1109 lines
39 KiB
Python
1109 lines
39 KiB
Python
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import gzip
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import hashlib
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import json
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import os
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import shutil
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import time
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from contextlib import closing
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from functools import wraps
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from os.path import join
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from typing import Callable, Optional, Dict, Tuple, List, Any, Union
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from tempfile import TemporaryDirectory
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from urllib.error import HTTPError, URLError
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from urllib.request import urlopen, Request
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from warnings import warn
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import numpy as np
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from . import get_data_home
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from ._arff_parser import load_arff_from_gzip_file
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from ..utils import Bunch
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from ..utils import check_pandas_support # noqa
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__all__ = ["fetch_openml"]
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_OPENML_PREFIX = "https://openml.org/"
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_SEARCH_NAME = "api/v1/json/data/list/data_name/{}/limit/2"
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_DATA_INFO = "api/v1/json/data/{}"
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_DATA_FEATURES = "api/v1/json/data/features/{}"
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_DATA_QUALITIES = "api/v1/json/data/qualities/{}"
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_DATA_FILE = "data/v1/download/{}"
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OpenmlQualitiesType = List[Dict[str, str]]
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OpenmlFeaturesType = List[Dict[str, str]]
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def _get_local_path(openml_path: str, data_home: str) -> str:
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return os.path.join(data_home, "openml.org", openml_path + ".gz")
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def _retry_with_clean_cache(
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openml_path: str,
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data_home: Optional[str],
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no_retry_exception: Optional[Exception] = None,
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) -> Callable:
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"""If the first call to the decorated function fails, the local cached
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file is removed, and the function is called again. If ``data_home`` is
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``None``, then the function is called once. We can provide a specific
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exception to not retry on usign `no_retry_exception` parameter.
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"""
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def decorator(f):
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@wraps(f)
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def wrapper(*args, **kw):
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if data_home is None:
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return f(*args, **kw)
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try:
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return f(*args, **kw)
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except URLError:
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raise
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except Exception as exc:
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if no_retry_exception is not None and isinstance(
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exc, no_retry_exception
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):
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raise
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warn("Invalid cache, redownloading file", RuntimeWarning)
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local_path = _get_local_path(openml_path, data_home)
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if os.path.exists(local_path):
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os.unlink(local_path)
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return f(*args, **kw)
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return wrapper
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return decorator
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def _retry_on_network_error(
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n_retries: int = 3, delay: float = 1.0, url: str = ""
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) -> Callable:
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"""If the function call results in a network error, call the function again
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up to ``n_retries`` times with a ``delay`` between each call. If the error
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has a 412 status code, don't call the function again as this is a specific
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OpenML error.
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The url parameter is used to give more information to the user about the
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error.
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"""
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def decorator(f):
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@wraps(f)
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def wrapper(*args, **kwargs):
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retry_counter = n_retries
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while True:
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try:
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return f(*args, **kwargs)
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except (URLError, TimeoutError) as e:
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# 412 is a specific OpenML error code.
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if isinstance(e, HTTPError) and e.code == 412:
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raise
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if retry_counter == 0:
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raise
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warn(
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f"A network error occurred while downloading {url}. Retrying..."
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)
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retry_counter -= 1
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time.sleep(delay)
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return wrapper
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return decorator
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def _open_openml_url(
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openml_path: str, data_home: Optional[str], n_retries: int = 3, delay: float = 1.0
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):
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"""
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Returns a resource from OpenML.org. Caches it to data_home if required.
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Parameters
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----------
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openml_path : str
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OpenML URL that will be accessed. This will be prefixes with
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_OPENML_PREFIX.
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data_home : str
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Directory to which the files will be cached. If None, no caching will
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be applied.
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n_retries : int, default=3
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Number of retries when HTTP errors are encountered. Error with status
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code 412 won't be retried as they represent OpenML generic errors.
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delay : float, default=1.0
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Number of seconds between retries.
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Returns
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-------
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result : stream
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A stream to the OpenML resource.
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"""
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def is_gzip_encoded(_fsrc):
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return _fsrc.info().get("Content-Encoding", "") == "gzip"
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req = Request(_OPENML_PREFIX + openml_path)
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req.add_header("Accept-encoding", "gzip")
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if data_home is None:
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fsrc = _retry_on_network_error(n_retries, delay, req.full_url)(urlopen)(req)
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if is_gzip_encoded(fsrc):
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return gzip.GzipFile(fileobj=fsrc, mode="rb")
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return fsrc
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local_path = _get_local_path(openml_path, data_home)
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dir_name, file_name = os.path.split(local_path)
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if not os.path.exists(local_path):
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os.makedirs(dir_name, exist_ok=True)
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try:
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# Create a tmpdir as a subfolder of dir_name where the final file will
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# be moved to if the download is successful. This guarantees that the
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# renaming operation to the final location is atomic to ensure the
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# concurrence safety of the dataset caching mechanism.
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with TemporaryDirectory(dir=dir_name) as tmpdir:
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with closing(
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_retry_on_network_error(n_retries, delay, req.full_url)(urlopen)(
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req
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)
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) as fsrc:
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opener: Callable
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if is_gzip_encoded(fsrc):
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opener = open
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else:
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opener = gzip.GzipFile
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with opener(os.path.join(tmpdir, file_name), "wb") as fdst:
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shutil.copyfileobj(fsrc, fdst)
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shutil.move(fdst.name, local_path)
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except Exception:
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if os.path.exists(local_path):
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os.unlink(local_path)
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raise
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# XXX: First time, decompression will not be necessary (by using fsrc), but
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# it will happen nonetheless
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return gzip.GzipFile(local_path, "rb")
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class OpenMLError(ValueError):
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"""HTTP 412 is a specific OpenML error code, indicating a generic error"""
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pass
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def _get_json_content_from_openml_api(
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url: str,
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error_message: Optional[str],
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data_home: Optional[str],
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n_retries: int = 3,
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delay: float = 1.0,
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) -> Dict:
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"""
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Loads json data from the openml api.
