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Merge pull request #147 from martindurant/intake2
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,74 +1,22 @@ | ||
| from . import __version__ | ||
| from intake.source.base import DataSource, Schema | ||
| class IntakeXarraySourceAdapter: | ||
| container = "xarray" | ||
| name = "xarray" | ||
| version = "" | ||
|
|
||
| def to_dask(self): | ||
| if "chunks" not in self.reader.kwargs: | ||
| return self.reader(chunks={}).read() | ||
| else: | ||
| return self.reader.read() | ||
|
|
||
| class DataSourceMixin(DataSource): | ||
| """Common behaviours for plugins in this repo""" | ||
| version = __version__ | ||
| container = 'xarray' | ||
| partition_access = True | ||
|
|
||
| def _get_schema(self): | ||
| """Make schema object, which embeds xarray object and some details""" | ||
| from .xarray_container import serialize_zarr_ds | ||
|
|
||
| self.urlpath = self._get_cache(self.urlpath)[0] | ||
|
|
||
| if self._ds is None: | ||
| self._open_dataset() | ||
| def __call__(self, *args, **kwargs): | ||
| return self | ||
|
|
||
| metadata = { | ||
| 'dims': dict(self._ds.dims), | ||
| 'data_vars': {k: list(self._ds[k].coords) | ||
| for k in self._ds.data_vars.keys()}, | ||
| 'coords': tuple(self._ds.coords.keys()), | ||
| } | ||
| if getattr(self, 'on_server', False): | ||
| metadata['internal'] = serialize_zarr_ds(self._ds) | ||
| metadata.update(self._ds.attrs) | ||
| self._schema = Schema( | ||
| datashape=None, | ||
| dtype=None, | ||
| shape=None, | ||
| npartitions=None, | ||
| extra_metadata=metadata) | ||
| return self._schema | ||
| get = __call__ | ||
|
|
||
| def read(self): | ||
| """Return a version of the xarray with all the data in memory""" | ||
| self._load_metadata() | ||
| return self._ds.load() | ||
| return self.reader(chunks=None).read() | ||
|
|
||
| def read_chunked(self): | ||
| """Return xarray object (which will have chunks)""" | ||
| self._load_metadata() | ||
| return self._ds | ||
|
|
||
| def read_partition(self, i): | ||
| """Fetch one chunk of data at tuple index i | ||
| """ | ||
| import numpy as np | ||
| self._load_metadata() | ||
| if not isinstance(i, (tuple, list)): | ||
| raise TypeError('For Xarray sources, must specify partition as ' | ||
| 'tuple') | ||
| if isinstance(i, list): | ||
| i = tuple(i) | ||
| if hasattr(self._ds, 'variables') or i[0] in self._ds.coords: | ||
| arr = self._ds[i[0]].data | ||
| i = i[1:] | ||
| else: | ||
| arr = self._ds.data | ||
| if isinstance(arr, np.ndarray): | ||
| return arr | ||
| # dask array | ||
| return arr.blocks[i].compute() | ||
|
|
||
| def to_dask(self): | ||
| """Return xarray object where variables are dask arrays""" | ||
| return self.read_chunked() | ||
| discover = read | ||
|
|
||
| def close(self): | ||
| """Delete open file from memory""" | ||
| self._ds = None | ||
| self._schema = None | ||
| read_chunked = to_dask |
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