From 0833c375555014a3d2f66c2693b3e552d2389754 Mon Sep 17 00:00:00 2001 From: k204247 Date: Wed, 15 Oct 2025 11:58:46 +0200 Subject: [PATCH 1/3] implementation for archive extension --- xpystac/core.py | 165 +++++++++++++++++++++++++++++++++++++----------- 1 file changed, 128 insertions(+), 37 deletions(-) diff --git a/xpystac/core.py b/xpystac/core.py index 8f22e2d..3128917 100644 --- a/xpystac/core.py +++ b/xpystac/core.py @@ -3,6 +3,8 @@ import pystac import xarray +import os +from tqdm import tqdm from xpystac.utils import _import_optional_dependency, _is_item_search @@ -83,49 +85,138 @@ def _( return xarray.Dataset(bands, attrs=da.attrs) +def _extract_tar_file(obj): + + tarfile=_import_optional_dependency("tarfile") + tempfile=_import_optional_dependency("tempfile") + pathlib=_import_optional_dependency("pathlib") + # Extract the archive:href from obj->href ( *.tar ) to a temp dir and pass + # this temp dir as the obj.href to xarray + #print(f"Encountered tar file:{obj.href}") + tmppath=os.getenv("STAC_TMP_DIR") + with tempfile.TemporaryDirectory(dir=tmppath,delete=False) as tmpdirname: + print(f"tar arch ext file:{obj.extra_fields}") + mytar = tarfile.open(obj.href) + myvar = obj.extra_fields["archive:href"] + myvarFiles = [ tarinfo for tarinfo in mytar.getmembers() if tarinfo.name.startswith(myvar)] + #Check if the 'archive:href' string ends with '.zarr' .i.e., extract the entire zarr store + if myvar.endswith(('.zarr','.zarr/')): + #case -1 : tar of zarr .. Complete zarr store + new_href = os.path.join(tmpdirname,obj.extra_fields["archive:href"]) + # myvarFiles = [ tarinfo for tarinfo in mytar.getmembers() if tarinfo.name.startswith(myvar) ] + #myvarFiles = [ tarinfo for tarinfo in mytar.getmembers() if tarinfo.name.startswith(myvar)] + else: + #case -2 : tar of var or #case -3 : tar of chunk .. Incomplete zarr store + myvarFiles.extend( [ tarinfo for tarinfo in mytar.getmembers() if tarinfo.name.endswith('.zmetadata') ] ) + myvarFiles.extend( [ tarinfo for tarinfo in mytar.getmembers() if tarinfo.name.endswith('.zgroup') ] ) + zarr_path = obj.extra_fields["archive:href"].split('.zarr')[0] + '.zarr' + new_href = os.path.join(tmpdirname,zarr_path) + #print(myvarFiles) + + # TODO: Add a progress bar to help the user + mytar.extractall(tmpdirname,myvarFiles) + + #print("Extraction Done!!!") + #print(f"tar file new:{new_href}") + return new_href + @to_xarray.register def _( - obj: pystac.Asset, + obj: Union[ pystac.Asset,list], stacking_library: Union[Literal["odc.stac", "stackstac"], None] = None, **kwargs, ) -> xarray.Dataset: + + # MKM 18 Oct 2024 + #TODO : Check if the obj is list instance or pystac.Asset instance and + # accordingly if just one asset pass it through xarray, + # else, collect the assets and pass to xarray as open_mfdataset. + # In case of tar balls, extract each of them and the store these paths + # send the list of these zarr stores to xarray.open_mfdataset() + # It should work. + default_kwargs: Mapping = {"chunks": {}} - open_kwargs = obj.extra_fields.get("xarray:open_kwargs", {}) - - storage_options = obj.extra_fields.get("xarray:storage_options", None) - if storage_options: - open_kwargs["storage_options"] = storage_options - - if obj.media_type == pystac.MediaType.JSON and {"index", "references"}.intersection( - set(obj.roles) if obj.roles else set() - ): - requests = _import_optional_dependency("requests") - fsspec = _import_optional_dependency("fsspec") - r = requests.get(obj.href) - r.raise_for_status() - try: - import planetary_computer # type: ignore - refs = planetary_computer.sign(r.json()) - except ImportError: - refs = r.json() - - mapper = fsspec.get_mapper("reference://", fo=refs) - default_kwargs = { - **default_kwargs, - "engine": "zarr", - "consolidated": False, - } - return xarray.open_dataset( - mapper, **{**default_kwargs, **open_kwargs, **kwargs} - ) - - if obj.media_type == pystac.MediaType.COG: - _import_optional_dependency("rioxarray") - default_kwargs = {**default_kwargs, "engine": "rasterio"} - elif obj.media_type == "application/vnd+zarr": - _import_optional_dependency("zarr") + # Check the type of the 'obj' + if isinstance(obj, pystac.Asset): + print("Asset as input!",flush=True) + open_kwargs = obj.extra_fields.get("xarray:open_kwargs", {}) + + storage_options = obj.extra_fields.get("xarray:storage_options", None) + if storage_options: + open_kwargs["storage_options"] = storage_options + + if obj.media_type == pystac.MediaType.JSON and {"index", "references"}.intersection( + set(obj.roles) if obj.roles else set() + ): + requests = _import_optional_dependency("requests") + fsspec = _import_optional_dependency("fsspec") + r = requests.get(obj.href) + r.raise_for_status() + try: + import planetary_computer # type: ignore + + refs = planetary_computer.sign(r.json()) + except ImportError: + refs = r.json() + + mapper = fsspec.get_mapper("reference://", fo=refs) + default_kwargs = { + **default_kwargs, + "engine": "zarr", + "consolidated": False, + } + return xarray.open_dataset( + mapper, **{**default_kwargs, **open_kwargs, **kwargs} + ) + + if obj.media_type == pystac.MediaType.COG: + _import_optional_dependency("rioxarray") + default_kwargs = {**default_kwargs, "engine": "rasterio"} + elif obj.media_type == "application/vnd+zarr": + _import_optional_dependency("zarr") + default_kwargs = {**default_kwargs, "engine": "zarr"} + # MKM added for handling the 'archive' extension, as of now only plain '*.tar' + # not zipped tarfiles. + elif obj.media_type == "application/x-tar": + new_href=_extract_tar_file(obj) + print("Extraction Done!!!") + print(f"Extracted tar file:{new_href}") + # Check the archive:type and set the appropriate engine (as of now 'tar' of 'zarr', + # hence 'zarr' engine) to the xarray + default_kwargs = {**default_kwargs, "engine": "zarr"} + # Pass the new_href and the kwargs to xarray + return xarray.open_dataset(new_href, **{**default_kwargs, **open_kwargs, **kwargs}) + ds = xarray.open_dataset(obj.href, **{**default_kwargs, **open_kwargs, **kwargs}) + return ds + + elif isinstance(obj, list): + print("List of Assets as input!",flush=True) + # Create a list of assets from the list of items. + # Prepare a dictionary to map the item, asset (tar ball) and the path where the tar ball has been extracted to. + # Concate all the zarr stores from each tar ball and create the xarray + # Return the xarray created above, with engine as 'zarr' ( for this particular use case ) + + open_kwargs = obj[0].extra_fields.get("xarray:open_kwargs", {}) + + storage_options = obj[0].extra_fields.get("xarray:storage_options", None) + if storage_options: + open_kwargs["storage_options"] = storage_options + + ref_media_type = obj[0].media_type + zarr_store_list = [] + for i in tqdm(obj): + # Check the type of the assets -- for homogenity ( all are tar balls ) + if i.media_type != ref_media_type: + print(f"Encountered {i.to_dict()} which differs with {ref_media_type}!") + return xarray.Dataset(data_vars=None, coords=None, attrs=None) # Empty Dataset + + if ref_media_type == "application/x-tar": + print(f"Extracting tar file:{i.href}") + new_href=_extract_tar_file(i) + zarr_store_list.append(new_href) + default_kwargs = {**default_kwargs, "engine": "zarr"} + # Pass the new_href and the kwargs to