import gzip import json import os import shutil from os.path import join from warnings import warn from contextlib import closing from functools import wraps import itertools from collections.abc import Generator from collections import OrderedDict from functools import partial from urllib.request import urlopen, Request import numpy as np import scipy.sparse from ..externals import _arff from . import get_data_home from urllib.error import HTTPError from ..utils import Bunch from ..utils import get_chunk_n_rows from ..utils import _chunk_generator from ..utils import check_pandas_support # noqa from ..utils.validation import _deprecate_positional_args __all__ = ['fetch_openml'] _OPENML_PREFIX = "https://openml.org/" _SEARCH_NAME = "api/v1/json/data/list/data_name/{}/limit/2" _DATA_INFO = "api/v1/json/data/{}" _DATA_FEATURES = "api/v1/json/data/features/{}" _DATA_QUALITIES = "api/v1/json/data/qualities/{}" _DATA_FILE = "data/v1/download/{}" def _get_local_path(openml_path, data_home): return os.path.join(data_home, 'openml.org', openml_path + ".gz") def _retry_with_clean_cache(openml_path, data_home): """If the first call to the decorated function fails, the local cached file is removed, and the function is called again. If ``data_home`` is ``None``, then the function is called once. """ def decorator(f): @wraps(f) def wrapper(*args, **kw): if data_home is None: return f(*args, **kw) try: return f(*args, **kw) except HTTPError: raise except Exception: warn("Invalid cache, redownloading file", RuntimeWarning) local_path = _get_local_path(openml_path, data_home) if os.path.exists(local_path): os.unlink(local_path) return f(*args, **kw) return wrapper return decorator def _open_openml_url(openml_path, data_home): """ Returns a resource from OpenML.org. Caches it to data_home if required. Parameters ---------- openml_path : str OpenML URL that will be accessed. This will be prefixes with _OPENML_PREFIX data_home : str Directory to which the files will be cached. If None, no caching will be applied. Returns ------- result : stream A stream to the OpenML resource """ def is_gzip(_fsrc): return _fsrc.info().get('Content-Encoding', '') == 'gzip' req = Request(_OPENML_PREFIX + openml_path) req.add_header('Accept-encoding', 'gzip') if data_home is None: fsrc = urlopen(req) if is_gzip(fsrc): return gzip.GzipFile(fileobj=fsrc, mode='rb') return fsrc local_path = _get_local_path(openml_path, data_home) if not os.path.exists(local_path): try: os.makedirs(os.path.dirname(local_path)) except OSError: # potentially, the directory has been created already pass try: with closing(urlopen(req)) as fsrc: if is_gzip(fsrc): with open(local_path, 'wb') as fdst: shutil.copyfileobj(fsrc, fdst) else: with gzip.GzipFile(local_path, 'wb') as fdst: shutil.copyfileobj(fsrc, fdst) except Exception: if os.path.exists(local_path): os.unlink(local_path) raise # XXX: First time, decompression will not be necessary (by using fsrc), but # it will happen nonetheless return gzip.GzipFile(local_path, 'rb') def _get_json_content_from_openml_api(url, error_message, raise_if_error, data_home): """ Loads json data from the openml api Parameters ---------- url : str The URL to load from. Should be an official OpenML endpoint error_message : str or None The error message to raise if an acceptable OpenML error is thrown (acceptable error is, e.g., data id not found. Other errors, like 404's will throw the native error message) raise_if_error : bool Whether to raise an error if OpenML returns an acceptable error (e.g., date not found). If this argument is set to False, a None is returned in case of acceptable errors. Note that all other errors (e.g., 404) will still be raised as normal. data_home : str or None Location to cache the response. None if no cache is required. Returns ------- json_data : json or None the json result from the OpenML server if the call was successful; None otherwise iff raise_if_error was set to False and the error was ``acceptable`` """ @_retry_with_clean_cache(url, data_home) def _load_json(): with closing(_open_openml_url(url, data_home)) as response: return json.loads(response.read().decode("utf-8")) try: return _load_json() except HTTPError as error: # 412 is an OpenML specific error code, indicating a generic error # (e.g., data not found) if error.code != 412: raise error # 412 error, not in except for nicer traceback if raise_if_error: raise ValueError(error_message) return None def _split_sparse_columns(arff_data, include_columns): """ obtains several columns from sparse arff representation. Additionally, the column indices are re-labelled, given the columns that are not included. (e.g., when including [1, 2, 3], the columns will be relabelled to [0, 1, 2]) Parameters ---------- arff_data : tuple A tuple of three lists of equal size; first list indicating the value, second the x coordinate and the third the y coordinate. include_columns : list A list of columns to include. Returns ------- arff_data_new : tuple Subset of arff data with only the include columns indicated by the include_columns argument. """ arff_data_new = (list(), list(), list()) reindexed_columns = {column_idx: array_idx for array_idx, column_idx in enumerate(include_columns)} for val, row_idx, col_idx in zip(arff_data[0], arff_data[1], arff_data[2]): if col_idx in include_columns: arff_data_new[0].append(val) arff_data_new[1].append(row_idx) arff_data_new[2].append(reindexed_columns[col_idx]) return arff_data_new def _sparse_data_to_array(arff_data, include_columns): # turns the sparse data back into an array (can't use toarray() function, # as this does only work on numeric data) num_obs = max(arff_data[1]) + 1 y_shape = (num_obs, len(include_columns)) reindexed_columns = {column_idx: array_idx for array_idx, column_idx in enumerate(include_columns)} # TODO: improve for efficiency y = np.empty(y_shape, dtype=np.float64) for val, row_idx, col_idx in zip(arff_data[0], arff_data[1], arff_data[2]): if col_idx in include_columns: y[row_idx, reindexed_columns[col_idx]] = val return y def _convert_arff_data(arff, col_slice_x, col_slice_y, shape=None): """ converts the arff object into the appropriate matrix type (np.array or scipy.sparse.csr_matrix) based on the 'data part' (i.e., in the liac-arff dict, the object from the 'data' key) Parameters ---------- arff : dict As obtained from liac-arff object. col_slice_x : list The column indices that are sliced from the original array to return as X data col_slice_y : list The column indices that are sliced from the original array to return as y data Returns ------- X : np.array or scipy.sparse.csr_matrix y : np.array """ arff_data = arff['data'] if isinstance(arff_data, Generator): if shape[0] == -1: count = -1 else: count = shape[0] * shape[1] data = np.fromiter(itertools.chain.from_iterable(arff_data), dtype='float64', count=count) data = data.reshape(*shape) X = data[:, col_slice_x] y = data[:, col_slice_y] return X, y elif isinstance(arff_data, tuple): arff_data_X = _split_sparse_columns(arff_data, col_slice_x) num_obs = max(arff_data[1]) + 1 X_shape = (num_obs, len(col_slice_x)) X = scipy.sparse.coo_matrix( (arff_data_X[0], (arff_data_X[1], arff_data_X[2])), shape=X_shape, dtype=np.float64) X = X.tocsr() y = _sparse_data_to_array(arff_data, col_slice_y) return X, y else: # This should never happen raise ValueError('Unexpected Data Type obtained from arff.') def _feature_to_dtype(feature): """Map feature to dtype for pandas DataFrame """ if feature['data_type'] == 'string': return object elif feature['data_type'] == 'nominal': return 'category' # only numeric, integer, real are left elif (feature['number_of_missing_values'] != '0' or feature['data_type'] in ['numeric', 'real']): # cast to floats when there are any missing values return np.float64 elif feature['data_type'] == 'integer': return np.int64 raise ValueError('Unsupported feature: {}'.format(feature)) def _convert_arff_data_dataframe(arff, columns, features_dict): """Convert the ARFF object into a pandas DataFrame. Parameters ---------- arff : dict As obtained from liac-arff object. columns : list Columns from dataframe to return. features_dict : dict Maps feature name to feature info from openml. Returns ------- result : tuple tuple with the resulting dataframe """ pd = check_pandas_support('fetch_openml with as_frame=True') attributes = OrderedDict(arff['attributes']) arff_columns = list(attributes) # calculate chunksize first_row = next(arff['data']) first_df = pd.DataFrame([first_row], columns=arff_columns) row_bytes = first_df.memory_usage(deep=True).sum() chunksize = get_chunk_n_rows(row_bytes) # read arff data with chunks columns_to_keep = [col for col in arff_columns if col in columns] dfs = [] dfs.append(first_df[columns_to_keep]) for data in _chunk_generator(arff['data'], chunksize): dfs.append(pd.DataFrame(data, columns=arff_columns)[columns_to_keep]) df = pd.concat(dfs, ignore_index=True) for column in columns_to_keep: dtype = _feature_to_dtype(features_dict[column]) if dtype == 'category': dtype = pd.api.types.CategoricalDtype(attributes[column]) df[column] = df[column].astype(dtype, copy=False) return (df, ) def _get_data_info_by_name(name, version, data_home): """ Utilizes the openml dataset listing api to find a dataset by name/version OpenML api function: https://www.openml.org/api_docs#!