"""NetworkX ``GraphMLDataSet`` loads and saves graphs to a GraphML file using an underlying
filesystem (e.g.: local, S3, GCS). ``NetworkX`` is used to create GraphML data.
"""
from copy import deepcopy
from pathlib import PurePosixPath
from typing import Any, Dict
import fsspec
import networkx
from kedro.io.core import (
AbstractVersionedDataset,
Version,
get_filepath_str,
get_protocol_and_path,
)
# NOTE: kedro.extras.datasets will be removed in Kedro 0.19.0.
# Any contribution to datasets should be made in kedro-datasets
# in kedro-plugins (https://github.com/kedro-org/kedro-plugins)
[docs]class GraphMLDataSet(AbstractVersionedDataset[networkx.Graph, networkx.Graph]):
"""``GraphMLDataSet`` loads and saves graphs to a GraphML file using an
underlying filesystem (e.g.: local, S3, GCS). ``NetworkX`` is used to
create GraphML data.
See https://networkx.org/documentation/stable/tutorial.html for details.
Example:
::
>>> from kedro.extras.datasets.networkx import GraphMLDataSet
>>> import networkx as nx
>>> graph = nx.complete_graph(100)
>>> graph_dataset = GraphMLDataSet(filepath="test.graphml")
>>> graph_dataset.save(graph)
>>> reloaded = graph_dataset.load()
>>> assert nx.is_isomorphic(graph, reloaded)
"""
DEFAULT_LOAD_ARGS = {} # type: Dict[str, Any]
DEFAULT_SAVE_ARGS = {} # type: Dict[str, Any]
[docs] def __init__( # noqa: too-many-arguments
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 ``GraphMLDataSet``.
Args:
filepath: Filepath in POSIX format to the NetworkX GraphML file.
load_args: Arguments passed on to ``networkx.read_graphml``.
See the details in
https://networkx.org/documentation/stable/reference/readwrite/generated/networkx.readwrite.graphml.read_graphml.html
save_args: Arguments passed on to ``networkx.write_graphml``.
See the details in
https://networkx.org/documentation/stable/reference/readwrite/generated/networkx.readwrite.graphml.write_graphml.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 {}
protocol, path = get_protocol_and_path(filepath, version)
if protocol == "file":
_fs_args.setdefault("auto_mkdir", True)
self._protocol = protocol
self._fs = fsspec.filesystem(self._protocol, **_credentials, **_fs_args)
super().__init__(
filepath=PurePosixPath(path),
version=version,
exists_function=self._fs.exists,
glob_function=self._fs.glob,
)
# 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
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:
return networkx.read_graphml(fs_file, **self._load_args)
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_graphml(data, fs_file, **self._save_args)
self._invalidate_cache()
def _exists(self) -> bool:
load_path = get_filepath_str(self._get_load_path(), self._protocol)
return self._fs.exists(load_path)
def _describe(self) -> Dict[str, Any]:
return {
"filepath": self._filepath,
"protocol": self._load_args,
"save_args": self._save_args,
"version": self._version,
}
def _release(self) -> None:
super()._release()
self._invalidate_cache()
def _invalidate_cache(self) -> None:
"""Invalidate underlying filesystem caches."""
filepath = get_filepath_str(self._filepath, self._protocol)
self._fs.invalidate_cache(filepath)