dmlc--dgl
643 行
22 KiB
Python
643 行
22 KiB
Python
"""GraphBolt OnDiskDataset."""
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import os
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from copy import deepcopy
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from typing import Dict, List, Union
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import pandas as pd
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import torch
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import yaml
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import dgl
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from ...base import dgl_warning
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from ...data.utils import download, extract_archive
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from ..base import etype_str_to_tuple
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from ..dataset import Dataset, Task
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from ..internal import copy_or_convert_data, get_attributes, read_data
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from ..itemset import ItemSet, ItemSetDict
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from ..sampling_graph import SamplingGraph
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from .fused_csc_sampling_graph import from_dglgraph, FusedCSCSamplingGraph
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from .ondisk_metadata import (
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OnDiskGraphTopology,
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OnDiskMetaData,
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OnDiskTaskData,
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OnDiskTVTSet,
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)
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from .torch_based_feature_store import TorchBasedFeatureStore
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__all__ = ["OnDiskDataset", "preprocess_ondisk_dataset", "BuiltinDataset"]
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def preprocess_ondisk_dataset(
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dataset_dir: str, include_original_edge_id: bool = False
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) -> str:
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"""Preprocess the on-disk dataset. Parse the input config file,
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load the data, and save the data in the format that GraphBolt supports.
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Parameters
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----------
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dataset_dir : str
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The path to the dataset directory.
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include_original_edge_id : bool, optional
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Whether to include the original edge id in the FusedCSCSamplingGraph.
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Returns
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-------
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output_config_path : str
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The path to the output config file.
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"""
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# Check if the dataset path is valid.
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if not os.path.exists(dataset_dir):
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raise RuntimeError(f"Invalid dataset path: {dataset_dir}")
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# Check if the dataset_dir is a directory.
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if not os.path.isdir(dataset_dir):
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raise RuntimeError(
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f"The dataset must be a directory. But got {dataset_dir}"
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)
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# 0. Check if the dataset is already preprocessed.
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preprocess_metadata_path = os.path.join("preprocessed", "metadata.yaml")
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if os.path.exists(os.path.join(dataset_dir, preprocess_metadata_path)):
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print("The dataset is already preprocessed.")
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return os.path.join(dataset_dir, preprocess_metadata_path)
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print("Start to preprocess the on-disk dataset.")
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processed_dir_prefix = "preprocessed"
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# Check if the metadata.yaml exists.
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metadata_file_path = os.path.join(dataset_dir, "metadata.yaml")
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if not os.path.exists(metadata_file_path):
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raise RuntimeError("metadata.yaml does not exist.")
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# Read the input config.
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with open(metadata_file_path, "r") as f:
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input_config = yaml.safe_load(f)
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# 1. Make `processed_dir_abs` directory if it does not exist.
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os.makedirs(os.path.join(dataset_dir, processed_dir_prefix), exist_ok=True)
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output_config = deepcopy(input_config)
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# 2. Load the edge data and create a DGLGraph.
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if "graph" not in input_config:
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raise RuntimeError("Invalid config: does not contain graph field.")
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is_homogeneous = "type" not in input_config["graph"]["nodes"][0]
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if is_homogeneous:
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# Homogeneous graph.
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num_nodes = input_config["graph"]["nodes"][0]["num"]
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edge_data = pd.read_csv(
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os.path.join(
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dataset_dir, input_config["graph"]["edges"][0]["path"]
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),
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names=["src", "dst"],
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)
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src, dst = edge_data["src"].to_numpy(), edge_data["dst"].to_numpy()
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g = dgl.graph((src, dst), num_nodes=num_nodes)
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else:
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# Heterogeneous graph.
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# Construct the num nodes dict.
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num_nodes_dict = {}
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for node_info in input_config["graph"]["nodes"]:
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num_nodes_dict[node_info["type"]] = node_info["num"]
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# Construct the data dict.
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data_dict = {}
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for edge_info in input_config["graph"]["edges"]:
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edge_data = pd.read_csv(
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os.path.join(dataset_dir, edge_info["path"]),
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names=["src", "dst"],
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)
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src = torch.tensor(edge_data["src"])
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dst = torch.tensor(edge_data["dst"])
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data_dict[etype_str_to_tuple(edge_info["type"])] = (src, dst)
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# Construct the heterograph.
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g = dgl.heterograph(data_dict, num_nodes_dict)
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# 3. Load the sampling related node/edge features and add them to
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# the sampling-graph.