/data/get_data_list_data_name_data_name Parameters ---------- name : str name of the dataset version : int or str If version is an integer, the exact name/version will be obtained from OpenML. If version is a string (value: "active") it will take the first version from OpenML that is annotated as active. Any other string values except "active" are treated as integer. data_home : str or None Location to cache the response. None if no cache is required. Returns ------- first_dataset : json json representation of the first dataset object that adhired to the search criteria """ if version == "active": # situation in which we return the oldest active version url = _SEARCH_NAME.format(name) + "/status/active/" error_msg = "No active dataset {} found.".format(name) json_data = _get_json_content_from_openml_api(url, error_msg, True, data_home) res = json_data['data']['dataset'] if len(res) > 1: warn("Multiple active versions of the dataset matching the name" " {name} exist. Versions may be fundamentally different, " "returning version" " {version}.".format(name=name, version=res[0]['version'])) return res[0] # an integer version has been provided url = (_SEARCH_NAME + "/data_version/{}").format(name, version) json_data = _get_json_content_from_openml_api(url, None, False, data_home) if json_data is None: # 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 # given name / version regardless of active, deactivated, etc. ) # TODO: feature request OpenML. url += "/status/deactivated" error_msg = "Dataset {} with version {} not found.".format(name, version) json_data = _get_json_content_from_openml_api(url, error_msg, True, data_home) return json_data['data']['dataset'][0] def _get_data_description_by_id(data_id, data_home): # OpenML API function: https://www.openml.org/api_docs#!/data/get_data_id url = _DATA_INFO.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, True, data_home) return json_data['data_set_description'] def _get_data_features(data_id, data_home): # 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, True, data_home) return json_data['data_features']['feature'] def _get_data_qualities(data_id, data_home): # 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, True, data_home) try: return json_data['data_qualities']['quality'] except KeyError: # the qualities might not be available, but we still try to process # the data return None def _get_num_samples(data_qualities): """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 if data_qualities is None: return default_n_samples qualities = {d['name']: d['value'] for d in data_qualities} return int(float(qualities.get('NumberOfInstances', default_n_samples))) def _load_arff_response(url, data_home, return_type, encode_nominal, parse_arff): """Load arff data with url and parses arff response with parse_arff""" response = _open_openml_url(url, data_home) with closing(response): # Note that if the data is dense, no reading is done until the data # generator is iterated. arff = _arff.load((line.decode('utf-8') for line in response), return_type=return_type, encode_nominal=encode_nominal) return parse_arff(arff) def _download_data_to_bunch(url, sparse, data_home, *, as_frame, features_list, data_columns, target_columns, shape): """Download OpenML ARFF and convert to Bunch of data """ # NB: this function is long in order to handle retry for any failure # during the streaming parse of the ARFF. # Prepare which columns and data types should be returned for the X and y features_dict = {feature['name']: feature for feature in features_list} # XXX: col_slice_y should be all nominal or all numeric _verify_target_data_type(features_dict, target_columns) col_slice_y = [int(features_dict[col_name]['index']) for col_name in target_columns] col_slice_x = [int(features_dict[col_name]['index']) for col_name in data_columns] for col_idx in col_slice_y: feat = features_list[col_idx] nr_missing = int(feat['number_of_missing_values']) if nr_missing > 0: raise ValueError('Target column {} has {} missing values. ' 'Missing values are not supported for target ' 'columns. '.format(feat['name'], nr_missing)) # Access an ARFF file on the OpenML server. Documentation: # https://www.openml.org/api_data_docs#!