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Parameters
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----------
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url : str
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The URL to load from. Should be an official OpenML endpoint.
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error_message : str or None
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The error message to raise if an acceptable OpenML error is thrown
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(acceptable error is, e.g., data id not found. Other errors, like 404's
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will throw the native error message).
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data_home : str or None
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Location to cache the response. None if no cache is required.
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n_retries : int, default=3
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Number of retries when HTTP errors are encountered. Error with status
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code 412 won't be retried as they represent OpenML generic errors.
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delay : float, default=1.0
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Number of seconds between retries.
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Returns
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-------
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json_data : json
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the json result from the OpenML server if the call was successful.
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An exception otherwise.
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"""
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@_retry_with_clean_cache(url, data_home=data_home)
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def _load_json():
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with closing(
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_open_openml_url(url, data_home, n_retries=n_retries, delay=delay)
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) as response:
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return json.loads(response.read().decode("utf-8"))
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try:
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return _load_json()
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except HTTPError as error:
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# 412 is an OpenML specific error code, indicating a generic error
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# (e.g., data not found)
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if error.code != 412:
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raise error
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# 412 error, not in except for nicer traceback
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raise OpenMLError(error_message)
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def _get_data_info_by_name(
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name: str,
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version: Union[int, str],
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data_home: Optional[str],
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n_retries: int = 3,
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delay: float = 1.0,
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):
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"""
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Utilizes the openml dataset listing api to find a dataset by
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name/version
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OpenML api function:
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https://www.openml.org/api_docs#!/data/get_data_list_data_name_data_name
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Parameters
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----------
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name : str
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name of the dataset
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version : int or str
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If version is an integer, the exact name/version will be obtained from
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OpenML. If version is a string (value: "active") it will take the first
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version from OpenML that is annotated as active. Any other string
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values except "active" are treated as integer.
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data_home : str or None
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Location to cache the response. None if no cache is required.
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n_retries : int, default=3
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Number of retries when HTTP errors are encountered. Error with status
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code 412 won't be retried as they represent OpenML generic errors.
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delay : float, default=1.0
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Number of seconds between retries.
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Returns
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-------
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first_dataset : json
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json representation of the first dataset object that adhired to the
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search criteria
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"""
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if version == "active":
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# situation in which we return the oldest active version
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url = _SEARCH_NAME.format(name) + "/status/active/"
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error_msg = "No active dataset {} found.".format(name)
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json_data = _get_json_content_from_openml_api(
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url,
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error_msg,
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data_home=data_home,
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n_retries=n_retries,
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delay=delay,
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)
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res = json_data["data"]["dataset"]
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if len(res) > 1:
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warn(
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"Multiple active versions of the dataset matching the name"
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" {name} exist. Versions may be fundamentally different, "
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"returning version"
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" {version}.".format(name=name, version=res[0]["version"])
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)
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return res[0]
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# an integer version has been provided
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url = (_SEARCH_NAME + "/data_version/{}").format(name, version)
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try:
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json_data = _get_json_content_from_openml_api(
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url,
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error_message=None,
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data_home=data_home,
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n_retries=n_retries,
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delay=delay,
|
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)
|
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|
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except OpenMLError:
|
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|
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# we can do this in 1 function call if OpenML does not require the
|
||
|
|
# specification of the dataset status (i.e., return datasets with a
|
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|
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# given name / version regardless of active, deactivated, etc. )
|
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|
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# TODO: feature request OpenML.
|
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url += "/status/deactivated"
|
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|
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error_msg = "Dataset {} with version {} not found.".format(name, version)
|
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json_data = _get_json_content_from_openml_api(
|
||
|
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url,
|
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error_msg,
|
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|
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data_home=data_home,
|
||
|
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n_retries=n_retries,
|
||
|
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delay=delay,
|
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)
|
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|
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|
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|
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return json_data["data"]["dataset"][0]
|
||
|
|
|
||
|
|
|
||
|
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def _get_data_description_by_id(
|
||
|
|
data_id: int,
|
||
|
|
data_home: Optional[str],
|
||
|
|
n_retries: int = 3,
|
||
|
|
delay: float = 1.0,
|
||
|
|
) -> Dict[str, Any]:
|
||
|
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# OpenML API function: https://www.openml.org/api_docs#!/data/get_data_id
|
||
|
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url = _DATA_INFO.format(data_id)
|
||
|
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error_message = "Dataset with data_id {} not found.".format(data_id)
|
||
|
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json_data = _get_json_content_from_openml_api(
|
||
|
|
url,
|
||
|
|
error_message,
|
||
|
|
data_home=data_home,
|
||
|
|
n_retries=n_retries,
|
||
|
|
delay=delay,
|
||
|
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)
|
||
|
|
return json_data["data_set_description"]
|
||
|
|
|
||
|
|
|
||
|
|
def _get_data_features(
|
||
|
|
data_id: int,
|
||
|
|
data_home: Optional[str],
|
||
|
|
n_retries: int = 3,
|
||
|
|
delay: float = 1.0,
|
||
|
|
) -> OpenmlFeaturesType:
|
||
|
|
# OpenML function:
|
||
|
|
# https://www.openml.org/api_docs#!/data/get_data_features_id
|
||
|
|
url = _DATA_FEATURES.format(data_id)
|
||
|
|
error_message = "Dataset with data_id {} not found.".format(data_id)
|
||
|
|
json_data = _get_json_content_from_openml_api(
|
||
|
|
url,
|
||
|
|
error_message,
|
||
|
|
data_home=data_home,
|
||
|
|
n_retries=n_retries,
|
||
|
|
delay=delay,
|
||
|
|
)
|
||
|
|
return json_data["data_features"]["feature"]
|
||
|
|
|
||
|
|
|
||
|
|
def _get_data_qualities(
|
||
|
|
data_id: int,
|
||
|
|
data_home: Optional[str],
|
||
|
|
n_retries: int = 3,
|
||
|
|
delay: float = 1.0,
|
||
|
|
) -> OpenmlQualitiesType:
|
||
|
|
# OpenML API function:
|
||
|
|
# https://www.openml.org/api_docs#!/data/get_data_qualities_id
|
||
|
|
url = _DATA_QUALITIES.format(data_id)
|
||
|
|
error_message = "Dataset with data_id {} not found.".format(data_id)
|
||
|
|
json_data = _get_json_content_from_openml_api(
|
||
|
|
url,
|
||
|
|
error_message,
|
||
|
|
data_home=data_home,
|
||
|
|
n_retries=n_retries,
|
||
|
|
delay=delay,
|
||
|
|
)
|
||
|
|
# the qualities might not be available, but we still try to process
|
||
|
|
# the data
|
||
|
|
return json_data.get("data_qualities", {}).get("quality", [])
|
||
|
|
|
||
|
|
|
||
|
|
def _get_num_samples(data_qualities: OpenmlQualitiesType) -> int:
|
||
|
|
"""Get the number of samples from data qualities.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
data_qualities : list of dict
|
||
|
|
Used to retrieve the number of instances (samples) in the dataset.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
n_samples : int
|
||
|
|
The number of samples in the dataset or -1 if data qualities are
|
||
|
|
unavailable.