xarray + return xarray.open_mfdataset(zarr_store_list, **{**default_kwargs, **open_kwargs, **kwargs}) - ds = xarray.open_dataset(obj.href, **{**default_kwargs, **open_kwargs, **kwargs}) - return ds From ca5e89b7ffe52be288c7d410aa79eae73bb0d70e Mon Sep 17 00:00:00 2001 From: k204247 Date: Thu, 16 Oct 2025 16:53:31 +0200 Subject: [PATCH 2/3] merging from public main branch --- .../data-cube-kerchunk-item-collection.json | 16021 ++++++++++++++++ tests/data/virtual-icechunk-collection.json | 401 + tests/utils.py | 41 + uv.lock | 2357 +++ xpystac/_icechunk.py | 112 + xpystac/_xstac_kerchunk.py | 28 + xpystac/core.py | 189 +- 7 files changed, 19055 insertions(+), 94 deletions(-) create mode 100644 tests/data/data-cube-kerchunk-item-collection.json create mode 100644 tests/data/virtual-icechunk-collection.json create mode 100644 tests/utils.py create mode 100644 uv.lock create mode 100644 xpystac/_icechunk.py create mode 100644 xpystac/_xstac_kerchunk.py diff --git a/tests/data/data-cube-kerchunk-item-collection.json b/tests/data/data-cube-kerchunk-item-collection.json new file mode 100644 index 0000000..0ff2811 --- /dev/null +++ b/tests/data/data-cube-kerchunk-item-collection.json @@ -0,0 +1,16021 @@ +{ + "type": "FeatureCollection", + "features": [ + { + "type": "Feature", + "stac_version": "1.0.0", + "id": "20230920-short_range-conus-channel_rt-0-1", + "properties": { + "nwm:model_configuration": "short_range", + "nwm:model_domain": "conus", + "nwm:file_output_type": "channel_rt", + "nwm:forecast_hour": 1, + "cube:dimensions": { + "time": { + "extent": [ + "2023-09-20T01:00:00Z", + "2023-09-20T01:00:00Z" + ], + "description": "valid output time", + "type": "temporal", + "kerchunk:zarray": { + "chunks": [ + 1024 + ], + "compressor": { + "id": "zlib", + "level": 2 + }, + "dtype": " tuple[bool, pytest.MarkDecorator]: + try: + mod = importlib.import_module(modname) + has = True + if minversion is not None: + v = getattr(mod, "__version__", "999") + if Version(v) < Version(minversion): + raise ImportError("Minimum version not satisfied") + except ImportError: + has = False + + reason = f"requires {modname}" + if minversion is not None: + reason += f">={minversion}" + func = pytest.mark.skipif(not has, reason=reason) + return has, func + + +has_planetary_computer, requires_planetary_computer = _importorskip( + "planetary_computer" +) + + +has_icechunk, requires_icechunk = _importorskip("icechunk") + + +# copied from https://github.com/stac-utils/pystac-client/blob/v0.6.0/tests/helpers.py#L7-L11 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b/xpystac/_icechunk.py @@ -0,0 +1,112 @@ +import warnings + +import icechunk +import pystac +import xarray as xr + +warnings.filterwarnings( + "ignore", + message="Numcodecs codecs are not in the Zarr version 3 specification*", + category=UserWarning, +) + + +def construct_virtual_containers_config( + collection: pystac.Collection, asset: pystac.Asset +): + # --- Configure icechunk storage for data store + data_buckets = asset.extra_fields["vrt:hrefs"] + + if len(data_buckets) != 1: + raise ValueError("Only supports one vrt:href per asset") + + data_asset = collection.assets[data_buckets[0]["key"]] + data_href = data_asset.href + + data_storage_refs = data_asset.extra_fields["storage:refs"] + if len(data_storage_refs) != 1: + raise ValueError("Only supports one storage:ref per data asset") + + data_storage_scheme = collection.extra_fields["storage:schemes"].get( + data_storage_refs[0] + ) + if not data_storage_scheme["type"] == "aws-s3": + raise ValueError("Only S3 buckets are currently supported") + + data_region = data_storage_scheme["region"] + data_anonymous = data_storage_scheme.get("anonymous", False) + + config = icechunk.RepositoryConfig.default() + config.set_virtual_chunk_container( + icechunk.VirtualChunkContainer(data_href, icechunk.s3_store(region=data_region)) + ) + if data_anonymous: + credentials = icechunk.s3_anonymous_credentials() + else: + credentials = icechunk.s3_from_env_credentials() + + virtual_credentials = icechunk.containers_credentials({data_href: credentials}) + return config, virtual_credentials + + +def read_icechunk(asset: pystac.Asset) -> xr.Dataset: + """Read a icechunk asset + + The asset's parent must contain: + * "storage:schemes" where at least one key matches "storage:ref" in the asset + + For virtual assets the parent must contain: + * another asset that matches the key in the primary asset's ["vrt:hrefs"] list + """ + # --- Get storage schemes off the parent + collection = asset.owner + storage_schemes = collection.extra_fields["storage:schemes"] + + # --- Create icechunk storage from asset fields + storage_refs = asset.extra_fields["storage:refs"] + if len(storage_refs) != 1: + raise ValueError("Only supports one storage:ref per asset") + + storage_scheme = storage_schemes.get(storage_refs[0]) + if not storage_scheme["type"] == "aws-s3": + raise ValueError("Only S3 buckets are currently supported") + + bucket = storage_scheme["bucket"] + region = storage_scheme["region"] + anonymous = storage_scheme.get("anonymous", False) + prefix = asset.href.split(f"{bucket}/")[1] + + storage = icechunk.s3_storage( + bucket=bucket, + prefix=prefix, + region=region, + anonymous=anonymous, + from_env=not anonymous, + ) + + if "virtual" in asset.roles: + config, virtual_credentials = construct_virtual_containers_config( + collection, asset + ) + repo_kwargs = dict( + config=config, authorize_virtual_chunk_access=virtual_credentials + ) + else: + repo_kwargs = dict(config=icechunk.RepositoryConfig.default()) + + repo = icechunk.Repository.open(storage=storage, **repo_kwargs) + + # --- Open icechunk session at a particular branch/tag/snapshot + if version := asset.extra_fields.get("version"): + if version in repo.list_branches(): + session_kwargs = {"branch": version} + elif version in repo.list_tags(): + session_kwargs = {"tag": version} + else: + session_kwargs = {"snapshot_id": version} + else: + session_kwargs = {"branch": "main"} + + session = repo.readonly_session(**session_kwargs) + + return xr.open_zarr(session.store, zarr_format=3, consolidated=False) diff --git a/xpystac/_xstac_kerchunk.py b/xpystac/_xstac_kerchunk.py new file mode 100644 index 0000000..bad1116 --- /dev/null +++ b/xpystac/_xstac_kerchunk.py @@ -0,0 +1,28 @@ +import json +from typing import Any, Dict + +import pystac + + +def _stac_to_kerchunk(item: pystac.Item, kerchunk_version: int = 1) -> Dict[str, Any]: + """ + Copied from xstac to support python < 3.10 + ref: https://github.com/stac-utils/xstac/blob/1.2.0/xstac/_kerchunk.py + + Derive Kerchunk indices from a STAC item. + """ + refs = {} + refs[".zgroup"] = json.dumps(item.properties["kerchunk:zgroup"]) + refs[".zattrs"] = json.dumps(item.properties["kerchunk:zattrs"]) + + for attr in ["cube:dimensions", "cube:variables"]: + cd = item.properties[attr] + for k in cd: + refs[f"{k}/.zarray"] = json.dumps(cd[k]["kerchunk:zarray"]) + # TODO: derive from datacube stuff, ARRAY_DIMENSIONS + refs[f"{k}/.zattrs"] = json.dumps(cd[k]["kerchunk:zattrs"]) + for i in cd[k]["kerchunk:value"]: + refs[f"{k}/{i}"] = cd[k]["kerchunk:value"][i] + + d = {"version": kerchunk_version, "refs": refs} + return d diff --git a/xpystac/core.py b/xpystac/core.py index 3128917..8a76ec6 