressor":null,"dtype":"<i2","fill_value":null,"filters":null,"order":"C","shape":[2920,25,53],"zarr_format":2}',
  'air/.zattrs': '{"GRIB_id":11,"GRIB_name":"TMP","_ARRAY_DIMENSIONS":["time","lat","lon"],"actual_range":[185.16000366210938,322.1000061035156],"dataset":"NMC Reanalysis","level_desc":"Surface","long_name":"4xDaily Air temperature at sigma level 995","parent_stat":"Other","precision":2,"scale_factor":0.01,"statistic":"Individual Obs","units":"degK","var_desc":"Air temperature"}',
  'air/0.0.0': ['air.nc', 15419, 7738000],
  'lat/.zarray': '{"chunks":[25],"compressor":null,"dtype":"<f4","fill_value":"NaN","filters":null,"order":"C","shape":[25],"zarr_format":2}',
  'lat/.zattrs': '{"_ARRAY_DIMENSIONS":["lat"],"axis":"Y","long_name":"Latitude","standard_name":"latitude","units":"degrees_north"}',
  'lat/0': ['air.nc', 5179, 100],
  'lon/.zarray': '{"chunks":[53],"compressor":null,"dtype":"<f4","fill_value":"NaN","filters":null,"order":"C","shape":[53],"zarr_format":2}',
  'lon/.zattrs': '{"_ARRAY_DIMENSIONS":["lon"],"axis":"X","long_name":"Longitude","standard_name":"longitude","units":"degrees_east"}',
  'lon/0': ['air.nc', 5279, 212],
  'time/.zarray': '{"chunks":[2920],"compressor":null,"dtype":"<f4","fill_value":"NaN","filters":null,"order":"C","shape":[2920],"zarr_format":2}',
  'time/.zattrs': '{"_ARRAY_DIMENSIONS":["time"],"calendar":"standard","long_name":"Time","standard_name":"time","units":"hours since 1800-01-01"}',
  'time/0': ['air.nc', 7757515, 11680]}}

Notice that this is only partially decoded - the top two levels are nested python dictionaries, but below that the various zarr attributes are stored as long strings, e.g:

'{"chunks":[2920,25,53],"compressor":null,"dtype":"<i2","fill_value":null,"filters":null,"order":"C","shape":[2920,25,53],"zarr_format":2}'

This seems silly, why not just decode the whole thing properly at the beginning so you can always treat it like a nested python dictionary? (Or even better use a dedicated abstraction like suggested in #375)

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start at kerchunk.backends.SingleHdf5ToZarr and its translate() output, using the provided air_temperature example to inspect how zarr metadata strings are decoded. Done means nested zarr attributes such as .zarray and .zattrs are represented as dictionaries rather than long JSON strings.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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