|
||
|
|
"""
|
||
|
|
# If the data qualities are unavailable, we return -1
|
||
|
|
default_n_samples = -1
|
||
|
|
|
||
|
|
qualities = {d["name"]: d["value"] for d in data_qualities}
|
||
|
|
return int(float(qualities.get("NumberOfInstances", default_n_samples)))
|
||
|
|
|
||
|
|
|
||
|
|
def _load_arff_response(
|
||
|
|
url: str,
|
||
|
|
data_home: Optional[str],
|
||
|
|
parser: str,
|
||
|
|
output_type: str,
|
||
|
|
openml_columns_info: dict,
|
||
|
|
feature_names_to_select: List[str],
|
||
|
|
target_names_to_select: List[str],
|
||
|
|
shape: Optional[Tuple[int, int]],
|
||
|
|
md5_checksum: str,
|
||
|
|
n_retries: int = 3,
|
||
|
|
delay: float = 1.0,
|
||
|
|
):
|
||
|
|
"""Load the ARFF data associated with the OpenML URL.
|
||
|
|
|
||
|
|
In addition of loading the data, this function will also check the
|
||
|
|
integrity of the downloaded file from OpenML using MD5 checksum.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
url : str
|
||
|
|
The URL of the ARFF file on OpenML.
|
||
|
|
|
||
|
|
data_home : str
|
||
|
|
The location where to cache the data.
|
||
|
|
|
||
|
|
parser : {"liac-arff", "pandas"}
|
||
|
|
The parser used to parse the ARFF file.
|
||
|
|
|
||
|
|
output_type : {"numpy", "pandas", "sparse"}
|
||
|
|
The type of the arrays that will be returned. The possibilities are:
|
||
|
|
|
||
|
|
- `"numpy"`: both `X` and `y` will be NumPy arrays;
|
||
|
|
- `"sparse"`: `X` will be sparse matrix and `y` will be a NumPy array;
|
||
|
|
- `"pandas"`: `X` will be a pandas DataFrame and `y` will be either a
|
||
|
|
pandas Series or DataFrame.
|
||
|
|
|
||
|
|
openml_columns_info : dict
|
||
|
|
The information provided by OpenML regarding the columns of the ARFF
|
||
|
|
file.
|
||
|
|
|
||
|
|
feature_names_to_select : list of str
|
||
|
|
The list of the features to be selected.
|
||
|
|
|
||
|
|
target_names_to_select : list of str
|
||
|
|
The list of the target variables to be selected.
|
||
|
|
|
||
|
|
shape : tuple or None
|
||
|
|
With `parser="liac-arff"`, when using a generator to load the data,
|
||
|
|
one needs to provide the shape of the data beforehand.
|
||
|
|
|
||
|
|
md5_checksum : str
|
||
|
|
The MD5 checksum provided by OpenML to check the data integrity.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
X : {ndarray, sparse matrix, dataframe}
|
||
|
|
The data matrix.
|
||
|
|
|
||
|
|
y : {ndarray, dataframe, series}
|
||
|
|
The target.
|
||
|
|
|
||
|
|
frame : dataframe or None
|
||
|
|
A dataframe containing both `X` and `y`. `None` if
|
||
|
|
`output_array_type != "pandas"`.
|
||
|
|
|
||
|
|
categories : list of str or None
|
||
|
|
The names of the features that are categorical. `None` if
|
||
|
|
`output_array_type == "pandas"`.
|
||
|
|
"""
|
||
|
|
gzip_file = _open_openml_url(url, data_home, n_retries=n_retries, delay=delay)
|
||
|
|
with closing(gzip_file):
|
||
|
|
md5 = hashlib.md5()
|
||
|
|
for chunk in iter(lambda: gzip_file.read(4096), b""):
|
||
|
|
md5.update(chunk)
|
||
|
|
actual_md5_checksum = md5.hexdigest()
|
||
|
|
|
||
|
|
if actual_md5_checksum != md5_checksum:
|
||
|
|
raise ValueError(
|
||
|
|
f"md5 checksum of local file for {url} does not match description: "
|
||
|
|
f"expected: {md5_checksum} but got {actual_md5_checksum}. "
|
||
|
|
"Downloaded file could have been modified / corrupted, clean cache "
|
||
|
|
"and retry..."