100644 --- a/xpystac/core.py +++ b/xpystac/core.py @@ -1,18 +1,21 @@ import functools -from typing import List, Literal, Mapping, Union +from collections.abc import Callable import pystac import xarray import os from tqdm import tqdm -from xpystac.utils import _import_optional_dependency, _is_item_search +from xpystac._xstac_kerchunk import _stac_to_kerchunk +from xpystac.utils import _import_optional_dependency @functools.singledispatch def to_xarray( obj, - stacking_library: Union[Literal["odc.stac", "stackstac"], None] = None, + *, + patch_url: None | Callable[[str], str] = None, + allow_kerchunk: bool = True, **kwargs, ) -> xarray.Dataset: """Given a PySTAC object return an xarray dataset. @@ -24,65 +27,57 @@ def to_xarray( dataset. If the asset points to a COG, read that. * Item: stacks all the assets into a dataset with 1 more dimension than any given asset. - * ItemCollection (output of pystac_client.search): stacks all the - assets in all the items into a dataset with 2 more dimensions than - any given asset. Parameters ---------- obj : PySTAC object (Item, ItemCollection, Asset) The object from which to read data. - stacking_library : "odc.stac", "stackstac", optional - When stacking multiple items, this argument determines which library - to use. Defaults to ``odc.stac`` if available and otherwise ``stackstac``. + patch_url : Callable, optional + Function that takes a string or pystac object and returns an altered + version. Normally used to sign urls before trying to read data from + them. For instance when working with Planetary Computer this argument + should be set to ``pc.sign``. + allow_kerchunk : bool, (True by default) + Control whether this reader tries to interpret kerchunk attributes + if provided (either in the data-cube extension or as a regular asset + with ``references`` or ``index`` as the role). """ - if _is_item_search(obj): - item_collection = obj.item_collection() - return to_xarray(item_collection, stacking_library=stacking_library, **kwargs) raise TypeError @to_xarray.register(pystac.Item) -@to_xarray.register(pystac.ItemCollection) def _( - obj: Union[pystac.Item, pystac.ItemCollection], - drop_variables: Union[str, List[str], None] = None, - stacking_library: Union[Literal["odc.stac", "stackstac"], None] = None, + obj: pystac.Item, + drop_variables: str | list[str] | None = None, + patch_url: None | Callable[[str], str] = None, + allow_kerchunk: bool = True, **kwargs, ) -> xarray.Dataset: if drop_variables is not None: raise KeyError("``drop_variables`` not implemented for pystac items") - if stacking_library is None: - try: - _import_optional_dependency("odc.stac") - stacking_library = "odc.stac" - except ImportError: - _import_optional_dependency("stackstac") - stacking_library = "stackstac" - elif stacking_library not in ["odc.stac", "stackstac"]: - raise ValueError(f"{stacking_library=} is not a valid option") - - if stacking_library == "odc.stac": - odc_stac = _import_optional_dependency("odc.stac") - if isinstance(obj, pystac.Item): - items = [obj] - else: - items = [i for i in obj] - return odc_stac.load(items, **{"chunks": {"x": 1024, "y": 1024}, **kwargs}) - elif stacking_library == "stackstac": - stackstac = _import_optional_dependency("stackstac") - da = stackstac.stack(obj, **kwargs) - bands = {} - for band in da.band.values: - b = da.sel(band=band) - scalar_coords = {k: v.item() for k, v in b.coords.items() if v.shape == ()} - b = b.assign_attrs( - **{k: v for k, v in scalar_coords.items() if v is not None} - ) - b = b.drop_vars(scalar_coords) - bands[band] = b - return xarray.Dataset(bands, attrs=da.attrs) + if allow_kerchunk: + first_obj = obj if isinstance(obj, pystac.Item) else next(i for i in obj) + is_kerchunked = any("kerchunk:" in k for k in first_obj.properties.keys()) + if is_kerchunked: + kerchunk_combine = _import_optional_dependency("kerchunk.combine") + fsspec = _import_optional_dependency("fsspec") + + if isinstance(obj, (list, pystac.ItemCollection)): + refs = kerchunk_combine.MultiZarrToZarr( + [_stac_to_kerchunk(item) for item in obj], + concat_dims=kwargs.get("concat_dims", "time"), + ).translate() + else: + refs = _stac_to_kerchunk(obj) + + mapper = fsspec.filesystem("reference", fo=refs).get_mapper() + default_kwargs = { + "engine": "zarr", + "consolidated": False, + } + + return xarray.open_dataset(mapper, **{**default_kwargs, **kwargs}) def _extract_tar_file(obj): @@ -92,7 +87,6 @@ def _extract_tar_file(obj): pathlib=_import_optional_dependency("pathlib") # Extract the archive:href from obj->href ( *.tar ) to a temp dir and pass # this temp dir as the obj.href to xarray - #print(f"Encountered tar file:{obj.href}") tmppath=os.getenv("STAC_TMP_DIR") with tempfile.TemporaryDirectory(dir=tmppath,delete=False) as tmpdirname: print(f"tar arch ext file:{obj.extra_fields}") @@ -103,29 +97,26 @@ def _extract_tar_file(obj): if myvar.endswith(('.zarr','.zarr/')): #case -1 : tar of zarr .. Complete zarr store new_href = os.path.join(tmpdirname,obj.extra_fields["archive:href"]) - # myvarFiles = [ tarinfo for tarinfo in mytar.getmembers() if tarinfo.name.startswith(myvar) ] - #myvarFiles = [ tarinfo for tarinfo in mytar.getmembers() if tarinfo.name.startswith(myvar)] else: #case -2 : tar of var or #case -3 : tar of chunk .. Incomplete zarr store myvarFiles.extend( [ tarinfo for tarinfo in mytar.getmembers() if tarinfo.name.endswith('.zmetadata') ] ) myvarFiles.extend( [ tarinfo for tarinfo in mytar.getmembers() if tarinfo.name.endswith('.zgroup') ] ) zarr_path = obj.extra_fields["archive:href"].split('.zarr')[0] + '.zarr' new_href = os.path.join(tmpdirname,zarr_path) - #print(myvarFiles) # TODO: Add a progress bar to help the user mytar.extractall(tmpdirname,myvarFiles) - #print("Extraction Done!!!") - #print(f"tar file new:{new_href}") return new_href @to_xarray.register def _( - obj: Union[ pystac.Asset,list], - stacking_library: Union[Literal["odc.stac", "stackstac"], None] = None, + obj: pystac.Asset, + patch_url: None | Callable[[str], str] = None, + allow_kerchunk: bool = True, **kwargs, ) -> xarray.Dataset: + open_kwargs = obj.extra_fields.get("xarray:open_kwargs", {}) # MKM 18 Oct 2024 #TODO : Check if the obj is list instance or pystac.Asset instance and @@ -140,54 +131,64 @@ def _( # Check the type of the 'obj' if isinstance(obj, pystac.Asset): print("Asset as input!",flush=True) - open_kwargs = obj.extra_fields.get("xarray:open_kwargs", {}) + #open_kwargs = obj.extra_fields.get("xarray:open_kwargs", {}) storage_options = obj.extra_fields.get("xarray:storage_options", None) if storage_options: open_kwargs["storage_options"] = storage_options - if obj.media_type == pystac.MediaType.JSON and {"index", "references"}.intersection( - set(obj.roles) if obj.roles else set() - ): - requests = _import_optional_dependency("requests") - fsspec = _import_optional_dependency("fsspec") - r = requests.get(obj.href) - r.raise_for_status() - try: - import planetary_computer # type: ignore + if ( + allow_kerchunk + and obj.media_type == pystac.MediaType.JSON + and {"index", "references"}.intersection(set(obj.roles) if obj.roles else set()) + ): + requests = _import_optional_dependency("requests") + r = requests.get(obj.href) + r.raise_for_status() + + refs = r.json() + if patch_url is not