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if input_config["graph"].get("feature_data", None):
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for graph_feature in input_config["graph"]["feature_data"]:
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in_memory = (
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True
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if "in_memory" not in graph_feature
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else graph_feature["in_memory"]
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)
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if graph_feature["domain"] == "node":
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node_data = read_data(
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os.path.join(dataset_dir, graph_feature["path"]),
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graph_feature["format"],
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in_memory=in_memory,
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)
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g.ndata[graph_feature["name"]] = node_data
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if graph_feature["domain"] == "edge":
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edge_data = read_data(
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os.path.join(dataset_dir, graph_feature["path"]),
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graph_feature["format"],
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in_memory=in_memory,
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)
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g.edata[graph_feature["name"]] = edge_data
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# 4. Convert the DGLGraph to a FusedCSCSamplingGraph.
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fused_csc_sampling_graph = from_dglgraph(
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g, is_homogeneous, include_original_edge_id
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)
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# 5. Save the FusedCSCSamplingGraph and modify the output_config.
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output_config["graph_topology"] = {}
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output_config["graph_topology"]["type"] = "FusedCSCSamplingGraph"
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output_config["graph_topology"]["path"] = os.path.join(
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processed_dir_prefix, "fused_csc_sampling_graph.pt"
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)
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torch.save(
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fused_csc_sampling_graph,
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os.path.join(
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dataset_dir,
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output_config["graph_topology"]["path"],
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),
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)
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del output_config["graph"]
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# 6. Load the node/edge features and do necessary conversion.
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if input_config.get("feature_data", None):
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for feature, out_feature in zip(
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input_config["feature_data"], output_config["feature_data"]
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):
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# Always save the feature in numpy format.
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out_feature["format"] = "numpy"
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out_feature["path"] = os.path.join(
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processed_dir_prefix, feature["path"].replace("pt", "npy")
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)
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in_memory = (
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True if "in_memory" not in feature else feature["in_memory"]
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)
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copy_or_convert_data(
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os.path.join(dataset_dir, feature["path"]),
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os.path.join(dataset_dir, out_feature["path"]),
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feature["format"],
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output_format=out_feature["format"],
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in_memory=in_memory,
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is_feature=True,
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)
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# 7. Save tasks and train/val/test split according to the output_config.
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if input_config.get("tasks", None):
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for input_task, output_task in zip(
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input_config["tasks"], output_config["tasks"]
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):
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for set_name in ["train_set", "validation_set", "test_set"]:
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if set_name not in input_task:
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continue
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for input_set_per_type, output_set_per_type in zip(
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input_task[set_name], output_task[set_name]
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):
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for input_data, output_data in zip(
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input_set_per_type["data"], output_set_per_type["data"]
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):
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# Always save the feature in numpy format.
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output_data["format"] = "numpy"
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output_data["path"] = os.path.join(
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processed_dir_prefix,
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input_data["path"].replace("pt", "npy"),
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)
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copy_or_convert_data(
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os.path.join(dataset_dir, input_data["path"]),
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os.path.join(dataset_dir, output_data["path"]),
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input_data["format"],
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output_data["format"],
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)
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# 8. Save the output_config.
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output_config_path = os.path.join(dataset_dir, preprocess_metadata_path)
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with open(output_config_path, "w") as f:
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yaml.dump(output_config, f)
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print("Finish preprocessing the on-disk dataset.")
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# 9. Return the absolute path of the preprocessing yaml file.
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return output_config_path
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class OnDiskTask:
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"""An on-disk task.
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An on-disk task is for ``OnDiskDataset``. It contains the metadata and the
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train/val/test sets.
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"""
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def __init__(
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self,
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metadata: Dict,
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train_set: Union[ItemSet, ItemSetDict],
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validation_set: Union[ItemSet, ItemSetDict],
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test_set: Union[ItemSet, ItemSetDict],
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):
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"""Initialize a task.
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Parameters
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----------
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metadata : Dict
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Metadata.
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train_set : Union[ItemSet, ItemSetDict]
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Training set.
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validation_set : Union[ItemSet, ItemSetDict]
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Validation set.
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test_set : Union[ItemSet, ItemSetDict]
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Test set.
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"""
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self._metadata = metadata
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self._train_set = train_set
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self._validation_set = validation_set
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self._test_set = test_set
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@property
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def metadata(self) -> Dict:
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"""Return the task metadata."""
