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Unverified Commit 129e75f3 authored by keli-wen's avatar keli-wen Committed by GitHub
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[Graphbolt] Update `preprocess` to Accept Dataset Path Instead of YAML File Path (#6091)

parent bcb5be4a
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Showing with 170 additions and 109 deletions
python/dgl/graphbolt/impl/ondisk_dataset.py
View file @ 129e75f3
......@@ -4,7 +4,6 @@ import os
import shutil
from copy import deepcopy
from pathlib import Path
from typing import List
import pandas as pd
......@@ -29,46 +28,80 @@ from .torch_based_feature_store import TorchBasedFeatureStore
__all__ = ["OnDiskDataset", "preprocess_ondisk_dataset"]
def preprocess_ondisk_dataset(input_config_path: str) -> str:
def _copy_or_convert_data(
input_path,
output_path,
input_format,
output_format="numpy",
in_memory=True,
):
"""Copy or convert the data from input_path to output_path."""
os.makedirs(os.path.dirname(output_path), exist_ok=True)
if input_format == "numpy":
# If the original format is numpy, just copy the file.
shutil.copyfile(input_path, output_path)
else:
# If the original format is not numpy, convert it to numpy.
data = read_data(input_path, input_format, in_memory)
save_data(data, output_path, output_format)
def preprocess_ondisk_dataset(dataset_dir: str) -> str:
"""Preprocess the on-disk dataset. Parse the input config file,
load the data, and save the data in the format that GraphBolt supports.
Parameters
----------
input_config_path : str
The path to the input config file.
dataset_dir : str
The path to the dataset directory.
Returns
-------
output_config_path : str
The path to the output config file.
"""
# 0. Load the input_config.
with open(input_config_path, "r") as f:
input_config = yaml.safe_load(f)
# Check if the dataset path is valid.
if not os.path.exists(dataset_dir):
raise RuntimeError(f"Invalid dataset path: {dataset_dir}")
# Check if the dataset_dir is a directory.
if not os.path.isdir(dataset_dir):
raise RuntimeError(
f"The dataset must be a directory. But got {dataset_dir}"
)
# If the input config does not contain the "graph" field, then we
# assume that the input config is already preprocessed.
if "graph" not in input_config:
print("The input config is already preprocessed.")
return input_config_path
# 0. Check if the dataset is already preprocessed.
if os.path.exists(os.path.join(dataset_dir, "preprocessed/metadata.yaml")):
print("The dataset is already preprocessed.")
return os.path.join(dataset_dir, "preprocessed/metadata.yaml")
print("Start to preprocess the on-disk dataset.")
# Infer the dataset path from the input config path.
dataset_path = Path(os.path.dirname(input_config_path))
processed_dir_prefix = Path("preprocessed")
processed_dir_prefix = os.path.join(dataset_dir, "preprocessed")
# Check if the metadata.yaml exists.
metadata_file_path = os.path.join(dataset_dir, "metadata.yaml")
if not os.path.exists(metadata_file_path):
raise RuntimeError("metadata.yaml does not exist.")
# Read the input config.
with open(metadata_file_path, "r") as f:
input_config = yaml.safe_load(f)
# 1. Make `processed_dir_prefix` directory if it does not exist.
os.makedirs(dataset_path / processed_dir_prefix, exist_ok=True)
# 1. Make `processed_dir_abs` directory if it does not exist.
os.makedirs(processed_dir_prefix, exist_ok=True)
output_config = deepcopy(input_config)
# 2. Load the edge data and create a DGLGraph.
if "graph" not in input_config:
raise RuntimeError("Invalid config: does not contain graph field.")
is_homogeneous = "type" not in input_config["graph"]["nodes"][0]
if is_homogeneous:
# Homogeneous graph.
num_nodes = input_config["graph"]["nodes"][0]["num"]
edge_data = pd.read_csv(
dataset_path / input_config["graph"]["edges"][0]["path"],
os.path.join(
dataset_dir, input_config["graph"]["edges"][0]["path"]
),
names=["src", "dst"],
)
src, dst = edge_data["src"].to_numpy(), edge_data["dst"].to_numpy()
......@@ -84,7 +117,8 @@ def preprocess_ondisk_dataset(input_config_path: str) -> str:
data_dict = {}
for edge_info in input_config["graph"]["edges"]:
edge_data = pd.read_csv(
dataset_path / edge_info["path"], names=["src", "dst"]
os.path.join(dataset_dir, edge_info["path"]),
names=["src", "dst"],
)
src = torch.tensor(edge_data["src"])
dst = torch.tensor(edge_data["dst"])
......@@ -98,14 +132,14 @@ def preprocess_ondisk_dataset(input_config_path: str) -> str:
for graph_feature in input_config["graph"]["feature_data"]:
if graph_feature["domain"] == "node":
node_data = read_data(
dataset_path / graph_feature["path"],
os.path.join(dataset_dir, graph_feature["path"]),
graph_feature["format"],
in_memory=graph_feature["in_memory"],
)
g.ndata[graph_feature["name"]] = node_data
if graph_feature["domain"] == "edge":
edge_data = read_data(
dataset_path / graph_feature["path"],
os.path.join(dataset_dir, graph_feature["path"]),
graph_feature["format"],
in_memory=graph_feature["in_memory"],
)
......@@ -117,13 +151,12 @@ def preprocess_ondisk_dataset(input_config_path: str) -> str:
# 5. Save the CSCSamplingGraph and modify the output_config.
output_config["graph_topology"] = {}
output_config["graph_topology"]["type"] = "CSCSamplingGraph"
output_config["graph_topology"]["path"] = str(
processed_dir_prefix / "csc_sampling_graph.tar"
output_config["graph_topology"]["path"] = os.path.join(
processed_dir_prefix, "csc_sampling_graph.tar"
)
save_csc_sampling_graph(
csc_sampling_graph,
str(dataset_path / output_config["graph_topology"]["path"]),
csc_sampling_graph, output_config["graph_topology"]["path"]
)
del output_config["graph"]
......@@ -134,31 +167,15 @@ def preprocess_ondisk_dataset(input_config_path: str) -> str:
):
# Always save the feature in numpy format.
out_feature["format"] = "numpy"
out_feature["path"] = str(
processed_dir_prefix / feature["path"].replace("pt", "npy")
out_feature["path"] = os.path.join(
processed_dir_prefix, feature["path"].replace("pt", "npy")
)
if feature["format"] == "numpy":
# If the original format is numpy, just copy the file.
os.makedirs(
dataset_path / os.path.dirname(out_feature["path"]),
exist_ok=True,
)
shutil.copyfile(
dataset_path / feature["path"],
dataset_path / out_feature["path"],
)
else:
# If the original format is not numpy, convert it to numpy.
data = read_data(
dataset_path / feature["path"],
_copy_or_convert_data(
os.path.join(dataset_dir, feature["path"]),
out_feature["path"],
feature["format"],
in_memory=feature["in_memory"],
)
save_data(
data,
dataset_path / out_feature["path"],
out_feature["format"],
feature["in_memory"],
)
# 7. Save the train/val/test split according to the output_config.
......@@ -173,38 +190,25 @@ def preprocess_ondisk_dataset(input_config_path: str) -> str:
):
# Always save the feature in numpy format.
output_data["format"] = "numpy"
output_data["path"] = str(
processed_dir_prefix
/ input_data["path"].replace("pt", "npy")
output_data["path"] = os.path.join(
processed_dir_prefix,
input_data["path"].replace("pt", "npy"),
)
if input_data["format"] == "numpy":
# If the original format is numpy, just copy the file.
os.makedirs(
dataset_path / os.path.dirname(output_data["path"]),
exist_ok=True,
)
shutil.copy(
dataset_path / input_data["path"],
dataset_path / output_data["path"],
)
else:
# If the original format is not numpy, convert it to numpy.
input_set = read_data(
dataset_path / input_data["path"],
_copy_or_convert_data(
os.path.join(dataset_dir, input_data["path"]),
output_data["path"],
input_data["format"],
)
save_data(
input_set,
dataset_path / output_data["path"],
output_set_per_type["format"],
output_data["format"],
)
# 8. Save the output_config.
output_config_path = dataset_path / "output_config.yaml"
output_config_path = os.path.join(dataset_dir, "preprocessed/metadata.yaml")
with open(output_config_path, "w") as f:
yaml.dump(output_config, f)
print("Finish preprocessing the on-disk dataset.")
return str(output_config_path)
# 9. Return the absolute path of the preprocessing yaml file.
return output_config_path
class OnDiskDataset(Dataset):
......
tests/python/pytorch/graphbolt/test_ondisk_dataset.py
View file @ 129e75f3
import os
import re
import tempfile
import gb_test_utils as gbt
......@@ -16,7 +17,8 @@ from dgl import graphbolt as gb
def test_OnDiskDataset_TVTSet_exceptions():
"""Test excpetions thrown when parsing TVTSet."""