/data/get_download_id if sparse is True: return_type = _arff.COO else: return_type = _arff.DENSE_GEN frame = nominal_attributes = None if as_frame: columns = data_columns + target_columns parse_arff = partial(_convert_arff_data_dataframe, columns=columns, features_dict=features_dict) def postprocess(frame): # type:ignore X = frame[data_columns] if len(target_columns) >= 2: y = frame[target_columns] elif len(target_columns) == 1: y = frame[target_columns[0]] else: y = None return X, y, frame, nominal_attributes else: def parse_arff(arff): X, y = _convert_arff_data(arff, col_slice_x, col_slice_y, shape) # nominal attributes is a dict mapping from the attribute name to # the possible values. Includes also the target column (which will # be popped off below, before it will be packed in the Bunch # object) nominal_attributes = {k: v for k, v in arff['attributes'] if isinstance(v, list) and k in data_columns + target_columns} return X, y, nominal_attributes def postprocess(X, y, nominal_attributes): # type:ignore is_classification = {col_name in nominal_attributes for col_name in target_columns} if not is_classification: # No target pass elif all(is_classification): y = np.hstack([ np.take( np.asarray(nominal_attributes.pop(col_name), dtype='O'), y[:, i:i + 1].astype(int, copy=False)) for i, col_name in enumerate(target_columns) ]) elif any(is_classification): raise ValueError('Mix of nominal and non-nominal targets is ' 'not currently supported') # reshape y back to 1-D array, if there is only 1 target column; # back to None if there are not target columns if y.shape[1] == 1: y = y.reshape((-1,)) elif y.shape[1] == 0: y = None return X, y, frame, nominal_attributes out = _retry_with_clean_cache(url, data_home)( _load_arff_response)(url, data_home, return_type=return_type, encode_nominal=not as_frame, parse_arff=parse_arff) X, y, frame, nominal_attributes = postprocess(*out) return Bunch(data=X, target=y, frame=frame, categories=nominal_attributes, 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('Could not find 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('target_column={} has flag is_ignore.'.format( target_column)) if features_dict[target_column]['is_row_identifier'] == 'true': warn('target_column={} has flag is_row_identifier.'.format( target_column)) 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 @_deprecate_positional_args def fetch_openml(name=None, *, version='active', data_id=None, data_home=None, target_column='default-target', cache=True, return_X_y=False, as_frame=False): """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 `. .. versionadded:: 0.20 .. note:: EXPERIMENTAL The API is experimental (particularly the return value structure), and might have small backward-incompatible changes in future releases. Parameters ---------- name : str or None String identifier of the dataset. Note that OpenML can have multiple datasets with the same name. version : integer 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 or 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 : string or None, 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 : string, 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 : boolean, default=True Whether to cache downloaded datasets using joblib. return_X_y : boolean, 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 : boolean, default=False 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. 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) """ data_home = get_data_home(data_home=data_home) data_home = join(data_home, 'openml') if cache is False: # no caching will be applied data_home = None # 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) 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, name)) 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'])) return_sparse = False if data_description['format'].lower() == 'sparse_arff': return_sparse = True if as_frame and return_sparse: raise ValueError('Cannot return dataframe with sparse data') # 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) # 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=as_frame, features_list=features_list, shape=shape, target_columns=target_columns, data_columns=data_columns) 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