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return self._metadata
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@property
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def train_set(self) -> Union[ItemSet, ItemSetDict]:
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"""Return the training set."""
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return self._train_set
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@property
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def validation_set(self) -> Union[ItemSet, ItemSetDict]:
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"""Return the validation set."""
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return self._validation_set
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@property
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def test_set(self) -> Union[ItemSet, ItemSetDict]:
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"""Return the test set."""
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return self._test_set
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def __repr__(self) -> str:
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return _ondisk_task_str(self)
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class OnDiskDataset(Dataset):
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"""An on-disk dataset which reads graph topology, feature data and
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Train/Validation/Test set from disk.
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Due to limited resources, the data which are too large to fit into RAM will
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remain on disk while others reside in RAM once ``OnDiskDataset`` is
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initialized. This behavior could be controled by user via ``in_memory``
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field in YAML file. All paths in YAML file are relative paths to the
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dataset directory.
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A full example of YAML file is as follows:
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.. code-block:: yaml
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dataset_name: graphbolt_test
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graph:
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nodes:
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- type: paper # could be omitted for homogeneous graph.
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num: 1000
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- type: author
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num: 1000
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edges:
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- type: author:writes:paper # could be omitted for homogeneous graph.
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format: csv # Can be csv only.
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path: edge_data/author-writes-paper.csv
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- type: paper:cites:paper
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format: csv
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path: edge_data/paper-cites-paper.csv
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feature_data:
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- domain: node
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type: paper # could be omitted for homogeneous graph.
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name: feat
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format: numpy
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in_memory: false # If not specified, default to true.
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path: node_data/paper-feat.npy
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- domain: edge
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type: "author:writes:paper"
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name: feat
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format: numpy
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in_memory: false
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path: edge_data/author-writes-paper-feat.npy
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tasks:
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- name: "edge_classification"
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num_classes: 10
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train_set:
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- type: paper # could be omitted for homogeneous graph.
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data: # multiple data sources could be specified.
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- name: node_pairs
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format: numpy # Can be numpy or torch.
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in_memory: true # If not specified, default to true.
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path: set/paper-train-node_pairs.npy
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- name: labels
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format: numpy
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path: set/paper-train-labels.npy
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validation_set:
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- type: paper
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data:
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- name: node_pairs
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format: numpy
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path: set/paper-validation-node_pairs.npy
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- name: labels
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format: numpy
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path: set/paper-validation-labels.npy
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test_set:
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- type: paper
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data:
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- name: node_pairs
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format: numpy
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path: set/paper-test-node_pairs.npy
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- name: labels
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format: numpy
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path: set/paper-test-labels.npy
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Parameters
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----------
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path: str
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The YAML file path.
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include_original_edge_id: bool, optional
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Whether to include the original edge id in the FusedCSCSamplingGraph.
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"""
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def __init__(
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self, path: str, include_original_edge_id: bool = False
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) -> None:
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# Always call the preprocess function first. If already preprocessed,
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# the function will return the original path directly.
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self._dataset_dir = path
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yaml_path = preprocess_ondisk_dataset(path, include_original_edge_id)
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with open(yaml_path) as f:
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self._yaml_data = yaml.load(f, Loader=yaml.loader.SafeLoader)
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self._loaded = False
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def _convert_yaml_path_to_absolute_path(self):
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"""Convert the path in YAML file to absolute path."""
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if "graph_topology" in self._yaml_data:
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self._yaml_data["graph_topology"]["path"] = os.path.join(
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self._dataset_dir, self._yaml_data["graph_topology"]["path"]
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)
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if "feature_data" in self._yaml_data:
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for feature in self._yaml_data["feature_data"]:
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feature["path"] = os.path.join(
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self._dataset_dir, feature["path"]
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)
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if "tasks" in self._yaml_data:
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for task in self._yaml_data["tasks"]:
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for set_name in ["train_set", "validation_set", "test_set"]:
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if set_name not in task:
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continue
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for set_per_type in task[set_name]:
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for data in set_per_type["data"]:
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data["path"] = os.path.join(
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self._dataset_dir, data["path"]
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)
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def load(self):
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"""Load the dataset."""