with tempfile.TemporaryDirectory() as test_dir:
yaml_file = os.path.join(test_dir, "test.yaml")
os.makedirs(os.path.join(test_dir, "preprocessed"), exist_ok=True)
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
# Case 1: ``format`` is invalid.
yaml_content = """
......@@ -26,13 +28,14 @@ def test_OnDiskDataset_TVTSet_exceptions():
- format: torch_invalid
path: set/paper-train.pt
"""
yaml_file = os.path.join(test_dir, "test.yaml")
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
with pytest.raises(pydantic.ValidationError):
_ = gb.OnDiskDataset(yaml_file)
_ = gb.OnDiskDataset(test_dir)
# Case 2: ``type`` is not specified while multiple TVT sets are specified.
# Case 2: ``type`` is not specified while multiple TVT sets are
# specified.
yaml_content = """
train_set:
- type: null
......@@ -50,7 +53,7 @@ def test_OnDiskDataset_TVTSet_exceptions():
AssertionError,
match=r"Only one TVT set is allowed if type is not specified.",
):
_ = gb.OnDiskDataset(yaml_file)
_ = gb.OnDiskDataset(test_dir)
def test_OnDiskDataset_TVTSet_ItemSet_id_label():
......@@ -109,11 +112,12 @@ def test_OnDiskDataset_TVTSet_ItemSet_id_label():
in_memory: true
path: {test_labels_path}
"""
yaml_file = os.path.join(test_dir, "test.yaml")
os.makedirs(os.path.join(test_dir, "preprocessed"), exist_ok=True)
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
dataset = gb.OnDiskDataset(yaml_file)
dataset = gb.OnDiskDataset(test_dir)
# Verify train set.
train_set = dataset.train_set
......@@ -151,11 +155,11 @@ def test_OnDiskDataset_TVTSet_ItemSet_id_label():
- format: numpy
path: {train_ids_path}
"""
yaml_file = os.path.join(test_dir, "test.yaml")
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
dataset = gb.OnDiskDataset(yaml_file)
dataset = gb.OnDiskDataset(test_dir)
assert dataset.train_set is not None
assert dataset.validation_set is None
assert dataset.test_set is None
......@@ -232,11 +236,12 @@ def test_OnDiskDataset_TVTSet_ItemSet_node_pair_label():
in_memory: true
path: {test_labels_path}
"""
yaml_file = os.path.join(test_dir, "test.yaml")
os.makedirs(os.path.join(test_dir, "preprocessed"), exist_ok=True)
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
dataset = gb.OnDiskDataset(yaml_file)
dataset = gb.OnDiskDataset(test_dir)
# Verify train set.
train_set = dataset.train_set
......@@ -344,11 +349,12 @@ def test_OnDiskDataset_TVTSet_ItemSet_node_pair_negs():
in_memory: true
path: {test_neg_dst_path}
"""
yaml_file = os.path.join(test_dir, "test.yaml")
os.makedirs(os.path.join(test_dir, "preprocessed"), exist_ok=True)
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
dataset = gb.OnDiskDataset(yaml_file)
dataset = gb.OnDiskDataset(test_dir)
# Verify train set.
train_set = dataset.train_set
......@@ -434,11 +440,12 @@ def test_OnDiskDataset_TVTSet_ItemSetDict_id_label():
- format: numpy
path: {test_path}
"""
yaml_file = os.path.join(test_dir, "test.yaml")
os.makedirs(os.path.join(test_dir, "preprocessed"), exist_ok=True)
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
dataset = gb.OnDiskDataset(yaml_file)
dataset = gb.OnDiskDataset(test_dir)
# Verify train set.
train_set = dataset.train_set
......@@ -536,11 +543,12 @@ def test_OnDiskDataset_TVTSet_ItemSetDict_node_pair_label():
- format: numpy
path: {test_path}
"""
yaml_file = os.path.join(test_dir, "test.yaml")
os.makedirs(os.path.join(test_dir, "preprocessed"), exist_ok=True)
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
dataset = gb.OnDiskDataset(yaml_file)
dataset = gb.OnDiskDataset(test_dir)
# Verify train set.
train_set = dataset.train_set
......@@ -636,11 +644,12 @@ def test_OnDiskDataset_Feature_heterograph():
in_memory: true
path: {edge_data_label_path}
"""
yaml_file = os.path.join(test_dir, "test.yaml")
os.makedirs(os.path.join(test_dir, "preprocessed"), exist_ok=True)
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
dataset = gb.OnDiskDataset(yaml_file)
dataset = gb.OnDiskDataset(test_dir)
# Verify feature data storage.
feature_data = dataset.feature
......@@ -714,11 +723,12 @@ def test_OnDiskDataset_Feature_homograph():
in_memory: true
path: {edge_data_label_path}
"""
yaml_file = os.path.join(test_dir, "test.yaml")
os.makedirs(os.path.join(test_dir, "preprocessed"), exist_ok=True)
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
dataset = gb.OnDiskDataset(yaml_file)
dataset = gb.OnDiskDataset(test_dir)