|
||
|
|
)
|
||
|
|
|
||
|
|
def _open_url_and_load_gzip_file(url, data_home, n_retries, delay, arff_params):
|
||
|
|
gzip_file = _open_openml_url(url, data_home, n_retries=n_retries, delay=delay)
|
||
|
|
with closing(gzip_file):
|
||
|
|
return load_arff_from_gzip_file(gzip_file, **arff_params)
|
||
|
|
|
||
|
|
arff_params = dict(
|
||
|
|
parser=parser,
|
||
|
|
output_type=output_type,
|
||
|
|
openml_columns_info=openml_columns_info,
|
||
|
|
feature_names_to_select=feature_names_to_select,
|
||
|
|
target_names_to_select=target_names_to_select,
|
||
|
|
shape=shape,
|
||
|
|
)
|
||
|
|
try:
|
||
|
|
X, y, frame, categories = _open_url_and_load_gzip_file(
|
||
|
|
url, data_home, n_retries, delay, arff_params
|
||
|
|
)
|
||
|
|
except Exception as exc:
|
||
|
|
if parser == "pandas":
|
||
|
|
from pandas.errors import ParserError
|
||
|
|
|
||
|
|
if isinstance(exc, ParserError):
|
||
|
|
# A parsing error could come from providing the wrong quotechar
|
||
|
|
# to pandas. By default, we use a double quote. Thus, we retry
|
||
|
|
# with a single quote before to raise the error.
|
||
|
|
arff_params["read_csv_kwargs"] = {"quotechar": "'"}
|
||
|
|
X, y, frame, categories = _open_url_and_load_gzip_file(
|
||
|
|
url, data_home, n_retries, delay, arff_params
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
raise
|
||
|
|
|
||
|
|
return X, y, frame, categories
|
||
|
|
|
||
|
|
|
||
|
|
def _download_data_to_bunch(
|
||
|
|
url: str,
|
||
|
|
sparse: bool,
|
||
|
|
data_home: Optional[str],
|
||
|
|
*,
|
||
|
|
as_frame: bool,
|
||
|
|
openml_columns_info: List[dict],
|
||
|
|
data_columns: List[str],
|
||
|
|
target_columns: List[str],
|
||
|
|
shape: Optional[Tuple[int, int]],
|
||
|
|
md5_checksum: str,
|
||
|
|
n_retries: int = 3,
|
||
|
|
delay: float = 1.0,
|
||
|
|
parser: str,
|
||
|
|
):
|
||
|
|
"""Download ARFF data, load it to a specific container and create to Bunch.
|
||
|
|
|
||
|
|
This function has a mechanism to retry/cache/clean the data.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
url : str
|
||
|
|
The URL of the ARFF file on OpenML.
|
||
|
|
|
||
|
|
sparse : bool
|
||
|
|
Whether the dataset is expected to use the sparse ARFF format.
|
||
|
|
|
||
|
|
data_home : str
|
||
|
|
The location where to cache the data.
|
||
|
|
|
||
|
|
as_frame : bool
|
||
|
|
Whether or not to return the data into a pandas DataFrame.
|
||
|
|
|
||
|
|
openml_columns_info : list of dict
|
||
|
|
The information regarding the columns provided by OpenML for the
|
||
|
|
ARFF dataset. The information is stored as a list of dictionaries.
|
||
|
|
|
||
|
|
data_columns : list of str
|
||
|
|
The list of the features to be selected.
|
||
|
|
|
||
|
|
target_columns : list of str
|
||
|
|
The list of the target variables to be selected.
|
||
|
|
|
||
|
|
shape : tuple or None
|
||
|
|
With `parser="liac-arff"`, when using a generator to load the data,
|
||
|
|
one needs to provide the shape of the data beforehand.
|
||
|
|
|
||
|
|
md5_checksum : str
|
||
|
|
The MD5 checksum provided by OpenML to check the data integrity.
|
||
|
|
|
||
|
|
n_retries : int, default=3
|
||
|
|
Number of retries when HTTP errors are encountered. Error with status
|
||
|
|
code 412 won't be retried as they represent OpenML generic errors.
|
||
|
|
|
||
|
|
delay : float, default=1.0
|
||
|
|
Number of seconds between retries.
|
||
|
|
|
||
|
|
parser : {"liac-arff", "pandas"}
|
||
|
|
The parser used to parse the ARFF file.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
data : :class:`~sklearn.utils.Bunch`
|
||
|
|
Dictionary-like object, with the following attributes.
|
||
|
|
|
||
|
|
X : {ndarray, sparse matrix, dataframe}
|
||
|
|
The data matrix.
|
||
|
|
y : {ndarray, dataframe, series}
|
||
|
|
The target.
|
||
|
|
frame : dataframe or None
|
||
|
|
A dataframe containing both `X` and `y`. `None` if
|
||
|
|
`output_array_type != "pandas"`.
|
||
|
|
categories : list of str or None
|
||
|
|
The names of the features that are categorical. `None` if
|
||
|
|
`output_array_type == "pandas"`.
|
||
|
|
"""
|
||
|
|
# Prepare which columns and data types should be returned for the X and y
|
||
|
|
features_dict = {feature["name"]: feature for feature in openml_columns_info}
|
||
|
|
|
||
|
|
if sparse:
|
||
|
|
output_type = "sparse"
|
||
|
|
elif as_frame:
|
||
|
|
output_type = "pandas"
|
||
|
|
else:
|
||
|
|
output_type = "numpy"
|
||
|
|
|
||
|
|
# XXX: target columns should all be categorical or all numeric
|
||
|
|
_verify_target_data_type(features_dict, target_columns)
|
||
|
|
for name in target_columns:
|
||
|
|
column_info = features_dict[name]
|
||
|
|
n_missing_values = int(column_info["number_of_missing_values"])
|
||
|
|
if n_missing_values > 0:
|
||
|
|
raise ValueError(
|
||
|
|
f"Target column '{column_info['name']}' has {n_missing_values} missing "
|
||
|
|
"values. Missing values are not supported for target columns."
