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from __future__ import annotations
from collections.abc import Iterable
from typing import TYPE_CHECKING, Any
import numpy as np
from xarray.backends.common import (
BACKEND_ENTRYPOINTS,
AbstractDataStore,
BackendArray,
BackendEntrypoint,
T_PathFileOrDataStore,
_normalize_path,
datatree_from_dict_with_io_cleanup,
robust_getitem,
)
from xarray.backends.store import StoreBackendEntrypoint
from xarray.core import indexing
from xarray.core.utils import (
Frozen,
FrozenDict,
close_on_error,
is_remote_uri,
)
from xarray.core.variable import Variable
from xarray.namedarray.pycompat import integer_types
if TYPE_CHECKING:
import os
from xarray.core.dataset import Dataset
from xarray.core.datatree import DataTree
from xarray.core.types import ReadBuffer
class PydapArrayWrapper(BackendArray):
def __init__(self, array):
self.array = array
@property
def shape(self) -> tuple[int, ...]:
return self.array.shape
@property
def dtype(self):
return self.array.dtype
def __getitem__(self, key):
return indexing.explicit_indexing_adapter(
key, self.shape, indexing.IndexingSupport.BASIC, self._getitem
)
def _getitem(self, key):
result = robust_getitem(self.array, key, catch=ValueError)
# in some cases, pydap doesn't squeeze axes automatically like numpy
result = np.asarray(result)
axis = tuple(n for n, k in enumerate(key) if isinstance(k, integer_types))
if result.ndim + len(axis) != self.array.ndim and axis:
result = np.squeeze(result, axis)
return result
def get_group(ds, group):
if group in {None, "", "/"}:
# use the root group
return ds
else:
try:
return ds[group]
except KeyError as e:
# wrap error to provide slightly more helpful message
raise KeyError(f"group not found: {group}", e) from e
class PydapDataStore(AbstractDataStore):
"""Store for accessing OpenDAP datasets with pydap.
This store provides an alternative way to access OpenDAP datasets that may
be useful if the netCDF4 library is not available.
"""
def __init__(self, dataset, group=None):
"""
Parameters
----------
ds : pydap DatasetType
group: str or None (default None)
The group to open. If None, the root group is opened.
"""
self.dataset = dataset
self.group = group
@classmethod
def open(
cls,
url,
group=None,
application=None,
session=None,
output_grid=None,
timeout=None,
verify=None,
user_charset=None,
):
from pydap.client import open_url
from pydap.net import DEFAULT_TIMEOUT
if output_grid is not None:
# output_grid is no longer passed to pydap.client.open_url
from xarray.core.utils import emit_user_level_warning
emit_user_level_warning(
"`output_grid` is deprecated and will be removed in a future version"
" of xarray. Will be set to `None`, the new default. ",
DeprecationWarning,
)
output_grid = False # new default behavior
kwargs = {
"url": url,
"application": application,
"session": session,
"output_grid": output_grid or False,
"timeout": timeout or DEFAULT_TIMEOUT,
"verify": verify or True,
"user_charset": user_charset,
}
if isinstance(url, str):
# check uit begins with an acceptable scheme
dataset = open_url(**kwargs)
elif hasattr(url, "ds"):
# pydap dataset
dataset = url.ds
args = {"dataset": dataset}
if group:
# only then, change the default
args["group"] = group
return cls(**args)
def open_store_variable(self, var):
data = indexing.LazilyIndexedArray(PydapArrayWrapper(var))
try:
dimensions = [
dim.split("/")[-1] if dim.startswith("/") else dim for dim in var.dims
]
except AttributeError:
# GridType does not have a dims attribute - instead get `dimensions`
# see https://github.com/pydap/pydap/issues/485
dimensions = var.dimensions
return Variable(dimensions, data, var.attributes)
def get_variables(self):
# get first all variables arrays, excluding any container type like,
# `Groups`, `Sequence` or `Structure` types
try:
_vars = list(self.ds.variables())
_vars += list(self.ds.grids()) # dap2 objects
except AttributeError:
from pydap.model import GroupType
_vars = [
var
for var in self.ds.keys()
# check the key is not a BaseType or GridType
if not isinstance(self.ds[var], GroupType)
]
return FrozenDict((k, self.open_store_variable(self.ds[k])) for k in _vars)
def get_attrs(self):
"""Remove any opendap specific attributes"""
opendap_attrs = (
"configuration",
"build_dmrpp",
"bes",
"libdap",
"invocation",
"dimensions",
)
attrs = self.ds.attributes
list(map(attrs.pop, opendap_attrs, [None] * 6))
return Frozen(attrs)
def get_dimensions(self):
return Frozen(self.ds.dimensions)
@property
def ds(self):
return get_group(self.dataset, self.group)
class PydapBackendEntrypoint(BackendEntrypoint):
"""
Backend for steaming datasets over the internet using
the Data Access Protocol, also known as DODS or OPeNDAP
based on the pydap package.
This backend is selected by default for urls.