None: + refs = patch_url(refs) + + default_kwargs = { + "engine": "kerchunk", + } + return xarray.open_dataset(refs, **{**default_kwargs, **open_kwargs, **kwargs}) + - refs = planetary_computer.sign(r.json()) - except ImportError: - refs = r.json() + if obj.media_type == pystac.MediaType.COG: + _import_optional_dependency("rioxarray") + default_kwargs = {**default_kwargs, "engine": "rasterio"} + elif obj.media_type in ["application/vnd+zarr", "application/vnd.zarr"]: + _import_optional_dependency("zarr") + zarr_kwargs = {} + if "zarr:consolidated" in obj.extra_fields: + zarr_kwargs["consolidated"] = obj.extra_fields["zarr:consolidated"] + if "zarr:zarr_format" in obj.extra_fields: + zarr_kwargs["zarr_format"] = obj.extra_fields["zarr:zarr_format"] + default_kwargs = {**zarr_kwargs, "engine": "zarr"} + elif obj.media_type == "application/vnd.zarr+icechunk": + from xpystac._icechunk import read_icechunk + + return read_icechunk(obj) - mapper = fsspec.get_mapper("reference://", fo=refs) - default_kwargs = { - **default_kwargs, - "engine": "zarr", - "consolidated": False, - } - return xarray.open_dataset( - mapper, **{**default_kwargs, **open_kwargs, **kwargs} - ) + # MKM added for handling the 'archive' extension, as of now only plain '*.tar' + # not zipped tarfiles. + elif obj.media_type == "application/x-tar": + new_href=_extract_tar_file(obj) + print("Extraction Done!!!") + print(f"Extracted tar file:{new_href}") + # Check the archive:type and set the appropriate engine (as of now 'tar' of 'zarr', + # hence 'zarr' engine) to the xarray + default_kwargs = {**default_kwargs, "engine": "zarr"} + # Pass the new_href and the kwargs to xarray + return xarray.open_dataset(new_href, **{**default_kwargs, **open_kwargs, **kwargs}) - if obj.media_type == pystac.MediaType.COG: - _import_optional_dependency("rioxarray") - default_kwargs = {**default_kwargs, "engine": "rasterio"} - elif obj.media_type == "application/vnd+zarr": - _import_optional_dependency("zarr") - default_kwargs = {**default_kwargs, "engine": "zarr"} - # MKM added for handling the 'archive' extension, as of now only plain '*.tar' - # not zipped tarfiles. - elif obj.media_type == "application/x-tar": - new_href=_extract_tar_file(obj) - print("Extraction Done!!!") - print(f"Extracted tar file:{new_href}") - # Check the archive:type and set the appropriate engine (as of now 'tar' of 'zarr', - # hence 'zarr' engine) to the xarray - default_kwargs = {**default_kwargs, "engine": "zarr"} - # Pass the new_href and the kwargs to xarray - return xarray.open_dataset(new_href, **{**default_kwargs, **open_kwargs, **kwargs}) - ds = xarray.open_dataset(obj.href, **{**default_kwargs, **open_kwargs, **kwargs}) + href = obj.href + if patch_url is not None: + href = patch_url(href) + + ds = xarray.open_dataset(href, **{**default_kwargs, **open_kwargs, **kwargs}) return ds elif isinstance(obj, list): From 462fac6d2f701f53a81a2badb41994c9f36042fb Mon Sep 17 00:00:00 2001 From: k204247 Date: Thu, 16 Oct 2025 16:58:07 +0200 Subject: [PATCH 3/3] code cleanup --- xpystac/core.py | 102 ++++++++++++++++++++++++------------------------ 1 file changed, 51 insertions(+), 51 deletions(-) diff --git a/xpystac/core.py b/xpystac/core.py index 8a76ec6..4b08778 100644 --- a/xpystac/core.py +++ b/xpystac/core.py @@ -137,59 +137,59 @@ def _( if storage_options: open_kwargs["storage_options"] = storage_options - if ( - allow_kerchunk - and obj.media_type == pystac.MediaType.JSON - and {"index", "references"}.intersection(set(obj.roles) if obj.roles else set()) - ): - requests = _import_optional_dependency("requests") - r = requests.get(obj.href) - r.raise_for_status() - - refs = r.json() - if patch_url is not None: - refs = patch_url(refs) - - default_kwargs = { - "engine": "kerchunk", - } - return xarray.open_dataset(refs, **{**default_kwargs, **open_kwargs, **kwargs}) + if ( + allow_kerchunk + and obj.media_type == pystac.MediaType.JSON + and {"index", "references"}.intersection(set(obj.roles) if obj.roles else set()) + ): + requests = _import_optional_dependency("requests") + r = requests.get(obj.href) + r.raise_for_status() + + refs = r.json() + if patch_url is not None: + refs = patch_url(refs) - - if obj.media_type == pystac.MediaType.COG: - _import_optional_dependency("rioxarray") - default_kwargs = {**default_kwargs, "engine": "rasterio"} - elif obj.media_type in ["application/vnd+zarr", "application/vnd.zarr"]: - _import_optional_dependency("zarr") - zarr_kwargs = {} - if "zarr:consolidated" in obj.extra_fields: - zarr_kwargs["consolidated"] = obj.extra_fields["zarr:consolidated"] - if "zarr:zarr_format" in obj.extra_fields: - zarr_kwargs["zarr_format"] = obj.extra_fields["zarr:zarr_format"] - default_kwargs = {**zarr_kwargs, "engine": "zarr"} - elif obj.media_type == "application/vnd.zarr+icechunk": - from xpystac._icechunk import read_icechunk - - return read_icechunk(obj) - - # MKM added for handling the 'archive' extension, as of now only plain '*.tar' - # not zipped tarfiles. - elif obj.media_type == "application/x-tar": - new_href=_extract_tar_file(obj) - print("Extraction Done!!!") - print(f"Extracted tar file:{new_href}") - # Check the archive:type and set the appropriate engine (as of now 'tar' of 'zarr', - # hence 'zarr' engine) to the xarray - default_kwargs = {**default_kwargs, "engine": "zarr"} - # Pass the new_href and the kwargs to xarray - return xarray.open_dataset(new_href, **{**default_kwargs, **open_kwargs, **kwargs}) - - href = obj.href - if patch_url is not None: - href = patch_url(href) + default_kwargs = { + "engine": "kerchunk", + } + return xarray.open_dataset(refs, **{**default_kwargs, **open_kwargs, **kwargs}) + + + if obj.media_type == pystac.MediaType.COG: + _import_optional_dependency("rioxarray") + default_kwargs = {**default_kwargs, "engine": "rasterio"} + elif obj.media_type in ["application/vnd+zarr", "application/vnd.zarr"]: + _import_optional_dependency("zarr") + zarr_kwargs = {} + if "zarr:consolidated" in obj.extra_fields: + zarr_kwargs["consolidated"] = obj.extra_fields["zarr:consolidated"] + if "zarr:zarr_format" in obj.extra_fields: + zarr_kwargs["zarr_format"] = obj.extra_fields["zarr:zarr_format"] + default_kwargs = {**zarr_kwargs, "engine": "zarr"} + elif obj.media_type == "application/vnd.zarr+icechunk": + from xpystac._icechunk import read_icechunk + + return read_icechunk(obj) + + # MKM added for handling the 'archive' extension, as of now only plain '*.tar' + # not zipped tarfiles. + elif obj.media_type == "application/x-tar": + new_href=_extract_tar_file(obj) + print("Extraction Done!!!") + print(f"Extracted tar file:{new_href}") + # Check the archive:type and set the appropriate engine (as of now 'tar' of 'zarr', + # hence 'zarr' engine) to the xarray + default_kwargs = {**default_kwargs, "engine": "zarr"} + # Pass the new_href and the kwargs to xarray + return xarray.open_dataset(new_href, **{**default_kwargs, **open_kwargs, **kwargs}) + + href = obj.href + if patch_url is not None: + href = patch_url(href) - ds = xarray.open_dataset(href, **{**default_kwargs, **open_kwargs, **kwargs}) - return ds + ds = xarray.open_dataset(href, **{**default_kwargs, **open_kwargs, **kwargs}) + return ds elif isinstance(obj, list): print("List of Assets as input!",flush=True)