|
||
|
|
)
|
||
|
|
|
||
|
|
no_retry_exception = None
|
||
|
|
if parser == "pandas":
|
||
|
|
# If we get a ParserError with pandas, then we don't want to retry and we raise
|
||
|
|
# early.
|
||
|
|
from pandas.errors import ParserError
|
||
|
|
|
||
|
|
no_retry_exception = ParserError
|
||
|
|
|
||
|
|
X, y, frame, categories = _retry_with_clean_cache(
|
||
|
|
url, data_home, no_retry_exception
|
||
|
|
)(_load_arff_response)(
|
||
|
|
url,
|
||
|
|
data_home,
|
||
|
|
parser=parser,
|
||
|
|
output_type=output_type,
|
||
|
|
openml_columns_info=features_dict,
|
||
|
|
feature_names_to_select=data_columns,
|
||
|
|
target_names_to_select=target_columns,
|
||
|
|
shape=shape,
|
||
|
|
md5_checksum=md5_checksum,
|
||
|
|
n_retries=n_retries,
|
||
|
|
delay=delay,
|
||
|
|
)
|
||
|
|
|
||
|
|
return Bunch(
|
||
|
|
data=X,
|
||
|
|
target=y,
|
||
|
|
frame=frame,
|
||
|
|
categories=categories,
|
||
|
|
feature_names=data_columns,
|
||
|
|
target_names=target_columns,
|
||
|
|
)
|
||
|
|
|
||
|
|
|
||
|
|
def _verify_target_data_type(features_dict, target_columns):
|
||
|
|
# verifies the data type of the y array in case there are multiple targets
|
||
|
|
# (throws an error if these targets do not comply with sklearn support)
|
||
|
|
if not isinstance(target_columns, list):
|
||
|
|
raise ValueError("target_column should be list, got: %s" % type(target_columns))
|
||
|
|
found_types = set()
|
||
|
|
for target_column in target_columns:
|
||
|
|
if target_column not in features_dict:
|
||
|
|
raise KeyError(f"Could not find target_column='{target_column}'")
|
||
|
|
if features_dict[target_column]["data_type"] == "numeric":
|
||
|
|
found_types.add(np.float64)
|
||
|
|
else:
|
||
|
|
found_types.add(object)
|
||
|
|
|
||
|
|
# note: we compare to a string, not boolean
|
||
|
|
if features_dict[target_column]["is_ignore"] == "true":
|
||
|
|
warn(f"target_column='{target_column}' has flag is_ignore.")
|
||
|
|
if features_dict[target_column]["is_row_identifier"] == "true":
|
||
|
|
warn(f"target_column='{target_column}' has flag is_row_identifier.")
|
||
|
|
if len(found_types) > 1:
|
||
|
|
raise ValueError(
|
||
|
|
"Can only handle homogeneous multi-target datasets, "
|
||
|
|
"i.e., all targets are either numeric or "
|
||
|
|
"categorical."
|
||
|
|
)
|
||
|
|
|
||
|
|
|
||
|
|
def _valid_data_column_names(features_list, target_columns):
|
||
|
|
# logic for determining on which columns can be learned. Note that from the
|
||
|
|
# OpenML guide follows that columns that have the `is_row_identifier` or
|
||
|
|
# `is_ignore` flag, these can not be learned on. Also target columns are
|
||
|
|
# excluded.
|
||
|
|
valid_data_column_names = []
|
||
|
|
for feature in features_list:
|
||
|
|
if (
|
||
|
|
feature["name"] not in target_columns
|
||
|
|
and feature["is_ignore"] != "true"
|
||
|
|
and feature["is_row_identifier"] != "true"
|
||
|
|
):
|
||
|
|
valid_data_column_names.append(feature["name"])
|
||
|
|
return valid_data_column_names
|
||
|
|
|
||
|
|
|
||
|
|
def fetch_openml(
|
||
|
|
name: Optional[str] = None,
|
||
|
|
*,
|
||
|
|
version: Union[str, int] = "active",
|
||
|
|
data_id: Optional[int] = None,
|
||
|
|
data_home: Optional[str] = None,
|
||
|
|
target_column: Optional[Union[str, List]] = "default-target",
|
||
|
|
cache: bool = True,
|
||
|
|
return_X_y: bool = False,
|
||
|
|
as_frame: Union[str, bool] = "auto",
|
||
|
|
n_retries: int = 3,
|
||
|
|
delay: float = 1.0,
|
||
|
|
parser: Optional[str] = "warn",
|
||
|
|
):
|
||
|
|
"""Fetch dataset from openml by name or dataset id.
|
||
|
|
|
||
|
|
Datasets are uniquely identified by either an integer ID or by a
|
||
|
|
combination of name and version (i.e. there might be multiple
|
||
|
|
versions of the 'iris' dataset). Please give either name or data_id
|
||
|
|
(not both). In case a name is given, a version can also be
|
||
|
|
provided.
|
||
|
|
|
||
|
|
Read more in the :ref:`User Guide <openml>`.
|
||
|
|
|
||
|
|
.. versionadded:: 0.20
|
||
|
|
|
||
|
|
.. note:: EXPERIMENTAL
|
||
|
|
|
||
|
|
The API is experimental (particularly the return value structure),
|
||
|
|
and might have small backward-incompatible changes without notice
|
||
|
|
or warning in future releases.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
name : str, default=None
|
||
|
|
String identifier of the dataset. Note that OpenML can have multiple
|
||
|
|
datasets with the same name.
|
||
|
|
|
||
|
|
version : int or 'active', default='active'
|
||
|
|
Version of the dataset. Can only be provided if also ``name`` is given.
|
||
|
|
If 'active' the oldest version that's still active is used. Since
|
||
|
|
there may be more than one active version of a dataset, and those
|
||
|
|
versions may fundamentally be different from one another, setting an
|
||
|
|
exact version is highly recommended.
|
||
|
|
|
||
|
|
data_id : int, default=None
|
||
|
|
OpenML ID of the dataset. The most specific way of retrieving a
|
||
|
|
dataset. If data_id is not given, name (and potential version) are
|
||
|
|
used to obtain a dataset.
|
||
|
|
|
||
|
|
data_home : str, default=None
|
||
|
|
Specify another download and cache folder for the data sets. By default
|
||
|
|
all scikit-learn data is stored in '~/scikit_learn_data' subfolders.
