"ValueError: missing object_codec for object array"

Seeing the same VLEN string issue noted in https://github.com/fsspec/kerchunk/issues/102 when attempting to use SingleHdf5ToZarr with a single GEDI HDF5 file.

See this notebook https://nbviewer.org/gist/sharkinsspatial/b5938e2e3e0c96a1f1cef768d1b4da7e

I attempted testing against https://github.com/fsspec/kerchunk/pull/40 but did not see the reported segfault but the same originally reported “ValueError: missing object_codec for object array” exception.

predict_stratum appears to be the offending variable in this case as tests with a new intermediate HDF5 for a selected BEAM group with this variable dropped work as expected.

For more details on the GEDI data structure see https://github.com/ornldaac/gedi_tutorials/blob/main/3_gedi_l4a_exploring_data.ipynb

[sharkinsspatial]

@martindurant I would suggest that in the short term we include a parameter which allows users to select inlining or skipping for compound dtypes and VLEN strings. Once #40 is completed we can change the underlying storage mechanism without altering the use of the option parameter.

[martindurant]

@joshmoore , this is not actually related to VLEN: we have a complex dtype here that includes some object type fields, which are encoded using HDF5-specific pointers.