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self._convert_yaml_path_to_absolute_path()
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self._meta = OnDiskMetaData(**self._yaml_data)
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self._dataset_name = self._meta.dataset_name
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self._graph = self._load_graph(self._meta.graph_topology)
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self._feature = TorchBasedFeatureStore(self._meta.feature_data)
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self._tasks = self._init_tasks(self._meta.tasks)
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self._all_nodes_set = self._init_all_nodes_set(self._graph)
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self._loaded = True
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return self
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@property
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def yaml_data(self) -> Dict:
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"""Return the YAML data."""
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return self._yaml_data
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@property
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def tasks(self) -> List[Task]:
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"""Return the tasks."""
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self._check_loaded()
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return self._tasks
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@property
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def graph(self) -> SamplingGraph:
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"""Return the graph."""
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self._check_loaded()
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return self._graph
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@property
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def feature(self) -> TorchBasedFeatureStore:
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"""Return the feature."""
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self._check_loaded()
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return self._feature
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@property
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def dataset_name(self) -> str:
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"""Return the dataset name."""
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self._check_loaded()
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return self._dataset_name
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@property
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def all_nodes_set(self) -> Union[ItemSet, ItemSetDict]:
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"""Return the itemset containing all nodes."""
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self._check_loaded()
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return self._all_nodes_set
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def _init_tasks(self, tasks: List[OnDiskTaskData]) -> List[OnDiskTask]:
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"""Initialize the tasks."""
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ret = []
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if tasks is None:
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return ret
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for task in tasks:
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ret.append(
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OnDiskTask(
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task.extra_fields,
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self._init_tvt_set(task.train_set),
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self._init_tvt_set(task.validation_set),
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self._init_tvt_set(task.test_set),
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)
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)
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return ret
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def _check_loaded(self):
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assert self._loaded, (
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"Please ensure that you have called the OnDiskDataset.load() method"
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+ " to properly load the data."
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)
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def _load_graph(
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self, graph_topology: OnDiskGraphTopology
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) -> FusedCSCSamplingGraph:
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"""Load the graph topology."""
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if graph_topology is None:
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return None
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if graph_topology.type == "FusedCSCSamplingGraph":
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return torch.load(graph_topology.path)
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raise NotImplementedError(
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f"Graph topology type {graph_topology.type} is not supported."
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)
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def _init_tvt_set(
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self, tvt_set: List[OnDiskTVTSet]
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) -> Union[ItemSet, ItemSetDict]:
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"""Initialize the TVT set."""
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ret = None
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if (tvt_set is None) or (len(tvt_set) == 0):
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return ret
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if tvt_set[0].type is None:
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assert (
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len(tvt_set) == 1
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), "Only one TVT set is allowed if type is not specified."
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ret = ItemSet(
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tuple(
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read_data(data.path, data.format, data.in_memory)
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for data in tvt_set[0].data
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),
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names=tuple(data.name for data in tvt_set[0].data),
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)
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else:
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data = {}
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for tvt in tvt_set:
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data[tvt.type] = ItemSet(
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tuple(
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read_data(data.path, data.format, data.in_memory)
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for data in tvt.data
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),
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names=tuple(data.name for data in tvt.data),
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)
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ret = ItemSetDict(data)
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return ret
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def _init_all_nodes_set(self, graph) -> Union[ItemSet, ItemSetDict]:
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if graph is None:
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dgl_warning(
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"`all_node_set` is returned as None, since graph is None."
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)
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return None
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num_nodes = graph.num_nodes
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if isinstance(num_nodes, int):
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return ItemSet(num_nodes, names="seed_nodes")
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else:
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data = {
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node_type: ItemSet(num_node, names="seed_nodes")
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for node_type, num_node in num_nodes.items()
|
|
}
|
|
return ItemSetDict(data)
|
|
|
|
|
|
class BuiltinDataset(OnDiskDataset):
|
|
"""A utility class to download built-in dataset from AWS S3 and load it as
|
|
:class:`OnDiskDataset`.
|
|
|
|
Available built-in datasets include:
|
|
|
|
**cora**
|
|
The cora dataset is a homogeneous citation network dataset, which is
|
|
designed for the node classification task.
|
|
|
|
**ogbn-mag**
|
|
The ogbn-mag dataset is a heterogeneous network composed of a subset of
|
|
the Microsoft Academic Graph (MAG). See more details in
|
|
`ogbn-mag <https://ogb.stanford.edu/docs/nodeprop/#ogbn-mag>`_.
|
|
|
|
.. note::
|
|
Reverse edges are added to the original graph and duplicated
|
|
edges are removed.
