diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index fee53a7..706a105 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -18,8 +18,8 @@ jobs: os: - macos-latest - ubuntu-latest - python-version: [3.8, 3.9] - poetry-version: ["1.2.0"] + python-version: [3.8, 3.10] + poetry-version: ["1.8.3"] steps: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 diff --git a/.gitignore b/.gitignore index e75eb54..0a02ee6 100644 --- a/.gitignore +++ b/.gitignore @@ -197,7 +197,7 @@ target/ # pyenv # For a library or package, you might want to ignore these files since the code is # intended to run in multiple environments; otherwise, check them in: -# .python-version +.python-version # pipenv # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. @@ -345,9 +345,11 @@ $RECYCLE.BIN/ # End of https://www.toptal.com/developers/gitignore/api/macos,windows,linux,emacs,vim,visualstudiocode,python,jupyternotebooks # ================ -# Custom Setting +# Custom Setting # ================ data/ !openpack_toolkit/data/ !tests/data/ *.csv +wandb/ +outputs/ diff --git a/.secrets/.gitignore b/.secrets/.gitignore new file mode 100644 index 0000000..d6b7ef3 --- /dev/null +++ b/.secrets/.gitignore @@ -0,0 +1,2 @@ +* +!.gitignore diff --git a/openpack_toolkit/download/README.md b/openpack_toolkit/download/README.md new file mode 100644 index 0000000..960cfc4 --- /dev/null +++ b/openpack_toolkit/download/README.md @@ -0,0 +1,41 @@ +# Python-based Data Downloader + +Shell script-based data downloader is prepared in [open-pack/openpack-dataset](https://github.com/open-pack/openpack-dataset/blob/main/docs/DOWNLOAD.md). +However, it does not support downloading data from Google Drive and it is not easy to configure. +This download tool provides another option to set up datasets in your environment. + +## How to use + +```bash +poetry run python download.py +``` + +### Track data lineage with Weight and Biases + +(Optional) Create an artifact of the OpenPack Dataset on the cloud repository. + +```bash +poetry run python create_wandb_artifact.py zenodo +``` + +Download the dataset into your local using WandB. + +```bash +wandb login +poetry run python download_local.py --use-wandb +``` + +### Workflow + +```mermaid +graph LR + RepoZ[(Zenodo)] + RepoG[(GoogleDrive)] + LocalZipFolder[(`openpack/v.X.X.X/zip/`)] + LocalDsFolder[(`openpack/v.X.X.X/`)] + ProcDownload(Download) + ProcExtract(Extract) + RepoZ --> ProcDownload --> LocalZipFolder + RepoG --> ProcDownload --> LocalZipFolder + LocalZipFolder --> ProcExtract --> LocalDsFolder +``` diff --git a/openpack_toolkit/download/__init__.py b/openpack_toolkit/download/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/openpack_toolkit/download/const.py b/openpack_toolkit/download/const.py new file mode 100644 index 0000000..561a85b --- /dev/null +++ b/openpack_toolkit/download/const.py @@ -0,0 +1,44 @@ +WANDB_PROJECT_NAME_PUBLIC = "openpack-dataset" +WANDB_PROJECT_NAME_LOCAL = "openpack-dataset-local" +WANDB_JOB_TYPE_DOWNLOAD_DATASET = "download-dataset" +WANDB_ARTIFACT_TYPE_DATASET = "dataset" + +OPENPACK_DATASET_NAME_ON_ZENODO_TEMPLATE = "openpack-{version}-zenodo" +OPENPACK_DATASET_NAME_ON_GRDIVE_TEMPLATE = "openpack-{version}-gdrive" +OPENPACK_DATASET_NAME_ON_LOCAL_TEMPLATE = "openpack-{version}-local-{hostname}" + +OPENAPCK_ROOT_PATH_STR = "./openpack/v{version}" + +ZENODO_URLS = { + "v1.1.0": "https://zenodo.org/records/11059235", + "v1.0.0": "https://zenodo.org/records/8145223", +} + +GDRIVE_URLS = { + "v1.0.0": "https://drive.google.com/drive/folders/10hYJYkhPRgf-uTToUm5KR99EHkH2v9GB", +} + + +OPENPACK_USERS = ( + "U0101", + "U0102", + "U0103", + "U0104", + "U0105", + "U0106", + "U0107", + "U0108", + "U0109", + "U0110", + "U0111", + "U0201", + "U0202", + "U0203", + "U0204", + "U0205", + "U0206", + "U0207", + "U0208", + "U0209", + "U0210", +) diff --git a/openpack_toolkit/download/download_local.py b/openpack_toolkit/download/download_local.py new file mode 100644 index 0000000..622dc02 --- /dev/null +++ b/openpack_toolkit/download/download_local.py @@ -0,0 +1,154 @@ +import socket +import zipfile +from pathlib import Path + +import click +import requests +import wandb +from loguru import logger +from tqdm import tqdm + +from tools.download.const import ( + OPENPACK_DATASET_NAME_ON_LOCAL_TEMPLATE, + OPENPACK_DATASET_NAME_ON_ZENODO_TEMPLATE, + OPENPACK_USERS, + WANDB_ARTIFACT_TYPE_DATASET, + WANDB_JOB_TYPE_DOWNLOAD_DATASET, + WANDB_PROJECT_NAME_LOCAL, + WANDB_PROJECT_NAME_PUBLIC, + ZENODO_URLS, +) + +# _DEFAULT_OUTPUT_DIR = "../../data/datasets/openpack/" +_DEFAULT_OPENPACK_DIR = Path().cwd() / "data" / "datasets" / "openpack" + + +def download_file_with_progress_bar(src_uri: str, dest_path: Path): + if dest_path.exists(): + logger.warning(f"Zip file ({dest_path}) already exists. Skip downloading.") + return + + logger.info(f"Download zip file from {src_uri} and save it to {dest_path}.") + response = requests.get(src_uri, stream=True) + total_size = int(response.headers.get("content-length", 0)) + + dest_path.parent.mkdir(parents=True, exist_ok=True) + with open(dest_path, "wb") as f: + with tqdm( + desc=str(dest_path), total=total_size, unit="iB", unit_scale=True, unit_divisor=1024 + ) as bar: + for data in response.iter_content(chunk_size=1024): + size = f.write(data) + bar.update(size) + logger.info(f"Finish downloading zip file to {dest_path}.") + + +def extract_zip(zip_file_path: Path, extract_path: Path): + logger.info(f"Extract {zip_file_path} to {extract_path}.") + extract_path.mkdir(parents=True, exist_ok=True) + with zipfile.ZipFile(zip_file_path, "r") as zip_ref: + zip_ref.extractall(extract_path) + + +def download_from_zenodo( + version: str, user_id: str, zip_dir: Path, remote_artifact: wandb.Artifact = None +): + """Download a zip file from Zenodo. If the wandb is active, download using the artifact.""" + if remote_artifact is not None: + zip_path = remote_artifact.get_entry(f"{user_id}.zip").download( + root=zip_dir, skip_cache=True + ) + else: + base_uri = ZENODO_URLS[version] + uri = f"{base_uri}/files/{user_id}.zip?download=1" + zip_path = zip_dir / f"{user_id}.zip" + download_file_with_progress_bar(uri, zip_path) + return zip_path + + +def extract_zip_from_zenodo(zip_path: Path, user_dir: Path, local_artifact: wandb.Artifact = None): + """Extract a zip file downloaded from zenodo to the user_directory.""" + user_id = user_dir.name + logger.info(f"Extract zip file for {user_id}.") + extract_zip(zip_path, user_dir) + + # Log local data to WandB. + # Create artifact references for each data stream. + if local_artifact is not None: + logger.info(f"Log streams of {user_id} to WandB.") + for sensor_dir in user_dir.iterdir(): + for stream_dir in sensor_dir.iterdir(): + local_artifact.add_reference( + f"file://{stream_dir.absolute()}", + name=f"{user_id}/{sensor_dir.name}/{stream_dir.name}", + ) + + +@click.command() +@click.option( + "-v", + "--version", + type=click.Choice(ZENODO_URLS.keys()), + default="v1.1.0", + help="Version of the dataset to download.", +) +@click.option( + "-o", + "--openpack-dir", + type=click.Path(exists=True), + default=_DEFAULT_OPENPACK_DIR, + help="a root directory to download datasets.", +) +@click.option( + "--use-wandb", + "--wandb", + is_flag=True, + show_default=True, + default=True, + help="Log artifact with wandb.", +) +@click.option("--debug", is_flag=True, show_default=True, default=False, help="Run in debug mode.") +def main(version: str, openpack_dir: Path, use_wandb: bool = True, debug: bool = False): + # Init wandb. + if use_wandb is not None: + project_name = WANDB_PROJECT_NAME_LOCAL + if debug: + project_name += "-debug" + wandb_run = wandb.init(project=project_name, job_type=WANDB_JOB_TYPE_DOWNLOAD_DATASET) + remote_artifact = wandb_run.use_artifact( + f"{WANDB_PROJECT_NAME_PUBLIC}/{OPENPACK_DATASET_NAME_ON_ZENODO_TEMPLATE}:latest".format( + version=version + ) + ) + local_artifact = wandb.Artifact( + name=OPENPACK_DATASET_NAME_ON_LOCAL_TEMPLATE.format( + version=version, hostname=socket.gethostname() + ), + type=WANDB_ARTIFACT_TYPE_DATASET, + description=f"OpenPack Dataset ({version}) on {socket.gethostname()}", + ) + else: + wandb_run, remote_artifact, local_artifact = None, None, None + + # Init dataset directories. + openpack_dir = Path(openpack_dir) + zip_dir = openpack_dir / version / "zip" / "zenodo" + zip_dir.mkdir(parents=True, exist_ok=True) + users = OPENPACK_USERS + if debug: + users = users[:2] + + # Download and extract data for the first two users. + for user_id in users: + zip_path = download_from_zenodo(version, user_id, openpack_dir, remote_artifact) + + user_dir = openpack_dir / user_id + extract_zip_from_zenodo(zip_path, user_dir, local_artifact=local_artifact) + + # Save the artifact to W&B + wandb_run.log_artifact(local_artifact) + wandb_run.finish() + + +if __name__ == "__main__": + main() diff --git a/openpack_toolkit/download/metadata/README.md b/openpack_toolkit/download/metadata/README.md new file mode 100644 index 0000000..3137fd0 --- /dev/null +++ b/openpack_toolkit/download/metadata/README.md @@ -0,0 +1,3 @@ +# [Admin Tool] Dataset Metadata Generator + +This is a tool for OpenPack admin members to generate dataset metadata for creating a release. diff --git a/openpack_toolkit/download/metadata/__init__.py b/openpack_toolkit/download/metadata/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/openpack_toolkit/download/metadata/create_wandb_artifact.py b/openpack_toolkit/download/metadata/create_wandb_artifact.py new file mode 100644 index 0000000..0bdd871 --- /dev/null +++ b/openpack_toolkit/download/metadata/create_wandb_artifact.py @@ -0,0 +1,307 @@ +"""[Admin Command] Generate metadata for the OpenPack dataset and create a W&B artifact. +""" + +from __future__ import annotations + +import json +from pathlib import Path + +import attrs +import cattrs +import click +import google.auth.transport.requests +from google.auth.transport.requests import Request +from google.oauth2 import service_account +from google_auth_oauthlib.flow import InstalledAppFlow +from googleapiclient.discovery import build +from loguru import logger +from omegaconf import OmegaConf +from tqdm import tqdm + +import wandb +from openpack_toolkit.download.const import ( + GDRIVE_URLS, + OPENPACK_DATASET_NAME_ON_ZENODO_TEMPLATE, + OPENPACK_USERS, + WANDB_ARTIFACT_TYPE_DATASET, + WANDB_JOB_TYPE_DOWNLOAD_DATASET, + WANDB_PROJECT_NAME_PUBLIC, + ZENODO_URLS, +) + +OPENPACK_CACHE_DIR = Path(".cache/") +OPERNPACK_ZIP_DIR_ZENODO = OPENPACK_CACHE_DIR / "zenodo" +OPERNPACK_ZIP_DIR_GDRIVE = OPENPACK_CACHE_DIR / "zenodo" + +_DEFAULT_OUTPUT_DIR = Path("./outputs") +_DEFAULT_OUTPUT_PATH_ZENODO = _DEFAULT_OUTPUT_DIR / "dataset_metadata_zenodo.yaml" +_DEFAULT_OUTPUT_PATH_GDRIVE = _DEFAULT_OUTPUT_DIR / "dataset_metadata_gdrive.yaml" + +# ============= +# Data Models +# ============= + + +@attrs.define +class WebsiteList: + project: str = "https://open-pack.github.io/" + github: str = "https://github.com/open-pack/openpack-dataset" + release_note: str = "https://github.com/open-pack/openpack-dataset/tree/main/release/{version}" + + +@attrs.define +class DatasetObjectMetadata: + file_name: str + file_type: str + parent_dir: Path + uri: str | None = None # URI of the object that contains this object. + subject: str | None = None + session: str | None = None + + +@attrs.define +class DatasetMetadata: + name: str + version: str + repository: str + repository_url: str + website: WebsiteList = WebsiteList() + objects: list[DatasetObjectMetadata] = attrs.field(factory=list) + + def __attrs_post_init__(self): + self.website.release_note = self.website.release_note.format(version=self.version) + + +def get_converter() -> cattrs.Converter: + converter = cattrs.Converter() + converter.register_structure_hook(Path, lambda path_str, _: Path(path_str)) + converter.register_unstructure_hook(Path, str) + return converter + + +# ==================== +# Metadata Generator +# ==================== + + +def create_metadata_zenodo(version: str) -> DatasetMetadata: + metadata = DatasetMetadata( + name=OPENPACK_DATASET_NAME_ON_ZENODO_TEMPLATE.format(version=version), + version=version, + repository="zenodo", + repository_url=ZENODO_URLS[version], + ) + + # Add