# Verify feature data storage.
feature_data = dataset.feature
......@@ -757,7 +767,8 @@ def test_OnDiskDataset_Graph_Exceptions():
type: CSRSamplingGraph
path: /path/to/graph
"""
yaml_file = os.path.join(test_dir, "test.yaml")
os.makedirs(os.path.join(test_dir, "preprocessed"), exist_ok=True)
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
......@@ -765,7 +776,7 @@ def test_OnDiskDataset_Graph_Exceptions():
pydantic.ValidationError,
match="1 validation error for OnDiskMetaData",
):
_ = gb.OnDiskDataset(yaml_file)
_ = gb.OnDiskDataset(test_dir)
def test_OnDiskDataset_Graph_homogeneous():
......@@ -782,11 +793,12 @@ def test_OnDiskDataset_Graph_homogeneous():
type: CSCSamplingGraph
path: {graph_path}
"""
yaml_file = os.path.join(test_dir, "test.yaml")
os.makedirs(os.path.join(test_dir, "preprocessed"), exist_ok=True)
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
dataset = gb.OnDiskDataset(yaml_file)
dataset = gb.OnDiskDataset(test_dir)
graph2 = dataset.graph
assert graph.num_nodes == graph2.num_nodes
......@@ -824,11 +836,12 @@ def test_OnDiskDataset_Graph_heterogeneous():
type: CSCSamplingGraph
path: {graph_path}
"""
yaml_file = os.path.join(test_dir, "test.yaml")
os.makedirs(os.path.join(test_dir, "preprocessed"), exist_ok=True)
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
dataset = gb.OnDiskDataset(yaml_file)
dataset = gb.OnDiskDataset(test_dir)
graph2 = dataset.graph
assert graph.num_nodes == graph2.num_nodes
......@@ -854,11 +867,12 @@ def test_OnDiskDataset_Metadata():
num_classes: {num_classes}
num_labels: {num_labels}
"""
yaml_file = os.path.join(test_dir, "test.yaml")
os.makedirs(os.path.join(test_dir, "preprocessed"), exist_ok=True)
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
dataset = gb.OnDiskDataset(yaml_file)
dataset = gb.OnDiskDataset(test_dir)
assert dataset.dataset_name == dataset_name
assert dataset.num_classes == num_classes
assert dataset.num_labels == num_labels
......@@ -867,11 +881,11 @@ def test_OnDiskDataset_Metadata():
yaml_content = f"""
dataset_name: {dataset_name}
"""
yaml_file = os.path.join(test_dir, "test.yaml")
yaml_file = os.path.join(test_dir, "preprocessed/metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
dataset = gb.OnDiskDataset(yaml_file)
dataset = gb.OnDiskDataset(test_dir)
assert dataset.dataset_name == dataset_name
assert dataset.num_classes is None
assert dataset.num_labels is None
......@@ -969,10 +983,10 @@ def test_OnDiskDataset_preprocess_homogeneous():
- format: numpy
path: set/test.npy
"""
yaml_file = os.path.join(test_dir, "test.yaml")
yaml_file = os.path.join(test_dir, "metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
output_file = gb.ondisk_dataset.preprocess_ondisk_dataset(yaml_file)
output_file = gb.ondisk_dataset.preprocess_ondisk_dataset(test_dir)
with open(output_file, "rb") as f:
processed_dataset = yaml.load(f, Loader=yaml.Loader)
......@@ -996,3 +1010,46 @@ def test_OnDiskDataset_preprocess_homogeneous():
torch.tensor([fanout]),
)
assert len(list(subgraph.node_pairs.values())[0][0]) <= num_samples
def test_OnDiskDataset_preprocess_path():
"""Test if the preprocess function can catch the path error."""
with tempfile.TemporaryDirectory() as test_dir:
# All metadata fields are specified.
dataset_name = "graphbolt_test"
num_classes = 10
num_labels = 9
yaml_content = f"""
dataset_name: {dataset_name}
num_classes: {num_classes}
num_labels: {num_labels}
"""
yaml_file = os.path.join(test_dir, "metadata.yaml")
with open(yaml_file, "w") as f:
f.write(yaml_content)
# Case1. Test the passed in is the yaml file path.
with pytest.raises(
RuntimeError,
match="The dataset must be a directory. "
rf"But got {re.escape(yaml_file)}",
):
_ = gb.OnDiskDataset(yaml_file)
# Case2. Test the passed in is a fake directory.
fake_dir = os.path.join(test_dir, "fake_dir")
with pytest.raises(
RuntimeError,
match=rf"Invalid dataset path: {re.escape(fake_dir)}",
):
_ = gb.OnDiskDataset(fake_dir)
# Case3. Test the passed in is the dataset directory.
# But the metadata.yaml is not in the directory.
os.makedirs(os.path.join(test_dir, "fake_dir"), exist_ok=True)
with pytest.raises(
RuntimeError,
match=r"metadata.yaml does not exist.",
):
_ = gb.OnDiskDataset(fake_dir)
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