|
|
|
|
**ogbl-citation2**
|
|
The ogbl-citation2 dataset is a directed graph, representing the
|
|
citation network between a subset of papers extracted from MAG. See
|
|
more details in `ogbl-citation2
|
|
<https://ogb.stanford.edu/docs/linkprop/#ogbl-citation2>`_.
|
|
|
|
.. note::
|
|
Reverse edges are added to the original graph and duplicated
|
|
edges are removed.
|
|
|
|
**ogbn-arxiv**
|
|
The ogbn-arxiv dataset is a directed graph, representing the citation
|
|
network between all Computer Science (CS) arXiv papers indexed by MAG.
|
|
See more details in `ogbn-arxiv
|
|
<https://ogb.stanford.edu/docs/nodeprop/#ogbn-arxiv>`_.
|
|
|
|
.. note::
|
|
Reverse edges are added to the original graph and duplicated
|
|
edges are removed.
|
|
|
|
**ogbn-products**
|
|
The ogbn-products dataset is an undirected and unweighted graph,
|
|
representing an Amazon product co-purchasing network. See more details
|
|
in `ogbn-products
|
|
<https://ogb.stanford.edu/docs/nodeprop/#ogbn-products>`_.
|
|
|
|
.. note::
|
|
Reverse edges are added to the original graph.
|
|
Node features are stored as float32.
|
|
|
|
**ogb-lsc-mag240m**
|
|
The ogb-lsc-mag240m dataset is a heterogeneous academic graph extracted
|
|
from the Microsoft Academic Graph (MAG). See more details in
|
|
`ogb-lsc-mag240m <https://ogb.stanford.edu/docs/lsc/mag240m/>`_.
|
|
|
|
.. note::
|
|
Reverse edges are added to the original graph.
|
|
|
|
Parameters
|
|
----------
|
|
name : str
|
|
The name of the builtin dataset.
|
|
root : str, optional
|
|
The root directory of the dataset. Default ot ``datasets``.
|
|
"""
|
|
|
|
# For dataset that is smaller than 30GB, we use the base url.
|
|
# Otherwise, we use the accelerated url.
|
|
_base_url = "https://data.dgl.ai/dataset/graphbolt/"
|
|
_accelerated_url = (
|
|
"https://dgl-data.s3-accelerate.amazonaws.com/dataset/graphbolt/"
|
|
)
|
|
_datasets = [
|
|
"cora",
|
|
"ogbn-mag",
|
|
"ogbl-citation2",
|
|
"ogbn-products",
|
|
"ogbn-arxiv",
|
|
]
|
|
_large_datasets = ["ogb-lsc-mag240m"]
|
|
_all_datasets = _datasets + _large_datasets
|
|
|
|
def __init__(self, name: str, root: str = "datasets") -> OnDiskDataset:
|
|
dataset_dir = os.path.join(root, name)
|
|
if not os.path.exists(dataset_dir):
|
|
if name not in self._all_datasets:
|
|
raise RuntimeError(
|
|
f"Dataset {name} is not available. Available datasets are "
|
|
f"{self._all_datasets}."
|
|
)
|
|
url = (
|
|
self._accelerated_url
|
|
if name in self._large_datasets
|
|
else self._base_url
|
|
)
|
|
url += name + ".zip"
|
|
os.makedirs(root, exist_ok=True)
|
|
zip_file_path = os.path.join(root, name + ".zip")
|
|
download(url, path=zip_file_path)
|
|
extract_archive(zip_file_path, root, overwrite=True)
|
|
os.remove(zip_file_path)
|
|
super().__init__(dataset_dir)
|
|
|
|
|
|
def _ondisk_task_str(task: OnDiskTask) -> str:
|
|
final_str = "OnDiskTask("
|
|
indent_len = len(final_str)
|
|
|
|
def _add_indent(_str, indent):
|
|
lines = _str.split("\n")
|
|
lines = [lines[0]] + [" " * indent + line for line in lines[1:]]
|
|
return "\n".join(lines)
|
|
|
|
attributes = get_attributes(task)
|
|
attributes.reverse()
|
|
for name in attributes:
|
|
if name[0] == "_":
|
|
continue
|
|
val = getattr(task, name)
|
|
final_str += (
|
|
f"{name}={_add_indent(str(val), indent_len + len(name) + 1)},\n"
|
|
+ " " * indent_len
|
|
)
|
|
return final_str[:-indent_len] + ")"
|