files to the metadata + base_uri = ZENODO_URLS[version] + for user_id in OPENPACK_USERS: + uri = f"{base_uri}/files/{user_id}.zip?download=1" + obj_metadata = DatasetObjectMetadata( + file_name=f"{user_id}.zip", + file_type="zip", + parent_dir=OPERNPACK_ZIP_DIR_ZENODO, + uri=uri, + ) + metadata.objects.append(obj_metadata) + + return metadata + + +# 認証とトークンの保存 +def authenticate(service_account_file_path: Path): + creds = None + token_file = Path(".secrets/gcp_token.json") + + # 以前に保存したトークンがある場合、それをロードする + if token_file.exists(token_file): + with open(token_file, "r") as f: + creds = json.load(f) + + # トークンが有効でないか、存在しない場合、新しいトークンを取得する + if not creds or not creds.valid: + if creds and creds.expired and creds.refresh_token: + creds.refresh(Request()) + else: + flow = InstalledAppFlow.from_client_secrets_file(CLIENT_SECRET_FILE, SCOPES) + creds = flow.run_local_server(port=0) + + # 新しいトークンを保存する + with open(token_file, "w") as f: + json.dump(creds, f) + + return creds + + +def create_metadata_gdrive(version: str, service_account_file_path: Path) -> DatasetMetadata: + """Create metadata of a data on Google Drive.""" + metadata = DatasetMetadata( + name=OPENPACK_DATASET_NAME_ON_ZENODO_TEMPLATE.format(version=version), + version=version, + repository="google-drive", + repository_url=GDRIVE_URLS[version], + ) + + # Authentication + logger.info( + f"Authenticate with Google Drive using a service account from {service_account_file_path}." + ) + creds = service_account.Credentials.from_service_account_file( + service_account_file_path, scopes=["https://www.googleapis.com/auth/drive.readonly"] + ) + service = build("drive", "v3", credentials=creds) + + # List Items in the folder + folder_id = GDRIVE_URLS[version].split("/")[-1] + results = ( + service.files() + .list( + q=f"'{folder_id}' in parents and trashed = false", + fields="nextPageToken, files(id, name)", + ) + .execute() + ) + items = results.get("files", []) + logger.info(f"Found {len(items)} files in the folder.") + + if not items: + raise ValueError("No files found in the folder.") + else: + logger.info("Add files in the folder to the metadata.") + for item in items: + file_id = item["id"] + file_name = item["name"] + file_uri = f"https://drive.google.com/file/d/{file_id}/view" + # print(f"Name: {file_name}, URI: {file_uri}") + obj_metadata = DatasetObjectMetadata( + file_name=file_name, + file_type="file", + parent_dir=OPERNPACK_ZIP_DIR_GDRIVE, + uri=file_uri, + ) + metadata.objects.append(obj_metadata) + logger.info(f"Add {file_name} to the metadata.") + + return metadata + + +def create_wandb_artifacts_from_metadata(metadata: DatasetMetadata): + logger.info(f"Create a WandB artifact for {metadata.name}.") + metadata_dict = get_converter().unstructure(metadata) + version = metadata.version + + # Create a W&B artifact + wandb_run = wandb.init( + project=WANDB_PROJECT_NAME_PUBLIC, job_type=WANDB_JOB_TYPE_DOWNLOAD_DATASET, mode="offline" + ) + artifact = wandb.Artifact( + name=metadata.name, + type=WANDB_ARTIFACT_TYPE_DATASET, + description=( + f"OpenPack Dataset ({version}) on zenodo. " + "Visit https://open-pack.github.io/ for more details." + ), + metadata=metadata_dict, + ) + objects = sorted(list(metadata.objects), key=lambda x: x.file_name) + logger.info(f"Add {len(objects)} objects to the artifact.") + for obj_metadata in tqdm(objects): + artifact.add_reference(obj_metadata.uri, name=obj_metadata.file_name) + # Save the artifact to W&B + wandb_run.log_artifact(artifact) + wandb_run.finish() + + +# ========== +# Commands +# ========== + + +@click.group() +def cli(): + pass + + +@cli.command() +@click.option( + "-v", + "--version", + type=click.Choice(ZENODO_URLS.keys()), + default="v1.1.0", + help="Version of the dataset to download.", +) +@click.option( + "-o", + "--output-path", + type=click.Path(file_okay=True, path_type=Path), + default=_DEFAULT_OUTPUT_PATH_ZENODO, + show_default=True, + help="output file path.", +) +def zenodo( + version: str, + output_path: Path, +): + """Create metadata of a data on zenodo.""" + metadata = create_metadata_zenodo(version) + metadata_dict = get_converter().unstructure(metadata) + output_path.parent.mkdir(parents=True, exist_ok=True) + with output_path.open("w") as f: + OmegaConf.save(metadata_dict, f) + logger.info(f"Saved metadata to {output_path}") + + +@cli.command() +@click.option( + "-v", + "--version", + type=click.Choice(ZENODO_URLS.keys()), + default="v1.0.0", + help="Version of the dataset to download.", +) +@click.option( + "-o", + "--output-path", + type=click.Path(file_okay=True, path_type=Path), + default=_DEFAULT_OUTPUT_PATH_ZENODO, + show_default=True, + help="output file path.", +) +@click.option( + "-s", + "--service-account-file-path", + type=click.Path(exists=True, file_okay=True, path_type=Path), + help="Path to a service account file for Google Drive.", +) +def gdrive(version: str, output_path: Path, service_account_file_path: Path): + click.echo(f"Create a WandB artifact for Google Drive ({version}).") + metadata = create_metadata_gdrive(version, service_account_file_path) + metadata_dict = get_converter().unstructure(metadata) + output_path.parent.mkdir(parents=True, exist_ok=True) + with output_path.open("w") as f: + OmegaConf.save(metadata_dict, f) + logger.info(f"Saved metadata to {output_path}") + + +@cli.command() +@click.option( + "-i", + "--input-path", + type=click.Path(exists=True, file_okay=True, path_type=Path), + default=_DEFAULT_OUTPUT_PATH_ZENODO, + show_default=True, + help="output file path.", +) +def artifact(input_path: Path): + """Log the dataset as a WandB artifact.""" + with input_path.open("r") as f: + metadata_dict = OmegaConf.load(f) + metadata = get_converter().structure(metadata_dict, DatasetMetadata) + create_wandb_artifacts_from_metadata(metadata) + + +def main(): + cli() + + +if __name__ == "__main__": + main() diff --git a/openpack_toolkit/download/tests/test_download.py b/openpack_toolkit/download/tests/test_download.py new file mode 100644 index 0000000..87f59e6 --- /dev/null +++ b/openpack_toolkit/download/tests/test_download.py @@ -0,0 +1,53 @@ +from pathlib import Path +from unittest.mock import MagicMock, patch + +import pytest + +from tools.download.download import ( + download_and_extract_single_user_from_zenodo, + download_file_with_progress_bar, + extract_zip, +) + + +@patch("requests.get") +def test_download_file(mock_get: MagicMock, tmp_path: Path): + # Dummy address + url = "http://example.com/fake.zip" + download_path = Path(tmp_path, "data", "zip", "downloaded_file.zip") + # Mock for requests + mock_response = MagicMock() + mock_response.iter_content = lambda chunk_size: [b"a" * 1024] * 5 + mock_response.headers = {"content-length": f"{1024 * 5}"} + mock_get.return_value = mock_response + + download_file_with_progress_bar(url, download_path) + + assert download_path.exists() + + +@patch("zipfile.ZipFile") +def test_extract_zip(mock_zipfile: MagicMock): + file_path = "downloaded_file.zip" + extract_path = "extracted" + # Mock for zipfile.ZipFile + mock_zip = MagicMock() + mock_zipfile.return_value.__enter__.return_value = mock_zip + + result = extract_zip(file_path, extract_path) + + assert result == extract_path + mock_zip.extractall.assert_called_once_with(extract_path) + + +@patch("tools.download.download.download_file_with_progress_bar") +@patch("tools.download.download.extract_zip") +@patch("wandb.Artifact.add_reference") +def test_smoke_download_and_extract_single_user_from_zenodo( + mock_download: MagicMock, mock_extract: MagicMock, mock_add_reference: MagicMock +): + openpack_dir = Path("openpack") + version = "v1.0.0" + user_id = "U0101" + + download_and_extract_single_user_from_zenodo(openpack_dir, version, user_id) diff --git a/poetry.lock b/poetry.lock index 527a793..9738a56 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,74 +1,413 @@ +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. + [[package]] name = "antlr4-python3-runtime" version = "4.9.3" description = "ANTLR 4.9.3 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