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feat: networkx datasets gml and graphml
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| # Copyright 2021 QuantumBlack Visual Analytics Limited | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, | ||
| # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES | ||
| # OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND | ||
| # NONINFRINGEMENT. IN NO EVENT WILL THE LICENSOR OR OTHER CONTRIBUTORS | ||
| # BE LIABLE FOR ANY CLAIM, DAMAGES, OR OTHER LIABILITY, WHETHER IN AN | ||
| # ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF, OR IN | ||
| # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. | ||
| # | ||
| # The QuantumBlack Visual Analytics Limited ("QuantumBlack") name and logo | ||
| # (either separately or in combination, "QuantumBlack Trademarks") are | ||
| # trademarks of QuantumBlack. The License does not grant you any right or | ||
| # license to the QuantumBlack Trademarks. You may not use the QuantumBlack | ||
| # Trademarks or any confusingly similar mark as a trademark for your product, | ||
| # or use the QuantumBlack Trademarks in any other manner that might cause | ||
| # confusion in the marketplace, including but not limited to in advertising, | ||
| # on websites, or on software. | ||
| # | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
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| """NetworkX ``GMLDataSet`` loads and saves graphs to a graph modelling language (GML) | ||
| file using an underlying filesystem (e.g.: local, S3, GCS). ``NetworkX`` is used to | ||
| create GML data. | ||
| """ | ||
|
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| from copy import deepcopy | ||
| from pathlib import PurePosixPath | ||
| from typing import Any, Dict | ||
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| import fsspec | ||
| import networkx | ||
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| from kedro.io.core import ( | ||
| AbstractVersionedDataSet, | ||
| Version, | ||
| get_filepath_str, | ||
| get_protocol_and_path, | ||
| ) | ||
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| class GMLDataSet(AbstractVersionedDataSet): | ||
| """``GMLDataSet`` loads and saves graphs to a GML file using an | ||
| underlying filesystem (e.g.: local, S3, GCS). ``NetworkX`` is used to | ||
| create GML data. | ||
| See https://networkx.org/documentation/stable/tutorial.html for details. | ||
| Example: | ||
| :: | ||
| >>> from kedro.extras.datasets.networkx import GMLDataSet | ||
| >>> import networkx as nx | ||
| >>> graph = nx.complete_graph(100) | ||
| >>> graph_dataset = GMLDataSet(filepath="test.gml") | ||
| >>> graph_dataset.save(graph) | ||
| >>> reloaded = graph_dataset.load() | ||
| >>> assert nx.is_isomorphic(graph, reloaded) | ||
| """ | ||
|
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| DEFAULT_LOAD_ARGS = {} # type: Dict[str, Any] | ||
| DEFAULT_SAVE_ARGS = {} # type: Dict[str, Any] | ||
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| # pylint: disable=too-many-arguments | ||
| def __init__( | ||
| self, | ||
| filepath: str, | ||
| load_args: Dict[str, Any] = None, | ||
| save_args: Dict[str, Any] = None, | ||
| version: Version = None, | ||
| credentials: Dict[str, Any] = None, | ||
| fs_args: Dict[str, Any] = None, | ||
| ) -> None: | ||
| """Creates a new instance of ``GMLDataSet``. | ||
| Args: | ||
| filepath: Filepath in POSIX format to the NetworkX GML file. | ||
| load_args: Arguments passed on to ``networkx.read_gml``. | ||
| See the details in | ||
| https://networkx.org/documentation/stable/reference/readwrite/generated/networkx.readwrite.gml.read_gml.html | ||
| save_args: Arguments passed on to ``networkx.write_gml``. | ||
| See the details in | ||
| https://networkx.org/documentation/stable/reference/readwrite/generated/networkx.readwrite.gml.write_gml.html | ||
| version: If specified, should be an instance of | ||
| ``kedro.io.core.Version``. If its ``load`` attribute is | ||
| None, the latest version will be loaded. If its ``save`` | ||
| attribute is None, save version will be autogenerated. | ||
| credentials: Credentials required to get access to the underlying filesystem. | ||
| E.g. for ``GCSFileSystem`` it should look like `{"token": None}`. | ||
| fs_args: Extra arguments to pass into underlying filesystem class constructor | ||
| (e.g. `{"project": "my-project"}` for ``GCSFileSystem``), as well as | ||
| to pass to the filesystem's `open` method through nested keys | ||
| `open_args_load` and `open_args_save`. | ||
| Here you can find all available arguments for `open`: | ||
| https://filesystem-spec.readthedocs.io/en/latest/api.html#fsspec.spec.AbstractFileSystem.open | ||
| All defaults are preserved, except `mode`, which is set to `r` when loading | ||
| and to `w` when saving. | ||
| """ | ||
| _fs_args = deepcopy(fs_args) or {} | ||
| _fs_open_args_load = _fs_args.pop("open_args_load", {}) | ||
| _fs_open_args_save = _fs_args.pop("open_args_save", {}) | ||
| _credentials = deepcopy(credentials) or {} | ||
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| protocol, path = get_protocol_and_path(filepath, version) | ||
| if protocol == "file": | ||
| _fs_args.setdefault("auto_mkdir", True) | ||
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| self._protocol = protocol | ||
| self._fs = fsspec.filesystem(self._protocol, **_credentials, **_fs_args) | ||
|
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| super().__init__( | ||
| filepath=PurePosixPath(path), | ||
| version=version, | ||
| exists_function=self._fs.exists, | ||
| glob_function=self._fs.glob, | ||
| ) | ||
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| # Handle default load and save arguments | ||
| self._load_args = deepcopy(self.DEFAULT_LOAD_ARGS) | ||
| if load_args is not None: | ||
| self._load_args.update(load_args) | ||
| self._save_args = deepcopy(self.DEFAULT_SAVE_ARGS) | ||
| if save_args is not None: | ||
| self._save_args.update(save_args) | ||
| _fs_open_args_load.setdefault("mode", "rb") | ||
| _fs_open_args_save.setdefault("mode", "wb") | ||
| self._fs_open_args_load = _fs_open_args_load | ||
| self._fs_open_args_save = _fs_open_args_save | ||
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| def _load(self) -> networkx.Graph: | ||
| load_path = get_filepath_str(self._get_load_path(), self._protocol) | ||
| with self._fs.open(load_path, **self._fs_open_args_load) as fs_file: | ||
| data = networkx.read_gml(fs_file, **self._load_args) | ||
| return data | ||
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| def _save(self, data: networkx.Graph) -> None: | ||
| save_path = get_filepath_str(self._get_save_path(), self._protocol) | ||
| with self._fs.open(save_path, **self._fs_open_args_save) as fs_file: | ||
| networkx.write_gml(data, fs_file, **self._save_args) | ||
| self._invalidate_cache() | ||
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| def _exists(self) -> bool: | ||
| load_path = get_filepath_str(self._get_load_path(), self._protocol) | ||
| return self._fs.exists(load_path) | ||
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| def _describe(self) -> Dict[str, Any]: | ||
| return dict( | ||
| filepath=self._filepath, | ||
| protocol=self._protocol, | ||
| load_args=self._load_args, | ||
| save_args=self._save_args, | ||
| version=self._version, | ||
| ) | ||
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| def _release(self) -> None: | ||
| super()._release() | ||
| self._invalidate_cache() | ||
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| def _invalidate_cache(self) -> None: | ||
| """Invalidate underlying filesystem caches.""" | ||
| filepath = get_filepath_str(self._filepath, self._protocol) | ||
| self._fs.invalidate_cache(filepath) |
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