|
||
|
|
|
||
|
|
target_column : str, list or None, default='default-target'
|
||
|
|
Specify the column name in the data to use as target. If
|
||
|
|
'default-target', the standard target column a stored on the server
|
||
|
|
is used. If ``None``, all columns are returned as data and the
|
||
|
|
target is ``None``. If list (of strings), all columns with these names
|
||
|
|
are returned as multi-target (Note: not all scikit-learn classifiers
|
||
|
|
can handle all types of multi-output combinations).
|
||
|
|
|
||
|
|
cache : bool, default=True
|
||
|
|
Whether to cache the downloaded datasets into `data_home`.
|
||
|
|
|
||
|
|
return_X_y : bool, default=False
|
||
|
|
If True, returns ``(data, target)`` instead of a Bunch object. See
|
||
|
|
below for more information about the `data` and `target` objects.
|
||
|
|
|
||
|
|
as_frame : bool or 'auto', default='auto'
|
||
|
|
If True, the data is a pandas DataFrame including columns with
|
||
|
|
appropriate dtypes (numeric, string or categorical). The target is
|
||
|
|
a pandas DataFrame or Series depending on the number of target_columns.
|
||
|
|
The Bunch will contain a ``frame`` attribute with the target and the
|
||
|
|
data. If ``return_X_y`` is True, then ``(data, target)`` will be pandas
|
||
|
|
DataFrames or Series as describe above.
|
||
|
|
|
||
|
|
If `as_frame` is 'auto', the data and target will be converted to
|
||
|
|
DataFrame or Series as if `as_frame` is set to True, unless the dataset
|
||
|
|
is stored in sparse format.
|
||
|
|
|
||
|
|
If `as_frame` is False, the data and target will be NumPy arrays and
|
||
|
|
the `data` will only contain numerical values when `parser="liac-arff"`
|
||
|
|
where the categories are provided in the attribute `categories` of the
|
||
|
|
`Bunch` instance. When `parser="pandas"`, no ordinal encoding is made.
|
||
|
|
|
||
|
|
.. versionchanged:: 0.24
|
||
|
|
The default value of `as_frame` changed from `False` to `'auto'`
|
||
|
|
in 0.24.
|
||
|
|
|
||
|
|
n_retries : int, default=3
|
||
|
|
Number of retries when HTTP errors or network timeouts are encountered.
|
||
|
|
Error with status code 412 won't be retried as they represent OpenML
|
||
|
|
generic errors.
|
||
|
|
|
||
|
|
delay : float, default=1.0
|
||
|
|
Number of seconds between retries.
|
||
|
|
|
||
|
|
parser : {"auto", "pandas", "liac-arff"}, default="liac-arff"
|
||
|
|
Parser used to load the ARFF file. Two parsers are implemented:
|
||
|
|
|
||
|
|
- `"pandas"`: this is the most efficient parser. However, it requires
|
||
|
|
pandas to be installed and can only open dense datasets.
|
||
|
|
- `"liac-arff"`: this is a pure Python ARFF parser that is much less
|
||
|
|
memory- and CPU-efficient. It deals with sparse ARFF dataset.
|
||
|
|
|
||
|
|
If `"auto"` (future default), the parser is chosen automatically such that
|
||
|
|
`"liac-arff"` is selected for sparse ARFF datasets, otherwise
|
||
|
|
`"pandas"` is selected.
|
||
|
|
|
||
|
|
.. versionadded:: 1.2
|
||
|
|
.. versionchanged:: 1.4
|
||
|
|
The default value of `parser` will change from `"liac-arff"` to
|
||
|
|
`"auto"` in 1.4. You can set `parser="auto"` to silence this
|
||
|
|
warning. Therefore, an `ImportError` will be raised from 1.4 if
|
||
|
|
the dataset is dense and pandas is not installed.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
data : :class:`~sklearn.utils.Bunch`
|
||
|
|
Dictionary-like object, with the following attributes.
|
||
|
|
|
||
|
|
data : np.array, scipy.sparse.csr_matrix of floats, or pandas DataFrame
|
||
|
|
The feature matrix. Categorical features are encoded as ordinals.
|
||
|
|
target : np.array, pandas Series or DataFrame
|
||
|
|
The regression target or classification labels, if applicable.
|
||
|
|
Dtype is float if numeric, and object if categorical. If
|
||
|
|
``as_frame`` is True, ``target`` is a pandas object.
|
||
|
|
DESCR : str
|
||
|
|
The full description of the dataset.
|
||
|
|
feature_names : list
|
||
|
|
The names of the dataset columns.
|
||
|
|
target_names: list
|
||
|
|
The names of the target columns.
|
||
|
|
|
||
|
|
.. versionadded:: 0.22
|
||
|
|
|
||
|
|
categories : dict or None
|
||
|
|
Maps each categorical feature name to a list of values, such
|
||
|
|
that the value encoded as i is ith in the list. If ``as_frame``
|
||
|
|
is True, this is None.
|
||
|
|
details : dict
|
||
|
|
More metadata from OpenML.
|
||
|
|
frame : pandas DataFrame
|
||
|
|
Only present when `as_frame=True`. DataFrame with ``data`` and
|
||
|
|
``target``.
|
||
|
|
|
||
|
|
(data, target) : tuple if ``return_X_y`` is True
|
||
|
|
|
||
|
|
.. note:: EXPERIMENTAL
|
||
|
|
|
||
|
|
This interface is **experimental** and subsequent releases may
|
||
|
|
change attributes without notice (although there should only be
|
||
|
|
minor changes to ``data`` and ``target``).
|
||
|
|
|
||
|
|
Missing values in the 'data' are represented as NaN's. Missing values
|
||
|
|
in 'target' are represented as NaN's (numerical target) or None
|
||
|
|
(categorical target).