For more information about the underlying library, visit:
https://pydap.github.io/pydap/en/intro.html
See Also
--------
backends.PydapDataStore
"""
description = "Open remote datasets via OPeNDAP using pydap in Xarray"
url = "https://docs.xarray.dev/en/stable/generated/xarray.backends.PydapBackendEntrypoint.html"
def guess_can_open(self, filename_or_obj: T_PathFileOrDataStore) -> bool:
return isinstance(filename_or_obj, str) and is_remote_uri(filename_or_obj)
def open_dataset(
self,
filename_or_obj: (
str | os.PathLike[Any] | ReadBuffer | bytes | memoryview | AbstractDataStore
),
*,
mask_and_scale=True,
decode_times=True,
concat_characters=True,
decode_coords=True,
drop_variables: str | Iterable[str] | None = None,
use_cftime=None,
decode_timedelta=None,
group=None,
application=None,
session=None,
output_grid=None,
timeout=None,
verify=None,
user_charset=None,
) -> Dataset:
store = PydapDataStore.open(
url=filename_or_obj,
group=group,
application=application,
session=session,
output_grid=output_grid,
timeout=timeout,
verify=verify,
user_charset=user_charset,
)
store_entrypoint = StoreBackendEntrypoint()
with close_on_error(store):
ds = store_entrypoint.open_dataset(
store,
mask_and_scale=mask_and_scale,
decode_times=decode_times,
concat_characters=concat_characters,
decode_coords=decode_coords,
drop_variables=drop_variables,
use_cftime=use_cftime,
decode_timedelta=decode_timedelta,
)
return ds
def open_datatree(
self,
filename_or_obj: T_PathFileOrDataStore,
*,
mask_and_scale=True,
decode_times=True,
concat_characters=True,
decode_coords=True,
drop_variables: str | Iterable[str] | None = None,
use_cftime=None,
decode_timedelta=None,
group: str | None = None,
application=None,
session=None,
timeout=None,
verify=None,
user_charset=None,
) -> DataTree:
groups_dict = self.open_groups_as_dict(
filename_or_obj,
mask_and_scale=mask_and_scale,
decode_times=decode_times,
concat_characters=concat_characters,
decode_coords=decode_coords,
drop_variables=drop_variables,
use_cftime=use_cftime,
decode_timedelta=decode_timedelta,
group=group,
application=None,
session=None,
timeout=None,
verify=None,
user_charset=None,
)
return datatree_from_dict_with_io_cleanup(groups_dict)
def open_groups_as_dict(
self,
filename_or_obj: T_PathFileOrDataStore,
*,
mask_and_scale=True,
decode_times=True,
concat_characters=True,
decode_coords=True,
drop_variables: str | Iterable[str] | None = None,
use_cftime=None,
decode_timedelta=None,
group: str | None = None,
application=None,
session=None,
timeout=None,
verify=None,
user_charset=None,
) -> dict[str, Dataset]:
from xarray.core.treenode import NodePath
filename_or_obj = _normalize_path(filename_or_obj)
store = PydapDataStore.open(
url=filename_or_obj,
application=application,
session=session,
timeout=timeout,
verify=verify,
user_charset=user_charset,
)
# Check for a group and make it a parent if it exists
if group:
parent = str(NodePath("/") / NodePath(group))
else:
parent = str(NodePath("/"))
groups_dict = {}
group_names = [parent]
# construct fully qualified path to group
try:
# this works for pydap >= 3.5.1
Groups = store.ds[parent].groups()
except AttributeError:
# THIS IS ONLY NEEDED FOR `pydap == 3.5.0`
# `pydap>= 3.5.1` has a new method `groups()`
# that returns a dict of group names and their paths
def group_fqn(store, path=None, g_fqn=None) -> dict[str, str]:
"""To be removed for pydap > 3.5.0.
Derives the fully qualifying name of a Group."""
from pydap.model import GroupType
if not path:
path = "/" # parent
if not g_fqn:
g_fqn = {}
groups = [
store[key].id
for key in store.keys()
if isinstance(store[key], GroupType)
]
for g in groups:
g_fqn.update({g: path})
subgroups = [
var for var in store[g] if isinstance(store[g][var], GroupType)
]
if len(subgroups) > 0:
npath = path + g
g_fqn = group_fqn(store[g], npath, g_fqn)
return g_fqn
Groups = group_fqn(store.ds)
group_names += [
str(NodePath(path_to_group) / NodePath(group))
for group, path_to_group in Groups.items()
]
for path_group in group_names:
# get a group from the store
store.group = path_group
store_entrypoint = StoreBackendEntrypoint()
with close_on_error(store):
group_ds = store_entrypoint.open_dataset(
store,
mask_and_scale=mask_and_scale,
decode_times=decode_times,
concat_characters=concat_characters,
decode_coords=decode_coords,
drop_variables=drop_variables,
use_cftime=use_cftime,
decode_timedelta=decode_timedelta,
)
if group:
group_name = str(NodePath(path_group).relative_to(parent))
else:
group_name = str(NodePath(path_group))
groups_dict[group_name] = group_ds
return groups_dict
BACKEND_ENTRYPOINTS["pydap"] = ("pydap", PydapBackendEntrypoint)
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