wehub-resource-sync
215 lines
7.6 KiB
Python
215 lines
7.6 KiB
Python
import os
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import numpy as np
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from .. import backend as F
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from ..base import DGLError
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from .dgl_dataset import DGLDataset
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from .utils import load_graphs, save_graphs, Subset
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class CSVDataset(DGLDataset):
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"""Dataset class that loads and parses graph data from CSV files.
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This class requires the following additional packages:
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- pyyaml >= 5.4.1
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- pandas >= 1.1.5
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- pydantic >= 1.9.0
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The parsed graph and feature data will be cached for faster reloading. If
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the source CSV files are modified, please specify ``force_reload=True``
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to re-parse from them.
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Parameters
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----------
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data_path : str
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Directory which contains 'meta.yaml' and CSV files
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force_reload : bool, optional
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Whether to reload the dataset. Default: False
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verbose: bool, optional
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Whether to print out progress information. Default: True.
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ndata_parser : dict[str, callable] or callable, optional
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Callable object which takes in the ``pandas.DataFrame`` object created from
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CSV file, parses node data and returns a dictionary of parsed data. If given a
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dictionary, the key is node type and the value is a callable object which is
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used to parse data of corresponding node type. If given a single callable
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object, such object is used to parse data of all node type data. Default: None.
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If None, a default data parser is applied which load data directly and tries to
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convert list into array.
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edata_parser : dict[(str, str, str), callable], or callable, optional
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Callable object which takes in the ``pandas.DataFrame`` object created from
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CSV file, parses edge data and returns a dictionary of parsed data. If given a
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dictionary, the key is edge type and the value is a callable object which is
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used to parse data of corresponding edge type. If given a single callable
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object, such object is used to parse data of all edge type data. Default: None.
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If None, a default data parser is applied which load data directly and tries to
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convert list into array.
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gdata_parser : callable, optional
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Callable object which takes in the ``pandas.DataFrame`` object created from
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CSV file, parses graph data and returns a dictionary of parsed data. Default:
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None. If None, a default data parser is applied which load data directly and
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tries to convert list into array.
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transform : callable, optional
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A transform that takes in a :class:`~dgl.DGLGraph` object and returns
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a transformed version. The :class:`~dgl.DGLGraph` object will be
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transformed before every access.
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Attributes
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----------
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graphs : :class:`dgl.DGLGraph`
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Graphs of the dataset
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data : dict
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any available graph-level data such as graph-level feature, labels.
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Examples
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--------
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Please refer to :ref:`guide-data-pipeline-loadcsv`.
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"""
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META_YAML_NAME = "meta.yaml"
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def __init__(
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self,
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data_path,
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force_reload=False,
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verbose=True,
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ndata_parser=None,
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edata_parser=None,
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gdata_parser=None,
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transform=None,
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):
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from .csv_dataset_base import (
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DefaultDataParser,
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load_yaml_with_sanity_check,
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)
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self.graphs = None
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self.data = None
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self.ndata_parser = {} if ndata_parser is None else ndata_parser
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self.edata_parser = {} if edata_parser is None else edata_parser
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self.gdata_parser = gdata_parser
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self.default_data_parser = DefaultDataParser()
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meta_yaml_path = os.path.join(data_path, CSVDataset.META_YAML_NAME)
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if not os.path.exists(meta_yaml_path):
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raise DGLError(
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"'{}' cannot be found under {}.".format(
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CSVDataset.META_YAML_NAME, data_path
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)
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)
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self.meta_yaml = load_yaml_with_sanity_check(meta_yaml_path)
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ds_name = self.meta_yaml.dataset_name
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super().__init__(
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ds_name,
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raw_dir=os.path.dirname(meta_yaml_path),
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force_reload=force_reload,
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verbose=verbose,
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transform=transform,
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)
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def process(self):
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"""Parse node/edge data from CSV files and construct DGL.Graphs"""
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from .csv_dataset_base import (
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DGLGraphConstructor,
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EdgeData,
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GraphData,
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NodeData,
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)
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meta_yaml = self.meta_yaml
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base_dir = self.raw_dir
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node_data = []
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for meta_node in meta_yaml.node_data:
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if meta_node is None:
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continue
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ntype = meta_node.ntype
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data_parser = (
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self.ndata_parser
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if callable(self.ndata_parser)
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else self.ndata_parser.get(ntype, self.default_data_parser)
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)
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ndata = NodeData.load_from_csv(
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meta_node,
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base_dir=base_dir,
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separator=meta_yaml.separator,
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data_parser=data_parser,
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)
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node_data.append(ndata)
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edge_data = []
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for meta_edge in meta_yaml.edge_data:
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if meta_edge is None:
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continue
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etype = tuple(meta_edge.etype)
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data_parser = (
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self.edata_parser
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if callable(self.edata_parser)
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else self.edata_parser.get(etype, self.default_data_parser)
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)
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edata = EdgeData.load_from_csv(
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meta_edge,
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base_dir=base_dir,
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separator=meta_yaml.separator,
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data_parser=data_parser,
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)
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edge_data.append(edata)
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graph_data = None
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if meta_yaml.graph_data is not None:
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meta_graph = meta_yaml.graph_data
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data_parser = (
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self.default_data_parser
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if self.gdata_parser is None
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else self.gdata_parser
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)
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graph_data = GraphData.load_from_csv(
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meta_graph,
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base_dir=base_dir,
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separator=meta_yaml.separator,
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data_parser=data_parser,
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)
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# construct graphs
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self.graphs, self.data = DGLGraphConstructor.construct_graphs(
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node_data, edge_data, graph_data
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)
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if len(self.data) == 1:
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self.labels = list(self.data.values())[0]
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def has_cache(self):
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graph_path = os.path.join(self.save_path, self.name + ".bin")
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if os.path.exists(graph_path):
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return True
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return False
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def save(self):
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if self.graphs is None:
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raise DGLError("No graphs available in dataset")
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graph_path = os.path.join(self.save_path, self.name + ".bin")
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save_graphs(graph_path, self.graphs, labels=self.data)
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def load(self):
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graph_path = os.path.join(self.save_path, self.name + ".bin")
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self.graphs, self.data = load_graphs(graph_path)
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if len(self.data) == 1:
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self.labels = list(self.data.values())[0]
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def __getitem__(self, i):
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if F.is_tensor(i) and F.ndim(i) == 1:
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return Subset(self, F.copy_to(i, F.cpu()))
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if self._transform is None:
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g = self.graphs[i]
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else:
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g = self._transform(self.graphs[i])
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if len(self.data) == 1:
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return g, self.labels[i]
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elif len(self.data) > 0:
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data = {k: v[i] for (k, v) in self.data.items()}
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return g, data
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else:
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return g
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def __len__(self):
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return len(self.graphs)
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