|
||
|
|
|
||
|
|
Notes
|
||
|
|
-----
|
||
|
|
The `"pandas"` and `"liac-arff"` parsers can lead to different data types
|
||
|
|
in the output. The notable differences are the following:
|
||
|
|
|
||
|
|
- The `"liac-arff"` parser always encodes categorical features as `str` objects.
|
||
|
|
To the contrary, the `"pandas"` parser instead infers the type while
|
||
|
|
reading and numerical categories will be casted into integers whenever
|
||
|
|
possible.
|
||
|
|
- The `"liac-arff"` parser uses float64 to encode numerical features
|
||
|
|
tagged as 'REAL' and 'NUMERICAL' in the metadata. The `"pandas"`
|
||
|
|
parser instead infers if these numerical features corresponds
|
||
|
|
to integers and uses panda's Integer extension dtype.
|
||
|
|
- In particular, classification datasets with integer categories are
|
||
|
|
typically loaded as such `(0, 1, ...)` with the `"pandas"` parser while
|
||
|
|
`"liac-arff"` will force the use of string encoded class labels such as
|
||
|
|
`"0"`, `"1"` and so on.
|
||
|
|
- The `"pandas"` parser will not strip single quotes - i.e. `'` - from
|
||
|
|
string columns. For instance, a string `'my string'` will be kept as is
|
||
|
|
while the `"liac-arff"` parser will strip the single quotes. For
|
||
|
|
categorical columns, the single quotes are stripped from the values.
|
||
|
|
|
||
|
|
In addition, when `as_frame=False` is used, the `"liac-arff"` parser
|
||
|
|
returns ordinally encoded data where the categories are provided in the
|
||
|
|
attribute `categories` of the `Bunch` instance. Instead, `"pandas"` returns
|
||
|
|
a NumPy array were the categories are not encoded.
|
||
|
|
"""
|
||
|
|
if cache is False:
|
||
|
|
# no caching will be applied
|
||
|
|
data_home = None
|
||
|
|
else:
|
||
|
|
data_home = get_data_home(data_home=data_home)
|
||
|
|
data_home = join(data_home, "openml")
|
||
|
|
|
||
|
|
# check valid function arguments. data_id XOR (name, version) should be
|
||
|
|
# provided
|
||
|
|
if name is not None:
|
||
|
|
# OpenML is case-insensitive, but the caching mechanism is not
|
||
|
|
# convert all data names (str) to lower case
|
||
|
|
name = name.lower()
|
||
|
|
if data_id is not None:
|
||
|
|
raise ValueError(
|
||
|
|
"Dataset data_id={} and name={} passed, but you can only "
|
||
|
|
"specify a numeric data_id or a name, not "
|
||
|
|
"both.".format(data_id, name)
|
||
|
|
)
|
||
|
|
data_info = _get_data_info_by_name(
|
||
|
|
name, version, data_home, n_retries=n_retries, delay=delay
|
||
|
|
)
|
||
|
|
data_id = data_info["did"]
|
||
|
|
elif data_id is not None:
|
||
|
|
# from the previous if statement, it is given that name is None
|
||
|
|
if version != "active":
|
||
|
|
raise ValueError(
|
||
|
|
"Dataset data_id={} and version={} passed, but you can only "
|
||
|
|
"specify a numeric data_id or a version, not "
|
||
|
|
"both.".format(data_id, version)
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
raise ValueError(
|
||
|
|
"Neither name nor data_id are provided. Please provide name or data_id."
|
||
|
|
)
|
||
|
|
|
||
|
|
data_description = _get_data_description_by_id(data_id, data_home)
|
||
|
|
if data_description["status"] != "active":
|
||
|
|
warn(
|
||
|
|
"Version {} of dataset {} is inactive, meaning that issues have "
|
||
|
|
"been found in the dataset. Try using a newer version from "
|
||
|
|
"this URL: {}".format(
|
||
|
|
data_description["version"],
|
||
|
|
data_description["name"],
|
||
|
|
data_description["url"],
|
||
|
|
)
|
||
|
|
)
|
||
|
|
if "error" in data_description:
|
||
|
|
warn(
|
||
|
|
"OpenML registered a problem with the dataset. It might be "
|
||
|
|
"unusable. Error: {}".format(data_description["error"])
|
||
|
|
)
|
||
|
|
if "warning" in data_description:
|
||
|
|
warn(
|
||
|
|
"OpenML raised a warning on the dataset. It might be "
|
||
|
|
"unusable. Warning: {}".format(data_description["warning"])
|
||
|
|
)
|
||
|
|
|
||
|
|
# TODO(1.4): remove "warn" from the valid parser
|
||
|
|
valid_parsers = ("auto", "pandas", "liac-arff", "warn")
|
||
|
|
if parser not in valid_parsers:
|
||
|
|
raise ValueError(
|
||
|
|
f"`parser` must be one of {', '.join(repr(p) for p in valid_parsers)}. Got"
|
||
|
|
f" {parser!r} instead."
|
||
|
|
)
|
||
|
|
|
||
|
|
if parser == "warn":
|
||
|
|
# TODO(1.4): remove this warning
|
||
|
|
parser = "liac-arff"
|
||
|
|
warn(
|
||
|
|
"The default value of `parser` will change from `'liac-arff'` to "
|
||
|
|
"`'auto'` in 1.4. You can set `parser='auto'` to silence this "
|
||
|
|
"warning. Therefore, an `ImportError` will be raised from 1.4 if "
|
||
|
|
"the dataset is dense and pandas is not installed. Note that the pandas "
|
||
|
|
"parser may return different data types. See the Notes Section in "
|
||
|
|
"fetch_openml's API doc for details.",
|
||
|
|
FutureWarning,
|
||
|
|
)
|
||
|
|
|
||
|
|
if as_frame not in ("auto", True, False):
|
||
|
|
raise ValueError(
|
||
|
|
f"`as_frame` must be one of 'auto', True, or False. Got {as_frame} instead."
