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ENH: Support Kerchunk Files #480

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merged 6 commits into from
Jun 4, 2022
Merged

ENH: Support Kerchunk Files #480

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62f0b0e
add kerchunk option
mgrover1 Jun 1, 2022
3b949ca
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 1, 2022
70f8f94
fix bug in the kerchunk open
mgrover1 Jun 1, 2022
795edd3
Merge branch 'intake:main' into add-kerchunk
mgrover1 Jun 4, 2022
dfcab1a
Update spec
mgrover1 Jun 4, 2022
25b5e91
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 4, 2022
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10 changes: 5 additions & 5 deletions docs/source/explanation/esm-catalog-spec.md
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Original file line number Diff line number Diff line change
Expand Up @@ -96,11 +96,11 @@ The column names can optionally be associated with a controlled vocabulary, such

An assets object describes the columns in the CSV file relevant for opening the actual data files.

| Element | Type | Description |
| ------------------ | ------ | ---------------------------------------------------------------------------------------------------------------------------------- |
| column_name | string | **REQUIRED.** The name of the column containing the path to the asset. Must be in the header of the CSV file. |
| format | string | The data format. Valid values are `netcdf` and `zarr`. If specified, it means that all data in the catalog is the same type. |
| format_column_name | string | The column name which contains the data format, allowing for variable data types in one catalog. Mutually exclusive with `format`. |
| Element | Type | Description |
| ------------------ | ------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| column_name | string | **REQUIRED.** The name of the column containing the path to the asset. Must be in the header of the CSV file. |
| format | string | The data format. Valid values are `netcdf`, `zarr`, or `reference` ([`kerchunk`](https://github.com/fsspec/kerchunk) reference files). If specified, it means that all data in the catalog is the same type. |
| format_column_name | string | The column name which contains the data format, allowing for variable data types in one catalog. Mutually exclusive with `format`. |

### Aggregation Control Object

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10 changes: 10 additions & 0 deletions intake_esm/source.py
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Expand Up @@ -44,10 +44,19 @@ def _open_dataset(
requested_variables=None,
additional_attrs=None,
expand_dims=None,
data_format=None,
):

_can_be_local = fsspec.utils.can_be_local(urlpath)
storage_options = xarray_open_kwargs.get('backend_kwargs', {}).get('storage_options', {})

# Support kerchunk datasets, setting the file object (fo) and urlpath
if data_format == 'reference':
if 'storage_options' not in xarray_open_kwargs.keys():
xarray_open_kwargs['storage_options'] = {}
xarray_open_kwargs['storage_options']['fo'] = urlpath
urlpath = 'reference://'

if xarray_open_kwargs['engine'] == 'zarr':
url = urlpath
elif _can_be_local:
Expand Down Expand Up @@ -220,6 +229,7 @@ def _open_dataset(self):
if agg.type.value == 'join_new'
},
requested_variables=self.requested_variables,
data_format=record['_data_format_'],
additional_attrs=record.to_dict(),
)
for _, record in self.df.iterrows()
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