|
||
|
|
)
|
||
|
|
|
||
|
|
return_sparse = data_description["format"].lower() == "sparse_arff"
|
||
|
|
as_frame = not return_sparse if as_frame == "auto" else as_frame
|
||
|
|
if parser == "auto":
|
||
|
|
parser_ = "liac-arff" if return_sparse else "pandas"
|
||
|
|
else:
|
||
|
|
parser_ = parser
|
||
|
|
|
||
|
|
if as_frame or parser_ == "pandas":
|
||
|
|
try:
|
||
|
|
check_pandas_support("`fetch_openml`")
|
||
|
|
except ImportError as exc:
|
||
|
|
if as_frame:
|
||
|
|
err_msg = (
|
||
|
|
"Returning pandas objects requires pandas to be installed. "
|
||
|
|
"Alternatively, explicitely set `as_frame=False` and "
|
||
|
|
"`parser='liac-arff'`."
|
||
|
|
)
|
||
|
|
raise ImportError(err_msg) from exc
|
||
|
|
else:
|
||
|
|
err_msg = (
|
||
|
|
f"Using `parser={parser_!r}` requires pandas to be installed. "
|
||
|
|
"Alternatively, explicitely set `parser='liac-arff'`."
|
||
|
|
)
|
||
|
|
if parser == "auto":
|
||
|
|
# TODO(1.4): In version 1.4, we will raise an error instead of
|
||
|
|
# a warning.
|
||
|
|
warn(
|
||
|
|
"From version 1.4, `parser='auto'` with `as_frame=False` "
|
||
|
|
"will use pandas. Either install pandas or set explicitely "
|
||
|
|
"`parser='liac-arff'` to preserve the current behavior.",
|
||
|
|
FutureWarning,
|
||
|
|
)
|
||
|
|
parser_ = "liac-arff"
|
||
|
|
else:
|
||
|
|
raise ImportError(err_msg) from exc
|
||
|
|
|
||
|
|
if return_sparse:
|
||
|
|
if as_frame:
|
||
|
|
raise ValueError(
|
||
|
|
"Sparse ARFF datasets cannot be loaded with as_frame=True. "
|
||
|
|
"Use as_frame=False or as_frame='auto' instead."
|
||
|
|
)
|
||
|
|
if parser_ == "pandas":
|
||
|
|
raise ValueError(
|
||
|
|
f"Sparse ARFF datasets cannot be loaded with parser={parser!r}. "
|
||
|
|
"Use parser='liac-arff' or parser='auto' instead."
|
||
|
|
)
|
||
|
|
|
||
|
|
# download data features, meta-info about column types
|
||
|
|
features_list = _get_data_features(data_id, data_home)
|
||
|
|
|
||
|
|
if not as_frame:
|
||
|
|
for feature in features_list:
|
||
|
|
if "true" in (feature["is_ignore"], feature["is_row_identifier"]):
|
||
|
|
continue
|
||
|
|
if feature["data_type"] == "string":
|
||
|
|
raise ValueError(
|
||
|
|
"STRING attributes are not supported for "
|
||
|
|
"array representation. Try as_frame=True"
|
||
|
|
)
|
||
|
|
|
||
|
|
if target_column == "default-target":
|
||
|
|
# determines the default target based on the data feature results
|
||
|
|
# (which is currently more reliable than the data description;
|
||
|
|
# see issue: https://github.com/openml/OpenML/issues/768)
|
||
|
|
target_columns = [
|
||
|
|
feature["name"]
|
||
|
|
for feature in features_list
|
||
|
|
if feature["is_target"] == "true"
|
||
|
|
]
|
||
|
|
elif isinstance(target_column, str):
|
||
|
|
# for code-simplicity, make target_column by default a list
|
||
|
|
target_columns = [target_column]
|
||
|
|
elif target_column is None:
|
||
|
|
target_columns = []
|
||
|
|
elif isinstance(target_column, list):
|
||
|
|
target_columns = target_column
|
||
|
|
else:
|
||
|
|
raise TypeError(
|
||
|
|
"Did not recognize type of target_column"
|
||
|
|
"Should be str, list or None. Got: "
|
||
|
|
"{}".format(type(target_column))
|
||
|
|
)
|
||
|
|
data_columns = _valid_data_column_names(features_list, target_columns)
|
||
|
|
|
||
|
|
shape: Optional[Tuple[int, int]]
|
||
|
|
# determine arff encoding to return
|
||
|
|
if not return_sparse:
|
||
|
|
# The shape must include the ignored features to keep the right indexes
|
||
|
|
# during the arff data conversion.
|
||
|
|
data_qualities = _get_data_qualities(data_id, data_home)
|
||
|
|
shape = _get_num_samples(data_qualities), len(features_list)
|
||
|
|
else:
|
||
|
|
shape = None
|
||
|
|
|
||
|
|
# obtain the data
|
||
|
|
url = _DATA_FILE.format(data_description["file_id"])
|
||
|
|
bunch = _download_data_to_bunch(
|
||
|
|
url,
|
||
|
|
return_sparse,
|
||
|
|
data_home,
|
||
|
|
as_frame=bool(as_frame),
|
||
|
|
openml_columns_info=features_list,
|
||
|
|
shape=shape,
|
||
|
|
target_columns=target_columns,
|
||
|
|
data_columns=data_columns,
|
||
|
|
md5_checksum=data_description["md5_checksum"],
|
||
|
|
n_retries=n_retries,
|
||
|
|
delay=delay,
|
||
|
|
parser=parser_,
|
||
|
|
)
|
||
|
|
|
||
|
|
if return_X_y:
|
||
|
|
return bunch.data, bunch.target
|
||
|
|
|
||
|
|
description = "{}\n\nDownloaded from openml.org.".format(
|
||
|
|
data_description.pop("description")
|
||
|
|
)
|
||
|
|
|
||
|
|
bunch.update(
|
||
|
|
DESCR=description,
|
||
|
|
details=data_description,
|
||
|
|
url="https://www.openml.org/d/{}".format(data_id),
|
||
|
|
)
|
||
|
|
|
||
|
|
return bunch
|